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Recent studies suggest that hypolimnetic respiration may be responsible for greenhouse gas (GHG) emissions from deep reservoirs. Currently, quantitative evaluation of aerobic vs. anaerobic processes and priming (enhanced processing of organic matter due to the addition of labile carbon) in regulating GHG production and emissions across the reservoir-downstream continuum remains largely unknown. High-resolution, annual time-series observations in a large, subtropical reservoir (Shuikou) experiencing seasonal hypoxia in southeast China indicate that aerobic hypolimnetic CO2 production dominated in most periods of the stratified spring/summer with higher rates at higher temperatures. In addition, anaerobic production of hypolimnetic CO2 occurred in the late stratified spring/summer period, which stimulated hypolimnetic production of CH4 and N2O. Incubation experiments showed that priming in spring enhanced both aerobic and anaerobic production of excess GHGs. A late spring flood event generated the highest daily efflux of CO2 through the flushing of GHG-enriched hypolimnion waters. Turbine degassing contributed 59%, 93%, and 63% of annual CO2, CH4, and N2O effluxes, respectively. Moreover, annual downstream GHG emissions were similar to those in the transition/lacustrine zone of the Shuikou reservoir. Diurnal variation observations revealed net CO2 emissions even during algal bloom seasons. The reservoir-downstream river continuum was a year-round source of GHGs (218.5 ± 18.9 Gg CO2-equivalent yr−1; CO2 contributed 91%). However, the loss of oxygen also leads to increased production and storage of recalcitrant dissolved organic carbon (RDOC). Thus, identifying mechanisms controlling both GHG emissions and RDOC production is crucial to constrain the carbon neutrality issue of hydroelectric reservoirs in the context of climate change mitigation strategies.

To understand the extent of anthropogenic noise in the ocean, it is essential to compare the differences between modern noise environments and their pre-industrial equivalents. The Santa Barbara Channel, off the coast of Southern California, is a corridor for the transportation of goods to and from the busiest shipping ports in the Western hemisphere. Commercial ships introduce high levels of underwater noise into the marine environment. To quantify the extent of noise in the region, we modeled pre-industrial ocean noise levels, driven by wind, and modern ocean noise levels, resulting from the presence of both ships and wind. By comparing pre-industrial and modern underwater noise levels, the low-frequency (50 Hz) acoustic environment was found to be degraded by more than 15 dB. These results can be used to identify regions for noise reduction efforts, as well as to model scenarios to identify those with the greatest potential to support marine conservation efforts.

Data from Bering-Chukchi-Beaufort Seas bowhead whales (Balaena mysticetus), harvested during 1973–2021 by aboriginal subsistence hunters, were used to estimate reproductive parameters: length at sexual maturity (LSM), age at sexual maturity (ASM), pregnancy rate (PR), and calving interval. Sexual maturity (N = 187 females) was determined from the presence/absence of corpora in the ovaries, or a fetus. Using sampling bias-corrected logistic regression, LSM was estimated at 13.5 m, 95% CI [13.0, 13.8]. There was a downward trend in LSM over time, statistically significant with one method but marginal with another. A growth model translated this estimate to an ASM estimate of 23.5 years, 95% CI [20.4, 26.7]. Pregnancy rate was determined from mature females (N = 125), and from a subset limited to certain autumn-caught whales (n = 37) to reduce bias. The PR was estimated at 0.46 globally, 95% CI [0.36, 0.55] and 0.38 for the autumn sample, 95% CI [0.20, 0.51]. Both estimated PRs are consistent with a 3-year calving interval, because the larger estimate includes two cohorts of pregnant whales harvested in spring, and bowhead whale gestation is longer than 12 months. These analyses represent the most conclusive empirical estimates of ASM, LSM, and PR for this bowhead whale stock from the largest available data sets to date.

Abstract: Organic carbon in seawater plays a significant role in the global carbon cycle. The concentration and composition of dissolved organic carbon reflect the activity of the biological community and chemical reactions that occur in seawater. From 2016 to 2019, we repeatedly sampled the oligotrophic northwest Sargasso Sea in the vicinity of the Bermuda Atlantic Time‐series Study site (BATS) to quantitatively follow known compounds within the pool of dissolved organic matter in the upper 1000 m of the water column. Most metabolites showed surface enrichment, and 83% of the metabolites had significantly lower concentrations with increasing depth. Dissolved metabolite concentrations most notably revealed temporal variability. Fourteen metabolites displayed seasonality that was repeated in each of the 4 yr sampled. Concentrations of vitamins, including pantothenic acid (vitamin B5) and riboflavin (vitamin B2), increased annually during winter periods when mixed layer depths were deepest. During diel sampling, light‐sensitive riboflavin decreased significantly during daylight hours. The temporal variability in metabolites at BATS was less than the spatial variability in metabolites from a previous sample set collected over a broad latitudinal range in the western Atlantic Ocean. The metabolites examined in this study are all components of central carbon metabolism. By examining these metabolites at finer resolution and in a time‐series, we begin to provide insights into the chemical compounds that may be exchanged by microorganisms in marine systems, data which are fundamental to understanding the chemical response of marine systems to future changes in climate.

