Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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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_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_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_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 | |||||
| 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 | ||||||||||||
| 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 |