Publications

@article{nokey,

title = {Rana Boylii (Foothill Yellow-legged Frog) Reproductive Behavior and Habitat Use},

author = {Sarah J. Kupferberg },

year  = {2021},

date = {2021-12-17},

journal = {Herpetological Review},

volume = {52},

number = {4},

keywords = {natural history notes, Rana boylii},

pubstate = {published},

tppubtype = {article}

}

@article{Golla2021,

title = {The evolution of lithium isotope signatures in fluids draining actively weathering hillslopes},

author = {J.K. Golla and M.L. Kuessner and M.J. Henehan and J. Bouchez and D.M. Rempe and J.L. Druhan},

doi = {10.1016/j.epsl.2021.116988},

year  = {2021},

date = {2021-08-01},

journal = {Earth and Planetary Science Letters},

volume = {567},

number = {1},

abstract = {The stable isotopes of lithium (Li) serve as a robust proxy of silicate weathering. The fate and transport of these isotopes in the dissolved load of major rivers have been characterized to infer changes in both contemporary weathering regimes and paleo-conditions. In this contribution, we deconvolve this integrated signal into the individual processes that fractionate Li at the inception of silicate weathering by directly measuring Li isotope ratios of waters (Li) transiting through a rapidly eroding first-order hillslope. We use these data to develop a multicomponent reactive transport framework, which shows that net dissolution of weathered material generates light Li signatures (as low as −9.2‰) in the shallow portion of the vadose zone. An increase in Li deeper into the vadose zone (as much as +18‰) reflects an increasing contribution of secondary mineral formation. Below the water table, congruent weathering occurs and imparts elevated cation concentrations and bedrock Li. Silicate weathering continues within the saturated zone as groundwater travels downslope (Li = +13 to + 24‰) to the stream. The stream signatures (Li = +28 to +29‰) reflect the terminus of this network of silicate weathering reactions and the relative magnitude of each contributing process (e.g., transitions in secondary mineral formation, dissolution of weathered material). We show that fluid progressing through the weathering profile of this first-order hillslope is distinguished by a sequence of characteristic Li isotope signatures, which can be reproduced in a forward, process-based model framework. This model development offers an improved quantitative basis for the use of metal(loid) stable isotopes in disentangling catchment-scale chemical weathering fluxes.



},

keywords = {Critical Zone, ERCZO, lithium isotopes, reactive transport, silicate weathering},

pubstate = {published},

tppubtype = {article}

}

@article{Muller2021,

title = {Catchment processes can amplify the effect of increasing rainfall variability},

author = {M.F. Muller and K.R. Roche and D.N. Dralle},

doi = {https://doi.org/10.1088/1748-9326/ac153e},

year  = {2021},

date = {2021-07-29},

urldate = {2021-07-29},

journal = {Environmental Research Letters},

volume = {16},

number = {8},

abstract = {By filtering the incoming climate signal when producing streamflow, river basins can attenuate—or amplify—projected increases in rainfall variability. A common perception is that river systems dampen rainfall variability by averaging spatial and temporal variations in their watersheds. However, by analyzing 671 watersheds throughout the United States, we find that many catchments actually amplify the coefficient of variation of rainfall, and that these catchments also likely amplify changes in rainfall variability. Based on catchment-scale water balance principles, we relate that faculty to the interplay between two fundamental hydrological processes: water uptake by vegetation and the storage and subsequent release of water as discharge. By increasing plant water uptake, warmer temperatures might exacerbate the amplifying effect of catchments. More variable precipitations associated with a warmer climate are therefore expected to lead to even more variable river flows—a significant potential challenge for river transportation, ecosystem sustainability and water supply reliability.},

keywords = {climate change, ERCZO, rainfall, Stream Flow, water resources},

pubstate = {published},

tppubtype = {article}

}

@article{Vadeboncoeur2021,

title = {Blue Waters, Green Bottoms: Benthic Filamentous Algal Blooms Are an Emerging Threat to Clear Lakes Worldwide},

