Publications by authors named "Mary E Power"

38 Publications

Blue Waters, Green Bottoms: Benthic Filamentous Algal Blooms Are an Emerging Threat to Clear Lakes Worldwide.

Bioscience 2021 Oct 7;71(10):1011-1027. Epub 2021 Jul 7.

Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.

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.
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http://dx.doi.org/10.1093/biosci/biab049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8490932PMC
October 2021

Microcoleus (Cyanobacteria) form watershed-wide populations without strong gradients in population structure.

Mol Ecol 2022 01 21;31(1):86-103. Epub 2021 Oct 21.

Earth and Planetary Science Department, University of California, Berkeley, California, USA.

The relative importance of separation by distance and by environment to population genetic diversity can be conveniently tested in river networks, where these two drivers are often independently distributed over space. To evaluate the importance of dispersal and environmental conditions in shaping microbial population structures, we performed genome-resolved metagenomic analyses of benthic Microcoleus-dominated cyanobacterial mats collected in the Eel and Russian River networks (California, USA). The 64 Microcoleus genomes were clustered into three species that shared >96.5% average nucleotide identity (ANI). Most mats were dominated by one strain, but minor alleles within mats were often shared, even over large spatial distances (>300 km). Within the most common Microcoleus species, the ANI between the dominant strains within mats decreased with increasing spatial separation. However, over shorter spatial distances (tens of kilometres), mats from different subwatersheds had lower ANI than mats from the same subwatershed, suggesting that at shorter spatial distances environmental differences between subwatersheds in factors like canopy cover, conductivity, and mean annual temperature decreases ANI. Since mats in smaller creeks had similar levels of nucleotide diversity (π) as mats in larger downstream subwatersheds, within-mat genetic diversity does not appear to depend on the downstream accumulation of upstream-derived strains. The four-gamete test and sequence length bias suggest recombination occurs between almost all strains within each species, even between populations separated by large distances or living in different habitats. Overall, our results show that, despite some isolation by distance and environmental conditions, sufficient gene-flow occurs among cyanobacterial strains to prevent either driver from producing distinctive population structures across the watershed.
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http://dx.doi.org/10.1111/mec.16208DOI Listing
January 2022

Author Correction: Priority effects in microbiome assembly.

Nat Rev Microbiol 2022 Feb;20(2):122

Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.

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http://dx.doi.org/10.1038/s41579-021-00643-3DOI Listing
February 2022

Priority effects in microbiome assembly.

Nat Rev Microbiol 2022 02 27;20(2):109-121. Epub 2021 Aug 27.

Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.

Advances in next-generation sequencing have enabled the widespread measurement of microbiome composition across systems and over the course of microbiome assembly. Despite substantial progress in understanding the deterministic drivers of community composition, the role of historical contingency remains poorly understood. The establishment of new species in a community can depend on the order and/or timing of their arrival, a phenomenon known as a priority effect. Here, we review the mechanisms of priority effects and evidence for their importance in microbial communities inhabiting a range of environments, including the mammalian gut, the plant phyllosphere and rhizosphere, soil, freshwaters and oceans. We describe approaches for the direct testing and prediction of priority effects in complex microbial communities and illustrate these with re-analysis of publicly available plant and animal microbiome datasets. Finally, we discuss the shared principles that emerge across study systems, focusing on eco-evolutionary dynamics and the importance of scale. Overall, we argue that predicting when and how current community state impacts the success of newly arriving microbial taxa is crucial for the management of microbiomes to sustain ecological function and host health. We conclude by discussing outstanding conceptual and practical challenges that are faced when measuring priority effects in microbiomes.
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http://dx.doi.org/10.1038/s41579-021-00604-wDOI Listing
February 2022

Synthetic threads through the web of life.

Authors:
Mary E Power

Proc Natl Acad Sci U S A 2021 06 30;118(22). Epub 2021 Apr 30.

Department of Integrative Biology, University of California, Berkeley, CA 94720

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.
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http://dx.doi.org/10.1073/pnas.2004833118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8179130PMC
June 2021

The Functional Significance of Bacterial Predators.

mBio 2021 04 27;12(2). Epub 2021 Apr 27.

Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA.

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 and , 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 and 81% higher for the , 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. The word "predator" may conjure images of leopards killing and eating impala on the African savannah or of great white sharks attacking elephant seals off the coast of California. But microorganisms are also predators, including bacteria that kill and eat other bacteria. While predatory bacteria have been found in many environments, it has been challenging to document their importance in nature. This study quantified the growth of predatory and nonpredatory bacteria in soils (and one stream) by tracking isotopically labeled substrates into newly synthesized DNA. Predatory bacteria were more active than nonpredators, and obligate predators, such as and , increased in growth rate in response to added substrates at the base of the food chain, strong evidence of trophic control. This work provides quantitative measures of predator activity and suggests that predatory bacteria-along with protists, nematodes, and phages-are active and important in microbial food webs.
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http://dx.doi.org/10.1128/mBio.00466-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8092244PMC
April 2021

Clades of huge phages from across Earth's ecosystems.

Nature 2020 02 12;578(7795):425-431. Epub 2020 Feb 12.

Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA.

Bacteriophages typically have small genomes and depend on their bacterial hosts for replication. 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.
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http://dx.doi.org/10.1038/s41586-020-2007-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162821PMC
February 2020

Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network.

ISME J 2019 06 26;13(6):1618-1634. Epub 2019 Feb 26.

Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.

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.
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http://dx.doi.org/10.1038/s41396-019-0374-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6776057PMC
June 2019

Landscapes of Fear: Spatial Patterns of Risk Perception and Response.

Trends Ecol Evol 2019 04 8;34(4):355-368. Epub 2019 Feb 8.

Department of Environmental Science, Policy, and Management, University of California Berkeley, 130 Mulford Hall #3114, Berkeley, CA 94720, USA.

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.
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http://dx.doi.org/10.1016/j.tree.2019.01.004DOI Listing
April 2019

Diverse effects of the common hippopotamus on plant communities and soil chemistry.

Oecologia 2018 Nov 11;188(3):821-835. Epub 2018 Aug 11.

Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA.

The ecological importance of the common hippopotamus (Hippopotamus amphibius) in aquatic ecosystems is becoming increasingly well known. These unique megaherbivores are also likely to have a formative influence on the terrestrial ecosystems in which they forage. In this study, we employed a novel exclosure design to exclude H. amphibius from experimental plots on near-river grasslands. Our three-year implementation of this experiment revealed a substantial influence of H. amphibius removal on both plant communities and soil chemistry. H. amphibius significantly reduced grassland canopy height, increased the leafiness of common grasses, reduced woody plant abundance and size, and increased the concentrations of several soil elements. Many of the soil chemistry changes that we experimentally induced by exclusion of H. amphibius were mirrored in the soil chemistry differences between naturally occurring habitats of frequent (grazing lawns) and infrequent (shrub forest) use by H. amphibius and other grazing herbivores. In contrast to existing hypotheses regarding grazing species, we found that H. amphibius had little effect on local plant species richness. Simultaneous observations of exclosures designed to remove all large herbivores revealed that H. amphibius removal had ecologically significant impacts, but that the removal of all species of large herbivores generated more pronounced impacts than the removal of H. amphibius alone. In aggregate, our results suggest that H. amphibius have myriad effects on their terrestrial habitats that likely improve the quality of forage available for other herbivores. We suggest that ongoing losses of this vulnerable megaherbivore are likely to cause significant ecological change.
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http://dx.doi.org/10.1007/s00442-018-4243-yDOI Listing
November 2018

Widespread anatoxin-a detection in benthic cyanobacterial mats throughout a river network.

PLoS One 2018 18;13(5):e0197669. Epub 2018 May 18.

Department of Integrative Biology, University of California, Berkeley, California, United States of America.

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 Anabaena-dominated 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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0197669PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5959195PMC
December 2018

Effects of the hippopotamus on the chemistry and ecology of a changing watershed.

