Multiomics in the central Arctic Ocean for benchmarking biodiversity change.

Multiomics approaches need to be applied in the central Arctic Ocean to benchmark biodiversity change and to identify novel species and their genes. As part of MOSAiC, EcoOmics will therefore be essential for conservation and sustainable bioprospecting in one of the least explored ecosystems on Earth.

Coping with extreme free cortisol levels: Seasonal stress axis changes in sympatric North American flying squirrels.

Most environments exhibit predictable yearly changes, permitting animals to anticipate them. The hypothalamic-pituitary-adrenal (HPA) axis is a key physiological pathway that enables animals to cope with such changes. Monitoring glucocorticoid (the end products of the HPA axis) levels in wild animals throughout the year can improve our understanding of how this pathway responds to different conditions. For this study, we collected 18 months of data on two species of North American flying squirrels (Glaucomys sabrinus and G. volans) living in a southern Ontario forest where temperature and food availability fluctuate dramatically throughout the year. These squirrels are active year-round, nest communally, and rely on scatter hoarded foods in the winter months. Flying squirrels have extremely high levels of free plasma cortisol relative to other mammals, but it is unknown how these levels are affected by environmental and reproductive factors. For both species, our goals were to (1) validate an enzyme immunoassay (EIA) to measure their fecal glucocorticoid metabolite (FGM) concentrations and (2) assess yearly differences, seasonal changes, and the influence of sex, reproduction, and ambient temperature on FGM concentrations in each species. In the lab, we successfully validated the use of antibody 5α-pregnane-3ß, 11ß, 21-triol-20-one EIA for FGM analysis in both species. In the field, neither sex nor reproductive status (breeding condition or not) were linked to FGM concentrations in either species. FGM concentrations were higher in autumn compared to the spring and summer. There were no other seasonal differences. We discuss possible explanations for the autumn peak in FGM concentrations (increased energy expenditure and social nesting changes), as well as outline possible avenues for future research. Understanding how individuals and populations respond to environmental change is a critical goal in evolutionary ecology, particularly in the context of a rapidly changing Anthropocene.

Gut Microbial Ecosystem in Parkinson Disease: New Clinicobiological Insights from Multi-Omics.

OBJECTIVE: Gut microbiome alterations in Parkinson disease (PD) have been reported repeatedly, but their functional relevance remains unclear. Fecal metabolomics, which provide a functional readout of microbial activity, have scarcely been investigated. We investigated fecal microbiome and metabolome alterations in PD, and their clinical relevance. METHODS: Two hundred subjects (104 patients, 96 controls) underwent extensive clinical phenotyping. Stool samples were analyzed using 16S rRNA gene sequencing. Fecal metabolomics were performed using two platforms, nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry. RESULTS: Fecal microbiome and metabolome composition in PD was significantly different from controls, with the largest effect size seen in NMR-based metabolome. Microbiome and NMR-based metabolome compositional differences remained significant after comprehensive confounder analyses. Differentially abundant fecal metabolite features and predicted functional changes in PD versus controls included bioactive molecules with putative neuroprotective effects (eg, short chain fatty acids [SCFAs], ubiquinones, and salicylate) and other compounds increasingly implicated in neurodegeneration (eg, ceramides, sphingosine, and trimethylamine N-oxide). In the PD group, cognitive impairment, low body mass index (BMI), frailty, constipation, and low physical activity were associated with fecal metabolome compositional differences. Notably, low SCFAs in PD were significantly associated with poorer cognition and low BMI. Lower butyrate levels correlated with worse postural instability-gait disorder scores. INTERPRETATION: Gut microbial function is altered in PD, characterized by differentially abundant metabolic features that provide important biological insights into gut-brain pathophysiology. Their clinical relevance further supports a role for microbial metabolites as potential targets for the development of new biomarkers and therapies in PD. ANN NEUROL 2021;89:546-559.

Recurrent microbial community types driven by nearshore and seasonal processes in coastal Southern California.