author = {Yvonne Vadeboncoeur and Marianne V Moore and Simon D Stewart and Sudeep Chandra and Karen S Atkins and Jill S Baron and Keith Bouma-Gregson and Soren Brothers and Steven N Francoeur and Laurel Genzoli and Scott N Higgins and Sabine Hilt and Leon R Katona and David Kelly and Isabella A Oleksy and Ted Ozersky and Mary E Power and Derek Roberts and Adrianne P Smits and Oleg Timoshkin and Flavia Tromboni and M Jake Vander Zanden and Ekaterina A Volkova and Sean Waters and Susanna A Wood and Masumi Yamamuro},

url = {https://angelo.berkeley.edu/biab049-2/},

doi = {10.1093/biosci/biab049},

year  = {2021},

date = {2021-07-07},

journal = {BioScience},

volume = {71},

number = {10},

pages = {1011–1027},

abstract = {Nearshore (littoral) habitats of clear lakes with high water quality are increasingly experiencing unexplained proliferations of filamentous algae that grow on submerged surfaces. These filamentous algal blooms (FABs) are sometimes associated with nutrient pollution in groundwater, but complex changes in climate, nutrient transport, lake hydrodynamics, and food web structure may also facilitate this emerging threat to clear lakes. A coordinated effort among members of the public, managers, and scientists is needed to document the occurrence of FABs, to standardize methods for measuring their severity, to adapt existing data collection networks to include nearshore habitats, and to mitigate and reverse this profound structural change in lake ecosystems. Current models of lake eutrophication do not explain this littoral greening. However, a cohesive response to it is essential for protecting some of the world's most valued lakes and the flora, fauna, and ecosystem services they sustain.},

keywords = {attached filamentous algae, eutrophication, global change, littoral, periphyton},

pubstate = {published},

tppubtype = {article}

}

@article{Dralle2021,

title = {Technical note: Accounting for snow in the estimation of root zone water storage capacity from precipitation and evapotranspiration fluxes},

author = {D.N. Dralle and W.J. Hahm and K.D. Chadwick and E. McCormick and D.M. Rempe},

doi = {10.5194/hess-25-2861-2021},

year  = {2021},

date = {2021-05-27},

journal = {Hydrology and Earth System Sciences},

volume = {25},

number = {5},

pages = {2861–2867},

abstract = {A common parameter in hydrological modeling frameworks is root zone water storage capacity (SR[L]), which mediates plant water availability during dry periods as well as the partitioning of rainfall between runoff and evapotranspiration. Recently, a simple flux-tracking-based approach was introduced to estimate the value of SR (Wang-Erlandsson et al., 2016). Here, we build upon this original method, which we argue may overestimate SR in snow-dominated catchments due to snow melt and evaporation processes. We propose a simple extension to the method presented by Wang-Erlandsson et al. (2016) and show that the approach provides a lower estimate of SR in snow-dominated watersheds. This SR dataset is available at a 1 km resolution for the continental USA, along with the full analysis code, on the Google Colab and Earth Engine platforms. We highlight differences between the original and new methods across the rain–snow transition in the Southern Sierra Nevada, California, USA. As climate warms and precipitation increasingly arrives as rain instead of snow, the subsurface may be an increasingly important reservoir for storing plant-available water between wet and dry seasons; therefore, improved estimates of SR will better clarify the future role of the subsurface as a storage reservoir that can sustain forests during seasonal dry periods and episodic drought.},

keywords = {ERCZO, evapotranspiration, hydrologic modeling, root zone, snow melt, water storage},

pubstate = {published},

tppubtype = {article}

}

@article{Hood2021,

title = {Longitudinal patterns and linkages in benthic fine particulate organic matter composition, respiration, and nutrient uptake},

author = {James M. Hood and Lyndsie M. Collis and John D. Schade and Rebecca A. Stark and Jacques C. Finlay },

