Search

We investigated long-term changes in the abundance and species composition of hyperiid amphipods in the Southern California Bight and nearby waters from twelve springime CalCOFI cruises spanning the period 1951-1997. Sixty-two hyperiid species were detected in the study region. We found dimunition in species diversity and in total hyperiid abundance during the studied period. Despite high interannual variability, there was higher species richness, evenness of species numbers, and abundances of hyperiids in an earlier time period (1951 to 1972) and generally lower species richness, evenness, and abundances in a more recent time period (1979 to 1997). Variations in abundance of total hyperiids were significantly correlated with variations in abundance of presumed gelatinous zooplankton hosts, especially salps, physonect siphonophores, and pyrosomes. Species-specific correlations showed significant associations between ten species of hyperiids and different species of salps, siphonphores, and medusae. Some amphipods were correlated with more than one host. Hyperiid amphipod assemblages appear to be sensitive to large-scale climate changes in the NE Pacific, through either direct responses or indirectly through their association as parasitoids on gelatinous hosts.

El Niño-Southern Oscillation (ENSO) events activate long-distance teleconnections through the atmosphere and ocean that can dramatically impact marine ecosystems along the West Coast of NorthAmerica, affecting diverse organisms ranging from plankton to exploitable and protected species. Such ENSO-related changes to marine ecosystems can ultimately affect humans in many ways, including via depressed plankton and fish production, dramatic range shifts formany protected and exploited species, inaccessibility of traditionally fished resources, more prevalent harmful algal blooms, altered oxygen and pH of waters used in mariculture, and proliferation of pathogens. Theprincipal objective of the Forecasting ENSO Impacts on Marine Ecosystems of the US West Coast workshop was to develop a scientific framework for building an ENSO-related forecast system of ecosystem indicators along the West Coast of North America, including major biological and biogeochemical responses. Attendees realized thata quantitative, biologically-focused forecast system is a much more challenging objective than forecasting the physical system alone; it requires an understanding of the ocean-atmospheric physical system and of diverse organism-level, population-level, and geochemicalresponses that, in aggregate, lead to altered ecosystem states.

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.

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.

Multiple processes transport carbon into the deep ocean as part of the biological carbon pump, leading to long-term carbon sequestration. However, our ability to predict future changes in these processes is hampered by the absence of studies that have simultaneously quantified all carbon pump pathways. Here, we quantify carbon export and sequestration in the California Current Ecosystem resulting from (1) sinking particles, (2) active transport by diel vertical migration, and (3) the physical pump (subduction + vertical mixing of particles). We find that sinking particles are the most important and export 9.0 mmol C m-2 d-1 across 100-m depth while sequestering 3.9 Pg C. The physical pump exports more carbon from the shallow ocean than active transport (3.8 vs. 2.9 mmol C m-2 d-1), although active transport sequesters more carbon (1.0 vs. 0.8 Pg C) because of deeper remineralization depths. We discuss the implications of these results for understanding biological carbon pump responses to climate change.

Abstract. Observations and theory have suggested that ocean fronts are ecological hotspots, associated with higher diversity and biomass across many trophic levels. The hypothesis that these hotspots are driven by frontal nutrient injections is seemingly supported by the frequent observation of opportunistic diatoms at fronts, but the behavior of the rest of the plankton community is largely unknown.Here we investigate the organization of planktonic communities across fronts by analyzing eight high-resolution transects in the California Current Ecosystem containing extensive data for 24 groups of bacteria, phytoplankton, and zooplankton.We find that a distinct frontal plankton community characterized by enhanced biomass of not only diatoms and copepods but many other groups of plankton such as chaetognaths, rhizarians, and appendicularians emerges over most fronts. Importantly, we find spatial variability at a finer scale (typically 1–5 km) than the width of the front itself (typically 10–30 km) with peaks of different plankton taxa at different locations across the width of a front. Our results suggest that multiple processes, including horizontal stirring and biotic interactions, are responsible for creating this fine-scale patchiness.

Abstract: Long-term ocean time series have proven to be the most robust approach for direct observation of climate change processes such as Ocean Acidification. The California Cooperative Oceanic Fisheries Investigations (CalCOFI) program has collected quarterly samples for seawater inorganic carbon since 1983. The longest time series is at CalCOFI line 90 station 90 from 1984–present, with a gap from 2002 to 2008. Here we present the first analysis of this 37- year time series, the oldest in the Pacific. Station 90.90 exhibits an unambiguous acidification signal in agreement with the global surface ocean (decrease in pH of −0.0015 ± 0.0001 yr−1), with a distinct seasonal cycle driven by temperature and total dissolved inorganic carbon. This provides direct evidence that the unique carbon chemistry signature (compared to other long standing time series) results in a reduced uptake rate of carbon dioxide (CO2) due to proximity to a mid-latitude eastern boundary current upwelling zone. Comparison to an independent empirical model estimate and climatology at the same location reveals regional differences not captured in the existing models.

abstract 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.

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.

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 autonomous Zooglider revealed 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 12 Zooglider missions 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.

Metabarcoding of zooplankton communities is becoming more common, but molecular results must be interpreted carefully and validated with morphology-based analyses, where possible. To evaluate our metabarcoding approach within the California Current Ecosystem, we tested whether physical subsampling and PCR replication affects observed community composition; whether community composition resolved by metabarcoding is comparable to morphological analyses by digital imaging; and whether pH neutralization of ethanol with ammonium hydroxide affects molecular diversity. We found that (1) PCR replication was important to accurately resolve alpha diversity and that physical subsampling can decrease sensitivity to rare taxa; (2) there were significant correlations between relative read abundance and proportions of carbon biomass for most taxonomic groups analyzed, but such relationships showed better agreement for the more dominant taxonomic groups; and (3) ammonium hydroxide in ethanol had no effect on molecular diversity. Together, these results indicate that with appropriate replication, paired metabarcoding and morphological analyses can characterize zooplankton community structure and biomass, and that metabarcoding methods are to some extent indicative of relative community composition when absolute measures of abundance or biomass are not available.