A multitude of concurrent biological and physical processes contribute to microbial community turnover, especially in highly dynamic coastal environments. Characterizing what factors contribute most to shifts in microbial community structure and the specific organisms that correlate with changes in the products of photosynthesis improves our understanding of nearshore microbial ecosystem functions. We conducted high frequency sampling in nearshore Southern California in order to capture sub-weekly microbial community dynamics. Microbial communities were characterized by flow cytometry and 16S rRNA gene sequencing, and placed in the context of physicochemical parameters. Within our time-series, season and nutrient availability corresponded to changes in dominant microbial community members. Concurrent aseasonal drivers with overlapping scales of variability were also apparent when we used network analysis to assess the microbial community as subsets of the whole. Our analyses revealed the microbial community as a mosaic, with overlapping groups of taxa that varied on different timescales and correlated with unique abiotic and biotic factors. Specifically, a subnetwork associated with chlorophyll a exhibited rapid turnover, indicating that ecologically important subsets of the microbial community can change on timescales different than and in response to factors other than those that govern turnover of most members of the assemblage.

Current state of athalassohaline deep-sea hypersaline anoxic basin research-recommendations for future work and relevance to astrobiology.

Deep-sea hypersaline anoxic basins (DHABs) are uniquely stratified polyextreme environments generally found in enclosed seas. These environments select for elusive and widely uncharacterized microbes that may be living below the currently recognized window of life on Earth. Still, there is strong evidence of highly specialized active microbial communities in the Kryos, Discovery, and Hephaestus basins located in the Eastern Mediterranean Sea; the only known athalassohaline DHABs. Life is further constrained in these DHABs as near-saturated concentrations of magnesium chloride significantly reduces water activity (aw ) and exerts extreme chaotropic stress, the tendency of a solution to disorder biomolecules. In this review, we provide an overview of microbial adaptations to polyextremes focusing primarily on chaotropicity, summarize current evidence of microbial life within athalassohaline DHABs and describe the difficulties of life detection approaches and sampling within these environments. We also reveal inconsistent measurements of chaotropic activity in the literature highlighting the need for a new methodology. Finally, we generate recommendations for future investigations and discuss the importance of athalassohaline DHAB research to help inform extraterrestrial life detection missions.

Microbial diversity and activity in Southern California salterns and bitterns: analogues for remnant ocean worlds.

Concurrent osmotic and chaotropic stress make MgCl2 -rich brines extremely inhospitable environments. Understanding the limits of life in these brines is essential to the search for extraterrestrial life on contemporary and relict ocean worlds, like Mars, which could host similar environments. We sequenced environmental 16S rRNA genes and quantified microbial activity across a broad range of salinity and chaotropicity at a Mars-analogue salt harvesting facility in Southern California, where seawater is evaporated in a series of ponds ranging from kosmotropic NaCl brines to highly chaotropic MgCl2 brines. Within NaCl brines, we observed a proliferation of specialized halophilic Euryarchaeota, which corresponded closely with the dominant taxa found in salterns around the world. These communities were characterized by very slow growth rates and high biomass accumulation. As salinity and chaotropicity increased, we found that the MgCl2 -rich brines eventually exceeded the limits of microbial activity. We found evidence that exogenous genetic material is preserved in these chaotropic brines, producing an unexpected increase in diversity in the presumably sterile MgCl2 -saturated brines. Because of their high potential for biomarker preservation, chaotropic brines could therefore serve as repositories of genetic biomarkers from nearby environments (both on Earth and beyond) making them prime targets for future life-detection missions.

Detection of Sulfate-Reducing Bacteria as an Indicator for Successful Mitigation of Sulfide Production.