Proc Natl Acad Sci U S A 2018 05 14;115(22):E5028-E5037. Epub 2018 May 14.

Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720.

Cross-boundary transfers of nutrients can profoundly shape the ecology of recipient systems. The common hippopotamus, , is a significant vector of such subsidies from terrestrial to river ecosystems. We compared river pools with high and low densities of to determine how subsidies shape the chemistry and ecology of aquatic communities. Our study watershed, like many in sub-Saharan Africa, has been severely impacted by anthropogenic water abstraction reducing dry-season flow to zero. We conducted observations for multiple years over wet and dry seasons to identify how hydrological variability influences the impacts of During the wet season, when the river was flowing, we detected no differences in water chemistry and nutrient parameters between pools with high and low densities of Likewise, the diversity and abundance of fish and aquatic insect communities were indistinguishable. During the dry season, however, high-density s pools differed drastically in almost all measured attributes of water chemistry and exhibited depressed fish and insect diversity and fish abundance compared with low-density pools. Scaled up to the entire watershed, we estimate that in this hydrologically altered watershed reduces dry-season fish abundance and indices of gamma-level diversity by 41% and 16%, respectively, but appears to promote aquatic invertebrate diversity. Widespread human-driven shifts in hydrology appear to redefine the role of , altering their influence on ecosystem diversity and functioning in a fashion that may be more severe than presently appreciated.
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http://dx.doi.org/10.1073/pnas.1800407115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5984519PMC
May 2018

Eighty years of food-web response to interannual variation in discharge recorded in river diatom frustules from an ocean sediment core.

Proc Natl Acad Sci U S A 2017 09 5;114(38):10155-10159. Epub 2017 Sep 5.

Department of Integrative Biology, University of California, Berkeley, CA 94720;

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 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.
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http://dx.doi.org/10.1073/pnas.1611884114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617238PMC
September 2017

Robert Treat Paine III (1933-2016).

Proc Natl Acad Sci U S A 2017 07 19;114(27):6881-6882. Epub 2017 Jun 19.

Department of Integrative Biology, University of California, Berkeley, CA 94720.

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http://dx.doi.org/10.1073/pnas.1706692114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502649PMC
July 2017

Rise and fall of toxic benthic freshwater cyanobacteria (Anabaena spp.) in the Eel river: Buoyancy and dispersal.

Harmful Algae 2017 06 24;66:79-87. Epub 2017 May 24.

UMR 6553 ECOBIO CNRS, University of Rennes 1, Campus de Beaulieu, bat 14a, 35042 Rennes, France; Department of Civil and Environmental Engineering, University of California, 1 Shields Avenue, Davis, CA 95616, USA. Electronic address:

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 4days, while in low light mats begin to sink in <24h. 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 30,693ng/gDW) than microcystin (median 30, max 37ng/gDW). 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.
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http://dx.doi.org/10.1016/j.hal.2017.05.007DOI Listing
June 2017

A keystone ecologist: Robert Treat Paine, 1933-2016.

Ecology 2016 11;97(11):2905-2909

Nicholas School of the Environment, Duke University, Durham, North Carolina, 27708, USA.

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.
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http://dx.doi.org/10.1002/ecy.1572DOI Listing
November 2016

High Time for Conservation: Adding the Environment to the Debate on Marijuana Liberalization.

Bioscience 2015 Aug 19;65(8):822-829. Epub 2015 Jun 19.