We use Zooglider, a low-power optical zooplankton-sensing glider, to test the covariability of the fine-scale vertical distributions of six omnivorous zooplankton taxa with three different representations of their potential prey field: small suspended particles (equivalent circular diameter [ECD] between 0.25 and 0.45 mm), marine snow (ECD ≥ 0.45 mm), and chlorophyll a (Chl a), in the San Diego Trough. All three prey fields tend to be highly correlated from 100 m to the depth of the subsurface Chl a maximum layer (SCML), while correlations between the prey fields are weaker or nonexistent from the SCML to the surface. An index of spatial overlap (Local Index of Collocation) showed stronger overlap of zooplankton with marine snow or small particles than with Chl a in most cases. Moreover, generalized additive models revealed marine snow distributions or small particles as the primary explanatory variable, by percent deviance explained, for all zooplankton taxa tested. Chl a distributions were a secondary explanatory variable for four of the six taxa tested (small copepods, appendicularia-Fritillaria, and both night and day large copepods), and an insignificant explanatory variable for the remaining two (appendicularia-others and large protists). The distributions of suspended particles, during our year-round study in the San Diego Trough, were more informative for explaining distributions of omnivorous zooplankton than Chl a alone.

We investigated long-term changes in the abundance and species composition of hyperiid amphipods in the Southern California Bight and nearby waters from twelve springime CalCOFI cruises spanning the period 1951-1997. Sixty-two hyperiid species were detected in the study region. We found dimunition in species diversity and in total hyperiid abundance during the studied period. Despite high interannual variability, there was higher species richness, evenness of species numbers, and abundances of hyperiids in an earlier time period (1951 to 1972) and generally lower species richness, evenness, and abundances in a more recent time period (1979 to 1997). Variations in abundance of total hyperiids were significantly correlated with variations in abundance of presumed gelatinous zooplankton hosts, especially salps, physonect siphonophores, and pyrosomes. Species-specific correlations showed significant associations between ten species of hyperiids and different species of salps, siphonphores, and medusae. Some amphipods were correlated with more than one host. Hyperiid amphipod assemblages appear to be sensitive to large-scale climate changes in the NE Pacific, through either direct responses or indirectly through their association as parasitoids on gelatinous hosts.

El Niño-Southern Oscillation (ENSO) events activate long-distance teleconnections through the atmosphere and ocean that can dramatically impact marine ecosystems along the West Coast of NorthAmerica, affecting diverse organisms ranging from plankton to exploitable and protected species. Such ENSO-related changes to marine ecosystems can ultimately affect humans in many ways, including via depressed plankton and fish production, dramatic range shifts formany protected and exploited species, inaccessibility of traditionally fished resources, more prevalent harmful algal blooms, altered oxygen and pH of waters used in mariculture, and proliferation of pathogens. Theprincipal objective of the Forecasting ENSO Impacts on Marine Ecosystems of the US West Coast workshop was to develop a scientific framework for building an ENSO-related forecast system of ecosystem indicators along the West Coast of North America, including major biological and biogeochemical responses. Attendees realized thata quantitative, biologically-focused forecast system is a much more challenging objective than forecasting the physical system alone; it requires an understanding of the ocean-atmospheric physical system and of diverse organism-level, population-level, and geochemicalresponses that, in aggregate, lead to altered ecosystem states.

Ecosystems across the United States are changing in complex ways that are difficult to predict. Coordinated long-term research and analysis are required to assess how these changes will affect a diverse array of ecosystem services. This paper is part of a series that is a product of a synthesis effort of the U.S. National Science Foundation’s Long Term Ecological Research (LTER) network. This effort revealed that each LTER site had at least one compelling scientific case study about “what their site would look like” in 50 or 100 yr. As the site results were prepared, themes emerged, and the case studies were grouped into separate papers along five themes: state change, connectivity, resilience, time lags, and cascading effects and compiled into this special issue. This paper addresses the time lags theme with five examples from diverse biomes including tundra (Arctic), coastal upwelling (California Current Ecosystem), montane forests (Coweeta), and Everglades freshwater and coastal wetlands (Florida Coastal Everglades) LTER sites. Its objective is to demonstrate the importance of different types of time lags, in different kinds of ecosystems, as drivers of ecosystem structure and function and how these can effectively be addressed with long-term studies. The concept that slow, interactive, compounded changes can have dramatic effects on ecosystem structure, function, services, and future scenarios is apparent in many systems, but they are difficult to quantify and predict. The case studies presented here illustrate the expanding scope of thinking about time lags within the LTER network and beyond. Specifically, they examine what variables are best indicators of lagged changes in arctic tundra, how progressive ocean warming can have profound effects on zooplankton and phytoplankton in waters off the California coast, how a series of species changes over many decades can affect Eastern deciduous forests, and how infrequent, extreme cold spells and storms can have enduring effects on fish populations and wetland vegetation along the Southeast coast and the Gulf of Mexico. The case studies highlight the need for a diverse set of LTER (and other research networks) sites to sort out the multiple components of time lag effects in ecosystems.

