Oceanographic and biological effects of shoaling of the oxygen minimum zone

The vulnerability of sharks, skates, and rays to ocean deoxygenation: Physiological mechanisms, behavioral responses, and ecological impacts

Levels of dissolved oxygen in open ocean and coastal waters are decreasing (ocean deoxygenation), with poorly understood effects on marine megafauna. All of the more than 1000 species of elasmobranchs (sharks, skates, and rays) are obligate water breathers, with a variety of life-history strategies and oxygen requirements. This review demonstrates that although many elasmobranchs typically avoid hypoxic water, they also appear capable of withstanding mild to moderate hypoxia with changes in activity, ventilatory responses, alterations to circulatory and hematological parameters, and morphological alterations to gill structures. However, such strategies may be insufficient to withstand severe, progressive, or prolonged hypoxia or anoxia where anaerobic metabolic pathways may be used for limited periods. As water temperatures increase with climate warming, ectothermic elasmobranchs will exhibit elevated metabolic rates and are likely to be less able to tolerate the effects of even mild hypoxia associated with deoxygenation. As a result, sustained hypoxic conditions in warmer coastal or surface-pelagic waters are likely to lead to shifts in elasmobranch distributions. Mass mortalities of elasmobranchs linked directly to deoxygenation have only rarely been observed but are likely underreported. One key concern is how reductions in habitat volume as a result of expanding hypoxia resulting from deoxygenation will influence interactions between elasmobranchs and industrial fisheries. Catch per unit of effort of threatened pelagic sharks by longline fisheries, for instance, has been shown to be higher above oxygen minimum zones compared to adjacent, normoxic regions, and attributed to vertical habitat compression of sharks overlapping with increased fishing effort. How a compound stressor such as marine heatwaves alters vulnerability to deoxygenation remains an open question. With over a third of elasmobranch species listed as endangered, a priority for conservation and management now lies in understanding and mitigating ocean deoxygenation effects in addition to population declines already occurring from overfishing.

Aquatic connectivity: challenges and solutions in a changing climate

The challenge of managing aquatic connectivity in a changing climate is exacerbated in the presence of additional anthropogenic stressors, social factors, and economic drivers. Here we discuss these issues in the context of structural and functional connectivity for aquatic biodiversity, specifically fish, in both the freshwater and marine realms. We posit that adaptive management strategies that consider shifting baselines and the socio-ecological implications of climate change will be required to achieve management objectives. The role of renewable energy expansion, particularly hydropower, is critically examined for its impact on connectivity. We advocate for strategic spatial planning that incorporates nature-positive solutions, ensuring climate mitigation efforts are harmonized with biodiversity conservation. We underscore the urgency of integrating robust scientific modelling with stakeholder values to define clear, adaptive management objectives. Finally, we call for innovative monitoring and predictive decision-making tools to navigate the uncertainties inherent in a changing climate, with the goal of ensuring the resilience and sustainability of aquatic ecosystems.

Hg and Se in Muscle and Liver of Blue Shark (Prionace glauca) from the Entrance of the Gulf of California: An Insight to the Potential Risk to Human Health

The blue shark (Prionace glauca) is the most commonly caught species of Elasmobranchii at the entrance to the Gulf of California. Although fins are the primary target commodity, the entire organism is consumed. This study examined the concentration of Hg and Se in muscle and liver to understand the antagonistic process that occurs between these two elements within the organism. Twenty-two individuals were captured at the Gulf of California inlet between September 2019 and March 2021. Hg was measured by cold vapor atomic absorption, and Se by atomic absorption spectrophotometry in a graphite furnace. All individuals studied showed higher concentrations (µg g-1 wet weight) of Hg (0.69) and Se (2.49) in liver than in muscle (Hg 0.63 and Se 0.08). Although the mean Hg values were below the maximum allowable limits (Hg 1.0 µg g-1 wet weight), the molar ratio (< 1.0) and the negative health benefit value of selenium (HBVSe) in muscle show that additional caution should be taken when consuming this species. We recommend a more thorough study of the antagonistic interaction between Hg and Se to accurately assess the health risk for consumers of blue shark.

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

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 timescale ranging from 2 to 10 years. This tool will be critical in predicting marine habitat shifts in face of a changing climate.

MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets

Our knowledge of viral sequence space has exploded with advancing sequencing technologies and large-scale sampling and analytical efforts. Though archaea are important and abundant prokaryotes in many systems, our knowledge of archaeal viruses outside of extreme environments is limited. This largely stems from the lack of a robust, high-throughput, and systematic way to distinguish between bacterial and archaeal viruses in datasets of curated viruses. Here we upgrade our prior text-based tool (MArVD) via training and testing a random forest machine learning algorithm against a newly curated dataset of archaeal viruses. After optimization, MArVD2 presented a significant improvement over its predecessor in terms of scalability, usability, and flexibility, and will allow user-defined custom training datasets as archaeal virus discovery progresses. Benchmarking showed that a model trained with viral sequences from the hypersaline, marine, and hot spring environments correctly classified 85% of the archaeal viruses with a false detection rate below 2% using a random forest prediction threshold of 80% in a separate benchmarking dataset from the same habitats.

Three stages in the variation of the depth of hypoxia in the California Current System 2003-2020 by satellite estimation

The depth of hypoxia (DOH) is the shallowest depth at which the waters become hypoxic (oxygen concentration < 60 μmol kg^-1), is a crucial indicator of the formation and expansion of oxygen minimum zones (OMZs). In this study, a nonlinear polynomial regression inversion model was developed to estimate the DOH in the California Current System (CCS), based on the dissolved oxygen profile detected by the Biogeochemical-Argo (BGC-Argo) float and remote sensing data. Satellite-derived net community production was used in the algorithm development, to denote the combined effect of phytoplankton photosynthesis and O₂ consumption. Our model performs well, with a coefficient of determination of 0.82 and a root mean square error of 37.69 m (n = 80) from November 2012 to August 2016. Then, it was used to reconstruct the variation in satellite-derived DOH in the CCS from 2003 to 2020, and three stages of the DOH variation trend were identified. From 2003 to 2013, the DOH showed a significant shallowing trend due to the intense subsurface O₂ consumption caused by strong phytoplankton production in the CCS coastal region. The trend was interrupted by two successive strong climate oscillation events from 2014 to 2016, which led to a significant deepening of the DOH and a slowing, or even reversal, of the variations in other environmental parameters. After 2017, the effects of climate oscillation events gradually disappeared, and the shallowing pattern in the DOH recovered slightly. However, by 2020, the DOH had not returned to the pre-2014 shallowing characteristic, which would lead to continuing complex ecosystem responses in the context of global warming. Based on the satellite inversion model of DOH in the CCS, we provide a new insight on the high-resolution spatiotemporal OMZ variations during an 18-year period in the CCS, which will aid in the evaluation and prediction of local ecosystems variation.

Carbon sequestration by multiple biological pump pathways in a coastal upwelling biome

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

Acoustic micronektonic distribution and density is structured by macroscale oceanographic processes across 17-48° N latitudes in the North Atlantic Ocean

This study investigates the large-scale distribution patterns of the acoustic scattering layers and micronekton density across the Northeast Atlantic Ocean during daylight hours. A research cruise on board R/V "Kronprins Haakon" was conducted during May 2019 from Cape Verde to Bay of Biscay. Hydrological data were obtained at 20 conductivity-temperature-depth sensor (CTD) stations. To estimate the micronekton densities in front of the trawl, an autonomous echo sounder (120 or 200 kHz) on the headrope of the macroplankton trawl was used. Acoustic data were also collected along the cruise track using ship-mounted multi-frequency echo sounders (backscatter at 18 and 38 kHz was analyzed). Acoustic observations (both at 18, 38 and 120/200 kHz) showed clear patterns in the horizontal distribution of the micronekton during daytime with higher backscatter and echo densities in the south of the study area (from 17 to 37° N), and the absence of high backscatter in the surface from 37 to 45° N. Backscatter and echo densities were found to be significantly influenced by: temperature, salinity, and oxygen, as well as depth and time of the day.

Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin

Secondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds. Here, we use metagenomics and metatranscriptomics to analyze BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela. We recovered 565 bacterial and archaeal metagenome-assembled genomes (MAGs) and identified 1154 diverse BGCs. We show that differences in water redox potential and microbial lifestyle (particle-associated vs. free-living) are associated with variations in the predicted composition and production of secondary metabolites. Our results indicate that microbes, including understudied clades such as Planctomycetota, potentially produce a wide range of secondary metabolites in these anoxic/euxinic waters.

Vertical Microbial Profiling of Arabian Sea Oxygen Minimal Zone Reveals Complex Bacterial Communities and Distinct Functional Implications

Arabian Sea harbours one of the largest oxygen minimal zones (OMZs) among the global oceans wherein biogeochemical cycles are regulated through dominant and complex microbial processes. The present study investigated the bacterial communities at various depths of the Arabian Sea OMZ using high-throughput sequencing of the v3-v4 hyper variable region of 16S rRNA gene. A total of 10 samples which included water samples from 8 different depths and 2 sediment samples were analyzed in this study. About 2.7 million sequences were obtained from all the samples. The sequence analysis revealed high bacterial diversity at deep waters and sediment samples and comparatively less species richness at the core OMZ depths. Number of OTUs ranged from 114 to 14441.Taxonomic assignments of the obtained OTUs showed dominant presence of Proteobacteria, Bacteriodetes, and Chloroflexi across all the samples. The identified OTUs were further affiliated to the phyla Marinimicrobia, Colwellia, Nitrospina, Tepidicaulis, Shewanella, Pseudoalteromonas, Woeseia at various depths along the water column. Correlation with abiotic factors suggested distinct variation in bacterial community composition with change in depth and dissolved oxygen (DO) levels. Predictive functional annotation based on bacterial phylotypes suggested presence of active nitrogen, sulphur, carbon, and methane metabolic cycles along the vertical transect of the studied region. Presence of nitrogen reduction bacterial group below the core OMZ depths may potentially provide insight into the expansion of OMZ region in Arabian Sea. Functional profiling further revealed presence of genes related to xenobiotic degradation in the water and sediment samples indicating a potential hotspot for bio-prospection.

Oxygen sensing and transcriptional regulation under hypoxia exposure in the mollusk Crassostrea gigas

Hypoxia caused by global climate change and anthropogenic pollution has exposed marine species to increasing stress. Oxygen sensing mediated by prolyl hydroxylase (PHD) is regarded as the first line of defense under hypoxia exposure; however, the function of PHD in marine molluscan species remains unclear. In this study, we identified two PHD2 gene in the oyster Crassostrea gigas using phylogenetic tree analysis with 36 species, namely, CgPHD2A/B. Under hypoxia, the mRNA and protein expression of CgPHD2A displayed a time-dependent pattern, revealing a critical role in the response to hypoxia-induced stress. Observation of interactions between CgPHD2 and CgHIF-1α proteins under normoxia using co-immunoprecipitation and GST-pull down experiments showed that the β2β3 loop in CgPHD2A hydroxylates CgHIF-1α to promote its ubiquitination with CgVHL. With the protein recombination and site-directed mutagenesis, the hydroxylation domain and two target proline loci (P404A and 504A) in CgPHDs and CgHIF-1α were identified respectively. Moreover, the electrophoretic mobility-shift assay (EMSA) and luciferase double reporter gene assay revelaed that CgHIF-1α could regulate CgPHD2A expression through binding with the hypoxia-responsive element in the promoter region (320 bp upstream), forming a feedback loop. However, protein structure analysis indicated that six extra amino acids formed an α-helix in the β2β3 loop of CgPHD2B, inhibiting its activity. Overall, this study revealed that two CgPHD2 proteins have evolved, which encode enzymes with different activities in oyster, potentially representing a specific hypoxia-sensing mechanism in mollusks. Illustrating the functional diversity of CgPHDs could help to assess the physiological status of oyster and guide their aquaculture.

Oxygen Variability in the Offshore Northern Benguela Upwelling System From Glider Data

Despite their role in modulating the marine ecosystem, variability and drivers of low-oxygen events in the offshore northern Benguela Upwelling System (BenUS) have been rarely investigated due to the events' episodicity which is difficult to resolve using shipboard measurements. We address this issue using 4 months of high-resolution glider data collected between February and June 2018, 100 km offshore at 18°S. We find that oxygen (O₂) concentrations in the offshore northern Benguela are determined by the subsurface alternation of low-oxygen Angola-derived water and oxygenated water from the south at 100-500 m depth. We observe intermittent hypoxia (O₂ < 60 μmol kg^-1) which occurs on average for ∼30% of the 4 months deployment and is driven by the time-varying subsurface pulses of Angola-derived tropical water. Hypoxic events are rather persistent at depths of 300-450 m, while they are more sporadic and have weekly duration at shallower depths (100-300 m). We find extreme values of hypoxia, with O₂ minima of 16 μmol kg^-1, associated with an anticyclonic eddy spinning from the undercurrent flowing on the BenUS shelf and showing no surface signature. Fine-scale patchiness and water mass mixing are associated with cross-frontal stirring by a large anticyclone recirculating tropical water into the northern BenUS. The dominance of physical drivers and their high variability on short time scales reveal a dynamic coupling between Angola and Benguela, calling for long-term and high-resolution measurements and studies focusing on future changes of both tropical O₂ minima and lateral fluxes in this region.

Using deep-sea images to examine ecosystem services associated with methane seeps

Deep-sea images are routinely collected during at-sea expeditions and represent a repository of under-utilized knowledge. We leveraged dive videos collected by the remotely-operated vehicle Hercules (deployed from E/V Nautilus, operated by the Ocean Exploration Trust), and adapted biological trait analysis, to develop an approach that characterizes ecosystem services. Specifically, fisheries and climate-regulating services related to carbon are assessed for three southern California methane seeps: Point Dume (∼725 m), Palos Verdes (∼506 m), and Del Mar (∼1023 m). Our results enable qualitative intra-site comparisons that suggest seep activity influences ecosystem services differentially among sites, and site-to-site comparisons that suggest the Del Mar site provides the highest relative contributions to fisheries and carbon services. This study represents a first step towards ecosystem services characterization and quantification using deep-sea images. The results presented herein are foundational, and continued development should help guide research and management priorities by identifying potential sources of ecosystem services.

Elevated Mercury Concentrations and Isotope Signatures (N, C, Hg) in Yellowfin Tuna (Thunnus albacares) from the Galápagos Marine Reserve and Waters off Ecuador

We examined how dietary factors recorded by C and N influence Hg uptake in 347 individuals of yellowfin tuna (Thunnus albacares), an important subsistence resource from the Galápagos Marine Reserve (Ecuador) and the Ecuadorian mainland coast in 2015-2016. We found no differences in total Hg (THg) measured in red muscle between the two regions and no seasonal differences, likely due to the age of the fish and slow elimination rates of Hg. Our THg concentrations are comparable to those of other studies in the Pacific (0.20-9.60 mg/kg wet wt), but a subset of individuals exhibited the highest Hg concentrations yet reported in yellowfin tuna. Mercury isotope values differed between Δ¹⁹⁹ Hg and δ202Hg in both regions (Δ¹⁹⁹ Hg = 2.86 ± 0.04‰ vs. Δ¹⁹⁹ Hg = 2.33 ± 0.07‰), likely related to shifting food webs and differing photochemical processing of Hg prior to entry into the food web. There were significantly lower values of both δ¹⁵ N and δ¹³ C in tuna from Galápagos Marine Reserve (δ¹⁵ N: 8.5-14.2‰, δ¹³ C: -18.5 to -16.1‰) compared with those from the Ecuadorian mainland coast (δ¹⁵ N: 8.3-14.4‰, δ¹³ C: -19.4 to -11.9‰), of which δ¹³ C values suggest spatially constrained movements of tuna. Results from the pooled analysis, without considering region, indicated that variations in δ¹³ C and δ¹⁵ N values tracked changes of Hg stable isotopes. Our data indicate that the individual tuna we used were resident fish of each region and were heavily influenced by upwellings related to the eastern Pacific oxygen minimum zone and the Humboldt Current System. The isotopes C, N, and Hg reflect foraging behavior mainly on epipelagic prey in shallow waters and that food web shifts drive Hg variations between these populations of tuna. Environ Toxicol Chem 2022;41:2732-2744. © 2022 SETAC.

