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2020 |
Rossi, Gabriel J Food, Phenology, and Flow—How Prey Phenology and Streamflow Dynamics Affect the Behavior, Ecology, and Recovery of Pacific Salmon PhD Thesis 2020. BibTeX | Tags: behavior, food webs, mediterranean stream, Oncorhynchus mykiss, phenology @phdthesis{Rossi2020, title = {Food, Phenology, and Flow—How Prey Phenology and Streamflow Dynamics Affect the Behavior, Ecology, and Recovery of Pacific Salmon}, author = {Gabriel J Rossi}, year = {2020}, date = {2020-05-31}, keywords = {behavior, food webs, mediterranean stream, Oncorhynchus mykiss, phenology}, pubstate = {published}, tppubtype = {phdthesis} } |
Uno, Hiromi; Pneh, Shelley Ecological Research, 35 (3), pp. 474-481, 2020. Abstract | Links | BibTeX | Tags: diversity, ecological function, predator-prey dynamics, Riparian, STREAM @article{Uno2020b, title = {Effect of source habitat spatial heterogeneity and species diversity on the temporal stability of aquatic‐to‐terrestrial subsidy by emerging aquatic insects}, author = {Hiromi Uno and Shelley Pneh}, doi = {10.1111/1440-1703.12125}, year = {2020}, date = {2020-05-25}, journal = {Ecological Research}, volume = {35}, number = {3}, pages = {474-481}, abstract = {Duration and temporal stability of resource subsidy largely affect the response of recipient communities. Factors that influence the temporal dynamics of resource subsidy from aquatic‐to‐terrestrial habitats by emerging aquatic insects were examined in this study. By measuring the flux of aquatic insect emergence from six habitats in a river over summer, we found that the timing of emergence varied by habitats for each dominant taxa, and that different species emerged at different times of the summer sequentially. We found that spatial variation in the emergence timing caused by the spatial heterogeneity of the water temperature, and so on in the source habitat can temporally stabilize the subsidy of each species from the whole river. Similarly, we found that the variation in emergence timing between species contributed to the temporal stability of subsidies from each habitat. The contribution of spatial heterogeneity to the temporal stability varied by the focal species and the contribution of species diversity varied by habitats. This study demonstrates how the ecological function of spatial heterogeneity and species diversity crosses the boundary of ecosystems by temporally stabilizing resource subsidies.}, keywords = {diversity, ecological function, predator-prey dynamics, Riparian, STREAM}, pubstate = {published}, tppubtype = {article} } Duration and temporal stability of resource subsidy largely affect the response of recipient communities. Factors that influence the temporal dynamics of resource subsidy from aquatic‐to‐terrestrial habitats by emerging aquatic insects were examined in this study. By measuring the flux of aquatic insect emergence from six habitats in a river over summer, we found that the timing of emergence varied by habitats for each dominant taxa, and that different species emerged at different times of the summer sequentially. We found that spatial variation in the emergence timing caused by the spatial heterogeneity of the water temperature, and so on in the source habitat can temporally stabilize the subsidy of each species from the whole river. Similarly, we found that the variation in emergence timing between species contributed to the temporal stability of subsidies from each habitat. The contribution of spatial heterogeneity to the temporal stability varied by the focal species and the contribution of species diversity varied by habitats. This study demonstrates how the ecological function of spatial heterogeneity and species diversity crosses the boundary of ecosystems by temporally stabilizing resource subsidies. |
Wang, Terrance; Kelson, Suzanne J; Greer, George; Thompson, Sally E; Carlson., Stephanie M Tributary confluences are dynamic thermal refuges for a juvenile salmonid in a warming river network Journal Article River Research and Applications, 2020. Abstract | Links | BibTeX | Tags: climate change, Eel river, microhabitat, Oncorhynchus mykiss, stream temperatures, thermal refuges, thermal tolerance @article{Wang2020, title = {Tributary confluences are dynamic thermal refuges for a juvenile salmonid in a warming river network}, author = {Terrance Wang and Suzanne J. Kelson and George Greer and Sally E. Thompson and Stephanie M. Carlson. }, doi = {10.1002/rra.3634}, year = {2020}, date = {2020-04-28}, journal = {River Research and Applications}, abstract = {As rivers warm, cold‐water fish species may alleviate thermal stress by moving into localized thermal refuges such as cold‐water plumes created by cool tributary inflows. We quantified use of two tributary confluence plumes by juvenile steelhead, Oncorhynchus mykiss , throughout the summer, including how trout positioned themselves in relation to temperature within confluence plumes. At two confluences, Cedar and Elder creeks, along the South Fork Eel River, California, USA, we monitored temperatures using in situ logger grids throughout summer 2016. Fish were counted within confluences via snorkel surveys five times a day on 5 days at each site. We found diel and seasonal dependence on confluence use by steelhead, especially at the Cedar Creek confluence, where mainstem temperatures exceeded 28°C. At this site, fish moved into the confluence on the warmest days and warmest times of the day. Fish observed within the Cedar Creek confluence plume were most common in locations between 20–22°C, rather than the coldest locations (14.5°C). At Elder Creek, where mainstem temperatures remained below 24°C, there was little relationship between mainstem temperature and steelhead presence in the confluence plume. At both sites, steelhead distribution within plumes was influenced by spatial variation of temperature and mean temperature in surveyed grid cells. Our results show that cool tributaries flowing into warmer mainstem reaches (over 24°C) likely create important thermal refuges for juvenile steelhead. As mainstem rivers warm with climate change, cool‐water tributary inputs may become more important for sustaining cold‐water salmonids near the southern end of their range.}, keywords = {climate change, Eel river, microhabitat, Oncorhynchus mykiss, stream temperatures, thermal refuges, thermal tolerance}, pubstate = {published}, tppubtype = {article} } As rivers warm, cold‐water fish species may alleviate thermal stress by moving into localized thermal refuges such as cold‐water plumes created by cool tributary inflows. We quantified use of two tributary confluence plumes by juvenile steelhead, Oncorhynchus mykiss , throughout the summer, including how trout positioned themselves in relation to temperature within confluence plumes. At two confluences, Cedar and Elder creeks, along the South Fork Eel River, California, USA, we monitored temperatures using in situ logger grids throughout summer 2016. Fish were counted within confluences via snorkel surveys five times a day on 5 days at each site. We found diel and seasonal dependence on confluence use by steelhead, especially at the Cedar Creek confluence, where mainstem temperatures exceeded 28°C. At this site, fish moved into the confluence on the warmest days and warmest times of the day. Fish observed within the Cedar Creek confluence plume were most common in locations between 20–22°C, rather than the coldest locations (14.5°C). At Elder Creek, where mainstem temperatures remained below 24°C, there was little relationship between mainstem temperature and steelhead presence in the confluence plume. At both sites, steelhead distribution within plumes was influenced by spatial variation of temperature and mean temperature in surveyed grid cells. Our results show that cool tributaries flowing into warmer mainstem reaches (over 24°C) likely create important thermal refuges for juvenile steelhead. As mainstem rivers warm with climate change, cool‐water tributary inputs may become more important for sustaining cold‐water salmonids near the southern end of their range. |
Kelson, Suzanne J; Power, Mary E; Finlay, Jacques C; Carlson, Stephanie M Partial migration alters population ecology and food chain length: evidence from a salmonid fish Journal Article Ecosphere, 11 (2), pp. e03044, 2020. Abstract | Links | BibTeX | Tags: eco-evolutionary dynamics, extended phenotype, food chain length, intraspecific variation, life history, O. mykiss, Oncorhynchus mykiss, partial migration, population ecology, size structure, steelhead/rainbow trout @article{Kelson2020b, title = {Partial migration alters population ecology and food chain length: evidence from a salmonid fish}, author = {Suzanne J. Kelson and Mary E. Power and Jacques C. Finlay and Stephanie M. Carlson }, url = {https://angelo.berkeley.edu/wp-content/uploads/ecs2.3044.pdf}, doi = {10.1002/ecs2.3044}, year = {2020}, date = {2020-02-21}, journal = {Ecosphere}, volume = {11}, number = {2}, pages = {e03044}, abstract = {Many migratory species, from monarch butterflies to wildebeest, express partial migration, where only a subset of a population migrates. This intraspecific variation is likely to have large ecological consequences. We studied the ecological consequences of partial migration in a salmonid fish, Oncorhynchus mykiss, in coastal streams in California, USA. One ecotype, steelhead trout, migrates to the ocean, whereas the other, rainbow trout, completes its lifecycle in freshwater. Migration has a strong genetic basis in O. mykiss. In one stream, we found differences in the frequency of migration‐linked genotypes below and above a waterfall barrier (migratory allele frequency of 60% below vs. 31% above). Below the waterfall, in the migratory‐dominated region, the density of young fish (<1 yr old) was approximately twice that in the resident‐dominated region above the waterfall (0.46 vs. 0.26 individuals/m2, respectively), presumably reflecting the higher fecundity of migratory females. Additionally, there were half as many older fish (>1 yr old) in pools downstream of the waterfall (0.05 vs. 0.13 individuals/m2). In a second stream, between‐year variation in the dominance of migratory vs. resident fish allowed us to explore differences in fish density and size structure through time, and we found a consistent pattern. In brief, when migratory genotypes dominated, we found higher densities of young fish and lower densities of older fish, resulting in a simpler size structure, compared to when resident genotypes dominated. Moreover, large resident trout had a slightly higher trophic position than young fish (3.92 vs. 3.42 in one creek and 3.77 vs. 3.17 in the other), quantified with stable isotope data. The difference in fish size structure did not generate trophic cascades. Partial migration is widespread among migratory populations, as is phenotypic divergence between resident and migratory forms, suggesting the potential for widespread ecological effects arising from this common form of intraspecific variation.}, keywords = {eco-evolutionary dynamics, extended phenotype, food chain length, intraspecific variation, life history, O. mykiss, Oncorhynchus mykiss, partial migration, population ecology, size structure, steelhead/rainbow trout}, pubstate = {published}, tppubtype = {article} } Many migratory species, from monarch butterflies to wildebeest, express partial migration, where only a subset of a population migrates. This intraspecific variation is likely to have large ecological consequences. We studied the ecological consequences of partial migration in a salmonid fish, Oncorhynchus mykiss, in coastal streams in California, USA. One ecotype, steelhead trout, migrates to the ocean, whereas the other, rainbow trout, completes its lifecycle in freshwater. Migration has a strong genetic basis in O. mykiss. In one stream, we found differences in the frequency of migration‐linked genotypes below and above a waterfall barrier (migratory allele frequency of 60% below vs. 31% above). Below the waterfall, in the migratory‐dominated region, the density of young fish (<1 yr old) was approximately twice that in the resident‐dominated region above the waterfall (0.46 vs. 0.26 individuals/m2, respectively), presumably reflecting the higher fecundity of migratory females. Additionally, there were half as many older fish (>1 yr old) in pools downstream of the waterfall (0.05 vs. 0.13 individuals/m2). In a second stream, between‐year variation in the dominance of migratory vs. resident fish allowed us to explore differences in fish density and size structure through time, and we found a consistent pattern. In brief, when migratory genotypes dominated, we found higher densities of young fish and lower densities of older fish, resulting in a simpler size structure, compared to when resident genotypes dominated. Moreover, large resident trout had a slightly higher trophic position than young fish (3.92 vs. 3.42 in one creek and 3.77 vs. 3.17 in the other), quantified with stable isotope data. The difference in fish size structure did not generate trophic cascades. Partial migration is widespread among migratory populations, as is phenotypic divergence between resident and migratory forms, suggesting the potential for widespread ecological effects arising from this common form of intraspecific variation. |
Al-Shayeb, Basem; Sachdeva, Rohan; Chen, Lin-Xing; Ward, Fred; Munk, Patrick; Devoto, Audra; Castelle, Cindy J; Olm, Matthew R; Bouma-Gregson, Keith; Amano, Yuki; He, Christine; Méheust, Raphaël; Brooks, Brandon; Thomas, Alex; Lavy, Adi; Matheus-Carnevali, Paula; Sun, Christine; Goltsman, Daniela S A; Borton, Mikayla A; Sharrar, Allison; Jaffe, Alexander L; Nelson, Tara C; Kantor, Rose; Keren, Ray; Lane, Katherine R; Farag, Ibrahim F; Lei, Shufei; Finstad, Kari; Amundson, Ronald; Anantharaman, Karthik; Zhou, Jinglie; Probst, Alexander J; Power, Mary E; Tringe, Susannah G; Li, Wen-Jun; Wrighton, Kelly; Harrison, Sue; Morowitz, Michael; Relman, David A; Doudna, Jennifer A; Lehours, Anne-Catherine; Warren, Lesley; Cate, Jamie H D; Santini, Joanne M; Banfield, Jillian F Clades of huge phages from across Earth’s ecosystems Journal Article Nature, 578 , pp. 425-431, 2020. Abstract | Links | BibTeX | Tags: bacteriophage, metagenomes, metagenomic sequencing @article{Al-Shayeb2020, title = {Clades of huge phages from across Earth’s ecosystems}, author = {Basem Al-Shayeb and Rohan Sachdeva and Lin-Xing Chen and Fred Ward and Patrick Munk and Audra Devoto and Cindy J. Castelle and Matthew R. Olm and Keith Bouma-Gregson and Yuki Amano and Christine He and Raphaël Méheust and Brandon Brooks and Alex Thomas and Adi Lavy and Paula Matheus-Carnevali and Christine Sun and Daniela S. A. Goltsman and Mikayla A. Borton and Allison Sharrar and Alexander L. Jaffe and Tara C. Nelson and Rose Kantor and Ray Keren and Katherine R. Lane and Ibrahim F. Farag and Shufei Lei and Kari Finstad and Ronald Amundson and Karthik Anantharaman and Jinglie Zhou and Alexander J. Probst and Mary E. Power and Susannah G. Tringe and Wen-Jun Li and Kelly Wrighton and Sue Harrison and Michael Morowitz and David A. Relman and Jennifer A. Doudna and Anne-Catherine Lehours and Lesley Warren and Jamie H. D. Cate and Joanne M. Santini and Jillian F. Banfield}, doi = {10.1038/s41586-020-2007-4}, year = {2020}, date = {2020-02-12}, journal = {Nature}, volume = {578}, pages = {425-431}, abstract = {Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is—to our knowledge—the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR–Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR–Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR–Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth’s ecosystems.}, keywords = {bacteriophage, metagenomes, metagenomic sequencing}, pubstate = {published}, tppubtype = {article} } Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is—to our knowledge—the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR–Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR–Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR–Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth’s ecosystems. |
Kelson, Suzanne J; Miller, Michael R; Thompson, Tasha Q; O'Rourke, Sean M; Carlson, Stephanie M Temporal dynamics of migration‐linked genetic variation are driven by streamflows and riverscape permeability Journal Article Molecular Ecology, 29 (5), pp. 870-885, 2020. Abstract | Links | BibTeX | Tags: ecology, genetic variation, landscape genetics, life history, O. mykiss, Oncorhynchus mykiss, partial barrier, partial migration, river networks @article{Kelson2020, title = {Temporal dynamics of migration‐linked genetic variation are driven by streamflows and riverscape permeability}, author = {Suzanne J. Kelson and Michael R. Miller and Tasha Q. Thompson and Sean M. O'Rourke and Stephanie M. Carlson}, url = {https://angelo.berkeley.edu/wp-content/uploads/mec.15367-1.pdf}, doi = {10.1111/mec.15367}, year = {2020}, date = {2020-02-03}, journal = {Molecular Ecology}, volume = {29}, number = {5}, pages = {870-885}, abstract = {Landscape permeability is often explored spatially, but may also vary temporally. Landscape permeability, including partial barriers, influences migratory animals that move across the landscape. Partial barriers are common in rivers where barrier passage varies with streamflow. We explore the influence of partial barriers on the spatial and temporal distribution of migration‐linked genotypes of Oncorhynchus mykiss, a salmonid fish with co‐occurring resident and migratory forms, in tributaries to the South Fork Eel River, California, USA, Elder and Fox Creeks. We genotyped >4,000 individuals using RAD‐capture and classified individuals as resident, heterozygous or migratory genotypes using life history‐associated loci. Across four years of study (2014–2017), the permeability of partial barriers varied across dry and wet years. In Elder Creek, the largest waterfall was passable for adults migrating up‐river 4–39 days each year. In this stream, the overall spatial pattern, with fewer migratory genotypes above the waterfall, remained true across dry and wet years (67%–76% of migratory alleles were downstream of the waterfall). We also observed a strong relationship between distance upstream and proportion of migratory alleles. In Fox Creek, the primary barrier is at the mouth, and we found that the migratory allele frequency varied with the annual timing of high flow events. In years when rain events occurred during the peak breeding season, migratory allele frequency was high (60%–68%), but otherwise it was low (30% in two years). We highlight that partial barriers and landscape permeability can be temporally dynamic, and this effect can be observed through changing genotype frequencies in migratory animals.}, keywords = {ecology, genetic variation, landscape genetics, life history, O. mykiss, Oncorhynchus mykiss, partial barrier, partial migration, river networks}, pubstate = {published}, tppubtype = {article} } Landscape permeability is often explored spatially, but may also vary temporally. Landscape permeability, including partial barriers, influences migratory animals that move across the landscape. Partial barriers are common in rivers where barrier passage varies with streamflow. We explore the influence of partial barriers on the spatial and temporal distribution of migration‐linked genotypes of Oncorhynchus mykiss, a salmonid fish with co‐occurring resident and migratory forms, in tributaries to the South Fork Eel River, California, USA, Elder and Fox Creeks. We genotyped >4,000 individuals using RAD‐capture and classified individuals as resident, heterozygous or migratory genotypes using life history‐associated loci. Across four years of study (2014–2017), the permeability of partial barriers varied across dry and wet years. In Elder Creek, the largest waterfall was passable for adults migrating up‐river 4–39 days each year. In this stream, the overall spatial pattern, with fewer migratory genotypes above the waterfall, remained true across dry and wet years (67%–76% of migratory alleles were downstream of the waterfall). We also observed a strong relationship between distance upstream and proportion of migratory alleles. In Fox Creek, the primary barrier is at the mouth, and we found that the migratory allele frequency varied with the annual timing of high flow events. In years when rain events occurred during the peak breeding season, migratory allele frequency was high (60%–68%), but otherwise it was low (30% in two years). We highlight that partial barriers and landscape permeability can be temporally dynamic, and this effect can be observed through changing genotype frequencies in migratory animals. |
Uno, Hiromi; Stillman, Jonathon H Lifetime eurythermy by seasonally matched thermal performance of developmental stages in an annual aquatic insect Journal Article Oecologia, 192 (3), pp. 647-656, 2020. Abstract | Links | BibTeX | Tags: Aquatic insect, life cycle, season, STREAM, temperature @article{Uno2020, title = {Lifetime eurythermy by seasonally matched thermal performance of developmental stages in an annual aquatic insect}, author = {Hiromi Uno and Jonathon H. Stillman}, url = {https://angelo.berkeley.edu/oecologia-2020-uno/}, doi = {10.1007/s00442-020-04605-z}, year = {2020}, date = {2020-01-27}, journal = {Oecologia}, volume = {192}, number = {3}, pages = {647-656}, abstract = {Organisms with annual life cycles are exposed to life stage specific thermal environments across seasons. Seasonal variation in thermal environments can vary across years and among sites. We investigated how organisms with annual life cycles respond to predictable seasonal changes in temperature and unpredictable thermal variation between habitats and years throughout their lives. Field surveys and historical records reveal that the spatially and temporally heterogeneous thermal environments inhabited by the annual mayfly Ephemerella maculata (Ephemerellidae) shift the date for transition to the next, life stage, so that the thermal phenotype of each life stage matches the thermal environment of the specific habitat and year. Laboratory studies of three distinct life stages of this mayfly reveal that life stage transitions are temperature dependent, facilitating timing shifts that are synchronized with the current season’s temperatures. Each life stage exhibited specific thermal sensitivity and performance phenotypes that matched the ambient temperature typically experienced during that life stage. Our study across the whole life cycle reveals mechanisms that allow organisms to achieve lifetime eurythermy in a dynamic seasonal environment, despite having narrower thermal ranges for growth and development in each life stage.}, keywords = {Aquatic insect, life cycle, season, STREAM, temperature}, pubstate = {published}, tppubtype = {article} } Organisms with annual life cycles are exposed to life stage specific thermal environments across seasons. Seasonal variation in thermal environments can vary across years and among sites. We investigated how organisms with annual life cycles respond to predictable seasonal changes in temperature and unpredictable thermal variation between habitats and years throughout their lives. Field surveys and historical records reveal that the spatially and temporally heterogeneous thermal environments inhabited by the annual mayfly Ephemerella maculata (Ephemerellidae) shift the date for transition to the next, life stage, so that the thermal phenotype of each life stage matches the thermal environment of the specific habitat and year. Laboratory studies of three distinct life stages of this mayfly reveal that life stage transitions are temperature dependent, facilitating timing shifts that are synchronized with the current season’s temperatures. Each life stage exhibited specific thermal sensitivity and performance phenotypes that matched the ambient temperature typically experienced during that life stage. Our study across the whole life cycle reveals mechanisms that allow organisms to achieve lifetime eurythermy in a dynamic seasonal environment, despite having narrower thermal ranges for growth and development in each life stage. |