We analyzed spatial distributions of 10 euphausiid species in the southern California Current System across seven El Niño events (1951–2018) and the 2014–15 Warm Anomaly to determine variations in habitat utilization and reproduction during Eastern Pacific (EP) and Central Pacific (CP) Niños. Our goal was to characterize the main forcing mechanisms by which El Niño events influence these dominant species. Our findings suggest cool-water euphausiids respond predominantly to changing in situ habitat conditions during El Niño, while subtropical species require initial advection to increase in the southern CCS. Cool-water coastally-associated species (Euphausia pacifica, Thysanoessa spinifera) compress shoreward and retract poleward to upwelling waters during EP Niños, likely in response to offshore warming. A subtropical coastal species (Nyctiphanes simplex) extends poleward nearshore during EP Niños, suggesting anomalous advection, but increases only moderately and variably off southern California during CP Niños. A Tropical Pacific-Baja California species (Euphausia eximia) only appears off southern California in spring during El Niño years (EP, some CP), suggesting direct advection and low tolerance for cooler, fresher conditions. Subtropical offshore species (Euphausia gibboides, Euphausia recurva, Stylocheiron affine, Euphausia hemigibba) expand shoreward during most Niños (strongest during 2014–15 Warm Anomaly) and show moderate in situ post-event persistence, suggesting combined influence of advection and temporarily favorable habitat nearshore. Regionwide temperate species (Nematoscelis difficilis, Thysanoessa gregaria) contract only moderately shoreward during some Niños. Predictions of Year 2100 distributions using generalized additive models suggest future non-Niño conditions and CP Niños will produce regionwide in situ increases in subtropical species and moderate poleward and onshore expansions, while EP Niños will produce continued nearshore habitat compression and reduced abundance of coastal species. Understanding zooplankton spatial responses to El Niño can help predict community compositional shifts under other ocean changes (e.g., long-term trends, basin-wide warm anomalies).

Model representations of plankton structure and dynamics have consequences for a broad spectrum of ocean processes. Here we focus on the representation of zooplankton and their grazing dynamics in such models. It remains unclear whether phytoplankton community composition, growth rates, and spatial patterns in plankton ecosystem models are especially sensitive to the specific means of representing zooplankton grazing. We conduct a series of numerical experiments that explicitly address this question. We focus our study on the form of the functional response to changes in prey density, including the formulation of a grazing refuge. We use a contemporary biogeochemical model based on continuum size-structured organization, including phytoplankton diversity, coupled to a physical model of the California Current System. This region is of particular interest because it exhibits strong spatial gradients. We find that small changes in grazing refuge formulation across a range of plausible functional forms drive fundamental differences in spatial patterns of plankton concentrations, species richness, pathways of grazing fluxes, and underlying seasonal cycles. An explicit grazing refuge, with refuge prey concentration dependent on grazers' body size, using allometric scaling, is likely to provide more coherent plankton ecosystem dynamics compared to classic formulations or size-independent threshold refugia. We recommend that future plankton ecosystem models pay particular attention to the grazing formulation and implement a threshold refuge incorporating size-dependence, and we call for a new suite of experimental grazing studies.

The Rhizaria is a super-group of amoeboid protists with ubiquitous distributions, from the euphotic zone to the twilight zone and beyond. While rhizarians have been recently described as important contributors to both biogenic silica and carbon fluxes, we lack the most basic information about their ecological habitats and preferences. Here, using in situ imaging (Underwater Vision Profiler 5), we characterize the vertical ecological niches of different test-bearing pelagic rhizarian taxa in the southern California Current Ecosystem. We define three vertical layers between 0 and 500 m occupied, respectively, by (1) surface dwelling and mostly symbiont-bearing rhizarians (Acantharia and Collodaria), (2) flux-feeding phaeodarians in the lower epipelagic (100–200 m), and (3) Foraminifera and Phaeodaria populations adjacent to the oxygen minimum zone. We then use Generalized Additive Models to analyze the response of each rhizarian category to a suite of environmental variables. The models explain between 9% and 93% of the total variance observed for the different groups. While temperature and the depth of the deep chlorophyll maximum appear as the main abiotic factors influencing populations in the upper 200 m, dissolved silicon concentration is related to the abundance of mesopelagic phaeodarians, though it explains only a portion of the variance. The importance of biotic interactions (e.g., prey availability, predation, parasitism, symbiosis) is still to be considered, in order to fully incorporate the dynamics of test-bearing pelagic rhizarians in ecological and biogeochemical models.

Compound-specific isotopic analysis of amino acids (CSIA-AA) is increasingly used in ecological and biogeochemical studies tracking the origin and fate of nitrogen (N). Its advantages include the potential for resolving finer-scale trophic dynamics than possible with standard bulk SIA and for reconstructing historical changes in the food webs of consumers from analyses of specimens in preserved sample archives. For the latter, assessing the effects of chemical preservatives on δ15NAA has been inconclusive because the conventional CSIA approach for derivatized AAs by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) has analytical errors (0.4–1.0‰) in the range expected from chemical preservation. Here, we show improved analytical precision (0.15 ± 0.08‰) for 11 underivatized AA standards analyzed by high-pressure liquid chromatography followed by offline elemental analysis-IRMS (HPLC/EA-IRMS). Using this method, we report the first high-precision tests of preservation effects on δ15NAA in Northern Anchovy (Engraulis mordax) kept 1.5-yr in ethanol and up to 27-yr in formaldehyde. We found minimal methodological induced fractionation for eight AAs, and preservation effects on δ15N were similar regardless of duration and preservative used. Although some of the AAs differed significantly from frozen control samples (AA average +1.0 ± 0.8‰), changes in δ15N in the source AA phenylalanine and trophic position estimates were statistically insignificant. Our results are encouraging for resolving fine-scale natural variability using HPLC/EA-IRMS on chemically preserved specimens and for ultimately reconstructing biogeochemical records and trophic dynamics over long time scales.

