@article{Tune2023,

title = {Deep root activity overprints weathering of petrogenic organic carbon in shale},

author = {AK Tune and JL Druhan and CR Lawrence and DM Rempe},

editor = {A Jacobson},

doi = {10.1016/j.epsl.2023.118048},

year  = {2023},

date = {2023-04-01},

journal = {Earth and Planetary Science Letters},

volume = {607},

number = {118048},

keywords = {root zone, Weathering},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{Rempe2022,

title = {Resilience of woody ecosystems to precipitation variability},

author = {D Rempe and EL McCormick and WJ Hahm and GG Persad and C Cummins},

doi = {https://doi.org/10.31223/X5XW7D},

year  = {2022},

date = {2022-12-31},

urldate = {2022-12-31},

journal = {EarthArXiv},

keywords = {climate change, Drought, precipitation, woody plants},

pubstate = {published},

tppubtype = {article}

}

@article{Lapides2022,

title = {Missing snowmelt runoff following drought explained by root-zone storage deficits},

author = {D Lapides and WJ Hahm and D Rempe and DN Dralle},

doi = {http://doi.org/10.31223/X5591F },

year  = {2022},

date = {2022-12-31},

urldate = {2022-12-31},

journal = {PNAS},

keywords = {Drought, root zone, snow melt},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{Hudson-Rasmussen2022,

title = {Mapping variations in bedrock weathering with slope aspect under a sedimentary ridge-valley system using near-surface geophysics and drilling},

author = {B Hudson-Rasmussen and MH Huang and WJ Hahm and D Rempe and DN Dralle},

doi = {https://doi.org/10.1002/essoar.10512033.1},

year  = {2022},

date = {2022-12-31},

urldate = {2022-12-31},

journal = {ESSOAr},

keywords = {bedrock weathering, hillslopes, Mapping},

pubstate = {published},

tppubtype = {article}

}

@article{Hill2022,

title = {Direct and indirect interactions of spiders, herbivorous insects, and native plants in native perennial vs exotic annual grass patches},

author = {K Hill and ME Power},

year  = {2022},

date = {2022-12-31},

urldate = {2022-12-31},

journal = {Ecology},

keywords = {ecology, exotic plants, grasses, spiders},

pubstate = {published},

tppubtype = {article}

}

@article{Golla2022,

title = {Subsurface weathering signatures in stream chemistry during an intense storm},

author = {JK Golla and J Bouchez and ML Kuessner and DM Rempe and JL Druhan},

url = {https://angelo.berkeley.edu/golla_subsurface_weathering/},

doi = {https://doi.org/10.1016/j.epsl.2022.117773},

year  = {2022},

date = {2022-10-01},

journal = {Earth and Planetary Science Letters},

volume = {595},

keywords = {bedrock weathering, hydrochemistry, streams},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{Rossi2022,

title = {Seasonal growth potential of Oncorhynchus mykiss in streams with contrasting prey phenology and streamflow},

author = {G Rossi and ME Power and SM Carlson and TE Grantham},

url = {https://angelo.berkeley.edu/ecs24211/},

doi = {https://doi.org/10.1002/ecs2.4211},

year  = {2022},

date = {2022-06-16},

urldate = {2022-06-16},

journal = {Ecosphere},

keywords = {predator-prey dynamics, steelhead/rainbow trout, streams},

pubstate = {published},

tppubtype = {article}

}

@article{Hahm2022,

title = {Bedrock vadose zone storage dynamics under extreme drought: consequences for plant water availability, recharge, and runoff},

author = {WJ Hahm and DN Dralle and M Sanders and AB Bryk and KE Fauria and MH Huang and B Hudson-Rasmussen and MD Nelson and MA Pedrazas and L Schmidt and et al.},