2019 |
Diamond, Spencer; Andeer, Peter F; Li, Zhou; Crits-Christoph, Alexander; Burstein, David; Anantharaman, Karthik; Lane, Katherine R; Thomas, Brian C; Pan, Chongle; Northen, Trent R; Banfield, Jillian F Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Journal Article Nature Microbiology, 4 , pp. 1356-1367, 2019. Abstract | Links | BibTeX | Tags: metagenomics, soil microbes @article{Diamond2019, title = {Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. }, author = {Spencer Diamond and Peter F. Andeer and Zhou Li and Alexander Crits-Christoph and David Burstein and Karthik Anantharaman and Katherine R. Lane and Brian C. Thomas and Chongle Pan and Trent R. Northen and Jillian F. Banfield}, url = {https://angelo.berkeley.edu/wp-content/uploads/41564_2019_Article_449.pdf}, doi = {10.1038/s41564-019-0449-y}, year = {2019}, date = {2019-05-20}, journal = {Nature Microbiology}, volume = {4}, pages = {1356-1367}, abstract = {Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C1 metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C1, nitrate and ammonia transformations, and constrain factors that impact their distributions in soil.}, keywords = {metagenomics, soil microbes}, pubstate = {published}, tppubtype = {article} } Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C1 metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C1, nitrate and ammonia transformations, and constrain factors that impact their distributions in soil. |
Kelson, Suzanne J; Carlson, Stephanie M Do precipitation extremes drive growth and migration timing of a Pacific salmonid fish in Mediterranean‐climate streams? Journal Article Ecosphere, 10 (3), pp. e02618, 2019. Abstract | Links | BibTeX | Tags: Drought, growth, headwaters, migration, Oncorhynchus mykiss, salmonids, stream flows @article{Kelson2019, title = {Do precipitation extremes drive growth and migration timing of a Pacific salmonid fish in Mediterranean‐climate streams?}, author = {Suzanne J. Kelson and Stephanie M. Carlson }, url = {https://angelo.berkeley.edu/wp-content/uploads/ecs2.2618.pdf}, doi = {10.1002/ecs2.2618}, year = {2019}, date = {2019-03-20}, journal = {Ecosphere}, volume = {10}, number = {3}, pages = {e02618}, abstract = {Climate change is expected to increase weather extremes and variability, including more frequent weather whiplashes or extreme swings between severe drought and extraordinarily wet years. Shifts in precipitation patterns will alter stream flow regimes, affecting critical life history stages of sensitive aquatic organisms. Understanding how threatened fish species, such as steelhead/rainbow trout (Oncorhynchus mykiss), are affected by stream flows in years with contrasting environmental conditions is important for their conservation. Here, we report how extreme wet and dry years, from 2015 to 2018, affected stream flow patterns in two tributaries to the South Fork Eel River, California, USA, and aspects of O. mykiss ecology, including over‐summer fish growth and body condition as well as spring out‐migration timing. We found that stream flow patterns differed across years in the timing and magnitude of large winter–spring flow events and in summer low‐flow levels. We were surprised to find that differences in stream flows did not impact growth, body condition, or timing of out‐migration of O. mykiss. Fish growth was limited in the late summer in these streams (average of 0.02 ± 0.05 mm/d), but was similar across dry and wet years, and so was end‐of‐summer body condition and pool‐specific biomass loss from the beginning to the end of the summer. Similarly, O. mykiss migrated out of tributaries during the last week of March/first week of April regardless of the timing of spring flow events. We suggest that the muted response to inter‐annual hydrologic variability is due to the high quality of habitat provided by these unimpaired, groundwater‐fed tributaries. Similar streams that are likely to maintain cool temperatures and sufficient base flows, even in the driest years, should be a high priority for conservation and restoration efforts.}, keywords = {Drought, growth, headwaters, migration, Oncorhynchus mykiss, salmonids, stream flows}, pubstate = {published}, tppubtype = {article} } Climate change is expected to increase weather extremes and variability, including more frequent weather whiplashes or extreme swings between severe drought and extraordinarily wet years. Shifts in precipitation patterns will alter stream flow regimes, affecting critical life history stages of sensitive aquatic organisms. Understanding how threatened fish species, such as steelhead/rainbow trout (Oncorhynchus mykiss), are affected by stream flows in years with contrasting environmental conditions is important for their conservation. Here, we report how extreme wet and dry years, from 2015 to 2018, affected stream flow patterns in two tributaries to the South Fork Eel River, California, USA, and aspects of O. mykiss ecology, including over‐summer fish growth and body condition as well as spring out‐migration timing. We found that stream flow patterns differed across years in the timing and magnitude of large winter–spring flow events and in summer low‐flow levels. We were surprised to find that differences in stream flows did not impact growth, body condition, or timing of out‐migration of O. mykiss. Fish growth was limited in the late summer in these streams (average of 0.02 ± 0.05 mm/d), but was similar across dry and wet years, and so was end‐of‐summer body condition and pool‐specific biomass loss from the beginning to the end of the summer. Similarly, O. mykiss migrated out of tributaries during the last week of March/first week of April regardless of the timing of spring flow events. We suggest that the muted response to inter‐annual hydrologic variability is due to the high quality of habitat provided by these unimpaired, groundwater‐fed tributaries. Similar streams that are likely to maintain cool temperatures and sufficient base flows, even in the driest years, should be a high priority for conservation and restoration efforts. |
Bouma-Gregson, Keith; Olm, Matthew R; Probst, Alexander J; Anantharaman, Karthik; Power, Mary E; Banfield, Jillian F Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network Journal Article The ISME Journal, 13 , pp. 1618–1634, 2019. Abstract | Links | BibTeX | Tags: algae, cyanobacteria @article{Bouma-Gregson2019, title = {Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network}, author = {Keith Bouma-Gregson and Matthew R. Olm and Alexander J. Probst and Karthik Anantharaman and Mary E. Power and Jillian F. Banfield}, url = {https://angelo.berkeley.edu/wp-content/uploads/ACFrOgCi6hBdMfYejhSBBRhowH7uEzKdYcuAjfK9v1rJWg3ajgn9fFrFZmnWAY1cjZKhRQuhAhjSjhR6b_fShyPM32lKV7Coi7lFfnbS4xgM02VVqWdiTojYom8fl1nvtqMdQfs3mn-oTmwNlMoG-1.pdf}, doi = {10.1038/s41396-019-0374-3}, year = {2019}, date = {2019-02-26}, journal = {The ISME Journal}, volume = {13}, pages = {1618–1634}, abstract = {Blooms of planktonic cyanobacteria have long been of concern in lakes, but more recently, harmful impacts of riverine benthic cyanobacterial mats been recognized. As yet, we know little about how various benthic cyanobacteria are distributed in river networks, or how environmental conditions or other associated microbes in their consortia affect their biosynthetic capacities. We performed metagenomic sequencing for 22 Oscillatoriales-dominated (Cyanobacteria) microbial mats collected across the Eel River network in Northern California and investigated factors associated with anatoxin-a producing cyanobacteria. All microbial communities were dominated by one or two cyanobacterial species, so the key mat metabolisms involve oxygenic photosynthesis and carbon oxidation. Only a few metabolisms fueled the growth of the mat communities, with little evidence for anaerobic metabolic pathways. We genomically defined four cyanobacterial species, all which shared <96% average nucleotide identity with reference Oscillatoriales genomes and are potentially novel species in the genus Microcoleus. One of the Microcoleus species contained the anatoxin-a biosynthesis genes, and we describe the first anatoxin-a gene cluster from the Microcoleus clade within Oscillatoriales. Occurrence of these four Microcoleus species in the watershed was correlated with total dissolved nitrogen and phosphorus concentrations, and the species that contains the anatoxin-a gene cluster was found in sites with higher nitrogen concentrations. Microbial assemblages in mat samples with the anatoxin-a gene cluster consistently had a lower abundance of Burkholderiales (Betaproteobacteria) species than did mats without the anatoxin-producing genes. The associations of water nutrient concentrations and certain co-occurring microbes with anatoxin-a producing Microcoleus motivate further exploration for their roles as potential controls on the distributions of toxigenic benthic cyanobacteria in river networks.}, keywords = {algae, cyanobacteria}, pubstate = {published}, tppubtype = {article} } Blooms of planktonic cyanobacteria have long been of concern in lakes, but more recently, harmful impacts of riverine benthic cyanobacterial mats been recognized. As yet, we know little about how various benthic cyanobacteria are distributed in river networks, or how environmental conditions or other associated microbes in their consortia affect their biosynthetic capacities. We performed metagenomic sequencing for 22 Oscillatoriales-dominated (Cyanobacteria) microbial mats collected across the Eel River network in Northern California and investigated factors associated with anatoxin-a producing cyanobacteria. All microbial communities were dominated by one or two cyanobacterial species, so the key mat metabolisms involve oxygenic photosynthesis and carbon oxidation. Only a few metabolisms fueled the growth of the mat communities, with little evidence for anaerobic metabolic pathways. We genomically defined four cyanobacterial species, all which shared <96% average nucleotide identity with reference Oscillatoriales genomes and are potentially novel species in the genus Microcoleus. One of the Microcoleus species contained the anatoxin-a biosynthesis genes, and we describe the first anatoxin-a gene cluster from the Microcoleus clade within Oscillatoriales. Occurrence of these four Microcoleus species in the watershed was correlated with total dissolved nitrogen and phosphorus concentrations, and the species that contains the anatoxin-a gene cluster was found in sites with higher nitrogen concentrations. Microbial assemblages in mat samples with the anatoxin-a gene cluster consistently had a lower abundance of Burkholderiales (Betaproteobacteria) species than did mats without the anatoxin-producing genes. The associations of water nutrient concentrations and certain co-occurring microbes with anatoxin-a producing Microcoleus motivate further exploration for their roles as potential controls on the distributions of toxigenic benthic cyanobacteria in river networks. |
Kelson, Suzanne J; Miller, Michael R; Thompson, Tasha Q; O'Rourke, Sean M; Carlson, Stephanie M Do genomics and sex predict migration in a partially migratory salmonid fish, Oncorhynchus mykiss? Journal Article Canadian Journal of Fisheries and Aquatic Sciences, 76 (11), pp. 2080-2088, 2019. Abstract | Links | BibTeX | Tags: genetic variation, O. mykiss, partial migration @article{Kelson2019b, title = {Do genomics and sex predict migration in a partially migratory salmonid fish, Oncorhynchus mykiss?}, author = {Suzanne J. Kelson and Michael R. Miller and Tasha Q. Thompson and Sean M. O'Rourke and Stephanie M. Carlson}, url = {https://angelo.berkeley.edu/wp-content/uploads/cjfas-2018-0394-1.pdf}, doi = {10.1139/cjfas-2018-0394}, year = {2019}, date = {2019-02-14}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, volume = {76}, number = {11}, pages = {2080-2088}, abstract = {Partial migration is a common phenomenon wherein populations include migratory and resident individuals. Whether an individual migrates or not has important ecological and management implications, particularly within protected populations. Within partially migratory populations of Oncorhynchus mykiss, migration is highly correlated with a specific genomic region, but it is unclear how well this region predicts migration at the individual level. Here, we relate sex and life history genotype, determined using >400 single nucleotide polymorphisms (SNPs) on the migratory-linked genomic region, to life history expression of marked juvenile O. mykiss from two tributaries to the South Fork Eel River, northern California. Most resident fish were resident genotypes (57% resident, 37% heterozygous, 6% migratory genotype) and male (78%). Most migratory fish were female (62%), but were a mixture of genotypes (30% resident, 45% heterozygous, 25% migratory genotype). Sex was more strongly correlated with life history expression than genotype, but the best-supported model included both. Resident genotypes regularly migrated, highlighting the importance of conserving the full suite of life history and genetic diversity in partially migratory populations.}, keywords = {genetic variation, O. mykiss, partial migration}, pubstate = {published}, tppubtype = {article} } Partial migration is a common phenomenon wherein populations include migratory and resident individuals. Whether an individual migrates or not has important ecological and management implications, particularly within protected populations. Within partially migratory populations of Oncorhynchus mykiss, migration is highly correlated with a specific genomic region, but it is unclear how well this region predicts migration at the individual level. Here, we relate sex and life history genotype, determined using >400 single nucleotide polymorphisms (SNPs) on the migratory-linked genomic region, to life history expression of marked juvenile O. mykiss from two tributaries to the South Fork Eel River, northern California. Most resident fish were resident genotypes (57% resident, 37% heterozygous, 6% migratory genotype) and male (78%). Most migratory fish were female (62%), but were a mixture of genotypes (30% resident, 45% heterozygous, 25% migratory genotype). Sex was more strongly correlated with life history expression than genotype, but the best-supported model included both. Resident genotypes regularly migrated, highlighting the importance of conserving the full suite of life history and genetic diversity in partially migratory populations. |
Gaynor, Kaitlyn M; Brown, Joel S; Middleton, Arthur D; Power, Mary E; Brashares, Justin S Landscapes of Fear: Spatial Patterns of Risk Perception and Response. Journal Article Trends in Ecology & Evolution , 34 (4), pp. 355-368, 2019. Abstract | Links | BibTeX | Tags: anti-predator defenses, predator–prey interaction, risk effects @article{Gaynor2019, title = {Landscapes of Fear: Spatial Patterns of Risk Perception and Response.}, author = {Kaitlyn M. Gaynor and Joel S. Brown and Arthur D. Middleton and Mary E. Power and Justin S. Brashares}, doi = {10.1016/j.tree.2019.01.004}, year = {2019}, date = {2019-02-08}, journal = {Trends in Ecology & Evolution }, volume = {34}, number = {4}, pages = {355-368}, abstract = {Animals experience varying levels of predation risk as they navigate heterogeneous landscapes, and behavioral responses to perceived risk can structure ecosystems. The concept of the landscape of fear has recently become central to describing this spatial variation in risk, perception, and response. We present a framework linking the landscape of fear, defined as spatial variation in prey perception of risk, to the underlying physical landscape and predation risk, and to resulting patterns of prey distribution and antipredator behavior. By disambiguating the mechanisms through which prey perceive risk and incorporate fear into decision making, we can better quantify the nonlinear relationship between risk and response and evaluate the relative importance of the landscape of fear across taxa and ecosystems. }, keywords = {anti-predator defenses, predator–prey interaction, risk effects}, pubstate = {published}, tppubtype = {article} } Animals experience varying levels of predation risk as they navigate heterogeneous landscapes, and behavioral responses to perceived risk can structure ecosystems. The concept of the landscape of fear has recently become central to describing this spatial variation in risk, perception, and response. We present a framework linking the landscape of fear, defined as spatial variation in prey perception of risk, to the underlying physical landscape and predation risk, and to resulting patterns of prey distribution and antipredator behavior. By disambiguating the mechanisms through which prey perceive risk and incorporate fear into decision making, we can better quantify the nonlinear relationship between risk and response and evaluate the relative importance of the landscape of fear across taxa and ecosystems. |
2018 |
Crits-Christoph, Alexander; Diamond, Spencer; Butterfield, Cristina N; Thomas, Brian C; Banfield, Jillian F Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis Journal Article Nature, 558 , pp. 440-444, 2018. Abstract | Links | BibTeX | Tags: metagenomic sequencing, soil microbes @article{Crits-Christoph2018, title = {Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis}, author = {Alexander Crits-Christoph and Spencer Diamond and Cristina N. Butterfield and Brian C. Thomas and Jillian F. Banfield}, doi = {10.1038/s41586-018-0207-y}, year = {2018}, date = {2018-06-13}, journal = {Nature}, volume = {558}, pages = {440-444}, abstract = {In soil ecosystems, microorganisms produce diverse secondary metabolites such as antibiotics, antifungals and siderophores that mediate communication, competition and interactions with other organisms and the environment. Most known antibiotics are derived from a few culturable microbial taxa, and the biosynthetic potential of the vast majority of bacteria in soil has rarely been investigated. Here we reconstruct hundreds of near-complete genomes from grassland soil metagenomes and identify microorganisms from previously understudied phyla that encode diverse polyketide and nonribosomal peptide biosynthetic gene clusters that are divergent from well-studied clusters. These biosynthetic loci are encoded by newly identified members of the Acidobacteria, Verrucomicobia and Gemmatimonadetes, and the candidate phylum Rokubacteria. Bacteria from these groups are highly abundant in soils, but have not previously been genomically linked to secondary metabolite production with confidence. In particular, large numbers of biosynthetic genes were characterized in newly identified members of the Acidobacteria, which is the most abundant bacterial phylum across soil biomes5. We identify two acidobacterial genomes from divergent lineages, each of which encodes an unusually large repertoire of biosynthetic genes with up to fifteen large polyketide and nonribosomal peptide biosynthetic loci per genome. To track gene expression of genes encoding polyketide synthases and nonribosomal peptide synthetases in the soil ecosystem that we studied, we sampled 120 time points in a microcosm manipulation experiment and, using metatranscriptomics, found that gene clusters were differentially co-expressed in response to environmental perturbations. Transcriptional co-expression networks for specific organisms associated biosynthetic genes with two-component systems, transcriptional activation, putative antimicrobial resistance and iron regulation, linking metabolite biosynthesis to processes of environmental sensing and ecological competition. We conclude that the biosynthetic potential of abundant and phylogenetically diverse soil microorganisms has previously been underestimated. These organisms may represent a source of natural products that can address needs for new antibiotics and other pharmaceutical compounds.}, keywords = {metagenomic sequencing, soil microbes}, pubstate = {published}, tppubtype = {article} } In soil ecosystems, microorganisms produce diverse secondary metabolites such as antibiotics, antifungals and siderophores that mediate communication, competition and interactions with other organisms and the environment. Most known antibiotics are derived from a few culturable microbial taxa, and the biosynthetic potential of the vast majority of bacteria in soil has rarely been investigated. Here we reconstruct hundreds of near-complete genomes from grassland soil metagenomes and identify microorganisms from previously understudied phyla that encode diverse polyketide and nonribosomal peptide biosynthetic gene clusters that are divergent from well-studied clusters. These biosynthetic loci are encoded by newly identified members of the Acidobacteria, Verrucomicobia and Gemmatimonadetes, and the candidate phylum Rokubacteria. Bacteria from these groups are highly abundant in soils, but have not previously been genomically linked to secondary metabolite production with confidence. In particular, large numbers of biosynthetic genes were characterized in newly identified members of the Acidobacteria, which is the most abundant bacterial phylum across soil biomes5. We identify two acidobacterial genomes from divergent lineages, each of which encodes an unusually large repertoire of biosynthetic genes with up to fifteen large polyketide and nonribosomal peptide biosynthetic loci per genome. To track gene expression of genes encoding polyketide synthases and nonribosomal peptide synthetases in the soil ecosystem that we studied, we sampled 120 time points in a microcosm manipulation experiment and, using metatranscriptomics, found that gene clusters were differentially co-expressed in response to environmental perturbations. Transcriptional co-expression networks for specific organisms associated biosynthetic genes with two-component systems, transcriptional activation, putative antimicrobial resistance and iron regulation, linking metabolite biosynthesis to processes of environmental sensing and ecological competition. We conclude that the biosynthetic potential of abundant and phylogenetically diverse soil microorganisms has previously been underestimated. These organisms may represent a source of natural products that can address needs for new antibiotics and other pharmaceutical compounds. |
