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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| log in | [16S microbiome data for artificial reef sponges and seawater] - 16S microbiome metadata collected from shallow artificial reef sponges and seawater in the Florida Keys, USA from Apr 2021 to Aug 2021 (Collaborative Research: Investigations into microbially mediated ecological diversification in sponges) | Sponges are a dominant component of coral reefs worldwide and in the Caribbean, where their biomass exceeds that of reef-building corals. For almost a quarter century, the success of sponges in the Caribbean has been linked to their filter-feeding ability. However, recent work demonstrated that coexisting sponges on Caribbean reefs host unique communities of bacteria that might allow sponges to access multiple pools of nutrients that are not available to other organisms. In this project, the investigators will test the hypothesis that ecologically dominant sponge species in the Caribbean have unique metabolic strategies that are mediated by their associations with microbes that live within the sponge body.\n\nIn this dataset, we present the 16S rRNA microbiome NCBI accession and sample collection metadata for an artificial reef experiment where sponges of 10 species were placed on this temporary reef from April to August of 2021 and sampled using VacuSIP. VacuSIP methods capture incurrent (In) and excurrent (Ex) water from each sponge specimen. Incurrent represents the bacteria that are available for the sponge to consume via filter feeding and excurrent represents the bacteria that remain once sponges have consumed their preferred taxa. Additionally, we have provided microbiome metadata for the host sponges for several of these paired In/Ex samples. See the related dataset, NCBI Bioproject PRJNA1179970, for all sequence data. Microbiome data was generated using protocols from the Earth Microbiome project and sequencing was conducted on an Illumina MiSeq at Middle Tennessee State University. The data available at NCBI represents raw sequencing data, and no quality checks or sequencing filtering has been done on the uploaded sequences.\n\ncdm_data_type = Other\nVARIABLES:\ncollection_date (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\naccession (unitless)\nsample_name (unitless)\nspecies_ab (unitless)\nsample_type (unitless)\norganism (unitless)\n... (6 more variables)\n | BCO-DMO | bcodmo_dataset_953999_v1 | ||||||||||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_955739_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_955739_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_955739_v1/ | public | [Acarta tonsa and A. hudsonica seasonal thermal limits (LD50)] - Upper thermal limits (LD50) for two common coastal copepods during thermal experiments with individuals collected from Long Island Sound between July 2017 and November 2019 (Linking eco-evolutionary dynamics of thermal adaptation and grazing in copepods from highly seasonal environments) | These data include estimates of upper thermal limits for two common coastal copepods collected from Long Island Sound between July 2017 and November 2019. Individual survival measurements were made for both field and laboratory acclimated individuals exposed to temperatures ranging from 10°C to 39°C. These data highlight how acclimation and rapid adaptation may influence responses of populations to rapid climate change. Data were collected by Dr. Matthew Sasaki at the University of Connecticut.\n\ncdm_data_type = Other\nVARIABLES:\nspecies (unitless)\nacclimation (unitless)\ncollection_id (unitless)\ncollection_date (unitless)\ncollection_month (unitless)\ncollection_year (unitless)\ncollection_temp (degrees Celsius)\nacclimation_temp (degrees Celsius)\nLD50 (degrees Celsius)\nSE (degrees Celsius)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_955739_v1/index.htmlTable | https://osprey.bco-dmo.org/dataset/955739
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_955739_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_955739_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_955739_v1 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_818482_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_818482_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_818482_v1/ | public | [Acartia tonsa Body Size] - Sex-specific body size measurements from two copepod populations in the Coastal Northwest Atlantic Surface Waters from 2017-07-16 to 2017-08-25 (Collaborative Research: Response of marine copepods to warming temperature and ocean acidification) | Sex-specific body size measurements from two copepod populations in the Coastal Northwest Atlantic Surface Waters from 2017-07-16 to 2017-08-25\n\ncdm_data_type = Other\nVARIABLES:\nIndividual (unitless)\nPop (unitless)\nDev (degrees Celsius)\nSex (unitless)\nBL (millimeters)\nCollection_Date (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_818482_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_818482_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_818482_v1/index.htmlTable | https://osprey.bco-dmo.org/dataset/818482
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_818482_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_818482_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_818482_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_817999_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_817999_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_817999_v1/ | public | [Acartia tonsa Egg Production] - Individual egg production measurements from 10 copepod populations from 2017-07-15 to 2018-07-26 in coastal northwest Atlantic surface waters (Collaborative Research: Response of marine copepods to warming temperature and ocean acidification) | Individual egg production measurements from 10 copepod populations from 2017-07-15 to 2018-07-26 in coastal northwest Atlantic surface waters\n\ncdm_data_type = Other\nVARIABLES:\nIndividual (unitless)\nPopulation (unitless)\nTemp (degrees Celsius (C))\nTotal (unitless)\nHatched (unitless)\nHatching_Success (unitless)\nEggs_per_day (eggs per day)\nCollection_Date (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_817999_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_817999_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_817999_v1/index.htmlTable | https://osprey.bco-dmo.org/dataset/817999
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_817999_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_817999_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_817999_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_818042_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_818042_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_818042_v1/ | public | [Acartia tonsa heat shock survivorship] - Individual thermal stress survivorship measurements from 10 copepod populations from Coastal Northwest Atlantic Surface Waters from 2017-07-15 to 2018-07-26 (Collaborative Research: Response of marine copepods to warming temperature and ocean acidification) | Individual thermal stress survivorship measurements from 10 copepod populations from Coastal Northwest Atlantic Surface Waters from 2017-07-15 to 2018-07-26.\n\ncdm_data_type = Other\nVARIABLES:\nPopulation (unitless)\nStress_temp (degrees Celsius (C))\nDev_temp (degrees Celsius (C))\nIndividual (unitless)\nSurvivorship (unitless)\nCollection_Date (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_818042_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_818042_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_818042_v1/index.htmlTable | https://osprey.bco-dmo.org/dataset/818042
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_818042_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_818042_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_818042_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_955742_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_955742_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_955742_v1/ | public | [Acartia tonsa seasonal variation in body size] - Acartia tonsa prosome length measurements from copepods collected in Long Island Sound in summer and fall of 2019 (Linking eco-evolutionary dynamics of thermal adaptation and grazing in copepods from highly seasonal environments) | Copepods with short generation times experience seasonal environmental variation across, rather than within, generations. This data includes body size measurements for both male and female individuals from seasonal collections of Acartia tonsa from Eastern Long Island Sound in Summer and Fall 2019. The body size measurements in this dataset correspond to the 2019 collections (laboratory acclimation groups).\nAdditional body size measurements (as prosome lengths) were made on individuals from a split-brood experiment after several generations of common garden acclimation. The observed variation in size can therefore be attributed to the effects of both genetic variation and phenotypic plasticity. Data were collected by Dr. Matthew Sasaki at the University of Connecticut.\n\ncdm_data_type = Other\nVARIABLES:\ncollection_id (unitless)\ncollection_date (unitless)\ncollection_temp (degrees Celsius)\nacclimation_temp (degrees Celsius)\nsex (unitless)\nlength (millimeter (mm))\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_955742_v1/index.htmlTable | https://osprey.bco-dmo.org/dataset/955742
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_955742_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_955742_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_955742_v1 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_818108_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_818108_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_818108_v1/ | public | [Acartia tonsa thermal tolerance] - Sex-specific thermal stress survivorship measurements from two copepod populations in the Coastal Northwest Atlantic Surface Waters from 2017-07-16 to 2017-08-25 (Collaborative Research: Response of marine copepods to warming temperature and ocean acidification) | Sex-specific thermal stress survivorship measurements from two copepod populations in the Coastal Northwest Atlantic Surface Waters from 2017-07-16 to 2017-08-25\n\ncdm_data_type = Other\nVARIABLES:\nPop (unitless)\nDev (degrees Celsius)\nStress (degrees Celsius (degC))\nSex (unitless)\nSurv (unitless)\nCollection_Date (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_818108_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_818108_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_818108_v1/index.htmlTable | https://osprey.bco-dmo.org/dataset/818108
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_818108_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_818108_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_818108_v1 | |||