Jennifer K. Carah is an ecologist, Jeanette K. Howard is the lead freshwater scientist, Lisa L. Hulette is a senior project director, and Stefanie L. Martin was an associate project director at The Nature Conservancy of California, in San Francisco. Jennifer works on stream and salmonid habitat conservation and restoration. Jeanette works on freshwater systems conservation planning and water resource sustainability. Lisa directs The Nature Conservancy of California's Salmon Program, and Stefanie is a conservation program manager who focuses on evaluating the economic value of conservation and the effects of market dynamics on conservation approaches. Sally E. Thompson is an ecohydrologist who studies hydrology, spatial ecology, and water resource sustainability and David N. Dralle is a graduate student who studies mathematical methods in ecohydrology in the Department of Civil and Environmental Engineering at the University of California, Berkeley. Stephanie M. Carlson is an ecologist who studies ecology and conservation of freshwater fishes in the Department of Environmental Science, Policy, and Management and Mary E. Power is an ecologist who studies river food webs and upland river-coastal ocean linkages in the Department of Integrative Biology at the University of California, Berkeley. Anne G. Short Gianotti is a geographer in the Department of Earth and Environment at Boston University; she studies human-environment relations, environmental governance, and sustainable development. Scott D. Bauer is a senior environmental scientist with the California Department of Fish and Wildlife (CDFW) in Eureka; he works on CDFW's Watershed Enforcement Team, a program created in the summer of 2014 to regulate and enforce existing environmental laws at marijuana cultivation sites. Mourad W. Gabriel is the executive director for the Integral Ecology Research Center, a nonprofit research organization in Blue Lake, California; he studies wildlife disease ecology and the environmental impacts associated with marijuana cultivation. Brian J. Johnson is California director of Trout Unlimited in Berkeley. Curtis A. Knight is executive director of California Trout in San Francisco. Sarah J. Kupferberg is an ecologist with McBain Associates, in Arcata, California. Sarah studies stream ecology, amphibian biology, and the impacts of hydropower facilities on aquatic resources. Rosamond L. Naylor is an economist in the Department of Environmental Earth Science at Stanford University. She studies the economic and biophysical dimensions of food security and the environmental impacts of crop and animal production. E-mail:

The liberalization of marijuana policies, including the legalization of medical and recreational marijuana, is sweeping the United States and other countries. Marijuana cultivation can have significant negative collateral effects on the environment that are often unknown or overlooked. Focusing on the state of California, where by some estimates 60%-70% of the marijuana consumed in the United States is grown, we argue that (a) the environmental harm caused by marijuana cultivation merits a direct policy response, (b) current approaches to governing the environmental effects are inadequate, and
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http://dx.doi.org/10.1093/biosci/biv083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776720PMC
August 2015

Mainstem-tributary linkages by mayfly migration help sustain salmonids in a warming river network.

Ecol Lett 2015 Oct 6;18(10):1012-20. Epub 2015 Aug 6.

Department of Integrative Biology, University of California Berkeley, Berkeley, CA, 94720, USA.

Animal migrations can link ecosystems across space. We discovered an aquatic insect that migrates between a river mainstem and its tributaries, and provides an important trophic subsidy for tributary predators. A mayfly, Ephemerella maculata, rears in a warm, sunlit productive river mainstem, then migrates as adults to cool, shaded unproductive tributaries where they oviposit and die. This migration tripled insect flux into a tributary for 1 month in summer. A manipulative field experiment showed that this E. maculata subsidy nearly tripled the growth of the young of the year steelhead trout (Oncorhynchus mykiss) in the recipient tributary over the summer months, and was more important than terrestrial invertebrate subsidies, which have been considered the primary food source for predators in small, forested creeks. By delivering food subsidies from productive but warming river mainstems to cool but food-limited tributaries, aquatic insect migrations could enhance resilience to cool-water predators in warming river networks.
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http://dx.doi.org/10.1111/ele.12483DOI Listing
October 2015

Variation in terrestrial and aquatic sources of methylmercury in stream predators as revealed by stable mercury isotopes.

Environ Sci Technol 2014 Sep 18;48(17):10128-35. Epub 2014 Aug 18.

Department of Biology, University of North Carolina at Greensboro , Greensboro, North Carolina 27402, United States.

