For five decades, Jim A. Estes studied sea otters in the Aleutian archipelago of Alaska, discovering how otters structured entire communities. By consuming sea urchins, otters released kelp from herbivory, kelp beds flourished, and kelps sheltered a diversity of fishes, and invertebrates. When otters were extirpated by paleohumans, modern humans, or killer whales, urchins proliferated, reduced kelp forests to "urchin barrens," and species-rich assemblages of fishes and invertebrates were lost. These losses affected seals, eagles, sea gulls, fishes, and sea stars that depended on these prey as well as adjacent habitats that had been nourished by exported kelp production. Jim's research became the poster child for keystone species, trophic cascades, and the critical role of predators in structuring ecosystems. Similar discoveries followed in freshwaters, forests, and grasslands.

Climate change is redistributing life on Earth, with profound impacts for ecosystems and human well-being. While repeat surveys separated by multidecadal intervals can determine whether observed shifts are in the expected direction (e.g., poleward or upslope due to climate change), they do not reveal their mechanisms or time scales: whether they were gradual responses to environmental trends or punctuated responses to disturbance events. Here, we document population reductions and temporary range contractions at multiple sites resulting from drought for three Pacific salmonids at their ranges' trailing edge. During California's 2012 to 2016 historic multiyear drought, the 2013 to 2014 winter stood apart because rainfall was both reduced and delayed. Extremely low river flows during the breeding season ("flow-phenology mismatch") reduced or precluded access to breeding habitat. While Chinook (Oncorhynchus tshawytscha) experienced a down-river range shift, entire cohorts failed in individual tributaries (steelhead trout, O. mykiss) and in entire watersheds (coho salmon, O. kisutch). Salmonids returned to impacted sites in subsequent years, rescued by reserves in the ocean, life history diversity, and, in one case, a conservation broodstock program. Large population losses can, however, leave trailing-edge populations vulnerable to extinction due to demographic stochasticity, making permanent range contraction more likely. When only a few large storms occur during high flow season, the timing of particular storms plays an outsized role in determining which migratory fish species are able to access their riverine breeding grounds and persist.

Microscale symbioses can be critical to ecosystem functions, but the mechanisms of these interactions in nature are often cryptic. Here, we use a combination of stable isotope imaging and tracing to reveal carbon (C) and nitrogen (N) exchanges among three symbiotic primary producers that fuel a salmon-bearing river food web. Bulk isotope analysis, nanoSIMS (secondary ion mass spectrometry) isotope imaging, and density centrifugation for quantitative stable isotope probing enabled quantification of organism-specific C- and N-fixation rates from the subcellular scale to the ecosystem. After winters with riverbed-scouring floods, the macroalga Cladophora glomerata uses nutrients in spring runoff to grow streamers up to 10 m long. During summer flow recession, riverine N concentrations wane and Cladophora becomes densely epiphytized by three species of Epithemia, diatoms with N-fixing endosymbionts (proto-organelles) descended from a free-living Crocosphaera cyanobacterium. Over summertime epiphyte succession on Cladophora, N-fixation rates increased as Epithemia spp. became dominant, Cladophora C-fixation declined to near zero, and Epithemia C-fixation increased. Carbon transfer to caddisflies grazing on Cladophora with high densities of Epithemia was 10-fold higher than C transfer to caddisflies grazing Cladophora with low Epithemia loads. In response to demand for N, Epithemia allocates high levels of newly fixed C to its endosymbiont. Consequently, these endosymbionts have the highest rates of C and N accumulation of any taxon in this tripartite symbiosis during the biologically productive season and can produce one of the highest areal rates of N-fixation reported in any river ecosystem.

Mobile consumers track fluctuating resources across heterogeneous landscapes to grow and survive. In river networks, the abundance and accessibility of food and the energetic consequences of foraging vary among habitats and through time, providing a shifting mosaic of growth opportunities for mobile consumers. However, a framework integrating the spatiotemporal dynamics of growth potential within riverscapes has been lacking. We present the concept of foodscapes to depict the dynamic changes in food abundance, food accessibility, and consumer physiology that contribute to spatial and temporal variation of fish growth in rivers. Drawing on case studies of salmonid fishes from Alaska to California, we illustrate how foodscapes can provide a plethora of foraging, growth, and life history opportunities that potentially contribute to population resilience. We identify knowledge gaps in understanding foodscapes and approaches for stewardship that focus on restoring diverse foraging and growth opportunities for fish and other mobile consumers in river networks.