Abstract: Climate change is increasing the frequency, severity, and extent of wildfires and drought in many parts of the world, with numerous repercussions for the physical, chemical, and biological characteristics of streams. However, information on how these perturbations affect top predators and their impacts on lower trophic levels in streams is limited. The top aquatic predator in southern California streams is native Oncorhynchus mykiss, the endangered southern California steelhead trout (trout). To examine relationships among the distribution of trout, environmental factors, and stream invertebrate resources and assemblages, we sampled pools in 25 stream reaches that differed in the presence (nine reaches) or absence (16 reaches) of trout over 12 years, including eight reaches where trout were extirpated during the study period by drought or post‐fire flood disturbances. Trout were present in deep pools with high water and habitat quality. Invertebrate communities in trout pools were dominated by a variety of medium‐sized collector–gatherer and shredder invertebrate taxa with non‐seasonal life cycles, whereas tadpoles and large, predatory invertebrates (Odonata, Coleoptera, Hemiptera [OCH]), often with atmospheric breather traits, were more abundant in troutless than trout pools. Structural equation modelling of the algal‐based food web indicated a trophic cascade from trout to predatory invertebrates to collector–gatherer taxa and weaker direct negative trout effects on grazers; however, both grazers and collector–gatherers also were positively related to macroalgal biomass. Structural equation modelling also suggested that bottom‐up interactions and abiotic factors drove the detritus‐based food web, with shredder abundance being positively related to leaf litter (coarse particulate organic matter) levels, which, in turn, were positively related to canopy cover and negatively related to flow. These results emphasise the context dependency of trout effects on prey communities and of the relative importance of top‐down versus bottom‐up interactions on food webs, contingent on environmental conditions (flow, light, nutrients, disturbances) and the abundances and traits of component taxa. Invertebrate assemblage structure changed from a trout to a troutless configuration within a year or two after trout were lost owing to post‐fire scouring flows or drought. Increases in OCH abundance after trout were lost were much more variable after drought than after fire. The reappearance of trout in one stream resulted in quick, severe reductions in OCH abundance. These results indicate that climate‐change induced disturbances can result in the extirpation of a top predator, with cascading repercussions for stream communities and food webs. This study also emphasises the importance of preserving or restoring refuge habitats, such as deep, shaded, perennial, cool stream pools with high habitat and water quality, to prevent the extirpation of sensitive species and preserve native biodiversity during a time of climate change.

Open science is a global movement happening across all research fields. Enabled by technology and the open web, it builds on years of efforts by individuals, grassroots organizations, institutions, and agencies. The goal is to share knowledge and broaden participation in science, from early ideation to making research outputs openly accessible to all (open access). With an emphasis on transparency and collaboration, the open science movement dovetails with efforts to increase diversity, equity, inclusion, and belonging in science and society. The US Biden-Harris Administration and many other US government agencies have declared 2023 the Year of Open Science, providing a great opportunity to boost participation in open science for the oceans. For researchers day-to-day, open science is a critical piece of modern analytical workflows with increasing amounts of data. Therefore, we focus this article on open data science-the tooling and people enabling reproducible, transparent, inclusive practices for data-intensive research-and its intersection with the marine sciences. We discuss the state of various dimensions of open science and argue that technical advancements have outpaced our field's culture change to incorporate them. Increasing inclusivity and technical skill building are interlinked and must be prioritized within the marine science community to find collaborative solutions for responding to climate change and other threats to marine biodiversity and society.

Abstract: Salt marshes exist at the terrestrial-marine interface, providing important ecosystem services such as nutrient cycling and carbon sequestration. Tidal inputs play a dominant role in salt marsh porewater mixing, and terrestrially derived freshwater inputs are increasingly recognized as important sources of water and solutes to intertidal wetlands. However, there remains a critical gap in understanding the role of freshwater inputs on salt marsh hydrology, and how this may impact marsh subsurface salinity and plant productivity. Here, we address this knowledge gap by examining the hydrologic behavior, porewater salinity, and pickleweed (Sarcocornia pacifica also known as Salicornia pacifica) plant productivity along a salt marsh transect in an estuary along the central coast of California. Through the installation of a suite of hydrometric sensors and routine porewater sampling and vegetation surveys, we sought to understand how seasonal changes in terrestrial freshwater inputs impact salt marsh ecohydrologic processes. We found that salt marsh porewater salinity, shallow subsurface saturation, and pickleweed productivity are closely coupled with elevated upland water level during the winter and spring, and more influenced by tidal inputs during the summer and fall. This seasonal response indicates a switch in salt marsh hydrologic connectivity with the terrestrial upland that impacts ecosystem functioning. Through elucidating the interannual impacts of drought on salt marsh hydrology, we found that the severity of drought and historical precipitation can impact contemporary hydrologic behavior and the duration and timing of the upland-marsh hydrologic connectivity. This implies that the sensitivity of salt marshes to climate change involves a complex interaction between sea level rise and freshwater inputs that vary at seasonal to interannual timescales.

Female Weddell seals (Leptonychotes weddellii) display a mixed capital-income breeding strategy, losing up to 40% of their body mass between birthing and weaning their pups. How and when they regain energy stores, however, remains to be fully explored. To better understand the foraging by lactating Weddell seals, we fitted time-depth recorders and head-mounted cameras on 26 seals in Erebus Bay, Ross Sea, for ~ 5 days in November and December 2018 and 2019. We aimed to (1) identify prey species and foraging depth and (2) investigate relationships between seal physiology and demographics and probability of foraging. We recorded 2782 dives, 903 of which were > 50 m, maximum depth was 449.3 m and maximum duration was 31.1 min. Pup age likely contributes to the probability of a lactating Weddell seal foraging (Est. = 1.21 (SD = 0.61), z = 1.97, p = 0.0484). Among 846 prey encounters, the most frequent prey items were crustaceans (46.2%) and Antarctic silverfish (Pleuragramma antarcticum, 19.0%); two encounters were observed with juvenile Antarctic toothfish (Dissostichus mawsoni, 0.2%). We identified substantial variability in foraging behaviour, individually and between locations, and found that lactating seals target many species and some may specialise on certain prey groups.