Investigating ocean deoxygenation and the oxygen minimum zone in the Central Indo Pacific region based on the hindcast datasets

Deoxygenation is increasingly recognized as a significant environmental threat to the ocean following sea temperature rises due to global warming and climate change. Considering the cruciality of the deoxygenation impacts, it is important to assess the current status and predict the future possibility of ocean deoxygenation, for instance, within the Central Indo Pacific (CIP) regions represent climate-regulated marine areas. This study divided CIP into five regions then investigated the deoxygenation parameters (dissolved oxygen, temperature, salinity, and pH) collected from 1993 to 2021 sourced from in situ measurement and long-term hindcast data. The overall error statistics indicate a good accuracy of hindcast data and are comparable to the in situ values. The surface waters were identified to have the most fluctuated seasonal pattern of dissolved oxygen (DO) concentration compared to other water columns. However, DO fluctuation occurred in a different pattern in each region. The study shows ocean deoxygenation is accelerated in all five regions over decades. The strongest oxygen minimum zone (OMZ) is identified in the Bay of Bengal and the Arafura Sea with the lowest oxygen concentration less than 0.5 mmol/m³, while the weakest OMZ is located in the South China Sea with 60 mmol/m³ of DO concentration. The deoxygenation rates in CIP regions are varied by 0.09-2.75 mmol/m³/year depending on the different controlling factors that work in the five regions. Our results indicate that deoxygenation is attributed to ocean warming, seawater salinity increases, and ocean acidification and possibly continue in the future with continued global changes.

Reduced Oxygen Impairs Photobehavior in Marine Invertebrate Larvae

AbstractOrganisms in coastal waters experience naturally high oxygen variability and steep oxygen gradients with depth, in addition to ocean deoxygenation. They often undergo diel vertical migration involving a change in irradiance that initiates a visual behavior. Retinal function has been shown to be highly sensitive to oxygen loss; here we assess whether visual behavior (photobehavior) in paralarvae of the squid Doryteuthis opalescens and the octopus Octopus bimaculatus is affected by low oxygen conditions, using a novel behavioral paradigm. Larvae showed an irradiance-dependent, descending photobehavior after extinction of the light stimulus, measured through the change in vertical position of larvae in the chamber. The magnitude of photobehavior was decreased as oxygen was reduced, and the response was entirely gone at <6.4 kPa partial pressure of oxygen (<74.7 μmol kg^-1 at 15.3 °C) in D. opalescens paralarvae. Oxygen also affected photobehavior in O. bimaculatus paralarvae. The mean vertical velocity of paralarvae was unaffected by exposure to reduced oxygen, indicating that oxygen deficits selectively affect vision prior to locomotion. These findings suggest that variable and declining oxygen conditions in coastal upwelling areas and elsewhere will impair photobehavior and likely affect the distribution, migration behavior, and survival of highly visual marine species.

Physical-chemical factors influencing the vertical distribution of phototrophic pico-nanoplankton in the Oxygen Minimum Zone (OMZ) off Northern Chile: The relative influence of low pH/low O2 conditions

The vertical distribution of phytoplankton is of fundamental importance in the structure, dynamic, and biogeochemical pathways in marine ecosystems. Nevertheless, what are the main factors determining this distribution remains as an open question. Here, we evaluated the relative influence of environmental factors that might control the coexistence and vertical distribution of pico-nanoplankton associated with the OMZ off northern Chile. Our results showed that in the upper layer Synechococcus-like cells were numerically important at all sampling stations. Pico-nano eukaryotes and phototrophic nanoflagellates (PNF) also showed high abundances in the upper layer decreasing in abundance down to the upper oxycline, while only Prochlorococcus showed high abundances under oxycline and within the oxygen-depleted layer. Statistical analyses evidenced that temperature, oxygen, and carbonate chemistry parameters (pH and dissolved inorganic carbon, DIC) influenced significantly the vertical distribution of phototrophic pico-nanoplankton. Additionally, we experimentally-evaluated the combined effect of low pH/low O₂ conditions on a nanophytoplankton species, the haptophyte Imantonia sp. Under control conditions (pH = 8.1; O₂ = 287.5 μM, light = 169.6 μEm^-2s^-1), Imantonia sp. in vivo fluorescence increased over fifty times, inducing supersaturated O₂ conditions (900 μM) and an increasing pH (8.5), whereas upon an experimental treatment mimicking OMZ conditions (pH = 7.5; O₂ = 55.6 μM; light = 169.6 μEm^-2s^-1), in vivo fluorescence declined dramatically, suggesting that Imantonia sp. did not survive. Although preliminary, our study provides evidence about the role of low pH/low O₂ conditions on the vertical distribution of nanophytoplankton, which deserve future attention through both fieldwork and more extended experimental experiences.

Mercury stable isotopes suggest reduced foraging depth in oxygen minimum zones for blue sharks

Oxygen minimum zones (OMZs) are currently expanding across the global ocean due to climate change, leading to a compression of usable habitat for several marine species. Mercury stable isotope compositions provide a spatially and temporally integrated view of marine predator foraging habitat and its variability with environmental conditions. Here, we analyzed mercury isotopes in blue sharks Prionace glauca from normoxic waters in the northeastern Atlantic and from the world's largest and shallowest OMZ, located in the northeastern Pacific (NEP). Blue sharks from the NEP OMZ area showed higher Δ¹⁹⁹Hg values compared to sharks from the northeastern Atlantic, indicating a reduction in foraging depth of approximately 200 m. Our study suggests for the first time that blue shark feeding depth is altered by expanding OMZs and illustrates the use of mercury isotopes to assess the impacts of ocean deoxygenation on the vertical foraging habitat of pelagic predators.

Different patterns of hypoxia aggravate the toxicity of polystyrene nanoplastics in the mussels Mytilus galloprovincialis: Environmental risk assessment of plastics under global climate change

Hypoxia, largely triggered by anthropogenic activities and global climate change, exerts widespread and expanding stress on marine ecosystems. As an emerging contaminant, the influence of nanoplastics on marine organisms has also attracted attention in recent years. However, the impact of hypoxia on the risk assessments of nanoplastics is rarely considered. This study investigated the toxicity of PS-NPs (0, 0.5, and 5 mg/L) to the coastal mussels Mytilus galloprovincialis under different patterns of hypoxia (normoxia, constant hypoxia, and fluctuating hypoxia). The results showed that constant hypoxia might reduce the accumulation of PS-NPs in mussels by decreasing the standard metabolic rate. The impairment of PS-NPs on mussel immunity was also exacerbated by constant hypoxia. Fluctuating hypoxia did not affect the accumulation of PS-NPs, but aggravated the oxidative damage caused by PS-NPs. These findings emphasize the importance of environmental factors and their temporal variability in plastic risk assessment.

