Preserving biodiversity is a global challenge requiring data on species’ distribution and abundance over large geographic and temporal scales. However, traditional methods to survey mobile species’ distribution and abundance in marine environments are often inefficient, environmentally destructive, or resource‐intensive. Metabarcoding of environmental DNA (eDNA) offers a new means to assess biodiversity and on much larger scales, but adoption of this approach for surveying whole animal communities in large, dynamic aquatic systems has been slowed by significant unknowns surrounding error rates of detection and relevant spatial resolution of eDNA surveys. Here, we report the results of a 2.5 km eDNA transect surveying the vertebrate fauna present along a gradation of diverse marine habitats associated with a kelp forest ecosystem. Using PCR primers that target the mitochondrial 12S rRNA gene of marine fishes and mammals, we generated eDNA sequence data and compared it to simultaneous visual dive surveys. We find spatial concordance between individual species’ eDNA and visual survey trends, and that eDNA is able to distinguish vertebrate community assemblages from habitats separated by as little as ~60 m. eDNA reliably detected vertebrates with low false‐negative error rates (1/12 taxa) when compared to the surveys, and revealed cryptic species known to occupy the habitats but overlooked by visual methods. This study also presents an explicit accounting of false negatives and positives in metabarcoding data, which illustrate the influence of gene marker selection, replication, contamination, biases impacting eDNA count data and ecology of target species on eDNA detection rates in an open ecosystem.

Long-term declines in oxygen concentrations are evident throughout much of the ocean interior and are particularly acute in midwater oxygen minimum zones (OMZs). These regions are defined by extremely low oxygen concentrations (<20-45 μmol kg(-1)), cover wide expanses of the ocean, and are associated with productive oceanic and coastal regions. OMZs have expanded over the past 50 years, and this expansion is predicted to continue as the climate warms worldwide. Shoaling of the upper boundaries of the OMZs accompanies OMZ expansion, and decreased oxygen at shallower depths can affect all marine organisms through multiple direct and indirect mechanisms. Effects include altered microbial processes that produce and consume key nutrients and gases, changes in predator-prey dynamics, and shifts in the abundance and accessibility of commercially fished species. Although many species will be negatively affected by these effects, others may expand their range or exploit new niches. OMZ shoaling is thus likely to have major and far-reaching consequences.

Long-term changes in nutrient supply and primary production reportedly foreshadow substantial declines in global marine fishery production. These declines combined with current overfishing, habitat degradation, and pollution paint a grim picture for the future of marine fisheries and ecosystems. However, current models forecasting such declines do not account for the effects of ocean fronts as biogeochemical hotspots. Here we apply a fundamental technique from fluid dynamics to an ecosystem model to show how fronts increase total ecosystem biomass, explain fishery production, cause regime shifts, and contribute significantly to global biogeochemical budgets by channeling nutrients through alternate trophic pathways. We then illustrate how ocean fronts affect fishery abundance and yield, using long-term records of anchovy-sardine regimes and salmon abundances in the California Current. These results elucidate the fundamental importance of biophysical coupling as a driver of bottom-up vs. top-down regulation and high productivity in marine ecosystems.fronts | aggregation | trophic interactions | Reynolds decomposition G lobally, marine primary production is considered to set the limits of fishery production (1), drive ecosystem functioning (2), and contribute substantially to biogeochemical cycles (3). Recent evidence of increased ocean temperatures (4, 5) and declines in global nutrient supply and primary production (6), combined with overfishing and other increasing human demands on the ocean (7-9), therefore raises significant concerns about fishery sustainability, ecosystem health, and maintaining global biogeochemical cycles (10). However, the degree of patchiness, instead of total biomass, may be the primary regulator of marine production and food web structure (11-16). Fronts in the ocean are boundaries between distinct water masses with sharp gradients in temperature or salinity (density) that can increase patchiness through flow convergence and, for density fronts, increase vertical mixing and nutrient supply (11,17). Due to flow convergence at fronts, the spatiotemporal overlap of prey and predators can be immense, leading to a cascade of impacts across multiple scales from local prey size structure to global biogeochemical fluxes (11-13). However, the effects of fronts as fishery productivity and biogeochemical cycling hotspots have not been included in models that assess fisheries production and ecosystem health (18) or addressed at scales (tens to hundreds of kilometers) relevant to climate change (19).Here we use an ecosystem model to explore why fronts appear to have a strong influence on marine fishery production and biogeochemical cycling. Existing ecosystem models currently account only for the mean concentration of predator and prey with relatively large grid cells (20). In a simple case of a single autotrophic prey (A) and a single heterotrophic predator (B) the governing equations are[1]These equations describe the change in biomass of predator and prey relative to nutrient supply (N), intrins...

