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| griddap | Subset | tabledap | Make A Graph | wms | files | Accessible | Title | Summary | FGDC | ISO 19115 | Info | Background Info | RSS | Institution | Dataset ID | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_964227_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_964227_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_964227_v1/ | public | [16S rRNA amplicon sequence metadata from water samples and biofilms] - 16S rRNA gene amplicon sequences metadata collected from water samples and biofilms on mineral substrates deployed in the Lau Basin (Tonga) during R/V Thompson cruise TN401 from Mar to Apr 2022 (RUI: Collaborative Research: The impact of symbiont-larval interactions on species distributions across southwestern Pacific hydrothermal vents) | 16S rRNA gene amplicon sequences were generated from biofilms present on crushed substrates deployed at Lau Basin hydrothermal vents for approximately two weeks during R/V Thompson cruise TN401 from March to April 2022, typically in diffuse fluid flow. 16S rRNA gene amplicon sequences were generated from seawater or hydrothermal fluid samples collected on to filters via ROV deployed instruments. This dataset contains NCBI accession metadata and sample collection information.\n\ncdm_data_type = Other\nVARIABLES:\nSample_ID (unitless)\nBioproject_accession (unitless)\nBiosample_accession (unitless)\nCollection_date (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\ndepth (m)\nSample_type (unitless)\nColonizer_No (unitless)\nSRA_Study (unitless)\nSRA_accession (unitless)\nSequencing_technologies (unitless)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_964227_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_964227_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_964227_v1/index.htmlTable | https://osprey.bco-dmo.org/dataset/964227
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_964227_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_964227_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_964227_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745527.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745527 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745527.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_745527/ | public | [18S rRNA gene tag sequences from DNA and RNA] - NCBI accession metadata for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014 (Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series) | Raw DNA and RNA V4 tag sequences include spatially and temporally distinct samples from coastal California. Samples were collected in Niskin bottles with a CTD rosette at the San Pedro Ocean Time-series (SPOT) between April of 2013 and January of 2014. This dataset contains sequence data accession numbers and metadata for the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (SRA Study ID: SRP070577, BioProject: PRJNA311248).\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nsample_name (unitless)\nSRA_run_ID (unitless)\nSRA_run_link (unitless)\nlibrary_ID (unitless)\nSRA_study_ID (unitless)\nSRA_title (unitless)\nlibrary_strategy (unitless)\nlibrary_source (unitless)\nlibrary_selection (unitless)\nlibrary_layout (unitless)\nplatform (unitless)\ninstrument_model (unitless)\ndesign_description (unitless)\nfiletype (unitless)\nfilename (unitless)\nfiletpe2 (unitless)\nfilename2 (unitless)\ndepth2 (Depth, various)\nlatitude (degrees_north)\nlongitude (degrees_east)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_745527_fgdc.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_745527/index.htmlTable | https://www.bco-dmo.org/dataset/745527
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_745527.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_745527&showErrors=false&email= | BCO-DMO | bcodmo_dataset_745527 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_847425_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_847425_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_847425_v1/ | public | [Acropora cervicornis bleaching sequences] - Sequences from the coral Acropora cervicornis determined before and after bleaching at the Mote Marine Laboratory in August and September 2015 (Collaborative Research: Tracking the interacting roles of the environment, host genotype, and a novel Rickettsiales in coral disease susceptibility) | This dataset contains information about sequences of coral the Acropora cervicornis collected from host colonies (genets) at the Mote Marine Laboratory in situ coral nursery in Looe Key, Lower Florida Keys, USA in August and September of 2015. The sequence data can be found in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database under accession number SRP267474 with the associated BioProject PRJNA639601.\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nsample_name (unitless)\nSRA_run_ID (unitless)\nSRA_study_ID (unitless)\nSRA_title (unitless)\nlibrary_strategy (unitless)\nlibrary_source (unitless)\nlibrary_selection (unitless)\nlibrary_layout (unitless)\nplatform (unitless)\ninstrument_model (unitless)\ndesign (unitless)\nfiletype (unitless)\nfilename (unitless)\nfiletype2 (unitless)\nfilename2 (unitless)\nsite (unitless)\ncollection_date (unitless)\nlat (degrees_north)\nlongitude (degrees_east)\nHost_organism (unitless)\ngenotype (unitless)\nbleach_status (unitless)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_847425_v1/index.htmlTable | https://www.bco-dmo.org/dataset/847425
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_847425_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_847425_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_847425_v1 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_785167.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_785167 | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_785167/ | public | [Crassostrea virginica gonad MBD-BSseq] - Eastern oyster gonad methylation patterns in response to experimental ocean acidification (Collaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters?) | Eastern oyster gonad methylation patterns in response to experimental ocean acidification at pCO2 levels 400 and 2800 ppm. Oysters were collected from an intertidal oyster reef in Plum Island Sound, MA, Gulf of Maine in mid-July 2016. This dataset includes GenBank BioProject PRJNA513384 metadata.\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nbiosample_accession (unitless)\nlibrary_ID (unitless)\ntitle (unitless)\nlibrary_strategy (unitless)\nlibrary_source (unitless)\nlibrary_selection (unitless)\nlibrary_layout (unitless)\nplatform (unitless)\ninstrument_model (unitless)\ndesign_description (unitless)\nfiletype (unitless)\nfilename (unitless)\nfilename2 (unitless)\nMBD_cv_id (unitless)\npCO2_treatment (P CO2 Treatment, ppm)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_785167/index.htmlTable | https://www.bco-dmo.org/dataset/785167