As human-caused climate changes accelerate, California will experience hydrologic and temperature conditions different than any encountered in recorded history. How will these changes affect the state’s freshwater ecosystems? Rivers, lakes, and wetlands are managed as a water resource, but they also support a complex web of life, ranging from bacteria, fungi, and algae to macrophytes, woody plants, invertebrates, fish, amphibians, reptiles, birds, and mammals. In much of the state, native freshwater organisms already struggle to survive massive water diversions and dams, deteriorating water quality, extensive land cover modification for agriculture and urban development, and invasions of exotic species. In the face of climate change, we need to expand efforts to recover degraded ecosystems and to protect the resilience, health, and viability of existing ecosystems. For this, more process-based understanding of river, lake, and wetlands ecosystems is needed to forecast how systems will respond to future climate change and to our interventions. This will require 1) expanding our ability to model mechanistically how freshwater biota and ecosystems respond to environmental change; 2) hypothesis-driven monitoring and field studies; 3) education and training to build research, practitioner, stewardship, and policy capabilities; and 4) developing tools and policies for building resilient ecosystems. A goals-driven, hypothesis-informed collaboration among tribes, state (and federal) agencies, nongovernmental organizations, academicians, and consultants is needed to accomplish these goals and to advance the skills and knowledge of the future workforce of practitioners, regulators, and researchers who must live with the climate changes that are already upon us and will intensify.

Rapid climate change and invasive species introductions threaten ecological communities across the globe. Freshwaters are particularly vulnerable and impacted, especially when these stresses coincide. We document the migration of an invasive piscine predator, the Sacramento pikeminnow ( Ptychocheilus grandis ), within its introduced range, the South Fork Eel River, California, USA. Snorkel surveys and temperature monitoring in 2015–2019 showed that pikeminnow migrate upstream during spring and early summer, with earlier migration in warmer years. We developed a statistical temperature model to forecast the timing and extent of upstream migration by pikeminnow under varying combinations of discharge and air temperature. Modeled river temperature increased with air temperature and downstream and decreased with discharge. In years with low discharge and high air temperature, we predict pikeminnow will move upstream earlier, increasing spatial and temporal overlap in their summer range with native fishes. Managing conditions that reduce pikeminnow co-occurrence with native fishes (i.e., decreasing river temperature) could increase amount and duration of predator-free habitat for native fishes. We predict invasive pikeminnow will have larger impacts on invaded riverine communities with global warming and increasing drought severity. Knowledge of life history and phenology, for pikeminnow and other organisms, can guide effective management as conditions change and help to limit adverse impacts of introduced organisms on native species.

Water in rivers is delivered via the critical zone that mantles landscapes. Consequently, the success of stream-rearing salmonids depends on the structure and resulting water storage and release processes of this zone. Physical processes below the land surface (the subsurface component of the critical zone) ultimately determine how landscapes ‘filter’ climate to manifest ecologically significant stream flow and temperature regimes. Subsurface water storage capacity of the critical zone has emerged as a key hydrologic variable that integrates many of these subsurface processes, helping to explain flow regimes and terrestrial plant community composition. Here, we investigate how subsurface storage controls flow, temperature and energetic regimes that matter for salmonids. We illustrate the explanatory power of broadly applicable, storage-based frameworks across a lithological gradient that spans the Eel River watershed of California. Study sites are climatically similar but differ in their geologies and consequent subsurface critical zone structure that dictates water storage dynamics, leading to dramatically different hydrographs, temperature, and riparian regimes – with consequences for every aspect of salmonid life history. Lithological controls on the development of key subsurface critical zone properties like storage capacity suggest a heretofore unexplored link between salmonids and geology, adding to a rich literature that highlights various fluvial and geomorphic influences on salmonid diversity and distribution. Rapidly advancing methods for estimating and observing subsurface water storage dynamics at large scales present new opportunities for more clearly identifying landscape features that constrain the distributions and abundances of organisms, including salmonids, at watershed scales.