| 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 | |||||
| log in | [Adult black sea bass winter survival and lipid dynamics: Laboratory-mesocosm experiment] - Adult Black Sea Bass (Centropristis striata) winter survival and lipid accumulation under varying diet and temperature conditions from a laboratory mesocosm experiment (Oct 2022 to Apr 2023) with individuals collected in Long Island Sound (Collaborative research: The genomic underpinnings of local adaptation despite gene flow along a coastal environmental cline) | This dataset contains measurements from a laboratory mesocosm experiment (Oct 2022 to Apr 2023) with adult Black Sea Bass (Centropristis striata) collected in Long Island Sound. Fish in this experiment were collected concurrently with fish sampled for a related wild-caught dataset (see 'Related Datasets' section).\n\nStudy description:\n\nWe experimentally examined overwintering potential of adult Black Sea Bass (Centropristis striata), an ecologically and economically important fish that seasonally migrates from offshore overwintering grounds to coastal feeding and nursery areas. We collected adults from Long Island Sound in September 2022 and reared them in a laboratory-mesocosm experiment under a contemporary seasonal temperature profile for Long Island Sound (LIS; October 2022 – April 2023) to assess their potential to survive and accumulate lipids throughout the winter. We also fed experimental adults two diet items (blue mussels and Atlantic herring), which are commonly found in Long Island Sound. \n\nIn addition, we sampled fish from the same reef in LIS at the start (October) and end (April) of the experiment to identify lipid dynamics in wild fish that migrate offshore (see \"Related Datasets\" section for wild fish data). Experimental C. striata growth throughout the winter was negligible with high mortality (> 50% observed). \n\nWhile survivors fed herring had higher tissue lipid contents, mortality was 2x higher than for fish fed mussels. In contrast, to the experimental fish, wild-captured fish in the spring had higher gonadosmatic indices than that for survivors across both diet treatments, which was most similar to fall-captured fish. While some fish survived throughout the winter, current winter bottom temperatures still preclude a year-round C. striata presence within Long Island Sound. Overwintering inshore is still disadvantageous compared to seasonally migrating due to surviving experimental fish having lower gonadosomatic indices, suggesting that the offshore overwintering period is a time to build energy reserves. However, as coastal waters continue to warm, changing conditions could lead populations to become year-round residents of Long Island Sound, thus increasing C. striata abundance.\n\ncdm_data_type = Other\nVARIABLES:\nSpecies (unitless)\n... (44 more variables)\n | BCO-DMO | bcodmo_dataset_938004_v1 | ||||||||||||
| log in | [Adult black sea bass winter survival and lipid dynamics: Wild fish] - Adult Black Sea Bass (Centropristis striata) winter survival and lipid accumulation in wild-caught fish in Long Island Sound in Sept of 2022 to Apr of 2023 (Collaborative research: The genomic underpinnings of local adaptation despite gene flow along a coastal environmental cline) | This dataset contains adult Black Sea Bass (Centropristis striata) winter survival and lipid accumulation in wild-caught fish in Long Island Sound (September 2022 to April 2023). This dataset includes data from fish collected concurrently with those used in a related mesocosm experiment (run Oct 2022 to Apr 2023), with fish collected at the same reef (see 'Related Datasets' section).\n\nStudy description:\n\nWe experimentally examined overwintering potential of adult Black Sea Bass (Centropristis striata), an ecologically and economically important fish that seasonally migrates from offshore overwintering grounds to coastal feeding and nursery areas. We collected adults from Long Island Sound in September 2022 and reared them in a laboratory-mesocosm experiment under a contemporary seasonal temperature profile for Long Island Sound (LIS; October 2022 – April 2023) to assess their potential to survive and accumulate lipids throughout the winter. We also fed experimental adults two diet items (blue mussels and Atlantic herring), which are commonly found in Long Island Sound. \n\nIn addition, we sampled fish from the same reef in LIS at the start (October) and end (April) of the experiment to identify lipid dynamics in wild fish that migrate offshore. Experimental C. striata growth throughout the winter was negligible with high mortality (> 50% observed). \n\nWhile survivors fed herring had higher tissue lipid contents, mortality was 2x higher than for fish fed mussels. In contrast, to the experimental fish, wild-captured fish in the spring had higher gonadosmatic indices than that for survivors across both diet treatments, which was most similar to fall-captured fish. While some fish survived throughout the winter, current winter bottom temperatures still preclude a year-round C. striata presence within Long Island Sound. Overwintering inshore is still disadvantageous compared to seasonally migrating due to surviving experimental fish having lower gonadosomatic indices, suggesting that the offshore overwintering period is a time to build energy reserves. However, as coastal waters continue to warm, changing conditions could lead populations to become year-round residents of Long Island Sound, thus increasing C. striata abundance.\n\ncdm_data_type = Other\nVARIABLES:\nSpecies (unitless)\n... (34 more variables)\n | BCO-DMO | bcodmo_dataset_938012_v1 | ||||||||||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_780386 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_780386.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_780386/ | public | [Anderson & Rynearson 2020: Skeletonema CHN] - Elemental carbon and nitrogen data for Skeletonema species as analyzed in Anderson and Rynearson, 2020 (Dimensions: Collaborative Research: Genetic, functional and phylogenetic diversity determines marine phytoplankton community responses to changing temperature and nutrients) | Elemental concentrations for Skeletonema species (n=2), as analyzed in Anderson and Rynearson, 2020. This dataset includes carbon, nitrogen, and volume measurements for S. marinoi (n=3) and S. pseudocostatum (n=4) evaluated at the thermal minimum, maximum, and optimum for each strain. Strains were isolated from Narragansett Bay, Rhode Island.\n\ncdm_data_type = Other\nVARIABLES:\nSpecies (unitless)\nStrain (unitless)\nGenBank (Gen Bank, unitless)\nCollection_date (unitless)\nlatitude (Isolation Lat, degrees_north)\nlongitude (Isolation Lon, degrees_east)\nIsolation_Temperature (degrees C)\nTemperature (degrees C)\nmeanC (Mean C, picomol carbon per cell)\nseC (Se C, picomol carbon per cell)\nmeanN (Mean N, picomol nitrogen per cell)\nseN (Se N, picomol nitrogen per cell)\nmeanCN (Mean CN, unitless)\nseCN (Se CN, unitless)\nmeanV (Mean V, cubic micrometers (um3))\nseV (Se V, cubic micrometers (um3))\nmean_cd (femtomol/cubic micrometers (fmol um-3))\nse_cd (femtomol/cubic micrometers (fmol um-3))\nmean_nd (femtomol/cubic micrometers (fmol um-3))\nse_nd (femtomol/cubic micrometers (fmol um-3))\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_780386_fgdc.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_780386/index.htmlTable | https://www.bco-dmo.org/dataset/780386
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_780386.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_780386&showErrors=false&email= | BCO-DMO | bcodmo_dataset_780386 | ||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_774996 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_774996.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_774996/ | public | [Anderson & Rynearson 2020: Skeletonema thermal growth] - Thermal growth for Skeletonema species as analyzed in Anderson and Rynearson, 2020 (Dimensions: Collaborative Research: Genetic, functional and phylogenetic diversity determines marine phytoplankton community responses to changing temperature and nutrients) | Thermal growth rates for 24 strains representing 5 species from the diatom genus Skeletonema, as analyzed in Anderson and Rynearson, 2020. Strains were grown at temperatures ranging from -2 to 36C to assess how inter- and intraspecific thermal trait variability could explain diatom community dynamics.\n\ncdm_data_type = Other\nVARIABLES:\nSpecies (unitless)\nStrain (unitless)\nTemperature (degrees C)\nIsolation_Temperature (degrees C)\nGrowth (per day)\nGenBank (Gen Bank, unitless)\nCollection_date (unitless)\nlatitude (Isolation Lat, degrees_north)\nlongitude (Isolation Lon, degrees_east)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_774996_fgdc.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_774996/index.htmlTable | https://www.bco-dmo.org/dataset/774996
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_774996.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_774996&showErrors=false&email= | BCO-DMO | bcodmo_dataset_774996 | ||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_935908_v1 | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_935908_v1/ | public | [Bacterial communities and relative abundances of the pathogen Vibrio coralliilyticus in feces of coral reef fish] - Bacterial communities and relative abundances of the pathogen Vibrio coralliilyticus in feces of coral reef fish collected on the north shore of Mo’orea, French Polynesia, Oct 2020 (CAREER: Testing the effects of predator-derived feces on host symbiont acquisition and health) | Understanding how microbial communities in consumer feces may impact ecosystem health may improve conservation and restoration efforts. To test how microbial communities in fish feces may affect coral reef health, we collected fecal samples from ten fish species, ranging from obligate corallivore to grazer/detritivore. Additionally, samples of corals, algae, sediments, and seawater were collected to test whether bacterial taxa in these samples were also represented in fish feces (N = 5-14 per fish, coral, or algae species/genus). All collections were conducted in October 2020 from the back reef (1-2 m depth) and fore reef (5-10 m depth) in Moorea, between LTER sites 1 and 2 of the Moorea Coral Reef (MCR) Long Term Ecological Research (LTER) site. We conducted bacterial 16S rRNA gene metabarcoding on all samples and found that fecal communities of bacteria differed among fish guilds (obligate corallivores, facultative corallivores, grazer/detritivores). We also used real-time PCR to quantify abundances of Vibrio coralliilyticus, a known coral pathogen, in all fecal samples. Samples were collected and processed, and data were analyzed, by the authors of Grupstra et al., 2023.\n\ncdm_data_type = Other\nVARIABLES:\nsample_name (unitless)\nSRA (unitless)\nBioSample (unitless)\norganism (unitless)\nstrain (unitless)\nisolation_source (unitless)\ncollection_date (unitless)\ngeo_loc_name (unitless)\ndepth_r (Depth, m)\nenv_broad_scale (unitless)\nhost_description (unitless)\nhost_tissue_sampled (unitless)\nhost_diet (unitless)\nhost_feces_dCT (cycles)\nhost_AphiaID (unitless)\nhost_ScientificName (unitless)\nhost_LSID (unitless)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_935908_v1/index.htmlTable | https://www.bco-dmo.org/dataset/935908
