Recent sio_iod items

Resolving abrupt frontal gradients in zooplankton community composition and marine snow fields with an autonomous Zooglider

Thu, 18 Jun 2026 00:00:00 +0000

Abstract An autonomous Zooglider navigated across the California Current Front into low salinity, minty waters characteristic of the California Current proper in both summers of 2019 and 2021. Diving to 400 m depth, Zooglider transited another near‐surface frontal gradient somewhat inshore. These frontal gradients were generally associated with changes in intensity, size composition, and Diel Vertical Migration responses of acoustic backscatterers. They were also associated with pronounced changes in zooplankton community composition, as assessed by a shadowgraph imaging Zoocam. Zoocam detected a decline in concentrations of copepods, appendicularians, and marine snow in the offshore direction, and an overall shift in community structure to a higher proportion of carnivorous taxa (and, in 2019, of planktonic rhizaria). No taxon was consistently elevated at all the peak frontal gradients, but appendicularians, copepods, and rhizarians sometimes showed front‐related increases in...

Diverse sampling programs highlight pulses of Velella velella along the US West Coast.

Thu, 18 Jun 2026 00:00:00 +0000

Sporadic mass strandings of the hydrozoan, Velella velella, along the US West Coast fascinate beachcombers and perplex oceanographers. Velella often arrive to the coast in the spring concurrent with a shift in onshore winds and after winters with warmer water temperatures. Understanding the factors that bring Velella to coastal waters provides new information about the ecological impacts of local and basin-scale environmental variability in the northeast Pacific. We summarize several compelling, non-exclusive hypotheses that could explain the recent increase in Velella, including increased population size, larger surface patches and enhanced coastward transport. We compiled a comprehensive dataset spanning planktonic larval to colonial adult life stages from 10 sources covering ~1900-2025. We highlight pulses of Velella and an unprecedented number of strandings and at-sea observations since 2014. We found that wind patterns in the central-east...

Fine scale zooplankton distribution across the North Balearic Front during late spring

Thu, 18 Jun 2026 00:00:00 +0000

Observations, models and theory have suggested that ocean fronts are ecological hotspots, generally associated with higher diversity and biomass across many trophic levels. Nutrient injections are often associated with higher chlorophyll concentrations at fronts, but the response of the zooplankton community is largely unknown. The present study investigates mesozooplankton stocks and composition during late spring, northeast of Menorca along two north-south transects that crossed the North Balearic Front (NBF) separating central water of the Northwestern Mediterranean Sea (NWMS) gyre from peripheral waters originating from the Algerian basin. During the BioSWOT-Med campaign, samples were collected using vertical triple net tows at three depths (100 m, 200 m, 400 m) with 200 μm and 500 μm mesh nets, processed with ZooScan, and the organisms assigned to eight taxonomic groups. Zooplankton distributions were analysed for the surface (0–100 m), intermediate (100–200 m), and deeper...

Relationships Between Plankton Size Spectra, Net Primary Production, and the Biological Carbon Pump

Thu, 18 Jun 2026 00:00:00 +0000

Abstract Photosynthesis in the surface ocean and subsequent export of a fraction of this fixed carbon leads to carbon dioxide sequestration in the deep ocean. Ecological relationships among plankton functional groups and theoretical relationships between particle size and sinking rate suggest that carbon export from the euphotic zone is more efficient when communities are dominated by large organisms. However, this hypothesis has never been tested against measured size spectra spanning the >5 orders of magnitude found in plankton communities. Using data from five ocean regions (California Current Ecosystem, North Pacific subtropical gyre, Costa Rica Dome, Gulf of Mexico, and Southern Ocean subtropical front), we quantified carbon‐based plankton size spectra from heterotrophic bacteria to metazoan zooplankton (size class cutoffs varied slightly between regions) and their relationship to net primary production and sinking particle flux. Slopes of the normalized biomass size spectra...

Beyond transfer learning: Leveraging ancillary images in automated classification of plankton

Thu, 18 Jun 2026 00:00:00 +0000

Abstract 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...

Influences of Dispersal and Environmental Selection on Zooplankton Distributions Across the Upper 1000 m of the North Pacific

Thu, 18 Jun 2026 00:00:00 +0000

ABSTRACT Aim Test the response of mesopelagic zooplankton community composition and distributional ranges to dispersal potential and environment, in comparison with the epipelagic zooplankton community. Location Epipelagic (0–200 m) and mesopelagic (200–1000 m) depth zones of the North Pacific Ocean. Taxon Multicellular zooplankton. Methods Metabarcoding of two molecular markers (18S and COI) in combination with a global ocean circulation model, analysed by General Dissimilarity Modelling. Results We found no significant difference in beta‐diversity across three depth strata (0–200, 200–500, and 500–1000 m), calculated from the nMDS dispersion of samples within each stratum. Similarity in beta‐diversity within the three depth strata indicates that epipelagic and mesopelagic zooplankton communities have similar levels of spatial turnover in species composition despite differences in the magnitude of environmental gradients and dispersal potential. There were no differences...

Disturbance ecology in a pelagic upwelling biome: Lagrangian frameworks for studying succession

Thu, 18 Jun 2026 00:00:00 +0000

Abstract Disturbance ecology is underdeveloped in marine pelagic ecosystems relative to terrestrial and aquatic benthic habitats, in part because, when measured relative to a fixed location, postdisturbance recovery involves the advection of entire communities in addition to biotic interactions. A Lagrangian frame-of-reference perspective alleviates this issue. Using results from the California Current Ecosystem, we highlight three approaches: in situ Lagrangian, synthetic Lagrangian, and simulated Lagrangian studies. Within a Lagrangian context, extratropical marine heatwaves and El Niños represent press disturbances or alterations to the disturbance regime. Individual upwelling events are more appropriately viewed as pulse disturbances. Upwelling disturbances stimulate rapid growth of pioneer species (diatoms), with herbivores (copepods) lagging these blooms by approximately 3 weeks. The climax community is an assemblage of small low-nutrient specialists with high Shannon diversity....

Elucidating the Role of Marine Benthic Carbon in a Changing World

Thu, 4 Jun 2026 00:00:00 +0000

Abstract The ocean plays a major role in controlling atmospheric carbon at decadal to millennial timescales, with benthic carbon representing the only geologic‐scale storage of oceanic carbon. Despite its importance, detailed benthic ocean observations are limited and representation of the benthic carbon cycle in ocean and Earth system models (ESMs) is mostly empirical with little prognostic capacity, which hinders our ability to properly understand the long‐term evolution of the carbon cycle and climate change‐related feedbacks. The Benthic Ecosystem and Carbon Synthesis (BECS) working group, with the support of the US Ocean Carbon & Biogeochemistry Program (OCB), identified key challenges limiting our understanding of benthic systems, opportunities to act on these challenges, and pathways to increase the representation of these systems in global modeling and observational efforts. We propose a set of priorities to advance mechanistic understanding and better quantify the...

CMIP7 data request: Earth system priorities and opportunities

Thu, 14 May 2026 00:00:00 +0000

Abstract. This paper presents a comprehensive overview of the Coupled Model Intercomparison Project Phase 7 (CMIP7) request for data pertaining to Earth systems science, and provides justification for the resources needed to produce this data. Topics within the CMIP7 Earth System (CMIP7-ES) theme centre around tracking of flows of energy, carbon, water and other fluxes across domains, and constraining feedbacks between these cycles and the climate system. These topics are summarized in this paper as scientific “opportunities” describing specific model intercomparison experiments and use cases for next-generation Earth System Model (ESM) output. These opportunities were submitted by modelling groups and scientific consortia following an extended public consultation process. Contained within each opportunity are requests for groups of Climate & Forecasting (CF) variables, which are bundled into variable groups representing all data required to address...

An Explicit Test of Kill the Winner: Protistan Grazing and Phage Lysis Differentially Impact Fast-Growing Bacterial Taxa in the Coastal Antarctic.

Tue, 17 Feb 2026 00:00:00 +0000

Protists and bacteriophages exert top-down control on bacterial populations. Previous work in the coastal Antarctic demonstrates the potential for intra-seasonal variability of this top-down control driven by the extreme seasonal contrast in bacterial growth rates. We evaluated whether predators kill the winner wherein protists and phages preferentially impact the most abundant members of bacterial assemblages over an austral summer with weekly dilution experiments. Seawater from 10 m was divided into two serial dilutions with either 0.2 μm (to evaluate protist grazing) or 30 kDa (to evaluate protist grazing and lysis from bacteriophage) filtered water. We observed strong intra-seasonal change of bacteriophage and protistan contributions to mortality. A comparison of activity per ASV from amplicon sequencing over our dilution experiments to a predicted minimal doubling time indicates that kill the winner is occurring during the top-down control of only a few bacteria. As not all...

Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae

Wed, 10 Dec 2025 00:00:00 +0000

Phaeocystales, comprising the genus Phaeocystis and an uncharacterized sister lineage, are nanoplanktonic haptophytes widespread in the global ocean. Several species form mucilaginous colonies and influence key biogeochemical cycles, yet their underlying diversity and ecological strategies remain underexplored. Here, we present new genomic data from 13 strains, including three high-quality reference genomes (N50 > 30 kbp), and integrate previous metagenome-assembled genomes to resolve a robust phylogeny. Divergence timing of P. antarctica aligns with Miocene cooling and Southern Ocean isolation. Genomic traits reveal metabolic flexibility, including mixotrophic nitrogen acquisition in temperate waters and gene expansions linked to polar nutrient adaptation. Concordantly, transcriptomic comparisons between temperate and polar Phaeocystis suggest Southern Ocean populations experience iron and B12 limitation. We also identify signatures of horizontal gene transfer and endogenous...

Ocean conditions drive interannual variability in juvenile albacore tuna (Thunnus alalunga) muscle energy content in the California Current System

Fri, 5 Dec 2025 00:00:00 +0000

Juvenile albacore tuna (Thunnus alalunga) undertake long migrations across the North Pacific that they fuel by feeding in the California Current System (CCS) during the summer. The CCS is a highly dynamic system, which can lead to differences in foraging success that may be indicated by differences in body condition. Assessed through stomach content analysis, albacore diet composition by mean proportional weight showed high interannual variability including some years characterized by large increases in consumption of anchovy (2011 = 81%, 2017, 2022) and sardine (Sardinops sagax, 2022). We used a generalized additive model (GAM) to investigate the impact of albacore length, month of collection, diet composition, and environmental conditions on albacore muscle energy content. Two proxies for muscle energy content, the carbon to nitrogen ratio (C:N) and ash free dry weight (AFDW), were positively but weakly correlated. Albacore C:N increased with month, body size, and upwelling...