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_785167.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_785167&showErrors=false&email= | BCO-DMO | bcodmo_dataset_785167 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_966488_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_966488_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_966488_v1/ | public | [Field survey coral microbiome composition] - Accession numbers for 16S rRNA genes from microbial communities from four stony coral species collected across sites in Bahia Almirante, Panama in summer of 2021 (Collaborative Research: Biodiversity and resilience of corals and their microbiomes in response to ocean deoxygenation) | This dataset includes accession numbers and related information for 16S rRNA genes from microbial communities from four stony coral species in Bahia Almirante, Panama. Coral microbiomes were sampled by SCUBA divers in summer 2021 from 5 sites at both shallow (3 meters) and deep (10 to 13 meters) depths. These sites span a roughly east-west range representing a gradient of conditions within the bay where western sites are further from the mouth of the bay and eastern sites are closer to the mouth of the bay. Coral species include Agaricia tenuifolia, Montastraea cavernosa, Siderastrea siderea, and Stephenocoenia intersepta. Sequence data is available in NCBI Genbank under BioProject accession PRJNA939210.\n\ncdm_data_type = Other\nVARIABLES:\nSRA_accession (unitless)\nsample_name (unitless)\nbioproject_accession (unitless)\norganism (unitless)\ncollection_date (unitless)\nenv_broad_scale (unitless)\nenv_local_scale (unitless)\nenv_medium (unitless)\ngeo_loc_name (unitless)\nhost (unitless)\ndepth (m)\nlatitude (degrees_north)\nlongitude (degrees_east)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_966488_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_966488_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_966488_v1/index.htmlTable | https://osprey.bco-dmo.org/dataset/966488
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_966488_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_966488_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_966488_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_747872.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_747872 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_747872.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_747872/ | public | [Heterosigma akashiwo acclimation] - NCBI accessions of the harmful alga Heterosigma akashiwo (CCMP2393) grown under a range of CO2 concentrations from 200-1000 ppm (Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2) | This dataset includes metadata associated with NCBI BioProject PRJNA377729 \\Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2\\ PRJNA377729: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA377729. The alga Heterosigma akashiwo was grown at CO2 levels from about 200 to 1000 ppm and then the DNA and RNA were sequenced.\n\ncdm_data_type = Other\nVARIABLES:\nsample_name (unitless)\nsample_title (unitless)\nbioproject_accession (unitless)\norganism (unitless)\nstrain (unitless)\nisolate (unitless)\nhost (unitless)\nisolation_source (unitless)\ntime (Collection Date, seconds since 1970-01-01T00:00:00Z)\ngeo_loc_name (unitless)\nsample_type (unitless)\nbiomaterial_provider (unitless)\ncollected_by (unitless)\ndepth (m)\nenv_biome (unitless)\ngenotype (unitless)\nlat_lon (Latitude, decimal degrees)\npassage_history (unitless)\nsamp_size (unitless)\ntemp_C (degrees Celsius)\nlight_level_umol_m2_s (micromol photons m-2 s-1)\nlight_dark_hr (hours)\nMedia (unitless)\nCO2_ppm (parts per million)\nAlkalinity (micromol per kilogram (umol/kg))\npH (Sea Water Ph Reported On Total Scale, unitless; pH scale)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_747872/index.htmlTable | https://www.bco-dmo.org/dataset/747872
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_747872.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_747872&showErrors=false&email= | BCO-DMO | bcodmo_dataset_747872 | ||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_658497.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_658497 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_658497.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_658497/ | public | [Isolation culturing and sequencing of bacteria and viruses] - Isolation, culturing, and sequencing of bacteria and viruses collected in Canoe Cove, Nahant, MA during 2010 (Marine Bacterial Viruses project) (How can bacterial viruses succeed in the marine environment?) | Isolation, culturing, and sequencing of bacteria and viruses collected in Canoe Cove, Nahant, MA during 2010 (Marine Bacterial Viruses project)\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nenv_biome (unitless)\ngeo_loc_name (unitless)\norganism_type (unitless)\ncollection_date (unitless)\nisolation_source (unitless)\nsample_name (unitless)\norganism (unitless)\nstrain (unitless)\nisolate (unitless)\nhost (unitless)\nlab_host (unitless)\nsample_type (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\ntemp (Temperature, degrees celsius)\nordinal_day_of_isolation (unitless)\ndescription (unitless)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_658497_fgdc.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_658497/index.htmlTable | https://www.bco-dmo.org/dataset/658497
