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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.

The uptake of³H‐labeled leucine into proteins, a widely used method for estimating bacterial carbon production (BCP), is suggested to underestimate or overestimate bacterial growth in the open ocean by a factor of 40 uncertainty. Meanwhile, an alternative BCP approach, by the dilution method, has untested concerns about potential overestimation of bacterial growth from dissolved substrates released by filtration. We compared BCP_Diland BCP_Leuestimates from three cruises across a broad trophic gradient, from offshore oligotrophy to coastal upwelling, in the California Current Ecosystem. Our initial analyses based on midday microscopical estimates of bacterial size and a priori assumptions of conversions relationships revealed a mean two‐fold difference in BCP estimates (BCP_Dilhigher), but no systematic bias between low and high productivity stations. BCP_Diland BCP_Leuboth demonstrated strong relationships with bacteria cell abundance. Reanalysis of results, involving a different cell carbon‐biovolume relationship and informed by forward angle light scatter from flow cytometry as a relative cell size index, demonstrated that BCP_Diland BCP_Leuare fully compatible, with a 1 : 1 fit for bacteria of 5 fg C cell⁻¹. Based on these results and considering different strengths of the methods, the combined use of³H‐labeled leucine and dilution techniques provide strong mutually supportive constraints on bacterial biomass and production.

The marine coastal region makes up just 10% of the total area of the global ocean but contributes nearly 20% of its total primary production and over 80% of fisheries landings. Unicellular phytoplankton dominate primary production. Climate variability has had impacts on various marine ecosystems, but most sites are just approaching the age at which ecological responses to longer term, unidirectional climate trends might be distinguished. All five marine pelagic sites in the US Long Term Ecological Research (LTER) network are experiencing warming trends in surface air temperature. The marine physical system is responding at all sites with increasing mixed layer temperatures and decreasing depth and with declining sea ice cover at the two polar sites. Their ecological responses are more varied. Some sites show multiple population or ecosystem changes, whereas, at others, changes have not been detected, either because more time is needed or because they are not being measured.

The last two decades have shown the importance of Rhizaria in the biogeochemical cycles of carbon and silicon in modern oceans. This eukaryotic supergroup, which includes Radiolaria and Phaeodaria, represents an important part of zooplanktonic carbon biomass and contributes to carbon and silica export. Still, accurate estimations of their carbon biomass are hindered by poor knowledge of their elemental composition, contrasting with well‐established allometric carbon‐to‐volume relationships for smaller protists such as phytoplankton. Here, we directly measured carbon, nitrogen, and biogenic silica content as well as silicon uptake rates of planktonic Rhizaria. We highlight that size can be used as a predictor of elemental content for a broad variety of planktonic Rhizaria ranging from 200 μm to several mm, whereas size is weakly correlated with silicon uptake rates. Our results indicate that the scaling exponent of the carbon‐to‐volume allometry is significantly lower than those for smaller protists, underlining the low carbon strategy of these organisms. Still, we show that carbon and nitrogen densities span over four orders of magnitude, possibly accounting for the differences in depth ranges, nutritional modes and colonial or solitary forms. We estimate Rhizaria sinking speeds by combining carbon, nitrogen, and silica content data and show that great variability exists among the different taxa. Besides giving a better understanding of rhizarian ecology and biogeochemistry, these analyses, at the individual scale, are a first step to subsequent biomass and flux estimations at larger scales.

The ecological and oceanographic processes that drive the response of pelagic ocean microbiomes to environmental changes remain poorly understood, particularly in coastal upwelling ecosystems. Here we show that seasonal and interannual variability in coastal upwelling predicts pelagic ocean microbiome diversity and community structure in the Southern California Current region. Ribosomal RNA gene sequencing, targeting prokaryotic and eukaryotic microbes, from samples collected seasonally during 2014-2020 indicate that nitracline depth is the most robust predictor of spatial microbial community structure and biodiversity in this region. Striking ecological changes occurred due to the transition from a warm anomaly during 2014-2016, characterized by intense stratification, to cooler conditions in 2017-2018, representative of more typical upwelling conditions, with photosynthetic eukaryotes, especially diatoms, changing most strongly. The regional slope of nitracline depth exerts strong control on the relative proportion of highly diverse offshore communities and low biodiversity, but highly productive nearshore communities.