url = {https://aslopubs.onlinelibrary.wiley.com/doi/10.1002/lno.11781},

doi = {10.1002/lno.11781},

year  = {2021},

date = {2021-05-01},

journal = {Limnology and Oceanography},

abstract = {Longitudinal changes in the structure and function of river ecosystems have long been recognized, yet our understanding of how such patterns shape elemental cycles remains limited. In particular, while benthic fine particulate organic matter (POM, 0.7–1000 μm) may control many stream nutrient cycles, less is known about longitudinal patterns or controls of benthic POM‐associated nutrient uptake. We conducted a survey of benthic POM‐associated respiration and nutrient uptake as well as microbial biomass (bacteria and algae) and benthic POM composition in four size classes (0.7–53 μm, 53–106 μm, 106–250 μm, and 250–1000 μm) in six streams in the forested South Fork Eel River watershed (California), encompassing a longitudinal gradient in light availability and primary production. Benthic POM at downstream sites was composed of smaller particles with lower organic matter content that were richer in nitrogen and autotrophic material. Areal respiration and nutrient uptake rates increased 11‐ to 67‐fold with stream size. While microbial activity rates did not increase with stream size, benthic POM‐associated microbial biomass increased 20‐fold with stream size, and closely tracked a 15‐fold increase in light availability, and primary production. Thus, microbial biomass, not activity, determined longitudinal patterns in benthic POM‐associated areal nutrient uptake and respiration rates. We attribute longitudinal patterns in microbial biomass to increases in light availability and primary production. Our findings help clarify the role of local (primary production) and upstream processes in shaping ecosystem structure and function.},

keywords = {benthic, fine particulate organic matter, microbial biomass, Nutrient Cycling, Stream Ecology},

pubstate = {published},

tppubtype = {article}

}

@article{Power2021,

title = {Synthetic threads through the web of life},

author = {Mary E. Power },

doi = {10.1073/pnas.2004833118},

year  = {2021},

date = {2021-04-30},

journal = {PNAS},

abstract = {CRISPR-Cas gene editing tools have brought us to an era of synthetic biology that will change the world. Excitement over the breakthroughs these tools have enabled in biology and medicine is balanced, justifiably, by concern over how their applications might go wrong in open environments. We do not know how genomic processes (including regulatory and epigenetic processes), evolutionary change, ecosystem interactions, and other higher order processes will affect traits, fitness, and impacts of edited organisms in nature. However, anticipating the spread, change, and impacts of edited traits or organisms in heterogeneous, changing environments is particularly important with “gene drives on the horizon.” To anticipate how “synthetic threads” will affect the web of life on Earth, scientists must confront complex system interactions across many levels of biological organization. Currently, we lack plans, infrastructure, and funding for field science and scientists to track new synthetic organisms, with or without gene drives, as they move through open environments.},

keywords = {CRISPR, ecological impacts, gene drives, interaction strength, scale linkages},

pubstate = {published},

tppubtype = {article}

}

@article{Bilir2021,

title = {Slope-Aspect Induced Climate Differences Influence How Water Is Exchanged Between the Land and Atmosphere},

author = {T. Eren Bilir and Inez Fung and Todd E. Dawson

},

url = { https://doi.org/10.1029/2020JG006027},

doi = {10.1029/2020JG006027},

year  = {2021},

date = {2021-04-27},

journal = {JGR Biogeosciences},

volume = {126},

number = {5},

abstract = {Cross-slope climate differences in the midlatitudes are ecologically important, and impact vegetation-mediated water balance between the earth surface and the atmosphere. We made high-resolution in situ observations of air temperature, relative humidity, soil moisture, insolation, and sap velocity observations on 14 Pacific madrone trees (Arbutus menziesii) spanning adjacent north and south slopes at the University of California's Angelo Coast Range Reserve. To understand the cross-slope response of sap velocity, a proxy for transpiration, to microclimate, we modeled the sap velocity on each slope using a transpiration model driven by ambient environment and parameterized with a Markov Chain Monte Carlo parameter estimation process. The results show that trees on opposing slopes do not follow a shared pattern of physiological response to transpiration drivers. This means that the observed sap velocity differences are not due entirely to observed microclimate differences, but also due to population-level physiological differences, which indicates acclimation to inhabited microclimate. While our present data set and analytical tools do not identify mechanisms of acclimation, we speculate that differing proportions of sun-adapted and shade-adapted leaves, differences in stomatal regulation, and cross-slope root zone moisture differences could explain some of the observed and modeled differences.},