Physiological Consequences of Oceanic Environmental Variation: Life from a Pelagic Organism's Perspective

To better understand life in the sea, marine scientists must first quantify how individual organisms experience their environment, and then describe how organismal performance depends on that experience. In this review, we first explore marine environmental variation from the perspective of pelagic organisms, the most abundant life forms in the ocean. Generation time, the ability to move relative to the surrounding water (even slowly), and the presence of environmental gradients at all spatial scales play dominant roles in determining the variation experienced by individuals, but this variation remains difficult to quantify. We then use this insight to critically examine current understanding of the environmental physiology of pelagic marine organisms. Physiologists have begun to grapple with the complexity presented by environmental variation, and promising frameworks exist for predicting and/or interpreting the consequences for physiological performance. However, new technology needs to be developed and much difficult empirical work remains, especially in quantifying response times to environmental variation and the interactions among multiple covarying factors. We call on the field of global-change biology to undertake these important challenges.

Microbial community structures and important taxa across oxygen gradients in the Andaman Sea and eastern Bay of Bengal epipelagic waters

In oceanic oxygen minimum zones (OMZs), the abundances of aerobic organisms significantly decrease and energy shifts from higher trophic levels to microorganisms, while the microbial communities become critical drivers of marine biogeochemical cycling activities. However, little is known of the microbial ecology of the Andaman Sea and eastern Bay of Bengal (BoB) OMZs. In the present study, a total of 131 samples which from the Andaman Sea and eastern BoB epipelagic waters were analyzed. The microbial community distribution patterns across oxygen gradients, including oxygenic zones (OZs, dissolved oxygen [DO] ≥ 2 mg/L), oxygen limited zones (OLZs, 0.7 mg/L < DO < 2 mg/L), and OMZs (DO ≤ 0.7 mg/L), were investigated. Mantel tests and Spearman's correlation analysis revealed that DO was the most important driver of microbial community structures among several environmental factors. Microbial diversity, richness, and evenness were highest in the OLZs and lowest in the OZs. The microbial community compositions of OZ and OMZ waters were significantly different. Random forest analysis revealed 24 bioindicator taxa that differentiated OZ, OLZ, and OMZ water communities. These bioindicator taxa included Burkholderiaceae, HOC36, SAR11 Clade IV, Thioglobaceae, Nitrospinaceae, SAR86, and UBA10353. Further, co-occurrence network analysis revealed that SAR202, AEGEAN-169, UBA10353, SAR406, and Rhodobacteraceae were keystone taxa among the entire interaction network of the microbial communities. Functional prediction further indicated that the relative abundances of microbial populations involved in nitrogen and sulfur cycling were higher in OMZs. Several microbial taxa, including the Thioglobaceae, Nitrospinaceae, SAR202, SAR406, WPS-2, UBA10353, and Woeseiaceae, may be involved in nitrogen and/or sulfur cycling, while also contributing to oxygen consumption in these waters. This study consequently provides new insights into the microbial community structures and potentially important taxa that contribute to oxygen consumption in the Andaman Sea and eastern BoB OMZ.

Substantial oxygen consumption by aerobic nitrite oxidation in oceanic oxygen minimum zones

Oceanic oxygen minimum zones (OMZs) are globally significant sites of biogeochemical cycling where microorganisms deplete dissolved oxygen (DO) to concentrations <20 µM. Amid intense competition for DO in these metabolically challenging environments, aerobic nitrite oxidation may consume significant amounts of DO and help maintain low DO concentrations, but this remains unquantified. Using parallel measurements of oxygen consumption rates and ¹⁵N-nitrite oxidation rates applied to both water column profiles and oxygen manipulation experiments, we show that the contribution of nitrite oxidation to overall DO consumption systematically increases as DO declines below 2 µM. Nitrite oxidation can account for all DO consumption only under DO concentrations <393 nM found in and below the secondary chlorophyll maximum. These patterns are consistent across sampling stations and experiments, reflecting coupling between nitrate reduction and nitrite-oxidizing Nitrospina with high oxygen affinity (based on isotopic and omic data). Collectively our results demonstrate that nitrite oxidation plays a pivotal role in the maintenance and biogeochemical dynamics of OMZs.

Moving on up: Vertical distribution shifts in rocky reef fish species during climate-driven decline in dissolved oxygen from 1995 to 2009

Anthropogenic climate change has resulted in warming temperatures and reduced oxygen concentrations in the global oceans. Much remains unknown on the impacts of reduced oxygen concentrations on the biology and distribution of marine fishes. In the Southern California Channel Islands, visual fish surveys were conducted frequently in a manned submersible at three rocky reefs between 1995 and 2009. This area is characterized by a steep bathymetric gradient, with the surveyed sites Anacapa Passage, Footprint and Piggy Bank corresponding to depths near 50, 150 and 300 m. Poisson models were developed for each fish species observed consistently in this network of rocky reefs to determine the impact of depth and year on fish peak distribution. The interaction of depth and year was significant in 23 fish types, with 19 of the modelled peak distributions shifting to a shallower depth over the surveyed time period. Across the 23 fish types, the peak distribution shoaled at an average rate of 8.7 m of vertical depth per decade. Many of the species included in the study, including California sheephead, copper rockfish and blue rockfish, are targeted by commercial and recreational fisheries. CalCOFI hydrographic samples are used to demonstrate significant declines in dissolved oxygen at stations near the survey sites which are forced by a combination of natural multidecadal oscillations and anthropogenic climate change. This study demonstrates in situ fish depth distribution shifts over a 15-year period concurrent with oxygen decline. Climate-driven distribution shifts in response to deoxygenation have important implications for fisheries management, including habitat reduction, habitat compression, novel trophic dynamics and reduced body condition. Continued efforts to predict the formation and severity of hypoxic zones and their impact on fisheries dynamics will be essential to guiding effective placement of protected areas and fisheries regulations.

Microbial Ecology of Oxygen Minimum Zones Amidst Ocean Deoxygenation

Oxygen minimum zones (OMZs) have substantial effects on the global ecology and biogeochemical processes of marine microbes. However, the diversity and activity of OMZ microbes and their trophic interactions are only starting to be documented, especially in regard to the potential roles of viruses and protists. OMZs have expanded over the past 60 years and are predicted to expand due to anthropogenic climate change, furthering the need to understand these regions. This review summarizes the current knowledge of OMZ formation, the biotic and abiotic factors involved in OMZ expansion, and the microbial ecology of OMZs, emphasizing the importance of bacteria, archaea, viruses, and protists. We describe the recognized roles of OMZ microbes in carbon, nitrogen, and sulfur cycling, the potential of viruses in altering host metabolisms involved in these cycles, and the control of microbial populations by grazers and viruses. Further, we highlight the microbial community composition and roles of these organisms in oxic and anoxic depths within the water column and how these differences potentially inform how microbial communities will respond to deoxygenation. Additionally, the current literature on the alteration of microbial communities by other key climate change parameters such as temperature and pH are considered regarding how OMZ microbes might respond to these pressures. Finally, we discuss what knowledge gaps are present in understanding OMZ microbial communities and propose directions that will begin to close these gaps.

Distribution, associations and role in the biological carbon pump of Pyrosoma atlanticum (Tunicata, Thaliacea) off Cabo Verde, NE Atlantic

Gelatinous zooplankton are increasingly acknowledged to contribute significantly to the carbon cycle worldwide, yet many taxa within this diverse group remain poorly studied. Here, we investigate the pelagic tunicate Pyrosoma atlanticum in the waters surrounding the Cabo Verde Archipelago. By using a combination of pelagic and benthic in situ observations, sampling, and molecular genetic analyses (barcoding, eDNA), we reveal that: P. atlanticum abundance is most likely driven by local island-induced productivity, that it substantially contributes to the organic carbon export flux and is part of a diverse range of biological interactions. Downward migrating pyrosomes actively transported an estimated 13% of their fecal pellets below the mixed layer, equaling a carbon flux of 1.96-64.55 mg C m^-2 day^-1. We show that analysis of eDNA can detect pyrosome material beyond their migration range, suggesting that pyrosomes have ecological impacts below the upper water column. Moribund P. atlanticum colonies contributed an average of 15.09 ± 17.89 (s.d.) mg C m^-2 to the carbon flux reaching the island benthic slopes. Our pelagic in situ observations further show that P. atlanticum formed an abundant substrate in the water column (reaching up to 0.28 m² substrate area per m²), with animals using pyrosomes for settlement, as a shelter and/or a food source. In total, twelve taxa from four phyla were observed to interact with pyrosomes in the midwater and on the benthos.