Blue whales need to time their migration from their breeding grounds to their feeding grounds to avoid missing peak prey abundances, but the cues they use for this are unknown. We examine migration timing (inferred from the local onset and cessation of blue whale calls recorded on seafloor-mounted hydrophones), environmental conditions (e.g., sea surface temperature anomalies and chlorophyll a), and prey (spring krill biomass from annual net tow surveys) during a 10 year period (2008-2017) in waters of the Southern California Region where blue whales feed in the summer. Colder sea surface temperature anomalies the previous season were correlated with greater krill biomass the following year, and earlier arrival by blue whales. Our results demonstrate a plastic response of blue whales to interannual variability and the importance of krill as a driving force behind migration timing. A decadal-scale increase in temperature due to climate change has led to blue whales extending their overall time in Southern California. By the end of our 10-year study, whales were arriving at the feeding grounds more than one month earlier, while their departure date did not change. Conservation strategies will need to account for increased anthropogenic threats resulting from longer times at the feeding grounds.

Trait-based simplifications of plankton community structure require accurate assessment of trait values as expressed in situ. Yet planktonic organisms live suspended in a fluid medium and often bear elongate appendages, delicate feeding structures, and mucous houses that are badly damaged upon capture or removal from the fluid environment. Fixatives further distort organisms. In situ imaging of zooplankton from a fully autonomous Zooglider reveals a suite of trait characteristics that often differ markedly from those inferred from conventionally sampled plankton. In situ images show fragile feeding appendages in natural hunting postures, including reticulate networks of rhizopods, feeding tentacles of cnidarians, and tentilla of ctenophores; defensive spines and setae of copepods; intact mucous houses of appendicularians; and other structures that are not discernible in conventionally collected zooplankton. Postures characteristic of dormant copepods can be identified and the presence of egg sacs detected. Intact, elongate diatom chains that are much longer than measured in sampled specimens are resolvable in situ. The ability to image marine snow, as well as small-scale fluid deformations, reveals micro-habitat structure that may alter organismal behaviour. Trait-based representations of planktonic organisms in biogeochemical cycles need to consider naturally occurring traits expressed by freely suspended planktonic organisms in situ.

Spines and rhizopodia play an important role in the feeding behavior, symbiont ecology, shell geochemistry, and density and drag of planktonic foraminifera. However, there are few empirical data on planktonic foraminifera in situ, and these delicate structures are disturbed on capture. Here, we report spine and rhizopod measurements from underwater images obtained in the California Current System near La Jolla, California by Zooglider, a new autonomous zooplankton-sensing glider. Across all observed species, we find that spine length and flexibility correlate with test size and that spines increase the effective prey encounter volume of spinose foraminifera by two to three orders of magnitude. Our data also yielded several novel observations regarding hastigerinid foraminifera (Hastigerinella digitata and Hastigerina pelagica), a group of ! unusually large planktonic foraminifera that are abundant in our dataset below 250 m. First, the effective encounter volume of hastigerinid foraminifera can be very large: our largest specimen occupies almost 40 cm3 (about the size of a golf ball), while the median specimen occupies 5.3 cm3 (about the size of a cherry). Second, the majority of hastigerinid foraminifera in our dataset have asymmetric bubble capsules, which are most frequently oriented with their bubbles on the upward side of the test, consistent with the hypothesis that the bubble capsule is positively buoyant. Third, 16% of hastigerinid foraminifera in our dataset have dispersed bubble capsules with detached bubbles distributed along the spines and rhizopodia, consistent with a regular source of natural disturbance. Taken together, our observations suggest that hastigerinid foraminifera play a larger role as mesopelagic predators in the California Current System than previously recognized.

We analyzed impacts of the 2014–2015 Pacific Warm Anomaly and 2015–2016 El Niño on physical and biogeochemical variables at two southern California Current System moorings (CCE2, nearshore upwelling off Point Conception; CCE1, offshore California Current). Nitrate and Chl-a fluorescence were

We analyzed coastal sediments of the Santa Barbara Basin, California, for historical changes in microplastic deposition using a box core that spanned 1834-2009. The sediment was visually sorted for plastic, and a subset was confirmed as plastic polymers via FTIR (Fourier transform infrared) spectroscopy. After correcting for contamination introduced during sample processing, we found an exponential increase in plastic deposition from 1945 to 2009 with a doubling time of 15 years. This increase correlated closely with worldwide plastic production and southern California coastal population increases over the same period. Increased plastic loading in sediments has unknown consequences for deposit-feeding benthic organisms. This increase in plastic deposition in the post-World War II years can be used as a geological proxy for the Great Acceleration of the Anthropocene in the sedimentary record.

Advances in both hardware and software are enabling rapid proliferation of in situ plankton imaging methods, requiring more effective machine learning approaches to image classification. Deep Learning methods, such as convolutional neural networks (CNNs), show marked improvement over traditional feature-based supervised machine learning algorithms, but require careful optimization of hyperparameters and adequate training sets. Here, we document some best practices in applying CNNs to zooplankton and marine snow images and note where our results differ from contemporary Deep Learning findings in other domains. We boost the performance of CNN classifiers by incorporating metadata of different types and illustrate how to assimilate metadata beyond simple concatenation. We utilize both geotemporal (e.g., sample depth, location, time of day) and hydrographic (e.g., temperature, salinity, chlorophyll a) metadata and show that either type by itself, or both combined, can substantially reduce error rates. Incorporation of context metadata also boosts performance of the feature-based classifiers we evaluated: Random Forest, Extremely Randomized Trees, Gradient Boosted Classifier, Support Vector Machines, and Multilayer Perceptron. For our assessments, we use an original data set of 350,000 in situ images (roughly 50% marine snow and 50% non-snow sorted into 26 categories) from a novel in situ Zooglider. We document asymptotically increasing performance with more computationally intensive techniques, such as substantially deeper networks and artificially augmented data sets. Our best model achieves 92.3% accuracy with our 27-class data set. We provide guidance for further refinements that are likely to provide additional gains in classifier accuracy.