keywords = {MCMC, plant acclimation, sap velocity, topographic effect, transpiration drivers, transpiration modeling},

pubstate = {published},

tppubtype = {article}

}

@article{Hungate2021,

title = {The Functional Significance of Bacterial Predators},

author = {Bruce A. Hungate and Jane C. Marks and Mary E. Power and Egbert Schwartz and Kees Jan van Groenigen and Steven J. Blazewicz and Peter Chuckran and Paul Dijkstra and Brianna K. Finley and Mary K. Firestone and Megan Foley and Alex Greenlon and Michaela Hayer and Kirsten S. Hofmockel and Benjamin J. Koch and Michelle C. Mack and Rebecca L. Mau and Samantha N. Miller and Ember M. Morrissey and Jeffrey R. Propster and Alicia M. Purcell and Ella Sieradzki and Evan P. Starr and Bram W. G. Stone and César Terrer and Jennifer Pett-Ridge},

doi = {10.1128/mBio.00466-21},

year  = {2021},

date = {2021-04-27},

journal = {mBio},

volume = {12},

number = {e00466-21},

abstract = {Predation structures food webs, influences energy flow, and alters rates and pathways of nutrient cycling through ecosystems, effects that are well documented for macroscopic predators. In the microbial world, predatory bacteria are common, yet little is known about their rates of growth and roles in energy flows through microbial food webs, in part because these are difficult to quantify. Here, we show that growth and carbon uptake were higher in predatory bacteria compared to nonpredatory bacteria, a finding across 15 sites, synthesizing 82 experiments and over 100,000 taxon-specific measurements of element flow into newly synthesized bacterial DNA. Obligate predatory bacteria grew 36% faster and assimilated carbon at rates 211% higher than nonpredatory bacteria. These differences were less pronounced for facultative predators (6% higher growth rates, 17% higher carbon assimilation rates), though high growth and carbon assimilation rates were observed for some facultative predators, such as members of the genera Lysobacter and Cytophaga, both capable of gliding motility and wolf-pack hunting behavior. Added carbon substrates disproportionately stimulated growth of obligate predators, with responses 63% higher than those of nonpredators for the Bdellovibrionales and 81% higher for the Vampirovibrionales, whereas responses of facultative predators to substrate addition were no different from those of nonpredators. This finding supports the ecological theory that higher productivity increases predator control of lower trophic levels. These findings also indicate that the functional significance of bacterial predators increases with energy flow and that predatory bacteria influence element flow through microbial food webs.},

keywords = {18O-H2O, Bdellovibrio, food webs, predator, qSIP, stable isotope probing, top-down control, trophic interactions},

pubstate = {published},

tppubtype = {article}

}

@article{Pedrazas2021,

title = {The Relationship Between Topography, Bedrock Weathering, and Water Storage Across a Sequence of Ridges and Valleys},

author = {Michelle A. Pedrazas and W. Jesse Hahm and Mong-Han Huang and David Dralle and Mariel D. Nelson and Rachel E. Breunig and Kristen E. Fauria and Alexander B. Bryk and William E. Dietrich and Daniella M. Rempe},

url = {https://angelo.berkeley.edu/jgr-earth-surface-2021-pedrazas-the-relationship-between-topography-bedrock-weathering-and-water-storage-across-a-1/},