Climate change has rapidly altered marine ecosystems and is expected to continue to push systems and species beyond historical baselines into novel conditions. Projecting responses of organisms and populations to these novel environmental conditions often requires extrapolations beyond observed conditions, challenging the predictive limits of statistical modeling capabilities. Bioenergetics modeling provides the mechanistic basis for projecting climate change effects on marine living resources in novel conditions, has a long history of development, and has been applied widely to fish and other taxa. We provide our perspective on 4 opportunities that will advance the ability of bioenergetics-based models to depict changes in the productivity and distribution of fishes and other marine organisms, leading to more robust projections of climate impacts. These are (1) improved depiction of bioenergetics processes to derive realistic individual-level response(s) to complex changes in environmental conditions, (2) innovations in scaling individual-level bioenergetics to project responses at the population and food web levels, (3) more realistic coupling between spatial dynamics and bioenergetics to better represent the local- to regional-scale differences in the effects of climate change on the spatial distributions of organisms, and (4) innovations in model validation to ensure that the next generation of bioenergetics-based models can be used with known and sufficient confidence. Our focus on specific opportunities will enable critical advancements in bioenergetics modeling and position the modeling community to make more accurate and robust projections of the effects of climate change on individuals, populations, food webs, and ecosystems.

Abstract: The combination of taxa and size classes of phytoplankton that coexist at any location affects the structure of the marine food web and the magnitude of carbon fluxes to the deep ocean. But what controls the patterns of this community structure across environmental gradients remains unclear. Here, we focus on the North East Pacific Transition Zone, a ~ 10° region of latitude straddling warm, nutrient‐poor subtropical and cold, nutrient‐rich subpolar gyres. Data from three cruises to the region revealed intricate patterns of phytoplankton community structure: poleward increases in the number of cell size classes; increasing biomass of picoeukaryotes and diatoms; decreases in diazotrophs and Prochlorococcus; and both increases and decreases in Synechococcus. These patterns can only be partially explained by existing theories. Using data, theory, and numerical simulations, we show that the patterns of plankton distributions across the transition zone are the result of gradients in nutrient supply rates, which control a range of complex biotic interactions. We examine how interactions such as size‐specific grazing, multiple trophic strategies, shared grazing between several phytoplankton size classes and heterotrophic bacteria, and competition for multiple resources can individually explain aspects of the observed community structure. However, it is the combination of all these interactions together that is needed to explain the bulk compositional patterns in phytoplankton across the North East Pacific Transition Zone. The synthesis of multiple mechanisms is essential for us to begin to understand the shaping of community structure over large environmental gradients.

Abstract: The effects of environmental change on zooplankton communities, and more broadly, pelagic ecosystems are difficult to predict due to the high diversity of ecological strategies and complex interspecific interactions within the zooplankton. Trait‐based approaches can define zooplankton functional groups with distinct responses to environmental change. Analyses across multiple mesozooplankton groups can help identify key organizing traits. Here, we use the pronounced cross‐shore environmental gradient within the California Current Ecosystem in a space‐for‐time substitution to test potential effects of ocean warming and increased stratification on zooplankton communities. Along a horizontal gradient in sea‐surface temperature, water column stratification, and light attenuation, we test whether there are changes in zooplankton species composition, trait composition, and vertical habitat use. We employ DNA metabarcoding at two loci (18S‐V4 and COI) and digital ZooScan imaging of zooplankton sampled in a Lagrangian manner. We find that vertical distributions of many mesozooplankton taxa shift to deeper depths in the cross‐shore direction, and light attenuation is the strongest predictor of magnitude of change. Vertical habitat shifts vary among functional groups, with changes in vertical distribution most pronounced among carnivorous taxa. Herbivorous taxa remain associated with the chlorophyll maximum, especially in clear offshore waters. Our results suggest that increased stratification of this ocean region will lead to deeper depths occupied by some components of epipelagic mesozooplankton communities, and may result in zooplankton communities with more specialized feeding strategies, increased egg brooding, and more asexual reproduction.

Maturation schedules shape the age structure of a population and influence productivity and exposure to fishing. Fish cultivated and raised in artificial environments such as hatcheries may mature at different ages compared to their natural-origin counterparts. We evaluated whether endangered Sacramento River winter-run Chinook salmon Oncorhynchus tshawytscha produced in a conservation hatchery had different maturation schedules compared to naturalorigin fish, and how any differences affected their exposure to, and impact from, the ocean salmon fishery. Using coded-wire tags collected from hatchery fish in the ocean and in-river fisheries and on the spawning grounds, and scales collected from natural-origin spawner carcasses, we reconstructed the life history of hatchery and natural-origin cohorts from 2002-2015 brood years. Hatchery fish had similar age-2 maturation rates but higher age-3 maturation rates compared to natural-origin fish, resulting in fewer age-4 individuals and an overall more truncated age structure. Because natural-origin winter-run Chinook salmon were more likely to remain at sea until age 4, they were exposed to fishing for an additional year and experienced greater reduction in escapement. Compared to natural-origin males, hatchery-origin males were much less likely to return at an older age, possibly because sexual selection that is occurring on the spawning grounds is not occurring to the same extent in the hatchery. Identifying how reproductive maturation differs across sources, sex, and life histories is critical to understanding how fisheries can disproportionately impact subsets of a population and affect its long-term population dynamics and sustainability.

A diverse group of toothed whale species inhabits the pelagic habitats of the western North Atlantic, competing for overlapping prey resources. Historical data deficits have limited fundamental research into many of these species, such as establishing baselines of distribution and abundance, so their occurrence and habitat use patterns are not well characterized. Periodic cycles in activity have been reported at a range of temporal scales for odontocetes in other regions, such as seasonal movements, foraging activity modulated by lunar cycles, and diel activity patterns. A variety of spatial, temporal, and behavioral separation strategies have also been observed among predator guilds in both marine and terrestrial systems, and these may also contribute to observed spatiotemporal patterns in activity. Recently, passive acoustic data has been applied to monitor odontocete species continuously, with improved detection and species discrimination for some cryptic species. We used a long-term passive acoustic data set collected at sites spanning the western North Atlantic shelf-break region to quantify presence and characterize seasonal, lunar, and diel activity patterns for 10 species. Our results demonstrated strong regional preferences and clear patterns of spatiotemporal separation between species with similar foraging ecology. Latitudinal shifts in seasonal presence peaks may suggest meridional seasonal migrations for some dolphin species. We also observed strong diel activity patterns that were modulated by both seasonal and lunar cycles. This study reveals complex behavioral patterns arising in response to natural cycles playing out over multiple temporal scales and provides new insights into habitat partitioning among toothed whale species.

