Search for: All records

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. 

The Antarctic marine environment is a dynamic ecosystem where microorganisms play an important role in key biogeochemical cycles. Despite the role that microbes play in this ecosystem, little is known about the genetic and metabolic diversity of Antarctic marine microbes. In this study we leveraged DNA samples collected by the Palmer Long Term Ecological Research (LTER) project to sequence shotgun metagenomes of 48 key samples collected across the marine ecosystem of the western Antarctic Peninsula (wAP). We developed an in silico metagenomics pipeline (iMAGine) for processing metagenomic data and constructing metagenome-assembled genomes (MAGs), identifying a diverse genomic repertoire related to the carbon, sulfur, and nitrogen cycles. A novel analytical approach based on gene coverage was used to understand the differences in microbial community functions across depth and region. Our results showed that microbial community functions were partitioned based on depth. Bacterial members harbored diverse genes for carbohydrate transformation, indicating the availability of processes to convert complex carbons into simpler bioavailable forms. We generated 137 dereplicated MAGs giving us a new perspective on the role of prokaryotes in the coastal wAP. In particular, the presence of mixotrophic prokaryotes capable of autotrophic and heterotrophic lifestyles indicated a metabolically flexible community, which we hypothesize enables survival under rapidly changing conditions. Overall, the study identified key microbial community functions and created a valuable sequence library collection for future Antarctic genomics research. 

Abstract. Heterotrophic marine bacteria utilize organic carbon for growth and biomass synthesis. Thus, their physiological variability is key to the balancebetween the production and consumption of organic matter and ultimately particle export in the ocean. Here we investigate a potential link betweenbacterial traits and ecosystem functions in the rapidly warming West Antarctic Peninsula (WAP) region based on a bacteria-oriented ecosystemmodel. Using a data assimilation scheme, we utilize the observations of bacterial groups with different physiological traits to constrain thegroup-specific bacterial ecosystem functions in the model. We then examine the association of the modeled bacterial and other key ecosystemfunctions with eight recurrent modes representative of different bacterial taxonomic traits. Both taxonomic and physiological traits reflect thevariability in bacterial carbon demand, net primary production, and particle sinking flux. Numerical experiments under perturbed climate conditionsdemonstrate a potential shift from low nucleic acid bacteria to high nucleic acid bacteria-dominated communities in the coastal WAP. Our studysuggests that bacterial diversity via different taxonomic and physiological traits can guide the modeling of the polar marine ecosystem functionsunder climate change. 

The transition from winter to spring represents a major shift in the basal energy source for the Antarctic marine ecosystem from lipids and other sources of stored energy to sunlight. Because sea ice imposes a strong control on the transmission of sunlight into the water column during the polar spring, we hypothesized that the timing of the sea ice retreat influences the timing of the transition from stored energy to photosynthesis. To test the influence of sea ice on water column microbial energy utilization we took advantage of unique sea ice conditions in Arthur Harbor, an embayment near Palmer Station on the western Antarctic Peninsula, during the 2015 spring–summer seasonal transition. Over a 5-week period we sampled water from below land-fast sea ice, in the marginal ice zone at nearby Palmer Station B, and conducted an ice removal experiment with incubations of water collected below the land-fast ice. Whole-community metatranscriptomes were paired with lipidomics to better understand how lipid production and utilization was influenced by light conditions. We identified several different phytoplankton taxa that responded similarly to light by the number of genes up-regulated, and in the transcriptional complexity of this response. We applied a principal components analysis to these data to reduce their dimensionality, revealing that each of these taxa exhibited a strikingly different pattern of gene up-regulation. By correlating the changes in lipid concentration to the first principal component of log fold-change for each taxa we could make predictions about which taxa were associated with different changes in the community lipidome. We found that genes coding for the catabolism of triacylglycerol storage lipids were expressed early on in phytoplankton associated with aFragilariopsis kerguelensisreference transcriptome. Phytoplankton associated with aCorethron pennatumreference transcriptome occupied an adjacent niche, responding favorably to higher light conditions thanF. kerguelensis. Other diatom and dinoflagellate taxa had distinct transcriptional profiles and correlations to lipids, suggesting diverse ecological strategies during the polar winter–spring transition. 