doi = {10.1029/2020JF005848},

year  = {2021},

date = {2021-03-23},

urldate = {2021-03-23},

journal = {JGR Earth Surface},

volume = {126},

number = {4},

abstract = {Bedrock weathering regulates nutrient mobilization, water storage, and soil production. Relative to the mobile soil layer, little is known about the relationship between topography and bedrock weathering. Here, we identify a common pattern of weathering and water storage across a sequence of three ridges and valleys in the sedimentary Great Valley Sequence in Northern California that share a tectonic and climate history. Deep drilling, downhole logging, and characterization of chemistry and porosity reveal two weathering fronts. The shallower front is ∼7 m deep at the ridge of all three hillslopes, and marks the extent of pervasive fracturing and oxidation of pyrite and organic carbon. A deeper weathering front marks the extent of open fractures and discoloration. This front is 11 m deep under two ridges of similar ridge-valley spacing, but 17.5 m deep under a ridge with nearly twice the ridge-valley spacing. Hence, at ridge tops, the fraction of the hillslope relief that is weathered scales with hillslope length. In all three hillslopes, below this second weathering front, closed fractures and unweathered bedrock extend about one-half the hilltop elevation above the adjacent channels. Neutron probe surveys reveal that seasonally dynamic moisture is stored to approximately the same depth as the shallow weathering front. Under the channels that bound our study hillslopes, the two weathering fronts coincide and occur within centimeters of the ground surface. Our findings provide evidence for feedbacks between erosion and weathering in mountainous landscapes that result in systematic subsurface structuring and water routing.},

keywords = {bedrock weathering, Critical Zone, hillslope, unsaturated zone, water storage, Weathering},

pubstate = {published},

tppubtype = {article}

}

@article{Bouma-Gregson2021,

title = {Taxon-specific photosynthetic responses of attached algal assemblages to experimental translocation between river habitats},

author = {Keith Bouma-Gregson and Mary E. Power and Paula C. Furey and Casey J. Huckins and Yvonne Vadeboncoeur},

url = {https://www.journals.uchicago.edu/doi/pdf/10.1086/713095},

doi = {10.1086/713095},

year  = {2021},

date = {2021-02-25},

journal = {Freshwater Science},

volume = {40},

number = {1},

abstract = {Attached algal and cyanobacterial taxa differ in their ability to exploit and tolerate the diversity of flow, irradiance, and temperature regimes typical of a heterogeneous riverscape. Understanding the drivers of the small-scale variation in algal taxonomic composition helps us predict the riverscape-scale effects of altered flow regimes, but microhabitat-scale variation in algal taxonomy complicates the interpretation of ecosystem-scale estimates of biomass or primary production. Using pulse-amplitude modulated (PAM) fluorometry, we performed 2 manipulative field experiments (in 2014 and 2015) to measure photosynthetic responses of algae and cyanobacteria to depth, temperature, and flow modifications. In 2014, we exposed 6 attached algal assemblages common to the South Fork Eel River (California, USA) to a 24-h incubation on either the river bottom (20 cm deep) or floating at the water surface. In 2015, we incubated 3 algal assemblages for 1 wk in either the thalweg or at the river’s edge. For PAM measurements, we developed a novel method (Photosynthesis–Irradiance Periphyton Experimental System [PIPES]) for manipulating attached filamentous algae, a morphology common in aquatic habitats but underrepresented in photosynthesis experiments. To make the PIPES, we sandwiched thin (<1 mm) layers of filamentous attached algae between 2 layers of mesh so that the algae could be isolated and manipulated for repeated PAM measurements. In the 2014 experiment, incubating Cladophora, Rivularia, Microcoleus, and Anabaena at the water surface tended to decrease photosynthetic rates relative to submerged controls, whereas for Nostoc, the photosynthetic rates were higher in floating treatments. In the 2015 experiment, Cladophora and Oedogonium incubated in the warmer, low-flow river margin had persistently lower photosynthesis rates than their counterparts incubated in the thalweg. The PIPES method improves our ability to make PAM measurements on attached algae. PIPES can be used in conjunction with other methods to evaluate taxon-specific responses to environmental conditions and to help us predict how algal assemblages will shift in dominance under different river management regimes.},