Bouma-Gregson, Keith; Kudela, Raphael M; Power, Mary Widespread anatoxin-a detection in benthic cyanobacterial mats throughout a river network Journal Article PLoS One, 13 (5), 2018. Abstract | Links | BibTeX | Tags: algae, biodiversity @article{Bouma-Gregson2018, title = {Widespread anatoxin-a detection in benthic cyanobacterial mats throughout a river network}, author = {Keith Bouma-Gregson and Raphael M. Kudela and Mary Power}, doi = {https://doi.org/10.1371/journal.pone.0197669}, year = {2018}, date = {2018-05-18}, journal = {PLoS One}, volume = {13}, number = {5}, abstract = {Benthic algae fuel summer food webs in many sunlit rivers, and are hotspots for primary and secondary production and biogeochemical cycling. Concerningly, riverine benthic algal assemblages can become dominated by toxic cyanobacteria, threatening water quality and public health. In the Eel River in Northern California, over a dozen dog deaths have been attributed to cyanotoxin poisonings since 2000. During the summers of 2013–2015, we documented spatial and temporal patterns of cyanotoxin concentrations in the watershed, showing widespread distribution of anatoxin-a in benthic cyanobacterial mats. Solid phase adsorption toxin tracking (SPATT) samplers were deployed weekly to record dissolved microcystin and anatoxin-a levels at 10 sites throughout the watershed, and 187 Anabaenadominated or Phormidium-dominated cyanobacterial mat samples were collected from 27 locations to measure intracellular anatoxin-a (ATX) and microcystins (MCY). Anatoxin-a levels were higher than microcystin for both SPATT (mean MCY = 0.8 and ATX = 4.8 ng g resin-1 day-1) and cyanobacterial mat samples (mean MCY = 0.074 and ATX = 1.89 μg g-1 DW). Of the benthic mats sampled, 58.9% had detectable anatoxin-a (max = 70.93 μg g-1 DW), while 37.6% had detectable microcystins (max = 2.29 μg g-1 DW). SPATT cyanotoxin levels peaked in mid-summer in warm mainstem reaches of the watershed. This is one of the first documentations of widespread anatoxin-a occurrence in benthic cyanobacterial mats in a North American watershed.}, keywords = {algae, biodiversity}, pubstate = {published}, tppubtype = {article} } Benthic algae fuel summer food webs in many sunlit rivers, and are hotspots for primary and secondary production and biogeochemical cycling. Concerningly, riverine benthic algal assemblages can become dominated by toxic cyanobacteria, threatening water quality and public health. In the Eel River in Northern California, over a dozen dog deaths have been attributed to cyanotoxin poisonings since 2000. During the summers of 2013–2015, we documented spatial and temporal patterns of cyanotoxin concentrations in the watershed, showing widespread distribution of anatoxin-a in benthic cyanobacterial mats. Solid phase adsorption toxin tracking (SPATT) samplers were deployed weekly to record dissolved microcystin and anatoxin-a levels at 10 sites throughout the watershed, and 187 Anabaenadominated or Phormidium-dominated cyanobacterial mat samples were collected from 27 locations to measure intracellular anatoxin-a (ATX) and microcystins (MCY). Anatoxin-a levels were higher than microcystin for both SPATT (mean MCY = 0.8 and ATX = 4.8 ng g resin-1 day-1) and cyanobacterial mat samples (mean MCY = 0.074 and ATX = 1.89 μg g-1 DW). Of the benthic mats sampled, 58.9% had detectable anatoxin-a (max = 70.93 μg g-1 DW), while 37.6% had detectable microcystins (max = 2.29 μg g-1 DW). SPATT cyanotoxin levels peaked in mid-summer in warm mainstem reaches of the watershed. This is one of the first documentations of widespread anatoxin-a occurrence in benthic cyanobacterial mats in a North American watershed. |
Rempe, Daniella; Dietrich, William Direct observations of rock moisture, a hidden component of the hydrologic cycle Journal Article Proceedings of the National Academy of Science of the United States of America, 115 (11), pp. 2664-2669, 2018. Abstract | Links | BibTeX | Tags: Critical Zone, deep vadose zone, evapotranspiration, rock moisture, water budget @article{daniellaRempe2018, title = {Direct observations of rock moisture, a hidden component of the hydrologic cycle}, author = {Daniella Rempe and William Dietrich}, url = {https://angelo.berkeley.edu/wp-content/uploads/Proceedings-of-the-National-Academy-of-Sciences-2018-Rempe.pdf}, doi = {https://doi.org/10.1073/pnas.1800141115 }, year = {2018}, date = {2018-03-13}, journal = {Proceedings of the National Academy of Science of the United States of America}, volume = {115}, number = {11}, pages = {2664-2669}, abstract = {Recent theory and field observations suggest that a systematically varying weathering zone, that can be tens of meters thick, commonly develops in the bedrock underlying hillslopes. Weathering turns otherwise poorly conductive bedrock into a dynamic water storage reservoir. Infiltrating precipitation typically will pass through unsaturated weathered bedrock before reaching groundwater and running off to streams. This invisible and difficult to access unsaturated zone is virtually unexplored compared with the surface soil mantle. We have proposed the term “rock moisture” to describe the exchangeable water stored in the unsaturated zone in weathered bedrock, purposely choosing a term parallel to, but distinct from, soil moisture, because weathered bedrock is a distinctly different material that is distributed across landscapes independently of soil thickness. Here, we report a multiyear intensive campaign of quantifying rock moisture across a hillslope underlain by a thick weathered bedrock zone using repeat neutron probe measurements in a suite of boreholes. Rock moisture storage accumulates in the wet season, reaches a characteristic upper value, and rapidly passes any additional rainfall downward to groundwater. Hence, rock moisture storage mediates the initiation and magnitude of recharge and runoff. In the dry season, rock moisture storage is gradually depleted by trees for transpiration, leading to a common lower value at the end of the dry season. Up to 27% of the annual rainfall is seasonally stored as rock moisture. Significant rock moisture storage is likely common, and yet it is missing from hydrologic and land-surface models used to predict regional and global climate.}, keywords = {Critical Zone, deep vadose zone, evapotranspiration, rock moisture, water budget}, pubstate = {published}, tppubtype = {article} } Recent theory and field observations suggest that a systematically varying weathering zone, that can be tens of meters thick, commonly develops in the bedrock underlying hillslopes. Weathering turns otherwise poorly conductive bedrock into a dynamic water storage reservoir. Infiltrating precipitation typically will pass through unsaturated weathered bedrock before reaching groundwater and running off to streams. This invisible and difficult to access unsaturated zone is virtually unexplored compared with the surface soil mantle. We have proposed the term “rock moisture” to describe the exchangeable water stored in the unsaturated zone in weathered bedrock, purposely choosing a term parallel to, but distinct from, soil moisture, because weathered bedrock is a distinctly different material that is distributed across landscapes independently of soil thickness. Here, we report a multiyear intensive campaign of quantifying rock moisture across a hillslope underlain by a thick weathered bedrock zone using repeat neutron probe measurements in a suite of boreholes. Rock moisture storage accumulates in the wet season, reaches a characteristic upper value, and rapidly passes any additional rainfall downward to groundwater. Hence, rock moisture storage mediates the initiation and magnitude of recharge and runoff. In the dry season, rock moisture storage is gradually depleted by trees for transpiration, leading to a common lower value at the end of the dry season. Up to 27% of the annual rainfall is seasonally stored as rock moisture. Significant rock moisture storage is likely common, and yet it is missing from hydrologic and land-surface models used to predict regional and global climate. |
Power, Mary; Estes, James; Kareiva, Peter; Simon Levin, ; Lubchenco, Jane; Palumbi, Stephen Biographical Memoire: Robert Paine Miscellaneous 2018. Abstract | Links | BibTeX | Tags: keystone species, memoire, patch dynamics, trophic cascades @misc{Power2018, title = {Biographical Memoire: Robert Paine}, author = {Mary Power and James Estes and Peter Kareiva and Simon Levin and Jane Lubchenco and Stephen Palumbi}, url = {https://angelo.berkeley.edu/wp-content/uploads/PNAS-2018-Power.pdf}, year = {2018}, date = {2018-01-01}, journal = {Proceedings of the National Academy of Science of the United States of America}, number = {1}, pages = {1-20}, abstract = {Robert Paine changed the science of ecology profoundly. Fascinated with nature and greatly skilled as a naturalist, he took delight in linking results from field experiments to general, often novel concepts. Paine’s development of the concepts of keystone species, trophic cascades, and patch dynamics are milestones in community ecology. He will long be revered for his remarkable humanity, including his devotion to and respect for students, both his own and the many others he encouraged and guided. Paine took a bachelor’s degree in paleontology from Harvard in 1954. After service in the army he earned a Ph.D. in zoology from the University of Michigan in 1961 followed by a brief but influential postdoc at the Scripps Institution of Oceanography. He then joined the faculty of the University of Washington where he spent the remainder of his career.}, keywords = {keystone species, memoire, patch dynamics, trophic cascades}, pubstate = {published}, tppubtype = {misc} } Robert Paine changed the science of ecology profoundly. Fascinated with nature and greatly skilled as a naturalist, he took delight in linking results from field experiments to general, often novel concepts. Paine’s development of the concepts of keystone species, trophic cascades, and patch dynamics are milestones in community ecology. He will long be revered for his remarkable humanity, including his devotion to and respect for students, both his own and the many others he encouraged and guided. Paine took a bachelor’s degree in paleontology from Harvard in 1954. After service in the army he earned a Ph.D. in zoology from the University of Michigan in 1961 followed by a brief but influential postdoc at the Scripps Institution of Oceanography. He then joined the faculty of the University of Washington where he spent the remainder of his career. |
2017 |
Bouma-Gregson, Keith The Ecology of Benthic Toxigenic Anabaena and Phormidium (Cyanobacteria) in the Eel River, California PhD Thesis University of California, Berkeley, 2017, ISBN: 978-0-355-94920-9. Abstract | BibTeX | Tags: Anabaena, Anatoxin-a, Biological sciences, cyanobacteria, Cyanotoxin, metagenomics, Phormidium @phdthesis{Bouma-Gregson2017c, title = {The Ecology of Benthic Toxigenic Anabaena and Phormidium (Cyanobacteria) in the Eel River, California}, author = {Keith Bouma-Gregson}, isbn = {978-0-355-94920-9}, year = {2017}, date = {2017-12-31}, school = {University of California, Berkeley}, abstract = {Cyanobacteria are ubiquitous in aquatic ecosystems across the earth. In many environments they are present at low abundances, however under certain environmental conditions cyanobacteria bloom and become one of the dominant organisms in an waterbody, degrading aquatic food webs and water quality. Cyanobacteria evolved over 2 billion years ago, and cyanobacterial harmful algal blooms (cyanoHABs) have been documented for decades. Of particular concern is the production of cyanotoxins, secondary metabolites toxic to humans and other organisms, by certain strains of cyanobacteria. Most research of cyanoHABs has been of planktonic blooms in lakes or estuaries, and cyanotoxin production by benthic cyanobacteria in rivers has been more recent, but in many rivers benthic cyanobacteria are the primary source of cyanotoxins. With field surveys and monitoring, manipulative field experiments, and genome-resolved metagenomics, this dissertation investigated the ecology of benthic cyanobacteria in the Eel River, California. }, keywords = {Anabaena, Anatoxin-a, Biological sciences, cyanobacteria, Cyanotoxin, metagenomics, Phormidium}, pubstate = {published}, tppubtype = {phdthesis} } Cyanobacteria are ubiquitous in aquatic ecosystems across the earth. In many environments they are present at low abundances, however under certain environmental conditions cyanobacteria bloom and become one of the dominant organisms in an waterbody, degrading aquatic food webs and water quality. Cyanobacteria evolved over 2 billion years ago, and cyanobacterial harmful algal blooms (cyanoHABs) have been documented for decades. Of particular concern is the production of cyanotoxins, secondary metabolites toxic to humans and other organisms, by certain strains of cyanobacteria. Most research of cyanoHABs has been of planktonic blooms in lakes or estuaries, and cyanotoxin production by benthic cyanobacteria in rivers has been more recent, but in many rivers benthic cyanobacteria are the primary source of cyanotoxins. With field surveys and monitoring, manipulative field experiments, and genome-resolved metagenomics, this dissertation investigated the ecology of benthic cyanobacteria in the Eel River, California. |
Vadeboncoeur, Yvonne; Power, Mary Attached Algae: The Cryptic Base of Inverted Trophic Pyramids in Freshwaters Journal Article Annual Review of Ecology, Evolution, and Systematics, 48 (1), pp. 255-279, 2017. Abstract | Links | BibTeX | Tags: Cladophora, cyanobacteria, diatoms, grazers, lakes, microphytobenthos, periphyton, primary consumer, primary producer, rivers @article{Vadeboncoeur2017, title = { Attached Algae: The Cryptic Base of Inverted Trophic Pyramids in Freshwaters}, author = {Yvonne Vadeboncoeur and Mary Power}, url = {https://angelo.berkeley.edu/wp-content/uploads/Annu.-Rev.-Ecol.-Evol.-Syst.-2017-Vadeboncoeur.pdf}, doi = {https://doi.org/10.1146/annurev-ecolsys-121415-032340}, year = {2017}, date = {2017-08-11}, journal = {Annual Review of Ecology, Evolution, and Systematics}, volume = {48}, number = {1}, pages = {255-279}, abstract = {It seems improbable that a thin veneer of attached algae coating submerged surfaces in lakes and rivers could be the foundation of many freshwater food webs, but increasing evidence from chemical tracers supports this view. Attached algae grow on any submerged surface that receives enough light for photosynthesis, but animals often graze attached algae down to thin, barely perceptible biofilms. Algae in general are more nutritious and digestible than terrestrial plants or detritus, and attached algae are particularly harvestable, being concentrated on surfaces. Diatoms, a major component of attached algal assemblages, are especially nutritious and tolerant of heavy grazing. Algivores can track attached algal productivity over a range of spatial scales and consume a high proportion of new attached algal growth in high-light, low-nutrient ecosystems. The subsequent efficient conversion of the algae into consumer production in freshwater food webs can lead to low-producer, high-consumer biomass, patterns that Elton (1927) described as inverted trophic pyramids. Human perturbations of nutrient, sediment, and carbon loading into freshwaters and of thermal and hydrologic regimes can weaken consumer control of algae and promote nuisance attached algal blooms.}, keywords = {Cladophora, cyanobacteria, diatoms, grazers, lakes, microphytobenthos, periphyton, primary consumer, primary producer, rivers}, pubstate = {published}, tppubtype = {article} } It seems improbable that a thin veneer of attached algae coating submerged surfaces in lakes and rivers could be the foundation of many freshwater food webs, but increasing evidence from chemical tracers supports this view. Attached algae grow on any submerged surface that receives enough light for photosynthesis, but animals often graze attached algae down to thin, barely perceptible biofilms. Algae in general are more nutritious and digestible than terrestrial plants or detritus, and attached algae are particularly harvestable, being concentrated on surfaces. Diatoms, a major component of attached algal assemblages, are especially nutritious and tolerant of heavy grazing. Algivores can track attached algal productivity over a range of spatial scales and consume a high proportion of new attached algal growth in high-light, low-nutrient ecosystems. The subsequent efficient conversion of the algae into consumer production in freshwater food webs can lead to low-producer, high-consumer biomass, patterns that Elton (1927) described as inverted trophic pyramids. Human perturbations of nutrient, sediment, and carbon loading into freshwaters and of thermal and hydrologic regimes can weaken consumer control of algae and promote nuisance attached algal blooms. |
Sculley, John; Lowe, Rex L; Nittrouer, Charles; Drexler, Tina; Power, Mary Eighty years of food-web response to interannual variation in discharge recorded in river diatom frustules from an ocean sediment core Journal Article Proceedings of the National Academy of Science of the United States of America, 114 (38), pp. 10155–10159, 2017. Abstract | Links | BibTeX | Tags: diatom frustule, ecological upscaling, food-web controls, paleoproxy, river discharge, variation @article{Sculley2017, title = {Eighty years of food-web response to interannual variation in discharge recorded in river diatom frustules from an ocean sediment core}, author = {John Sculley and Rex L. Lowe and Charles Nittrouer and Tina Drexler and Mary Power}, url = {https://angelo.berkeley.edu/wp-content/uploads/Proceedings-of-the-National-Academy-of-Sciences-2017-Sculley.pdf}, doi = {https://doi.org/10.1073/pnas.1611884114}, year = {2017}, date = {2017-07-13}, journal = {Proceedings of the National Academy of Science of the United States of America}, volume = {114}, number = {38}, pages = {10155–10159}, abstract = {Little is known about the importance of food-web processes as controls of river primary production due to the paucity of both long term studies and of depositional environments which would allow retrospective fossil analysis. To investigate how freshwater algal production in the Eel River, northern California, varied over eight decades, we quantified siliceous shells (frustules) of freshwater diatoms from a well-dated undisturbed sediment core in a nearshore marine environment. Abundances of freshwater diatom frustules exported to Eel Canyon sediment from 1988 to 2001 were positively correlated with annual biomass of Cladophora surveyed over these years in upper portions of the Eel basin. Over 28 years of contemporary field research, peak algal biomass was generally higher in summers following bankfull, bed-scouring winter floods. Field surveys and experiments suggested that bed-mobilizing floods scour away overwintering grazers, releasing algae from spring and early summer grazing. During wet years, growth conditions for algae could also be enhanced by increased nutrient loading from the watershed, or by sustained summer base flows. Total annual rainfall and frustule densities in laminae over a longer 83-year record were weakly and negatively correlated, however, suggesting that positive effects of floods on annual algal production were primarily mediated by “top-down” (consumer release) rather than “bottom-up” (growth promoting) controls.}, keywords = {diatom frustule, ecological upscaling, food-web controls, paleoproxy, river discharge, variation}, pubstate = {published}, tppubtype = {article} } Little is known about the importance of food-web processes as controls of river primary production due to the paucity of both long term studies and of depositional environments which would allow retrospective fossil analysis. To investigate how freshwater algal production in the Eel River, northern California, varied over eight decades, we quantified siliceous shells (frustules) of freshwater diatoms from a well-dated undisturbed sediment core in a nearshore marine environment. Abundances of freshwater diatom frustules exported to Eel Canyon sediment from 1988 to 2001 were positively correlated with annual biomass of Cladophora surveyed over these years in upper portions of the Eel basin. Over 28 years of contemporary field research, peak algal biomass was generally higher in summers following bankfull, bed-scouring winter floods. Field surveys and experiments suggested that bed-mobilizing floods scour away overwintering grazers, releasing algae from spring and early summer grazing. During wet years, growth conditions for algae could also be enhanced by increased nutrient loading from the watershed, or by sustained summer base flows. Total annual rainfall and frustule densities in laminae over a longer 83-year record were weakly and negatively correlated, however, suggesting that positive effects of floods on annual algal production were primarily mediated by “top-down” (consumer release) rather than “bottom-up” (growth promoting) controls. |
Bouma-Gregson, Keith; Power, Mary; Bormans, Myriam Rise and fall of toxic benthic freshwater cyanobacteria (Anabaena spp.) in the Eel river: Buoyancy and dispersal Journal Article Harmful Algae, 66 (1), pp. 79-87, 2017. Abstract | Links | BibTeX | Tags: Benthic cyanobacteria Anabaena Buoyancy Harmful algal bloom Anatoxin-a Dispersal @article{Bouma-Gregson2017, title = {Rise and fall of toxic benthic freshwater cyanobacteria (Anabaena spp.) in the Eel river: Buoyancy and dispersal}, author = {Keith Bouma-Gregson and Mary Power and Myriam Bormans}, doi = {https://doi.org/10.1016/j.hal.2017.05.007}, year = {2017}, date = {2017-05-13}, journal = {Harmful Algae}, volume = {66}, number = {1}, pages = {79-87}, abstract = {Benthic cyanobacteria in rivers produce cyanotoxins and affect aquatic food webs, but knowledge of their ecology lags behind planktonic cyanobacteria. The buoyancy of benthic Anabaena spp. mats was studied to understand implications for Anabaena dispersal in the Eel River, California. Field experiments were used to investigate the effects of oxygen bubble production and dissolution on the buoyancy of Anabaena dominated benthic mats in response to light exposure. Samples of Anabaena dominated mats were harvested from the South Fork Eel River and placed in settling columns to measure floating and sinking velocities, or deployed into in situ ambient and low light treatments to measure the effect of light on flotation. Floating and sinking occurred within minutes and were driven by oxygen bubbles produced during photosynthesis, rather than intracellular changes in carbohydrates or gas vesicles. Light experiment results showed that in a natural ambient light regime, mats remained floating for at least 4 days, while in low light mats begin to sink in <24 h. Floating Anabaena samples were collected from five sites in the watershed and found to contain the cyanotoxins anatoxin-a and microcystin, with higher concentrations of anatoxin-a (median 560, max 30,693 ng/g DW) than microcystin (median 30, max 37 ng/g DW). The ability of Anabaena mats to maintain their buoyancy will markedly increase their downstream dispersal distances. Increased buoyancy also allows toxin-containing mats to collect along shorelines, increasing threats to human and animal public health.}, keywords = {Benthic cyanobacteria Anabaena Buoyancy Harmful algal bloom Anatoxin-a Dispersal}, pubstate = {published}, tppubtype = {article} } Benthic cyanobacteria in rivers produce cyanotoxins and affect aquatic food webs, but knowledge of their ecology lags behind planktonic cyanobacteria. The buoyancy of benthic Anabaena spp. mats was studied to understand implications for Anabaena dispersal in the Eel River, California. Field experiments were used to investigate the effects of oxygen bubble production and dissolution on the buoyancy of Anabaena dominated benthic mats in response to light exposure. Samples of Anabaena dominated mats were harvested from the South Fork Eel River and placed in settling columns to measure floating and sinking velocities, or deployed into in situ ambient and low light treatments to measure the effect of light on flotation. Floating and sinking occurred within minutes and were driven by oxygen bubbles produced during photosynthesis, rather than intracellular changes in carbohydrates or gas vesicles. Light experiment results showed that in a natural ambient light regime, mats remained floating for at least 4 days, while in low light mats begin to sink in <24 h. Floating Anabaena samples were collected from five sites in the watershed and found to contain the cyanotoxins anatoxin-a and microcystin, with higher concentrations of anatoxin-a (median 560, max 30,693 ng/g DW) than microcystin (median 30, max 37 ng/g DW). The ability of Anabaena mats to maintain their buoyancy will markedly increase their downstream dispersal distances. Increased buoyancy also allows toxin-containing mats to collect along shorelines, increasing threats to human and animal public health. |