Osmolyte chemical diversity in Lingulaulax polyedra red tides: a critical overlooked factor to respiratory irritations?

Thu, 4 Dec 2025 00:00:00 +0000

The detrimental effects on human health sometimes observed during blooms of Lingulaulax polyedra have been formerly attributed to the yessotoxin analogs this species produces. In this paper we show that natural concentrations of yessotoxin analogs present in seawater and sea spray aerosols during an unprecedented L. polyedra bloom in 2020 in Southern California did not induce inflammation in mammal macrophage cells, questioning the role played by yessotoxin in causing respiratory irritations. This bloom was associated with unprecedented levels of particulate dimethylsulfoniopropionate (2.74 ± 1.63 to 10.11 ± 1.39 µM), gonyol and several new structural analogs ofgonyol . We profiled the metabolic content of dinoflagellate cells and recorded increasing amounts of quaternary amines of the betaine family (carnitine, actinin, ectoine) as the bloom progressed. Being precursors of sulfur and nitrogenous small volatile compounds, we hypothesize that, in addition to their recognized role...

Phytoplankton dynamics in nearshore regions of the western Antarctic Peninsula in relation to a variable frontal zone in the Gerlache Strait

Tue, 28 Oct 2025 00:00:00 +0000

The Gerlache Strait is a narrow channel that separates the western coast of the Antarctic Peninsula (WAP) from the Palmer Archipelago. This area is characterized by the presence of interconnected fjords, bays, islands, and channels that serve as a refuge for megafauna during summer. Through the framework of FjordPhyto – a citizen science collaboration with the International Association of Antarctica Tour Operators (IAATO) vessels – we assessed phytoplankton biomass and composition in surface waters of six under-explored nearshore areas connected to the Gerlache Strait (between 64° and 65° S) during three consecutive seasons, from November to March (2016–2019). During the first two seasons, we found significant differences in the phytoplankton community distribution and successional patterns to the north and south of the sampling area; the greatest differences were evidenced mainly in the months of high biomass, December and January. During December, cryptophytes bloomed in the...

An undescribed species within the Gymnodinium sensu stricto group found responsible for an exceptional bloom in the Southern Ocean

Tue, 28 Oct 2025 00:00:00 +0000

Naked dinoflagellates are a regular component of the Antarctic phytoplankton but remain poorly studied. In December 2016, the first massive bloom (9.5 × 10⁶ cells · L^-1) of small (~15 μm) naked dinoflagellates was recorded in the western Antarctic Peninsula. To identify these organisms, we performed Illumina next-generation sequencing analysis on field samples to obtain genetic information (SSU rDNA 18SV9 and 16SV4-V5). In addition, we performed polymerase chain reaction (PCR) amplification and Sanger sequencing using dinoflagellate-specific primers (LSU rDNA D1-D3 and ITS/5.8S), as well as traditional light and scanning electron microscopy observations. Phylogenetic analyses revealed that these organisms belonged to the Gymnodinium sensu stricto group and may represent an undescribed species. These analyses also indicated that the observed organisms were closely related to the species Gymnodinium dorsalisulcum, G. impudicum, Barrufeta bravensis, and B. resplendens,...

Can a citizen science project enrich travellers’ experience in Antarctica? Case study of a preliminary evaluation of the FjordPhyto project

Tue, 28 Oct 2025 00:00:00 +0000

Expedition cruise vessels travelling to Antarctica offer several educational opportunities, with Citizen Science (CS) projects being the most prominent way to engage participants in polar science. FjordPhyto is a CS project where travellers onboard expedition cruise vessels gather data and samples for five months (from November to March) during the Antarctic summer season to help researchers understand changes in microalgae communities in response to melting glaciers. Since its inception in 2016, FjordPhyto has involved over 8,000 Antarctic travellers. To understand travellers’ perceptions engaging with the program during its first two years, 81 voluntary feedback surveys were collected from participants during 2017–2018 and 2018–2019 seasons. When analysing open-ended questions, three main themes associated with participant experience emerged: educational, enjoyable, and motivational. Results showed that ‘educational’ was the most frequent category in responses when describing...

Seasonal changes in physical oceanography modulate cetacean predator-prey dynamics in the San Diego Trough

Thu, 28 Aug 2025 00:00:00 +0000

In marine ecosystems, cetaceans are large mobile predators that depend on maximizing foraging efficiency. Their presence within a habitat can therefore be strongly related to the modulation of local prey by oceanographic conditions. Understanding how cetaceans are impacted by prey responses to the physical environment is challenging due to the difficulty of collecting presence data of cetaceans and their prey over long, comparable time periods. We used passive and active acoustic recordings collected from moorings within the San Diego Trough, along with physical oceanographic sampling (i.e. in situ, satellite-derived, and ocean general circulation model measurements), to elucidate relationships between cetaceans, their prey, and the physical environment. Our results show that the predator-prey dynamics of some cetaceans within the San Diego Trough are influenced by seasonal changes in the physical oceanographic conditions and processes that shape their prey resources. Specifically,...

Open Ocean Versus Upwelling Regimes: Air‐Sea CO2 Fluxes and pCO2 Inter‐Annual Variability in the Southern California Current System

Thu, 28 Aug 2025 00:00:00 +0000

Abstract Two moorings equipped with autonomous air‐sea CO 2 instrumentation located in the Southern California Current System were used to examine the seasonal and interannual variability of the surface partial pressure of carbon dioxide in seawater ( p CO 2,sw ) and the air‐sea CO 2 flux between 2008 and 2022. These two moorings are in two distinct oceanographic regimes: offshore, centered in the California Current (CCE1), and nearshore within the coastal upwelling regime (CCE2). The offshore seasonal cycles of the surface p CO 2,sw and CO 2 flux are driven by sea surface temperature (SST) seasonality and at the nearshore site by dissolved inorganic carbon (DIC) concentration changes linked with seasonal upwelling. The resulting net annual CO 2 flux at CCE1 is −0.52 molC m −2 year −1 (sink), while at CCE2, the best estimate for the long‐term CO 2 flux mean is 0.23 molC m −2 year −1 (source). The interannual variability at the offshore site is mainly controlled by...

Assessment of Submarine Groundwater Discharge (SGD) as a Source of Dissolved Radium and Nutrients to Moorea (French Polynesia) Coastal Waters

Mon, 11 Aug 2025 00:00:00 +0000

Previous work has documented large fluxes of freshwater and nutrients from submarine groundwater discharge (SGD) into the coastal waters of a few volcanic oceanic islands. However, on the majority of such islands, including Moorea (French Polynesia), SGD has not been studied. In this study, we used radium (Ra) isotopes and salinity to investigate SGD and associated nutrient inputs at five coastal sites and Paopao Bay on the north shore of Moorea. Ra activities were highest in coastal groundwater, intermediate in coastal ocean surface water, and lowest in offshore surface water, indicating that high-Ra groundwater was discharging into the coastal ocean. On average, groundwater nitrate and nitrite (N + N), phosphate, ammonium, and silica concentrations were 12, 21, 29, and 33 times greater, respectively, than those in coastal ocean surface water, suggesting that groundwater discharge could be an important source of nutrients to the coastal ocean. Ra and salinity mass balances...

Potential impacts of marine carbon dioxide removal on ocean oxygen

Thu, 17 Jul 2025 00:00:00 +0000

Abstract: Global warming is a main cause for current ocean deoxygenation. A deployment of marine carbon dioxide removal (CDR) for mitigating global warming could therefore also be viewed as a measure for mitigating ocean deoxygenation if, and only if, the respective CDR measure itself does not lead to a larger oxygen loss than the reduction in atmospheric CO2 would prevent. We here review the current state of knowledge regarding the potential impacts of various marine CDR (mCDR) options onto ocean oxygen, a key ocean state variable and an essential element for all higher forms of marine life. Using results from global model simulations, we show that biotic approaches, such as ocean fertilization, macroalgae cultivation and sinking, and placement of organic matter that is prone to remineralization, can lead to a loss in seawater dissolved oxygen that is 4–40 times larger than the oxygen gain that would result from the CDR-induced reduction in global warming only....

Deep Fjords Are Excellent Natural Infrastructure for Climate Impact Studies

Thu, 17 Jul 2025 00:00:00 +0000

ABSTRACT: Fjords provide valuable research opportunities for marine scientists. They are excellent natural infrastructure for climate impact studies associated with hypoxic episodes and consequences for mesopelagic and deep‐sea ecosystems involving oceanographic circulation processes and basin water renewals. Repeated sampling from the same populations is possible, making fjords excellent systems for developing time series of data for climate impact studies. We provide an overview of the 14 years of data from Norwegian West Coast fjords, focusing on Masfjorden, and report major findings from Oslofjorden in Eastern Norway, exhibiting recurrent hypoxia in the basin waters. We document that the oxygen levels in Masfjorden decreased rapidly by over 60% at 450 m depth in < 8 years, which is much faster than the average rate of deoxygenation in the global ocean. We also discuss the increase in the deep‐sea and low‐light‐adapted coronate jellyfish Periphylla periphylla in view of...

Illuminating deep-sea considerations and experimental approaches for mCDR proposals

Thu, 17 Jul 2025 00:00:00 +0000

Illuminating deep-sea considerations and experimental approaches for mCDR proposals

Methane-powered sea spiders: Diverse, epibiotic methanotrophs serve as a source of nutrition for deep-sea methane seep Sericosura

Thu, 17 Jul 2025 00:00:00 +0000

Methane seeps harbor uncharacterized animal-microbe symbioses with unique nutritional strategies. Three undescribed sea spider species (family Ammotheidae; genus Sericosura) endemic to methane seeps were found along the eastern Pacific margin, from California to Alaska, hosting diverse methane- and methanol-oxidizing bacteria on their exoskeleton. δ¹³C tissue isotope values of in situ specimens corroborated methane assimilation (-45‰, on average). Live animal incubations with ¹³C-labeled methane and methanol, followed by nanoscale secondary ion mass spectrometry, confirmed that carbon derived from both compounds was actively incorporated into the tissues within five days. Methano- and methylotrophs of the bacterial families Methylomonadaceae, Methylophagaceae and Methylophilaceae were abundant, based on environmental metagenomics and 16S rRNA sequencing, and fluorescence and electron microscopy confirmed dense epibiont aggregations on the sea spider...