Climate change is affecting marine ecosystems in many ways, including raising temperatures and leading to ocean acidification. From 2014 to 2016, an extensive marine heat wave extended along the west coast of North America and had devastating effects on numerous species, including bull kelp (Nereocystis luetkeana). Bull kelp is an important foundation species in coastal ecosystems and can be affected by marine heat waves and ocean acidification; however, the impacts have not been investigated on sensitive early life stages. To determine the effects of changing temperatures and carbonate levels on Northern California's bull kelp populations, we collected sporophylls from mature bull kelp individuals in Point Arena, CA. At the Bodega Marine Laboratory, we released spores from field-collected bull kelp, and cultured microscopic gametophytes in a common garden experiment with a fully factorial design crossing modern conditions (11.63 ± 0.54°C and pH 7.93 ± 0.26) with observed extreme climate conditions (15.56 ± 0.83°C and 7.64 ± 0.32 pH). Our results indicated that both increased temperature and decreased pH influenced growth and egg production of bull kelp microscopic stages. Increased temperature resulted in decreased gametophyte survival and offspring production. In contrast, decreased pH had less of an effect but resulted in increased gametophyte survival and offspring production. Additionally, increased temperature significantly impacted reproductive timing by causing female gametophytes to produce offspring earlier than under ambient temperature conditions. Our findings can inform better predictions of the impacts of climate change on coastal ecosystems and provide key insights into environmental dynamics regulating the bull kelp lifecycle.

Eclipse Sound, in the northeastern Canadian Arctic, has experienced a substantial increase in ship traffic due to growing tourism and industrial development in the region. This study aims to describe the natural soundscape as well as to assess the noise levels associated with shipping. Underwater sound recordings were collected at two locations: Eastern Eclipse Sound (72° 43.730 N, 76° 13.519 W, 670 m) leading to Baffin Bay, and Milne Inlet (72° 15.260 N, 80° 34.205 W, 313 m) situated near the southwest end of Eclipse Sound. To capture the dynamic nature of the soundscape, the data from these two locations were divided into three seasons: late spring, summer, and early fall. These periods were selected to account for the changing contribution of sea ice to the soundscape during the sea ice break-up, two months of open water, and the sea ice freeze-up. By analyzing ship tracks and underwater acoustic recordings, we identified patterns of ship traffic and estimated underwater noise levels due to ships. Noise emitted by ships is quantified by vessel type, including three cargo ship types, passenger ships, pleasure craft, and icebreakers. Individual ship transits through the region introduce transient noise at frequencies from 20 kHz, with durations lasting from a few minutes to >6 h. The impact of ship noise on the soundscape is significant, resulting in increases in sound levels by 15 to >30 dB when ships are within 10 km and measurable ship noise below 200 Hz at distances of >50 km.

Bacteria are an important component of the aquatic ecosystem playing a key role in the transformation and mineralisation of allochthonous organic matter, nutrients and pollutants. However, there is no clear understanding of spatio-temporal patterns of particle-attached versus free-living bacterial abundances, diversities and communities, which limits our in-depth understanding of hypereutrophic urban river ecosystems and the mechanisms regulating nutrient cycling and biogeochemical transformations. In order to investigate spatio-temporal patterns and associated factors for aquatic particle-attached versus free-living bacterial communities, we conducted a 2-year study of four contrasting habitats in a hypereutrophic urban river network of eastern China. Bacterial abundance and community structure in relation to various environmental variables were assessed by epifluorescence microscopy and high-throughput sequencing techniques. Results revealed that particle-attached bacterial abundance depended mainly on suspended particle concentrations, whereas free-living bacterial abundance was correlated with nutrient availability and water temperature. Organic carbon was related to a decrease of free-living and particle-attached bacterial richness, and particulate matter input increased free-living bacterial diversity. Seasonal changes of water temperature were linked to the temporal dynamics of bacterial community composition, and the differences in total organic carbon concentrations contributed to spatial differences in bacterial community composition. There were significant differences in bacterial community composition between particle-attached and free-living assemblages in low-turbidity/low-nutrient rivers found in land areas comprising mainly natural vegetation. These differences were especially prominent for the relative abundances of Cyanobacteria and Actinobacteria, which were higher in the particle-attached and free-living fractions, respectively. However, no significant differences were found in turbid/nutrient-rich rivers. Total organic carbon was the most significant factor shaping the composition similarity between particle-attached and free-living bacterial communities. Our findings indicate that spatio-temporal variations in water temperature, suspended particle and resource availability, especially for organic carbon, appreciably contribute to changes in the abundance, diversity and composition of aquatic particle-attached versus free-living bacterial communities in the hypereutrophic urban river network. Considering that biodiversity is important for supporting ecosystem functioning, this study informs spatio-temporal patterns of particle-attached and free-living bacterial abundance, diversity and composition of communities, and their underlying control mechanisms, thereby providing fundamental knowledge of microbial ecological functions for remediation and sustainable management of hypereutrophic urban river ecosystems.

Pseudo-nitzschia species with the ability to produce the neurotoxin domoic acid (DA) are the main cause of harmful algal blooms (HABs) along the U.S. West Coast, with major impacts on ecosystems, fisheries, and human health. While most Pseudo-nitzschia (PN) HAB studies to date have focused on their characteristics at specific sites, few cross-regional comparisons exist, and mechanistic understanding of large-scale HAB drivers remains incomplete. To close these gaps, we compiled a nearly 20-year time series of in situ particulate DA and environmental observations to characterize similarities and differences in PN HAB drivers along the California coast. We focus on three DA hotspots with the greatest data density: Monterey Bay, the Santa Barbara Channel, and the San Pedro Channel. Coastwise, DA outbreaks are strongly correlated with upwelling, chlorophyll-a, and silicic acid limitation relative to other nutrients. Clear differences also exist across the three regions, with contrasting responses to climate regimes across a north to south gradient. In Monterey Bay, PN HAB frequency and intensity increase under relatively nutrient-poor conditions during anomalously low upwelling intensities. In contrast, in the Santa Barbara and San Pedro Channels, PN HABs are favored under cold, nitrogen-rich conditions during more intense upwelling. These emerging patterns provide insights on ecological drivers of PN HABs that are consistent across regions and support the development of predictive capabilities for DA outbreaks along the California coast and beyond.