Variability in community composition is often attributed to underlying differences in physical environments. However, predator–prey interactions can play an equally important role in structuring communities. Although environmental differences select for different species assemblages, less is known about their impacts on trait compositions. We develop a trait-based analysis of plankton communities of the southern California Current System across multiple trophic levels, from bacteria to mesozooplankton, and over a gradient of environmental conditions, from the oligotrophic open ocean to coastal upwelling. Across a factor of four differences in total community biomass, we observe similarities in the size structure along the environmental gradient, with the most pronounced departures from proportional variations in the biomasses found in the largest protists (> 40 µm). Differences in the trait distributions emerge within a small range of size groups: greater biomass contribution of larger autotrophs (> 10 µm) is observed only for the upwelling region.

Some planktonic patches have markedly higher concentrations of organisms compared to ambient conditions and are

RationaleIt is imperative to understand how chemical preservation alters tissue isotopic compositions before using historical samples in ecological studies. Specifically, although compound-specific isotope analysis of amino acids (CSIA-AA) is becoming a widely used tool, there is little information on how preservation techniques affect amino acid δ15 N values.MethodsWe evaluated the effects of chemical preservatives on bulk tissue δ13 C and δ15 N and amino acid δ15 N values, measured by gas chromatography/isotope ratio mass spectrometry (GC/IRMS), of (a) tuna (Thunnus albacares) and squid (Dosidicus gigas) muscle tissues that were fixed in formaldehyde and stored in ethanol for 2 years and (b) two copepod species, Calanus pacificus and Eucalanus californicus, which were preserved in formaldehyde for 24-25 years.ResultsTissues in formaldehyde-ethanol had higher bulk δ15 N values (+1.4, D. gigas; +1.6‰, T. albacares), higher δ13 C values for D. gigas (+0.5‰), and lower δ13 C values for T. albacares (-0.8‰) than frozen samples. The bulk δ15 N values from copepods were not different those from frozen samples, although the δ13 C values from both species were lower (-1.0‰ for E. californicus and -2.2‰ for C. pacificus) than those from frozen samples. The mean amino acid δ15 N values from chemically preserved tissues were largely within 1‰ of those of frozen tissues, but the phenylalanine δ15 N values were altered to a larger extent (range: 0.5-4.5‰).ConclusionsThe effects of preservation on bulk δ13 C values were variable, where the direction and magnitude of change varied among taxa. The changes in bulk δ15 N values associated with chemical preservation were mostly minimal, suggesting that storage in formaldehyde or ethanol will not affect the interpretation of δ15 N values used in ecological studies. The preservation effects on amino acid δ15 N values were also mostly minimal, mirroring bulk δ15 N trends, which is promising for future CSIA-AA studies of archived specimens. However, there were substantial differences in phenylalanine and valine δ15 N values, which we speculate resulted from interference in the chromatographic resolution of unknown compounds rather than alteration of tissue isotopic composition due to chemical preservation.

We investigated variability in the C:234Th ratio of sinking particles and its relationship to changing water column characteristics and plankton ecological dynamics during 29 Lagrangian experiments conducted on six cruises of the California Current Ecosystem Long-Term Ecological Research (CCE-LTER) Program. C:234Th ratios of sinking particles collected by a surface-tethered sediment trap (C:234ThST) varied from 2.3 to 20.5 μmol C dpm−1 over a depth range of 47–150 m. C:234ThST was significantly greater (by a factor of 1.8) than C:234Th ratios of suspended >51-μm particles collected in the same water parcels with in situ pumps. C:234Th ratios of large (>200-μm) sinking particles also exceeded those of smaller sinking particles. C:234ThST decreased with depth from the base of the euphotic zone through the upper twilight zone. C:234ThST was positively correlated with several indices of ecosystem productivity including particulate organic carbon (POC) and chlorophyll (Chl) concentrations, mesozooplankton biomass, and the fraction of Chl >20-μm. Principal component analysis and multiple linear regression suggested that decaying phytoplankton blooms exhibited higher C:234ThST than actively growing blooms at similar biomass levels. C:234ThST was positively correlated with indices of the fractional contribution of fecal pellets in sediment traps when the proportion of fecal pellets was low in the traps, likely because of a correlation between mesozooplankton biomass and other indices of ecosystem productivity. However, when fecal pellets were a more important component of sinking material, C:234ThST decreased with increasing fecal pellet content. C:234ThST was also positively correlated with the Si:C ratio of sinking particles. Across the dataset (and across depths) a strong correlation was found between C:234ThST and the ratio of vertically-integrated POC to vertically-integrated total water column 234Th (vC:234Thtot). A mechanistic one-layer, two-box model of thorium sorption and desorption was invoked to explain this correlation. Two empirical models (one using vC:234Thtot; one using depth and vertically-integrated Chl) were developed to predict C:234Th ratios in this coastal upwelling biome. The former regression (log10(C:234ThST) = 0.43 × log10(vC:234Thtot) + 0.53) was found to also be a reasonable predictor for C:234ThST from diverse regions including the Southern Ocean, Sargasso Sea, Subarctic North Pacific, and Eastern Tropical North Pacific.

We present the design and preliminary results from ocean deployments of Zooglider, a new autonomous zooplankton-sensing glider. Zooglider is a modified Spray glider that includes a low-power camera (Zoocam) with telecentric lens and a custom dual frequency Zonar (200 and 1000 kHz). The Zoocam quantifies zooplankton and marine snow as they flow through a defined volume inside a sampling tunnel. Images are acquired on average every 5 cm from a maximum operating depth of ~ 400 m to the sea surface. Biofouling is mitigated using a dual approach: an ultraviolet light-emitting diode and a mechanical wiper. The Zonar permits differentiation of large and small acoustic backscatterers in larger volumes than can be sampled optically. Other sensors include a pumped conductivity, temperature, and depth unit and chlorophyll a fluorometer. Zooglider enables fully autonomous in situ measurements of mesozooplankton distributions, together with the three-dimensional orientation of organisms and marine snow in relation to other biotic and physical properties of the ocean water column. It is well suited to resolve thin layers and microscale ocean patchiness. Battery capacity supports 50 d of operations. Zooglider includes two-way communications via Iridium, permitting near-real–time transmission of data from each dive profile, as well as interactive instrument control from remote locations for adaptive sampling.