Mercury (Hg) is widely distributed in the environment, and its organic form, methylmercury (MeHg), can extensively bioaccumulate and biomagnify in aquatic and terrestrial food webs. Concentrations of MeHg in organisms are highly variable, and the sources in natural food webs are often not well understood. This study examined stable isotope ratios of MeHg (mass-dependent fractionation, as δ(202)HgMeHg; and mass-independent fractionation, as Δ(199)HgMeHg) in benthic invertebrates, juvenile steelhead trout (Oncorhynchus mykiss), and water striders (Gerris remigis) along a stream productivity gradient, as well as carnivorous terrestrial invertebrates, in a forested watershed at the headwater of South Fork Eel River in northern California. Throughout the sampling sites, δ(202)HgMeHg (after correction due to the effect of MeHg photodegradation) was significantly different between benthic (median = -1.40‰; range, -2.34 to -0.78‰; total number of samples = 29) and terrestrial invertebrates (median = +0.51‰; range, -0.37 to +1.40‰; total number of samples = 9), but no major difference between these two groups was found for Δ(199)HgMeHg. Steelhead trout (52 individual fishes) have MeHg of predominantly aquatic origins, with a few exceptions at the upstream locations (e.g., 1 fish collected in a tributary had a purely terrestrial MeHg source and 4 fishes had mixed aquatic and terrestrial MeHg sources). Water striders (seven pooled samples) derive MeHg largely from terrestrial sources throughout headwater sections. These data suggest that direct terrestrial subsidy (e.g., terrestrial invertebrates falling into water) can be important for some stream predators in headwater streams and could represent an important means of transfer of terrestrially derived MeHg (e.g., in situ methylation within forests, atmospheric sources) to aquatic ecosystems. Moreover, these findings show that terrestrial subsidies can enhance MeHg bioaccumulation of consumers in headwater streams where aqueous MeHg levels are very low.
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http://dx.doi.org/10.1021/es500517sDOI Listing
September 2014

Integrating the invisible fabric of nature into fisheries management.

Proc Natl Acad Sci U S A 2014 Jan 23;111(2):581-4. Epub 2013 Dec 23.

Department of Biological Science, Florida State University, Tallahassee, FL 32306.

Overfishing and environmental change have triggered many severe and unexpected consequences. As existing communities have collapsed, new ones have become established, fundamentally transforming ecosystems to those that are often less productive for fisheries, more prone to cycles of booms and busts, and thus less manageable. We contend that the failure of fisheries science and management to anticipate these transformations results from a lack of appreciation for the nature, strength, complexity, and outcome of species interactions. Ecologists have come to understand that networks of interacting species exhibit nonlinear dynamics and feedback loops that can produce sudden and unexpected shifts. We argue that fisheries science and management must follow this lead by developing a sharper focus on species interactions and how disrupting these interactions can push ecosystems in which fisheries are embedded past their tipping points.
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http://dx.doi.org/10.1073/pnas.1305853111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3896161PMC
January 2014

Predicting and detecting reciprocity between indirect ecological interactions and evolution.

Am Nat 2013 May 21;181 Suppl 1:S76-99. Epub 2013 Mar 21.

Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, CA 95060, USA.

Living nature can be thought of as a tapestry, defined not only by its constituent parts but also by how these parts are woven together. The weaving of this tapestry is a metaphor for species interactions, which can be divided into three broad classes: competitive, mutualistic, and consumptive. Direct interactions link together as more complex networks, for example, the joining of consumptive interactions into food webs. Food web dynamics are driven, in turn, by changes in the abundances of web members, whose numbers or biomass respond to bottom-up (resource limitation) and top-down (consumer limitation) forcing. The relative strengths of top-down and bottom-up forcing on the abundance of a given web member depend on its ecological context, including its topological position within the food web. Top-down effects by diverse consumers are nearly ubiquitous, in many cases influencing the structure and operation of ecosystems. While the ecological effects of such interactions are well known, far less is known of their evolutionary consequences. In this essay, we describe sundry consequences of these interaction chains on species and ecosystem processes, explain several known or suspected evolutionary effects of consumer-induced interaction chains, and identify areas where reciprocity between ecology and evolution involving the indirect effects of consumer-prey interaction chains might be further explored.
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http://dx.doi.org/10.1086/668120DOI Listing
May 2013

Effects of flow regimes altered by dams on survival, population declines, and range-wide losses of California river-breeding frogs.