Abstract: Detection of the effects of climate change on ocean ecosystems is often limited by the short duration of available time series. Here, we use ocean transparency measurements (the Secchi disk depth, ZSD) in the California Current Ecosystem since 1949 and combine them with satellite estimates. Historic in situ measurements of ZSD were irregular in space and time and are difficult to interpret in time series due to biases introduced by changing locations and timing. We normalize historic ZSD measurements with satellite‐derived mean climatology and create a merged in situ—satellite time series of ZSD for the last ~ 73 yr. Although interannual variability in ZSD is dominated by El Niño Southern Oscillation‐related variability (~ 50% of the total variance in many areas), a secular trend of decreasing transparency that is correlated with increasing productivity is detected 0–300 km from the coast in an area affected by coastal upwelling north of 27°N. In contrast, increasing transparency (correlated with decreasing productivity) is detected offshore (> 1000 km from the coast). In addition to those general trends, transparency is also increasing in coastal area off Baja California south of 27°N.

Abstract: Separating microplastics (MPs) (smaller particle size,

The organic carbon (Corg) stored in seagrass meadows is globally significant and could be relevant in strategies to mitigate increasing CO2 concentration in the atmosphere. Most of that stored Corg is in the soils that underlie the seagrasses. We explored how seagrass and soil characteristics vary among seagrass meadows across the geographic range of turtlegrass (Thalassia testudinum) with a goal of illuminating the processes controlling soil organic carbon (Corg) storage spanning 23° of latitude. Seagrass abundance (percent cover, biomass, and canopy height) varied by over an order of magnitude across sites, and we found high variability in soil characteristics, with Corg ranging from 0.08 to 12.59% dry weight. Seagrass abundance was a good predictor of the Corg stocks in surficial soils, and the relative importance of seagrass-derived soil Corg increased as abundance increased. These relationships suggest that first-order estimates of surficial soil Corg stocks can be made by measuring seagrass abundance and applying a linear transfer function. The relative availability of the nutrients N and P to support plant growth was also correlated with soil Corg stocks. Stocks were lower at N-limited sites than at P-limited ones, but the importance of seagrass-derived organic matter to soil Corg stocks was not a function of nutrient limitation status. This finding seemed at odds with our observation that labile standard substrates decomposed more slowly at N-limited than at P-limited sites, since even though decomposition rates were 55% lower at N-limited sites, less Corg was accumulating in the soils. The dependence of Corg stocks and decomposition rates on nutrient availability suggests that eutrophication is likely to exert a strong influence on carbon storage in seagrass meadows.

Processes regulating the rate of oxygen depletion determine whether hypoxia occurs and the extent to which greenhouse gases accumulate in seasonally ice-covered lakes. Here, we investigate the oxygen budget of four arctic lakes using high-frequency data during two winters in three shallow lakes (9–13 m maximal depth) and four winters in 24 m deep main basin of Toolik Lake. Incubation experiments measured sediment metabolism. Volume-averaged oxygen depletion measured in situ was independent of water temperature and duration of the ice-covered period. Average rates were between 0.2 and 0.39 g O2 m−2 d−1 in the shallow lakes and between 0.03 and 0.14 g O2 m−2 d−1 in Toolik Lake, with higher rates in smaller lakes with their larger sediment area to volume ratio. Rates decreased to ~ 20%–50% of initial values in late winter in the shallow lakes but less or not at all in Toolik. The lack of a decline in Toolik Lake points to continued oxygen transport to the sediment–water interface where oxygen consumption occurs. In all lakes, lower in situ oxygen depletion than in incubation measurements points toward increasing anoxia in the lower water column depressing loss rates. In Toolik, oxygen loss during early winter was less in years with minimal snow cover. Penetrative convection occurred, which could mix downwards oxygen produced by photosynthesis or excluded during ice formation. Estimates of these terms exceeded photosynthesis measured in sediment incubations. Modeling under ice-oxygen dynamics requires consideration of optical properties and biological and transport processes that modify oxygen concentrations and distributions.

Abstract: The San Francisco Estuary, in central California, has several long-running monitoring programs that have been used to reveal human-induced changes throughout the estuary in the last century. Here, we pair synoptic records of particulate organic matter (POM) composition from 1990–1996 and 2007–2016 with more robust long-term monitoring program records of total suspended sediment (TSS) concentrations generally starting in the mid-1970s to better understand how POM and TSS sources and transport have shifted. Specifically, POM C:N ratios and stable isotope values were used as indicators of POM source and to separate the bulk POC pool into detrital and phytoplankton components. We found that TSS and POC sources have shifted significantly across the estuary in time and space from declines in terrestrial inputs. Landward freshwater and brackish water sites, in the Delta and near Suisun Bay, witnessed long-term declines in TSS (32 to 52%), while seaward sites, near San Pablo Bay, recorded recent increases in TSS (16 to 121%) that began to trend downwards at the end of the record considered. Bulk POM C:N ratios shifted coeval with the TSS concentration changes at nearly all sites, with mean declines of 12 to 27% between 1990–1996 and 2007–2016. The widespread declines in bulk POM C:N ratios and inferred changes in POC concentrations from TSS trends, along with the substantial declines in upstream TSS supply through time (56%), suggest measurable reductions in terrestrial inputs to the system. Changes in terrestrial TSS and POM inputs have implications for biotic (e.g., food web dynamics) and abiotic organic matter cycling (e.g., burial, export) along the estuarine continuum. This work demonstrates how human-generated environmental changes can propagate spatially and temporally through a large river-estuary system. More broadly, we show how underutilized monitoring program datasets can be paired with existing (and often imperfect) synoptic records to generate new system insight in lieu of new data collection.