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_935908_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_935908_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_935908_v1 | ||||||
| log in | [Carpinteria Salt Marsh Elemental and Isotope Composition Data for Sediment and Biomass] - Elemental and isoptopic composition of sediment and biomass from the Carpinteria Salt March sampled in 2020 and 2021 (Carbon Storage in Mangrove Ecosystems via Abiotic Sulfurization) | Here we provide data that help to evaluate organic matter sulfurization and pyrite formation in a salt marsh in California. We collected six sediment cores from three habitat types at Carpinteria Salt Marsh Reserve (34.41336°N, 119.84365°W) in July 2020. One core was used to establish dry bulk density, while the other was reserved for geochemical measurements. Both cores were kept at -20°C until analysis could be carried out. We provide elemental concentrations (organic C/N/S, Fe, pyrite) and isotopic compositions (δ13C, δ34S) of important carbon, iron and sulfur sediment pools. Additional biomass samples were collected between 2020 and 2023 and were also analyzed for elemental (C/N/S) and isotopic compositions (δ13C, δ34S). Data will be useful for those interested in assessing organic matter sulfurization and pyrite formation in blue carbon ecosystems such as mangroves, seagrass meadows and salt marshes. Data will also be informative for researchers investigating organic and inorganic sulfur cycling. Samples were collected by Lena Capece and Morgan Raven, data were interpreted by Lena Capece and Morgan Raven.\n\ncdm_data_type = Other\nVARIABLES:\ncollection_date (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\ntype (unitless)\nlocation (unitless)\ndepth (m)\ndepth_bin (unitless)\nhabitat (unitless)\nOC (weight percent carbon (wt. %C))\nCPK (weight percent carbon (wt. %C))\nOS (unitless)\nSPK (unitless)\nCN (weight percent sulfur (wt. %S))\nCNPK (weight percent sulfur (wt. %S))\nSC (unitless)\nSCPK (unitless)\n... (10 more variables)\n | BCO-DMO | bcodmo_dataset_938709_v1 | ||||||||||||
| log in | [Carpinteria Salt Marsh Sulfur Speciation in Sediments and Biomass] - Sulfur speciation of sediment and biomass from the Carpinteria Salt March sampled in 2020 and 2021 (Carbon Storage in Mangrove Ecosystems via Abiotic Sulfurization) | Here we provide data that help to evaluate organic matter sulfurization and pyrite formation in a salt marsh in California. We collected six sediment cores from three habitat types at Carpinteria Salt Marsh Reserve (34.41336°N, 119.84365°W) in July 2020. One core was used to establish dry bulk density, while the other was reserved for geochemical measurements. Both cores were kept at -20°C until analysis could be carried out. We provide data on the speciation of sulfur in acid hydrolysis resistant organic matter and biomass samples. Data will be useful for those interested in assessing organic matter sulfurization in blue carbon ecosystems such as mangroves, seagrass meadows and salt marshes. Data will also be informative for researchers investigating organic sulfur cycling. Samples were collected by Lena Capece and Morgan Raven, data were interpreted by Lena Capece and Morgan Raven.\n\ncdm_data_type = Other\nVARIABLES:\ncollection_date (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\ntype (unitless)\nlocation (unitless)\nhabitat (unitless)\ndepth_core (Depth, cm)\ndisulfide (fraction as a decimal)\nmonosulfide (fraction as a decimal)\naromatic (fraction as a decimal)\nsulfoxide (fraction as a decimal)\nsulfonate (fraction as a decimal)\nsulfate_ester (fraction as a decimal)\nchi_sq (unitless)\nreduced (fraction as a decimal)\noxidized (fraction as a decimal)\n | BCO-DMO | bcodmo_dataset_938382_v1 | ||||||||||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_782025 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_782025.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_782025/ | public | [Chemistry and cell counts] - Chemistry and cell counts of formation fluids from North Pond, western flank of the Mid-Atlantic Ridge, from 2012-2014 (Collaborative Research: Characterization of Microbial Transformations in Basement Fluids, from Genes to Geochemical Cycling) | Chemistry and cell counts of formation fluids from North Pond\n\ncdm_data_type = Other\nVARIABLES:\nsample (unitless)\nbioproject_id (unitless)\ncollection_date (unitless)\ndescription (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\ndepth_minimum (Depth, meters)\ndepth_maximum (Depth, meters)\nCell_counts (cells per mililiter (cells/mL))\nconfidence_level_95pcnt (cells per mililiter (cells/mL))\nO2 (micromole per Liter (umol/L))\nNO3 (Mole Concentration Of Nitrate In Sea Water, micromole per Liter (umol/L))\nSi (Mass Concentration Of Silicate In Sea Water, micromole per Liter (umol/L))\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_782025_fgdc.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_782025/index.htmlTable | https://www.bco-dmo.org/dataset/782025
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_782025.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_782025&showErrors=false&email= | BCO-DMO | bcodmo_dataset_782025 | ||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_914491_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_914491_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_914491_v1/ | public | [Consensus Reference Material Collection Data] - Consensus Reference Material Collection Data of marine dissolved organic matter collected in the Florida Strait between 2019 and 2023 (Preparation and Distribution of DOC Consensus Reference Materials) | The laboratory of Prof. Dennis A. Hansell at the University of Miami is supported by the U.S. National Science Foundation to provide the international community of marine dissolved organic matter analysts the reference waters needed for testing their analytical results against those of a select group of expert analysts. \n\nThree depths of the water column are sampled in the Florida Strait, typically twice each year, to collect and distribute those waters as reference materials. The deepest water (i.e., deep seawater reference (DSR)) is collected in the Florida Straits at 700 m depth. A mid depth seawater reference (MSR), is collected at 150 m depth and surface seawater reference (SSR) is collected at 5 m. In the data table that follows, the relevant information for each collection during NSF Grant OCE-1844886, awarded to the Hansell laboratory, is provided. These details include the ship employed and its cruise designations, the dates of collection, the batch and lot numbers designated for the reference waters, the locations and depths sampled, the concentrations of dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) in each lot. Finally, hyperlinks to the associated CTD and underway data, archived by RVDATA.US, are provided.\n\ncdm_data_type = Other\nVARIABLES:\nCruise_ID (unitless)\nCollection_Date (unitless)\nLatitude (degrees_north)\nlongitude (degrees_east)\nBatch_ID (unitless)\nDesignations (unitless)\nSampling_Depths (unitless)\nDOC_Conc_uM_Min (micromoles carbon per liter (uM/L))\nDOC_Conc_uM_Max (micromoles carbon per liter (uM/L))\nTDN_Conc_uM_Min (micromoles nitrogen per liter (uM/L))\nTDN_Conc_uM_Max (micromoles nitrogen per liter (uM/L))\nShip (unitless)\nShip_Data (unitless)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_914491_v1/index.htmlTable | https://www.bco-dmo.org/dataset/914491
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_914491_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_914491_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_914491_v1 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_845039_v2 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_845039_v2.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_845039_v2/ | public | [Coral Associated Microbes on Mo'orean Coral Reefs] - Coral associated microbes on coral, sediment and water sampled from coral reefs in Mo'orea, French Polynesia in 2017 and 2018 (Collaborative Research: Viral Reefscapes: The Role of Viruses in Coral Reef Health, Disease, and Biogeochemical Cycling) | Three species of coral, plus water and sediment, were sampled at 21 sites around the island of Mo'orea, French Polynesia during the dry and rainy seasons in 2017 and 2018. Coral associated microbes (bacteria and archaea) were investigated and their community composition characterized through sequencing of the 16S rRNA gene.\n\ncdm_data_type = Other\nVARIABLES:\nBioSample_accession (unitless)\nSample_name (unitless)\nOrganism (unitless)\nCollection_date (unitless)\nDepth (meters (m))\nEnv_Local_Scale (unitless)\nGeo_Loc_Name (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nHost (unitless)\nHost_Subject_ID (unitless)\nSequencing_Replicate (unitless)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_845039_v2_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_845039_v2_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_845039_v2/index.htmlTable | https://www.bco-dmo.org/dataset/845039
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_845039_v2.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_845039_v2&showErrors=false&email= | BCO-DMO | bcodmo_dataset_845039_v2 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_933832_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_933832_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_933832_v1/ | public | [Coral lesion frequencies and sizes after fish feces treatment] - Lesion frequencies and sizes after fish feces treatment on coral samples collected on the north shore of Mo’orea, French Polynesia, Oct 2020 to Jun 2021 (CAREER: Testing the effects of predator-derived feces on host symbiont acquisition and health) | This datafile contains frequencies and sizes (number of polyps killed) developed in coral tissues after the application and removal of fish feces to test whether fish from different guilds affect coral health in distinct ways.There were five treatments: fresh feces from a corallivorous butterflyfish (FC); fresh feces from a grazer/detritivore (FG); sterilized feces from a corallivorous butterflyfish (SC); sterilized feces from a grazer/detritivore (SG); no-feces control (C). For the fresh feces treatments (FC, FG), we applied 100 µl of fresh feces isolated from the hindgut of the butterflyfish Chaetodon ornatissimus (FC) or the grazer/detritivore Ctenochaetus striatus (FG) directly onto each coral fragment. For the sterilized feces treatments (SC, SG), fecal pellets were sterilized in a pressure cooker for 40 minutes at 120°C and then applied in the same manner as fresh feces. The experiment ran for ~22 hours. The experiment was conducted in three iterations in Mo'orea, French Polynesia, over two years (2020, 2021).\n\ncdm_data_type = Other\nVARIABLES:\nSample_ID (unitless)\nCollection_Date (unitless)\nExperiment (unitless)\nTreatment (unitless)\nColony (unitless)\nReplicate (unitless)\nHealth (unitless)\nDead_Polyps (unitless)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_933832_v1/index.htmlTable | https://www.bco-dmo.org/dataset/933832