Stable isotope analysis (SIA) of highly migratory marine pelagic animals can improve understanding of their migratory patterns and trophic ecology. However, accurate interpretation of isotopic analyses relies on knowledge of isotope turnover rates and tissue-diet isotope discrimination factors. Laboratory-derived turnover rates and discrimination factors have been difficult to obtain due to the challenges of maintaining these species in captivity. We conducted a study to determine tissue- (white muscle and liver) and isotope- (nitrogen and carbon) specific turnover rates and trophic discrimination factors (TDFs) using archived tissues from captive Pacific bluefin tuna (PBFT), Thunnus orientalis, 1–2914 days after a diet shift in captivity. Half-life values for 15N turnover in white muscle and liver were 167 and 86 days, and for 13C were 255 and 162 days, respectively. TDFs for white muscle and liver were 1.9 and 1.1‰ for δ 15N and 1.8 and 1.2‰ for δ 13C, respectively. Our results demonstrate that turnover of 15N and 13C in bluefin tuna tissues is well described by a single compartment first-order kinetics model. We report variability in turnover rates between tissue types and their isotope dynamics, and hypothesize that metabolic processes play a large role in turnover of nitrogen and carbon in PBFT white muscle and liver tissues. 15N in white muscle tissue showed the most predictable change with diet over time, suggesting that white muscle δ 15N data may provide the most reliable inferences for diet and migration studies using stable isotopes in wild fish. These results allow more accurate interpretation of field data and dramatically improve our ability to use stable isotope data from wild tunas to better understand their migration patterns and trophic ecology.

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Eastern boundary currents are often described as ‘wasp-waist’ ecosystems in which one or few mid-level forage species support a high diversity of larger predators that are highly susceptible to fluctuations in prey biomass. The assumption of wasp-waist control has not been empirically tested in all such ecosystems. This study used stable isotope analysis to test the hypothesis of wasp-waist control in the southern California Current large marine ecosystem (CCLME). We analyzed prey and predator tissue for δ13C and δ15N and used Bayesian mixing models to provide estimates of CCLME trophic dynamics from 2007–2010. Our results show high omnivory, planktivory by some predators, and a higher degree of trophic connectivity than that suggested by the wasp-waist model. Based on this study period, wasp-waist models oversimplify trophic dynamics within the CCLME and potentially other upwelling, pelagic ecosystems. Higher trophic connectivity in the CCLME likely increases ecosystem stability and resilience to perturbations.

Stable isotope analysis (SIA) is becoming a commonly used tool to study the ecology of elasmobranchs. However, the retention of urea by elasmobranchs for osmoregulatory purposes may bias the analysis and interpretation of SIA data. We examined the effects of removing urea and lipid on the stable isotope composition of 14 species of sharks, skates, and rays from the eastern North Pacific Ocean. While effects were variable across taxa, removal of urea generally increased δ15N and C:N. Urea removal had less influence on δ13C, whereas extracting urea and lipid generally increased δ15N, C:N, and δ13C. Because C:N values of nonextracted tissues are often used to infer lipid content and adjust δ13C, shifts in C:N following urea extraction will change the inferred lipid content and bias any mathematical adjustment of δ13C. These results highlight the importance of urea and lipid extraction and demonstrate the confounding effects of these compounds, making it impossible to use C:N of non-urea-extracted samples as a diagnostic tool to estimate and correct for lipid content in elasmobranch tissues.