Why aquatic deoxygenation belongs in the planetary boundary framework

Thu, 17 Jul 2025 00:00:00 +0000

Why aquatic deoxygenation belongs in the planetary boundary framework

Multi‐Trophic Level Responses to Marine Heatwave Disturbances in the California Current Ecosystem

Mon, 14 Jul 2025 00:00:00 +0000

Marine heatwaves (MHWs) caused by multiple phenomena with days to months duration are increasingly common disturbances in ocean ecosystems. We investigated the impacts of MHWs on pelagic communities using spatially resolved time-series of multiple trophic levels from the Southern California Current Ecosystem. Indices of phytoplankton biomass mostly declined during MHWs because of reduced nutrient supply (excepting Prochlorococcus) and were generally more sensitive to marine heatwave intensity than duration. By contrast, mesozooplankton (as estimated by zooplankton displacement volume) were somewhat more strongly correlated with MHW duration than intensity. Zooplankton anomalies were also positively correlated with fucoxanthin (diatom) anomalies, highlighting possible bottom-up influences during MHWs. Mobile consumers (forage fish) showed more complex responses, with fish egg abundance declining during MHWs but not correlating with any MHW characteristics. Our findings provide...

Estimating Directional Wave Spectra Properties in Nonbreaking Waves from a UAS-Mounted Multibeam Lidar

Thu, 3 Jul 2025 00:00:00 +0000

Abstract: Wave spectra and directional moment measurements are of scientific and engineering interest and are routinely estimated with wave buoys. Recently, both fixed-location and uncrewed aircraft system (UAS)-mounted lidar have estimated surfzone wave spectra. However, nearshore wave statistics seaward of the surfzone have not been measured with lidar due to low return number, and nearshore directional moments have not been measured at all. We use a multibeam scanning lidar mounted on a gasoline-powered UAS to estimate wave spectra, wave slope spectra, and directional moments on the inner shelf in ≈10-m water depth from an 11-min hover and compare to a collocated wave buoy. Lidar returns within circular sampling regions with varying radius R are fit to a plane and a 2D parabola, providing sea surface and slope time series. Wave spectra across the sea–swell (0.04–0.4 Hz) band are robustly estimated for R ≥ 0.8 m. Estimating slope spectra is more challenging. Large R works...

Climatic and economic fluctuations revealed by decadal ocean soundscapes

Thu, 19 Jun 2025 00:00:00 +0000

Decadal variations of ocean soundscapes are intricately linked to large-scale climatic and economic fluctuations. This study draws on over 15 years of acoustic recordings at six sites within the Southern California Bight, investigating interannual, seasonal, and diel variations. By examining acoustic energy from fin and blue whales along with sounds from ships and wind, we identified changes in soundscape over time and space. This study reveals that sound levels associated with both biological and non-biological sound sources varied seasonally and correlated with large-scale climatic patterns and long-term oceanographic fluctuations. Baleen whale sound levels before, during, and after a marine heatwave were assessed; sound levels decreased in southern sites and increased in northern sites adjacent to the California Current, underscoring the potential for range shifts and habitat compression during warm years for these species. Ship-generated sound levels at high-traffic sites...

Yessotoxin production and aerosolization during the unprecedented red tide of 2020 in southern California

Thu, 19 Jun 2025 00:00:00 +0000

An April–May 2020 bloom of the red tide microalga Lingulodinium polyedra developed to an unprecedented size, extending from northern Baja California to the Santa Barbara Channel. The L. polyedra strain is native to coastal California and is known to produce low levels of a toxic di-sulfated polyether named yessotoxin (YTX). In order to assess the evolution of the YTX content throughout the bloom and its transfer to water and aerosols, the concentration of YTX analogs was measured in the particulate and the dissolved organic matter of the sea surface water as well as in onshore sea spray aerosols. The YTX cell content was characteristic of Californian strains of L. polyedra. A lower production of YTX analogs by the cells at the peak of the bloom was detected, yielding total YTX content (particulate + dissolved) ranging from below the detection limit to 6.89 ng L−1 at that time. Yessotoxin and homo-yessotoxin were detected in sea spray aerosol measured onshore (from below detection...

Informing the spatial management of Silky Shark (Carcharhinus falciformis) in the Eastern Pacific Ocean

Tue, 13 May 2025 00:00:00 +0000

Abstract: The Silky Shark (Carcharhinus falciformis) is highly vulnerable to population decline, yet leads shark bycatch in some of the world’s largest tuna fisheries. As such, this species provides an appropriate case study for regional fisheries management organizations—exemplified by the Inter-American Tropical Tuna Commission—to develop conceptual population assessment frameworks that integrate diverse data streams to elucidate population structure and dynamics of assessed species. Using genetic, movement, life history, and small- and large-scale fishery-dependent data from across much of the Silky Shark’s Pacific Ocean range, we found preliminary evidence for a three-stock model—southern, central, and northern—in the eastern Pacific Ocean (EPO). Length distributions of Silky Sharks varied with latitude and across fishery gears and strategies. The predominance of small juveniles, including neonates, caught on or near the continental shelf by small-scale fisheries...

Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection

Mon, 12 May 2025 00:00:00 +0000

Many eukaryotic viruses require membrane-bound compartments for replication, but no such organelles are known to be formed by prokaryotic viruses. Bacteriophages of the Chimalliviridae family sequester their genomes within a phage-generated organelle, the phage nucleus, which is enclosed by a lattice of the viral protein ChmA. We show that inhibiting phage nucleus formation arrests infections at an early stage in which the injected phage genome is enclosed within a membrane-bound early phage infection (EPI) vesicle. Early phage genes are expressed from the EPI vesicle, demonstrating its functionality as a prokaryotic, transcriptionally active, membrane-bound organelle. We also show that the phage nucleus is essential, with genome replication beginning after the injected DNA is transferred from the EPI vesicle to the phage nucleus. Our results show that Chimalliviridae require two sophisticated subcellular compartments of distinct compositions and functions that facilitate successive...

A Mercury Times Series in the Southern California Upwelling Region

Thu, 8 May 2025 00:00:00 +0000

A Mercury Times Series in the Southern California Upwelling Region

Dethiothermospora halolimnae gen. nov., sp. nov., a novel moderately halophilic, thermotolerant, bacterium isolated from a brine lake

Thu, 8 May 2025 00:00:00 +0000

A novel, strictly anaerobic, slightly alkaliphilic, halotolerant, peptide- and amino acid-utilizing bacterial strain, SD1^T, was isolated from a hypersaline lake in Western Australia. The strain stained Gram-negative and was a motile, spore-forming rod. The strain grew between 15 and 50 °C (optimum 40 °C), 1-15% w/v sodium chloride (optimum 5%) and pH 6.0-10.0 (optimum 9.0). Major fatty acids included anteiso-C15 : 0 (24.9%), C14 : 0 dimethyl acetyl (13.2%), anteiso-C15 : 0 dimethyl acetyl (11.5%) and iso-C15 : 0 (10.4%). The DNA G+C content was 30.3 mol%. The isolate did not grow using any tested sugars but grew well on arginine and glycine. It is capable of using elemental sulfur and thiosulfate as alternate electron acceptors, but not sulfide, sulfate, nitrate or nitrite. 16S rRNA gene similarity indicates that the isolate is related to Sporosalibacterium tautonense MRo-4^T (94.33% identity). SD1^T showed 76.18%-76.31% average nucleotide...

Resource partitioning among pelagic predators remains stable despite annual variability in diet composition

Thu, 10 Apr 2025 00:00:00 +0000

Diet data are critical for describing predator resource use and partitioning among competitors. However, time series needed to properly assess variability in resource use and partitioning are limited, especially in pelagic (open ocean) ecosystems where predators and prey make broad use of horizontal and vertical habitats. We examined a diet time series spanning two decades (1998-2018) consisting of 2749 stomachs from 10 pelagic predators in the southern California Current Ecosystem (SCCE): albacore tuna (Thunnus alalunga), Pacific bluefin tuna (Thunnus orientalis), swordfish (Xiphias gladius), blue shark (Prionace glauca), shortfin mako (Isurus oxyrinchus), common thresher shark (Alopias vulpinus), bigeye thresher shark (Alopias superciliosus), short-beaked common dolphin (Delphinus delphis), long-beaked common dolphin (Delphinus capensis) and northern right whale dolphin (Lissodelphis borealis). We quantified feeding habits with respect to prey taxonomy, length, vertical habitat...

Continuing Long‐Term Shifts in Larval Fish Phenology in the Southern California Current Ecosystem Are Matched by Rapid Advances in the North

Thu, 10 Apr 2025 00:00:00 +0000

Changing environmental conditions are leading to shifts in the timing of seasonal events globally. In the ocean, environmental cues affecting larval fish (ichthyoplankton) abundance may not be synchronized with factors optimizing larval and juvenile survival, making the study of ichthyoplankton phenology in the context of a changing environment critical. In the southern California Current Ecosystem (CCE), a major eastern boundary current upwelling system, significant long-term shifts in larval fish phenology have been previously observed. To assess the stability of these estimates and extend them to the northern CCE, we evaluated multidecadal trends in ichthyoplankton abundance for 57 species from the California Cooperative Oceanic Fisheries Investigations (CalCOFI) and 25 species from the Newport Hydrographic Line (NH Line). We show that on average, larval fish phenology in the southern CCE has continued to advance with an estimated rate of -0.18 ± 0.05 day year^-1...