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_933832_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_933832_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_933832_v1 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_775229.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_775229 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_775229.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_775229/ | public | [Coral reef seawater microbial communities] - Diel, daily, and spatial variation of coral reef seawater microbial communities from US Virgin Islands, 2017 (Signature exometabolomes of Caribbean corals and influences on reef picoplankton) | Bacterial and archaeal diversity and composition, microbial cell abundances, inorganic nutrient concentrations, and physicochemical conditions were determined and measured in coral reef seawater over a three-day, diel time series on one reef in St. John, U.S. Virgin Islands.\n\ncdm_data_type = Other\nVARIABLES:\nSample_ID (unitless)\nNCBI_BioProject_accession_number (NCBI Bio Project Accession Number, unitless)\nNCBI_BioSample_accession_number (NCBI Bio Sample Accession Number, unitless)\nSample_type (unitless)\nCoral_Colony_or_sand (unitless)\nCollection_time (unitless)\nCollection_Date (unitless)\nCollection_location (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nProchlorococcus_cells_mL (Prochlorococcus Cells M L, cell/milliliter)\nSynechococcus_cells_mL (Synechococcus Cells M L, cell/milliliter)\nPicoeukaryotes_cells_mL (Picoeukaryotes Cells M L, cell/milliliter)\nUnpigmented_cells_cells_mL (Unpigmented Cells Cells M L, cell/milliliter)\nPhosphate_uM (Mass Concentration Of Phosphate In Sea Water, micromoles)\nSilicate_uM (Mass Concentration Of Silicate In Sea Water, micromoles)\nNitrate_uM (Mole Concentration Of Nitrate In Sea Water, micromoles)\nNitrite_uM (Mole Concentration Of Nitrite In Sea Water, micromoles)\nAmmonium_uM (Mole Concentration Of Ammonium In Sea Water, micromoles)\nTemperature_F (degrees Fahrenheit)\nDepth_Feet (Depth, feet)\nRelative_light_levels (lumens/foot^2)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_775229_fgdc.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_775229/index.htmlTable | https://www.bco-dmo.org/dataset/775229
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_775229.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_775229&showErrors=false&email= | BCO-DMO | bcodmo_dataset_775229 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_911338_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_911338_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_911338_v1/ | public | [Cyanobacteria cultures used to generate DNA reference library] - Cyanobacteria cultures used to generate DNA reference library from samples collected from sites in Alpena and Monroe, Michigan and Palm Coast, Florida between May and June 2022. (Collaborative Research: RUI: OCE-BO: Tango in the Mat World: Biogeochemistry of diurnal vertical migration in microbial mats of Lake Huron’s sinkholes) | These data are the information for each of the cultures generated from samples collected from three sites in Alpena, Michigan, one site in Monroe, Michigan, and one site in Palm Coast, Florida. Data are for cultures sequenced using Sanger sequencing and include taxonomic identification, location and sample type for samples used to develop the cultures.\nEach of these cultures was developed from high-sulfur, low-oxygen environments formed by underwater sinkholes and springs that create extreme habitats populated by microbial mat communities. Our study investigated previously undescribed diatom diversity in these habitats. Sequences from these cultures contribute to tying molecular data to morphologically identified isolates, providing a bridge between these two data types that can be used to improve metabarcoding analyses.\n\ncdm_data_type = Other\nVARIABLES:\nNCBI_Accession (unitless)\nCulture_ID (unitless)\nGenus (unitless)\nSpecies (unitless)\nMedia (unitless)\nCollection_Date (unitless)\nLocation (unitless)\nSample_Type (unitless)\nLat (degrees_north)\nlongitude (Long, degrees_east)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_911338_v1/index.htmlTable | https://www.bco-dmo.org/dataset/911338
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_911338_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_911338_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_911338_v1 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_911008_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_911008_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_911008_v1/ | public | [Diatom cultures used to generate DNA reference library] - Diatom cultures used to generate DNA reference library from samples collected from sites in Alpena, Michigan and Palm Coast, Florida between July 2021 & 2022. (Collaborative Research: RUI: OCE-BO: Tango in the Mat World: Biogeochemistry of diurnal vertical migration in microbial mats of Lake Huron’s sinkholes) | These data are the information for each of the cultures generated from samples collected from three sites in Alpena, Michigan, one site in Monroe, Michigan, and one site in Palm Coast, Florida. Data are for cultures sequenced using Sanger sequencing and include taxonomic identification, location and water parameter information from samples used to develop the cultures, and growth medium.\nEach of these cultures was developed from high-sulfur, low-oxygen environments formed by underwater sinkholes and springs that create extreme habitats populated by microbial mat communities. Our study investigated previously undescribed diatom diversity in these habitats. Sequences from these cultures contribute to tying molecular data to morphologically identified isolates, providing a bridge between these two data types that can be used to improve metabarcoding analyses.\n\ncdm_data_type = Other\nVARIABLES:\nNCBI_Accession (unitless)\nCulture_ID (unitless)\nGenus (unitless)\nSpecies (unitless)\nVariety (unitless)\nCollection_ID (unitless)\nMedia (unitless)\nCollection_Date (Month/Day/Year)\nLocation (unitless)\nSample_Type (unitless)\nLat (degrees_north)\nlongitude (Long, degrees_east)\nTemp (Celsius (°C))\nCond (Microsiemens / centimeter (μS/cm))\nTDS (Grams/liter (g/L))\npH (unitless)\nORP (Millivolts (mV))\nNTU (Nephelometric Turbidity Units (NTU))\nODO (Percentage saturation)\n... (6 more variables)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_911008_v1/index.htmlTable | https://www.bco-dmo.org/dataset/911008
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_911008_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_911008_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_911008_v1 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_753343.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_753343 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_753343.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_753343/ | public | [ESP 2016 Seq] - Metagenomic, metatranscriptomic, and single cell sequencing data from an Environmental Sample Processor deployment in Monterey Bay, CA in 2016. (Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere) | These metagenomic and metatranscriptomic time-series data cover a 52-day period in the fall of 2016 during an intense bloom of the dinoflagellate Akashiwo sanguinea in Monterey Bay, CA, USA. The dataset comprises 84 metagenomes, 82 metatranscriptomes, and 88 16S rRNA amplicon libraries that capture the functions and taxonomy the bacterial and archaeal community. In addition, 88 18S rRNA amplicon libraries describe the taxonomy of the eukaryotic community during the bloom. Microbial cells were collected at station M0 using the moored autonomous robotic Environmental Sample Processor (ESP) instrument and preserved with RNAlater in the instrument until retrieval.\n\ncdm_data_type = Other\nVARIABLES:\nGOLD_Project_ID (unitless)\nAnalysis_Project_Name (unitless)\nType (unitless)\nAssembly_Method (unitless)\nCollection_Date (unitless)\nInstrument (unitless)\nJGI_Contigs_Link (unitless)\nJGI_Project_ID (unitless)\nJGI_Sample_ID (unitless)\nJGI_Sequencing_Project_ID (unitless)\nJGI_Sequencing_Project_Name (unitless)\nLatitude_and_Longitude (Longitude, unitless)\nNCBI_BioProject_Accession (NCBI Bio Project Accession, unitless)\nNCBI_BioSample_Accession (NCBI Bio Sample Accession, unitless)\nNCBI_Project_ID (unitless)\nNCBI_SRA_Accession_ID (unitless)\nSample_Name (unitless)\nSequencing_Run_Mode (unitless)\nTotal_Bases (unitless)\nVolume_Seawater_Filtered (milliliters (mL))\nenv_biome (unitless)\n... (5 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_753343_fgdc.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_753343/index.htmlTable | https://www.bco-dmo.org/dataset/753343