The wave fields of coastal bays are comprised of waves generated by far-off storms that enter the bay to combine with waves generated locally by winds inside the bay and regionally outside the bay. In any given location, the resultant wave field varies spatially and temporally, and affects coastal features, such as beaches in estuaries and bays (BEBs). However, wave fields in enclosed bays with tidal shoals are poorly studied, limiting the efficacy of coastal protection and restoration projects in these systems, a critical focus in light of ongoing sea level rise. Here we present observations of the wave field in Tomales Bay, a 20-km-long, narrow, semi-enclosed embayment on the wave-dominated coast of Northern California (USA) with a spring-tide range of 2.5 m. We deployed pressure sensors near several beaches along the linear axis of the bay. Low-frequency waves (4 ∗ 10 - 2- 2.5 ∗ 10 - 1 Hz or 4–25-s period) were not observed further than 4 km of the mouth, delineating the “outer bay” region, where remotely generated swell and regionally generated wind waves could dominate. The wave spectrum of the landward “inner bay” was dominated by fetch-limited waves generated within the bay with frequency ≥ 2.5 ∗ 10 - 1 Hz. The energy of both ocean waves and locally generated wind waves across all sites were controlled by the tide, but the former by changes in attenuation and the latter likely by modulation of wave generation. Wave energies were low at low tide and high at high tide, but high-frequency wind wave energy was increased during ebb tides while lower-frequency swell energy was reduced during ebb tides, suggesting different mechanisms of tidal influences. Thus, in addition to fluctuations in winds and the presence of ocean waves, tides exert a strong control on the wave energy spectra at coastal features in mesotidal regions. In general, events that may be impactful for BEB morphology are expected to occur when waves due to high winds or high-swell event arrive during high-tide periods. However, no such events were observed during our study and questions remain as to how rarely such events occur across the bay.

Diatoms are significant primary producers especially in cold, turbulent, and nutrient-rich surface oceans. Hence, they are abundant in polar oceans, but also underpin most of the polar food webs and related biogeochemical cycles. The cold-adapted pennate diatom Fragilariopsis cylindrus is considered a keystone species in polar oceans and sea ice because it can thrive under different environmental conditions if temperatures are low. In this perspective paper, we provide insights into the latest molecular work that has been done on F. cylindrus and discuss its role as a model alga to understand cold-adapted life.

In recent years, harmful algal blooms (HABs) have increased in their severity and extent in many parts of the world and pose serious threats to local aquaculture, fisheries, and public health. In many cases, the mechanisms triggering and regulating HAB events remain poorly understood. Using underwater microscopy and Residual Neural Network (ResNet-18) to taxonomically classify imaged organisms, we developed a daily abundance record of four potentially harmful algae (Akashiwo sanguinea, Chattonella spp., Dinophysis spp., and Lingulodinium polyedra) and major grazer groups (ciliates, copepod nauplii, and copepods) from August 2017 to November 2020 at Scripps Institution of Oceanography pier, a coastal location in the Southern California Bight. Random Forest algorithms were used to identify the optimal combination of environmental and ecological variables that produced the most accurate abundance predictions for each taxon. We developed models with high prediction accuracy for A. sanguinea ((Formula presented.)), Chattonella spp. ((Formula presented.)), and L. polyedra ((Formula presented.)), whereas models for Dinophysis spp. showed lower prediction accuracy ((Formula presented.)). Offshore nutricline depth and indices describing climate variability, including El Niño Southern Oscillation, Pacific Decadal Oscillation, and North Pacific Gyre Oscillation, that influence regional-scale ocean circulation patterns and environmental conditions, were key predictor variables for these HAB taxa. These metrics of regional-scale processes were generally better predictors of HAB taxa abundances at this coastal location than the in situ environmental measurements. Ciliate abundance was an important predictor of Chattonella and Dinophysis spp., but not of A. sanguinea and L. polyedra. Our findings indicate that combining regional and local environmental factors with microzooplankton populations dynamics can improve real-time HAB abundance forecasts.

The world's eastern boundary upwelling systems (EBUSs) contribute disproportionately to global ocean productivity and provide critical ecosystem services to human society. The impact of climate change on EBUSs and the ecosystems they support is thus a subject of considerable interest. Here, we review hypotheses of climate-driven change in the physics, biogeochemistry, and ecology of EBUSs; describe observed changes over recent decades; and present projected changes over the twenty-first century. Similarities in historical and projected change among EBUSs include a trend toward upwelling intensification in poleward regions, mitigatedwarming in near-coastal regions where upwelling intensifies, and enhanced water-column stratification and a shoaling mixed layer. However, there remains significant uncertainty in how EBUSs will evolve with climate change, particularly in how the sometimes competing changes in upwelling intensity, source-water chemistry, and stratification will affect productivity and ecosystem structure. We summarize the commonalities and differences in historical and projected change in EBUSs and conclude with an assessment of key remaining uncertainties and questions. Future studies will need to address these questions to better understand, project, and adapt to climate-driven changes in EBUSs.

Photogrammetry is an emerging tool that allows scientists to measure important habitat characteristics of coral reefs at multiple spatial scales. However, the ecological benefits of using photogrammetry to measure reef habitat have rarely been assessed through direct comparison to traditional methods, especially in settings where manual measurements are more feasible and affordable. Here, we applied multiple methods to measure coral colonies (Pocillopora spp.) and asked whether photogrammetric or manual observations better describe short-term colony growth and links between colony size and the biodiversity of coral-dwelling fishes and invertebrates. Using photogrammetry, we measured patterns in changes in coral volume that were otherwise obscured by high variation from manual measurements. Additionally, we found that photogrammetry-based estimates of colony skeletal volume best predicted the abundance and richness of animals living within the coral. This study highlights that photogrammetry can improve descriptions of coral colony size, growth, and associated biodiversity compared to manual measurements.