Conserv Biol 2012 Jun;26(3):513-24

Department of Integrative Biology, University of California, Berkeley, 2033 Valley Life Sciences Building, Berkeley, CA 94702, USA.

Widespread alteration of natural hydrologic patterns by large dams combined with peak demands for power and water delivery during summer months have resulted in frequent aseasonal flow pulses in rivers of western North America. Native species in these ecosystems have evolved with predictable annual flood-drought cycles; thus, their likelihood of persistence may decrease in response to disruption of the seasonal synchrony between stable low-flow conditions and reproduction. We evaluated whether altered flow regimes affected 2 native frogs in California and Oregon (U.S.A.) at 4 spatial and temporal extents. We examined changes in species distribution over approximately 50 years, current population density in 11 regulated and 16 unregulated rivers, temporal trends in abundance among populations occupying rivers with different hydrologic histories, and within-year patterns of survival relative to seasonal hydrology. The foothill yellow-legged frog (Rana boylii), which breeds only in flowing water, is more likely to be absent downstream of large dams than in free-flowing rivers, and breeding populations are on average 5 times smaller in regulated rivers than in unregulated rivers. Time series data (range = 8 - 19 years) from 5 populations of yellow-legged frogs and 2 populations of California red-legged frogs (R. draytonii) across a gradient of natural to highly artificial timing and magnitude of flooding indicate that variability of flows in spring and summer is strongly correlated with high mortality of early life stages and subsequent decreases in densities of adult females. Flow management that better mimics natural flow timing is likely to promote persistence of these species and others with similar phenology.
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http://dx.doi.org/10.1111/j.1523-1739.2012.01837.xDOI Listing
June 2012

Structural and functional loss in restored wetland ecosystems.

PLoS Biol 2012 Jan 24;10(1):e1001247. Epub 2012 Jan 24.

Integrative Biology Department, University of California at Berkeley, Berkeley, California, United States of America.

Wetlands are among the most productive and economically valuable ecosystems in the world. However, because of human activities, over half of the wetland ecosystems existing in North America, Europe, Australia, and China in the early 20th century have been lost. Ecological restoration to recover critical ecosystem services has been widely attempted, but the degree of actual recovery of ecosystem functioning and structure from these efforts remains uncertain. Our results from a meta-analysis of 621 wetland sites from throughout the world show that even a century after restoration efforts, biological structure (driven mostly by plant assemblages), and biogeochemical functioning (driven primarily by the storage of carbon in wetland soils), remained on average 26% and 23% lower, respectively, than in reference sites. Either recovery has been very slow, or postdisturbance systems have moved towards alternative states that differ from reference conditions. We also found significant effects of environmental settings on the rate and degree of recovery. Large wetland areas (>100 ha) and wetlands restored in warm (temperate and tropical) climates recovered more rapidly than smaller wetlands and wetlands restored in cold climates. Also, wetlands experiencing more (riverine and tidal) hydrologic exchange recovered more rapidly than depressional wetlands. Restoration performance is limited: current restoration practice fails to recover original levels of wetland ecosystem functions, even after many decades. If restoration as currently practiced is used to justify further degradation, global loss of wetland ecosystem function and structure will spread.
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http://dx.doi.org/10.1371/journal.pbio.1001247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3265451PMC
January 2012

Trophic downgrading of planet Earth.

Science 2011 Jul;333(6040):301-6

Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA.

Until recently, large apex consumers were ubiquitous across the globe and had been for millions of years. The loss of these animals may be humankind's most pervasive influence on nature. Although such losses are widely viewed as an ethical and aesthetic problem, recent research reveals extensive cascading effects of their disappearance in marine, terrestrial, and freshwater ecosystems worldwide. This empirical work supports long-standing theory about the role of top-down forcing in ecosystems but also highlights the unanticipated impacts of trophic cascades on processes as diverse as the dynamics of disease, wildfire, carbon sequestration, invasive species, and biogeochemical cycles. These findings emphasize the urgent need for interdisciplinary research to forecast the effects of trophic downgrading on process, function, and resilience in global ecosystems.
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http://dx.doi.org/10.1126/science.1205106DOI Listing
July 2011

Light-mediated thresholds in stream-water nutrient composition in a river network.