Sulfate-reducing bacteria (SRBs) are one of the main sources of biogenic H2S generation in oil reservoirs. Excess H2S production in these systems leads to oil biosouring, which causes operational risks and health hazards and can increase the cost of refining crude oil. Nitrate salts are often added to the system to suppress sulfidogenesis. Because SRB populations can persist in biofilms even after nitrate treatment, identifying shifts in the sessile community is crucial for successful mitigation. However, sampling the sessile community is hampered by its inaccessibility. Here, we use the results of a long-term (148 days) ex situ experiment to identify particular sessile community members from observations of the sample waste stream. Microbial community structure was determined for 731 samples across 20 bioreactors using 16S rRNA gene sequencing. By associating microbial community structure with specific steps in the mitigation process, we could distinguish between taxa associated with H2S production and mitigation. After initiation of nitrate treatment, certain SRB populations increased in the planktonic community during critical time points, indicating the dissociation of SRBs from the biofilm. Predicted relative abundances of the dissimilatory sulfate reduction pathway also increased during the critical time points. Here, by analyzing the planktonic community structure, we describe a general method that uses high-throughput amplicon sequencing, metabolic inferences, and cell abundance data to identify successful biofilm mitigation. We anticipate that our approach is also applicable to other systems where biofilms must be mitigated but cannot be sampled easily. IMPORTANCE Microbial biofilms are commonly present in many industrial processes and can negatively impact performance and safety. Within the oil industry, subterranean biofilms cause biosouring with implications for oil quality, cost, occupational health, and the environment. Because these biofilms cannot be sampled directly, methods are needed to indirectly assess the success of mitigation measures. This study demonstrates how the planktonic microbial community can be used to assess the dissociation of sulfate-reducing bacterium (SRB)-containing biofilms. We found that an increase in the abundance of a specific SRB population in the effluent after nitrate treatment can be used as a potential indicator for the successful mitigation of biofilm-forming SRBs. Moreover, a method for determining critical time points for detecting potential indicators is suggested. This study expands our knowledge of improving mitigation strategies for biosouring and could have broader implications in other systems where biofilms lead to adverse consequences.

Extremophile enzyme optimization for low temperature and high salinity are fundamentally incompatible.

The evolutionary mechanisms behind cold and high-saline co-adaptation of proteins are not thoroughly understood. To explore how enzymes evolve in response to multiple environmental pressures we developed a novel in silico method to model the directed evolution of proteins, the Protein Evolution Parameter Calculator (PEPC). PEPC carries out single amino acid substitutions that lead to improvements in the selected user-defined parameters. To investigate the evolutionary relationship between increased flexibility and decreased isoelectric point, which are presumed indicators of cold and saline adaptation in proteins, we applied PEPC to a subset of core haloarchaea orthologous group (cHOG) proteins from the mesophilic Halobacterium salinarum NRC-1 and cold-tolerant Halorubrum lacusprofundi strain ATCC 49239. The results suggest that mutations that increase flexibility will also generally increase isoelectric point. These findings suggest that enzyme adaptation to low temperature and high salinity might be evolutionarily counterposed based on the structural characteristics of probable amino acid mutations. This may help to explain the apparent lack of truly psychrophilic halophiles in nature, and why microbes adapted to polar hypersaline environments typically have mesophilic temperature optima. A better understanding of protein evolution to extremely cold and salty conditions will aid in our understanding of where and how life is distributed on Earth and in our solar system.

Corticosterone response by Peromyscus mice to parasites, reproductive season, and age.

A common response to parasite infestations is increased production of glucocorticoid hormones that regulate immune function. We examined relationships between ectoparasite infestations and fecal corticosterone metabolites (FCM) in deer mice (Peromyscus maniculatus). Furthermore, we experimentally removed fleas to determine if reductions in ectoparasites affected FCM production. Individuals were assigned to control (no flea removal) or treatment (anti-flea application, physical combing) groups and individuals were recaptured to assess changes in FCM concentrations. There was a significant and negative effect of number of anti-flea treatment applications on FCM concentrations of deer mice. However, models including host biology traits and environmental predictors had a better model fit compared to models containing ectoparasite predictors. In particular, there was a significant relationship of deer mouse FCM with date and host age, where glucocorticoid production decreased towards the end of the breeding season and increased with age. Overall, adverse events associated with reproduction and age class, rather than ectoparasites, may be more important to variation in glucocorticoids of deer mice.

Spatial and environmental influences on selection in a clock gene coding trinucleotide repeat in Canada lynx (Lynx canadensis).

Clock genes exhibit substantial control over gene expression and ultimately life-histories using external cues such as photoperiod, and are thus likely to be critical for adaptation to shifting seasonal conditions and novel environments as species redistribute their ranges under climate change. Coding trinucleotide repeats (cTNRs) are found within several clock genes, and may be interesting targets of selection due to their containment within exonic regions and elevated mutation rates. Here, we conduct inter-specific characterization of the NR1D1 cTNR between Canada lynx and bobcat, and intra-specific spatial and environmental association analyses of neutral microsatellites and our functional cTNR marker, to investigate the role of selection on this locus in Canada lynx. We report signatures of divergent selection between lynx and bobcat, with the potential for hybrid-mediated gene flow in the area of range overlap. We also provide evidence that this locus is under selection across Canada lynx in eastern Canada, with both spatial and environmental variables significantly contributing to the explained variation, after controlling for neutral population structure. These results suggest that cTNRs may play an important role in the generation of functional diversity within some mammal species, and allow for contemporary rates of adaptation in wild populations in response to environmental change. We encourage continued investment into the study of cTNR markers to better understand their broader relevance to the evolution and adaptation of mammals.