Grant, Gordon E; Dietrich, William E The frontier beneath our feet Journal Article Water Resources Research, 53 (4), pp. 2605-2609, 2017. Abstract | Links | BibTeX | Tags: Critical Zone, environmental problems, field studies, groundwater, landscape development, water @article{Grant2017, title = {The frontier beneath our feet}, author = {Gordon E. Grant and William E. Dietrich}, doi = {https://doi.org/10.1002/2017WR020835 }, year = {2017}, date = {2017-04-20}, journal = {Water Resources Research}, volume = {53}, number = {4}, pages = {2605-2609}, abstract = {Following the simple question as to where water goes when it rains leads to one of the most exciting frontiers in earth science: the critical zone—Earth's dynamic skin. The critical zone extends from the top of the vegetation canopy through the soil and down to fresh bedrock and the bottom of the groundwater. Only recently recognized as a distinct zone, it is challenging to study because it is hard to observe directly, and varies widely across biogeoclimatic regions. Yet new ideas, instruments, and observations are revealing surprising and sometimes paradoxical insights, underscoring the value of field campaigns and long‐term observatories. These insights bear directly on some of the most pressing societal problems today: maintaining healthy forests, sustaining streamflow during droughts, and restoring productive terrestrial and aquatic ecosystems. The critical zone is critical because it supports all terrestrial life; it is the nexus where water and carbon is cycled, vegetation (hence food) grows, soil develops, landscapes evolve, and we live. No other frontier is so close to home. }, keywords = {Critical Zone, environmental problems, field studies, groundwater, landscape development, water}, pubstate = {published}, tppubtype = {article} } Following the simple question as to where water goes when it rains leads to one of the most exciting frontiers in earth science: the critical zone—Earth's dynamic skin. The critical zone extends from the top of the vegetation canopy through the soil and down to fresh bedrock and the bottom of the groundwater. Only recently recognized as a distinct zone, it is challenging to study because it is hard to observe directly, and varies widely across biogeoclimatic regions. Yet new ideas, instruments, and observations are revealing surprising and sometimes paradoxical insights, underscoring the value of field campaigns and long‐term observatories. These insights bear directly on some of the most pressing societal problems today: maintaining healthy forests, sustaining streamflow during droughts, and restoring productive terrestrial and aquatic ecosystems. The critical zone is critical because it supports all terrestrial life; it is the nexus where water and carbon is cycled, vegetation (hence food) grows, soil develops, landscapes evolve, and we live. No other frontier is so close to home. |
Schaaf, Cody J; Kelson, Suzanne J; Nusslé, Sébastien C; Carlson, Stephanie M Black spot infection in juvenile steelhead trout increases with stream temperature in northern California Journal Article Environmental Biology of Fishes, 100 (6), pp. 733-744, 2017. Abstract | Links | BibTeX | Tags: black spot disease, ecology, parasitism, steelhead trout, water temperature @article{Schaaf2017, title = {Black spot infection in juvenile steelhead trout increases with stream temperature in northern California}, author = {Cody J. Schaaf and Suzanne J. Kelson and Sébastien C. Nusslé and Stephanie M. Carlson}, doi = { 10.1007/s10641-017-0599-9}, year = {2017}, date = {2017-04-13}, journal = {Environmental Biology of Fishes}, volume = {100}, number = {6}, pages = {733-744}, abstract = {Climate change will increase water temperature in rivers and streams that provide critical habitat for imperiled species. Warmer water temperatures will influence the intensity and nature of biotic interactions, including parasitism. To better understand the factors influencing a neascus-type parasitic infection known as black spot disease, we examined the relationship between infection rate in juvenile steelhead trout (Oncorhynchus mykiss), abundance of another intermediate host (ramshorn snail, Planorbella trivolvis), and water temperature. We quantified infection patterns of trout at seven sites within the South Fork Eel River in northern California, visiting each site on three different occasions across the summer, and recording water temperature at each site. We also quantified infection patterns in trout captured from two tributaries to the South Fork Eel River. Overall, trout infection rates were highest in sites with the warmest temperatures. The abundance of ramshorn snails was positively related to both water temperature and black spot infection rates in juvenile trout. Both snail abundance and infection rates increased rapidly above a 23 °C daily maximum, suggesting a threshold effect at this temperature. We suggest that warmer temperatures are associated with environmental and biotic conditions that increase black spot disease prevalence in threatened steelhead trout. A comparison of our results with similar data collected from a more northern latitude suggests that salmonids in California may be warm-adapted in terms of their parasite susceptibility.}, keywords = {black spot disease, ecology, parasitism, steelhead trout, water temperature}, pubstate = {published}, tppubtype = {article} } Climate change will increase water temperature in rivers and streams that provide critical habitat for imperiled species. Warmer water temperatures will influence the intensity and nature of biotic interactions, including parasitism. To better understand the factors influencing a neascus-type parasitic infection known as black spot disease, we examined the relationship between infection rate in juvenile steelhead trout (Oncorhynchus mykiss), abundance of another intermediate host (ramshorn snail, Planorbella trivolvis), and water temperature. We quantified infection patterns of trout at seven sites within the South Fork Eel River in northern California, visiting each site on three different occasions across the summer, and recording water temperature at each site. We also quantified infection patterns in trout captured from two tributaries to the South Fork Eel River. Overall, trout infection rates were highest in sites with the warmest temperatures. The abundance of ramshorn snails was positively related to both water temperature and black spot infection rates in juvenile trout. Both snail abundance and infection rates increased rapidly above a 23 °C daily maximum, suggesting a threshold effect at this temperature. We suggest that warmer temperatures are associated with environmental and biotic conditions that increase black spot disease prevalence in threatened steelhead trout. A comparison of our results with similar data collected from a more northern latitude suggests that salmonids in California may be warm-adapted in terms of their parasite susceptibility. |
Alessandro Catenazzi, Sarah Kupferberg J Variation in thermal niche of a declining river-breeding frog:From counter-gradient responses to population distributionpatterns Journal Article Freshwater Biology, 62 (7), pp. 1255-1265, 2017. Abstract | Links | BibTeX | Tags: climate sensitivity, common-garden experiment, declining amphibians, hypolimnetic releases, Rana boylii @article{Catenazzi2017, title = {Variation in thermal niche of a declining river-breeding frog:From counter-gradient responses to population distributionpatterns}, author = {Alessandro Catenazzi, Sarah J. Kupferberg}, doi = {https://doi.org/10.1111/fwb.12942 }, year = {2017}, date = {2017-03-28}, journal = {Freshwater Biology}, volume = {62}, number = {7}, pages = {1255-1265}, abstract = {When dams or climate change alter the thermal regimes of rivers, conditions can shift outside optimal ranges for aquatic poikilothermic vertebrates. Plasticity in thermal performance and preference, however, may allow temperature‐vulnerable fauna to persist under challenging conditions. To determine the effects of thermal regime on Rana boylii (Ranidae), a threatened frog species endemic to rivers of California and Oregon, we quantified tadpole thermal preferences and performance in relation to thermal conditions. We monitored temperature and censused populations across a coastal to inland cline in six catchments where dams have altered thermal environments in close proximity to river reaches with natural conditions. We found geographic variation in population distribution and abundance based on river size combined with water temperature. The large inland rivers that supported breeding frogs, although cooler in spring due to snowmelt, became warmer during the summer than occupied coastal sites. Inland populations were constrained to reaches where the average temperature over the warmest 30 days ranged from 17.6 to 24.2°C, higher than coastal rainfall‐driven systems where averages ranged from 15.7 to 22.0°C. Frogs in rivers with hypolimnetic‐release dams bred in colder waters than they did in free‐flowing rivers. Common‐garden and field translocation experiments revealed local adaptations in larval growth and phenotypically plastic thermoregulatory behaviour. Tadpoles from all rivers had a positive linear growth response to temperature, but individuals from inland rivers displayed intrinsically higher growth rates. Consistent with a counter‐gradient model of selection in which the response to temperature change is in the opposite direction of the change, individuals from cooler rivers selected warmer temperatures. When reared under common conditions, however, tadpoles showed similar temperature preferences regardless of source river. Our results suggest a role for local growth rate adaptation in structuring the distribution of Rana boylii. Plastic thermoregulatory behaviour by tadpoles may explain how small populations are able to persist where dams release cold water. Management of edgewater habitats to increase the availability of warm micro‐sites may ameliorate this impact.}, keywords = {climate sensitivity, common-garden experiment, declining amphibians, hypolimnetic releases, Rana boylii}, pubstate = {published}, tppubtype = {article} } When dams or climate change alter the thermal regimes of rivers, conditions can shift outside optimal ranges for aquatic poikilothermic vertebrates. Plasticity in thermal performance and preference, however, may allow temperature‐vulnerable fauna to persist under challenging conditions. To determine the effects of thermal regime on Rana boylii (Ranidae), a threatened frog species endemic to rivers of California and Oregon, we quantified tadpole thermal preferences and performance in relation to thermal conditions. We monitored temperature and censused populations across a coastal to inland cline in six catchments where dams have altered thermal environments in close proximity to river reaches with natural conditions. We found geographic variation in population distribution and abundance based on river size combined with water temperature. The large inland rivers that supported breeding frogs, although cooler in spring due to snowmelt, became warmer during the summer than occupied coastal sites. Inland populations were constrained to reaches where the average temperature over the warmest 30 days ranged from 17.6 to 24.2°C, higher than coastal rainfall‐driven systems where averages ranged from 15.7 to 22.0°C. Frogs in rivers with hypolimnetic‐release dams bred in colder waters than they did in free‐flowing rivers. Common‐garden and field translocation experiments revealed local adaptations in larval growth and phenotypically plastic thermoregulatory behaviour. Tadpoles from all rivers had a positive linear growth response to temperature, but individuals from inland rivers displayed intrinsically higher growth rates. Consistent with a counter‐gradient model of selection in which the response to temperature change is in the opposite direction of the change, individuals from cooler rivers selected warmer temperatures. When reared under common conditions, however, tadpoles showed similar temperature preferences regardless of source river. Our results suggest a role for local growth rate adaptation in structuring the distribution of Rana boylii. Plastic thermoregulatory behaviour by tadpoles may explain how small populations are able to persist where dams release cold water. Management of edgewater habitats to increase the availability of warm micro‐sites may ameliorate this impact. |
Kim, Hyojin; Dietrich, William E; Thurnhoffer, Benjamin M; Bishop, Jim K B; Fung, Inez Y Water Resources Research, 53 (2), pp. 1424-1443, 2017. Abstract | Links | BibTeX | Tags: concentration-discharge relationships, critical zone structure, simultaneous observations of ground water and stream water @article{Kim2017, title = {Controls on solute concentration‐discharge relationships revealed by simultaneous hydrochemistry observations of hillslope runoff and stream flow: The importance of critical zone structure}, author = {Hyojin Kim and William E. Dietrich and Benjamin M. Thurnhoffer and Jim K. B. Bishop and Inez Y. Fung}, doi = {https://doi.org/10.1002/2016WR019722}, year = {2017}, date = {2017-01-27}, journal = {Water Resources Research}, volume = {53}, number = {2}, pages = {1424-1443}, abstract = {We investigated controls on concentration‐discharge relationships of a catchment underlain by argillite by monitoring both groundwater along a hillslope transect and stream chemistry. Samples were collected at 1–3 day intervals over 4 years (2009–2013) in Elder Creek in the Eel River Critical Zone Observatory in California. Runoff at our study hillslope is driven by vadose zone flux through deeply weathered argillite (5–25 m thick) to a perched, seasonally dynamic groundwater that then drains to Elder Creek. Low flow derives from the slowly draining deepest perched groundwater that reaches equilibrium between primary and secondary minerals and saturation with calcite under high subsurface pCO2. Arriving winter rains pass through the thick vadose zone, where they rapidly acquire solutes via cation exchange reactions (driven by high pCO2), and then recharge the groundwater that delivers runoff to the stream. These new waters displayed lower solute concentrations than the deep groundwater by less than a factor of 5 (except for Ca). Up to 74% of the total annual solute flux is derived from the vadose zone. The deep groundwater's Ca concentration decreased as it exfiltrates to the stream due to CO2 degassing and this Ca loss is equivalent of 30% of the total chemical weathering flux of Elder Creek. The thick vadose zone in weathered bedrock and the perched groundwater on underlying fresh bedrock result in two distinct processes that lead to the relatively invariant (chemostatic) concentration‐discharge behavior. The processes controlling solute chemistry are not evident from stream chemistry and runoff analysis alone.}, keywords = {concentration-discharge relationships, critical zone structure, simultaneous observations of ground water and stream water}, pubstate = {published}, tppubtype = {article} } We investigated controls on concentration‐discharge relationships of a catchment underlain by argillite by monitoring both groundwater along a hillslope transect and stream chemistry. Samples were collected at 1–3 day intervals over 4 years (2009–2013) in Elder Creek in the Eel River Critical Zone Observatory in California. Runoff at our study hillslope is driven by vadose zone flux through deeply weathered argillite (5–25 m thick) to a perched, seasonally dynamic groundwater that then drains to Elder Creek. Low flow derives from the slowly draining deepest perched groundwater that reaches equilibrium between primary and secondary minerals and saturation with calcite under high subsurface pCO2. Arriving winter rains pass through the thick vadose zone, where they rapidly acquire solutes via cation exchange reactions (driven by high pCO2), and then recharge the groundwater that delivers runoff to the stream. These new waters displayed lower solute concentrations than the deep groundwater by less than a factor of 5 (except for Ca). Up to 74% of the total annual solute flux is derived from the vadose zone. The deep groundwater's Ca concentration decreased as it exfiltrates to the stream due to CO2 degassing and this Ca loss is equivalent of 30% of the total chemical weathering flux of Elder Creek. The thick vadose zone in weathered bedrock and the perched groundwater on underlying fresh bedrock result in two distinct processes that lead to the relatively invariant (chemostatic) concentration‐discharge behavior. The processes controlling solute chemistry are not evident from stream chemistry and runoff analysis alone. |
Brett, Michael T; Bunn, Stuart E; Chandra, Sudeep; Galloway, Aaron W E; Guo, Fen; Kainz, Martin J; Kankaala, Paula; Lau, Danny C P; Moulton, Timothy P; Power, Mary E; Rasmussen, Joseph B; Taipale, Sami J; Thorp, James H; Wehr, John D How important are terrestrial organic carbon inputs for secondary production in freshwater ecosystems? Journal Article Freshwater Biology, 62 (5), pp. 833-853, 2017. Abstract | Links | BibTeX | Tags: allochthonous, autochthonous, biochemical composition, freshwater, resource utilisation @article{Wehr2017, title = {How important are terrestrial organic carbon inputs for secondary production in freshwater ecosystems?}, author = {Michael T. Brett and Stuart E. Bunn and Sudeep Chandra and Aaron W. E. Galloway and Fen Guo and Martin J. Kainz and Paula Kankaala and Danny C. P. Lau and Timothy P. Moulton and Mary E. Power and Joseph B. Rasmussen and Sami J. Taipale and James H. Thorp and John D. Wehr }, doi = {https://doi.org/10.1111/fwb.12909}, year = {2017}, date = {2017-01-19}, journal = {Freshwater Biology}, volume = {62}, number = {5}, pages = {833-853}, abstract = {Many freshwater systems receive substantial inputs of terrestrial organic matter. Terrestrially derived dissolved organic carbon (t‐DOC) inputs can modify light availability, the spatial distribution of primary production, heat, and oxygen in aquatic systems, as well as inorganic nutrient bioavailability. It is also well‐established that some terrestrial inputs (such as invertebrates and fruits) provide high‐quality food resources for consumers in some systems. In small to moderate‐sized streams, leaf litter inputs average approximately three times greater than the autochthonous production. Conversely, in oligo/mesotrophic lakes algal production is typically five times greater than the available flux of allochthonous basal resources. Terrestrial particulate organic carbon (t‐POC) inputs to lakes and rivers are comprised of 80%–90% biochemically recalcitrant lignocellulose, which is highly resistant to enzymatic breakdown by animal consumers. Further, t‐POC and heterotrophic bacteria lack essential biochemical compounds that are critical for rapid growth and reproduction in aquatic invertebrates and fishes. Several studies have directly shown that these resources have very low food quality for herbivorous zooplankton and benthic invertebrates. Much of the nitrogen assimilated by stream consumers is probably of algal origin, even in systems where there appears to be a significant terrestrial carbon contribution. Amino acid stable isotope analyses for large river food webs indicate that most upper trophic level essential amino acids are derived from algae. Similarly, profiles of essential fatty acids in consumers show a strong dependence on the algal food resources. Primary production to respiration ratios are not a meaningful index to assess consumer allochthony because respiration represents an oxidised carbon flux that cannot be utilised by animal consumers. Rather, the relative importance of allochthonous subsidies for upper trophic level production should be addressed by considering the rates at which terrestrial and autochthonous resources are consumed and the growth efficiency supported by this food. Ultimately, the biochemical composition of a particular basal resource, and not just its quantity or origin, determines how readily this material is incorporated into upper trophic level consumers. Because of its highly favourable biochemical composition and greater availability, we conclude that microalgal production supports most animal production in freshwater ecosystems. }, keywords = {allochthonous, autochthonous, biochemical composition, freshwater, resource utilisation}, pubstate = {published}, tppubtype = {article} } Many freshwater systems receive substantial inputs of terrestrial organic matter. Terrestrially derived dissolved organic carbon (t‐DOC) inputs can modify light availability, the spatial distribution of primary production, heat, and oxygen in aquatic systems, as well as inorganic nutrient bioavailability. It is also well‐established that some terrestrial inputs (such as invertebrates and fruits) provide high‐quality food resources for consumers in some systems. In small to moderate‐sized streams, leaf litter inputs average approximately three times greater than the autochthonous production. Conversely, in oligo/mesotrophic lakes algal production is typically five times greater than the available flux of allochthonous basal resources. Terrestrial particulate organic carbon (t‐POC) inputs to lakes and rivers are comprised of 80%–90% biochemically recalcitrant lignocellulose, which is highly resistant to enzymatic breakdown by animal consumers. Further, t‐POC and heterotrophic bacteria lack essential biochemical compounds that are critical for rapid growth and reproduction in aquatic invertebrates and fishes. Several studies have directly shown that these resources have very low food quality for herbivorous zooplankton and benthic invertebrates. Much of the nitrogen assimilated by stream consumers is probably of algal origin, even in systems where there appears to be a significant terrestrial carbon contribution. Amino acid stable isotope analyses for large river food webs indicate that most upper trophic level essential amino acids are derived from algae. Similarly, profiles of essential fatty acids in consumers show a strong dependence on the algal food resources. Primary production to respiration ratios are not a meaningful index to assess consumer allochthony because respiration represents an oxidised carbon flux that cannot be utilised by animal consumers. Rather, the relative importance of allochthonous subsidies for upper trophic level production should be addressed by considering the rates at which terrestrial and autochthonous resources are consumed and the growth efficiency supported by this food. Ultimately, the biochemical composition of a particular basal resource, and not just its quantity or origin, determines how readily this material is incorporated into upper trophic level consumers. Because of its highly favourable biochemical composition and greater availability, we conclude that microalgal production supports most animal production in freshwater ecosystems. |