A source of isotopically light organic carbon in a low-pH anoxic marine zone

Geochemical and stable isotope measurements in the anoxic marine zone (AMZ) off northern Chile during periods of contrasting oceanographic conditions indicate that microbial processes mediating sulfur and nitrogen cycling exert a significant control on the carbonate chemistry (pH, A_T, DIC and pCO₂) of this region. Here we show that in 2015, a large isotopic fractionation between DIC and POC, a DIC and N deficit in AMZ waters indicate the predominance of in situ dark carbon fixation by sulfur-driven autotrophic denitrification in addition to anammox. In 2018, however, the fractionation between DIC and POC was significantly lower, while the total alkalinity increased in the low-pH AMZ core, suggesting a predominance of heterotrophic processes. An isotope mass-balance model demonstrates that variations in the rates of sulfur- and nitrogen-mediated carbon fixation in AMZ waters contribute ~7–35% of the POC exported to deeper waters. Thus, dark carbon fixation should be included in assessments of future changes in carbon cycling and carbonate chemistry due to AMZ expansion.

Anoxic marine zones are expanding and intensifying with climate change. Here the authors show that microbial dark carbon fixation influences the carbonate system and the stable isotope composition in waters off Chile, contributing up to 35% of the organic carbon reaching the mesopelagic region.

Impacts of hypoxic events surpass those of future ocean warming and acidification

Over the past decades, three major challenges to marine life have emerged as a consequence of anthropogenic emissions: ocean warming, acidification and oxygen loss. While most experimental research has targeted the first two stressors, the last remains comparatively neglected. Here, we implemented sequential hierarchical mixed-model meta-analyses (721 control-treatment comparisons) to compare the impacts of oxygen conditions associated with the current and continuously intensifying hypoxic events (1-3.5 O₂ mg l^-1) with those experimentally yielded by ocean warming (+4 °C) and acidification (-0.4 units) conditions on the basis of IPCC projections (RCP 8.5) for 2100. In contrast to warming and acidification, hypoxic events elicited consistent negative effects relative to control biological performance-survival (-33%), abundance (-65%), development (-51%), metabolism (-33%), growth (-24%) and reproduction (-39%)-across the taxonomic groups (mollusks, crustaceans and fish), ontogenetic stages and climate regions studied. Our findings call for a refocus of global change experimental studies, integrating oxygen concentration drivers as a key factor of ocean change. Given potential combined effects, multistressor designs including gradual and extreme changes are further warranted to fully disclose the future impacts of ocean oxygen loss, warming and acidification.

Climate-driven deoxygenation elevates fishing vulnerability for the ocean's widest ranging shark

Climate-driven expansions of ocean hypoxic zones are predicted to concentrate pelagic fish in oxygenated surface layers, but how expanding hypoxia and fisheries will interact to affect threatened pelagic sharks remains unknown. Here, analysis of satellite-tracked blue sharks and environmental modelling in the eastern tropical Atlantic oxygen minimum zone (OMZ) shows shark maximum dive depths decreased due to combined effects of decreasing dissolved oxygen (DO) at depth, high sea surface temperatures, and increased surface-layer net primary production. Multiple factors associated with climate-driven deoxygenation contributed to blue shark vertical habitat compression, potentially increasing their vulnerability to surface fisheries. Greater intensity of longline fishing effort occurred above the OMZ compared to adjacent waters. Higher shark catches were associated with strong DO gradients, suggesting potential aggregation along suitable DO gradients contributed to habitat compression and higher fishing-induced mortality. Fisheries controls to counteract deoxygenation effects on shark catches will be needed as oceans continue warming.

In situ observations show vertical community structure of pelagic fauna in the eastern tropical North Atlantic off Cape Verde

Distribution patterns of fragile gelatinous fauna in the open ocean remain scarcely documented. Using epi-and mesopelagic video transects in the eastern tropical North Atlantic, which features a mild but intensifying midwater oxygen minimum zone (OMZ), we established one of the first regional observations of diversity and abundance of large gelatinous zooplankton. We quantified the day and night vertical distribution of 46 taxa in relation to environmental conditions. While distribution may be driven by multiple factors, abundance peaks of individual taxa were observed in the OMZ core, both above and below the OMZ, only above, or only below the OMZ whereas some taxa did not have an obvious distribution pattern. In the eastern eropical North Atlantic, OMZ expansion in the course of global climate change may detrimentally impact taxa that avoid low oxygen concentrations (Beroe, doliolids), but favour taxa that occur in the OMZ (Lilyopsis, phaeodarians, Cydippida, Colobonema, Haliscera conica and Halitrephes) as their habitat volume might increase. While future efforts need to focus on physiology and taxonomy of pelagic fauna in the study region, our study presents biodiversity and distribution data for the regional epi- and mesopelagic zones of Cape Verde providing a regional baseline to monitor how climate change may impact the largest habitat on the planet, the deep pelagic realm.

Diel vertical migration into anoxic and high-pCO2 waters: acoustic and net-based krill observations in the Humboldt Current

A select group of marine organisms can enter the Oxygen Minimum Zones (OMZs) and even anoxic waters, while performing diel vertical migration (DVM). DVM of the euphausiid Euphausia eximia off northern Chile in the spring of 2015 was documented based on acoustic measurements using an echo sounder along with net samplings. Dissolved oxygen (DO) concentrations were obtained using a vertical profiler, and water samples were collected to obtain in situ nitrite (NO₂⁻) concentrations as well as pH_T, total alkalinity (AT), and therefore carbon dioxide partial pressure (pCO₂) was estimated. Krill were found to migrate up to the surface (0–50 m) during the night and returned to ca. 200–300 m depth during the day, spending between 11 and 14 h at these layers. At the surface, DO and NO₂⁻ concentrations were 208 and 0.14 μM respectively, while pH_T was 8.04 and 405 μatm pCO₂. In contrast, at the deeper layers (200–300 m), DO and NO₂⁻ were < 3 and 6.3 μM respectively, with pH_T 7.53 and 1490 μatm pCO₂. The pH_T and high pCO₂ values at depths represent the conditions predicted for open ocean waters in a worst-case global warming scenario by 2150. The acoustic scatter suggested that > 60% of the krill swarms enter the OMZ and anoxic waters during the daytime. These frequent migrations suggest that krill can tolerate such extreme conditions associated with anoxic and high-pCO₂ waters. The inferences drawn from the observation of these migrations might have strong implications for the current oceanic carbon pump models, highlighting the need for understanding the molecular and physiological adaptations allowing these migrations.

Biogeochemistry and hydrography shape microbial community assembly and activity in the eastern tropical North Pacific Ocean oxygen minimum zone

Oceanic oxygen minimum zones (OMZs) play a pivotal role in biogeochemical cycles due to extensive microbial activity. How OMZ microbial communities assemble and respond to environmental variation is therefore essential to understanding OMZ functioning and ocean biogeochemistry. Sampling along depth profiles at five stations in the eastern tropical North Pacific Ocean (ETNP), we captured systematic variations in dissolved oxygen (DO) and associated variables (nitrite, chlorophyll, and ammonium) with depth and between stations. We quantitatively analysed relationships between oceanographic gradients and microbial community assembly and activity based on paired 16S rDNA and 16S rRNA sequencing. Overall microbial community composition and diversity were strongly related to regional variations in density, DO, and other variables (regression and redundancy analysis r²  = 0.68-0.82), displaying predictable patterns with depth and between stations. Although similar factors influenced the active community, diversity was substantially lower within the OMZ. We also identified multiple active microbiological networks that tracked specific gradients or features - particularly subsurface ammonium and nitrite maxima. Our findings indicate that overall microbial community assembly is consistently shaped by hydrography and biogeochemistry, while active segments of the community form discrete networks inhabiting distinct portions of the water column, and that both are tightly tuned to environmental conditions in the ETNP.

