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2020 |
Schmidt, Logan; Rempe, Daniella M Quantifying Dynamic Water Storage in Unsaturated Bedrock with Borehole Nuclear Magnetic Resonance Journal Article Geophysical Research Letters, 47 (22), pp. e2020GL089600, 2020. Abstract | Links | BibTeX | Tags: Critical Zone, ERCZO, hydrogeophysics, neutron moderation nuclear magnetic resonance, vadose zone, water storage @article{Schmidt2020, title = {Quantifying Dynamic Water Storage in Unsaturated Bedrock with Borehole Nuclear Magnetic Resonance}, author = {Logan Schmidt and Daniella M. Rempe }, doi = {10.1029/2020GL089600}, year = {2020}, date = {2020-11-02}, journal = {Geophysical Research Letters}, volume = {47}, number = {22}, pages = {e2020GL089600}, abstract = {Quantifying the volume of water that is stored in the subsurface is critical to studies of water availability to ecosystems, slope stability, and water‐rock interactions. In a variety of settings, water is stored in fractured and weathered bedrock as rock moisture. However, few techniques are available to measure rock moisture in unsaturated rock, making direct estimates of water storage dynamics difficult to obtain. Here, we use borehole nuclear magnetic resonance (NMR) at two sites in seasonally dry California to quantify dynamic rock moisture storage. We show strong agreement between NMR estimates of dynamic storage and estimates derived from neutron logging and mass balance techniques. The depths of dynamic storage are up to 9 m and likely reflect the depth extent of root water uptake. To our knowledge, these data are the first to quantify the volume and depths of dynamic water storage in the bedrock vadose zone via borehole NMR.}, keywords = {Critical Zone, ERCZO, hydrogeophysics, neutron moderation nuclear magnetic resonance, vadose zone, water storage}, pubstate = {published}, tppubtype = {article} } Quantifying the volume of water that is stored in the subsurface is critical to studies of water availability to ecosystems, slope stability, and water‐rock interactions. In a variety of settings, water is stored in fractured and weathered bedrock as rock moisture. However, few techniques are available to measure rock moisture in unsaturated rock, making direct estimates of water storage dynamics difficult to obtain. Here, we use borehole nuclear magnetic resonance (NMR) at two sites in seasonally dry California to quantify dynamic rock moisture storage. We show strong agreement between NMR estimates of dynamic storage and estimates derived from neutron logging and mass balance techniques. The depths of dynamic storage are up to 9 m and likely reflect the depth extent of root water uptake. To our knowledge, these data are the first to quantify the volume and depths of dynamic water storage in the bedrock vadose zone via borehole NMR. |
Sharrar, A M; Crits-Christoph, A; Méheust, R; Diamond, S; Starr, E P; Banfield, J F Bacterial secondary metabolite biosynthetic potential in soil varies with phylum, depth, and vegetation type. Journal Article mBio, 11 , pp. e00416-20, 2020. Abstract | Links | BibTeX | Tags: ERCZO, metagenomics, secondary metabolism, soil microbiology @article{Sharrar2020, title = {Bacterial secondary metabolite biosynthetic potential in soil varies with phylum, depth, and vegetation type.}, author = {A.M. Sharrar and A. Crits-Christoph and R. Méheust and S. Diamond and E.P. Starr and J.F. Banfield}, url = {https://mbio.asm.org/content/11/3/e00416-20}, doi = {10.1128/mBio.00416-20}, year = {2020}, date = {2020-06-16}, journal = {mBio}, volume = {11}, pages = {e00416-20}, abstract = {Bacteria isolated from soils are major sources of specialized metabolites, including antibiotics and other compounds with clinical value that likely shape interactions among microbial community members and impact biogeochemical cycles. Yet, isolated lineages represent a small fraction of all soil bacterial diversity. It remains unclear how the production of specialized metabolites varies across the phylogenetic diversity of bacterial species in soils and whether the genetic potential for production of these metabolites differs with soil depth and vegetation type within a geographic region. We sampled soils and saprolite from three sites in a northern California Critical Zone Observatory with various vegetation and bedrock characteristics and reconstructed 1,334 metagenome-assembled genomes containing diverse biosynthetic gene clusters (BGCs) for secondary metabolite production. We obtained genomes for prolific producers of secondary metabolites, including novel groups within the Actinobacteria, Chloroflexi, and candidate phylum “Candidatus Dormibacteraeota.” Surprisingly, one genome of a candidate phyla radiation (CPR) bacterium coded for a ribosomally synthesized linear azole/azoline-containing peptide, a capacity we found in other publicly available CPR bacterial genomes. Overall, bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with patterns of abundance of BGC type varying by taxonomy. }, keywords = {ERCZO, metagenomics, secondary metabolism, soil microbiology}, pubstate = {published}, tppubtype = {article} } Bacteria isolated from soils are major sources of specialized metabolites, including antibiotics and other compounds with clinical value that likely shape interactions among microbial community members and impact biogeochemical cycles. Yet, isolated lineages represent a small fraction of all soil bacterial diversity. It remains unclear how the production of specialized metabolites varies across the phylogenetic diversity of bacterial species in soils and whether the genetic potential for production of these metabolites differs with soil depth and vegetation type within a geographic region. We sampled soils and saprolite from three sites in a northern California Critical Zone Observatory with various vegetation and bedrock characteristics and reconstructed 1,334 metagenome-assembled genomes containing diverse biosynthetic gene clusters (BGCs) for secondary metabolite production. We obtained genomes for prolific producers of secondary metabolites, including novel groups within the Actinobacteria, Chloroflexi, and candidate phylum “Candidatus Dormibacteraeota.” Surprisingly, one genome of a candidate phyla radiation (CPR) bacterium coded for a ribosomally synthesized linear azole/azoline-containing peptide, a capacity we found in other publicly available CPR bacterial genomes. Overall, bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with patterns of abundance of BGC type varying by taxonomy. |
