Browse
Submit Data
Databases
API
Help

Dataset Information

26 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High spatial resolution global ocean metagenomes from Bio-GO-SHIP repeat hydrography transects.

ABSTRACT: Detailed descriptions of microbial communities have lagged far behind physical and chemical measurements in the marine environment. Here, we present 971 globally distributed surface ocean metagenomes collected at high spatio-temporal resolution. Our low-cost metagenomic sequencing protocol produced 3.65 terabases of data, where the median number of base pairs per sample was 3.41 billion. The median distance between sampling stations was 26 km. The metagenomic libraries described here were collected as a part of a biological initiative for the Global Ocean Ship-based Hydrographic Investigations Program, or "Bio-GO-SHIP." One of the primary aims of GO-SHIP is to produce high spatial and vertical resolution measurements of key state variables to directly quantify climate change impacts on ocean environments. By similarly collecting marine metagenomes at high spatiotemporal resolution, we expect that this dataset will help answer questions about the link between microbial communities and biogeochemical fluxes in a changing ocean.

SUBMITTER: Larkin AA

PROVIDER: S-EPMC8052323 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Southern Ocean Biogeochemical Float Deployment Strategy, With Example From the Greenwich Meridian Line (GO-SHIP A12).

Project description:Biogeochemical Argo floats, profiling to 2,000-m depth, are being deployed throughout the Southern Ocean by the Southern Ocean Carbon and Climate Observations and Modeling program (SOCCOM). The goal is 200 floats by 2020, to provide the first full set of annual cycles of carbon, oxygen, nitrate, and optical properties across multiple oceanographic regimes. Building from no prior coverage to a sparse array, deployments are based on prior knowledge of water mass properties, mean frontal locations, mean circulation and eddy variability, winds, air-sea heat/freshwater/carbon exchange, prior Argo trajectories, and float simulations in the Southern Ocean State Estimate and Hybrid Coordinate Ocean Model (HYCOM). Twelve floats deployed from the 2014-2015 Polarstern cruise from South Africa to Antarctica are used as a test case to evaluate the deployment strategy adopted for SOCCOM's 20 deployment cruises and 126 floats to date. After several years, these floats continue to represent the deployment zones targeted in advance: (1) Weddell Gyre sea ice zone, observing the Antarctic Slope Front, and a decadally-rare polynya over Maud Rise; (2) Antarctic Circumpolar Current (ACC) including the topographically steered Southern Zone chimney where upwelling carbon/nutrient-rich deep waters produce surprisingly large carbon dioxide outgassing; (3) Subantarctic and Subtropical zones between the ACC and Africa; and (4) Cape Basin. Argo floats and eddy-resolving HYCOM simulations were the best predictors of individual SOCCOM float pathways, with uncertainty after 2 years of order 1,000 km in the sea ice zone and more than double that in and north of the ACC.

| S-EPMC6472510 | biostudies-literature

Ocean-scale patterns in community respiration rates along continuous transects across the Pacific Ocean.

Project description:Community respiration (CR) of organic material to carbon dioxide plays a fundamental role in ecosystems and ocean biogeochemical cycles, as it dictates the amount of production available to higher trophic levels and for export to the deep ocean. Yet how CR varies across large oceanographic gradients is not well-known: CR is measured infrequently and cannot be easily sensed from space. We used continuous oxygen measurements collected by autonomous gliders to quantify surface CR rates across the Pacific Ocean. CR rates were calculated from changes in apparent oxygen utilization and six different estimates of oxygen flux based on wind speed. CR showed substantial spatial variation: rates were lowest in ocean gyres (mean of 6.93 mmol m(-3) d(-1)±8.0 mmol m(-3) d(-1) standard deviation in the North Pacific Subtropical Gyre) and were more rapid and more variable near the equator (8.69 mmol m(-3) d(-1)±7.32 mmol m(-3) d(-1) between 10°N and 10°S) and near shore (e.g., 5.62 mmol m(-3) d(-1)±45.6 mmol m(-3) d(-1) between the coast of California and 124°W, and 17.0 mmol m(-3) d(-1)±13.9 mmol m(-3) d(-1) between 156°E and the Australian coast). We examined how CR varied with coincident measurements of temperature, turbidity, and chlorophyll concentrations (a proxy for phytoplankton biomass), and found that CR was weakly related to different explanatory variables across the Pacific, but more strongly related to particular variables in different biogeographical areas. Our results indicate that CR is not a simple linear function of chlorophyll or temperature, and that at the scale of the Pacific, the coupling between primary production, ocean warming, and CR is complex and variable. We suggest that this stems from substantial spatial variation in CR captured by high-resolution autonomous measurements.