2016 |
Butterfield, Cristina N; Li, Zhou; Andeer, Peter F; Spaulding, Susan; Thomas, Brian C; Singh, Andrea; Hettich, Robert L; Suttle, Kenwyn B; Probst, Alexander J; Tringe, Susannah G; Northen, Trent; Pan, Chongle; Banfield, Jillian F Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. Journal Article PeerJ, 4 , pp. e2687, 2016. Abstract | Links | BibTeX | Tags: metagenomics, northern California, soil microbes @article{Butterfield2016, title = {Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone.}, author = {Cristina N. Butterfield and Zhou Li and Peter F. Andeer and Susan Spaulding and Brian C. Thomas and Andrea Singh and Robert L. Hettich and Kenwyn B. Suttle and Alexander J. Probst and Susannah G. Tringe and Trent Northen and Chongle Pan and Jillian F. Banfield}, url = {https://angelo.berkeley.edu/peerj-2687-2/}, doi = {10.7717/peerj.2687}, year = {2016}, date = {2016-11-08}, journal = {PeerJ}, volume = {4}, pages = {e2687}, abstract = {Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10 – 20 cm and 30 – 40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate. From ten samples, we reconstructed 198 metagenome-assembled genomes that represent all major phylotypes. We also quantified 6,835 proteins and 175 metabolites and showed that after the rain event the concentrations of many sugars and amino acids approach zero at the base of the soil profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that these abundant organisms contribute substantially to carbon turnover in the soil, given that methylotrophy proteins were among the most abundant proteins in the proteome. Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid degradation. Many of the other bacteria appear to breakdown other components of plant biomass, as evidenced by the prevalence of various sugar and amino acid transporters and corresponding hydrolyzing machinery in the proteome. Overall, our work provides organism-resolved insight into the spatial distribution of bacteria and archaea whose activities combine to degrade plant-derived organics, limiting the transport of methanol, amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously little known soil microbes, were made possible via the combination of metagenomics, proteomics, and metabolomics.}, keywords = {metagenomics, northern California, soil microbes}, pubstate = {published}, tppubtype = {article} } Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10 – 20 cm and 30 – 40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate. From ten samples, we reconstructed 198 metagenome-assembled genomes that represent all major phylotypes. We also quantified 6,835 proteins and 175 metabolites and showed that after the rain event the concentrations of many sugars and amino acids approach zero at the base of the soil profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that these abundant organisms contribute substantially to carbon turnover in the soil, given that methylotrophy proteins were among the most abundant proteins in the proteome. Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid degradation. Many of the other bacteria appear to breakdown other components of plant biomass, as evidenced by the prevalence of various sugar and amino acid transporters and corresponding hydrolyzing machinery in the proteome. Overall, our work provides organism-resolved insight into the spatial distribution of bacteria and archaea whose activities combine to degrade plant-derived organics, limiting the transport of methanol, amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously little known soil microbes, were made possible via the combination of metagenomics, proteomics, and metabolomics. |
Riebe, Clifford S; Hahm, Jesse W; Brantley, Susan L Controls on deep critical zone architecture: a historical review and four testable hypotheses Journal Article Earth Surface Processes and Landforms, 42 (1), pp. 128-156, 2016. Abstract | Links | BibTeX | Tags: regolith production; near-surface geophysics; weathering; fractures @article{Riebe2016, title = {Controls on deep critical zone architecture: a historical review and four testable hypotheses}, author = {Clifford S. Riebe and W. Jesse Hahm and Susan L. Brantley}, doi = {https://doi.org/10.1002/esp.4052 }, year = {2016}, date = {2016-08-16}, journal = {Earth Surface Processes and Landforms}, volume = {42}, number = {1}, pages = {128-156}, abstract = {The base of Earth's critical zone (CZ) is commonly shielded from study by many meters of overlying rock and regolith. Though deep CZ processes may seem far removed from the surface, they are vital in shaping it, preparing rock for infusion into the biosphere and breaking Earth materials down for transport across landscapes. This special issue highlights outstanding challenges and recent advances of deep CZ research in a series of articles that we introduce here in the context of relevant literature dating back to the 1500s. Building on several contributions to the special issue, we highlight four exciting new hypotheses about factors that drive deep CZ weathering and thus influence the evolution of life‐sustaining CZ architecture. These hypotheses have emerged from recently developed process‐based models of subsurface phenomena including: fracturing related to subsurface stress fields; weathering related to drainage of bedrock under hydraulic head gradients; rock damage from frost cracking due to subsurface temperature gradients; and mineral reactions with reactive fluids in subsurface chemical potential gradients. The models predict distinct patterns of subsurface weathering and CZ thickness that can be compared with observations from drilling, sampling and geophysical imaging. We synthesize the four hypotheses into an overarching conceptual model of fracturing and weathering that occurs as Earth materials are exhumed to the surface across subsurface gradients in stress, hydraulic head, temperature, and chemical potential. We conclude with a call for a coordinated measurement campaign designed to comprehensively test the four hypotheses across a range of climatic, tectonic and geologic conditions.}, keywords = {regolith production; near-surface geophysics; weathering; fractures}, pubstate = {published}, tppubtype = {article} } The base of Earth's critical zone (CZ) is commonly shielded from study by many meters of overlying rock and regolith. Though deep CZ processes may seem far removed from the surface, they are vital in shaping it, preparing rock for infusion into the biosphere and breaking Earth materials down for transport across landscapes. This special issue highlights outstanding challenges and recent advances of deep CZ research in a series of articles that we introduce here in the context of relevant literature dating back to the 1500s. Building on several contributions to the special issue, we highlight four exciting new hypotheses about factors that drive deep CZ weathering and thus influence the evolution of life‐sustaining CZ architecture. These hypotheses have emerged from recently developed process‐based models of subsurface phenomena including: fracturing related to subsurface stress fields; weathering related to drainage of bedrock under hydraulic head gradients; rock damage from frost cracking due to subsurface temperature gradients; and mineral reactions with reactive fluids in subsurface chemical potential gradients. The models predict distinct patterns of subsurface weathering and CZ thickness that can be compared with observations from drilling, sampling and geophysical imaging. We synthesize the four hypotheses into an overarching conceptual model of fracturing and weathering that occurs as Earth materials are exhumed to the surface across subsurface gradients in stress, hydraulic head, temperature, and chemical potential. We conclude with a call for a coordinated measurement campaign designed to comprehensively test the four hypotheses across a range of climatic, tectonic and geologic conditions. |
Estes, James; Dayton, Paul; Kareiva, Peter; Levin, Simon; Lubchenco, Jane; Menge, Bruce; Palumbi, Stephen; Mary, ; Power, ; Terborgh, John A keystone ecologist: Robert Treat Paine, 1933–2016 Journal Article Ecology, 97 (11), pp. 2905-2909, 2016. Abstract | Links | BibTeX | Tags: intermediate disturbance, keystone species, mentor, patch dynamics, tribute to life, trophic cascade, zonation @article{Estes2016, title = {A keystone ecologist: Robert Treat Paine, 1933–2016}, author = {James Estes and Paul Dayton and Peter Kareiva and Simon Levin and Jane Lubchenco and Bruce Menge and Stephen Palumbi and Mary and Power and John Terborgh }, doi = {https://doi.org/10.1002/ecy.1572 }, year = {2016}, date = {2016-08-13}, journal = {Ecology}, volume = {97}, number = {11}, pages = {2905-2909}, abstract = {Robert T. Paine, who passed away on 13 June 2016, is among the most influential people in the history of ecology. Paine was an experimentalist, a theoretician, a practitioner, and proponent of the “ecology of place,” and a deep believer in the importance of natural history to ecological understanding. His scientific legacy grew from the discovery of a link between top‐down forcing and species diversity, a breakthrough that led to the ideas of both keystone species and trophic cascades, and to our early understanding of the mosaic nature of biological communities, causes of zonation across physical gradients, and the intermediate‐disturbance hypothesis of species diversity. Paine's influence as a mentor was equally important to the growth of ecological thinking, natural resource conservation, and policy. He served ecology as an Ecological Society of America president, an editor of the Society's journals, a member of and contributor to the National Academy of Sciences and the National Research Council, and an in‐demand advisor to various state and federal agencies. Paine's broad interests, enthusiasm, charisma, and humor deeply affected our lives and the lives of so many others.}, keywords = {intermediate disturbance, keystone species, mentor, patch dynamics, tribute to life, trophic cascade, zonation}, pubstate = {published}, tppubtype = {article} } Robert T. Paine, who passed away on 13 June 2016, is among the most influential people in the history of ecology. Paine was an experimentalist, a theoretician, a practitioner, and proponent of the “ecology of place,” and a deep believer in the importance of natural history to ecological understanding. His scientific legacy grew from the discovery of a link between top‐down forcing and species diversity, a breakthrough that led to the ideas of both keystone species and trophic cascades, and to our early understanding of the mosaic nature of biological communities, causes of zonation across physical gradients, and the intermediate‐disturbance hypothesis of species diversity. Paine's influence as a mentor was equally important to the growth of ecological thinking, natural resource conservation, and policy. He served ecology as an Ecological Society of America president, an editor of the Society's journals, a member of and contributor to the National Academy of Sciences and the National Research Council, and an in‐demand advisor to various state and federal agencies. Paine's broad interests, enthusiasm, charisma, and humor deeply affected our lives and the lives of so many others. |
Lee, Jun-Hak; Biging, Gregory; Fisher, Joshua An Individual Tree-Based Automated Registration of Aerial Images to Lidar Data in a Forested Area Journal Article Photogrammetric Engineering & Remote Sensing, 82 (9), pp. 699-701, 2016. Abstract | Links | BibTeX | Tags: aerial images, LiDAR, tree tops @article{Jun-HakLee2016, title = {An Individual Tree-Based Automated Registration of Aerial Images to Lidar Data in a Forested Area}, author = {Jun-Hak Lee and Gregory Biging and Joshua Fisher}, doi = {https://doi.org/10.1016/S0099-1112(16)30121-5}, year = {2016}, date = {2016-08-01}, journal = {Photogrammetric Engineering & Remote Sensing}, volume = {82}, number = {9}, pages = {699-701}, abstract = {In this paper, we demonstrate an approach to align aerial images to airborne lidar data by using common object features (tree tops) from both data sets under the condition that conventional correlation-based approaches are challenging due to the fact that the spatial pattern of pixel gray-scale values in aerial images hardly exist in lidar data. We extracted tree tops by using an image processing technique called extended-maxima transformation from both aerial images and lidar data. Our approach was tested at the Angelo Coast Range Reserve on the South Fork Eel River forests in Mendocino County, California. Although the aerial images were acquired simultaneously with the lidar data, the images had only approximate exposure point locations and average flight elevation information, which mimicked the condition of limited information availability about the aerial images. Our results showed that this approach enabled us to align aerial images to airborne lidar data at the single-tree level with reasonable accuracy. With a local transformation model (piecewise linear model), the rmse and the median absolute deviation (mad) of the registration were 9.2 pixels (2.3 meters) and 6.8 pixels (1.41 meters), respectively. We expect our approach to be applicable to fine scale change detection for forest ecosystems and may serve to extract detailed forest biophysical parameters. }, keywords = {aerial images, LiDAR, tree tops}, pubstate = {published}, tppubtype = {article} } In this paper, we demonstrate an approach to align aerial images to airborne lidar data by using common object features (tree tops) from both data sets under the condition that conventional correlation-based approaches are challenging due to the fact that the spatial pattern of pixel gray-scale values in aerial images hardly exist in lidar data. We extracted tree tops by using an image processing technique called extended-maxima transformation from both aerial images and lidar data. Our approach was tested at the Angelo Coast Range Reserve on the South Fork Eel River forests in Mendocino County, California. Although the aerial images were acquired simultaneously with the lidar data, the images had only approximate exposure point locations and average flight elevation information, which mimicked the condition of limited information availability about the aerial images. Our results showed that this approach enabled us to align aerial images to airborne lidar data at the single-tree level with reasonable accuracy. With a local transformation model (piecewise linear model), the rmse and the median absolute deviation (mad) of the registration were 9.2 pixels (2.3 meters) and 6.8 pixels (1.41 meters), respectively. We expect our approach to be applicable to fine scale change detection for forest ecosystems and may serve to extract detailed forest biophysical parameters. |
Lind, Amy; Welsh, Hartwell; Wheeler, Clara Foothill yellow-legged frog (Rana boylii) oviposition site choice at multiple spatial scales Journal Article Journal of Herpetology, 50 (2), pp. 263-270, 2016. Abstract | Links | BibTeX | Tags: Rana boylii @article{Lind2016, title = {Foothill yellow-legged frog (Rana boylii) oviposition site choice at multiple spatial scales}, author = {Amy Lind and Hartwell Welsh and Clara Wheeler}, doi = {https://doi.org/10.1670/14-169}, year = {2016}, date = {2016-06-01}, journal = {Journal of Herpetology}, volume = {50}, number = {2}, pages = {263-270}, abstract = {Studies of resource selection at multiple scales are critical to understanding ecological and evolutionary attributes of a species. We analyzed relative abundance, habitat use, and oviposition site selection of Foothill Yellow-Legged Frogs (Rana boylii) at 11 localities across two geographic regions in California (northern Coast Range and Sierra Nevada) over 16 yr. We found narrow ranges for oviposition microhabitat characteristics (water depth, water velocity, and stream substrate) among study localities. At the Main and South forks of the Trinity River, variances of the habitat traits were lower for oviposition microsites than for random points within breeding areas, indicating fine-scale selection. On the South Fork Trinity, egg mass relative abundances were negatively associated with water depth and positively associated with distance from the shoreline, suggesting that breeding areas with high egg mass relative abundances generally occurred in wide shallow areas. We observed long-term repeated use of breeding sites. At the South Fork Trinity, 63% of potentially suitable breeding areas were used consecutively for 3 yr, and at Hurdygurdy Creek several areas were used in ≥11 yr. Oviposition site selection and microhabitat specificity may result in population stability even within the substantial temporal and spatial variability of stream environments. Management of stream environments and conservation plans for R. boylii could benefit by preserving hydrologic processes that produce these specific habitats and identifying and protecting high-use breeding areas. }, keywords = {Rana boylii}, pubstate = {published}, tppubtype = {article} } Studies of resource selection at multiple scales are critical to understanding ecological and evolutionary attributes of a species. We analyzed relative abundance, habitat use, and oviposition site selection of Foothill Yellow-Legged Frogs (Rana boylii) at 11 localities across two geographic regions in California (northern Coast Range and Sierra Nevada) over 16 yr. We found narrow ranges for oviposition microhabitat characteristics (water depth, water velocity, and stream substrate) among study localities. At the Main and South forks of the Trinity River, variances of the habitat traits were lower for oviposition microsites than for random points within breeding areas, indicating fine-scale selection. On the South Fork Trinity, egg mass relative abundances were negatively associated with water depth and positively associated with distance from the shoreline, suggesting that breeding areas with high egg mass relative abundances generally occurred in wide shallow areas. We observed long-term repeated use of breeding sites. At the South Fork Trinity, 63% of potentially suitable breeding areas were used consecutively for 3 yr, and at Hurdygurdy Creek several areas were used in ≥11 yr. Oviposition site selection and microhabitat specificity may result in population stability even within the substantial temporal and spatial variability of stream environments. Management of stream environments and conservation plans for R. boylii could benefit by preserving hydrologic processes that produce these specific habitats and identifying and protecting high-use breeding areas. |
Uno, Hiromi Spatial and temporal linkage of stream-riparian food webs by seasonal migration of mayfly Ephemerella maculata PhD Thesis University of California, Berkeley, 2016, ISBN: 978-1-369-05549-8. Abstract | BibTeX | Tags: Aquatic insect, Aquatic-terrestrial linkage, Biological sciences, food web, Spatial heterogeneity, subsidy, Temporal heterogeneity @phdthesis{Uno2016, title = {Spatial and temporal linkage of stream-riparian food webs by seasonal migration of mayfly Ephemerella maculata}, author = {Hiromi Uno}, isbn = {978-1-369-05549-8}, year = {2016}, date = {2016-05-30}, school = {University of California, Berkeley}, abstract = {Stream environments are spatially and temporally heterogeneous. Mainstem rivers are often wide, sunlit, warm and productive, while tributaries are shaded by riparian trees, unproductive, and remain cool in summer. Within mainstem rivers themselves there is substantial spatial heterogeneity in habitat structure and physical conditions, such as water temperature. River environments also change dramatically with season. Organisms that live in the riverine environment respond to and take advantage of such heterogeneous environments by moving between microhabitats or shifting their phenology. I studied the life cycle of a riverine mayfly, Ephemerella maculata (Ephemerellidae), in a northern California river system, its responses to spatial and temporal heterogeneity, and how its movements connect stream and riparian food webs in space and time. I discovered that E. maculata migrates between the mainstem and tributaries of rivers during its life cycle, thereby linking food webs in these two habitats, and enhancing predator growth in unproductive tributaries. The resource subsidy from productive but warm rivers to cool, unproductive tributaries associated with the mayfly migration increase the growth of stenothermic predators like juvenile salmonids in otherwise food-limited, cool thermal refuges, and increase their resilience to future warming. Furthermore, I examined the resilience of E. maculata to changes in water temperature using field surveys and lab rearing experiments. I discovered that different life stages of E. maculata have different thermal responses, and they shift their phenology depending on the water temperature, allowing each life stage to occur in the most desirable thermal condition. Therefore, as long as the natural seasonal pattern of the water temperature is sustained, E. maculata can resist temperature changes by shifting their phenology. Finally, I have shown that thermal spatial heterogeneity of rivers desynchronizes mayfly emergence timing, prolonging the subsidy period to riparian predators, and changing the predators’ responses to this subsidy.}, keywords = {Aquatic insect, Aquatic-terrestrial linkage, Biological sciences, food web, Spatial heterogeneity, subsidy, Temporal heterogeneity}, pubstate = {published}, tppubtype = {phdthesis} } Stream environments are spatially and temporally heterogeneous. Mainstem rivers are often wide, sunlit, warm and productive, while tributaries are shaded by riparian trees, unproductive, and remain cool in summer. Within mainstem rivers themselves there is substantial spatial heterogeneity in habitat structure and physical conditions, such as water temperature. River environments also change dramatically with season. Organisms that live in the riverine environment respond to and take advantage of such heterogeneous environments by moving between microhabitats or shifting their phenology. I studied the life cycle of a riverine mayfly, Ephemerella maculata (Ephemerellidae), in a northern California river system, its responses to spatial and temporal heterogeneity, and how its movements connect stream and riparian food webs in space and time. I discovered that E. maculata migrates between the mainstem and tributaries of rivers during its life cycle, thereby linking food webs in these two habitats, and enhancing predator growth in unproductive tributaries. The resource subsidy from productive but warm rivers to cool, unproductive tributaries associated with the mayfly migration increase the growth of stenothermic predators like juvenile salmonids in otherwise food-limited, cool thermal refuges, and increase their resilience to future warming. Furthermore, I examined the resilience of E. maculata to changes in water temperature using field surveys and lab rearing experiments. I discovered that different life stages of E. maculata have different thermal responses, and they shift their phenology depending on the water temperature, allowing each life stage to occur in the most desirable thermal condition. Therefore, as long as the natural seasonal pattern of the water temperature is sustained, E. maculata can resist temperature changes by shifting their phenology. Finally, I have shown that thermal spatial heterogeneity of rivers desynchronizes mayfly emergence timing, prolonging the subsidy period to riparian predators, and changing the predators’ responses to this subsidy. |