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_658497.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_658497&showErrors=false&email= | BCO-DMO | bcodmo_dataset_658497 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_930084_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_930084_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_930084_v1/ | public | [Kāneʻohe Bay Time-series - microbial community] - Flow cytometry, 16S rRNA gene amplicons, chlorophyll a, and surface seawater measurements taken between August 2017 to June 2019 Kāneʻohe Bay, Oʻahu, Hawaiʻi (Population genomics and ecotypic divergence in the most dominant lineage of marine bacteria) | These data include temperature, pH, salinity, chlorophyll a concentrations, cellular abundances of Prochlorococcus, Synechococcus, photosynthetic picoeukaryotes, and heterotrophic bacteria, and 16S ribosomal RNA gene amplicon libraries from 200 surface seawater samples collected as part of the Kāneʻohe Bay Time-series (KByT). Near-monthly sampling of surface seawater was conducted between August 2017 to June 2019 at 10 sites within coastal waters of Kāneʻohe Bay, Oʻahu, Hawaiʻi and in the adjacent offshore. Instruments used were a YSI 6,600 sonde, a Turner 10AU fluorometer, an EPICS ALTRA flow cytometer, and an Illumina MiSeq v2 platform.\n\nThese data characterize the partitioning of microbial communities across sharp physiochemical gradients in surface seawaters connecting nearshore and offshore waters in the tropical Pacific. This study provides evidence for the ecological differentiation of SAR11 marine bacteria across nearshore to offshore waters in the tropical Pacific and further increases our understanding of how SAR11 genetic diversity partitions into distinct ecological units. Data were collected by Sarah J. Tucker, Kelle C. Freel, Elizabeth A. Monaghan, Clarisse E. S. Sullivan, Oscar Ramfelt, Yoshimi M. Rii, and Michael S. Rappé.\n\ncdm_data_type = Other\nVARIABLES:\nSample_ID (unitless)\ncollection_date (unitless)\ndepth (m)\nenv_broad_scale (unitless)\nenv_local_scale (unitless)\nenv_medium (unitless)\ngeo_loc_name (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nSite_name (unitless)\nchlorophyll_a_ug_per_L (micrograms per Liter)\nph (no unit)\nsalinity (ppt)\n... (21 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_930084_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_930084_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_930084_v1/index.htmlTable | https://www.bco-dmo.org/dataset/930084
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_930084_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_930084_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_930084_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_700961.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_700961 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_700961.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_700961/ | public | [Metabarcoding zooplankton at station ALOHA: NCBI SRA accession numbers] - NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files for each zooplankton community sample (Plankton Population Genetics project) (Basin-scale genetics of marine zooplankton) | These data include sample information and accession links to sequence data at\nThe National Center for Biotechnology Information (NCBI) Sequence Read Archive\n(SRA).\n \nThis data submission consists of metabarcoding data for the zooplankton\ncommunity in the epipelagic, mesopelagic and upper bathypelagic zones\n(0-1500m) of the North Pacific Subtropical Gyre. The goal of this study was to\nassess the hidden diversity present in zooplankton assemblages in midwaters,\nand detect vertical gradients in species richness, depth distributions, and\ncommunity composition of the full zooplankton assemblage. Samples were\ncollected in June 2014 from Station ALOHA (22.75, -158) using a 1 meter square\nMultiple Opening and Closing Nets and Environmental Sampling System (MOCNESS,\n200um mesh), on R/V Falkor cruise FK140613. \\u00a0Next generation sequence\ndata (Illumina MiSeq, V3 chemistry, 300-bp paired-end) of the zooplankton\nassemblage derive from amplicons of the V1-V2 region of 18S rRNA (primers\ndescribed in Fonseca et al. 2010). The data includes sequences and read count\nabundance information for molecular OTUs from both holoplanktonic and\nmeroplanktonic taxa\n \nRelated dataset containing OTU tables and fasta sequences (representative /\nmost abundance read for each OTU): \n[Metabarcoding zooplankton at ](\\\\http://www.bco-\ndmo.org/dataset/700279\\\\)[station](\\\\http://www.bco-\ndmo.org/dataset/700279\\\\)[ ALOHA: OTU tables and ](\\\\http://www.bco-\ndmo.org/dataset/700279\\\\)[fasta](\\\\http://www.bco-\ndmo.org/dataset/700279\\\\)[ files](\\\\http://www.bco-\ndmo.org/dataset/700279\\\\)\n\ncdm_data_type = Other\nVARIABLES:\nanalysis_name (unitless)\n... (15 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_700961_fgdc.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_700961/index.htmlTable | https://www.bco-dmo.org/dataset/700961
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_700961.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_700961&showErrors=false&email= | BCO-DMO | bcodmo_dataset_700961 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_964236_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_964236_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_964236_v1/ | public | [Metagenomic sequence metadata] - NCBI Metagenomic metadata for Lau Basin (Tonga) mollusc gill tissue collected on R/V Thompson cruises TN235 and TN401 and R/V Falkor cruise FK160407 between May 2009 and Apr 2022 (RUI: Collaborative Research: The impact of symbiont-larval interactions on species distributions across southwestern Pacific hydrothermal vents) | Metagenomic sequence data from Lau Basin hydrothermal vent mollusc gill tissues that contain chemosynthetic bacterial symbionts. Samples were collected between May 2009 to April 2022 aboard R/V Thompson cruises TN235 (May-June 2009) and TN401 (April 2016) and R/V Falkor cruise FK160407 (April 2022) for population and comparative genomics analysis of host animal and bacterial symbionts.\n\ncdm_data_type = Other\nVARIABLES:\nSample_ID (unitless)\nBioproject_accession (unitless)\nBiosample_accession (unitless)\nHost_species (unitless)\nTissue_type (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nCollection_date (unitless)\nCruise (unitless)\ndepth (m)\nMAG_biosample_accession (unitless)\nSequencing_technologies (unitless)\nSRA_Study (unitless)\nSRA_accession (unitless)\nAssembly_methods (unitless)\nSymbiont_MAG_ID (unitless)\nMAG_acc (unitless)\nMAG_organism (unitless)\nHost_AphiaID_accepted (unitless)\nHost_LSID (unitless)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_964236_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_964236_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_964236_v1/index.htmlTable | https://osprey.bco-dmo.org/dataset/964236