Continuing Long‐Term Shifts in Larval Fish Phenology in the Southern California Current Ecosystem Are Matched by Rapid Advances in the North

Mon, 7 Apr 2025 00:00:00 +0000

Light cues drive community-wide transcriptional shifts in the hypersaline South Bay Salt Works

Fri, 4 Apr 2025 00:00:00 +0000

The transition from day to night brings sweeping change to both environments and the organisms within them. Diel shifts in gene expression have been documented across all domains of life but remain understudied in microbial communities, particularly those in extreme environments where small changes may have rippling effects on resource availability. In hypersaline environments, many prominent taxa are photoheterotrophs that rely on organic carbon for growth but can also generate significant ATP via light-powered rhodopsins. Previous research demonstrated a significant response to light intensity shifts in the model halophile Halobacterium salinarum, but these cycles have rarely been explored in situ. Here, we examined genome-resolved differential expression in a hypersaline saltern (water activity (aw)≅$$\cong$$0.83, total dissolved solids = 250.7 g L−1) throughout a 24-h period. We found increased transcription of genes related to phototrophy and anabolic metabolic processes...

Transportome remodeling of a symbiotic microalga inside a planktonic host

Tue, 1 Apr 2025 00:00:00 +0000

Metabolic exchange is one of the foundations of symbiotic associations between organisms and is a driving force in evolution. In the ocean, photosymbiosis between heterotrophic hosts and microalgae is powered by photosynthesis and relies on the transfer of organic carbon to the host (e.g. sugars). Yet, the identity of transferred carbohydrates as well as the molecular mechanisms that drive this exchange remain largely unknown, especially in unicellular photosymbioses that are widespread in the open ocean. Combining genomics, single-holobiont transcriptomics, and environmental metatranscriptomics, we revealed the transportome of the marine microalga Phaeocystis in symbiosis within acantharia, with a focus on sugar transporters. At the genomic level, the sugar transportome of Phaeocystis is comparable to non-symbiotic haptophytes. By contrast, we found significant remodeling of the expression of the transportome in symbiotic microalgae compared to the free-living stage. More particularly,...

Performance of a One-Dimensional Model of Wave-Driven Nearshore Alongshore Tracer Transport and Decay with Applications for Dry Weather Coastal Pollution

Tue, 1 Apr 2025 00:00:00 +0000

Dry weather pollution sources cause coastal water quality problems that are not accounted for in existing beach advisory metrics. A 1D wave-driven advection and loss model was developed for a 30 km nearshore domain spanning the United States/Mexico border region. Bathymetric nonuniformities, such as the inlet and shoal near the Tijuana River estuary mouth, were neglected. Nearshore alongshore velocities were estimated by using wave properties at an offshore location. The 1D model was evaluated using the hourly output of a 3D regional hydrodynamic model. The 1D model had high skill in reproducing the spatially averaged alongshore velocities from the 3D model. The 1D and 3D models agreed on tracer exceedance or nonexceedance above a human illness probability threshold for 87% of model time steps. 1D model tracer was well-correlated with targeted water samples tested for DNA-based human fecal indicators. This demonstrates that a simple, computationally fast, 1D nearshore wave-driven...

Metal mining on land versus the ocean in the context of the current Biodiversity Crisis

Thu, 27 Mar 2025 00:00:00 +0000

Metal mining on land versus the ocean in the context of the current Biodiversity Crisis

Draft Genome Sequence of Desulfurobacterium sp. Strain AV08, a Thermophilic Chemolithoautotroph Isolated from a Deep-Sea Hydrothermal Vent

Tue, 18 Mar 2025 00:00:00 +0000

A thermophilic chemolithoautotrophic bacterium was isolated from vent fluids at Axial Seamount, an active deep-sea volcano in the northeast Pacific Ocean. We present the draft genome sequence of Desulfurobacterium sp. strain AV08.

Ocean Observing in California: 2024 Conference Summary Report

Thu, 13 Mar 2025 00:00:00 +0000

Ocean Observing in California: 2024 Conference Summary Report

Maternal Effects and Trophodynamics Drive Interannual Larval Growth Variability of Atlantic Bluefin Tuna (Thunnus thynnus) from the Gulf of Mexico

Fri, 31 Jan 2025 00:00:00 +0000

Two cohorts of Atlantic bluefin tuna (Thunnus thynnus) larvae were sampled in 2017 and 2018 during the peak of spawning in the Gulf of Mexico (GOM). We examined environmental variables, daily growth, otolith biometry and stable isotopes and found that the GOM18 cohort grew at faster rates, with larger and wider otoliths. Inter and intra-population analyses (deficient vs. optimal growth groups) were carried out for pre- and post-flexion developmental stages to determine maternal and trophodynamic influences on larval growth variability based on larval isotopic signatures, trophic niche sizes and their overlaps. For the pre-flexion stages in both years, the optimal growth groups had significantly lower δ¹⁵N, implying a direct relationship between growth potential and maternal inheritance. Optimal growth groups and stages for both years showed lower C:N ratios, reflecting a greater energy investment in growth. The results of this study illustrate the interannual...

A faunal inventory of methane seeps on the Pacific margin of Costa Rica

Thu, 30 Jan 2025 00:00:00 +0000

The methane seeps on the Pacific margin of Costa Rica support extensive animal diversity and offer insights into deep-sea biogeography. During five expeditions between 2009 and 2019, we conducted intensive faunal sampling via 63 submersible dives to 11 localities at depths of 300-3600 m. Based on these expeditions and published literature, we compiled voucher specimens, images, and 274 newly published DNA sequences to present a taxonomic inventory of macrofaunal and megafaunal diversity with a focus on invertebrates. In total 488 morphospecies were identified, representing the highest number of distinct morphospecies published from a single seep or vent region to date. Of these, 131 are described species, at least 58 are undescribed species, and the remainder include some degree of taxonomic uncertainty, likely representing additional undescribed species. Of the described species, 38 are known only from the Costa Rica seeps and their vicinity. Fifteen range extensions are also...

Applying a two-stage generalized synthetic control approach to quantify the heterogeneous health effects of extreme weather events: A 2018 large wildfire in California event as a case study

Sun, 26 Jan 2025 00:00:00 +0000

Extreme weather events, including wildfires, are becoming more intense, frequent, and expansive due to climate change, thus increasing negative health outcomes. However, such effects can vary across space, time, and population subgroups, requiring methods that can handle multiple exposed units, account for time-varying confounding, and capture heterogeneous treatment effects. In this article, we proposed an approach based on staggered generalized synthetic control methods to study heterogeneous health effects, using the 2018 California wildfire season as a case study. This study aimed to estimate the effects of the November 2018 California wildfires, one of the state's deadliest and most destructive wildfire seasons, on respiratory and circulatory health, document heterogeneity in health impacts, and investigate drivers of this heterogeneity. We applied a two-stage generalized synthetic control method to compare health outcomes in exposed (from 8 November to 5 December 2018) versus...

Effects of Mesoscale Eddies on Southern Ocean Biogeochemistry

Thu, 5 Dec 2024 00:00:00 +0000

The Southern Ocean is rich in highly dynamic mesoscale eddies and substantially modulates global biogeochemical cycles. However, the overall surface and subsurface effects of eddies on the Southern Ocean biogeochemistry have not been quantified observationally at a large scale. Here, we co-locate eddies, identified in the Meta3.2DT satellite altimeter-based product, with biogeochemical Argo floats to determine the effects of eddies on the dissolved inorganic carbon (DIC), nitrate, and dissolved oxygen concentrations in the upper 1,500 m of the ice-free Southern Ocean, as well as the eddy effects on the carbon fluxes in this region. DIC and nitrate concentrations are lower in anticyclonic eddies (AEs) and increased in cyclonic eddies (CEs), while dissolved oxygen anomalies switch signs above (CEs: positive, AEs: negative) and below the mixed layer (CEs: negative, AEs: positive). We attribute these anomalies primarily to eddy pumping (isopycnal heave), as well as eddy trapping...

Deepening the Decade: Collaborative Action for Advancing Deep‐Ocean Science and Policy in the United Nations Decade of Ocean Science for Sustainable Development

Thu, 5 Dec 2024 00:00:00 +0000

Abstract The current United Nations Decade of Ocean Science for Sustainable Development (2021–2030; hereafter, the Decade) offers a unique opportunity and framework to globally advance ocean science and policy. Achieving meaningful progress within the Decade requires collaboration and coordination across Decade Actions (Programs, Projects, and Centres). This coordination is particularly important for the deep ocean, which remains critically under‐sampled compared to other ecosystems. Despite the limited sampling, the deep ocean accounts for over 95% of Earth's habitable space, plays a crucial role in regulating the carbon cycle and global temperatures, and supports diverse ecosystems. To collectively advance deep‐ocean science, we gathered representatives from 20 Decade Actions that focus at least partially on the deep ocean. We identified five broad themes that aim to advance deep‐ocean science in alignment with the Decade's overarching 10 Challenges: natural capital and the...

Reviews and syntheses: Biological Indicators of Oxygen Stress in Water Breathing Animals

Thu, 5 Dec 2024 00:00:00 +0000

Abstract. Anthropogenic warming and nutrient over-enrichment of our oceans have resulted in significant, and often catastrophic, reductions in dissolved oxygen (deoxygenation). Stress on water-breathing animals from this deoxygenation has been shown to occur at all levels of biological organization: cellular; organ; individual; species; population; community; and ecosystem. Most climate forecasts predict increases in ocean deoxygenation, thus it is essential to develop reliable biological indicators of oxygen stress that can be used by regional and global oxygen monitoring efforts to detect and assess the impacts of deoxygenation on ocean life. This review focuses on indicators of low-oxygen stress that are manifest at different levels of biological organization and at a variety of spatial and temporal scales. We compare particular attributes of these indicators to the dissolved oxygen threshold of response, time-scales of response, sensitive life stages and taxa, and the ability...

Future directions for deep ocean climate science and evidence-based decision making

Wed, 4 Dec 2024 00:00:00 +0000

A defining aspect of the Intergovernmental Panel on Climate Change (IPCC) assessment reports (AR) is a formal uncertainty language framework that emphasizes higher certainty issues across the reports, especially in the executive summaries and short summaries for policymakers. As a result, potentially significant risks involving understudied components of the climate system are shielded from view. Here we seek to address this in the latest, sixth assessment report (AR6) for one such component—the deep ocean—by summarizing major uncertainties (based on discussions of low confidence issues or gaps) regarding its role in our changing climate system. The goal is to identify key research priorities to improve IPCC confidence levels in deep ocean systems and facilitate the dissemination of IPCC results regarding potentially high impact deep ocean processes to decision-makers. This will accelerate improvement of global climate projections and aid in informing efforts to mitigate climate...