url = {https://angelo.berkeley.edu/hahm_bedrock_vadose_storage/},

doi = {https://doi.org/10.1029/2021WR031781},

year  = {2022},

date = {2022-04-08},

urldate = {2022-04-08},

journal = {Water Resources Research},

volume = {58},

issue = {4},

keywords = {bedrock, Drought, water storage},

pubstate = {published},

tppubtype = {article}

}

@article{Lapides2022b,

title = {Controls on stream water age in a saturation overland flow-dominated catchment},

author = {D Lapides and WJ Hahm and DM Rempe and WE Dietrich and DN Dralle

},

url = {https://angelo.berkeley.edu/lapides_streamwater_age-compressed/},

doi = {https://doi.org/10.1029/2021WR031665},

year  = {2022},

date = {2022-04-01},

journal = {Water Resources Research},

volume = {58},

issue = {4},

keywords = {catchment, stream flows},

pubstate = {published},

tppubtype = {article}

}

@article{LaFollette2022,

title = {Multicriteria analysis on rock moisture and streamflow in a rainfall-runoff model improves accuracy of model results},

author = {PT LaFollette and WJ Hahm and DM Rempe and WE Dietrich and CC Brauer and AH Weerts and DN Dralle },

url = {https://angelo.berkeley.edu/lafollette_rockmoisture_streamflow_model/},

doi = {https://doi.org/10.1002/hyp.14536},

year  = {2022},

date = {2022-03-09},

journal = {Hydrological Processes},

volume = {36},

issue = {3},

keywords = {hydrologic modeling, rainfall, rock moisture, Stream Flow},

pubstate = {published},

tppubtype = {article}

}

@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{Peek2021,

title = {Actinemys marmorata (northwestern pond turtle) feeding on Dicamptodon tenebrosus (coastal giant salamander)},

author = {RA Peek and SJ Kupferberg and A Catenazzi and PB Georgakakos and ME Power},

url = {https://angelo.berkeley.edu/peek_pondturtle_salamander/},

doi = {https://doi.org/10.1898/1051-1733-102.3.261},

year  = {2021},

date = {2021-11-26},

journal = {Northwestern Naturalist},

volume = {102},

issue = {3},

keywords = {ecology},

pubstate = {published},

tppubtype = {article}

}

@article{Bouma-Gregson2021b,

title = {Microcoleus (Cyanobacteria) form watershed-wide populations without strong gradients in population structure},

author = {K Bouma-Gregson and A Crits-Christoph and MR Olm and ME Power and JF Banfield},

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

doi = {https://doi.org/10.1111/mec.16208},

year  = {2021},

date = {2021-10-04},

urldate = {2021-10-04},

journal = {Molecular Ecology},

volume = {31},

pages = {86-103},

keywords = {cyanobacteria, population ecology, population structure},

pubstate = {published},

tppubtype = {article}

}

@article{Debray2021,

title = {Priority effects in microbiome assembly},

author = {R Debray and R Herbert and A Jaffe and A Crits-Christoph and ME Power and B Koskella},

url = {https://angelo.berkeley.edu/debray_priority_effects_microbiome/},

doi = {https://doi.org/10.1038/s41579-021-00604-w },

year  = {2021},

date = {2021-08-27},

journal = {Nature Reviews Microbiology},

keywords = {microbial communities},

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{Vadeboncoeur2021b,

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

author = {Y Vadeboncoeur and MV Moore and SD Stewart and S Chandra and KS Atkins and JS Baron and K Bouma-Gregson and S Brothers and SN Francoeur and L Genzoli and SN Higgins and S Hilt and LR Katona and D Kelly and IA Oleksy and T Ozersky and ME Power and D Roberts and AP Smits and O Timoshkin and F Tromboni and MJ Vander Zanden and EA Volkova and AS Waters and SA Wood and M Yamamuro },

url = {https://angelo.berkeley.edu/vadebonceour_algal_blooms/},

doi = {https://doi.org/10.1093/biosci/biab049},

year  = {2021},

date = {2021-07-27},

urldate = {2021-07-27},

journal = {BioScience},

volume = {71},

keywords = {algal blooms, benthic, lakes},

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}

}