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_964236_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_964236_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_964236_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745518.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745518 | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_745518/ | public | [Microbial eukaryotic focused metatranscriptome data] - Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 2015 (Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series) | Seawater was collected via Niskin bottles mounted with a CTD from the San Pedro Ocean Time-series (SPOT) station off the coast of Southern California near the surface (5 m), 150 and 890 m, in late May 2015. Raw sequence data was generated as part of a metatranscriptome study targeting the protistan community. Raw sequences are available at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (SRA Study ID: SRP110974, BioProject: PRJNA391503). Sequences for BioProject PRJNA608423 will be available at NCBI on Jan 1st, 2021.\\r\\n\\r\\nThese data were published in Hu et al. (2018).\n\ncdm_data_type = Other\nVARIABLES:\nSRA_run (unitless)\nSRA_run_link (unitless)\nSRA_study (unitless)\nbioproject_accession (unitless)\nbiosample_accession (unitless)\nlibrary_ID (unitless)\ntitle (unitless)\nsample_name (unitless)\nlibrary_strategy (unitless)\nlibrary_source (unitless)\nlibrary_selection (unitless)\nlibrary_layout (unitless)\nplatform (unitless)\ninstrument_model (unitless)\ndesign_description (unitless)\nfiletype (unitless)\nfilename (unitless)\nfilename2 (unitless)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_745518/index.htmlTable | https://www.bco-dmo.org/dataset/745518
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_745518.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_745518&showErrors=false&email= | BCO-DMO | bcodmo_dataset_745518 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_906740_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_906740_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_906740_v1/ | public | [Microbiome dynamics of coral reef and cleanerfish] - Microbiome dynamics of coral reef and cleanerfish from ecological surveys, in situ manipulations, and laboratory experiments conducted from 2020-2021 (Collaborative Research: Cleaning stations as hubs for the maintenance and recovery of microbial diversity on coral reefs.) | Coral reefs host some of the most iconic symbiotic interactions in nature and are host to the highest diversity of life on the planet. Cleaning symbiosis, wherein small fish or shrimp remove external parasites and associated microorganisms from specific clients, is common on coral reefs. Sites on the reef occupied by cleaners, or \"cleaning stations\", attract a wide variety of fish species that engage in direct physical contact with the cleaner. In this study, we used a combination of ecological surveys, in situ manipulations, and laboratory experiments to examine the unique features of cleaning stations to understand transfer of bacterial and archaeal symbionts amongst fish and within coral reef environment. We used microbial 16S rRNA gene amplicons, environmental parameters, and other molecular tools to evaluate the dynamics between coral microbiomes, cleanerfish skin microbiomes, and the environment. This dataset contains metadata describing sequenced samples, including sample name, data deposition accession records, and measurements at the time of sample collection.\n\ncdm_data_type = Other\nVARIABLES:\nBioProject_accession (unitless)\nBioSample_accession (unitless)\nsample_name (unitless)\nSRA_accession (unitless)\ncollection_date (unitless)\ngeo_loc_name (unitless)\nhost (unitless)\nlat (degrees_north)\nlongitude (degrees_east)\nisolation_source (unitless)\nhost_common_name (unitless)\nhost_disease (unitless)\nhost_condition (unitless)\nhost_coral_cleaner_goby_pretreatment (unitless)\nhost_coral_reef_id (unitless)\nlocation_survey_date (unitless)\n... (13 more variables)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_906740_v1/index.htmlTable | https://www.bco-dmo.org/dataset/906740
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_906740_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_906740_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_906740_v1 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_926299_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_926299_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_926299_v1/ | public | [Microorganisms associated with doliolids] - Eukaryotic and prokaryotic microbial taxa retained by wild-caught doliolids collected during bloom events at three different shelf locations in the northern California Current system in June 2019. (Collaborative Research: Comparative feeding by gelatinous grazers on microbial prey) | Doliolids have a unique ability to impact the marine microbial community through bloom events and high filtration rates. Their predation on large eukaryotic microorganisms is established and evidence of predation on smaller prokaryotic microorganisms is beginning to emerge. We studied the retention of both eukaryotic and prokaryotic microbial taxa by wild-caught doliolids in the northern California Current system. Doliolids were collected during bloom events identified at three different shelf locations with variable upwelling intensity.\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nbiosample_accession (unitless)\nsample_name (unitless)\nsra_sample_accession (unitless)\nsample_accession_title (unitless)\norganism_name (unitless)\norganism_taxonomy_id (unitless)\norganism_taxonomy_name (unitless)\nkeyword (unitless)\nbiosample_package (unitless)\ncollection_date (unitless)\ndepth (m)\nenv_broad_scale (unitless)\nenv_local_scale (unitless)\nenv_medium (unitless)\ngeo_loc_name (unitless)\nlatitude (Sampling_lat, degrees_north)\nlongitude (Sampling_lon, degrees_east)\nsize_frac (unitless)\nhost (unitless)\nsource_material_id (unitless)\nstatus (unitless)\n... (5 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_926299_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_926299_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_926299_v1/index.htmlTable | https://www.bco-dmo.org/dataset/926299