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_753343.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_753343&showErrors=false&email= | BCO-DMO | bcodmo_dataset_753343 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_719379.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_719379 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_719379.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_719379/ | public | [Fatty acid profiles] - Fatty acid profiles of M. menidia females and their unfertilized eggs. (Collaborative research: Understanding the effects of acidification and hypoxia within and across generations in a coastal marine fish) | Gas chromatography was used to quantify the absolute (mg g dry weight-1) and\nrelative concentrations (% of total) of 27 FAs for each of 5 females (whole\nindividual) and their unfertilized eggs (~ 1 ml). Samples were first dried and\nthen homogenized in a solution of chloroform-methanol (2:1 v/v) and\ntricosanoic acid (23:0) as an internal standard for quantification of mg\ng\\u22121\\u00a0dry mass of fatty acids. Lipids were cold-extracted from\napproximately 50 mg of dry mass. A Shimadzu GC-2014 gas chromatograph set with\na Phenomenex ZB-WAX plus capillary column (30\\u00a0m long; 0.53 mm ID; 1.0 um\nthick) was used to quantify FAs, and individual FAs were identified by\ncomparison to commercial standards (Supelco, Inc).\\u00a0\n \nThese data are\\u00a0associated with the corresponding paper:\n \n[Snyder, J.T.*, Murray, C.S.*, and Baumann, H. (2017) Potential for maternal\neffects on offspring CO2-sensitivities in a coastal marine fish. Journal of\nExperimental Marine Biology and Ecology (in\npress).](\\\\https://doi.org/10.1016/j.jembe.2017.11.002\\\\)\n \nOther datasets related to this paper:\n \n[Survival, length, and growth responses of M. menidia offspring from different\nfemales exposed to contrasting CO2 environments.](\\\\https://www.bco-\ndmo.org/dataset/719420\\\\)\n\ncdm_data_type = Other\nVARIABLES:\nSpecies (unitless)\nCollection_site (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nCollection_date (unitless)\n... (6 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_719379_fgdc.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_719379/index.htmlTable | https://www.bco-dmo.org/dataset/719379
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_719379.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_719379&showErrors=false&email= | BCO-DMO | bcodmo_dataset_719379 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_908689_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_908689_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_908689_v1/ | public | [Gulf of Alaska copepods: annotated transcriptomes] - Annotated de novo transcriptomes generated from six co-occurring species of calanoid copepods from the R/V Tiglax TXF18, TXS19, TXF15, TXF17 in the Gulf of Alaska from 2015-2019 (Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska) | The dataset includes the annotation files of nine high-quality de novo transcriptomes generated from shotgun assemblies of short-sequence reads. The species are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. The de novo assemblies included one generated several years ago plus eight new ones generated from six co-occurring species of calanoid copepods in the Gulf of Alaska. The transcriptomes include the first published ones for Neocalanus plumchrus, Neocalanus cristatus, Eucalanus bungii and Metridia pacifica and three for Neocalanus flemingeri and two for Calanus marshallae. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Short-sequence reads were assembled with Trinity software and resulting transcripts were annotated using the SwissProt database with additional functional annotation using gene ontology terms and enzyme function. The annotations files are the first ones published for these species. The integrated dataset can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes using the annotations.\n\nThese data are further described in the following publications: Hartline, et al. (2023) (DOI: 10.1038/s41597-023-02130-1), Roncalli, et al. (2022) (DOI: 10.1111/mec.16354), and Roncalli, et al. (2019) (DOI: 10.1038/s42003-019-0565-5)\n\ncdm_data_type = Other\nVARIABLES:\nseq_id (unitless)\nGenbank_accession (unitless)\nSpecies (unitless)\nStation (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nCollection_date (unitless)\nDepth_range (meters (m))\nLife_stage (unitless)\nSex (unitless)\nEntry (unitless)\n... (20 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_908689_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_908689_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_908689_v1/index.htmlTable | https://www.bco-dmo.org/dataset/908689
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_908689_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_908689_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_908689_v1 | |||
| 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_897895_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_897895_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_897895_v1/ | public | [Juvenile Black sea bass winter growth and lipid accumulation under varying food and temperature conditions - Experiment 1] - Winter growth and lipid accumulation in juvenile Black sea bass exposed to varying food and temperature conditions during lab experiments conducted from September 2021 to April 2022 at UConn Avery Point (Collaborative research: Understanding the effects of acidification and hypoxia within and across generations in a coastal marine fish) | The northern stock of Black sea bass (BSB, Centropristis striata) has greatly expanded over the past decade, potentially due to warming Northwest Atlantic shelf waters affecting overwintering especially in juveniles. To gather better empirical data we quantified winter growth and lipid accumulation in BSB juveniles from Long Island Sound using two complementing experiments. The data from Experiment 1 are presented here.\n\nExperiment 1 measured individual length growth (GR), weight-specific growth (SGR), growth efficiency, and lipid content at constant food and three static temperatures: 6°, 12°, and 19° Celsius (C). Average GR (SGR) decreased from 0.24 millimeters per day (mm d-1) at 19°C (0.89% d-1) to 0.15 mm d-1 at 12°C (0.54% d-1) to 0.04 mm d-1 at 6°C (0.17% d-1). Even at the coldest temperature, most juveniles sustained positive GRs and SGRs; hence, the species' true thermal growth minimum may be below 6°C. However, lipid accumulation was greatest at 12°C, which is close to what overwintering juveniles likely encounter offshore.\n\nThe data from Experiment 2 are presented in a related dataset (https://www.bco-dmo.org/dataset/898012). In both experiments, juveniles disproportionally accumulated lipid over lean mass, with lipid proportions tripling in Exp2 from 4% at 65 mm to 12% at 120 mm.\n\ncdm_data_type = Other\nVARIABLES:\nCollection_site (unitless)\nlongitude (degrees_east)\nlatitude (degrees_north)\nCollection_date (unitless)\nSample_date (unitless)\nSpecies (unitless)\nBSB_ID (unitless)\nGroup (unitless)\nTemp (degree Celsius)\nDays_W (number of days)\n... (21 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_897895_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_897895_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_897895_v1/index.htmlTable | https://www.bco-dmo.org/dataset/897895
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_897895_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_897895_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_897895_v1 | |||
| log in | [Kelletia kelletii: DNA and RNA sequence] - Full genome and transcriptome sequence assembly of the non-model organism Kellet’s whelk, Kelletia kelletii (Collaborative Research: RUI: Combined spatial and temporal analyses of population connectivity during a northern range expansion) | Understanding the genomic characteristics of non-model organisms can bridge research gaps between ecology and evolution. However, the lack of a reference genome and transcriptome for these species makes their study challenging. Here, we complete the first full genome and transcriptome sequence assembly of the non-model organism Kellet's whelk, Kelletia kelletii, a marine gastropod exhibiting a poleward range expansion coincident with climate change. We used a combination of Oxford Nanopore Technologies, PacBio, and Illumina sequencing platforms and integrated a set of bioinformatic pipelines to create the most complete and contiguous genome documented among the Buccinoidea superfamily to date. Genome validation revealed relatively high completeness with low missing metazoan Benchmarking Universal Single-Copy Orthologs (BUSCO) and an average coverage of ∼70x for all contigs. Genome annotation identified a large number of protein-coding genes similar to some other closely related species, suggesting the presence of a complex genome structure. Transcriptome assembly and analysis of individuals during their period of peak embryonic development revealed highly expressed genes associated with specific Gene Ontology (GO) terms and metabolic pathways, most notably lipid, carbohydrate, glycan, and phospholipid metabolism. We also identified numerous heat shock proteins (HSPs) in the transcriptome and genome that may be related to coping with thermal stress during the sessile life history stage. A robust reference genome and transcriptome for the non-model organism K. kelletii provide resources to enhance our understanding of its ecology and evolution and potential mechanisms of range expansion for marine species facing environmental changes.\n\ncdm_data_type = Other\nVARIABLES:\nRun (unitless)\nAssay_Type (unitless)\nAvgSpotLen (unitless)\nBases (unitless)\nBioProject (unitless)\nBioSample (unitless)\nBioSampleModel (unitless)\nBytes (unitless)\nCenter_Name (unitless)\n... (29 more variables)\n | BCO-DMO | bcodmo_dataset_945292_v1 | ||||||||||||
| 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_949666_v1 | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_949666_v1/ | public | [Metadata for longread sequencing of Carcinus maenas] - Metadata for longread sequencing of Carcinus maenas collected from Buzzard's Bay, Massachusetts from May 2022 to Aug 2022 (Collaborative Research: Tracking fine-scale selection to temperature at the invasion front of a highly dispersive marine predator) | This project explores genomic changes in the invasive European green crab (Carcinus maenas), including at a putative inversion polymorphism. To begin to explore structural variation without a reference genome, we conducted semi-targeted longread sequencing of the C. maenas genome using MinION sequencing. This dataset includes individual metadata for 6 raw MinION reads, archived at GenBank's SRA under BioProject PRJNA1171011. This sequencing was conducted using crabs from Massachusetts waters.\n\ncdm_data_type = Other\nVARIABLES:\nsample_name (unitless)\nCollection_date (unitless)\nSRA_accession (unitless)\nbiosample_accession (unitless)\nembayment (unitless)\nstate (unitless)\nsex (unitless)\nlife_stage (unitless)\nrun_ID (unitless)\nsequencing_date (unitless)\nrun_day (days)\nprobe_set (unitless)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_949666_v1/index.htmlTable | https://www.bco-dmo.org/dataset/949666