Abstract: This study analysed threats to federally and State‐listed endangered and threatened animal taxa in California, United States, and how threats varied by taxa, habitat use, spatial extent, severity, geographical region and endemic status using threat categories from the International Union for Conservation of Nature (IUCN) Red List Threats Classification Scheme and information from scientific literature and reports. A majority of the taxa evaluated were associated with freshwater habitats and were endemic to California. The most threatened taxonomic groups were fish, followed by mammals and birds. The number of threats was mostly evenly distributed across the State's three geographical regions (i.e., North, Central and South), and no single region had a disproportionately high number of endangered animal taxa. Freshwater taxa were the most affected in nearly every threat category, suggesting that freshwater taxa are more threatened than their terrestrial and marine counterparts. In descending order, the most prominent threats across all taxa were habitat loss, invasive species, climate change and altered hydrology. Threats identified as high severity also tended to have a high spatial extent and vice versa. This study shows that the numerous freshwater faunas in California are disproportionately affected by threats also found in other freshwater systems and Mediterranean‐climate regions, highlighting the scope of the freshwater biodiversity crisis in California. Managing priorities to target the most pervasive threats to endangered freshwater taxa documented in this study will help safeguard freshwater biodiversity against human threats in California and beyond.

Habitat structural complexity is created by biotic and abiotic processes that operate over a range of scales. This can be seen clearly on coral reefs, where corals and reef geomorphology create structure from mm to km scales. Here, we quantified the relative contribution of biotic and abiotic structures to habitat complexity using ‘Structure from Motion’, a technology that allows accurate 3D models of environments to be reconstructed from overlapping photographs. We calculated the linear fractal dimension of these models using a virtual analogue of a profile gauge. By adjusting the spacing between profile gauge rods, we partitioned structural complexity into a series of scale intervals. We identified scales that were most indicative of coral cover (0.5-16 cm) and reef geomorphology (16-256 cm). We found that reefs in the Main Hawaiian Islands have more complexity at finer scales than reefs in the Northwest Hawaiian Islands, which we attribute to the latitudinal gradient in coral cover along the archipelago. At coarser scales, islands at each end of the archipelago have sites with high structural complexity, with less complexity in the center of the archipelago. These differences are consistent with geologic factors shaping island uplift, subsidence, and reef formation. In addition, we found that different coral genera and morphologies display unique patterns of fractal dimension, with branching Porites corals creating the greatest amount of habitat structure at nearly all scales. This study demonstrates how multi-scale approaches can be used to identify the processes responsible for reef structural complexity and changes in structure over time.

Abstract: We quantified cephalopods consumed by longnose lancetfish (Alepisaurus ferox, n = 1267 stomachs containing cephalopod remains) from 2009 to 2018 in the central North Pacific Ocean (between 0–35° N and 135–175° W). When cephalopods identified from beak remains in the stomach contents were included in diet analyses, clear increases in the abundance of gelatinous taxa and the inferred foraging depths of lancetfish were evident. Ontogeny in cephalopod consumption was evident for lancetfish, corroborating past diet studies. Small lancetfish (fork length

Estuaries are among the most productive of aquatic ecosystems. Yet the collective understanding of patterns and drivers of primary production in estuaries is incomplete, in part due to complex hydrodynamics and multiple controlling factors that vary at a range of temporal and spatial scales. A whole-ecosystem experiment was conducted in a deep, pelagically dominated terminal channel of the Sacramento-San Joaquin Delta (California, USA) that seasonally appears to become nitrogen limited, to test whether adding calcium nitrate would stimulate primary productivity or increase phytoplankton density. Production did not respond consistently to fertilization, in part because nitrate and phytoplankton were dispersed away from the manipulated area within 1–3 days. Temporal and spatial patterns of gross primary production were more strongly related to stratification and light availability (i.e., turbidity) than nitrogen, highlighting the role of hydrodynamics in regulating system production. Similarly, chlorophyll was positively related not only to stratification but also to nitrogen—with a positive interaction—suggesting stratification may trigger nutrient limitation. The average rate of primary production (4.3 g O2 m−2 d−1), metabolic N demand (0.023 mg N L−1 d−1), and ambient dissolved inorganic nitrogen concentration (0.03 mg N L−1) indicate that nitrogen can become limiting in time and space, especially during episodic stratification events when phytoplankton are isolated within the photic zone, or farther upstream where water clarity increases, dispersive flux decreases, and stratification is stronger and more frequent. The role of hydrodynamics in organizing habitat connectivity and regulating physical and chemical processes at multiple temporal and spatial scales is critical for determining resource availability and evaluating biogeochemical processes in estuaries.

Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for aquatic eDNA detection and interpretation were developed primarily in freshwater environments and have not been well established for estuaries and marine environments that are by nature dynamic, turbid, and hydrologically complex. Environmental context and species life history are critical for successful application of eDNA methods, and the challenges associated with eDNA detection in estuaries were the subject of a symposium held at the University of California Davis on January 29, 2020 (https://marinescience.ucdavis.edu/engagement/past-events/edna). Here, we elaborate upon topics addressed in the symposium to evaluate eDNA methods in the context of monitoring and biodiversity studies in estuaries. We first provide a concise overview of eDNA science and methods, and then examine the San Francisco Estuary (SFE) as a case study to illustrate how eDNA detection can complement traditional monitoring programs and provide regional guidance on future potential eDNA applications. Additionally, we offer recommendations for enhancing communication between eDNA scientists and natural resource managers, which is essential for integrating eDNA methods into existing monitoring programs. Our intent is to create a resource that is accessible to those outside the field of eDNA, especially managers, without oversimplifying the challenges or advantages of these methods.