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_926299_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_926299_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_926299_v1 | |||
| log in | [Microorganisms associated with pyrosomes] - High-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry of pyrosome-associated microorganisms compared to seawater sampled during a Pyrosoma atlanticum bloom in the Northern California Current System in July 2018. (Collaborative Research: Comparative feeding by gelatinous grazers on microbial prey) | Pyrosomes are widely distributed pelagic tunicates that have the potential to reshape marine food webs when they bloom. However, their grazing preferences and interactions with the background microbial community are poorly understood. The diversity, relative abundance, and taxonomy of pyrosome-associated microorganisms were compared to seawater during a Pyrosoma atlanticum bloom in the Northern California Current System using high-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry.\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nbiosample_accession (unitless)\nsample_name (unitless)\nsra_sample_accession (unitless)\nsample_accession_title (unitless)\norganism_name (unitless)\norganism_taxonomy_id (unitless)\norganism_taxonomy_name (unitless)\nkeywords (unitless)\nbiosample_package (unitless)\ncollection_date (unitless)\nenv_broad_scale (unitless)\nenv_local_scale (unitless)\nenv_medium (unitless)\ngeo_loc_name (unitless)\nhost (unitless)\nlatitude (Sampling_lat, degrees_north)\nlongitude (Sampling_lon, degrees_east)\ndepth (m)\nhost_length (centimeter (cm))\nsource_material_id (unitless)\nstatus (unitless)\n... (20 more variables)\n | BCO-DMO | bcodmo_dataset_926093_v1 | ||||||||||||
| log in | [Northern California Current Microorganisms] - 16S rRNA gene of microorganisms sampled along the Newport Hydrographic (NH) and Trinidad Head (TR) lines, in OR and CA in 2018 and 2019 (Collaborative Research: Comparative feeding by gelatinous grazers on microbial prey) | The Northern California Current ecosystem is a productive system which supports major fisheries. To determine how the microbial community responds to variable upwelling, we examined the 16S rRNA gene of microorganisms from two size fractions, 0.2-1.6µm and greater than 1.6µm along the Newport Hydrographic (NH) and Trinidad Head (TR) lines, in OR and CA.\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nbiosample_accession (unitless)\nmessage (unitless)\nsample_name (unitless)\norganism (unitless)\ncollection_date (unitless)\ndepth (m)\nenv_broad_scale (unitless)\nenv_local_scale (unitless)\nenv_medium (unitless)\ngeo_loc_name (unitless)\nlatitude (Sampling_lat, degrees_north)\nlongitude (Sampling_lon, degrees_east)\nsize_frac (unitless)\nsra_run_accession (unitless)\nsra_study_accession (unitless)\nobject_status (unitless)\nlibrary_ID (unitless)\ntitle (unitless)\nlibrary_strategy (unitless)\nlibrary_source (unitless)\nlibrary_selection (unitless)\nlibrary_layout (unitless)\nplatform (unitless)\n... (5 more variables)\n | BCO-DMO | bcodmo_dataset_926850_v1 | ||||||||||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_924886_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_924886_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_924886_v1/ | public | [RADseq data from Atlantic silversides used for linkage and QTL mapping] - RADseq data from Atlantic silversides used for linkage and QTL mapping. (Collaborative research: The genomic underpinnings of local adaptation despite gene flow along a coastal environmental cline) | ddRADseq data from 568 Atlantic silversides (Menidia menidia) that are either F1 or F2 offspring to wild-caught parents from Georgia and New York used in a controlled breeding experiment. The data were used to build linkage maps for each of the separate populations and their inter-population cross, and to perform quantitative trait locus mapping.\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (units)\nbiosample_accession (units)\ntaxonomic_name (units)\nmother_f0_sampling_location (units)\nlat_mother (degrees_north)\nlon_mother (degrees_east)\nfather_f0_sampling_location (units)\nlat_father (degrees_north)\nlon_father (degrees_east)\nSRA_study_accession (units)\nSRA_experiment_accession (units)\nSRA_run_accession (units)\nlibrary_ID (units)\ntitle (units)\nlibrary_strategy (units)\nlibrary_source (units)\nlibrary_selection (units)\nlibrary_layout (units)\nplatform (units)\ninstrument_model (units)\ndesign_description (units)\nfiletype (units)\nsample_name (units)\nfilename (units)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_924886_v1/index.htmlTable | https://www.bco-dmo.org/dataset/924886
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_924886_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_924886_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_924886_v1 | |||||