Power, Mary E; Kupferberg, Sarah J; Cooper, Scott D; Deas, Michael L Ecosystems of California, Rivers Book Chapter Mooney, Harold; Zavaleta, Erika (Ed.): Chapter 33, pp. 713-752, University of California Press, 2016, ISBN: 0520278801. Abstract | Links | BibTeX | Tags: California rivers, ecosystem @inbook{Power2016, title = {Ecosystems of California, Rivers}, author = {Mary E. Power and Sarah J. Kupferberg and Scott D. Cooper and Michael L. Deas}, editor = {Harold Mooney and Erika Zavaleta}, url = {https://angelo.berkeley.edu/?attachment_id=2668 }, isbn = {0520278801}, year = {2016}, date = {2016-01-19}, pages = {713-752}, publisher = {University of California Press}, chapter = {33}, abstract = {This long-anticipated reference and sourcebook for California’s remarkable ecological abundance provides an integrated assessment of each major ecosystem type—its distribution, structure, function, and management. A comprehensive synthesis of our knowledge about this biologically diverse state, Ecosystems of California covers the state from oceans to mountaintops using multiple lenses: past and present, flora and fauna, aquatic and terrestrial, natural and managed. Each chapter evaluates natural processes for a specific ecosystem, describes drivers of change, and discusses how that ecosystem may be altered in the future. This book also explores the drivers of California’s ecological patterns and the history of the state’s various ecosystems, outlining how the challenges of climate change and invasive species and opportunities for regulation and stewardship could potentially affect the state’s ecosystems. The text explicitly incorporates both human impacts and conservation and restoration efforts and shows how ecosystems support human well-being. Edited by two esteemed ecosystem ecologists and with overviews by leading experts on each ecosystem, this definitive work will be indispensable for natural resource management and conservation professionals as well as for undergraduate or graduate students of California’s environment and curious naturalists.}, keywords = {California rivers, ecosystem}, pubstate = {published}, tppubtype = {inbook} } This long-anticipated reference and sourcebook for California’s remarkable ecological abundance provides an integrated assessment of each major ecosystem type—its distribution, structure, function, and management. A comprehensive synthesis of our knowledge about this biologically diverse state, Ecosystems of California covers the state from oceans to mountaintops using multiple lenses: past and present, flora and fauna, aquatic and terrestrial, natural and managed. Each chapter evaluates natural processes for a specific ecosystem, describes drivers of change, and discusses how that ecosystem may be altered in the future. This book also explores the drivers of California’s ecological patterns and the history of the state’s various ecosystems, outlining how the challenges of climate change and invasive species and opportunities for regulation and stewardship could potentially affect the state’s ecosystems. The text explicitly incorporates both human impacts and conservation and restoration efforts and shows how ecosystems support human well-being. Edited by two esteemed ecosystem ecologists and with overviews by leading experts on each ecosystem, this definitive work will be indispensable for natural resource management and conservation professionals as well as for undergraduate or graduate students of California’s environment and curious naturalists. |
Afkhami, Michelle E; Strauss, Sharon Y Native fungal endophytes suppress an exotic dominant and increase plant diversity over small and large spatial scales Journal Article Ecology, 97 (5), pp. 1159–1169, 2016. Abstract | Links | BibTeX | Tags: biodiversity, Bromus laevipes, Epichloë, evenness, fungal endophyte, grass, hidden players, invasive species, keystone species, mutualism, richness, symbiosis @article{Afkhami2016, title = {Native fungal endophytes suppress an exotic dominant and increase plant diversity over small and large spatial scales}, author = {Michelle E. Afkhami and Sharon Y. Strauss}, url = {https://angelo.berkeley.edu/wp-content/uploads/Afkhami_2016_Eco.pdf}, doi = {10.1890/15-1166.1}, year = {2016}, date = {2016-01-01}, journal = {Ecology}, volume = {97}, number = {5}, pages = {1159–1169}, abstract = {Understanding community dynamics and processes, such as the factors that generate and maintain biodiversity, drive succession, and affect invasion susceptibility, is a central goal in ecology and evolution. While most studies of how species interactions affect communities have focused on highly visible macroorganisms, we show that mutualistic microfungal endophytes have community-level effects across their host plant’s range and provide the first example of fungal endophytes enhancing plant diversity. A three-year field study in which we experimentally manipulated endophyte abundance in a native Californian grass showed that despite their minute biomass, endophytes dramatically increased plant community diversity (~110% greater increase with endophytes) by suppressing a dominant invasive grass, Bromus diandrus. This effect was also detectable, but smaller, across five additional common gardens spanning ecologically diverse habitats, different climates, and >400 km of the host grass’ range as well as at microspatial scales within gardens. Our study illustrates that mutualistic microbes, while often hidden players, can have unexpectedly large ecological impacts across a wide range of habitats and scales and may be important for promoting diverse communities and ecosystems.}, keywords = {biodiversity, Bromus laevipes, Epichloë, evenness, fungal endophyte, grass, hidden players, invasive species, keystone species, mutualism, richness, symbiosis}, pubstate = {published}, tppubtype = {article} } Understanding community dynamics and processes, such as the factors that generate and maintain biodiversity, drive succession, and affect invasion susceptibility, is a central goal in ecology and evolution. While most studies of how species interactions affect communities have focused on highly visible macroorganisms, we show that mutualistic microfungal endophytes have community-level effects across their host plant’s range and provide the first example of fungal endophytes enhancing plant diversity. A three-year field study in which we experimentally manipulated endophyte abundance in a native Californian grass showed that despite their minute biomass, endophytes dramatically increased plant community diversity (~110% greater increase with endophytes) by suppressing a dominant invasive grass, Bromus diandrus. This effect was also detectable, but smaller, across five additional common gardens spanning ecologically diverse habitats, different climates, and >400 km of the host grass’ range as well as at microspatial scales within gardens. Our study illustrates that mutualistic microbes, while often hidden players, can have unexpectedly large ecological impacts across a wide range of habitats and scales and may be important for promoting diverse communities and ecosystems. |
2015 |
Dralle, David; Karst, Nathaniel; Thompson, Sally E a, b careful: The challenge of scale invariance for comparative analyses in power law models of the streamflow recession Journal Article Geophysical Research Letters, 42 (21), 2015. Abstract | Links | BibTeX | Tags: Power Law, Stream Flow @article{Dralle2015, title = {a, b careful: The challenge of scale invariance for comparative analyses in power law models of the streamflow recession}, author = {David Dralle and Nathaniel Karst and Sally E. Thompson}, url = {https://angelo.berkeley.edu/wp-content/uploads/Dralle_2015_GeophyResLet.pdf}, doi = {10.1002/2015GL066007}, year = {2015}, date = {2015-10-21}, journal = {Geophysical Research Letters}, volume = {42}, number = {21}, abstract = {The falling limb of the hydrograph – the streamflow recession – is frequently well-approximated by power law functions, in the form dq/dt =− aqb, so that recessions are often characterized in terms of their power law parameters (a, b). The empirical determination and interpretation of the parameter a is typically biased by the presence of a ubiquitous mathematical artifact resulting from the scale-free properties of the power law function. This reduces the information available from recession parameter analysis, and creates several heretofore-unaddressed methodological ‘pitfalls’. This letter outlines the artifact, demonstrates its genesis, and presents an empirical re-scaling method to remove artifact effects from fitted recession parameters. The re-scaling process reveals underlying climatic patterns obscured in the original data, and, we suggest, could maximize the information content of fitted power laws. }, keywords = {Power Law, Stream Flow}, pubstate = {published}, tppubtype = {article} } The falling limb of the hydrograph – the streamflow recession – is frequently well-approximated by power law functions, in the form dq/dt =− aqb, so that recessions are often characterized in terms of their power law parameters (a, b). The empirical determination and interpretation of the parameter a is typically biased by the presence of a ubiquitous mathematical artifact resulting from the scale-free properties of the power law function. This reduces the information available from recession parameter analysis, and creates several heretofore-unaddressed methodological ‘pitfalls’. This letter outlines the artifact, demonstrates its genesis, and presents an empirical re-scaling method to remove artifact effects from fitted recession parameters. The re-scaling process reveals underlying climatic patterns obscured in the original data, and, we suggest, could maximize the information content of fitted power laws. |
Uno, Hiromi; Power, Mary E Mainstem-tributary linkages by mayfly migration help sustain salmonids in a warming river network Journal Article Ecology Letters, 18 (10), pp. 1012-1020, 2015. Abstract | Links | BibTeX | Tags: salmonids, warming @article{Uno2015, title = {Mainstem-tributary linkages by mayfly migration help sustain salmonids in a warming river network}, author = {Hiromi Uno and Mary E. Power}, url = {https://angelo.berkeley.edu/wp-content/uploads/Uno_2015_EcoLet.pdf}, doi = {10.1111/ele.12483}, year = {2015}, date = {2015-08-06}, journal = {Ecology Letters}, volume = {18}, number = {10}, pages = {1012-1020}, abstract = {Animal migrations can link ecosystems across space. We discovered an aquatic insect thatmigrates between a river mainstem and its tributaries, and provides an important trophic subsidyfor tributary predators. A mayfly,Ephemerella maculata, rears in a warm, sunlit productive rivermainstem, then migrates as adults to cool, shaded unproductive tributaries where they ovipositand die. This migration tripled insect flux into a tributary for 1 month in summer. A manipulativefield experiment showed that thisE. maculatasubsidy nearly tripled the growth of the young ofthe year steelhead trout (Oncorhynchus mykiss) in the recipient tributary over the summer months,and was more important than terrestrial invertebrate subsidies, which have been considered theprimary food source for predators in small, forested creeks. By delivering food subsidies from pro-ductive but warming river mainstems to cool but food-limited tributaries, aquatic insect migra-tions could enhance resilience to cool-water predators in warming river networks.}, keywords = {salmonids, warming}, pubstate = {published}, tppubtype = {article} } Animal migrations can link ecosystems across space. We discovered an aquatic insect thatmigrates between a river mainstem and its tributaries, and provides an important trophic subsidyfor tributary predators. A mayfly,Ephemerella maculata, rears in a warm, sunlit productive rivermainstem, then migrates as adults to cool, shaded unproductive tributaries where they ovipositand die. This migration tripled insect flux into a tributary for 1 month in summer. A manipulativefield experiment showed that thisE. maculatasubsidy nearly tripled the growth of the young ofthe year steelhead trout (Oncorhynchus mykiss) in the recipient tributary over the summer months,and was more important than terrestrial invertebrate subsidies, which have been considered theprimary food source for predators in small, forested creeks. By delivering food subsidies from pro-ductive but warming river mainstems to cool but food-limited tributaries, aquatic insect migra-tions could enhance resilience to cool-water predators in warming river networks. |
Carah, Jennifer K; Howard, Jeanette K; Thompson, Sally E; Gianotti, Anne Short G; Bauer, Scott D; Carlson, Stephanie M; Dralle, David N; Gabriel, Mourad W; Hulette, Lisa L; Johnson, Brian J; Knight, Curtis A; Kupferberg, Sarah J; Martin, Stefanie L; Naylor, Rosamond L; Power, Mary E High Time for Conservation: Adding the Environment to the Debate on Marijuana Liberalization Journal Article BioScience, 65 (8), pp. 822-829, 2015. Abstract | Links | BibTeX | Tags: Environment, Marijuana @article{Carah2015, title = {High Time for Conservation: Adding the Environment to the Debate on Marijuana Liberalization}, author = {Jennifer K. Carah and Jeanette K. Howard and Sally E. Thompson and Anne G. Short Gianotti and Scott D. Bauer and Stephanie M. Carlson and David N. Dralle and Mourad W. Gabriel and Lisa L. Hulette and Brian J. Johnson and Curtis A. Knight and Sarah J. Kupferberg and Stefanie L. Martin and Rosamond L. Naylor and Mary E. Power}, url = {https://angelo.berkeley.edu/wp-content/uploads/Carah_2015-Biosci.pdf}, doi = {10.1093/biosci/biv083}, year = {2015}, date = {2015-08-01}, journal = {BioScience}, volume = {65}, number = {8}, pages = {822-829}, abstract = {The liberalization of marijuana policies, including the legalization of medical and recreational marijuana, is sweeping the United States and other countries. Marijuana cultivation can have significant negative collateral effects on the environment that are often unknown or overlooked. Focusing on the state of California, where by some estimates 60%–70% of the marijuana consumed in the United States is grown, we argue that (a) the environmental harm caused by marijuana cultivation merits a direct policy response, (b) current approaches to governing the environmental effects are inadequate, and (c) neglecting discussion of the environmental impacts of cultivation when shaping future marijuana use and possession policies represents a missed opportunity to reduce, regulate, and mitigate environmental harm.}, keywords = {Environment, Marijuana}, pubstate = {published}, tppubtype = {article} } The liberalization of marijuana policies, including the legalization of medical and recreational marijuana, is sweeping the United States and other countries. Marijuana cultivation can have significant negative collateral effects on the environment that are often unknown or overlooked. Focusing on the state of California, where by some estimates 60%–70% of the marijuana consumed in the United States is grown, we argue that (a) the environmental harm caused by marijuana cultivation merits a direct policy response, (b) current approaches to governing the environmental effects are inadequate, and (c) neglecting discussion of the environmental impacts of cultivation when shaping future marijuana use and possession policies represents a missed opportunity to reduce, regulate, and mitigate environmental harm. |
F. Stuart Chapin, III ; Pickett, Steward T A; Power, Mary E; Jackson, Robert B; Carter, David M; Duke, Clifford Earth Stewardship: A Strategy for Social-Ecological Transformation to Reverse Planetary Degradation Book Chapter et al., Riccardo Rozzi (Ed.): 2 (1), Springer International Publishing, 2015, ISBN: 978-3-319-12132-1. Abstract | Links | BibTeX | Tags: Ecological Society of America, Ethics @inbook{Chapin2015, title = {Earth Stewardship: A Strategy for Social-Ecological Transformation to Reverse Planetary Degradation}, author = {F. Stuart Chapin, III and Steward T. A. Pickett and Mary E. Power and Robert B. Jackson and David M. Carter and Clifford Duke}, editor = {Riccardo Rozzi et al.}, url = {https://angelo.berkeley.edu/wp-content/uploads/Chapin_2015_EcoEthicThePract.pdf}, isbn = {978-3-319-12132-1}, year = {2015}, date = {2015-03-27}, volume = {2}, number = {1}, publisher = {Springer International Publishing}, abstract = {A century ago, stewards were responsible for managing estates or for keeping order at public events. Today, the Earth is one global estate, and improved stewardship is vital for maintaining social order and for preserving life on Earth. In this paper, we describe Earth Stewardship, a social-ecological framework for sustaining life in a rapidly changing world. The paper defines the components of Earth Stewardship, characterizes the scientific needs for its agenda, and discusses initial efforts to engage multiple disciplines and segments of society in its application. As a beginning, new knowledge for global stewardship must be generated by teams of physical, biological, and social scientists. However, other stakdersre needed for enerating and applying such knowledge, including people in communities of faith, professions involved in design, planning and restoration, and policy makers and managers. Communicating environmental problems and solutions must take into account the psychology of how people perceive problems, promoting positive stances toward the actions needed for an adaptive approach to Earth Stewardship. Successful long-term stewardship of the Earth will require a global partnership linking researchers, managers, policy makers, and citizens.}, keywords = {Ecological Society of America, Ethics}, pubstate = {published}, tppubtype = {inbook} } A century ago, stewards were responsible for managing estates or for keeping order at public events. Today, the Earth is one global estate, and improved stewardship is vital for maintaining social order and for preserving life on Earth. In this paper, we describe Earth Stewardship, a social-ecological framework for sustaining life in a rapidly changing world. The paper defines the components of Earth Stewardship, characterizes the scientific needs for its agenda, and discusses initial efforts to engage multiple disciplines and segments of society in its application. As a beginning, new knowledge for global stewardship must be generated by teams of physical, biological, and social scientists. However, other stakdersre needed for enerating and applying such knowledge, including people in communities of faith, professions involved in design, planning and restoration, and policy makers and managers. Communicating environmental problems and solutions must take into account the psychology of how people perceive problems, promoting positive stances toward the actions needed for an adaptive approach to Earth Stewardship. Successful long-term stewardship of the Earth will require a global partnership linking researchers, managers, policy makers, and citizens. |
Power, Mary E; Bouma-Gregson, Keith; Higgins, Patrick; Carlson, Stephanie M Copeia, 103 (1), pp. 200-211, 2015. Abstract | Links | BibTeX | Tags: cyanobacteria, Eel river, salmonids @article{Power2015, title = {The Thirsty Eel: Summer and Winter Flow Thresholds that Tilt the Eel River of Northwestern California from Salmon-Supporting to Cyanobacterially Degraded States}, author = {Mary E. Power and Keith Bouma-Gregson and Patrick Higgins and Stephanie M. Carlson}, url = {https://angelo.berkeley.edu/wp-content/uploads/Power_2015_Copeia.pdf}, doi = {10.1643/CE-14-086}, year = {2015}, date = {2015-03-05}, journal = {Copeia}, volume = {103}, number = {1}, pages = {200-211}, abstract = {Although it flows through regions of northwestern California that are thought to be relatively well watered, the Eel River is increasingly stressed by drought and water withdrawals. We discuss how critical threshold changes in summer discharge can potentially tilt the Eel from a recovering salmon-supporting ecosystem toward a cyanobacterially degraded one. To maintain food webs and habitats that support salmonids and suppress harmful cyanobacteria, summer discharge must be sufficient to connect mainstem pools hydrologically with gently moving, cool base flow. Rearing salmon and steelhead can survive even in pools that become isolated during summer low flows if hyporheic exchange is sufficient. But if the ground water discharge that sustains river flow during summer drought drops below critical levels, warm stagnant conditions will kill salmonids, and cyanobacteria will thrive. Challenges and opportunities for restoring the Eel and increasing its resilience to climate extremes, water diversions, and excessive loading of fine sediments point toward exploring how land use and terrestrial vegetation affect delivery from uplands of water, heat, sediments, solutes, organic matter, and organisms—in ways that either heal or damage rivers. }, keywords = {cyanobacteria, Eel river, salmonids}, pubstate = {published}, tppubtype = {article} } Although it flows through regions of northwestern California that are thought to be relatively well watered, the Eel River is increasingly stressed by drought and water withdrawals. We discuss how critical threshold changes in summer discharge can potentially tilt the Eel from a recovering salmon-supporting ecosystem toward a cyanobacterially degraded one. To maintain food webs and habitats that support salmonids and suppress harmful cyanobacteria, summer discharge must be sufficient to connect mainstem pools hydrologically with gently moving, cool base flow. Rearing salmon and steelhead can survive even in pools that become isolated during summer low flows if hyporheic exchange is sufficient. But if the ground water discharge that sustains river flow during summer drought drops below critical levels, warm stagnant conditions will kill salmonids, and cyanobacteria will thrive. Challenges and opportunities for restoring the Eel and increasing its resilience to climate extremes, water diversions, and excessive loading of fine sediments point toward exploring how land use and terrestrial vegetation affect delivery from uplands of water, heat, sediments, solutes, organic matter, and organisms—in ways that either heal or damage rivers. |