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_949666_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_949666_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_949666_v1 | ||||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_949682_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_949682_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_949682_v1/ | public | [Metadata for RNASeq of green crabs in the northeast Pacific] - Metadata for RNASeq of green crabs collected in the northeast Pacific from Apr 2017 to Aug 2021 (Collaborative Research: Tracking fine-scale selection to temperature at the invasion front of a highly dispersive marine predator) | This project explores genomic changes in the invasive European green crab (Carcinus maenas) in the northeast Pacific. It tracks the earliest stages of green crab invasion into a new environment where the species is predicted to have substantial ecological and economic impacts. Samples span time and space across the species range in the northeast Pacific, with a focus on areas where the species is currently expanding. This dataset includes individual metadata for 127 raw RNA-Seq reads, archived at GenBank's SRA under BioProject PRJNA1170986.\n\ncdm_data_type = Other\nVARIABLES:\nsample_name (unitless)\nSRA_accession (unitless)\nbiosample_accession (unitless)\nembayment (unitless)\nsite (unitless)\nstate (unitless)\nsex (unitless)\nsize_CW (Millimeters (mm))\ncolor (unitless)\ncollection_date (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\ncollector (unitless)\ncollector_affiliation (unitless)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_949682_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_949682_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_949682_v1/index.htmlTable | https://www.bco-dmo.org/dataset/949682
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_949682_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_949682_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_949682_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_949610_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_949610_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_949610_v1/ | public | [Metadata for targeted genotyping of green crabs in the northeast Pacific] - Metadata for targeted genotyping of green crabs collected in the northeast Pacific from Aug 2016 to Oct 2022 (Collaborative Research: Tracking fine-scale selection to temperature at the invasion front of a highly dispersive marine predator) | This project explores genetic changes in the invasive European green crab (Carcinus maenas) in the northeast Pacific, using targeted genotyping of SNPs identified in prior high-resolution population genomics in the region. It tracks the early stages of green crab invasion into a new environment, particularly through repeated sampling of multiple size-classes of crabs from the same sites over multiple years. Samples span time and space across the species range in the northeast Pacific, with a focus on the coast of Washington and Oregon. This dataset includes individual collection and accession metadata for 1,662 crabs, for which raw demultiplexed reads are archived at GenBank's SRA under BioProject PRJNA1177418.\n\ncdm_data_type = Other\nVARIABLES:\nsample_name (unitless)\nSRA_accession (unitless)\nbiosample_accession (unitless)\nembayment (unitless)\nsite (unitless)\nstate (unitless)\nsex (unitless)\nsize_CW (Millimeters (mm))\ncolor (unitless)\ncollection_date (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\ncollector (unitless)\ncollector_affiliation (unitless)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_949610_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_949610_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_949610_v1/index.htmlTable | https://www.bco-dmo.org/dataset/949610
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_949610_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_949610_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_949610_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_945915_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_945915_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_945915_v1/ | public | [Metagenome sequencing samples] - Contextual data for samples collected for metagenome sequencing from the deep subseafloor biosphere as accessed via CORKs along the Juan de Fuca Ridge flank in the Northeast Pacific Ocean between 2008 and 2014 (Collaborative Research: Illuminating microbes and their viruses within the dark ocean crust through strain-level approaches) | This dataset provides contextual information about samples used for metagenome sequencing. These samples were collected from pristine crustal fluids sampled via CORK observatories along the Juan de Fuca Ridge flank in the Northeast Pacific Ocean off the coast of North America. Also included are metadata for seawater and sediment metagenomes that have been sequenced as controls. All of the data are publicly available via the National Center for Biotechnology Information (NCBI) accession numbers provided in the dataset (BioProject numbers PRJNA655018 to PRJNA655040).\n\ncdm_data_type = Other\nVARIABLES:\nSample_Type (unitless)\nSample_Name (unitless)\nDNA_Isolation_Method (unitless)\nCollection_Date (unitless)\nCollection_Year (unitless)\nCollection_Month (unitless)\nCollection_Day (unitless)\nSample_Source (unitless)\nFluid_Delivery_Line (unitless)\nEnvironment (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nDepth (msb)\nArea (unitless)\nFull_Sample_Name_and_Description (unitless)\nIMG_Genome_ID (unitless)\nNCBI_Bioproject_Accession (unitless)\nNCBI_Biosample_Accession (unitless)\nSRA_ID (unitless)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_945915_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_945915_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_945915_v1/index.htmlTable | https://www.bco-dmo.org/dataset/945915
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_945915_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_945915_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_945915_v1 | |||
| 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 | [NCBI accessions for RNAseq data from apparently healthy and SCTLD-affected Montastraea cavernosa] - RNAseq data from apparently healthy and Stony Coral Tissue Loss Disease-affected Montastraea cavernosa coral collected from St. Thomas, US Virgin Islands in 2020 (RAPID: Collaborative Research: Predicting the Spread of Multi-Species Coral Disease Using Species Immune Traits) | These data include raw RNAseq reads from Montastraea cavernosa collected from two reefs in St. Thomas, United States Virgin Islands. Samples were collected from two reefs showing signs of active stony coral tissue loss disease (SCTLD) in February of 2020: Buck Island and Black Point. Black Point, a nearshore reef, first exhibited cases of SCTLD between December 2018 and January 2019, whereas Buck Island, situated near an offshore undeveloped island, recorded its first cases of SCTLD in October 2019. At both sites, one coral fragment was collected from each apparently health colony (Buck Island, n = 3; Black Point, n = 3), termed apparently healthy tissue on an apparently healthy colony (HH). Two fragments were collected from each diseased colony: one immediately adjacent to the SCTLD lesion line (Buck Island, n = 3: Black Point, n = 5), termed lesion tissue on a diseased colony (LD), and one as far away from the lesion line as possible (approximately 10 cm from the lesion line) (Buck Island, n = 3; Black Point, n = 5), termed apparently healthy tissue on a diseased colony (HD). Sample and data analysis was performed in January 2024. Sequences were used in a feature selection algorithm to identify the genes in M. cavernosa and its dominant algal endosymbiont, Cladocopium goreaui, that best discriminate between the three SCTLD health states. By characterizing the gene expression profiles associated with various tissue health states in M. cavernosa and C. goreaui, this data supports evidence that SCTLD causes dysbiosis between the coral host and its Symbiodiniaceae and describes the metabolic and immune shifts that occur as the holobiont transitions from an apparently healthy state to a diseased state.\n\ncdm_data_type = Other\nVARIABLES:\nSample_ID (unitless)\nNCBI_BioProject_accession (unitless)\nNCBI_BioSample_accession (unitless)\nNCBI_SRA_accession (unitless)\nSample_type (unitless)\nCoral_species (unitless)\nReef_Name (unitless)\nReef_type (unitless)\nCollection_Date (unitless)\nlatitude (degrees_north)\n... (15 more variables)\n | BCO-DMO | bcodmo_dataset_935630_v1 | ||||||||||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_914459_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_914459_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_914459_v1/ | public | [Neocalanus flemingeri incubation experiment: gene expression] - Gene expression profiles for Neocalanus flemingeri pre adults (CV) exposed to four different experimental food conditions collected from the M/V Dora in the Gulf of Alaska at station GAK1 from April 2019 (Collaborative Research: Molecular profiling of the ecophysiology of dormancy induction in calanid copepods of the Northern Gulf of Alaska LTER site) | This experimental dataset includes relative expression of individual Neocalanus flemingeri stage CV individuals incubated for different lengths of time and four different food treatments. The experimental protocol and results are described in detail in Roncalli et al., 2023. Briefly, field-collected N. flemingeri were allowed to molt into stage CV and then sorted into four different treatments: no food, low carbon, high carbon and high carbon with diatoms. After a one-week incubation, individuals from all four treatments were processed individually for RNA-Seq. In addition, following two and three-week incubations, copepods from the three fed treatments were processed individually for RNA-Seq. Short-sequence reads were mapped against a reference transcriptome and normalized gene expression was computed for each transcript. The dataset includes log-transformed relative gene expression in reads per kilobase per million reads (RPKM) (log2[RPKM+1]). The dataset also includes a list of differentially expressed genes and a look-up table that cross-references the hierarchical identifications of transcripts generated by the Trinity assembly software and the corresponding National Center for Biotechnology Information (NCBI) accession number. \n\nThese data are further described in the following publications: Roncalli, et al. (2023) (DOI: 10.1093/plankt/fbad045) and Roncalli, et al. (2019) (DOI: 10.1038/s42003-019-0565-5)\n\ncdm_data_type = Other\nVARIABLES:\nseq_id (unitless)\nGenbank_accession (unitless)\nOrganism_Name (unitless)\nStation (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nCollection_date (unitless)\nYear (unitless)\nMonth (unitless)\nDay (unitless)\nDepth_range (meters (m))\n... (33 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_914459_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_914459_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_914459_v1/index.htmlTable | https://www.bco-dmo.org/dataset/914459