| log in | [Salp and pteropod associated microorganisms] - Salp and pteropod associated microorganisms from the Western Edge of the Gulf Stream sampled in September 2019. (Collaborative Research: Comparative feeding by gelatinous grazers on microbial prey) | Microbial mortality impacts the structure of food webs, carbon flow, and the interactions that create dynamic patterns of abundance across gradients in space and time in diverse ecosystems. In the oceans, estimates of microbial mortality by viruses, protists, and small zooplankton do not account fully for observations of loss, suggesting the existence of underappreciated mortality sources. We examined how ubiquitous mucous mesh feeders (i.e. gelatinous zooplankton) could contribute to microbial mortality in the open ocean. We coupled capture of live animals by blue-water diving to sequence-based approaches to measure the enrichment and selectivity of feeding by two coexisting mucous grazer taxa (pteropods and salps) on numerically dominant marine prokaryotes. We show that mucous mesh grazers consume a variety of marine prokaryotes and select between coexisting lineages and similar cell sizes. We show that Prochlorococcus may evade filtration more than other cells and that planktonic archaea are consumed by macrozooplanktonic grazers. Discovery of these feeding relationships identifies a new source of mortality for Earth's dominant marine microbes and alters our understanding of how top-down processes shape microbial community and function.\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nbiosample_accession (unitless)\nmessage (unitless)\nsample_name (unitless)\nsample_title (unitless)\norganism (unitless)\ncollection_date (unitless)\ndepth_f (Depth, feet)\nenv_broad_scale (unitless)\nenv_local_scale (unitless)\nenv_medium (unitless)\ngeo_loc_name (unitless)\nlatitude (Sampling_lat, degrees_north)\nlongitude (Sampling_lon, degrees_east)\n... (15 more variables)\n | BCO-DMO | bcodmo_dataset_926841_v1 | ||||||||||||
| log in | [Sponge Coral Picoplankton Incubation Experiment - NCBI] - Microbiome profiling of bacterioplankton communities on sponge excurrent water, coral exudate water, and surface reef water. (Collaborative Research: The Influence of Sponge Holobiont Metabolism on Coral Reef Dissolved Organic Matter and Reef Microorganisms) | Sponge exhalent water was collected from Looe Key reef, coral exudates water was collected from a coral incubation at Mote Marine lab, and ambient reef water was collected from Looe Key Reef surface water. All seawater was 0.2 um filtered to use as media in 2L bottles for an incubation experiment. Inoculum from reef surface water (1.6 um filtered) was used for the incubation. Bottles were incubated in the dark for 48 hours and samples were taken at the start (T0) and end (T48) for nutrient and microbiome analysis.\n\ncdm_data_type = Other\nVARIABLES:\nBioproject_Accession (unitless)\nBiosample_accession (unitless)\nSample_Name (unitless)\nSRA_run_ID (unitless)\nSRA_run_link (unitless)\nSPUID (unitless)\nOrganism (unitless)\nTax_ID (unitless)\nlibrary_ID (unitless)\nSRA_study_ID (unitless)\nSRA_title (unitless)\nlibrary_strategy (unitless)\nlibrary_source (unitless)\nlibrary_selection (unitless)\nlibrary_layout (unitless)\nplatform (unitless)\ninstrument_model (unitless)\ndesign_description (unitless)\nfiletype (unitless)\nfilename (unitless)\nfiletype2 (unitless)\nfilename2 (unitless)\n... (4 more variables)\n | BCO-DMO | bcodmo_dataset_964182_v1 | ||||||||||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_963428_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_963428_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_963428_v1/ | public | [SRA accessions from Chesapeake Bay sediment samples 2017-2018] - SRA accession and collection metadata for sediments samples collected at two Chesapeake Bay stations from Mar 2017 to Aug 2018 (Collaborative Research: Probing the Metabolic and Electrical Interactions of Cable Bacteria in Anoxic Sediments) | To examine the seasonality of sulfur oxidizers in surface sediments in seasonality oxygen stressed sediments of the Chesapeake Bay, surface sediments (0-0.5 cm depth) were collected on 10 occasions spanning all seasons over the course of two years by gravity coring at a pair of stations with differing summer bottom water oxygen concentrations. Samples were collected from March of 2017 to August of 2018. One station was located in the central channel which experiences severe summer hypoxia (CB4.3C) and one station was located on an adjacent shoal where bottom waters are better ventilated (CB4.3W; station names associated with Chesapeake Bay Water Quality Monitoring Program). At both stations, the waters are mesohaline and the sediments are fine grained. The study was designed to enable a description of the seasonality of benthic microbial communities at paired locations with contrasting degrees of bioturbation.\nThis dataset includes collection metadata, Sequence Read Archive (SRA) and BioSample accessions under BioProject PRJNA613483 at The National Center for Biotechnology Information and are associated with BCO-DMO datasets, all listed under related datasets. The SRA project title is “Chesapeake Bay Surface Sediment Seasonal Study”.\n\ncdm_data_type = Other\nVARIABLES:\nsample_name (unitless)\nbioproject_accession (unitless)\ncollection_date (unitless)\nStation_Name (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_963428_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_963428_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_963428_v1/index.htmlTable | https://osprey.bco-dmo.org/dataset/963428
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_963428_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_963428_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_963428_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_958631_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_958631_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_958631_v1/ | public | [SRA archive of Magallana gigas] - NCBI accession numbers and related metadata for an SRA archive of the Pacific oyster, Magallana gigas (The genetic legacy of an Asian oyster introduction and its disease-causing parasite) | The massive geographic expansion of terrestrial plant crops, livestock, and marine aquacultured species during the 19th and 20th centuries provided local economic benefits, stabilized food demands, and altered local ecosystems. The invasion history of these translocations remains uncertain for most species, limiting our understanding of their future adaptive potential and historical roles as vectors for co-invaded species. We provide a framework for filling this gap in invasion biology using the widely transplanted Pacific oyster (Magallana gigas) as a case study. A two-dimensional summary of population-level variation in single nucleotide polymorphisms (SNPs) in native Japan reflected the geographical map of Japan and allowed identification of the source regions for the worldwide expansion. Pacific oysters proliferate in non-native areas with environmental temperatures similar to those areas where native lineages evolved.