Effects of hypoxia on the behavior and physiology of kelp forest fishes

Forecasts from climate models and oceanographic observations indicate increasing deoxygenation in the global oceans and an elevated frequency and intensity of hypoxic events in the coastal zone, which have the potential to affect marine biodiversity and fisheries. Exposure to low dissolved oxygen (DO) conditions may have deleterious effects on early life stages in fishes. This study aims to identify thresholds to hypoxia while testing behavioral and physiological responses of two congeneric species of kelp forest fish to four DO levels, ranging from normoxic to hypoxic (8.7, 6.0, 4.1, and 2.2 mg O2 /L). Behavioral tests identified changes in exploratory behavior and turning bias (lateralization), whereas physiological tests focused on determining changes in hypoxia tolerance (pCrit), ventilation rates, and metabolic rates, with impacts on the resulting capacity for aerobic activity. Our findings indicated that copper rockfish (Sebastes caurinus) and blue rockfish (Sebastes mystinus) express sensitivity to hypoxia; however, the strength of the response differed between species. Copper rockfish exhibited reduced absolute lateralization and increased escape time at the lowest DO levels, whereas behavioral metrics for blue rockfish did not vary with oxygen level. Both species exhibited decreases in aerobic scope (as a function of reduced maximum metabolic rate) and increases in ventilation rates to compensate for decreasing oxygen levels. Blue rockfish had a lower pCrit and stronger acclimation response compared to copper rockfish. The differences expressed by each species suggest that acclimatization to changing ocean conditions may vary, even among related species that recruit to the same kelp forest habitat, leading to winners and losers under future ocean conditions. Exposure to hypoxia can decrease individual physiological fitness through metabolic and aerobic depression and changes to anti-predator behavior, with implications for the outcome of ecological interactions and the management of fish stocks in the face of climate change.

Hypoxia Tolerance of 10 Euphausiid Species in Relation to Vertical Temperature and Oxygen Gradients

Oxygen Minimum Zones prevail in most of the world's oceans and are particularly extensive in Eastern Boundary Upwelling Ecosystems such as the Humboldt and the Benguela upwelling systems. In these regions, euphausiids are an important trophic link between primary producers and higher trophic levels. The species are known as pronounced diel vertical migrators, thus facing different levels of oxygen and temperature within a 24 h cycle. Declining oxygen levels may lead to vertically constrained habitats in euphausiids, which consequently will affect several trophic levels in the food web of the respective ecosystem. By using the regulation index (RI), the present study aimed at investigating the hypoxia tolerances of different euphausiid species from Atlantic, Pacific as well as from Polar regions. RI was calculated from 141 data sets and used to differentiate between respiration strategies using median and quartile (Q) values: low degree of oxyregulation (0.25 < RI median < 0.5); high degree of oxyregulation (0.5 < RI median < 1; Q1 > 0.25 or Q3 > 0.75); and metabolic suppression (RI median, Q1 and Q3 < 0). RI values of the polar (Euphausia superba, Thysanoessa inermis) and sub-tropical (Euphausia hanseni, Nyctiphanes capensis, and Nematoscelis megalops) species indicate a high degree of oxyregulation, whereas almost perfect oxyconformity (RI median ≈ 0; Q1 < 0 and Q3 > 0) was identified for the neritic temperate species Thysanoessa spinifera and the tropical species Euphausia lamelligera. RI values of Euphausia distinguenda and the Humboldt species Euphausia mucronata qualified these as metabolic suppressors. RI showed a significant impact of temperature on the respiration strategy of E. hanseni from oxyregulation to metabolic suppression. The species' estimated hypoxia tolerances and the degree of oxyconformity vs. oxyregulation were linked to diel vertical migration behavior and the temperature experienced during migration. The results highlight that the euphausiid species investigated have evolved various strategies to deal with different levels of oxygen, ranging from species showing a high degree of oxyconformity to strong oxyregulation. Neritic species may be more affected by hypoxia, as these are often short-distance-migrators and only adapted to a narrow range of environmental conditions.

An hypoxia-tolerant flatfish: consequences of sustained stress on the slender sole Lyopsetta exilis (Pleuronectidae) in the context of a changing ocean

Slender sole Lyopsetta exilis is an abundant groundfish on the continental shelf and inner waters of British Columbia, Canada, where it reaches a maximum standard length of 44 cm. Benthic image surveys coupled with oxygen measurements in Saanich Inlet document a dense population in bottom conditions near anoxia (0.03 ml l^-1 oxygen) where diel migrating zooplankton intersect the bottom; we confirm this species is a planktivore, which limits its depth range to the base of the migration layer. In a comparison with slender sole from a nearby well-oxygenated habitat, several probable effects of living in severe hypoxia emerge: both sexes are significantly smaller in Saanich and the sex ratio is male-skewed. Otoliths from the Saanich fish were difficult to read due to many checks, but both sexes were smaller at age with the largest female (20 cm) from the hypoxia zone registering 17 years. Hypoxia appears to have a direct consequence on growth despite good food supply in this productive basin. Hyperventilation, a low metabolic rate and a very low critical oxygen tension help this fish regulate oxygen uptake in severely hypoxic conditions; it will be particularly resilient as the incidence of hypoxia increases on the continental shelf. Data from small-mesh bottom-trawl surveys over four decades reveal an increase in mean annual catch per unit effort in southern regions of the province, including the outer shelf and the Strait of Georgia. The California Cooperative Oceanic Fisheries Investigations (CalCOFI) ichthyoplankton database records a general decline in fish larvae on the Oregon-California shelf since 1990, but slender sole larvae are increasing there, as they are in the Strait of Georgia. We project that the slender sole will gain relative benefits in the future warming, deoxygenated northeast Pacific Ocean.

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing

The Indian Ocean harbors oxygen minimum zones (OMZs) in the Arabian Sea and Bay of Bengal, with dissolved oxygen < 20 μM, located at the mid-depths of the water column. Till date, high-throughput sequence-data on depth-wise distribution of prokaryotic communities have rarely been reported from these OMZs. The present study aimed to characterize the prokaryotic diversity inhabiting Arabian Sea Time Series (ASTS) and India's Idea 2 (II2) in the Arabian Sea, and Bay of Bengal Time Series (BoBTS) in the Bay of Bengal OMZs based on amplicon sequencing of 16S rRNA gene regions, along six sampled depths in the water column. High prokaryotic richness was observed in the Arabian Sea and Bay of Bengal samples. Operational taxonomic units (OTUs) in the range of 1249-3298 were identified, wherein, less prokaryotic diversity was observed at surface and within oxygen minimum depths. At phylum level, most OTUs were affiliated to Bacteroidetes, Chloroflexi, Cyanobacteria, Marinimicrobia, Planctomycetes, and Proteobacteria. Prokaryotic community differed between ASTS, II2 and BoBTS locations along varying physicochemical conditions. Predictive functional profiling of the bacterial communities suggested the involvement of abundant microbes in nitrogen and sulfur metabolism pathways. Bacterial isolates belonging to genera from the clades, δ-Proteobacteria and γ-Proteobacteria, described previously for their participation in biogeochemical cycling of N-and-S in the OMZs were reported from deoxygenated waters of both the basins. Bacteria involved in anammox such as Candidatus Scalindua were found to be relatively high at ASTS and II2 locations in the Arabian Sea. Further studies are required to ascertain the role of abundant bacteria along the dynamic oceanographic processes in the OMZs.