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_914459_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_914459_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_914459_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_918545_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_918545_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_918545_v1/ | public | [Organic Alkalinity Discrete Data] - Organic alkalinity data from estuary transects in Coastal Gulf of Maine (Pleasant, Maine; St. John, New Brunswick) in May and October of 2018 and 2019 (Collaborative Research: Organic Alkalinity: Impacts of the [OTHER] Alkalinity on Estuary and Coastal Ocean Chemistry) | Four organic alkalinity estuary transects, in May and October of 2018 and 2019, were completed in the Pleasant (Maine, USA) and St. John (New Brunswick, Canada) estuaries. Discrete samples were collected at intervals of salinity along each estuary. An underway measurements system was also operated during each transect (see \"Related Datasets\" section). Discrete samples were analyzed via a number of methods described below. Underway measurements were collected using the procedures described in Hunt et al. (2013).\n\nOrganic alkalinity is a poorly understood component of the estuarine and coastal ocean acid-base system. This lack of understanding makes assessment of ocean acidification vulnerability and inorganic carbon dynamics more difficult. However, the methods used to quantify organic alkalinity and its effects on the acid-base system are not standardized. In this work we examined several approaches for the measurement of organic alkalinity, and their application to inorganic carbon dynamics.\n\ncdm_data_type = Other\nVARIABLES:\nID (unitless)\nCollection_Date (unitless)\nCollection_Time (unitless)\ntime (Iso_datetime_utc, seconds since 1970-01-01T00:00:00Z)\nLatitude (degrees_north)\nlongitude (degrees_east)\nSalinity (unitless)\nIn_Situ_Water_Temperature (degrees Celcius)\npHT (unitless (total scale))\npH_Method (unitless)\npCO2 (microatmospheres)\nDOC (micromoles carbon per liter)\nT_Alk (micromoles per kilogram)\nDIC (micromoles per kilogram)\nOrgAlk_from_Endpoint_Titration (micromoles per kilogram)\n... (9 more variables)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_918545_v1/index.htmlTable | https://www.bco-dmo.org/dataset/918545
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_918545_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_918545_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_918545_v1 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_782247.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_782247 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_782247.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_782247/ | public | [Otolith microstructure] - Otolith microstructure of young-of-year Atlantic silversides (Menidia menidia) from Mumford Cove during 2015 (Collaborative research: Understanding the effects of acidification and hypoxia within and across generations in a coastal marine fish) | Back-calculated age, hatch date, length-at-age, growth rate, and experienced temperature of young-of-year Atlantic silversides (Menidia menidia) collected during 3 successive collections in Mumford Cove, CT in fall 2015.\n\ncdm_data_type = Other\nVARIABLES:\nSpecies (unitless)\nCollection_Date (unitless)\nIndividual_number (unitless)\nTotal_length (centimeters (cm))\nTotal_length_class (centimeters (cm))\nTotal_length_group (unitless)\nSex (unitless)\nAge (days post hatch)\nHatch_Date (unitless)\nBiweekly_hatch_interval (unitless)\nHatch_check_radius (micrometer (um))\nOtolith_size (micrometer (um))\nHatch_check_flag (unitless)\nOtolith_flag (unitless)\nScaling_factor (unitless)\nIncrement_formation_date (unitless)\nTemperature (degrees Celsius)\nIncrement (Number)\nIncrement_width (micrometer (um))\nLength_at_age (millimeter (mm))\nGrowth_rate (millimeter per day (mm/d))\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_782247/index.htmlTable | https://www.bco-dmo.org/dataset/782247
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_782247.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_782247&showErrors=false&email= | BCO-DMO | bcodmo_dataset_782247 | ||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_945218_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_945218_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_945218_v1/ | public | [Parasite abundance in coral reef fishes] - Parasite abundance data collected from coral reef fishes across 19 islands in the central equatorial Pacific from 2009 to 2021 (Collaborative Research: Decomposing the effects of diversity on the abundance of marine parasites) | The loss of biological diversity is considered one of the principal environmental challenges of the 21st century, and there are hints that this massive reorganization of food webs could affect how parasites are transmitted among hosts. Parasites are often hidden and can be easy to overlook, but they are ecologically important and ubiquitous - so it is important to understand whether we should expect more or fewer of them as biodiversity disappears. Does biodiversity loss increase the abundance of parasites by eroding natural \"checks and balances\" on transmission? Or does it decrease parasite abundance by removing the free-living biodiversity on which parasites depend? Answers to these questions are urgently needed if we are to mitigate or prevent an uptick in parasite transmission for ecosystems experiencing biodiversity loss. \n\nIn a joint collaborative research project among the University of Washington, Scripps Institution of Oceanography at UC San Diego, and California State University Monterey Bay, we created a parasite dataset of unprecedented size and taxonomic resolution. We sampled parasites of coral reef fishes from 19 replicate islands in the central equatorial Pacific to study how biodiversity and parasite burden covary.\n\nIn this dataset, we present all of the data we collected on parasite abundance in coral reef fishes. We sampled 17 species (Acanthurus nigricans, Cephalopholis argus, Cephalopholis urodeta, Chromis iomelas, Chromis margaritifer, Ctenochaetus marginatus, Ctenochaetus striatus, Paracirrhites arcatus, Plectroglyphidodon dickii, Pseudanthias bartlettorum, Pseudanthias dispar, Pseudanthias mooreanus, Pseudanthias olivaceus, Pseudanthias pascalus, Pseudanthias spp., Stegastes aureus, Stegastes fasciolatus) across three archipelagos and 19 islands (Jarvis, Kingman, Kiritimati, Palmyra, Tabuaeran, and Teraina in the Northern Line Islands; Flint, Malden, Millennium, Starbuck, and Vostok in the Southern Line Islands; Huahine, Moorea, Raiatea, Rangiroa, Tahiti, Takapoto, Tetiaroa, and Tikehau in French Polynesia), for a total of 5,251 fish. These 17 broadly distributed host species represent a large spectrum of body sizes, including multiple taxonomic and trophic groups. Included in the dataset are specimens collected from expeditions mounted in 2009, 2010, 2011, 2013, 2019, 2020, and 2021. \n\nFish were collected with three-pronged spears and hand-nets, individually labeled and bagged, and frozen for transport before being thawed and evaluated for parasites. Parasitological dissections were designed to detect all multi-cellular (i.e., metazoan) parasites other than myxozoans, but would not have detected viral, bacterial, protozoal, or fungal parasites. Parasites were identified to the lowest possible taxonomic level and grouped into their broad parasite taxonomic grouping (i.e., Acanthocephalan, Cestoda, Copepoda, Isopoda, Monogenea, Other Crustacea, Trematoda, Nematoda) and transmission strategy (i.e., complex life cycle versus direct transmission).\n\ncdm_data_type = Other\nVARIABLES:\nfish_unique_code (units)\n... (19 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_945218_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_945218_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_945218_v1/index.htmlTable | https://www.bco-dmo.org/dataset/945218
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_945218_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_945218_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_945218_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_770638 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_770638.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_770638/ | public | [Porewater Composition] - Biogeochemical and sediment characteristics of the Cinder Cones Methane seep site in the Ross Sea from November 2016 (EAGER: Elucidating the Antarctic Methane Cycle at the Cinder Cones Reducing Habitat) | These data are samples of pore water collected from a methane seep on Ross Island. This seep had been active for 5 years at the time of sampling and were collected from 10m water depth.\n\ncdm_data_type = Other\nVARIABLES:\nSite_name (unitless)\nHabitat (unitless)\nCollection_Date (unitless)\nDate (unitless)\nlatitude (Geo Loc Lat, degrees_north)\nlongitude (Geo Loc Long, degrees_east)\ndepth (Water Depth, m)\nReplicate (unitless)\nSediment_Depth (centimeters (cm))\nsampling_approach (unitless)\nFluoride (millimole (mmol))\nAcetate (millimole (mmol))\nFormate (millimole (mmol))\nChloride (millimole (mmol))\nNitrite (Mole Concentration Of Nitrite In Sea Water, millimole (mmol))\nBromide (millimole (mmol))\nSulfate (millimole (mmol))\nThiosulfate (millimole (mmol))\nLithium (millimole (mmol))\nSodium (millimole (mmol))\nAmmonium (millimole (mmol))\nPotassium (millimole (mmol))\nMagnesium (millimole (mmol))\nCalcium (millimole (mmol))\nSulfide (millimole (mmol))\nMethane_porewater (nanomole per milliliter of porewater (nmol ml-1 porewater))\n... (4 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_770638_fgdc.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_770638/index.htmlTable | https://www.bco-dmo.org/dataset/770638
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_770638.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_770638&showErrors=false&email= | BCO-DMO | bcodmo_dataset_770638 | ||||