\n\ncdm_data_type = Other\nVARIABLES:\nsample_name (unitless)\naccession (unitless)\nbioproject_accession (unitless)\nbiosample_accession (unitless)\npop (unitless)\nPopulation (unitless)\nRegion (unitless)\nRegion2 (unitless)\nNatNon (unitless)\nCollection_Date (unitless)\nCollectionMonth (unitless)\nCollectionYear (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nCollector (unitless)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_958631_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_958631_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_958631_v1/index.htmlTable | https://osprey.bco-dmo.org/dataset/958631
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_958631_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_958631_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_958631_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_963432_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_963432_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_963432_v1/ | public | [SRA samples Chesapeake Bay Sediment Incubation Experiment 2019] - SRA accession and experiment metadata for Chesapeake Bay sediment incubation in 2019 (Collaborative Research: Probing the Metabolic and Electrical Interactions of Cable Bacteria in Anoxic Sediments) | Surficial sediment obtained from mesohaline zone of Chesapeake Bay were homogenized and incubated in sediment core liners for 64 days in aerated aquaria. Cable bacteria were allowed to grow unimpeded in a subset of cores. Downward growth of cable bacteria was inhibited by a barrier filter embedded at 0.5 cm in a subset of cores. Sediment cores were destructively sampled and sectioned at 0.5 cm depth increments at 6 times points over the approximately 2 months.\n\nThis dataset includes Sequence Read Archive (SRA) and BioSample accessions under BioProject PRJNA833464, accessions SAMN27993143 to SAMN27993196 and sampling metadata. These data were published in Liau et al. (2022).\n\ncdm_data_type = Other\nVARIABLES:\nsample_name (unitless)\nbioproject_accession (unitless)\nTreatment (unitless)\nDayfromStart (days)\nDepth_Top (cm)\nDepth_Bottom (cm)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_963432_v1/index.htmlTable | https://osprey.bco-dmo.org/dataset/963432
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_963432_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_963432_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_963432_v1 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_934800_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_934800_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_934800_v1/ | public | [Three-Prime Tag-Sequencing (3' Tag-Seq) Data for Pisaster ochraceus] - Bioproject accession information on tag-sequence data for Pisaster ochraceus samples collected from Bodega Bay, CA, in July 2019 (Collaborative Proposal: Selection and Genetic Succession in the Intertidal -- Population Genomics of Pisaster ochraceus During a Wasting Disease Outbreak and its Aftermath) | Outbreaks of sea star wasting (SSW) have killed millions of sea stars across over 20 taxa in the last decade alone, threatening the health and stability of coastal communities around the world. While the causative agent remains unknown, it has recently been postulated that hypoxia exposure may play a dominant role in the onset of SSW. We leveraged a study that subjected ochre sea stars to organic matter amendment in a controlled laboratory setting to induce hypoxia and used a repeated sampling design to collect non-invasive tissue samples from both healthy and wasting individuals. Following tag-based RNAseq (TagSeq), we analyzed differential gene expression (DGE) patterns among and within these individuals sampled strategically throughout the 15-day experiment. Transcriptional profiles reveal a progressive change in gene expression accompanying the advancement of SSW, reflecting a transition from asymptomatic stars to the onset of characteristic SSW lesions that progressively worsen until, in some cases, the star dies of their symptoms. Included in this dataset is the accession information for 89 individual TagSeq samples across 20 individual Pisaster ochraceus sea stars at multiple time points during the study to make them available for subsequent re-evaluation. The sequence data have been deposited into the NCBI archive under BioProject PRJNA1116313 and will be publicly available on 2025-08-01.\n\ncdm_data_type = Other\nVARIABLES:\nsample_name (unitless)\nbioproject_accession (unitless)\nbioproject_ncbi (unitless)\nassay_type (unitless)\norganism (unitless)\nisolate_id (unitless)\nisolation_source (unitless)\ncollection_date (unitless)\ngeo_loc_name (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\ntissue (unitless)\nbiomaterial_provider (unitless)\ncollected_by (unitless)\nhost_tissue_sampled (unitless)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_934800_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_934800_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_934800_v1/index.htmlTable | https://www.bco-dmo.org/dataset/934800