Jr., George Poinar; Walder, Larissa; Uno, Hiromi Systematic Parasitology, 90 (3), pp. 231-236, 2015, ISSN: 0165-5752. Abstract | Links | BibTeX | Tags: animal morphology, systematics, taxonomy, zoology @article{Poinar2015, title = {Anomalomermis ephemerophagis n. g., n. sp. (Nematoda: Mermithidae) parasitic in the mayfly Ephemerella maculata Traver (Ephermeroptera: Ephermerellidae) in California, USA}, author = {George Poinar Jr. and Larissa Walder and Hiromi Uno}, url = {https://angelo.berkeley.edu/?attachment_id=2641}, doi = {10.1007/s11230-015-9551-6}, issn = {0165-5752}, year = {2015}, date = {2015-02-19}, journal = {Systematic Parasitology}, volume = {90}, number = {3}, pages = {231-236}, abstract = {A new nematode, Anomalomermis ephemerophagis n. g., n. sp. (Nematoda: Mermithidae) is described from the mayfly Ephemerella maculata Traver (Ephermeroptera: Ephermerellidae) in California. The new species is characterised by six cephalic papillae and four additional disk papillae located on the head between the cephalic papillae and stoma. Additional diagnostic characters are: a terminal mouth opening; absence of X-fibers in the cuticle of both postparasitic juveniles and adults; paired, curved, medium-sized spicules; a straight barrow-shaped vagina and large eggs. Two infectious agents were present in some specimens. This is the first description of an adult nematode from a mayfly.}, keywords = {animal morphology, systematics, taxonomy, zoology}, pubstate = {published}, tppubtype = {article} } A new nematode, Anomalomermis ephemerophagis n. g., n. sp. (Nematoda: Mermithidae) is described from the mayfly Ephemerella maculata Traver (Ephermeroptera: Ephermerellidae) in California. The new species is characterised by six cephalic papillae and four additional disk papillae located on the head between the cephalic papillae and stoma. Additional diagnostic characters are: a terminal mouth opening; absence of X-fibers in the cuticle of both postparasitic juveniles and adults; paired, curved, medium-sized spicules; a straight barrow-shaped vagina and large eggs. Two infectious agents were present in some specimens. This is the first description of an adult nematode from a mayfly. |
2014 |
Bode, Collin; Limm, Michael; Power, Mary; Finlay, Jacques Subcanopy Solar Radiation model: Predicting solar radiation across a heavily vegetated landscape using LiDAR and GIS solar radiation models Journal Article Remote Sensing of Environment, 154 (SI), pp. 387-397, 2014, ISSN: 0034-4257. Abstract | Links | BibTeX | Tags: insolation, LiDAR, solar model, subcanopy, vegetation shading @article{Bode2014, title = {Subcanopy Solar Radiation model: Predicting solar radiation across a heavily vegetated landscape using LiDAR and GIS solar radiation models}, author = {Collin Bode and Michael Limm and Mary Power and Jacques Finlay}, url = {https://angelo.berkeley.edu/wp-content/uploads/2015/01/Bode_SSR_Methods_RSE2013.pdf}, doi = {DOI:10.1016/j.rse.2014.01.028}, issn = {0034-4257}, year = {2014}, date = {2014-11-14}, journal = {Remote Sensing of Environment}, volume = {154}, number = {SI}, pages = {387-397}, abstract = {Solar radiation flux, irradiance, is a fundamental driver of almost all hydrological and biological processes. Ecological models of these processes often require data at the watershed scale. GIS-based solar models that predict insolation at the watershed scale take topographic shading into account, but do not account for vegetative shading. Most methods that quantify subcanopy insolation do so only at a single point. Further, subcanopy model calibration requires significant field effort and knowledge of characteristics (species composition, leaf area index & mean leaf angle for each species), and upscaling to watersheds is a significant source of uncertainty. We propose an approach to modeling insolation that uses airborne LiDAR data to estimate canopy openness as a Light Penetration Index (LPI). We couple LPI with the GRASS GIS r.sun solar model to produce the Subcanopy Solar Radiation model (SSR). SSR accounts for both topographic shading and vegetative shading at a landscape scale. After calibrating the r.sun model to a weather station at our study site, we compare SSR model predictions to black thermopile pyranometer field measurements and to hemispherical photographs using Gap Light Analyzer software, a standard method for point estimation of subcanopy radiation. Both SSR and hemispherical models exhibit a similar linear relationship with pyranometer data, and the models predict similar total solar radiation flux across the range of canopy openness. This approach allows prediction of light regimes at watershed scales with resolution that was previously possible only for local point measurements. }, keywords = {insolation, LiDAR, solar model, subcanopy, vegetation shading}, pubstate = {published}, tppubtype = {article} } Solar radiation flux, irradiance, is a fundamental driver of almost all hydrological and biological processes. Ecological models of these processes often require data at the watershed scale. GIS-based solar models that predict insolation at the watershed scale take topographic shading into account, but do not account for vegetative shading. Most methods that quantify subcanopy insolation do so only at a single point. Further, subcanopy model calibration requires significant field effort and knowledge of characteristics (species composition, leaf area index & mean leaf angle for each species), and upscaling to watersheds is a significant source of uncertainty. We propose an approach to modeling insolation that uses airborne LiDAR data to estimate canopy openness as a Light Penetration Index (LPI). We couple LPI with the GRASS GIS r.sun solar model to produce the Subcanopy Solar Radiation model (SSR). SSR accounts for both topographic shading and vegetative shading at a landscape scale. After calibrating the r.sun model to a weather station at our study site, we compare SSR model predictions to black thermopile pyranometer field measurements and to hemispherical photographs using Gap Light Analyzer software, a standard method for point estimation of subcanopy radiation. Both SSR and hemispherical models exhibit a similar linear relationship with pyranometer data, and the models predict similar total solar radiation flux across the range of canopy openness. This approach allows prediction of light regimes at watershed scales with resolution that was previously possible only for local point measurements. |
Hood, James M; McNeely, Camille; Finlay, Jacques C; Sterner, Robert W Selective feeding determines patterns of nutrient release by stream invertebrates Journal Article Freshwater Science, 33 (4), pp. 1093-1107, 2014, ISSN: 2161-9549. Abstract | Links | BibTeX | Tags: nutrients, selective feeding, stream invertebrates @article{Hood2014, title = {Selective feeding determines patterns of nutrient release by stream invertebrates}, author = {James M. Hood and Camille McNeely and Jacques C. Finlay and Robert W. Sterner}, url = {https://angelo.berkeley.edu/wp-content/uploads/Hood_2014_FreshSci.pdf}, doi = {10.1086/678693}, issn = {2161-9549}, year = {2014}, date = {2014-09-19}, journal = {Freshwater Science}, volume = {33}, number = {4}, pages = {1093-1107}, abstract = {One common stoichiometric approach to predicting patterns of nutrient release (excretion + egestion) by animals in aquatic ecosystems is to base predictions on elemental mass-balance constrained by homeostatic maintenance. An easily measured resource composite (i.e., seston, epilithon, or leaf litter) often is used to represent ingested stoichiometry, but whether such a composite is a good indicator of food actually ingested is a relatively unexplored assumption. We examined the application of a stoichiometric model to the diets of 4 generalist stream invertebrates. We fed 3 trichopteran and 1 amphipod taxa rations consisting of cultured algae, stream epilithon, and several species of conditioned leaf litter. The rations ranged widely in C:N from 10 to 69 (molar) and in C: P from 165 to 3500. After a 2-d feeding period, we measured NH4+ and PO43- excretion, and C, N, and P egestion rates. The relationships observed between the stoichiometries of release and ration were unexpected. Total N: P release rates conformed to stoichiometric predictions for only 1 taxon. Excretion and egestion rates and ratios were generally similar across diets and rarely varied with ration stoichiometry. These patterns were the result of smaller-than-expected responses to leaf-litter rations, which were the most imbalanced relative to body stoichiometry. Analysis of the C:N stoichiometry of foregut material for 2 taxa showed selective ingestion of an N-rich fraction of leaf litter, in 1 case reducing an apparent 8.4:1 C:N imbalance between diet and body composition to 1.5:1. Our results show that selective feeding can reduce potential stoichiometric imbalances, altering patterns of nutrient release relative to expectations based on bulk-diet stoichiometry. Assuming that stream invertebrates consume materials stoichiometrically similar to a resource composite can obscure understanding of stoichiometric imbalances and the role of invertebrates in nutrient cycles.}, keywords = {nutrients, selective feeding, stream invertebrates}, pubstate = {published}, tppubtype = {article} } One common stoichiometric approach to predicting patterns of nutrient release (excretion + egestion) by animals in aquatic ecosystems is to base predictions on elemental mass-balance constrained by homeostatic maintenance. An easily measured resource composite (i.e., seston, epilithon, or leaf litter) often is used to represent ingested stoichiometry, but whether such a composite is a good indicator of food actually ingested is a relatively unexplored assumption. We examined the application of a stoichiometric model to the diets of 4 generalist stream invertebrates. We fed 3 trichopteran and 1 amphipod taxa rations consisting of cultured algae, stream epilithon, and several species of conditioned leaf litter. The rations ranged widely in C:N from 10 to 69 (molar) and in C: P from 165 to 3500. After a 2-d feeding period, we measured NH4+ and PO43- excretion, and C, N, and P egestion rates. The relationships observed between the stoichiometries of release and ration were unexpected. Total N: P release rates conformed to stoichiometric predictions for only 1 taxon. Excretion and egestion rates and ratios were generally similar across diets and rarely varied with ration stoichiometry. These patterns were the result of smaller-than-expected responses to leaf-litter rations, which were the most imbalanced relative to body stoichiometry. Analysis of the C:N stoichiometry of foregut material for 2 taxa showed selective ingestion of an N-rich fraction of leaf litter, in 1 case reducing an apparent 8.4:1 C:N imbalance between diet and body composition to 1.5:1. Our results show that selective feeding can reduce potential stoichiometric imbalances, altering patterns of nutrient release relative to expectations based on bulk-diet stoichiometry. Assuming that stream invertebrates consume materials stoichiometrically similar to a resource composite can obscure understanding of stoichiometric imbalances and the role of invertebrates in nutrient cycles. |
Kim, Hyojin; Bishop, James K B; Dietrich, William E; Funga, Inez Y Geochimica et Cosmochimica Acta, 140 , pp. 1-19, 2014. Abstract | Links | BibTeX | Tags: bedrock, hydrochemistry, solute flux @article{Kim2014, title = {Process dominance shift in solute chemistry as revealed by long-term high-frequency water chemistry observations of groundwater flowing through weathered argillite underlying a steep forested hillslope}, author = {Hyojin Kim and James K.B. Bishop and William E. Dietrich and Inez Y. Funga }, url = {https://angelo.berkeley.edu/wp-content/uploads/Kim_2014_GeochCosmoActa.pdf}, doi = {10.1016/j.gca.2014.05.011}, year = {2014}, date = {2014-09-01}, journal = {Geochimica et Cosmochimica Acta}, volume = {140}, pages = {1-19}, abstract = {Significant solute flux from the weathered bedrock zone – which underlies soils and saprolite – has been suggested by many studies. However, controlling processes for the hydrochemistry dynamics in this zone are poorly understood. This work reports the first results from a four-year (2009–2012) high-frequency (1–3 day) monitoring of major solutes (Ca, Mg, Na, K and Si) in the perched, dynamic groundwater in a 4000 m2 zero-order basin located at the Angelo Coast Range Reserve, Northern California. Groundwater samples were autonomously collected at three wells (downslope, mid-slope, and upslope) aligned with the axis of the drainage. Rain and throughfall samples, profiles of well headspace pCO2, vertical profiles and time series of groundwater temperature, and contemporaneous data from an extensive hydrologic and climate sensor network provided the framework for data analysis. All runoff at this soil-mantled site occurs by vertical unsaturated flow through a 5–25 m thick weathered argillite and then by lateral flows to the adjacent channel as groundwater perched over fresher bedrock. Driven by strongly seasonal rainfall, over each of the four years of observations, the hydrochemistry of the groundwater at each well repeats an annual cycle, which can be explained by two end-member processes. The first end-member process, which dominates during the winter high-flow season in mid- and upslope areas, is CO2 enhanced cation exchange reaction in the vadose zone in the more shallow conductive weathered bedrock. This process rapidly increases the cation concentrations of the infiltrated rainwater, which is responsible for the lowest cation concentration of groundwater. The second-end member process occurs in the deeper perched groundwater and either dominates year-round (at the downslope well) or becomes progressively dominant during low flow season at the two upper slope wells. This process is the equilibrium reaction with minerals such as calcite and clay minerals, but not with primary minerals, suggesting the critical role of the residence time of the water. Collectively, our measurements reveal that the hydrochemistry dynamics of the groundwater in the weathered bedrock zone is governed by two end-member processes whose dominance varies with critical zone structure, the relative importance of vadose versus groundwater zone processes, and thus with the seasonal variation of the chemistry of recharge and runoff.}, keywords = {bedrock, hydrochemistry, solute flux}, pubstate = {published}, tppubtype = {article} } Significant solute flux from the weathered bedrock zone – which underlies soils and saprolite – has been suggested by many studies. However, controlling processes for the hydrochemistry dynamics in this zone are poorly understood. This work reports the first results from a four-year (2009–2012) high-frequency (1–3 day) monitoring of major solutes (Ca, Mg, Na, K and Si) in the perched, dynamic groundwater in a 4000 m2 zero-order basin located at the Angelo Coast Range Reserve, Northern California. Groundwater samples were autonomously collected at three wells (downslope, mid-slope, and upslope) aligned with the axis of the drainage. Rain and throughfall samples, profiles of well headspace pCO2, vertical profiles and time series of groundwater temperature, and contemporaneous data from an extensive hydrologic and climate sensor network provided the framework for data analysis. All runoff at this soil-mantled site occurs by vertical unsaturated flow through a 5–25 m thick weathered argillite and then by lateral flows to the adjacent channel as groundwater perched over fresher bedrock. Driven by strongly seasonal rainfall, over each of the four years of observations, the hydrochemistry of the groundwater at each well repeats an annual cycle, which can be explained by two end-member processes. The first end-member process, which dominates during the winter high-flow season in mid- and upslope areas, is CO2 enhanced cation exchange reaction in the vadose zone in the more shallow conductive weathered bedrock. This process rapidly increases the cation concentrations of the infiltrated rainwater, which is responsible for the lowest cation concentration of groundwater. The second-end member process occurs in the deeper perched groundwater and either dominates year-round (at the downslope well) or becomes progressively dominant during low flow season at the two upper slope wells. This process is the equilibrium reaction with minerals such as calcite and clay minerals, but not with primary minerals, suggesting the critical role of the residence time of the water. Collectively, our measurements reveal that the hydrochemistry dynamics of the groundwater in the weathered bedrock zone is governed by two end-member processes whose dominance varies with critical zone structure, the relative importance of vadose versus groundwater zone processes, and thus with the seasonal variation of the chemistry of recharge and runoff. |
Tsui, Martin Tsz-Ki; Blum, Joel D; Finlay, Jacques C; Balogh, Steven J; Nollet, Yabing H; Palen, Wendy J; Power, Mary E Variation in Terrestrial and Aquatic Sources of Methylmercury in Stream Predators as Revealed by Stable Mercury Isotopes Journal Article Environmental Science & Technology, 48 (17), pp. 10128–10135, 2014. Abstract | Links | BibTeX | Tags: Mercury Isotope, Methylmercury @article{Tsui2014, title = {Variation in Terrestrial and Aquatic Sources of Methylmercury in Stream Predators as Revealed by Stable Mercury Isotopes}, author = {Martin Tsz-Ki Tsui and Joel D. Blum and Jacques C. Finlay and Steven J. Balogh and Yabing H. Nollet and Wendy J. Palen and Mary E. Power}, url = {https://angelo.berkeley.edu/wp-content/uploads/2015/01/Tsui_MethylMercuryinStream_EnvSciTech2014.pdf}, doi = {10.1021/es500517s}, year = {2014}, date = {2014-08-08}, journal = {Environmental Science & Technology}, volume = {48}, number = {17}, pages = {10128–10135}, abstract = {Mercury (Hg) is widely distributed in the environment, and its organic form, methylmercury (MeHg), can extensively bioaccumulate and biomagnify in aquatic and terrestrial food webs. Concentrations of MeHg in organisms are highly variable, and the sources in natural food webs are often not well understood. This study examined stable isotope ratios of MeHg (mass-dependent fractionation, as δ202HgMeHg; and mass-independent fractionation, as Δ199HgMeHg) in benthic invertebrates, juvenile steelhead trout (Oncorhynchus mykiss), and water striders (Gerris remigis) along a stream productivity gradient, as well as carnivorous terrestrial invertebrates, in a forested watershed at the headwater of South Fork Eel River in northern California. Throughout the sampling sites, δ202HgMeHg (after correction due to the effect of MeHg photodegradation) was significantly different between benthic (median = −1.40‰; range, −2.34 to −0.78‰; total number of samples = 29) and terrestrial invertebrates (median = +0.51‰; range, −0.37 to +1.40‰; total number of samples = 9), but no major difference between these two groups was found for Δ199HgMeHg. Steelhead trout (52 individual fishes) have MeHg of predominantly aquatic origins, with a few exceptions at the upstream locations (e.g., 1 fish collected in a tributary had a purely terrestrial MeHg source and 4 fishes had mixed aquatic and terrestrial MeHg sources). Water striders (seven pooled samples) derive MeHg largely from terrestrial sources throughout headwater sections. These data suggest that direct terrestrial subsidy (e.g., terrestrial invertebrates falling into water) can be important for some stream predators in headwater streams and could represent an important means of transfer of terrestrially derived MeHg (e.g., in situ methylation within forests, atmospheric sources) to aquatic ecosystems. Moreover, these findings show that terrestrial subsidies can enhance MeHg bioaccumulation of consumers in headwater streams where aqueous MeHg levels are very low.}, keywords = {Mercury Isotope, Methylmercury}, pubstate = {published}, tppubtype = {article} } Mercury (Hg) is widely distributed in the environment, and its organic form, methylmercury (MeHg), can extensively bioaccumulate and biomagnify in aquatic and terrestrial food webs. Concentrations of MeHg in organisms are highly variable, and the sources in natural food webs are often not well understood. This study examined stable isotope ratios of MeHg (mass-dependent fractionation, as δ202HgMeHg; and mass-independent fractionation, as Δ199HgMeHg) in benthic invertebrates, juvenile steelhead trout (Oncorhynchus mykiss), and water striders (Gerris remigis) along a stream productivity gradient, as well as carnivorous terrestrial invertebrates, in a forested watershed at the headwater of South Fork Eel River in northern California. Throughout the sampling sites, δ202HgMeHg (after correction due to the effect of MeHg photodegradation) was significantly different between benthic (median = −1.40‰; range, −2.34 to −0.78‰; total number of samples = 29) and terrestrial invertebrates (median = +0.51‰; range, −0.37 to +1.40‰; total number of samples = 9), but no major difference between these two groups was found for Δ199HgMeHg. Steelhead trout (52 individual fishes) have MeHg of predominantly aquatic origins, with a few exceptions at the upstream locations (e.g., 1 fish collected in a tributary had a purely terrestrial MeHg source and 4 fishes had mixed aquatic and terrestrial MeHg sources). Water striders (seven pooled samples) derive MeHg largely from terrestrial sources throughout headwater sections. These data suggest that direct terrestrial subsidy (e.g., terrestrial invertebrates falling into water) can be important for some stream predators in headwater streams and could represent an important means of transfer of terrestrially derived MeHg (e.g., in situ methylation within forests, atmospheric sources) to aquatic ecosystems. Moreover, these findings show that terrestrial subsidies can enhance MeHg bioaccumulation of consumers in headwater streams where aqueous MeHg levels are very low. |
Afkhami, Michelle E; McIntyre, Patrick J; Strauss, Sharon Y Mutualist-mediated effects on species’ range limits across large geographic scales Journal Article Ecology Letters, 17 (10), pp. 1265-1273, 2014. Abstract | Links | BibTeX | Tags: mutualism, species' range @article{Afkhami2014, title = {Mutualist-mediated effects on species’ range limits across large geographic scales}, author = {Michelle E. Afkhami and Patrick J. McIntyre and Sharon Y. Strauss}, url = {https://angelo.berkeley.edu/wp-content/uploads/Afkhami_2014_EcoLetters.pdf}, doi = {10.1111/ele.12332}, year = {2014}, date = {2014-07-22}, journal = {Ecology Letters}, volume = {17}, number = {10}, pages = {1265-1273}, abstract = {Understanding the processes determining species range limits is central to predicting species distributions under climate change. Projected future ranges are extrapolated from distribution models based on climate layers, and few models incorporate the effects of biotic interactions on species' distributions. Here, we show that a positive species interaction ameliorates abiotic stress, and has a profound effect on a species' range limits. Combining field surveys of 92 populations, 10 common garden experiments throughout the range, species distribution models and greenhouse experiments, we show that mutualistic fungal endophytes ameliorate drought stress and broaden the geographic range of their native grass host Bromus laevipes by thousands of square kilometres (~ 20% larger) into drier habitats. Range differentiation between fungal-associated and fungal-free grasses was comparable to species-level range divergence of congeners, indicating large impacts on range limits. Positive biotic interactions may be underappreciated in determining species' ranges and species' responses to future climates across large geographic scales.}, keywords = {mutualism, species' range}, pubstate = {published}, tppubtype = {article} } Understanding the processes determining species range limits is central to predicting species distributions under climate change. Projected future ranges are extrapolated from distribution models based on climate layers, and few models incorporate the effects of biotic interactions on species' distributions. Here, we show that a positive species interaction ameliorates abiotic stress, and has a profound effect on a species' range limits. Combining field surveys of 92 populations, 10 common garden experiments throughout the range, species distribution models and greenhouse experiments, we show that mutualistic fungal endophytes ameliorate drought stress and broaden the geographic range of their native grass host Bromus laevipes by thousands of square kilometres (~ 20% larger) into drier habitats. Range differentiation between fungal-associated and fungal-free grasses was comparable to species-level range divergence of congeners, indicating large impacts on range limits. Positive biotic interactions may be underappreciated in determining species' ranges and species' responses to future climates across large geographic scales. |