The persistent DDT footprint of ocean disposal, and ecological controls on bioaccumulation in fishes

Sat, 16 Nov 2024 00:00:00 +0000

Globally, ocean dumping of chemical waste is a common method of disposal and relies on the assumption that dilution, diffusion, and dispersion at ocean scales will mitigate human exposure and ecosystem impacts. In southern California, extensive dumping of agrochemical waste, particularly chlorinated hydrocarbon contaminants such as DDT, via sewage outfalls and permitted offshore barging occurred for most of the last century. This study compiled a database of existing sediment and fish DDT measurements to examine how this unique legacy of regional ocean disposal translates into the contemporary contamination of the coastal ocean. We used spatiotemporal modeling to derive continuous estimates of sediment DDT contamination and show that the spatial signature of disposal (i.e., high loadings near historic dumping sites) is highly conserved in sediments. Moreover, we demonstrate that the proximity of fish to areas of high sediment loadings explained over half of the variation in fish...

Deep-ocean macrofaunal assemblages on ferromanganese and phosphorite-rich substrates in the Southern California Borderland

Mon, 11 Nov 2024 00:00:00 +0000

Mineral-rich hardgrounds, such as ferromanganese (FeMn) crusts and phosphorites, occur on seamounts and continental margins, gaining attention for their resource potential due to their enrichment in valuable metals in some regions. This study focuses on the Southern California Borderland (SCB), an area characterized by uneven and heterogeneous topography featuring FeMn crusts, phosphorites, basalt, and sedimentary rocks that occur at varying depths and are exposed to a range of oxygen concentrations. Due to its heterogeneity, this region serves as an optimal setting for investigating the relationship between mineral-rich hardgrounds and benthic fauna. This study characterizes the density, diversity, and community composition of macrofauna (>300 μm) on hardgrounds as a function of substrate type and environment (depth and oxygen ranges). Rocks and their macrofauna were sampled quantitatively using remotely operated vehicles (ROVs) during expeditions in 2020 and 2021 at depths...

Microbial community composition predicts bacterial production across ocean ecosystems

Sat, 9 Nov 2024 00:00:00 +0000

Microbial ecological functions are an emergent property of community composition. For some ecological functions, this link is strong enough that community composition can be used to estimate the quantity of an ecological function. Here, we apply random forest regression models to compare the predictive performance of community composition and environmental data for bacterial production (BP). Using data from two independent long-term ecological research sites-Palmer LTER in Antarctica and Station SPOT in California-we found that community composition was a strong predictor of BP. The top performing model achieved an R2 of 0.84 and RMSE of 20.2 pmol L-1 hr-1 on independent validation data, outperforming a model based solely on environmental data (R2 = 0.32, RMSE = 51.4 pmol L-1 hr-1). We then operationalized our top performing model, estimating BP for 346 Antarctic samples from 2015 to 2020 for which only community composition data were available. Our...

Molecular forecasting of domoic acid during a pervasive toxic diatom bloom

Fri, 8 Nov 2024 00:00:00 +0000

In 2015, the largest recorded harmful algal bloom (HAB) occurred in the Northeast Pacific, causing nearly 100 million dollars in damages to fisheries and killing many protected marine mammals. Dominated by the toxic diatom Pseudo-nitzschia australis, this bloom produced high levels of the neurotoxin domoic acid (DA). Through molecular and transcriptional characterization of 52 near-weekly phytoplankton net-tow samples collected at a bloom hotspot in Monterey Bay, California, we identified active transcription of known DA biosynthesis (dab) genes from the three identified toxigenic species, including P. australis as the primary origin of toxicity. Elevated expression of silicon transporters (sit1) during the bloom supports the previously hypothesized role of dissolved silica (Si) exhaustion in contributing to bloom physiology and toxicity. We find that coexpression of the dabA and sit1 genes serves as a robust predictor of DA one week in...

Endemic, cosmopolitan, and generalist taxa and their habitat affinities within a coastal marine microbiome

Tue, 5 Nov 2024 00:00:00 +0000

The relative prevalence of endemic and cosmopolitan biogeographic ranges in marine microbes, and the factors that shape these patterns, are not well known. Using prokaryotic and eukaryotic amplicon sequence data spanning 445 near-surface samples in the Southern California Current region from 2014 to 2020, we quantified the proportion of taxa exhibiting endemic, cosmopolitan, and generalist distributions in this region. Using in-situ data on temperature, salinity, and nitrogen, we categorized oceanic habitats that were internally consistent but whose location varied over time. In this context, we defined cosmopolitan taxa as those that appeared in all regional habitats and endemics as taxa that only appeared in one habitat. Generalists were defined as taxa occupying more than one but not all habitats. We also quantified each taxon’s habitat affinity, defined as habitats where taxa were significantly more abundant than expected. Approximately 20% of taxa exhibited endemic...

Ecosystem service values support conservation and sustainable land development: Perspectives from four University of California campuses

Wed, 11 Sep 2024 00:00:00 +0000

Urban landscapes homogenize our world at global scales, contributing to “extinction of experience”, a progressive decline in human interactions with native greenspace that can disconnect people from the services it provides. College age adults report feeling disconnected from nature more than other demographics, making universities a logical place to explore interventions intended to restore a connection with nature. This study surveyed 1088 students and staff across four university campus communities in Southern California, USA and used multicriteria decision analysis to explore their landscape preferences and the implications of those preferences for combatting extinction of experience. Our results suggest that perspectives of, and preferences for, different greenspace forms vary significantly (i.e., they are not perceived as substitutable). Support for native ecosystems, particularly coastal sage scrub (top ranked landscape) was generally high, suggesting that disaffection...

Changes in microbial community structure of bio‐fouled polyolefins over a year‐long seawater incubation in Hawai'i

Tue, 27 Aug 2024 00:00:00 +0000

Plastic waste, especially positively buoyant polymers known as polyolefins, are a major component of floating debris in the marine environment. While plastic colonisation by marine microbes is well documented from environmental samples, the succession of marine microbial community structure over longer time scales (> > 1 month) and across different types and shapes of plastic debris is less certain. We analysed 16S rRNA and 18S rRNA amplicon gene sequences from biofilms on polyolefin debris floating in a flow-through seawater tank in Hawai'i to assess differences in microbial succession across the plastic types of polypropylene (PP) and both high-density polyethylene (HDPE) and low-density polyethylene (LDPE) made of different plastic shapes (rod, film and cube) under the same environmental conditions for 1 year. Regardless of type or shape, all plastic debris were dominated by the eukaryotic diatom Nitzschia, and only plastic type was significantly important for bacterial...

Metatranscriptomic response of deep ocean microbial populations to infusions of oil and/or synthetic chemical dispersant

Tue, 27 Aug 2024 00:00:00 +0000

Oil spills are a frequent perturbation to the marine environment that has rapid and significant impacts on the local microbiome. Previous studies have shown that exposure to synthetic dispersant alone did not enhance heterotrophic microbial activity or oxidation rates of specific hydrocarbon components but increased the abundance of some taxa (e.g., Colwellia). In contrast, exposure to oil, but not dispersants, increased the abundance of other taxa (e.g., Marinobacter) and stimulated hydrocarbon oxidation rates. Here, we advance these findings by interpreting metatranscriptomic data from this experiment to explore how and why specific components of the microbial community responded to distinct organic carbon exposure regimes. Dispersant alone was selected for a unique community and for dominant organisms that reflected treatment- and time-dependent responses. Dispersant amendment also led to diverging functional profiles among the different treatments. Similarly,...

Flexible B12 ecophysiology of Phaeocystis antarctica due to a fusion B12–independent methionine synthase with widespread homologues

Fri, 16 Aug 2024 00:00:00 +0000

Coastal Antarctic marine ecosystems are significant in carbon cycling because of their intense seasonal phytoplankton blooms. Southern Ocean algae are primarily limited by light and iron (Fe) and can be co-limited by cobalamin (vitamin B₁₂). Micronutrient limitation controls productivity and shapes the composition of blooms which are typically dominated by either diatoms or the haptophyte Phaeocystis antarctica. However, the vitamin requirements and ecophysiology of the keystone species P. antarctica remain poorly characterized. Using cultures, physiological analysis, and comparative omics, we examined the response of P. antarctica to a matrix of Fe-B₁₂ conditions. We show that P. antarctica is not auxotrophic for B₁₂, as previously suggested, and identify mechanisms underlying its B₁₂ response in cultures of predominantly solitary and colonial cells. A combination of proteomics and proteogenomics reveals...

Impact of Spatial Variability in Zooplankton Grazing Rates on Carbon Export Flux

Thu, 15 Aug 2024 00:00:00 +0000

Abstract: The biological carbon pump is a key controller of how much carbon is stored within the global ocean. This pathway is influenced by food web interactions between zooplankton and their prey. In global biogeochemical models, Holling Type functional responses are frequently used to represent grazing interactions. How these responses are parameterized greatly influences biomass and subsequent carbon export estimates. The half‐saturation constant, or k value, is central to the Holling functional response. Empirical studies show k can vary over three orders of magnitude, however, this variation is poorly represented in global models. This study derives zooplankton grazing dynamics from remote sensing products of phytoplankton biomass, resulting in global distribution maps of the grazing parameter k. The impact of these spatially varying k values on model skill and carbon export flux estimates is then considered. This study finds large spatial variation in k values across the...

From nutrients to fish: Impacts of mesoscale processes in a global CESM-FEISTY eddying ocean model framework

Thu, 15 Aug 2024 00:00:00 +0000

From nutrients to fish: Impacts of mesoscale processes in a global CESM-FEISTY eddying ocean model framework

Scenario setup and forcing data for impact model evaluation and impact attribution within the third round of the Inter-Sectoral Model Intercomparison Project (ISIMIP3a)

Thu, 15 Aug 2024 00:00:00 +0000

Abstract. This paper describes the rationale and the protocol of the first component of the third simulation round of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP3a, http://www.isimip.org, last access: 2 November 2023) and the associated set of climate-related and direct human forcing data (CRF and DHF, respectively). The observation-based climate-related forcings for the first time include high-resolution observational climate forcings derived by orographic downscaling, monthly to hourly coastal water levels, and wind fields associated with historical tropical cyclones. The DHFs include land use patterns, population densities, information about water and agricultural management, and fishing intensities. The ISIMIP3a impact model simulations driven by these observation-based climate-related and direct human forcings are designed to test to what degree the impact models can explain observed changes in natural and human systems. In a second set of ISIMIP3a...