keywords = {algae, benthic, Cladophora, cyanobacteria, electron transport rate, flow, Microcoleus, microhabitat, PAM, photosynthesis, temperature},

pubstate = {published},

tppubtype = {article}

}

@article{Rossi2021,

title = {Foraging modes and movements of Oncorhynchus mykiss as flow and invertebrate drift recede in a California stream},

author = {Gabriel J. Rossi and Mary E. Power and Shelley Pneh and Jason R. Neuswanger and Timothy J. Caldwell},

doi = {10.1139/cjfas-2020-0398},

year  = {2021},

date = {2021-02-12},

journal = {Canadian Journal of Fisheries and Aquatic Sciences},

abstract = {Salmonids frequently adapt their feeding and movement strategies to cope with seasonally fluctuating stream environments. Oncorhynchus mykiss tend to drift-forage in higher velocity habitat than other salmonids, yet their presence in streams with seasonally low velocity and drift suggests behavioral flexibility. We combined 3-D videogrammetry with measurements of invertebrate drift and stream hydraulics to investigate the drivers of O. mykiss foraging mode and movement during the seasonal recession in a California stream. From May to July (2016), foraging movement rate increased as prey concentration and velocity declined; however, movement decreased in August as pools became low and still. In May, 80% of O. mykiss were drift-foraging, while by July, over 70% used search or benthic-foraging modes. Velocity and riffle crest depth were significant predictors of foraging mode, while drift concentration was a poor univariate predictor. However top ranked additive models included both hydraulic variables and drift concentration. A drift-foraging bioenergetic model was a poor predictor of foraging mode. We suggest that infall and benthic prey, as well as risk aversion, may influence late-summer foraging decisions.},

keywords = {bioenergetics, ERCZO, foraging behavior, Mediterranean streams, Oncorhynchus mykiss, salmonids, stream hydraulics, video, videogrammetry},

pubstate = {published},

tppubtype = {article}

}

@article{McCormick2021,

title = {Evidence for widespread woody plant use of water stored in bedrock},

author = {E. McCormick and D.N. Dralle and W.J. Hahm and A.K. Tune and L.M. Schmidt and K.D. Chadwick and D.M. Rempe},

doi = {10.21203/rs.3.rs-138459/v1},

year  = {2021},

date = {2021-01-14},

journal = {Nature},

abstract = {Woody plant transpiration is a major control on Earth’s climate system, streamflow, and human water supply. Soils are widely considered to be the primary reservoir of water for woody plants, however, plants also access water stored in the fractures and pores of bedrock, either as rock moisture (water stored in the unsaturated zone) (Schwinning, 2010) or bedrock groundwater (below the water table) (Miller et al., 2010). Bedrock as a water source for plants has not been evaluated over large scales, and consequently, its importance to terrestrial water and carbon cycling is poorly known (Fan et al., 2019). Here, we show that woody plants routinely access significant quantities of water stored in bedrock —commonly as rock moisture —for transpiration across diverse climates and biomes. For example, in California, the volume of bedrock water transpired by woody vegetation annually exceeds that stored in man-made reservoirs, and woody vegetation that withdraws bedrock water accounts for over 50% of the aboveground carbon stocks in the state. Our findings show that bedrock water storage dynamics are a critical element of terrestrial water cycling and therefore necessary to capture the effect of shifting climate on woody ecosystems, above- and belowground carbon storage, and water resources.},

keywords = {bedrock water, ERCZO, root zone, transpiration, woody plants},

pubstate = {forthcoming},

tppubtype = {article}

}

@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}

}

@article{Wlostowski2020,

title = {Signatures of Hydrologic Function Across the Critical Zone Observatory Network},

author = {Adam N. Wlostowski and Noah Molotch and Suzanne P. Anderson and Susan L. Brantley and Jon Chorover and David Dralle and Praveen Kumar and Li Li and Kathleen A. Lohse and John M. Mallard and Jennifer C. McIntosh and Sheila F. Murphy and Eric Parrish and Mohammad Safeeq and Mark Seyfried and Yuning Shi and Ciaran Harman},