Rempe, Daniella M; Dietrich, William E A bottom-up control on fresh-bedrock topography under landscapes Journal Article PNAS, 111 (18), pp. 6576–6581, 2014. Abstract | Links | BibTeX | Tags: bedrock, topography @article{Rempe2014, title = {A bottom-up control on fresh-bedrock topography under landscapes}, author = {Daniella M. Rempe and William E. Dietrich}, url = {https://angelo.berkeley.edu/wp-content/uploads/Rempe_2014_PNAS.pdf}, doi = {10.1073/pnas.1404763111}, year = {2014}, date = {2014-05-06}, journal = {PNAS}, volume = {111}, number = {18}, pages = {6576–6581}, abstract = {The depth to unweathered bedrock beneath landscapes influences subsurface runoff paths, erosional processes, moisture availability to biota, and water flux to the atmosphere. Here we propose a quantitative model to predict the vertical extent of weathered rock underlying soil-mantled hillslopes. We hypothesize that once fresh bedrock, saturated with nearly stagnant fluid, is advected into the near surface through uplift and erosion, channel incision produces a lateral head gradient within the fresh bedrock inducing drainage toward the channel. Drainage of the fresh bedrock causes weathering through drying and permits the introduction of atmospheric and biotically controlled acids and oxidants such that the boundary between weathered and unweathered bedrock is set by the uppermost elevation of undrained fresh bedrock, Zb. The slow drainage of fresh bedrock exerts a “bottom up” control on the advance of the weathering front. The thickness of the weathered zone is calculated as the difference between the predicted topographic surface profile (driven by erosion) and the predicted groundwater profile (driven by drainage of fresh bedrock). For the steady-state, soil-mantled case, a coupled analytical solution arises in which both profiles are driven by channel incision. The model predicts a thickening of the weathered zone upslope and, consequently, a progressive upslope increase in the residence time of bedrock in the weathered zone. Two nondimensional numbers corresponding to the mean hillslope gradient and mean groundwater-table gradient emerge and their ratio defines the proportion of the hillslope relief that is unweathered. Field data from three field sites are consistent with model predictions.}, keywords = {bedrock, topography}, pubstate = {published}, tppubtype = {article} } The depth to unweathered bedrock beneath landscapes influences subsurface runoff paths, erosional processes, moisture availability to biota, and water flux to the atmosphere. Here we propose a quantitative model to predict the vertical extent of weathered rock underlying soil-mantled hillslopes. We hypothesize that once fresh bedrock, saturated with nearly stagnant fluid, is advected into the near surface through uplift and erosion, channel incision produces a lateral head gradient within the fresh bedrock inducing drainage toward the channel. Drainage of the fresh bedrock causes weathering through drying and permits the introduction of atmospheric and biotically controlled acids and oxidants such that the boundary between weathered and unweathered bedrock is set by the uppermost elevation of undrained fresh bedrock, Zb. The slow drainage of fresh bedrock exerts a “bottom up” control on the advance of the weathering front. The thickness of the weathered zone is calculated as the difference between the predicted topographic surface profile (driven by erosion) and the predicted groundwater profile (driven by drainage of fresh bedrock). For the steady-state, soil-mantled case, a coupled analytical solution arises in which both profiles are driven by channel incision. The model predicts a thickening of the weathered zone upslope and, consequently, a progressive upslope increase in the residence time of bedrock in the weathered zone. Two nondimensional numbers corresponding to the mean hillslope gradient and mean groundwater-table gradient emerge and their ratio defines the proportion of the hillslope relief that is unweathered. Field data from three field sites are consistent with model predictions. |
Tewksbury, Joshua J; Anderson, John G T; Bakker, Jonathan D; Billo, Timothy J; W. Dunwiddie, Peter; Groom, Martha J; Hampton, Stephanie E; Herman, Steven G; Levey, Douglas J; Machnicki, Noelle J; Rio, Carlos Martínez Del; Power, Mary E; Rowell, Kirsten; Salomon, Anne K; Stacey, Liam; Trombulak, Stephen C; Wheeler, Terry A Natural History’s Place in Science and Society Journal Article BioScience, 64 (4), pp. 300-310, 2014. Abstract | Links | BibTeX | Tags: ecological knowledge, environmental management, food security, human health, sustainability @article{Tewksbury2014, title = {Natural History’s Place in Science and Society}, author = {Joshua J. Tewksbury and John G. T. Anderson and Jonathan D. Bakker and Timothy J. Billo and Peter W. Dunwiddie and Martha J. Groom and Stephanie E. Hampton and Steven G. Herman and Douglas J. Levey and Noelle J. Machnicki and Carlos Martínez Del Rio and Mary E. Power and Kirsten Rowell and Anne K. Salomon and Liam Stacey and Stephen C. Trombulak and Terry A. Wheeler}, url = {https://angelo.berkeley.edu/wp-content/uploads/Tewksbury_NatHisSoc_BioSci2014.pdf http://www.nature.com/news/natural-decline-1.14966 http://www.independent.co.uk/news/science/the-natural-historian-faces-extinction-overspecialism-and-funding-cuts-could-end-a-vital-scientific-9256655.html}, doi = {10.1093/biosci/biu032}, year = {2014}, date = {2014-03-26}, journal = {BioScience}, volume = {64}, number = {4}, pages = {300-310}, abstract = {The fundamental properties of organisms—what they are, how and where they live, and the biotic and abiotic interactions that link them to communities and ecosystems—are the domain of natural history. We provide examples illustrating the vital importance of natural history knowledge to many disciplines, from human health and food security to conservation, management, and recreation. We then present several lines of evidence showing that traditional approaches to and support for natural history in developed economies has declined significantly over the past 40 years. Finally, we argue that a revitalization of the practice of natural history—one that is focused on new frontiers in a rapidly changing world and that incorporates new technologies—would provide significant benefits for both science and society.}, keywords = {ecological knowledge, environmental management, food security, human health, sustainability}, pubstate = {published}, tppubtype = {article} } The fundamental properties of organisms—what they are, how and where they live, and the biotic and abiotic interactions that link them to communities and ecosystems—are the domain of natural history. We provide examples illustrating the vital importance of natural history knowledge to many disciplines, from human health and food security to conservation, management, and recreation. We then present several lines of evidence showing that traditional approaches to and support for natural history in developed economies has declined significantly over the past 40 years. Finally, we argue that a revitalization of the practice of natural history—one that is focused on new frontiers in a rapidly changing world and that incorporates new technologies—would provide significant benefits for both science and society. |
Link, Percy; Simonin, Kevin; Maness, Holly; Oshun, Jasper; Dawson, Todd; Fung, Inez Water Resources Research, 50 (3), pp. 1869-1894, 2014. Abstract | Links | BibTeX | Tags: sap flow, seasonality, transpiration @article{Link2014, title = {Species differences in the seasonality of evergreen tree transpiration in a Mediterranean climate: Analysis of multiyear, half-hourly sap flow observations}, author = {Percy Link and Kevin Simonin and Holly Maness and Jasper Oshun and Todd Dawson and Inez Fung}, url = {https://angelo.berkeley.edu/wp-content/uploads/Link_2014_WaterResoRese.pdf}, doi = {10.1002/2013WR014023}, year = {2014}, date = {2014-03-01}, journal = {Water Resources Research}, volume = {50}, number = {3}, pages = {1869-1894}, abstract = {In Mediterranean climates, the season of water availability (winter) is out of phase with the season of light availability and atmospheric moisture demand (summer). We investigate the seasonality of evergreen tree transpiration in a Mediterranean climate, using observations from a small (4000 m2), forested, steep (32°) hillslope, in the northern California Coast Range. We analyze 3 years of half-hourly measurements from 39 sap flow sensors in 26 trees, six depth profiles of soil moisture measured by TDR, and spatially distributed measurements of micrometeorology from five locations. The sap flow measurements show that two common evergreen tree species have different seasons of peak transpiration. Douglas-firs (Pseudotsuga menziesii) maintain significant transpiration through the winter rainy season and transpire maximally in the spring, followed by a sharp decline in transpiration in the summer dry season. Pacific madrones (Arbutus menziesii), and to a lesser extent other broadleaf evergreen species (Quercus wislizeni, Notholithocarpus densiflorus, Umbellularia californica), in contrast, transpire maximally in the summer dry season. The seasonal patterns are quantified using principal component analysis. Markov chain Monte Carlo estimation of response to environmental variables shows that the difference in transpiration seasonality arises from different sensitivities to atmospheric evaporative demand and root-zone moisture. The different sensitivities to atmospheric evaporative demand also create species differences in transpiration variability at synoptic time scales. Using the sap flow measurements and a regional forest inventory, a bottom-up regional transpiration estimate is constructed. The estimate suggests that sensitivity of Douglas-fir transpiration to water stress suppresses dry season evapotranspiration at the regional scale.}, keywords = {sap flow, seasonality, transpiration}, pubstate = {published}, tppubtype = {article} } In Mediterranean climates, the season of water availability (winter) is out of phase with the season of light availability and atmospheric moisture demand (summer). We investigate the seasonality of evergreen tree transpiration in a Mediterranean climate, using observations from a small (4000 m2), forested, steep (32°) hillslope, in the northern California Coast Range. We analyze 3 years of half-hourly measurements from 39 sap flow sensors in 26 trees, six depth profiles of soil moisture measured by TDR, and spatially distributed measurements of micrometeorology from five locations. The sap flow measurements show that two common evergreen tree species have different seasons of peak transpiration. Douglas-firs (Pseudotsuga menziesii) maintain significant transpiration through the winter rainy season and transpire maximally in the spring, followed by a sharp decline in transpiration in the summer dry season. Pacific madrones (Arbutus menziesii), and to a lesser extent other broadleaf evergreen species (Quercus wislizeni, Notholithocarpus densiflorus, Umbellularia californica), in contrast, transpire maximally in the summer dry season. The seasonal patterns are quantified using principal component analysis. Markov chain Monte Carlo estimation of response to environmental variables shows that the difference in transpiration seasonality arises from different sensitivities to atmospheric evaporative demand and root-zone moisture. The different sensitivities to atmospheric evaporative demand also create species differences in transpiration variability at synoptic time scales. Using the sap flow measurements and a regional forest inventory, a bottom-up regional transpiration estimate is constructed. The estimate suggests that sensitivity of Douglas-fir transpiration to water stress suppresses dry season evapotranspiration at the regional scale. |
Travis, Joseph; Coleman, Felicia C; Auster, Peter J; Cury, Philippe M; Estes, James A; Orensanz, Jose; Peterson, Charles H; Power, Mary E; Steneck, Robert S; Wootton, Timothy J Integrating the invisible fabric of nature into fisheries management Journal Article PNAS, 111 (2), pp. 581-584, 2014. Abstract | Links | BibTeX | Tags: alternative states, ecosystem flips, fisheries collapse, ocean fisheries @article{Travis2013, title = {Integrating the invisible fabric of nature into fisheries management}, author = {Joseph Travis and Felicia C. Coleman and Peter J. Auster and Philippe M. Cury and James A. Estes and Jose Orensanz and Charles H. Peterson and Mary E. Power and Robert S. Steneck and J. Timothy Wootton}, url = {https://angelo.berkeley.edu/wp-content/uploads/Travis_NatFishManage_PNAS2014.pdf}, doi = {10.1073/pnas.1305853111}, year = {2014}, date = {2014-01-14}, journal = {PNAS}, volume = {111}, number = {2}, pages = {581-584}, abstract = {Overfishing and environmental change have triggered many severe and unexpected consequences. As existing communities have collapsed, new ones have become established, fundamentally transforming ecosystems to those that are often less productive for fisheries, more prone to cycles of booms and busts, and thus less manageable. We contend that the failure of fisheries science and management to anticipate these transformations results from a lack of appreciation for the nature, strength, complexity, and outcome of species interactions. Ecologists have come to understand that networks of interacting species exhibit nonlinear dynamics and feedback loops that can produce sudden and unexpected shifts. We argue that fisheries science and management must follow this lead by developing a sharper focus on species interactions and how disrupting these interactions can push ecosystems in which fisheries are embedded past their tipping points.}, keywords = {alternative states, ecosystem flips, fisheries collapse, ocean fisheries}, pubstate = {published}, tppubtype = {article} } Overfishing and environmental change have triggered many severe and unexpected consequences. As existing communities have collapsed, new ones have become established, fundamentally transforming ecosystems to those that are often less productive for fisheries, more prone to cycles of booms and busts, and thus less manageable. We contend that the failure of fisheries science and management to anticipate these transformations results from a lack of appreciation for the nature, strength, complexity, and outcome of species interactions. Ecologists have come to understand that networks of interacting species exhibit nonlinear dynamics and feedback loops that can produce sudden and unexpected shifts. We argue that fisheries science and management must follow this lead by developing a sharper focus on species interactions and how disrupting these interactions can push ecosystems in which fisheries are embedded past their tipping points. |
Hill, Kirsten E 2014. Abstract | Links | BibTeX | Tags: grasses, spiders @phdthesis{Hill2014, title = {Spiders in California’s grassland mosaic: The effects of native and non-native grasses on spiders, their prey, and their interactions}, author = {Kirsten E. Hill}, url = {https://angelo.berkeley.edu/wp-content/uploads/Hill_2014_UCBerkTheses.pdf}, year = {2014}, date = {2014-01-01}, abstract = {Found in nearly all terrestrial ecosystems, small in size and able to occupy a variety of hunting niches, spiders’ consumptive effects on other arthropods can have important impacts for ecosystems. This dissertation describes research into spider populations and their interactions with potential arthropod prey in California’s native and non-native grasslands. In meadows found in northern California, native and non-native grassland patches support different functional groups of arthropod predators, sap-feeders, pollinators, and scavengers and arthropod diversity is linked to native plant diversity. Wandering spiders’ ability to forage within the meadow’s interior is linked to the distance from the shaded woodland boundary. Native grasses offer a cooler conduit into the meadow interior than non-native annual grasses during midsummer heat. Juvenile spiders in particular, are more abundant in the more structurally complex native dominated areas of the grassland. Potential prey species and abundance differ along the trajectory from woodland boundary to meadow interior and may have consequences for the survival of juvenile spiders that reside primarily near the woodland boundary. Spiders’ ability to influence the eating habits of potential prey species is regulated by temperature and grassland characteristics. In experimental wolf spider enclosures, cooler habitats in which spiders were present evidenced lower herbivory by large chewing invertebrates. Herbivory differed across a gradient of temperature and sunlight but newly restored plants in exposed and warmer soil faced higher rates of herbivory than established plants; herbivory may be better mediated by spider activity in cooler environments.}, keywords = {grasses, spiders}, pubstate = {published}, tppubtype = {phdthesis} } Found in nearly all terrestrial ecosystems, small in size and able to occupy a variety of hunting niches, spiders’ consumptive effects on other arthropods can have important impacts for ecosystems. This dissertation describes research into spider populations and their interactions with potential arthropod prey in California’s native and non-native grasslands. In meadows found in northern California, native and non-native grassland patches support different functional groups of arthropod predators, sap-feeders, pollinators, and scavengers and arthropod diversity is linked to native plant diversity. Wandering spiders’ ability to forage within the meadow’s interior is linked to the distance from the shaded woodland boundary. Native grasses offer a cooler conduit into the meadow interior than non-native annual grasses during midsummer heat. Juvenile spiders in particular, are more abundant in the more structurally complex native dominated areas of the grassland. Potential prey species and abundance differ along the trajectory from woodland boundary to meadow interior and may have consequences for the survival of juvenile spiders that reside primarily near the woodland boundary. Spiders’ ability to influence the eating habits of potential prey species is regulated by temperature and grassland characteristics. In experimental wolf spider enclosures, cooler habitats in which spiders were present evidenced lower herbivory by large chewing invertebrates. Herbivory differed across a gradient of temperature and sunlight but newly restored plants in exposed and warmer soil faced higher rates of herbivory than established plants; herbivory may be better mediated by spider activity in cooler environments. |
Munshaw, Robin G; Atlas, W I; Palen, W J; Courcelles, Danielle M; Monteith, Zachary L Correlates and consequences of injury in a large, predatory stream salamander (Dicamptodon tenebrosus) Journal Article Amphibia-Reptilia, 35 (1), pp. 107-116, 2014, ISSN: 0173-5373. Abstract | Links | BibTeX | Tags: aggression, Dicamptodon tenebrosus, population structure, resource competition, territorialism @article{Munshaw2014, title = {Correlates and consequences of injury in a large, predatory stream salamander (Dicamptodon tenebrosus)}, author = { Robin G. Munshaw and W.I. Atlas and W.J. Palen and Danielle M. Courcelles and Zachary L. Monteith}, url = {https://angelo.berkeley.edu/wp-content/uploads/Munshaw_2014_AmphRept.pdf}, issn = {0173-5373}, year = {2014}, date = {2014-01-01}, journal = {Amphibia-Reptilia}, volume = {35}, number = {1}, pages = {107-116}, abstract = {Conspecific aggression is an important factor structuring population dynamics through intra- and interspecific interactions, but is rarely studied in un-manipulated populations. In this study, we evaluated rates of injury as a proxy for conspecific aggression using a depletion survey of predatory coastal giant salamanders (Dicamptodon tenebrosus) in a tributary of the South Fork Eel River, California. We tested a range of hypotheses including a suite of environmental and biotic factors for the rate of injury in a population by using an AIC model-selection approach that examined the weight of evidence for individual models. We examined both the probability of a given individual being injured, and the proportion of individuals within a given study pool being injured. We found strong support for models including salamander size, density of young-of-the-year steelhead, and density of the largest size-class of salamander as factors positively influencing the rate of injury at both the individual and habitat levels. We also found that density of older steelhead (1+ steelhead) had a strong, but highly variable positive impact on frequency of injury. This study shows that both conspecific and heterospecific factors influence intraspecific aggression for the dominant salamander throughout coastal Pacific Northwest streams. Our methodology demonstrates a non-manipulative approach to identifying correlates of natural injury in a cryptic species of amphibian. More work is needed to determine how these factors directly and indirectly influence the spatial distribution, individual fitness, and dynamics of salamander populations within streams.}, keywords = {aggression, Dicamptodon tenebrosus, population structure, resource competition, territorialism}, pubstate = {published}, tppubtype = {article} } Conspecific aggression is an important factor structuring population dynamics through intra- and interspecific interactions, but is rarely studied in un-manipulated populations. In this study, we evaluated rates of injury as a proxy for conspecific aggression using a depletion survey of predatory coastal giant salamanders (Dicamptodon tenebrosus) in a tributary of the South Fork Eel River, California. We tested a range of hypotheses including a suite of environmental and biotic factors for the rate of injury in a population by using an AIC model-selection approach that examined the weight of evidence for individual models. We examined both the probability of a given individual being injured, and the proportion of individuals within a given study pool being injured. We found strong support for models including salamander size, density of young-of-the-year steelhead, and density of the largest size-class of salamander as factors positively influencing the rate of injury at both the individual and habitat levels. We also found that density of older steelhead (1+ steelhead) had a strong, but highly variable positive impact on frequency of injury. This study shows that both conspecific and heterospecific factors influence intraspecific aggression for the dominant salamander throughout coastal Pacific Northwest streams. Our methodology demonstrates a non-manipulative approach to identifying correlates of natural injury in a cryptic species of amphibian. More work is needed to determine how these factors directly and indirectly influence the spatial distribution, individual fitness, and dynamics of salamander populations within streams. |