| S-EPMC4105538 | biostudies-literature

Shelf-ocean exchange and hydrography west of the Antarctic Peninsula: a review.

Project description:The West Antarctic Peninsula (WAP) is a highly productive marine ecosystem where extended periods of change have been observed in the form of glacier retreat, reduction of sea-ice cover and shifts in marine populations, among others. The physical environment on the shelf is known to be strongly influenced by the Antarctic Circumpolar Current flowing along the shelf slope and carrying warm, nutrient-rich water, by cold waters flooding into the northern Bransfield Strait from the Weddell Sea, by an extensive network of glaciers and ice shelves, and by strong seasonal to inter-annual variability in sea-ice formation and air-sea interactions, with significant modulation by climate modes like El Niño-Southern Oscillation and the Southern Annular Mode. However, significant gaps have remained in understanding the exchange processes between the open ocean and the shelf, the pathways and fate of oceanic water intrusions, the shelf heat and salt budgets, and the long-term evolution of the shelf properties and circulation. Here, we review how recent advances in long-term monitoring programmes, process studies and newly developed numerical models have helped bridge these gaps and set future research challenges for the WAP system.This article is part of the theme issue 'The marine system of the West Antarctic Peninsula: status and strategy for progress in a region of rapid change'.

| S-EPMC5954465 | biostudies-literature

Seawater physics and chemistry along the Med-SHIP transects in the Mediterranean Sea in 2016.

Project description:The Mediterranean Sea has been sampled irregularly by research vessels in the past, mostly by national expeditions in regional waters. To monitor the hydrographic, biogeochemical and circulation changes in the Mediterranean Sea, a systematic repeat oceanographic survey programme called Med-SHIP was recommended by the Mediterranean Science Commission (CIESM) in 2011, as part of the Global Ocean Ship-based Hydrographic Investigations Program (GO-SHIP). Med-SHIP consists of zonal and meridional surveys with different frequencies, where comprehensive physical and biogeochemical properties are measured with the highest international standards. The first zonal survey was done in 2011 and repeated in 2018. In addition, a network of meridional (and other key) hydrographic sections were designed: the first cycle of these sections was completed in 2016, with three cruises funded by the EU project EUROFLEETS2. This paper presents the physical and chemical data of the meridional and key transects in the Western and Eastern Mediterranean Sea collected during those cruises.

| S-EPMC10776779 | biostudies-literature

Mean hydrography on the continental shelf from 26 repeat glider deployments along Southeastern Australia.

Project description:Since 2008, 26 glider missions have been undertaken along the continental shelf of southeastern Australia. Typically these missions have spanned the continental shelf on the inshore edge of the East Australian Current from 29.5-33.5°S. This comprehensive dataset of over 33,600 CTD profiles from the surface to within 10?m of the bottom in water depths ranging 25-200?m provides new and unprecedented high resolution observations of the properties of the continental shelf waters adjacent to a western boundary current, straddling the region where it separates from the coast. The region is both physically and biologically significant, and is also in a hotspot of ocean warming. We present gridded mean fields for temperature, salinity and density, but also dissolved oxygen and chlorophyll-a fluorescence indicative of phytoplankton biomass. This data will be invaluable for understanding shelf stratification, circulation, biophysical and bio-geochemical interactions, as well as for the validation of high-resolution ocean models or serving as teaching material.

| S-EPMC5004588 | biostudies-literature

Secondary metabolite biosynthetic diversity in Arctic Ocean metagenomes.