Ecology 2011 Jan;92(1):140-50

Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108, USA.

The elemental composition of solutes transported by rivers reflects combined influences of surrounding watersheds and transformations within stream networks, yet comparatively little is known about downstream changes in effects of watershed loading vs. in-channel processes. In the forested watershed of a river under a mediterranean hydrologic regime, we examined the influence of longitudinal changes in environmental conditions on water-column nutrient composition during summer base flow across a network of sites ranging from strongly heterotrophic headwater streams to larger, more autotrophic sites downstream. Small streams (0.1-10 km2 watershed area) had longitudinally similar nutrient concentration and composition with low (approximately 2) dissolved nitrogen (N) to phosphorus (P) ratios. Abrupt deviations from this pattern were observed in larger streams with watershed areas > 100 km2 where insolation and algal abundance and production rapidly increased. Downstream, phosphorus and silica concentrations decreased by > 50% compared to headwater streams, and dissolved organic carbon and nitrogen increased by approximately 3-6 times. Decreasing dissolved P and increasing dissolved N raised stream-water N:P to 46 at the most downstream sites, suggesting a transition from N limitation in headwaters to potential P limitation in larger channels. We hypothesize that these changes were mediated by increasing algal photosynthesis and N fixation by benthic algal assemblages, which, in response to increasing light availability, strongly altered stream-water nutrient concentration and stoichiometry in larger streams and rivers.
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http://dx.doi.org/10.1890/09-2243.1DOI Listing
January 2011

Cultivation and quantitative proteomic analyses of acidophilic microbial communities.

ISME J 2010 Apr 24;4(4):520-30. Epub 2009 Dec 24.

Microbiology Graduate Group, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.

Acid mine drainage (AMD), an extreme environment characterized by low pH and high metal concentrations, can support dense acidophilic microbial biofilm communities that rely on chemoautotrophic production based on iron oxidation. Field determined production rates indicate that, despite the extreme conditions, these communities are sufficiently well adapted to their habitats to achieve primary production rates comparable to those of microbial communities occurring in some non-extreme environments. To enable laboratory studies of growth, production and ecology of AMD microbial communities, a culturing system was designed to reproduce natural biofilms, including organisms recalcitrant to cultivation. A comprehensive metabolic labeling-based quantitative proteomic analysis was used to verify that natural and laboratory communities were comparable at the functional level. Results confirmed that the composition and core metabolic activities of laboratory-grown communities were similar to a natural community, including the presence of active, low abundance bacteria and archaea that have not yet been isolated. However, laboratory growth rates were slow compared with natural communities, and this correlated with increased abundance of stress response proteins for the dominant bacteria in laboratory communities. Modification of cultivation conditions reduced the abundance of stress response proteins and increased laboratory community growth rates. The research presented here represents the first description of the application of a metabolic labeling-based quantitative proteomic analysis at the community level and resulted in a model microbial community system ideal for testing physiological and ecological hypotheses.
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http://dx.doi.org/10.1038/ismej.2009.139DOI Listing
April 2010

Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland.

ISME J 2009 Jun 12;3(6):738-44. Epub 2009 Mar 12.

Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.

Climate change impacts on soil microbial communities could alter the structure of terrestrial ecosystems and biogeochemical cycles of the Earth. We used 16S rRNA gene microarrays to evaluate changes in the composition of grassland soil microbial communities under rainfall amendments simulating alternative climate change scenarios, and to compare these to responses of overlying plants and invertebrates. Following 5 years of rainfall manipulation, soil bacteria and archaea in plots where natural rain was supplemented differed little from ambient controls, despite profound treatment-related changes in the overlying grassland. During the sixth and seventh year, seasonal differences in bacterial and archaeal assemblages emerged among treatments, but only when watering exacerbated or alleviated periods of particularly aberrant conditions in the ambient climate. In contrast to effects on plants and invertebrates, effects on bacteria and archaea did not compound across seasons or years, indicating that soil microbial communities may be more robust than associated aboveground macroorganisms to certain alterations in climate.
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http://dx.doi.org/10.1038/ismej.2009.16DOI Listing
June 2009

Impact of carbon nanotubes on the ingestion and digestion of bacteria by ciliated protozoa.