Ziphius cavirostris presence relative to the vertical and temporal variability of oceanographic conditions in the Southern California Bight

Fri, 2 Aug 2024 00:00:00 +0000

The oceanographic conditions of the Southern California Bight (SCB) dictate the distribution and abundance of prey resources and therefore the presence of mobile predators, such as goose-beaked whales (Ziphius cavirostris). Goose-beaked whales are deep-diving odontocetes that spend a majority of their time foraging at depth. Due to their cryptic behavior, little is known about how they respond to seasonal and interannual changes in their environment. This study utilizes passive acoustic data recorded from two sites within the SCB to explore the oceanographic conditions that goose-beaked whales appear to favor. Utilizing optimum multiparameter analysis, modeled temperature and salinity data are used to identify and quantify these source waters: Pacific Subarctic Upper Water (PSUW), Pacific Equatorial Water (PEW), and Eastern North Pacific Central Water (ENPCW). The interannual and seasonal variability in goose-beaked whale presence was related to the variability in El Niño...

Diversity and Detection of Nitrate Assimilation Genes in Marine Bacteria

Fri, 2 Aug 2024 00:00:00 +0000

A PCR approach was used to construct a database of nasA genes (called narB genes in cyanobacteria) and to detect the genetic potential for heterotrophic bacterial nitrate utilization in marine environments. A nasA-specific PCR primer set that could be used to selectively amplify the nasA gene from heterotrophic bacteria was designed. Using seawater DNA extracts obtained from microbial communities in the South Atlantic Bight, the Barents Sea, and the North Pacific Gyre, we PCR amplified and sequenced nasA genes. Our results indicate that several groups of heterotrophic bacterial nasA genes are common and widely distributed in oceanic environments.

Understanding and valuing human connections to deep-sea methane seeps off Costa Rica

Thu, 1 Aug 2024 00:00:00 +0000

Methane seeps are highly productive ecosystems that provide carbon sequestration services, host diverse communities including endemic species, and serve as habitats for commercial fisheries. Little is known about the economic value the public places on them. Discrete Choice Experiments (DCEs) are administered to a sample of Costa Rican taxpayers to evaluate their willingness to pay (WTP) in monetary terms using tradeoffs made in a survey context involving three of the main attributes of methane seep ecosystems to provide insights for future conservation and management efforts. Extensive effort is devoted to understanding how Costa Ricans view different aspects of the deep sea. We find that they associate it with strange animals, natural resources, the unknown, and being far from reach. Perhaps surprisingly, they underestimate how much they know about the deep sea. We find that WTP for methane seep protection is the highest for programs that protect seeps with endemic species,...

Improving impact assessments to reduce impacts of deep-sea fisheries on vulnerable marine ecosystems

Thu, 1 Aug 2024 00:00:00 +0000

Improving impact assessments to reduce impacts of deep-sea fisheries on vulnerable marine ecosystems

Sperm whale demographics in the Gulf of Alaska and Bering Sea/Aleutian Islands: An overlooked female habitat

Fri, 19 Jul 2024 00:00:00 +0000

Sperm whales exhibit sexual dimorphism and sex-specific latitudinal segregation. Females and their young form social groups and are usually found in temperate and tropical latitudes, while males forage at higher latitudes. Historical whaling data and rare sightings of social groups in high latitude regions of the North Pacific, such as the Gulf of Alaska (GOA) and Bering Sea/Aleutian Islands (BSAI), suggest a more complex distribution than previously understood. Sperm whales are the most sighted and recorded cetacean in marine mammal surveys in these regions but capturing their demographic composition and habitat use has proven challenging. This study detects sperm whale presence using passive acoustic data from seven sites in the GOA and BSAI from 2010 to 2019. Differences in click characteristics between males and females (i.e., inter-click and inter-pulse interval) was used as a proxy for animal size/sex to derive time series of animal detections. Generalized additive models...

Machine learning with taxonomic family delimitation aids in the classification of ephemeral beaked whale events in passive acoustic monitoring

Mon, 24 Jun 2024 00:00:00 +0000

Passive acoustic monitoring is an essential tool for studying beaked whale populations. This approach can monitor elusive and pelagic species, but the volume of data it generates has overwhelmed researchers' ability to quantify species occurrence for effective conservation and management efforts. Automation of data processing is crucial, and machine learning algorithms can rapidly identify species using their sounds. Beaked whale acoustic events, often infrequent and ephemeral, can be missed when co-occurring with signals of more abundant, and acoustically active species that dominate acoustic recordings. Prior efforts on large-scale classification of beaked whale signals with deep neural networks (DNNs) have approached the class as one of many classes, including other odontocete species and anthropogenic signals. That approach tends to miss ephemeral events in favor of more common and dominant classes. Here, we describe a DNN method for improved classification of beaked whale...

Relative Roles of Plume and Coastal Forcing on Exchange Flow Variability of a Glacial Fjord

Thu, 20 Jun 2024 00:00:00 +0000

Abstract: Glacial fjord circulation determines the import of oceanic heat to the Greenland Ice Sheet and the export of ice sheet meltwater to the ocean. However, limited observations and the presence of both glacial and coastal forcing—such as coastal‐trapped waves—make uncovering the physical mechanisms controlling fjord‐shelf exchange difficult. Here we use multi‐year, high‐resolution, realistically forced numerical simulations of Sermilik Fjord in southeast Greenland to evaluate the exchange flow. We compare models, with and without a plume, to differentiate between the exchange flow driven by shelf variability and that driven by subglacial discharge. We use the Total Exchange Flow framework to quantify the exchange volume transports. We find that a decline in offshore wind stress from January through July drives a seasonal reversal in the exchange flow increasing the presence of warm Atlantic Water at depth. We also find that including glacial plumes doubles the exchange...

Insights from the management of offshore energy resources: Toward an ecosystem-services based management approach for deep-ocean industries

Thu, 20 Jun 2024 00:00:00 +0000

The deep ocean comprises complex ecosystems made up of numerous community and habitat types that provide multiple services that benefit humans. As the industrialization of the deep sea proceeds, a standardized and robust set of methods and metrics need to be developed to monitor the baseline conditions and any anthropogenic and climate change-related impacts on biodiversity, ecosystem function, and ecosystem services. Here, we review what we have learned from studies involving offshore-energy industries, including state-of-the-art technologies and strategies for obtaining reliable metrics of deep-sea biodiversity and ecosystem function. An approach that includes the detection and monitoring of ecosystem services, with open access to baseline data from multiple sectors, can help to improve our global capacity for the management of the deep ocean.

Where’s Whaledo: A software toolkit for array localization of animal vocalizations

Mon, 10 Jun 2024 00:00:00 +0000

Where's Whaledo is a software toolkit that uses a combination of automated processes and user interfaces to greatly accelerate the process of reconstructing animal tracks from arrays of passive acoustic recording devices. Passive acoustic localization is a non-invasive yet powerful way to contribute to species conservation. By tracking animals through their acoustic signals, important information on diving patterns, movement behavior, habitat use, and feeding dynamics can be obtained. This method is useful for helping to understand habitat use, observe behavioral responses to noise, and develop potential mitigation strategies. Animal tracking using passive acoustic localization requires an acoustic array to detect signals of interest, associate detections on various receivers, and estimate the most likely source location by using the time difference of arrival (TDOA) of sounds on multiple receivers. Where's Whaledo combines data from two small-aperture volumetric arrays and a...

An essential and highly selective protein import pathway encoded by nucleus-forming phage

Thu, 30 May 2024 00:00:00 +0000

Targeting proteins to specific subcellular destinations is essential in prokaryotes, eukaryotes, and the viruses that infect them. Chimalliviridae phages encapsulate their genomes in a nucleus-like replication compartment composed of the protein chimallin (ChmA) that excludes ribosomes and decouples transcription from translation. These phages selectively partition proteins between the phage nucleus and the bacterial cytoplasm. Currently, the genes and signals that govern selective protein import into the phage nucleus are unknown. Here, we identify two components of this protein import pathway: a species-specific surface-exposed region of a phage intranuclear protein required for nuclear entry and a conserved protein, PicA (Protein importer of chimalliviruses A), that facilitates cargo protein trafficking across the phage nuclear shell. We also identify a defective cargo protein that is targeted to PicA on the nuclear periphery but fails to enter the nucleus, providing insight...

From microbial community structure to metabolic inference using paprica

Mon, 27 May 2024 00:00:00 +0000

Microbial taxonomic marker gene studies using 16S rRNA gene amplicon sequencing provide an understanding of microbial community structure and diversity; however, it can be difficult to infer the functionality of microbes in the ecosystem from these data. Here, we show how to predict metabolism from phylogeny using the paprica pipeline. This approach allows resolution at the strain and species level for select regions on the prokaryotic phylogenetic tree and provides an estimate of gene and metabolic pathway abundance. For complete details on the use and execution of this protocol, please refer to Erazo and Bowman (2021).

Using low volume eDNA methods to sample pelagic marine animal assemblages

Thu, 23 May 2024 00:00:00 +0000

Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380-1800 mL) collected at depths of 0-2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability...

Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron.

Fri, 17 May 2024 00:00:00 +0000

Iron is an essential nutrient for all microorganisms of the marine environment. Iron limitation of primary production has been well documented across a significant portion of the global surface ocean, but much less is known regarding the potential for iron limitation of the marine heterotrophic microbial community. In this work, we characterize the transcriptomic response of the heterotrophic bacterial community to iron additions in the California Current System, an eastern boundary upwelling system, to detect in situ iron stress of heterotrophic bacteria. Changes in gene expression in response to iron availability by heterotrophic bacteria were detected under conditions of high productivity when carbon limitation was relieved but when iron availability remained low. The ratio of particulate organic carbon to dissolved iron emerged as a biogeochemical proxy for iron limitation of heterotrophic bacteria in this system. Iron stress was characterized by high expression levels of...