Project description:Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are mega enzymes responsible for the biosynthesis of a large fraction of natural products (NPs). Molecular markers for biosynthetic genes, such as the ketosynthase (KS) domain of PKSs, have been used to assess the diversity and distribution of biosynthetic genes in complex microbial communities. More recently, metagenomic studies have complemented and enhanced this approach by allowing the recovery of complete biosynthetic gene clusters (BGCs) from environmental DNA. In this study, the distribution and diversity of biosynthetic genes and clusters from Arctic Ocean samples (NICE-2015 expedition), was assessed using PCR-based strategies coupled with high-throughput sequencing and metagenomic analysis. In total, 149 KS domain OTU sequences were recovered, 36 % of which could not be assigned to any known BGC. In addition, 74 bacterial metagenome-assembled genomes were recovered, from which 179 BGCs were extracted. A network analysis identified potential new NP families, including non-ribosomal peptides and polyketides. Complete or near-complete BGCs were recovered, which will enable future heterologous expression efforts to uncover the respective NPs. Our study represents the first report of biosynthetic diversity assessed for Arctic Ocean metagenomes and highlights the potential of Arctic Ocean planktonic microbiomes for the discovery of novel secondary metabolites. The strategy employed in this study will enable future bioprospection, by identifying promising samples for bacterial isolation efforts, while providing also full-length BGCs for heterologous expression.

| S-EPMC8767328 | biostudies-literature

Arctic Ocean metagenomes

Project description:Arctic Ocean metagenomes from HLY1502

| PRJEB14154 | ENA

Southern Ocean Metagenomes

Project description:SO-METAG

| PRJEB37465 | ENA

High-resolution repeat topography of drifting ice floes in the Arctic Ocean from terrestrial laser scanning.

Project description:Snow and ice topography impact and are impacted by fluxes of mass, energy, and momentum in Arctic sea ice. We measured the topography on approximately a 0.5 km2 drifting parcel of Arctic sea ice on 42 separate days from 18 October 2019 to 9 May 2020 via Terrestrial Laser Scanning (TLS). These data are aligned into an ice-fixed, lagrangian reference frame such that topographic changes (e.g., snow accumulation) can be observed for time periods of up to six months. Using in-situ measurements, we have validated the vertical accuracy of the alignment to ± 0.011 m. This data collection and processing workflow is the culmination of several prior measurement campaigns and may be generally applied for repeat TLS measurements on drifting sea ice. We present a description of the data, a software package written to process and align these data, and the philosophy of the data processing. These data can be used to investigate snow accumulation and redistribution, ice dynamics, surface roughness, and they can provide valuable context for co-located measurements.

| S-EPMC10787767 | biostudies-literature

Chemical Interactions Between Ship-Originated Air Pollutants and Ocean-Emitted Halogens.

Project description:Ocean-going ships supply products from one region to another and contribute to the world's economy. Ship exhaust contains many air pollutants and results in significant changes in marine atmospheric composition. The role of reactive halogen species (RHS) in the troposphere has received increasing recognition and oceans are the largest contributors to their atmospheric burden. However, the impact of shipping emissions on RHS and that of RHS on ship-originated air pollutants have not been studied in detail. Here, an updated Weather Research Forecasting coupled with Chemistry model is utilized to explore the chemical interactions between ship emissions and oceanic RHS over the East Asia seas in summer. The emissions and resulting chemical transformations from shipping activities increase the level of NO and NO2 at the surface, increase O3 in the South China Sea, but decrease O3 in the East China Sea. Such changes in pollutants result in remarkable changes in the levels of RHS (>200% increase of chlorine; ∼30% and ∼5% decrease of bromine and iodine, respectively) as well as in their partitioning. The abundant RHS, in turn, reshape the loadings of air pollutants (∼20% decrease of NO and NO2; ∼15% decrease of O3) and those of the oxidants (>10% reduction of OH and HO2; ∼40% decrease of NO3) with marked patterns along the ship tracks. We, therefore, suggest that these important chemical interactions of ship-originated emissions with RHS should be considered in the environmental policy assessments of the role of shipping emissions in air quality and climate.

| S-EPMC8008258 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data