Recurrent seascape units identify key ecological processes along the western Antarctic Peninsula.

The western Antarctic Peninsula (WAP) is a bellwether of global climate change and natural laboratory for identifying interactions between climate and ecosystems. The Palmer Long-Term Ecological Research (LTER) project has collected data on key ecological and environmental processes along the WAP since 1993. To better understand how key ecological parameters are changing across space and time, we developed a novel seascape classification approach based on in situ temperature, salinity, chlorophyll a, nitrate + nitrite, phosphate, and silicate. We anticipate that this approach will be broadly applicable to other geographical areas. Through the application of self-organizing maps (SOMs), we identified eight recurrent seascape units (SUs) in these data. These SUs have strong fidelity to known regional water masses but with an additional layer of biogeochemical detail, allowing us to identify multiple distinct nutrient profiles in several water masses. To identify the temporal and spatial distribution of these SUs, we mapped them across the Palmer LTER sampling grid via objective mapping of the original parameters. Analysis of the abundance and distribution of SUs since 1993 suggests two year types characterized by the partitioning of chlorophyll a into SUs with different spatial characteristics. By developing generalized linear models for correlated, time-lagged external drivers, we conclude that early spring sea ice conditions exert a strong influence on the distribution of chlorophyll a and nutrients along the WAP, but not necessarily the total chlorophyll a inventory. Because the distribution and density of phytoplankton biomass can have an impact on biomass transfer to the upper trophic levels, these results highlight anticipated links between the WAP marine ecosystem and climate.

Seasonal changes in acute stressor-mediated plasma glucocorticoid regulation in New World flying squirrels.

Southern flying squirrels have higher circulating cortisol levels than most vertebrates. However, regulation of tissue exposure to cortisol by the hormone's carrier protein, corticosteroid-binding globulin (CBG), appears to be altered due to lower-than-expected CBG expression levels, and a reduced affinity for cortisol. To assess the capacity of flying squirrels to regulate acute stress-mediated cortisol levels, we used the dexamethasone (DEX) suppression test followed by the adrenocorticotropic hormone (ACTH) stimulation test in both the breeding and non-breeding seasons, and quantified resultant changes in plasma cortisol and relative CBG levels. Regulation of cortisol via negative feedback, and the acute stress response appeared to function as they do in other vertebrates during the breeding season, but response to DEX in the non-breeding season showed that the sensitivity of the negative feedback mechanism changed across seasons. The relatively high concentrations of DEX required to induce negative feedback suggests that southern flying squirrels have a reduced sensitivity to cortisol compared with other vertebrates, and that high circulating cortisol levels may be required to compensate for low target tissue responsiveness in this species. Cortisol, but not CBG levels, were higher during the non-breeding than breeding season, and females had higher cortisol and CBG levels than males. Our data suggest that flying squirrel cortisol levels are regulated by negative feedback at a higher set point than in related species. Seasonal changes in cortisol levels, target tissue sensitivity to DEX, and in the capacity to respond to stressors appear to be part of the underlying physiology of southern flying squirrels, and may be required to maximize fitness in the face of tradeoffs between survival and reproduction.

Sex-specific graphs: Relating group-specific topology to demographic and landscape data.

Sex-specific genetic structure is a commonly observed pattern among vertebrate species. Facing differential selective pressures, individuals may adopt sex-specific life history traits that ultimately shape genetic variation among populations. Although differential dispersal dynamics are commonly detected in the literature, few studies have used genetic structure to investigate sex-specific functional connectivity. The recent use of graph theoretic approaches in landscape genetics has demonstrated network capacities to describe complex system behaviours where network topology represents genetic interaction among subunits. Here, we partition the overall genetic structure into sex-specific graphs, revealing different male and female dispersal dynamics of a fisher (Pekania [Martes] pennanti) metapopulation in southern Ontario. Our analyses based on network topologies supported the hypothesis of male-biased dispersal. Furthermore, we demonstrated that the effect of the landscape, identified at the population level, could be partitioned among sex-specific strata. We found that female connectivity was negatively correlated with snow depth, whereas connectivity among males was not. Our findings underscore the potential of conducting sex-specific analysis by identifying landscape elements or configuration that differentially promotes or impedes functional connectivity between sexes, revealing processes that may otherwise remain cryptic. We propose that the sex-specific graph approach would be applicable to other vagile species where differential sex-specific processes are expected to occur.