Euphausiids are important prey for many marine organisms and often occur in patchy aggregations. Euphausiid predators, such as blue whales, may become concentrated in the vicinity of these aggregations. We investigated an area called Nine Mile Bank (NMB) near San Diego, California, defined by an area of steep bathymetry, to determine whether the frequent whale sightings in that locality can be explained by the distribution of euphausiids across the bank and by the vertical distribution of euphausiids in the water column. Thysanoessa spinifera, the strongly preferred blue whale prey euphausiid in this area, was consistently more abundant on the bank or inshore of it than offshore. In contrast, Euphausia pacifica, a minor blue whale prey item, was much more abundant and distributed across the study region. Adults of both species were concentrated in a stratum corresponding to the feeding depth of blue whales. Other euphausiids that form a negligible part of the blue whale diet also showed no association with NMB. Both blue whales and their primary prey species Thysanoessa spinifera were more abundant on or inshore of the bank than offshore, suggesting that the bank may serve as an offshore limit of high prey abundance that helps to concentrate blue whales.

Zooplankton are important consumers of sinking particles in the ocean's twilight zone. However, the impact of different taxa depends on their feeding mode. In contrast to typical suspension-feeding zooplankton, flux-feeding taxa preferentially consume rapidly sinking particles that would otherwise penetrate into the deep ocean. To quantify the potential impact of two flux-feeding zooplankton taxa [Aulosphaeridae (Rhizaria), and Limacina helicina (euthecosome pteropod)] and the total suspension-feeding zooplankton community, we measured depth-stratified abundances of these organisms during six cruises in the California Current Ecosystem. Using allometric-scaling relationships, we computed the percentage of carbon flux intercepted by flux feeders and suspension feeders. These estimates were compared to direct measurements of carbon flux attenuation (CFA) made using drifting sediment traps and 238U-234Th disequilibrium. We found that CFA in the shallow twilight zone typically ranged from 500 to 1000 μmol organic C flux remineralized per 10-m vertical depth bin. This equated to approximately 6-10% of carbon flux remineralized/10 m. The two flux-feeding taxa considered in this study could account for a substantial proportion of this flux near the base of the euphotic zone. The mean flux attenuation attributable to Aulosphaeridae was 0.69%/10 m (median = 0.21%/10 m, interquartile range = 0.04-0.81%) at their depth of maximum abundance (~100 m), which would equate to ~10% of total flux attenuation in this depth range. The maximum flux attenuation attributable to Aulosphaeridae reached 4.2%/10 m when these protists were most abundant. L. helicina, meanwhile, could intercept 0.45-1.6% of carbon flux/10 m, which was slightly greater (on average) than the Aulosphaeridae. In contrast, suspension-feeding zooplankton in the mesopelagic (including copepods, euphausiids, appendicularians, and ostracods) had combined clearance rates of 2-81 L m-3 day-1 (mean of 19.6 L m-3 day-1). This implies a substantial impact on slowly sinking particles, but a negligible impact on the presumably rapidly sinking fecal pellets that comprised the majority of the material collected in sediment traps. Our results highlight the need for a greater research focus on the many taxa that potentially act as flux feeders in the oceanic twilight zone.

We used extensive ecological and biogeochemical measurements obtained from quasi-Lagrangian experiments during two California Current Ecosystem Long-Term Ecosystem Research cruises to analyze carbon fluxes between the epipelagic and mesopelagic zones using a linear inverse ecosystem model (LIEM). Measurement constraints on the model include 14C primary productivity, dilution-based microzooplankton grazing rates, gut pigment-based mesozooplankton grazing rates (on multiple zooplankton size classes), 234Th:238U disequilibrium and sediment trap measured carbon export, and metabolic requirements of micronekton, zooplankton, and bacteria. A likelihood approach (Markov Chain Monte Carlo) was used to estimate the resulting flow uncertainties from a sample of potential flux networks. Results highlight the importance of mesozooplankton active transport (i.e., diel vertical migration) in supplying the carbon demand of mesopelagic organisms and sequestering carbon dioxide from the atmosphere. In nine water parcels ranging from a coastal bloom to offshore oligotrophic conditions, mesozooplankton active transport accounted for 18–84% (median: 42%) of the total carbon transfer to the mesopelagic, with gravitational settling of POC (12–55%; median: 37%), and subduction (2–32%; median: 14%) providing the majority of the remainder. Vertically migrating zooplankton contributed to downward carbon flux through respiration and excretion at depth and via mortality losses to predatory zooplankton and mesopelagic fish (e.g., myctophids and gonostomatids). Sensitivity analyses showed that the results of the LIEM were robust to changes in nekton metabolic demand, rates of bacterial production, and mesozooplankton gross growth efficiency. This analysis suggests that prior estimates of zooplankton active transport based on conservative estimates of standard (rather than active) metabolism are likely too low.