Editorial: Constraining uncertainties in hindcasts and future projections of marine deoxygenation

Thu, 25 Apr 2024 00:00:00 +0000

Editorial: Constraining uncertainties in hindcasts and future projections of marine deoxygenation

Modeling future cliff-front waves during sea level rise and implications for coastal cliff retreat rates

Mon, 15 Apr 2024 00:00:00 +0000

It is often assumed that future coastal cliff retreat rates will accelerate as global sea level rises, but few studies have investigated how SLR (sea level rise) might change cliff-front wave dynamics. Using a new simple numerical model, this study simulates the number and type (breaking, broken, or unbroken) of cliff-front waves under future SLR scenarios. Previous research shows breaking waves deliver more energy to cliffs than broken waves, and unbroken waves generate minimal impact. Here, we investigated six cliff-platform profiles from three regions (USA, New Zealand, and UK) with varied tidal ranges and wave climates. Model inputs included 2013–2100 hindcast/forecast incident wave height and tidal water level, and three future SLR scenarios. Results show the number of both cliff-front breaking and broken waves generally increase for a high-elevation (relative to tide) cliff-platform junction. In contrast, breaking/broken wave occurrence decrease by 38–92% for a near-horizontal...

Sub-frontal niches of plankton communities driven by transport and trophic interactions at ocean fronts

Thu, 11 Apr 2024 00:00:00 +0000

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...

Anchovy booms and busts linked to trophic shifts in larval diet

Thu, 11 Apr 2024 00:00:00 +0000

Abstract: Biomass fluctuations of small coastal-pelagic fishes represent perhaps the most iconic temporal record of the impacts of natural climate variability on marine ecosystems1,2,3. These fishes are key constituents of the marine pelagic food web as primary feeders on plankton, prey to higher trophic level foragers such as birds, marine mammals, piscivore fishes4,5 and valued for human consumption and industry6. Despite over a century of research, the mechanisms governing their population volatility remain elusive7,8. Here, we use a 45-year record of nitrogen stable isotopes measured in larvae of Northern Anchovy (Engraulis mordax) in the California Current to assess patterns in food chain length. Larval trophic efficiency associated with a shortened food chain increased for boom periods of high adult biomass, during which the ratio of large to small larvae decreased by an order of magnitude. In contrast, the ratio increased during periods of low adult biomass, likely...

Multidecadal changes in ocean transparency: Decrease in a coastal upwelling region and increase offshore

Thu, 11 Apr 2024 00:00:00 +0000

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...

A 37-year record of ocean acidification in the Southern California current

Thu, 11 Apr 2024 00:00:00 +0000

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...

Climate change considerations are fundamental to management of deep‐sea resource extraction

Mon, 8 Apr 2024 00:00:00 +0000

Climate change manifestation in the ocean, through warming, oxygen loss, increasing acidification, and changing particulate organic carbon flux (one metric of altered food supply), is projected to affect most deep-ocean ecosystems concomitantly with increasing direct human disturbance. Climate drivers will alter deep-sea biodiversity and associated ecosystem services, and may interact with disturbance from resource extraction activities or even climate geoengineering. We suggest that to ensure the effective management of increasing use of the deep ocean (e.g., for bottom fishing, oil and gas extraction, and deep-seabed mining), environmental management and developing regulations must consider climate change. Strategic planning, impact assessment and monitoring, spatial management, application of the precautionary approach, and full-cost accounting of extraction activities should embrace climate consciousness. Coupled climate and biological modeling approaches applied in the water...

Understanding vessel noise across a network of marine protected areas

Mon, 1 Apr 2024 00:00:00 +0000

Protected areas are typically managed as a network of sites exposed to varying anthropogenic conditions. Managing these networks benefits from monitoring of conditions across sites to help prioritize coordinated efforts. Monitoring marine vessel activity and related underwater radiated noise impacts across a network of protected areas, like the U.S. National Marine Sanctuary system, helps managers ensure the quality of habitats used by a wide range of marine species. Here, we use underwater acoustic detections of vessels to quantify different characteristics of vessel noise at 25 locations within eight marine sanctuaries including the Hawaiian Archipelago and the U.S. east and west coasts. Vessel noise metrics, including temporal presence and sound levels, were paired with Automatic Identification System (AIS) vessel tracking data to derive a suite of robust vessel noise indicators for use across the network of marine protected areas. Network-wide comparisons revealed a spectrum...

The rise in climate change-induced federal fishery disasters in the United States

Fri, 22 Mar 2024 00:00:00 +0000

Commercial, recreational, and indigenous fisheries are critical to coastal economies and communities in the United States. For over three decades, the federal government has formally recognized the impact of fishery disasters via federal declarations. Despite these impacts, national syntheses of the dynamics, impacts, and causes of fishery disasters are lacking. We developed a nationwide Federal Fishery Disaster database using National Oceanic and Atmospheric Administration (NOAA) fishery disaster declarations and fishery revenue data. From 1989-2020, there were 71 federally approved fishery disasters (eleven are pending), which spanned every federal fisheries management region and coastal state in the country. To date, we estimate fishery disasters resulted in $2B (2019 USD) in Congressional allocations, and an additional, conservative estimate of $3.2B (2019 USD) in direct revenue loss. Despite this scale of impact, the disaster assistance process is largely ad hoc and lacks...

Modeling the past, present, and future distributions of endangered white abalone (Haliotis sorenseni) to inform recovery efforts in California

Fri, 22 Mar 2024 00:00:00 +0000

White abalone (Haliotis sorenseni) was once commonly found in coastal waters of the Southern California Bight (SCB) and south to Punta Abreojos, Baja California, Mexico. During the 1970s, white abalone supported a commercial fishery, which reduced the population and resulted in the closure of the fishery in 1996. When population levels continued to decline, National Marine Fisheries Service (NMFS) listed the species as endangered under the Endangered Species Act. The California Department of Fish and Wildlife and NMFS began surveying the wild populations, propagating specimens in captivity, and protecting its seabed habitat. We modeled coarse-scale (17 x 17 km) historical (using fishery-dependent data [1955-1996]) and contemporary (using fishery-independent data [1996-2017]) distributions of white abalone throughout its historical domain using random forests and maximum entropy (MaxEnt), respectively, and its fine-scale (10 x 10 m) contemporary distribution (fishery-independent...

Spatial ecology of the Giant Sea Bass, Stereolepis gigas, in a southern California kelp forest as determined by acoustic telemetry

Fri, 22 Mar 2024 00:00:00 +0000

The fisheries history of the Giant Sea Bass, Stereolepis gigas (Telostei: Polyprionidae), is closely linked to its spatial ecology. Its overharvest is directly associated with formation of spatially distinct spawning aggregations during summer, while its subsequent recovery is hypothesized to be the result of spatially explicit gear restrictions. Understanding the spatial ecology of Giant Sea Bass is a key part of efforts to assess contemporary threats such as commercial harvest and incidental catch by recreational fisheries. In this study, we used acoustic telemetry to characterize Giant Sea Bass space use in the La Jolla kelp forest using an acoustic array that encompasses two marine protected areas (MPAs) and heavily trafficked recreational fishing grounds. Five of the seven fish we tagged remained in the La Jolla array for at least 6 months. Two fish were resident across multiple years, with one fish consistently detected for 4 years. Only one fish was detected in the...

Protected fish spawning aggregations as self-replenishing reservoirs for regional recovery

Fri, 22 Mar 2024 00:00:00 +0000

Dispersal of eggs and larvae from spawning sites is critical to the population dynamics and conservation of marine fishes. For overfished species like critically endangered Nassau grouper (Epinephelus striatus), recovery depends on the fate of eggs spawned at the few remaining aggregation sites. Biophysical models can predict larval dispersal, yet these rely on assumed values of key parameters, such as diffusion and mortality rates, which have historically been difficult or impossible to estimate. We used in situ imaging to record three-dimensional positions of individual eggs and larvae in proximity to oceanographic drifters released into egg plumes from the largest known Nassau grouper spawning aggregation. We then estimated a diffusion-mortality model and applied it to previous years' drifter tracks to evaluate the possibility of retention versus export to nearby sites within 5 days of spawning. Results indicate that larvae were retained locally in 2011 and 2017,...

Organismal responses to deteriorating water quality during the historic 2020 red tide off Southern California

Thu, 21 Mar 2024 00:00:00 +0000

In April and May of 2020, a large phytoplankton bloom composed primarily of the dinoflagellate Lingulodinium polyedra reached historic levels in geographic expanse, duration, and density along the coast of southern California, United States, and Baja California Norte, Mexico. Here, we report the water quality parameters of dissolved oxygen and pH over the course of the red tide, as measured by multiple sensors deployed in various locations along San Diego County, and document the extent of mass organism mortality using field surveys and community science observations. We found that dissolved oxygen and pH corresponded with bloom dynamics, with extreme hypoxic and hyperoxic conditions occurring at multiple locations along the coast, most notably within select estuaries where dissolved oxygen reached 0 mg L−1 and hypoxia occurred for up to 254 consecutive hours, as well as along the inner shelf of the open coast where dissolved oxygen dropped as low as 0.05 mg L−1. Similarly, pH...

Rising sea levels and the increase of shoreline wave energy at American Samoa

Tue, 19 Mar 2024 00:00:00 +0000

American Samoa is experiencing rapid relative sea level rise due to increases in global sea level and significant post-2009 earthquake land subsidence, endangering homes and critical infrastructure. Wave and water-level observations collected over a fringing reef at Faga‘itua Bay, American Samoa, in 2017 reveal depth-limited shoreline sea-swell wave heights over the range of conditions sampled. Using field data to calibrate a one-dimensional, phase-resolving nonhydrostatic wave model (SWASH), we examine the influence of water level on wave heights over the reef for a range of current and future sea levels. Assuming a fixed reef bathymetry, model results predict rising sea levels will escalate nearshore extreme water levels that are dominated by an increase in nearshore sea-swell wave heights. Model results provide insight into how and at what reef depths rising sea levels reduce reef capacity to dissipate wave energy, compounding shoreline threats. This study aims to bring increased...