doi = {10.1029/2019WR026635},

year  = {2020},

date = {2020-10-18},

journal = {Water Resources Research},

volume = {57},

number = {3},

abstract = {Despite a multitude of small catchment studies, we lack a deep understanding of how variations in critical zone architecture lead to variations in hydrologic states and fluxes. This study characterizes hydrologic dynamics of 15 catchments of the U.S. Critical Zone Observatory (CZO) network where we hypothesized that our understanding of subsurface structure would illuminate patterns of hydrologic partitioning. The CZOs collect data sets that characterize the physical, chemical, and biological architecture of the subsurface, while also monitoring hydrologic fluxes such as streamflow, precipitation, and evapotranspiration. For the first time, we collate time series of hydrologic variables across the CZO network and begin the process of examining hydrologic signatures across sites. We find that catchments with low baseflow indices and high runoff sensitivity to storage receive most of their precipitation as rain and contain clay-rich regolith profiles, prominent argillic horizons, and/or anthropogenic modifications. In contrast, sites with high baseflow indices and low runoff sensitivity to storage receive the majority of precipitation as snow and have more permeable regolith profiles. The seasonal variability of water balance components is a key control on the dynamic range of hydraulically connected water in the critical zone. These findings lead us to posit that water balance partitioning and streamflow hydraulics are linked through the coevolution of critical zone architecture but that much work remains to parse these controls out quantitatively.},

keywords = {catchment sensitivity, critical zone structure, ERCZO, meta-analysis, water balance},

pubstate = {published},

tppubtype = {article}

}

@article{Ishikawa2020,

title = {Combined use of radiocarbon and stable carbon isotopes for the source mixing model in a stream food web},

author = {Naoto F. Ishikawa and Jacques C. Finlay and Hiromi Uno and Nanako O. Ogawa and Naohiko Ohkouchi and Ichiro Tayasu and Mary E. Power

},

doi = {10.1002/lno.11541},

year  = {2020},

date = {2020-07-06},

journal = {Limnology and Oceanography},

volume = {65},

number = {11},

pages = {2688-2696},

abstract = {Radiocarbon natural abundance (Δ14C) has emerged as a useful dietary tracer in freshwater ecology for the past decade, yet its applicability for separating aquatic and terrestrial resources has not been examined quantitatively. Here, we report Δ14C values of stream invertebrates in different functional feeding groups collected from the upper South Fork Eel River watershed, northern California. We found that algae‐grazing insect larvae show low Δ14C values (−43.1 ± 21.8‰, mean ± standard deviation, N = 6), reflecting the signal of dissolved inorganic carbon weathered from ancient inorganic carbon or respiration of old organic carbon. In contrast, the Δ14C values of leaf‐shredding insect larvae (21.7 ± 31.9‰, N = 5) were close to those of contemporary atmospheric CO2 except at the SF Eel River where algal production was highest. The Δ14C values of predators (−6.1 ± 35.7‰, N = 14) were intermediate between those of grazers and shredders. In a Bayesian mixing model, Δ14C provided a more ecologically realistic estimate for terrestrial vs. aquatic source contributions to invertebrates with lower uncertainty (i.e., narrower credible interval) than did the stable carbon isotopes (δ13C). These results demonstrate that Δ14C can be used, in combination with δ13C, to more precisely estimate organic matter sources to stream animals.},

keywords = {food web, freshwater ecosystem, stable isotopes, stream invertebrates},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}

@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/sites/59/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}

}

@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}

}

@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/sites/59/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}

}

@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}

}

@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}

}

@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/sites/59/41564_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}

}

@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/sites/59/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}

}

@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/sites/59/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}

}

@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/sites/59/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}

}

@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}

}

@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}

}

@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}

}

@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/sites/59/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}

}

@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/sites/59/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}

}

@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/sites/59/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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}