Fewer Copepods, Fewer Anchovies, and More Jellyfish: How Does Hypoxia Impact the Chesapeake Bay Zooplankton Community?

To understand dissolved oxygen deficiency in Chesapeake Bay and its direct impact on zooplankton and planktivorous fish communities, six research cruises were conducted at two sites in the Chesapeake Bay from spring to autumn in 2010 and 2011. Temperature, salinity, and dissolved oxygen were measured from hourly conductivity, temperature, and depth (CTD) casts, and crustacean zooplankton, planktivorous fish and gelatinous zooplankton were collected with nets and trawls. CTD data were grouped into three temperature groups and two dissolved oxygen-level subgroups using principal component analysis (PCA). Species concentrations and copepod nonpredatory mortalities were compared between oxygenated conditions within each temperature group. Under hypoxic conditions, there usually were significantly fewer copepods Acartia tonsa and bay anchovies Anchoa mitchilli, but more bay nettles Chyrsaora chesapeakei and lobate ctenophores Mnemiopsis leidyi. Neutral red staining of copepod samples confirmed that copepod nonpredatory mortalities were higher under hypoxic conditions than under normoxia, indicating that the sudden decline in copepod concentration in summer was directly associated with hypoxia. Because comparisons were made within each temperature group, the effects of temperature were isolated, and hypoxia was clearly shown to have contributed to copepod decreases, planktivorous fish decreases, and gelatinous zooplankton increases. This research quantified the direct effects of hypoxia and explained the interactions between seasonality and hypoxia on the zooplankton population.

A draft genome sequence of the elusive giant squid, Architeuthis dux

BACKGROUND

The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked.

FINDINGS

We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.

CONCLUSIONS

This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

The first global deep-sea stable isotope assessment reveals the unique trophic ecology of Vampire Squid Vampyroteuthis infernalis (Cephalopoda)

Vampyroteuthis infernalis Chun, 1903, is a widely distributed deepwater cephalopod with unique morphology and phylogenetic position. We assessed its habitat and trophic ecology on a global scale via stable isotope analyses of a unique collection of beaks from 104 specimens from the Atlantic, Pacific and Indian Oceans. Cephalopods typically are active predators occupying a high trophic level (TL) and exhibit an ontogenetic increase in δ¹⁵N and TL. Our results, presenting the first global comparison for a deep-sea invertebrate, demonstrate that V. infernalis has an ontogenetic decrease in δ¹⁵N and TL, coupled with niche broadening. Juveniles are mobile zooplanktivores, while larger Vampyroteuthis are slow-swimming opportunistic consumers and ingest particulate organic matter. Vampyroteuthis infernalis occupies the same TL (3.0–4.3) over its global range and has a unique niche in deep-sea ecosystems. These traits have enabled the success and abundance of this relict species inhabiting the largest ecological realm on the planet.

Microbes and macro-invertebrates show parallel β-diversity but contrasting α-diversity patterns in a marine natural experiment

Documenting ecological patterns across spatially, temporally and taxonomically diverse ecological communities is necessary for a general understanding of the processes shaping biodiversity. A major gap in our understanding remains the comparison of diversity patterns across a broad spectrum of evolutionarily and functionally diverse organisms, particularly in the marine realm. Here, we aim to narrow this gap by comparing the diversity patterns of free-living microbes and macro-invertebrates across a natural experiment provided by the marine lakes of Palau: geographically discrete and environmentally heterogeneous bodies of seawater with comparable geological and climatic history, and a similar regional species pool. We find contrasting patterns of α-diversity but remarkably similar patterns of β-diversity between microbial and macro-invertebrate communities among lakes. Pairwise dissimilarities in community composition among lakes are positively correlated between microbes and macro-invertebrates, and influenced to a similar degree by marked gradients in oxygen concentration and salinity. Our findings indicate that a shared spatio-temporal and environmental context may result in parallel patterns of β-diversity in microbes and macro-invertebrates, in spite of key trait differences between these organisms. This raises the possibility that parallel processes also influence transitions among regional biota across the tree of life, at least in the marine realm.

Environmental characteristics associated with the presence of the Spinetail devil ray (Mobula mobular) in the eastern tropical Pacific

In the eastern Pacific Ocean, the tropical tuna purse-seine fishery incidentally captures high numbers of five mobulid bycatch species; all of which are classified as mortalities by the Inter-American Tropical Tuna Commission due to uncertainties in post-release mortality rates. To date, the factors (operational or environmental) leading to the capture of these species by the fishery have not been well studied. Here, we developed Generalized Additive Models for fisheries observer data to analyze the relationships between the presence/absence of Mobula mobular bycatch and oceanographic conditions, the spatial and temporal variability in fishing location, and the set type (associated with dolphins, free-swimming tuna schools or floating objects). Our results suggest that chlorophyll concentration and sea surface height are the most important variables to describe the presence of M. mobular in conjunction with geographic location (latitude and longitude) and set type. Presence of the species was predicted in waters with chlorophyll concentrations between 0.5–1 mg·m^-3 and with sea surface height values close to 0; which indicates direct relationships with productive upwelling systems. Seasonally, M. mobular was observed more frequently during December-January and August-September. We also found the highest probability of presence observed in School sets, followed by Dolphin sets. Three areas were observed as important hotspots: the area close to the coastal upwelling of northern Peru, the area west to Islands Colon Archipelago (Galapagos) and the area close to the Costa Rica Dome. This information is crucial to identify the mobulids habitat and hotspots that could be managed and protected under dynamic spatial management measures to reduce the mortality of mobulid rays in the eastern Pacific purse-seine fishery and, hence, ensure the sustainability of the populations of these iconic species.

Shallow particulate organic carbon regeneration in the South Pacific Ocean

Particulate organic carbon (POC) produced in the surface ocean sinks through the water column and is respired at depth, acting as a primary vector sequestering carbon in the abyssal ocean. Atmospheric carbon dioxide levels are sensitive to the length (depth) scale over which respiration converts POC back to inorganic carbon, because shallower waters exchange with the atmosphere more rapidly than deeper ones. However, estimates of this carbon regeneration length scale and its spatiotemporal variability are limited, hindering the ability to characterize its sensitivity to environmental conditions. Here, we present a zonal section of POC fluxes at high vertical and spatial resolution from the GEOTRACES GP16 transect in the eastern tropical South Pacific, based on normalization to the radiogenic thorium isotope ²³⁰Th. We find shallower carbon regeneration length scales than previous estimates for the oligotrophic South Pacific gyre, indicating less efficient carbon transfer to the deep ocean. Carbon regeneration is strongly inhibited within suboxic waters near the Peru coast. Canonical Martin curve power laws inadequately capture POC flux profiles at suboxic stations. We instead fit these profiles using an exponential function with flux preserved at depth, finding shallow regeneration but high POC sequestration below 1,000 m. Both regeneration length scales and POC flux at depth closely track the depths at which oxygen concentrations approach zero. Our findings imply that climate warming will result in reduced ocean carbon storage due to expanding oligotrophic gyres, but opposing effects on ocean carbon storage from expanding suboxic waters will require modeling and future work to disentangle.

Hypoxia tolerance of giant axon-mediated escape jetting in California market squid (Doryteuthis opalescens)

Squids display a wide range of swimming behaviors, including powerful escape jets mediated by the giant axon system. For California market squid (Doryteuthis opalescens), maintaining essential behaviors like the escape response during environmental variations poses a major challenge as this species often encounters intrusions of cold, hypoxic offshore waters in its coastal spawning habitats. To explore the effects of hypoxia on locomotion and the underlying neural mechanisms, we made in vivo recordings of giant axon activity and simultaneous pressure inside the mantle cavity during escape jets in squid exposed to acute progressive hypoxia followed by return to normal dissolved oxygen (DO) concentration (normoxia). Compared with those in normoxia (>8 mg l^-1 DO), escape jets were unchanged in moderate hypoxia (4 and 2 mg l^-1 DO), but giant axon activity and associated mantle contractions significantly decreased while neuromuscular latency increased under severe hypoxia (0.5 mg l^-1 DO). Animals that survived exposure to severe hypoxia reliably produced escape jets under such conditions and fully recovered as more oxygen became available. The reduction in neuromuscular output under hypoxia suggests that market squid may suppress metabolic activity to maintain sufficient behavioral output, a common strategy in many hypoxia-tolerant species. The ability to recover from the deleterious effects of hypoxia suggests that this species is well adapted to cope with coastal hypoxic events that commonly occur in Monterey Bay, unless these events become more severe in the future as climate change progresses.