Sinking particles transport organic carbon produced in the surface ocean to the ocean interior, leading to net storage of atmospheric CO2 in the deep ocean. The rapid growth of in situ imaging technology has the potential to revolutionize our understanding of particle flux attenuation in the ocean; however, estimating particle flux from particle size and abundance (measured directly by in situ cameras) is challenging. Sinking rates are dependent on several factors, including particle excess density and porosity, which vary based on particle origin and type. Additionally, particle characteristics are transformed while sinking. We compare optically measured particle size spectra profiles (Underwater Vision Profiler 5, UVP) with contemporaneous measurements of particle flux made using sediment traps and 234Th:238U disequilibrium on six process cruises from the California Current Ecosystem (CCE) LTER Program. These measurements allow us to assess the efficacy of size-flux relationships for estimating fluxes from optical particle size measurements. We find that previously published parameterizations that estimate carbon flux from UVP profiles are a poor fit to direct flux measurements in the CCE. This discrepancy is found to result primarily from the important role of fecal pellets in particle flux. These pellets are primarily in a size range (i.e., 100–400 μm) that is not well-resolved as images by the UVP due to the resolution of the sensor. We develop new, CCE-optimized parameters for use in an algorithm estimating carbon flux from UVP data in the southern California Current (Flux = (Formula presented.)), with A = 15.4, B = 1.05, d = particle diameter (mm) and Flux in units of mg C m–2 d–1. We caution, however, that increased accuracy in flux estimates derived from optical instruments will require devices with greater resolution, the ability to differentiate fecal pellets from low porosity marine snow aggregates, and improved sampling of rapidly sinking fecal pellets. We also find that the particle size-flux relationships may be different within the euphotic zone than in the shallow twilight zone and hypothesize that the changing nature of sinking particles with depth must be considered when investigating the remineralization length scale of sinking particles in the ocean.

We assess whether a supervised machine learning algorithm, specifically a convolutional neural network (CNN), achieves higher accuracy on planktonic image classification when including non‐plankton and ancillary plankton during the training procedure. We focus on the case of optimizing the CNN for a single planktonic image source, while considering ancillary images to be plankton images from other instruments. We conducted two sets of experiments with three different types of plankton images (from a Zooglider, Underwater Vision Profiler 5, and Zooscan), and our results held across all three image types. First, we considered whether single‐stage transfer learning using non‐plankton images was beneficial. For this assessment, we used ImageNet images and the 2015 ImageNet contest‐winning model, ResNet‐152. We found increased accuracy using a ResNet‐152 model pretrained on ImageNet, provided the entire network was retrained rather than retraining only the fully connected layers. Next, we combined all three plankton image types into a single dataset with 3.3 million images (despite their differences in contrast, resolution, and pixel pitch) and conducted a multistage transfer learning assessment. We executed a transfer learning stage from ImageNet to the merged ancillary plankton dataset, then a second transfer learning stage from that merged plankton model to a single instrument dataset. We found that multistage transfer learning resulted in additional accuracy gains. These results should have generality for other image classification tasks. [ABSTRACT FROM AUTHOR]

Advances in in situ imaging allow enumeration of abundant populations of large Rhizarians that compose a substantial proportion of total mesozooplankton biovolume. Using a quasi-Lagrangian sampling scheme, we quantified the abundance, vertical distributions, and sinking-related mortality of Aulosphaeridae, an abundant family of Phaeodaria in the California Current Ecosystem. Inter-cruise variability was high, with average concentrations at the depth of maximum abundance ranging from < 10 to > 300 cells m−3, with seasonal and interannual variability associated with temperature-preferences and regional shoaling of the 10°C isotherm. Vertical profiles showed that these organisms were consistently most abundant at 100–150 m depth. Average turnover times with respect to sinking were 4.7–10.9 d, equating to minimum in situ population growth rates of ~ 0.1–0.2 d−1. Using simultaneous measurements of sinking organic carbon, we find that these organisms could only meet their carbon demand if their carbon : volume ratio were ~ 1 μg C mm−3. This value is substantially lower than previously used in global estimates of rhizarian biomass, but is reasonable for organisms that use large siliceous tests to inflate their cross-sectional area without a concomitant increase in biomass. We found that Aulosphaeridae alone can intercept > 20% of sinking particles produced in the euphotic zone before these particles reach a depth of 300 m. Our results suggest that the local (and likely global) carbon biomass of Aulosphaeridae, and probably the large Rhizaria overall, needs to be revised downwards, but that these organisms nevertheless play a major role in carbon flux attenuation in the twilight zone.

Oceanic fronts are sites of increased vertical exchange that are often associated with increased primary productivity, downward flux of organic carbon, and aggregation of plankton and higher trophic levels. Given the influence of fronts on the functioning of marine ecosystems, an improved understanding of the spatial and temporal variability of frontal activity is desirable. Here, we document changes in the frequency of sea-surface fronts and the surface concentration of chlorophyll-a (Chla) in the California Current System that occurred during the Northeast Pacific anomalous warming of 2014–2015 and El Niño of 2015–2016, and place those anomalies in the context of two decades of variability. Frontal frequency was detected with the automated histogram method using datasets of sea-surface temperature (SST) and Chla from multiple satellite sensors. During the anomalous 2014–2016 period, a drop in the frequency of fronts coincided with the largest negative Chla anomalies and positive SST anomalies in the whole period of satellite observations (1997–2017 for Chla and 1982–2017 for SST). These recent reductions in frontal frequency ran counter to a previously reported increasing trend, though it remains to be seen if they represent brief interruptions in that trend or a reversal that will persist going forward.