Nat Nanotechnol 2008 Jun 11;3(6):347-51. Epub 2008 May 11.

Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.

Research on the toxicity of carbon nanotubes has focused on human health risks, and little is known about their impact on natural ecosystems. The ciliated protozoan Tetrahymena thermophila has been widely studied by ecotoxicologists because of its role in the regulation of microbial populations through the ingestion and digestion of bacteria, and because it is an important organism in wastewater treatment and an indicator of sewage effluent quality. Here we show that single-walled carbon nanotubes are internalized by T. thermophila, possibly allowing the nanotubes to move up the food chain. The internalization also causes the protozoa to aggregate, which impedes their ability to ingest and digest their prey bacteria species, although it might also be possible to use nanotubes to improve the efficiency of wastewater treatment.
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http://dx.doi.org/10.1038/nnano.2008.109DOI Listing
June 2008

Evolutionary consequences of habitat loss for Pacific anadromous salmonids.

Evol Appl 2008 May;1(2):300-18

Oregon Department of Fish and Wildlife La Grande, OR.

Large portions of anadromous salmonid habitat in the western United States has been lost because of dams and other blockages. This loss has the potential to affect salmonid evolution through natural selection if the loss is biased, affecting certain types of habitat differentially, and if phenotypic traits correlated with those habitat types are heritable. Habitat loss can also affect salmonid evolution indirectly, by reducing genetic variation and changing its distribution within and among populations. In this paper, we compare the characteristics of lost habitats with currently accessible habitats and review the heritability of traits which show correlations with habitat/environmental gradients. We find that although there is some regional variation, inaccessible habitats tend to be higher in elevation, wetter and both warmer in the summer and colder in the winter than habitats currently available to anadromous salmonids. We present several case studies that demonstrate either a change in phenotypic or life history expression or an apparent reduction in genetic variation associated with habitat blockages. These results suggest that loss of habitat will alter evolutionary trajectories in salmonid populations and Evolutionarily Significant Units. Changes in both selective regime and standing genetic diversity might affect the ability of these taxa to respond to subsequent environmental perturbations. Both natural and anthropogenic and should be considered seriously in developing management and conservation strategies.
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http://dx.doi.org/10.1111/j.1752-4571.2008.00030.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3352431PMC
May 2008

Spatial variation in caddisfly grazing regimes within a northern California watershed.

Ecology 2007 Oct;88(10):2609-19

Department of Integrative Biology, University of California, Berkeley, California 94720, USA.

Ecologists seek better understanding of why species interactions change across space and time in natural communities. In streams, species effects on resources and community structure may change as physical characteristics of the stream environment change along drainage networks. We examined spatial and seasonal effects of armored grazers using a small-scale exclusion experiment that was replicated in streams of different drainage areas. Effects of grazing varied with stream size and were related to variation in grazer abundance and phenology. We identified three distinct grazing regimes and a stream size (drainage area [DA]) threshold corresponding to a shift from one to two functional trophic levels. In streams with DA < 1 km2, armored grazers did not reduce biomass of algal biofilms. In slightly larger streams (2-3 km2 DA), the armored grazer guild was dominated by bivoltine Glossosoma. These caddisflies persisted and limited algal biofilms throughout the summer in one of these streams. In the largest tributaries (DA > 10 km2), the grazer guild was dominated by univoltine caddisflies, and grazing limited algal biofilms in early summer, but not late summer, after caddisflies pupated. Drainage area is a useful predictor of spatial transitions in food web interactions within and among watersheds. Quantifying the drainage area threshold at which interactions change in catchments with differing geology, vegetation, hydrology, climate, land use, or species pools should help build the understanding we need to forecast ecological responses to environmental change.
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http://dx.doi.org/10.1890/06-0796.1DOI Listing
October 2007
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