Pseudo-nitzschia species are one of the leading causes of harmful algal blooms (HABs) along the western coast of the United States. Approximately half of known Pseudo-nitzschia strains can produce domoic acid (DA), a neurotoxin that can negatively impact wildlife and fisheries and put human life at risk through amnesic shellfish poisoning. Production and accumulation of DA, a secondary metabolite synthesized during periods of low primary metabolism, is triggered by environmental stressors such as nutrient limitation. To quantify and estimate the feedbacks between DA production and environmental conditions, we designed a simple mechanistic model of Pseudo-nitzschia and domoic acid dynamics, which we validate against batch and chemostat experiments. Our results suggest that, as nutrients other than nitrogen (i.e., silicon, phosphorus, and potentially iron) become limiting, DA production increases. Under Si limitation, we found an approximate doubling in DA production relative to N limitation. Additionally, our model indicates a positive relationship between light and DA production. These results support the idea that the relationship with nutrient limitation and light is based on direct impacts on Pseudo-nitzschia biosynthesis and biomass accumulation. Because it can easily be embedded within existing coupled physical-ecosystem models, our model represents a step forward toward modeling the occurrence of Pseudo-nitzschia HABs and DA across the U.S. West Coast.

Abstract: In California (USA), seasonal lagoons provide important oversummer rearing habitat for juvenile steelhead trout (anadromous Oncorhynchus mykiss). However, key water quality parameters such as temperature and dissolved oxygen concentration can periodically approach or exceed the physiological tolerances of steelhead during the protracted dry season. A field study employing distributed temperature sensing technology, water quality monitoring, habitat mapping, and mark-recapture sampling was conducted to examine how shifting environmental conditions affected the performance and behavior of juvenile steelhead in the Scott Creek estuary/lagoon (Santa Cruz County). Abiotic conditions were driven by episodic inputs of seawater to the typically freshwater lagoon. During midsummer, the water column was vertically stratified which reduced suitable lagoon rearing habitat by approximately 40%. Nevertheless, steelhead abundance, growth, and condition factor were high during the summer and decreased in autumn following lagoon destratification and cooling. Unlike previous work, this study identified limited emigration from the lagoon to riverine habitat during the summer. Instead, juvenile steelhead exhibited crepuscular movement patterns within the lagoon, with peaks in upstream (to upper lagoon habitat) and downstream (to lower lagoon habitat) movement occurring at dawn and dusk, respectively. This study underscores that habitat complexity and connectivity are critical for juvenile steelhead production and persistence and provides insight into steelhead habitat use and behavior in seasonal lagoons.

Plankton imaging systems supported by automated classification and analysis have improved ecologists' ability to observe aquatic ecosystems. Today, we are on the cusp of reliably tracking plankton populations with a suite of lab-based and in situ tools, collecting imaging data at unprecedentedly fine spatial and temporal scales. But these data have potential well beyond examining the abundances of different taxa; the individual images themselves contain a wealth of information on functional traits. Here, we outline traits that could be measured from image data, suggest machine learning and computer vision approaches to extract functional trait information from the images, and discuss promising avenues for novel studies. The approaches we discuss are data agnostic and are broadly applicable to imagery of other aquatic or terrestrial organisms.

AbstractDecades of research have revealed relationships between the abundance of coral reef taxa and local conditions, especially at small scales. However, a rigorous test of covariation requires a robust dataset collected across wide environmental or experimental gradients. Here, we surveyed spatial variability in the densities of major coral reef functional groups at 122 sites along a 70 km expanse of the leeward, forereef habitat of Curaçao in the southern Caribbean. These data were used to test the degree to which spatial variability in community composition could be predicted based on assumed functional relationships and site-specific anthropogenic, physical, and ecological conditions. In general, models revealed less power to describe the spatial variability of fish biomass than cover of reef builders (R2 of best-fit models: 0.25 [fish] and 0.64 [reef builders]). The variability in total benthic cover of reef builders was best described by physical (wave exposure and reef relief) and ecological (turf algal height and coral recruit density) predictors. No metric of anthropogenic pressure was related to spatial variation in reef builder cover. In contrast, total fish biomass showed a consistent (albeit weak) association with anthropogenic predictors (fishing and diving pressure). As is typical of most environmental gradients, the spatial patterns of both fish biomass density and reef builder cover were spatially autocorrelated. Residuals from the best-fit model for fish biomass retained a signature of spatial autocorrelation while the best-fit model for reef builder cover removed spatial autocorrelation, thus reinforcing our finding that environmental predictors were better able to describe the spatial variability of reef builders than that of fish biomass. As we seek to understand spatial variability of coral reef communities at the scale of most management units (i.e., at kilometer- to island-scales), distinct and scale-dependent perspectives will be needed when considering different functional groups.

Ocean warming endangers coastal ecosystems through increased risk of infectious disease, yet detection, surveillance, and forecasting of marine diseases remain limited. Eelgrass (Zostera marina) meadows provide essential coastal habitat and are vulnerable to a temperature-sensitive wasting disease caused by the protist Labyrinthula zosterae. We assessed wasting disease sensitivity to warming temperatures across a 3500 km study range by combining long-term satellite remote sensing of ocean temperature with field surveys from 32 meadows along the Pacific coast of North America in 2019. Between 11% and 99% of plants were infected in individual meadows, with up to 35% of plant tissue damaged. Disease prevalence was 3× higher in locations with warm temperature anomalies in summer, indicating that the risk of wasting disease will increase with climate warming throughout the geographic range for eelgrass. Large-scale surveys were made possible for the first time by the Eelgrass Lesion Image Segmentation Application, an artificial intelligence (AI) system that quantifies eelgrass wasting disease 5000× faster and with comparable accuracy to a human expert. This study highlights the value of AI in marine biological observing specifically for detecting widespread climate-driven disease outbreaks.