We analyzed seven El Niño events (springs 1958–59, 1983, 1992–93, 1998, 2003, 2010, and 2016) and the 2014–15 Pacific Warm Anomaly (spring 2015) for their impacts on zooplankton biomass and community composition in the southern sector of the California Current System (CCS). Although total mesozooplankton carbon biomass was only modestly affected during El Niño springs, community composition changed substantially. Carbon biomass of five major zooplankton taxa correlated negatively with San Diego sea level anomaly (SDSLA), a regional metric of El Niño physical impacts in the CCS. Additional taxa were negatively related to SDSLA via a time-lagged response reflected in an autoregressive-1 (AR-1) model. All five SDSLA-correlated taxa decreased in carbon biomass during most El Niño years compared to the surrounding years; the exception was the mild event of 2003. Principal Component Analysis revealed coherent species-level responses to El Niño within the euphausiids, copepods, and hyperiid amphipods. Percent similarity index (PSI) comparisons showed pronounced changes in the compositions of euphausiid and, to a lesser extent, calanoid copepod communities during El Niño. By grouping El Niños into Eastern Pacific (EP) versus Central Pacific (CP) events based on their expressions along the equator, we found that CCS zooplankton assemblages showed a tendency toward greater changes in species composition during EP than CP El Niños, although we had low statistical power for these comparisons. Several species showed consistent biomass changes across La Niña events as well, generally opposite in sign to El Niño responses, but overall community composition showed minimal change during La Niña. Carbon biomass and community composition returned to pre-Niño levels within 1–2 years following almost every event, suggesting high resilience of southern CCS zooplankton to El Niño perturbations to date.

This contribution provides an introduction to a sequence of five papers (CCE I- CCE V) that describe the impact of the Warm Anomaly of 2014–15 and El Niño 2015–16 on the pelagic food web of the southern California Current Ecosystem. These contributions analyze the influence of these two warm water perturbations on satellite-based measures of ocean fronts, export efficiency out of the euphotic zone, copepod egg production, mesozooplankton community structure, and a synthesis of primary production, mesozooplankton grazing, and gravitational fluxes of organic carbon.

Predicting marine carbon sequestration in a changing climate requires mechanistic understanding of the processes controlling sinking particle flux under different climatic conditions. The recent occurrence of a warm anomaly (2014–2015) followed by an El Niño (2015–2016) in the southern sector of the California Current System presented an opportunity to analyze changes in the biological carbon pump in response to altered climate forcing. We compare primary production, mesozooplankton grazing, and carbon export from the euphotic zone during quasi-Lagrangian experiments conducted in contrasting conditions: two cruises during warm years - one during the warm anomaly in 2014 and one toward the end of El Niño 2016 – and three cruises during El Niño-neutral years. Results showed no substantial differences in the relationships between vertical carbon export and its presumed drivers (primary production, mesozooplankton grazing) between warm and neutral years. Mesozooplankton fecal pellet enumeration and phaeopigment measurements both showed that fecal pellets were the dominant contributor to export in productive upwelling regions. In more oligotrophic regions, fluxes were dominated by amorphous marine snow with negligible pigment content. We found no evidence for a significant shift in the relationship between mesozooplankton grazing rate and chlorophyll concentration. However, mass-specific grazing rates were lower at low-to-moderate chlorophyll concentrations during warm years relative to neutral years. We also detected a significant difference in the relationship between phytoplankton primary production and photosynthetically active radiation between years: at similar irradiance and nutrient concentrations, productivity decreased during the warm events. Whether these changes resulted from species composition changes remains to be determined. Overall, our results suggest that the processes driving export remain similar during different climate conditions, but that species compositional changes or other structural changes require further attention.

We hypothesized that copepod egg production rates would be suppressed relative to their normal functional relationships with food availability during the NE Pacific warm anomalies of 2014–2015 and the El Niño event of 2015–2016. We also hypothesized that copepods would show increased rates of egg production and recruitment in association with ocean fronts. Three species of copepods (Calanus pacificus, Metridia pacifica, and Eucalanus californicus) were incubated at sea in simulated in situ conditions to ascertain egg production rates and egg hatching success during a sequence of 3–5 California Current Ecosystem-Long Term Ecological Research (CCE-LTER) cruises across diverse ocean conditions. Several indices of food availability were measured. The warm events had no significant effect on egg production rates measured in the experiments conducted here. Egg production and net naupliar production rates varied markedly among copepod species and across spatial gradients, but relationships with food concentration during warm events did not consistently diverge from functional relationships during El Niño-neutral conditions. Egg production was most commonly elevated inshore compared to offshore, but was not elevated within fronts. The egg production of C. pacificus was best explained by total Chl-a, while E. californicus was best explained by the > 20 size fraction of Chl-a. M. pacifica showed no relationship between egg production and any food metric tested. C. pacificus showed higher EPR than the other two species in virtually all conditions encountered, which may contribute to its numerical dominance throughout the region.

We describe the mandibular morphology of the eight most abundant euphausiid species in the California Current and report regression relationships between mandible size and body total length. We applied these species-specific characters to the mandibles recovered from fecal samples of 18 blue whales (Balaenoptera musculus (Linnaeus, 1758)) collected between 1998 to 2015 off Southern California to test for selective feeding on the euphausiid assemblage. The diets of blue whales were consistently and overwhelmingly dominated by the large neritic euphausiid Thysanoessa spinifera Holmes, 1900, even when other species were present or dominant in closely collected net samples. More than 99% of the ingested euphausiids were longer than 10 mm, indicating that blue whales in this region are highly selective by prey species and size class, and dependent upon aggregations of juveniles or adults of a limited number of coastally associated euphausiid species.

In marine ecosystems, many planktonic organisms precipitate biogenic silica (bSiO2) to build silicified skeletons. Among them, giant siliceous rhizarians (>500 μm), including Radiolaria and Phaeodaria, are important contributors to oceanic carbon pools but little is known about their contribution to the marine silica cycle. We report the first analyses of giant phaeodarians to bSiO2 export in the California Current Ecosystem. We measured the silica content of single rhizarian cells ranging in size from 470 to 3,920 μm and developed allometric equations to predict silica content (0.37–43.42 μg Si/cell) from morphometric measurements. Using sediment traps to measure phaeodarian fluxes from the euphotic zone on four cruises, we calculated bSiO2 export produced by two families, the Aulosphaeridae and Castanellidae. Biogenic silica export ranged from