In eastern boundary current systems, strong coastal upwelling brings deep, nutrient‐rich waters to the surface ocean, supporting a productive food web. The nitrate load in water masses that supply the region can be impacted by a variety of climate‐related processes that subsequently modulate primary productivity. In this study, two coastal upwelling regimes along central and southern California were sampled seasonally for nitrogen and oxygen stable isotopes of nitrate (i.e., nitrate isotopes) over several years (2010–2016) on 14 California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises. Seasonal, interannual, and spatial variations in euphotic zone nitrate isotopes were largely driven by the extent of nitrate utilization, sometimes linked to iron limitation of diatom productivity. Pronounced isotopic enrichment developed with the El Niño conditions in late 2015 and early 2016 which likely resulted from increased nitrate utilization linked to reduced nitrate supply to the euphotic zone. Differential enrichment of nitrogen and oxygen isotopes was observed in the surface ocean, suggesting that phytoplankton increased their reliance on locally nitrified (recycled) nitrate during warmer and more stratified periods. Overall, nitrate isotopes effectively differentiated important euphotic zone processes such as nitrate assimilation and nitrification, while archiving the influence of disparate controls such as iron limitation and climatic events through their effects on nitrate utilization and isotopic fractionation.

The Blob was the early manifestation of the Northeast Pacific marine heat wave from 2013 to 2016. While the upper ocean temperature in the Blob has been well described, the impacts on marine biogeochemistry have not been fully studied. Here, we characterize and develop understanding of Eastern North Pacific upper ocean biogeochemical properties during the Winter of 2013–2014 using in situ observations, an observation‐based product, and reconstructions from a collection of ocean models. We find that the Blob is associated with significant upper ocean biogeochemical anomalies: A 5% increase in aragonite saturation state (temporary reprieve of ocean acidification) and a 3% decrease in oxygen concentration (enhanced deoxygenation). Anomalous advection and mixing drive the aragonite saturation anomaly, while anomalous heating and air‐sea gas exchange drive the oxygen anomaly. Marine heatwaves do not necessarily serve as an analog for future change as they may enhance or mitigate long‐term trends.

Diel vertical migration (DVM) is a common behavior among marine organisms to balance the trade‐off between surface feeding opportunities and predation‐related mortality risk. Body size is a master trait that impacts predation risk to both visual and nonvisual predators. Acoustic measurements from the autonomousZoogliderrevealed size‐dependent DVM behaviors in the San Diego Trough. Dual frequency (200 and 1000 kHz) backscatter, in conjunction with physical properties of the ambient water and optical imaging of zooplankton, were recorded during 12Zooglidermissions over 2 yr. Acoustic size‐categories were identified based on the theoretical scattering properties of dominant taxonomic groups identified optically by the Zoocam. Acoustic modeling suggests that the measured acoustic backscatter in this region is largely dominated by copepods, with appreciable contributions from other taxa. We found that larger organisms migrated deeper (245–227 m) and faster (> 20 m h⁻¹) compared to smaller organisms (156 m, > 15 m h⁻¹). Larger organisms entered the upper layer of the water column later in the evening (0.2–1.5 h later) and descended into deeper water earlier in the morning (0.4–3.7 h earlier) than smaller‐bodied organisms, consistent with body size‐dependent visual predation risk. The variability in daytime depths occupied by small, intermediate, and large‐bodied backscatterers was related to the depth of the euphotic zone, again consistent with light‐dependent risk of predation.

Nitrification, the microbial conversion of ammonium to nitrite then to nitrate, occurs throughout the oceanic water column, yet the environmental factors influencing the production of nitrate in the euphotic zone (EZ) remain unclear. In this study, the natural abundances of N and O isotopes (δ¹⁵N and δ¹⁸O, respectively) in nitrate were used in an existing model framework to quantify nitrate contributed by EZ nitrification in the California Current Ecosystem (CCE) during two anomalously warm years. Model data estimated that between 6% and 36% of the EZ nitrate reservoirs were derived from the combined steps of nitrification within the EZ. The CCE data set found nitrification contributions to EZ nitrate to be positively correlated with nitrite concentrations () at the depth of the primary nitrite maximum (PNM). Building on this correlation, EZ nitrification in the southern California Current was estimated to contribute on average 20% ± 6% to EZ nitrate as inferred using the PNMof the long‐term California Cooperative Oceanic Fisheries Investigation (CalCOFI) survey record. A multiple linear regression analysis of the CalCOFI PNMtime series identified two conditions that led to positive deviations in. Enhanced PNM, and potentially enhanced EZ nitrification, may be linked to (1) reduced phytoplankton competition for ammonium () andas interpreted from particulate organic carbon:chlorophyll ratios, and/or (2) to increased supply of(and thenoxidation to) from the degradation of organic nitrogen as interpreted from particulate organic nitrogen concentrations.

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.