Vision is highly sensitive to oxygen availability in marine invertebrate larvae

For many animals, evolution has selected for complex visual systems despite the high energetic demands associated with maintaining eyes and their processing structures. The metabolic demands of visual systems therefore make them highly sensitive to fluctuations in available oxygen. In the marine environment, oxygen changes over daily, seasonal, and inter-annual time scales and there are large gradients of oxygen with depth. Vision is linked to survival in many marine animals, particularly among the crustaceans, cephalopods, and fish, and early life stages of these groups rely on vision for prey capture, predator detection, and their distribution in the water column. Using in vivo electroretinogram recordings, we show that there is a decrease in retinal sensitivity to light in marine invertebrates when exposed to reduced oxygen availability. We found a 60-100% reduction in retinal responses in the larvae of cephalopods and crustaceans: the market squid (Doryteuthis opalescens), two-spot octopus (Octopus bimaculatus), tuna crab (Pleuroncodes planipes), and brachyuran crab (Metacarcinus gracilis). A decline in oxygen also decreases the temporal resolution of vision in D. opalescens. These results are the first demonstration that vision in marine invertebrates is highly sensitive to oxygen availability and that the thresholds for visual impairment from reduced oxygen are species-specific. Oxygen-impaired retinal function may change the visual behaviors crucial to survival in these marine larvae. These findings may impact our understanding of species’ vulnerability to ocean oxygen loss and suggest that researchers conducting electrophysiology experiments should monitor oxygen levels, as even small changes in oxygen may affect the results.

The evolution of foraging capacity and gigantism in cetaceans

The extant diversity and rich fossil record of cetaceans provides an extraordinary evolutionary context for investigating the relationship between form, function and ecology. The transition from terrestrial to marine ecosystems is associated with a complex suite of morphological and physiological adaptations that were required for a fully aquatic mammalian life history. Two specific functional innovations that characterize the two great clades of cetaceans, echolocation in toothed whales (Odontoceti) and filter feeding in baleen whales (Mysticeti), provide a powerful comparative framework for integrative studies. Both clades exhibit gigantism in multiple species, but we posit that large body size may have evolved for different reasons and in response to different ecosystem conditions. Although these foraging adaptations have been studied using a combination of experimental and tagging studies, the precise functional drivers and consequences of morphological change within and among these lineages remain less understood. Future studies that focus at the interface of physiology, ecology and paleontology will help elucidate how cetaceans became the largest predators in aquatic ecosystems worldwide.

Rapid shift and millennial-scale variations in Holocene North Pacific Intermediate Water ventilation

The North Pacific hosts extensive oxygen minimum zones. Ventilation of North Pacific Intermediate Water mitigates hypoxia in thermocline waters not under influence of ocean–atmosphere processes. Instrumental datasets show recent decadal decreases in O₂, but millennial-scale natural variations in mesopelagic ventilation might be large and are not understood well. We reconstruct Holocene ventilation changes in a key region (Okhotsk Sea). Modern ventilation and O₂ levels are a relatively recent feature. In the warmer-than-present Early Holocene, middepth O₂ concentrations were 25 to 50% reduced, with significant millennial-scale variations. A sudden ventilation decrease six thousand years ago is linked to higher ocean temperatures, sea ice loss, and higher remineralization, corroborated by results from paleoclimate modeling, providing constraints for future warming scenarios.

The Pacific hosts the largest oxygen minimum zones (OMZs) in the world ocean, which are thought to intensify and expand under future climate change, with significant consequences for marine ecosystems, biogeochemical cycles, and fisheries. At present, no deep ventilation occurs in the North Pacific due to a persistent halocline, but relatively better-oxygenated subsurface North Pacific Intermediate Water (NPIW) mitigates OMZ development in lower latitudes. Over the past decades, instrumental data show decreasing oxygenation in NPIW; however, long-term variations in middepth ventilation are potentially large, obscuring anthropogenic influences against millennial-scale natural background shifts. Here, we use paleoceanographic proxy evidence from the Okhotsk Sea, the foremost North Pacific ventilation region, to show that its modern oxygenated pattern is a relatively recent feature, with little to no ventilation before six thousand years ago, constituting an apparent Early–Middle Holocene (EMH) threshold or “tipping point.” Complementary paleomodeling results likewise indicate a warmer, saltier EMH NPIW, different from its modern conditions. During the EMH, the Okhotsk Sea switched from a modern oxygenation source to a sink, through a combination of sea ice loss, higher water temperatures, and remineralization rates, inhibiting ventilation. We estimate a strongly decreased EMH NPIW oxygenation of ∼30 to 50%, and increased middepth Pacific nutrient concentrations and carbon storage. Our results (i) imply that under past or future warmer-than-present conditions, oceanic biogeochemical feedback mechanisms may change or even switch direction, and (ii) provide constraints on the high-latitude North Pacific’s influence on mesopelagic ventilation dynamics, with consequences for large oceanic regions.

Declining oxygen in the global ocean and coastal waters

Oxygen is fundamental to life. Not only is it essential for the survival of individual animals, but it regulates global cycles of major nutrients and carbon. The oxygen content of the open ocean and coastal waters has been declining for at least the past half-century, largely because of human activities that have increased global temperatures and nutrients discharged to coastal waters. These changes have accelerated consumption of oxygen by microbial respiration, reduced solubility of oxygen in water, and reduced the rate of oxygen resupply from the atmosphere to the ocean interior, with a wide range of biological and ecological consequences. Further research is needed to understand and predict long-term, global- and regional-scale oxygen changes and their effects on marine and estuarine fisheries and ecosystems.

Manifestation, Drivers, and Emergence of Open Ocean Deoxygenation

Oxygen loss in the ocean, termed deoxygenation, is a major consequence of climate change and is exacerbated by other aspects of global change. An average global loss of 2% or more has been recorded in the open ocean over the past 50-100 years, but with greater oxygen declines in intermediate waters (100-600 m) of the North Pacific, the East Pacific, tropical waters, and the Southern Ocean. Although ocean warming contributions to oxygen declines through a reduction in oxygen solubility and stratification effects on ventilation are reasonably well understood, it has been a major challenge to identify drivers and modifying factors that explain different regional patterns, especially in the tropical oceans. Changes in respiration, circulation (including upwelling), nutrient inputs, and possibly methane release contribute to oxygen loss, often indirectly through stimulation of biological production and biological consumption. Microbes mediate many feedbacks in oxygen minimum zones that can either exacerbate or ameliorate deoxygenation via interacting nitrogen, sulfur, and carbon cycles. The paleo-record reflects drivers of and feedbacks to deoxygenation that have played out through the Phanerozoic on centennial, millennial, and hundred-million-year timescales. Natural oxygen variability has made it difficult to detect the emergence of a climate-forced signal of oxygen loss, but new modeling efforts now project emergence to occur in many areas in 15-25 years. Continued global deoxygenation is projected for the next 100 or more years under most emissions scenarios, but with regional heterogeneity. Notably, even small changes in oxygenation can have significant biological effects. New efforts to systematically observe oxygen changes throughout the open ocean are needed to help address gaps in understanding of ocean deoxygenation patterns and drivers.