Wave, light, and dissolved oxygen exposures drive novel coastal eelgrass (Zostera pacifica) transplant performance

Thu, 29 Feb 2024 00:00:00 +0000

The high ecological and economic value of seagrass has been long recognized, with these foundational habitats providing myriad ecosystem services. Yet through cumulative anthropogenic impacts, seagrasses are exhibiting extensive declines globally. A litany of studies and active restoration trials have demonstrated practical methodologies to restore seagrass habitats and effectively return critical habitat functions to degraded coastal zone systems worldwide. Seagrass loss along the U.S. West Coast has precipitated decades of seagrass protection, conservation, and restoration efforts. Yet, mitigation transplanting efforts have prioritized Zostera marina (narrow-leaved eelgrass) in shallow, protected environments, while a dearth of information is available on species inhabiting offshore islands and exposed mainland coasts. In this study, we conducted a novel transplant of Zostera pacifica, a wide-leaved species found in depths of 7 – 20 m along the offshore islands and mainland...

The Ocean as a Classroom: Considering the Roles of Equity, Diversity, and Justice in Oceanographic Knowledge Production to Promote Accessibility for Future Generations

Thu, 29 Feb 2024 00:00:00 +0000

Understanding the history of how we studied our ocean in the past and how we study it now will help us develop approaches to make future oceanographic knowledge production more diverse, accessible, and inclusive. The motto of the UN Decade of Ocean Science for Sustainable Development (2021–2030) is, “The ocean we need for the future we want” (Singh et al., 2021). The Ocean Decade gives the ocean sciences community an opportunity to change the way it conducts research, to use ocean science to support sustainable development, and to energize the ocean sciences for future generations. With these goals in mind, we developed an introductory level, student-led graduate seminar that builds on the Ocean Decade framework. A research cruise involving seminar participants followed the seminar sessions. Here, we discuss how we conducted the seminar and highlight directions that are needed to energize future generations of ocean leaders and make ocean science more equitable, inclusive, and...

Development of Embryonic Market Squid, Doryteuthis opalescens, under Chronic Exposure to Low Environmental pH and [O2]

Sun, 25 Feb 2024 00:00:00 +0000

The market squid, Doryteuthis opalescens, is an important forage species for the inshore ecosystems of the California Current System. Due to increased upwelling and expansion of the oxygen minimum zone in the California Current Ecosystem, the inshore environment is expected to experience lower pH and [O2] conditions in the future, potentially impacting the development of seafloor-attached encapsulated embryos. To understand the consequences of this co-occurring environmental pH and [O2] stress for D. opalescens encapsulated embryos, we performed two laboratory experiments. In Experiment 1, embryo capsules were chronically exposed to a treatment of higher (normal) pH (7.93) and [O2] (242 μM) or a treatment of low pH (7.57) and [O2] (80 μM), characteristic of upwelling events and/or La Niña conditions. The low pH and low [O2] treatment extended embryo development duration by 5-7 days; embryos remained at less developed stages more often and had 54.7% smaller statolith area at a...

Predicted metabolic roles and stress responses provide insights into candidate phyla Hydrogenedentota and Sumerlaeota as members of the rare biosphere in biofilms from various environments

Thu, 22 Feb 2024 00:00:00 +0000

Pustular mats from Shark Bay, Western Australia, host complex microbial communities bound within an organic matrix. These mats harbour many poorly characterized organisms with low relative abundances (<1%), such as candidate phyla Hydrogenedentota and Sumerlaeota. Here, we aim to constrain the metabolism and physiology of these candidate phyla by analyzing two representative metagenome-assembled genomes (MAGs) from a pustular mat. Metabolic reconstructions of these MAGs suggest facultatively anaerobic, chemoorganotrophic lifestyles of both organisms and predict that both MAGs can metabolize a diversity of carbohydrate substrates. Ca. Sumerlaeota possesses genes involved in degrading chitin, cellulose and other polysaccharides, while Ca. Hydrogenedentota can metabolize cellulose derivatives in addition to glycerol, fatty acids and phosphonates. Both Ca. phyla can respond to nitrosative stress and participate in nitrogen metabolism. Metabolic comparisons of MAGs from Shark Bay...

Trait-based indicators of resource selection by albacore tuna in the California Current Large Marine Ecosystem

Thu, 15 Feb 2024 00:00:00 +0000

As global climate change reorganizes marine ecosystems, understanding how predators will respond to variable prey resources is critical to forecasting future community dynamics. Prey traits that affect the foraging process and recur across unrelated taxa offer a means to better anticipate predator resource use by simplifying complex foraging dynamics. Here we compare taxonomic and trait-based indicators of resource use and selection for albacore tuna (Thunnus alalunga), a commercially valuable pelagic predator undergoing climate-driven range shifts. We synthesized datasets from 2005 to 2019 to evaluate diets of albacore tuna in relation to prey availability estimates from shipboard surveys in the California Current Large Marine Ecosystem. Analyses with these data reveal that albacore and trawl surveys sample different aspects of the pelagic system, with albacore consuming a subset of taxa identified within trawls. Albacore consistently selected coastal prey that are schooling,...

Skillful multiyear prediction of marine habitat shifts jointly constrained by ocean temperature and dissolved oxygen

Mon, 5 Feb 2024 00:00:00 +0000

The ability to anticipate marine habitat shifts responding to climate variability has high scientific and socioeconomic value. Here we quantify interannual-to-decadal predictability of habitat shifts by combining trait-based aerobic habitat constraints with a suite of initialized retrospective Earth System Model forecasts, for diverse marine ecotypes in the North American Large Marine Ecosystems. We find that aerobic habitat viability, defined by joint constraints of temperature and oxygen on organismal energy balance, is potentially predictable in the upper-600 m ocean, showing a substantial improvement over a simple persistence forecast. The skillful multiyear predictability is dominated by the oxygen component in most ecosystems, yielding higher predictability than previously estimated based on temperature alone. Notable predictability differences exist among ecotypes differing in temperature sensitivity of hypoxia vulnerability, especially along the northeast coast with predictability...

The Pelagic Species Trait Database, an open data resource to support trait-based ocean research

Fri, 19 Jan 2024 00:00:00 +0000

Trait-based frameworks are increasingly used for predicting how ecological communities respond to ongoing global change. As species range shifts result in novel encounters between predators and prey, identifying prey ‘guilds’, based on a suite of shared traits, can distill complex species interactions, and aid in predicting food web dynamics. To support advances in trait-based research in open-ocean systems, we present the Pelagic Species Trait Database, an extensive resource documenting functional traits of 529 pelagic fish and invertebrate species in a single, open-source repository. We synthesized literature sources and online resources, conducted morphometric analysis of species images, as well as laboratory analyses of trawl-captured specimens to collate traits describing 1) habitat use and behavior, 2) morphology, 3) nutritional quality, and 4) population status information. Species in the dataset primarily inhabit the California Current system and broader NE Pacific Ocean,...

New framework reveals gaps in US ocean biodiversity protection

Thu, 18 Jan 2024 00:00:00 +0000

New framework reveals gaps in US ocean biodiversity protection

A space‐for‐time framework for forecasting the effects of ocean stratification on zooplankton vertical habitat use and trait composition

Thu, 18 Jan 2024 00:00:00 +0000

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...

Single-cell analysis in hypersaline brines predicts a water-activity limit of microbial anabolic activity

Mon, 15 Jan 2024 00:00:00 +0000

Hypersaline brines provide excellent opportunities to study extreme microbial life. Here, we investigated anabolic activity in nearly 6000 individual cells from solar saltern sites with water activities (a_w) ranging from 0.982 to 0.409 (seawater to extreme brine). Average anabolic activity decreased exponentially with a_w, with nuanced trends evident at the single-cell level: The proportion of active cells remained high (>50%) even after NaCl saturation, and subsets of cells spiked in activity as a_w decreased. Intracommunity heterogeneity in activity increased as seawater transitioned to brine, suggesting increased phenotypic heterogeneity with increased physiological stress. No microbial activity was detected in the 0.409-a_w brine (an MgCl₂-dominated site) despite the presence of cell-like structures. Extrapolating our data, we predict an a_w limit for detectable anabolic activity...

Anchovy boom and bust linked to trophic shifts in larval diet

Sat, 23 Dec 2023 00:00:00 +0000

Although massive biomass fluctuations of coastal-pelagic fishes are an iconic example of the impacts of climate variability on marine ecosystems, the mechanisms governing these dynamics are often elusive. We construct a 45-year record of nitrogen stable isotopes measured in larvae of Northern Anchovy (Engraulis mordax) in the California Current Ecosystem to assess patterns in food chain length. Larval trophic efficiency associated with a shortened food chain increased larval survival and produced boom periods of high adult biomass. In contrast, when larval food chain length increased, and energy transfer efficiency decreased, the population crashed. We propose the Trophic Efficiency in Early Life (TEEL) hypothesis, which states that larval fishes must consume prey that confer sufficient energy for survival, to help explain natural boom-bust dynamics of coastal pelagic fishes. Our findings illustrate a potential for trophic indicators to generally inform larval survival and adult...

Progress and challenges in exploring aquatic microbial communities using non-targeted metabolomics

Tue, 12 Dec 2023 00:00:00 +0000

Advances in bioanalytical technologies are constantly expanding our insights into complex ecosystems. Here, we highlight strategies and applications that make use of non-targeted metabolomics methods in aquatic chemical ecology research and discuss opportunities and remaining challenges of mass spectrometry-based methods to broaden our understanding of environmental systems.

Wide-Area Debris Field and Seabed Characterization of a Deep Ocean Dump Site Surveyed by Autonomous Underwater Vehicles

Wed, 29 Nov 2023 00:00:00 +0000

Disposal of industrial and hazardous waste in the ocean was a pervasive global practice in the 20th century. Uncertainty in the quantity, location, and contents of dumped materials underscores ongoing risks to marine ecosystems and human health. This study presents an analysis of a wide-area side-scan sonar survey conducted with autonomous underwater vehicles (AUVs) at a dump site in the San Pedro Basin, California. Previous camera surveys located 60 barrels and other debris. Sediment analysis in the region showed varying concentrations of the insecticidal chemical dichlorodiphenyltrichloroethane (DDT), of which an estimated 350-700 t were discarded in the San Pedro Basin between 1947 and 1961. A lack of primary historical documents specifying DDT acid waste disposal methods has contributed to the ambiguity surrounding whether dumping occurred via bulk discharge or containerized units. Barrels and debris observed during previous surveys were used for ground truth classification...