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_934800_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_934800_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_934800_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_746654.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_746654 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_746654.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_746654/ | public | [Trichodesmium AHL metatranscriptomes_AE1409] - Trichodesmium AHL amendment metatranscriptomic reads accessions and metadata (Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation) | Trichodesmium is a marine, diazotrophic cyanobacterium that plays a central role in the biogeochemical cycling of carbon and nitrogen. Colonies ubiquitously co-occur with a diverse microbiome of heterotrophic bacteria. Here we show that manipulation of the microbiome with quorum sensing acyl homoserine lactone (AHL) molecules significantly modulated rates of N2 fixation by Trichodesmium collected from the western North Atlantic, with both positive and negative effects of varied magnitude. Changes in Trichodesmium N2 fixation did not clearly correlate with changes in microbiome composition or geochemical patterns. Metatranscriptome sequencing revealed significant changes in the relative abundance of microbiome transcripts encoding metabolic functions consistent with quorum sensing responses in model bacteria. There was little overlap in specific microbiome transcriptional responses to AHL addition between stations, and this variability in microbiome gene expression may underpin the heterogeneous changes in Trichodesmium N2 fixation. These data suggest the microbiome could play a large and previously overlooked role in modulating Trichodesmium N2 fixation. This metadata form describes the metatranscriptomic sequencing reads that were used in the study.\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nbiosample_accession (unitless)\nlibrary_ID (unitless)\ntitle (unitless)\nlibrary_strategy (unitless)\nlibrary_source (unitless)\nlibrary_selection (unitless)\nlibrary_layout (unitless)\nplatform (unitless)\ninstrument_model (unitless)\ndesign_description (unitless)\nfiletype (unitless)\nassembly (unitless)\nfilename (unitless)\n... (7 more variables)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_746654/index.htmlTable | https://www.bco-dmo.org/dataset/746654
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_746654.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_746654&showErrors=false&email= | BCO-DMO | bcodmo_dataset_746654 | ||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_934772_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_934772_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_934772_v1/ | public | [Whole genome sequence data for Pisaster ochraceus] - Whole genome sequence data for Pisaster ochranceus samples collected from the Pacific coast of North America from July 2004 to May 2018 (Collaborative Proposal: Selection and Genetic Succession in the Intertidal -- Population Genomics of Pisaster ochraceus During a Wasting Disease Outbreak and its Aftermath) | This dataset includes collection and accession information for whole genome sequence (WGS) data from 65 Pisaster ochraceus (ochre sea star) collected across latitudes ranging from SE Alaska to southern California. The sequence data have been deposited into NCBI SRA archive under BioProject PRJNA1117092 and will be publicly available on 2025-08-01. These data are used to evaluate the population genomic diversity and divergence of spatially and environmentally separated populations of Pisaster ochraceus.\n\ncdm_data_type = Other\nVARIABLES:\nsample_name (unitless)\nbioproject_accession (unitless)\nbioproject_ncbi (unitless)\nassay_type (unitless)\norganism (unitless)\nisolation_source (unitless)\ncollection_date (unitless)\niso_collection_date (unitless)\ngeo_loc_name (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\ntissue (unitless)\nbiomaterial_provider (unitless)\ncollected_by (unitless)\nhost_tissue_sampled (unitless)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_934772_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_934772_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_934772_v1/index.htmlTable | https://www.bco-dmo.org/dataset/934772
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_934772_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_934772_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_934772_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_924786_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_924786_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_924786_v1/ | public | [Whole Genome Sequencing of Eelgrass Bodega and Tomales Bay] - Sample collection information and sequence accessions at the National Center for Biotechnology Information (NCBI) for whole genome sequencing of eelgrass (Zostera marina) collected at Bodega and Tomales Bay, CA, USA from July to September 2019 (Using genomics to link traits to ecosystem function in the eelgrass Zostera marina) | This dataset includes sample collection information and sequence accessions at the National Center for Biotechnology Information (NCBI) for whole genome sequencing of eelgrass (Zostera marina) collected at Bodega and Tomales Bay, California, USA from July and September of 2019. Sequence Read Archive (SRA) Experiments and BioSamples can be accessed from the NCBI BioProject PRJNA887384 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA887384/).\n\nResults summary as described in Scheibelhut, et al. (2023): We examine genomic signals of selection in the eelgrass Zostera marina across temperature gradients in adjacent embayments. Although we find many genomic regions with signals of selection within each bay there is very little overlap in signals of selection at the SNP level, despite most polymorphisms being shared across bays. We do find overlap at the gene level, potentially suggesting multiple mutational pathways to the same phenotype. Using polygenic models we find that some sets of candidate SNPs are able to predict temperature across both bays, suggesting that small but parallel shifts in allele frequencies may be missed by independent genome scans. Together, these results highlight the continuous rather than binary nature of parallel evolution in polygenic traits and the complexity of evolutionary predictability.\n\ncdm_data_type = Other\nVARIABLES:\naccession (unitless)\nsample_name (unitless)\nbioproject_accession (unitless)\nSite (unitless)\norganism (unitless)\ncollection_date (unitless)\nisolation_source (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_924786_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_924786_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_924786_v1/index.htmlTable | https://www.bco-dmo.org/dataset/924786
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_924786_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_924786_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_924786_v1 |