Abstract The growth of any organism depends on habitat conditions, food availability, and their seasonal interactions. Yet in the vast literature on Pacific salmon (Oncorhynchus), the seasonal interaction between habitat conditions and food availability has received relatively little attention. We examined juvenile Oncorhynchus mykiss rearing, physical habitat, and resource phenologies in two Mediterranean coastal streams—one perennial, cool, and shaded and the other intermittent, seasonally warm, and sunny. We used a bioenergetic model to investigate the timing and magnitude of growth potential for drift‐foraging O. mykiss during the spring and summer in both systems. Growth potential peaked at least 2 months earlier in the intermittent stream than in the perennial stream. By early summer (June), growth potential had declined in the intermittent stream, whereas growth rates were peaking in the perennial stream. However, the mid‐July lipid content of juvenile O. mykiss in the intermittent stream was nearly twice that of fish in the perennial stream. By late summer (August), foraging profitability declined in both streams, as abiotic conditions in the intermittent stream approached lethal. In contrast, the perennial stream maintained suitable abiotic conditions even though the growth rate was low. We suggest that the divergent resource phenologies and seasonal mortality risks experienced by anadromous O. mykiss rearing in these streams could drive diversification of traits governing size, age, and timing of outmigration.

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.

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.

The interface between terrestrial ecosystems and inland waters is an important link in the global carbon cycle. However, the extent to which allochthonous organic matter entering freshwater systems plays a major role in microbial and higher-trophic-level processes is under debate. Human perturbations can alter fluxes of terrestrial carbon to aquatic environments in complex ways. The biomass and production of aquatic microbes are traditionally thought to be resource limited via stoichiometric constraints such as nutrient ratios or the carbon standing stock at a given timepoint. Low concentrations of a particular constituent, however, can be strong evidence of its importance in food webs. High fluxes of a constituent are often associated with low concentrations due to high uptake rates, particularly in aquatic food webs. A focus on biomass rather than turnover can lead investigators to misconstrue dissolved organic carbon use by bacteria. By combining tracer methods with mass balance calculations, we reveal hidden patterns in aquatic ecosystems that emphasize fluxes, turnover rates, and molecular interactions. We suggest that this approach will improve forecasts of aquatic ecosystem responses to warming or altered nitrogen usage.

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.IMPORTANCE 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 Bdellovibrionales and Vampirovibrionales, 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.

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.

When unexpected predator-prey interactions are observed, abiotic conditions can reveal insights about the ecology of the species involved. During one of the warmest months of May in the last 30 y (2008), we observed an adult Northwestern Pond Turtle, Actinemys marmorata, preying upon a paedomorphic Coastal Giant Salamander, Dicamptodon tenebrosus, in the South Fork Eel River. Compiled records of temperatures when moribund, bitten, or dead D. tenebrosus were found in the sunny mainstem river highlight their vulnerability when facing thermal stress beyond their usual habitat in cool shaded tributaries.

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.

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 3D 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.

Radiocarbon natural abundance (Delta C-14) 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 Delta C-14 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 Delta C-14 values (-43.1 +/- 21.8 parts per thousand, 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 Delta C-14 values of leaf-shredding insect larvae (21.7 +/- 31.9 parts per thousand,N = 5) were close to those of contemporary atmospheric CO(2)except at the SF Eel River where algal production was highest. The Delta C-14 values of predators (-6.1 +/- 35.7 parts per thousand,N = 14) were intermediate between those of grazers and shredders. In a Bayesian mixing model, Delta C-14 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 (delta C-13). These results demonstrate that Delta C-14 can be used, in combination with delta C-13, to more precisely estimate organic matter sources to stream animals.

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.

Phage typically have small genomes and depend on their bacterial hosts for replication. DNA sequenced from many diverse ecosystems revealed hundreds of huge phage genomes, between 200 kbp and 716 kbp in length. Thirty-four genomes were manually curated to completion, including the largest phage genomes yet reported. Expanded genetic repertoires include diverse and new CRISPR-Cas systems, tRNAs, tRNA synthetases, tRNA modification enzymes, translation initiation and elongation factors, and ribosomal proteins. Phage CRISPR-Cas systems 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 phage may repurpose bacterial CRISPR-Cas systems to eliminate competing phage. We phylogenetically define major clades of huge phage from human and other animal microbiomes, oceans, lakes, sediments, soils and the built environment. We conclude that their large gene inventories reflect a conserved biological strategy, observed over a broad bacterial host range and across Earth’s ecosystems.