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, ERCZO, 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, ERCZO, 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, ERCZO, 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, ERCZO, 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, ERCZO, 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, ERCZO, 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, ERCZO, 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, ERCZO, 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, ERCZO, 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, ERCZO, 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, ERCZO, 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, ERCZO, 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. |
Dawson, T E; Hahm, W J; Crutchfield-Peters, K Digging deeper: what the critical zone perspective adds to the study of plant ecophysiology Journal Article New Phytologist, 226 (3), pp. 666-671, 2020. Abstract | Links | BibTeX | Tags: Critical Zone, ERCZO, nutrients, plant ecophysiology, soil, water, weathered bedrock @article{Dawson2020, title = {Digging deeper: what the critical zone perspective adds to the study of plant ecophysiology}, author = {T.E. Dawson and W.J. Hahm and K. Crutchfield-Peters}, url = {https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.16410}, doi = {10.1111/nph.16410}, year = {2020}, date = {2020-01-08}, journal = {New Phytologist}, volume = {226}, number = {3}, pages = {666-671}, abstract = {The emergence of critical zone (CZ) science has provided an integrative platform for investigating plant ecophysiology in the context of landscape evolution, weathering and hydrology. The CZ lies between the top of the vegetation canopy and fresh, chemically unaltered bedrock and plays a pivotal role in sustaining life. We consider what the CZ perspective has recently brought to the study of plant ecophysiology. We specifically highlight novel research demonstrating the importance of the deeper subsurface for plant water and nutrient relations. We also point to knowledge gaps and research opportunities, emphasising, in particular, greater focus on the roles of deep, nonsoil resources and how those resources influence and coevolve with plants as a frontier of plant ecophysiological research.}, keywords = {Critical Zone, ERCZO, nutrients, plant ecophysiology, soil, water, weathered bedrock}, pubstate = {published}, tppubtype = {article} } The emergence of critical zone (CZ) science has provided an integrative platform for investigating plant ecophysiology in the context of landscape evolution, weathering and hydrology. The CZ lies between the top of the vegetation canopy and fresh, chemically unaltered bedrock and plays a pivotal role in sustaining life. We consider what the CZ perspective has recently brought to the study of plant ecophysiology. We specifically highlight novel research demonstrating the importance of the deeper subsurface for plant water and nutrient relations. We also point to knowledge gaps and research opportunities, emphasising, in particular, greater focus on the roles of deep, nonsoil resources and how those resources influence and coevolve with plants as a frontier of plant ecophysiological research. |
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: ERCZO, 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 = {ERCZO, 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, ERCZO, 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, ERCZO, 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, ERCZO @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, ERCZO}, 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: ERCZO, 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 = {ERCZO, 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. |
2018 |
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, ERCZO @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, ERCZO}, 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, ERCZO, 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, ERCZO, 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. |
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, ERCZO, 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, ERCZO, 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. |
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, ERCZO @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, ERCZO}, 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, ERCZO, 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, ERCZO, 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, ERCZO, 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, ERCZO, 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. |
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, ERCZO, 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, ERCZO, 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. |
2016 |
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, ERCZO, 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, ERCZO, 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. |