Seasonal energetics and torpor use in North American flying squirrels.

Seasonal cold temperatures require mammals to use morphological, behavioural, or physiological traits to survive periods of extreme cold and food shortage. Torpor is a physiological state that minimizes energy requirements by decreasing resting metabolic rate (MR) and body temperature (Tb). Many rodent species are capable of torpor, however, evidence in northern and southern flying squirrels (Glaucomys sabrinus and Glaucomys volans, respectively) has remained anecdotal. We experimentally attempted to induce torpor in wild-caught flying squirrels by lowering ambient temperature (Ta) and measuring MR using open-flow respirometry. We also studied seasonal differences in MR and Tb at various Ta. Both MR and Tb provided evidence for torpor in flying squirrels, but only infrequent, shallow torpor. MR decreased infrequently and any decreases were rarely sustained for longer than one hour. We found a significant positive relationship between Ta and Tb only in G. volans, which suggests that G. volans is more susceptible to low Ta compared with G. sabrinus, possibly due to their small body size. We observed no substantive seasonal or interspecific differences in the relation between MR and Ta, with the exception that northern flying squirrels expended more energy at cold Ta during warm season trials than other species-season combinations. The infrequency of torpor use in our experiments suggests that other energy-saving strategies, such as social thermoregulation, may limit the reliance on torpor in this lineage.

A test of somatic mosaicism in the androgen receptor gene of Canada lynx (Lynx canadensis).

BACKGROUND: The androgen receptor, an X-linked gene, has been widely studied in human populations because it contains highly polymorphic trinucleotide repeat motifs that have been associated with a number of adverse human health and behavioral effects. A previous study on the androgen receptor gene in carnivores reported somatic mosaicism in the tissues of a number of species including Eurasian lynx (Lynx lynx). We investigated this claim in a closely related species, Canada lynx (Lynx canadensis). The presence of somatic mosaicism in lynx tissues could have implications for the future study of exonic trinucleotide repeats in landscape genomic studies, in which the accurate reporting of genotypes would be highly problematic. METHODS: To determine whether mosaicism occurs in Canada lynx, two lynx individuals were sampled for a variety of tissue types (lynx 1) and tissue locations (lynx 1 and 2), and 1,672 individuals of known sex were genotyped to further rule out mosaicism. RESULTS: We found no evidence of mosaicism in tissues from the two necropsied individuals, or any of our genotyped samples. CONCLUSIONS: Our results indicate that mosaicism does not manifest in Canada lynx. Therefore, the use of hide samples for further work involving trinucleotide repeat polymorphisms in Canada lynx is warranted.

Alkane hydroxylase genes in psychrophile genomes and the potential for cold active catalysis.

BACKGROUND: Psychrophiles are presumed to play a large role in the catabolism of alkanes and other components of crude oil in natural low temperature environments. In this study we analyzed the functional diversity of genes for alkane hydroxylases, the enzymes responsible for converting alkanes to more labile alcohols, as found in the genomes of nineteen psychrophiles for which alkane degradation has not been reported. To identify possible mechanisms of low temperature optimization we compared putative alkane hydroxylases from these psychrophiles with homologues from nineteen taxonomically related mesophilic strains. RESULTS: Seven of the analyzed psychrophile genomes contained a total of 27 candidate alkane hydroxylase genes, only two of which are currently annotated as alkane hydroxylase. These candidates were mostly related to the AlkB and cytochrome p450 alkane hydroxylases, but several homologues of the LadA and AlmA enzymes, significant for their ability to degrade long-chain alkanes, were also detected. These putative alkane hydroxylases showed significant differences in primary structure from their mesophile homologues, with preferences for specific amino acids and increased flexibility on loops, bends, and α-helices. CONCLUSION: A focused analysis on psychrophile genomes led to discovery of numerous candidate alkane hydroxylase genes not currently annotated as alkane hydroxylase. Gene products show signs of optimization to low temperature, including regions of increased flexibility and amino acid preferences typical of psychrophilic proteins. These findings are consistent with observations of microbial degradation of crude oil in cold environments and identify proteins that can be targeted in rate studies and in the design of molecular tools for low temperature bioremediation.