First-year sea-ice thickness, draft, salinity, temperature, and density were measured during near-weekly surveys at the main first-year ice coring site (MCS-FYI) during the MOSAiC expedition (legs 1 to 4). The ice cores were extracted either with a 9-cm (Mark II) or 7.25-cm (Mark III) internal diameter ice corers (Kovacs Enterprise, US). This data set includes data from 23 coring site visits and were performed from 28 October 2019 to 29 July 2020 at coring locations within 130 m to each other in the MOSAiC Central Observatory. During each coring event, ice temperature was measured in situ from a separate temperature core, using Testo 720 thermometers in drill holes with a length of half-core-diameter at 5-cm vertical resolution. Ice bulk practical salinity was measured from melted core sections at 5-cm resolution using a YSI 30 conductivity meter. Ice density was measured using the hydrostatic weighing method (Pustogvar and Kulyakhtin, 2016) from a density core in the freezer laboratory onboard Polarstern at the temperature of –15°C. Relative volumes of brine and gas were estimated from ice salinity, temperature and density using Cox and Weeks (1983) for cold ice and Leppäranta and Manninen (1988) for ice warmer than –2°C.The data contains the event label (1), time (2), and global coordinates (3,4) of each coring measurement and sample IDs (13, 15). Each salinity core has its manually measured ice thickness (5), ice draft (6), core length (7), and mean snow height (22). Each core section has the total length of its top (8) and bottom (9) measured in situ, as well estimated depth of section top (10), bottom (11), and middle (12). The depth estimates assume that the total length of all core sections is equal to the measured ice thickness. Each core section has the value of its practical salinity (14), isotopic values (16, 17, 18) (Meyer et al., 2000), as well as sea ice temperature (19) and ice density (20) interpolated to the depth of salinity measurements. The global coordinates of coring sites were measured directly. When it was not possible, coordinates of the nearby temperature buoy 2019T66 were used. Ice mass balance buoy 2019T66 installation is described in doi:10.1594/PANGAEA.938134. Brine volume (21) fraction estimates are presented only for fraction values from 0 to 30%. Each core section also has comments (23) describing if the sample is from a false bottom, from rafted ice or has any other special characteristics.Macronutrients from the salinity core, and more isotope data will be published in a subsequent version of this data set. 

We present sea ice temperature and salinity data from first-year ice (FYI) and second-year ice (SYI) relevant to the temporal development of sea ice permeability and brine drainage efficiency from the early growth phase in October 2019 to the onset of spring warming in May 2020. Our dataset was collected in the central Arctic Ocean during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) Expedition in 2019 to 2020. MOSAiC was an international transpolar drift expedition in which the German icebreaker RV Polarstern anchored into an ice floe to gain new insights into Arctic climate over a full annual cycle. In October 2019, RV Polarstern moored to an ice floe in the Siberian sector of the Arctic at 85 degrees north and 137 degrees east to begin the drift towards the North Pole and the Fram Strait via the Transpolar Drift Stream. The data presented here were collected during the first three legs of the expedition, so all the coring activities took place on the same floe. The end dates of legs 1, 2, and 3 were 13 December, 24 February, and 4 June, respectively. The dataset contributed to a baseline study entitled, Deciphering the properties of different Arctic ice types during the growth phase of the MOSAiC floes: Implications for future studies. The study highlights downward directed gas pathways in FYI and SYI by inferring sea ice permeability and potential brine release from several time series of temperature and salinity measurements. The physical properties presented in this paper lay the foundation for subsequent analyses on actual gas contents measured in the ice cores, as well as air-ice and ice-ocean gas fluxes. Sea ice cores were collected with a Kovacs Mark II 9 cm diameter corer. To measure ice temperatures, about 4.5 cm deep holes were drilled into the core (intervals varied by site and leg) . The temperatures were measured by a digital thermometer within minutes after the cores were retrieved. The ice cores were placed into pre-labelled plastic sleeves sealed at the bottom end. The ice cores were transported to RV Polarstern and stored in a -20 degrees Celsius freezer. Each of the cores was sub-sampled, melted at room temperature, and processed for salinity within one or two days. The practical salinity was estimated by measuring the electrical conductivity and temperature of the melted samples using a WTW Cond 3151 salinometer equipped with a Tetra-Con 325 four-electrode conductivity cell. The practical salinity represents the the salinity estimated from the electrical conductivity of the solution. The dataset also contains derived variables, including sea ice density, brine volume fraction, and the Rayleigh number. 

The West Antarctic Peninsula (henceforth “Peninsula”) is experiencing rapid warming and melting that is impacting the regional marine food web. The primary phytoplankton groups along the Peninsula are diatoms and cryptophytes. Relative to diatoms, there has been little focus on regional cryptophytes, and thus our understanding of their diversity and ecology is limited, especially at the species level. This gap is important, as diatoms and cryptophytes play distinct roles in the regional marine food web and biogeochemistry. Here, we use a phylogenetic placement approach with 18S rRNA gene amplicon sequence variants to assess surface ocean cryptophyte diversity and its drivers at a high taxonomic resolution along the Peninsula. Data were collected over 5 years (2012–2016) during the regional research cruises of the Palmer Long‐Term Ecological Research program. Our results indicate that there are two major cryptophyte taxa along the Peninsula, consisting of distinctGeminigeraspp., which in aggregate always comprise nearly 100% of the cryptophyte community (indicating low taxa evenness). The primary taxon dominates the cryptophyte community across all samples/years, which span a broad range of oceanographic conditions. A shift in cryptophyte community composition between a lower (higher) primary (secondary) taxon percentage is associated with distinct oceanographic conditions, including lower (higher) temperature, salinity, nutrients, and cryptophyte relative abundance (phytoplankton biomass and diatom relative abundance). These results emphasize the need for a full characterization of the ecology of these two taxa, as it is predicted that cryptophytes will increase along the Peninsula given projections of continued regional environmental change.