The subtle role of climate change on population genetic structure in Canada lynx.

Anthropogenically driven climatic change is expected to reshape global patterns of species distribution and abundance. Given recent links between genetic variation and environmental patterns, climate change may similarly impact genetic population structure, but we lack information on the spatial and mechanistic underpinnings of genetic-climate associations. Here, we show that current genetic variability of Canada lynx (Lynx canadensis) is strongly correlated with a winter climate gradient (i.e. increasing snow depth and winter precipitation from west-to-east) across the Pacific-North American (PNO) to North Atlantic Oscillation (NAO) climatic systems. This relationship was stronger than isolation by distance and not explained by landscape variables or changes in abundance. Thus, these patterns suggest that individuals restricted dispersal across the climate boundary, likely in the absence of changes in habitat quality. We propose habitat imprinting on snow conditions as one possible explanation for this unusual phenomenon. Coupling historical climate data with future projections, we also found increasingly diverging snow conditions between the two climate systems. Based on genetic simulations using projected climate data (2041-2070), we predicted that this divergence could lead to a threefold increase in genetic differentiation, potentially leading to isolated east-west populations of lynx in North America. Our results imply that subtle genetic structure can be governed by current climate and that substantive genetic differentiation and related ecological divergence may arise from changing climate patterns.

Bacterial diversity in snow on North Pole ice floes.

The microbial abundance and diversity in snow on ice floes at three sites near the North Pole was assessed using quantitative PCR and 454 pyrosequencing. Abundance of 16S rRNA genes in the samples ranged between 43 and 248 gene copies per millilitre of melted snow. A total of 291,331 sequences were obtained through 454 pyrosequencing of 16S rRNA genes, resulting in 984 OTUs at 97 % identity. Two sites were dominated by Cyanobacteria (72 and 61 %, respectively), including chloroplasts. The third site differed by consisting of 95 % Proteobacteria. Principal component analysis showed that the three sites clustered together when compared to the underlying environments of sea ice and ocean water. The Shannon indices ranged from 2.226 to 3.758, and the Chao1 indices showed species richness between 293 and 353 for the three samples. The relatively low abundances and diversity found in the samples indicate a lower rate of microbial input to this snow habitat compared to snow in the proximity of terrestrial and anthropogenic sources of microorganisms. The differences in species composition and diversity between the sites show that apparently similar snow habitats contain a large variation in biodiversity, although the differences were smaller than the differences to the underlying environment. The results support the idea that a globally distributed community exists in snow and that the global snow community can in part be attributed to microbial input from the atmosphere.

Ultrasound and ultraviolet: crypsis in gliding mammals.

Gliding is only present in six extant groups of mammals-interestingly, despite divergent evolutionary histories, all mammalian gliders are strictly nocturnal. Gliding mammals also seem to have relatively high rates of ultrasound use and ultraviolet-induced photoluminescence (UVP) in contrast with their close relatives. Therefore, we hypothesized that, despite diverging lineages, gliding mammals use similar modes of cryptic communication compared to their non-gliding counterparts. We developed two datasets containing the vocal range (minimum-maximum of the dominant harmonic; kHz) and UVP of 73 and 82 species, respectively; we report four novel vocal repertoires and 57 novel observations of the presence or absence of UVP. We complemented these datasets with information about body size, diel activity patterns, habitat openness, and sociality to explore possible covariates related to vocal production and UVP. We found that the maximum of the dominant harmonic was significant higher in gliding mammals when vocalizing than their non-gliding relatives. Additionally, we found that nocturnality was the only significant predictor of UVP, consistent with the previous hypothesis that luminophores primarily drive UVP in mammal fur. In contrast, however, we did not find UVP ubiquitous in nocturnal mammals, suggesting that some unknown process may contribute to variation in this trait.

Using low volume eDNA methods to sample pelagic marine animal assemblages.

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 in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.