| 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_911441_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_911441_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_911441_v1/ | public | [Samples Sequenced for Metabarcoding] - Cyanobacterial and diatom samples collecteced between April and September 2022, and sequenced for metabarcodig of 16S and rbcL. (Collaborative Research: RUI: OCE-BO: Tango in the Mat World: Biogeochemistry of diurnal vertical migration in microbial mats of Lake Huron’s sinkholes) | These data are the sample information for each of the samples collected for metabarcoding of 16S and rbcL to describe Cyanobacterial and diatom diversity, respectively, in three sites in Alpena, Michigan, one site in Monroe, Michigan, and one site in Palm Coast, Florida. Sample data are for sequenced samples and include their associated water parameter information that was collected simultaneously.\nEach of these sites are high-sulfur, low-oxygen environments formed by underwater sinkholes and springs that create extreme habitats populated by microbial mat communities. Our study investigated previously undescribed diatom diversity in these habitats, and further explored the bacterial communities as well. Our results provide novel information on microbial mat community composition, and present evidence that microbial biogeography influences these unique communities.\n\ncdm_data_type = Other\nVARIABLES:\nSampleID (unitless)\nCollection_ID (unitless)\nCollection_Date (unitless)\nLocation (unitless)\nLat (degrees_north)\nlongitude (Long, degrees_east)\nSample_Type (unitless)\nTemp (Celsius (°C))\nCond (Microsiemens / centimeter (μS/cm))\nTDS (Grams/liter (g/L))\npH (unitless)\nNTU (Nephelometric Turbidity Units (NTU))\nODO (Percentage saturation)\nODO_mg_L (Milligrams/liter (mg/L))\nCl_mg_L (Milligrams/liter (mg/L))\nSO4_mg_L (Milligrams/liter (mg/L))\nNO3_N_mg_L (Milligrams/liter (mg/L))\nSi_mg_L (Milligrams/liter (mg/L))\nSRP_P_mg_L (Milligrams/liter (mg/L))\nNCBI_BioProject (unitless)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_911441_v1/index.htmlTable | https://www.bco-dmo.org/dataset/911441
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_911441_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_911441_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_911441_v1 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_878631_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_878631_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_878631_v1/ | public | [Sciaenid egg identification] - Identity of sciaenid eggs collected from the Gulf of Mexico Estuary near Port Aransas, Texas from 2020 to 2022 (Counter-gradient Flow of Fatty Acids in Marine Food Webs Through Egg Boons) | This dataset represents the identity (based on PCR results) of sciaenid eggs from the Gulf of Mexico Estuary near Port Aransas, Texas. Egg samples were collected from 20 August, 2020 through 8 March, 2022 from the research pier at UTMSI, located in the Aransas Pass inlet. Egg samples were collected bi-weekly during the Red Drum spawning season (August – December) and monthly outside the Red drum spawning season from two locations. Eggs were sorted by morphology to isolate sciaenid eggs and molecular PCR techniques were applied to subsamples of eggs to confirm the species identification.\n\ncdm_data_type = Other\nVARIABLES:\nEgg_size (millimeters)\nCollection_date (unitless)\nUIN (unitless)\nSite (unitless)\nLatitude (degrees_north)\nlongitude (degrees_east)\nDNA_extraction_date (unitless)\nDate_analyzed (unitless)\nRed_Drum (unitless)\nGulf_Kingfish (unitless)\nSouthern_Kingfish (unitless)\nSpotted_Seatrout (unitless)\nAtlantic_Croaker (unitless)\nBlack_Drum (unitless)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_878631_v1/index.htmlTable | https://www.bco-dmo.org/dataset/878631
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_878631_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_878631_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_878631_v1 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_878631_v2 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_878631_v2.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_878631_v2/ | public | [Sciaenid egg identification] - Identity of sciaenid eggs collected from the Gulf of Mexico Estuary near Port Aransas, Texas from 2020 to 2022 (Counter-gradient Flow of Fatty Acids in Marine Food Webs Through Egg Boons) | This dataset represents the identity (based on PCR results) of sciaenid eggs from the Gulf of Mexico Estuary near Port Aransas, Texas. Egg samples were collected from 20 August, 2020 through 8 March, 2022 from the research pier at UTMSI, located in the Aransas Pass inlet. Egg samples were collected bi-weekly during the Red Drum spawning season (August – December) and monthly outside the Red drum spawning season from two locations. Eggs were sorted by morphology to isolate sciaenid eggs and molecular PCR techniques were applied to subsamples of eggs to confirm the species identification.\n\ncdm_data_type = Other\nVARIABLES:\nEgg_size (millimeters)\nCollection_date (unitless)\nUIN (unitless)\nSite (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nDNA_extraction_date (unitless)\nDate_analyzed (unitless)\nRed_Drum (unitless)\nGulf_Kingfish (unitless)\nSouthern_Kingfish (unitless)\nSpotted_Seatrout (unitless)\nAtlantic_Croaker (unitless)\nBlack_Drum (unitless)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_878631_v2_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_878631_v2_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_878631_v2/index.htmlTable | https://www.bco-dmo.org/dataset/878631
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_878631_v2.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_878631_v2&showErrors=false&email= | BCO-DMO | bcodmo_dataset_878631_v2 | |||
| log in | [Seagrass Microbiome Data] - (Collaborative Research: The role of a keystone pathogen in the geographic and local-scale ecology of eelgrass decline in the eastern Pacific) | This dataset includes sample collection information and sequence accessions for 16S rRNA amplicon sequencing of eelgrass leaf and surrounding water column bacteria from 32 eelgrass meadows across latitudes from 55 to 32° N in the Northeastern Pacific during July and August 2019. Sequence Read Archive (SRA) Experiments and BioSamples can be accessed from the NCBI BioProject PRJNA802566 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA802566/)\n\nEelgrass, Zostera marina, is impacted by outbreaks of wasting disease caused by the opportunistic pathogen Labyrinthula zosterae. We investigated how Z. marina phyllosphere microbial communities vary with rising wasting disease lesion prevalence and severity relative to plant and meadow characteristics like shoot density, longest leaf length, and temperature across 23° latitude in the Northeastern Pacific. We sampled 32 eelgrass meadows across latitudes from 55 to 32° N in the Northeastern Pacific during July and August 2019. This range included six regions (AK=Alaska, BC=British Columbia, WA=Washington, OR=Oregon, BB=Bodega Bay Northern California, SD=San Diego Southern California), with 5–6 meadows per region. The location of each region is AK: N 55° 32' 27.124” W 133° 11' 1.0546, BC: N 51° 48' 30.1469” W 128° 13' 27.2182, WA: N 48° 36' 4.9725” W 122° 59' 56.4203, OR: N 44° 69 43.717” W 124° 89 22.7337, BB: N 38° 14' 30.3218” W 122° 58' 32.5723, SD: N 32° 47' 37.5929” W 117° 12' 57.1071”. We selected eelgrass meadows within each region that had consistently high cover of eelgrass in recent years.\n\ncdm_data_type = Other\nVARIABLES:\nsample_title (unitless)\nSampleType (unitless)\nRegionName (unitless)\nSiteCode (unitless)\nTissueType (unitless)\nLesionStatus (unitless)\ncollection_date (unitless)\nLocationName (unitless)\nTidalHeight (unitless)\nTransect (unitless)\n... (8 more variables)\n | BCO-DMO | bcodmo_dataset_933635_v1 | ||||||||||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_924808_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_924808_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_924808_v1/ | public | [Shoots sampled for whole genome sequencing] - Shoot measurements (sheath length and width) for the eelgrass (Zostera marina) shoots sampled for whole genome sequencing collected from 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 provides shoot measurements for the shoots sampled for whole genome sequencing for Tomales Bay and Bodega Harbor (see related datasets for access to sequence data). Sheath width is measured on the terminal shoot using calipers at the abscission point (point where leaves emerge from the sheath). Sheath length is measured using a ruler to the nearest mm from the base to the abscission point. These data were used to record any differences in plant phenotype among the populations sampled. Shoot Length was not measured since it is susceptible to breakage and density was not measured as we could not ascribe density to a genetic individual.\n\ncdm_data_type = Other\nVARIABLES:\nINDV (unitless)\nSITE (unitless)\ncollection_date (unitless)\nLatitude (degrees_north)\nlongitude (degrees_east)\nsheath_length (millimeters (mm))\nsheath_width (millimeters (mm))\nsite_descrip (Depth, unitless)\nmean_temp_C (degrees Celsius)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_924808_v1/index.htmlTable | https://www.bco-dmo.org/dataset/924808
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_924808_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_924808_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_924808_v1 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_917239_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_917239_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_917239_v1/ | public | [Siphonophore CSIA-AA] - Compound-specific isotope analysis of amino acids (CSIA-AA) from a subset of siphophore samples collected during four research cruises on the R/V Wester Flyer in the California Current Ecosystem between 2019 and 2021 (Collaborative research: The effects of predator traits on the structure of oceanic food webs) | Samples of siphonophores (Cnidaria, Hydrozoa) were collected using blue‑water diving, midwater trawls, and remotely operated vehicles in the California Current Ecosystem, from 0 to 3,000 meters depth. Siphonophore samples were collected on four research cruises on the R/V Wester Flyer between 2019-2021. To remove potential biases associated with tissue‑specific variability in stable isotope values, the gelatinous swimming bells (nectophores) of siphonophores were sampled. This approach was possible for most specimens, except for physonect species that are extremely fragile or have nectosomes that are a small fraction of the colony length and are often not collected. For these species (e.g., Apolemia spp.), the gelatinous bracts and pieces of the siphosome, excluding gastrozooids, were used. For small individuals (Diphyes dispar, Nanomia bijuga, and Sphaeronectes koellikeri), nectophores from several colonies that were captured at the same time and sampling location were pooled to obtain an adequate mass for isotope analyses. A subset of samples was selected for compound-specific isotope analysis of amino acids. These specific taxa were selected as representatives of different depth habitats, suborders, and hypothesized diets. Bulk and compound-specific isotope analyses were performed at the University of Hawaii's Biogeochemistry Stable Isotope Facility. This dataset includes the compound-specific isotope analysis data.\n\ncdm_data_type = Other\nVARIABLES:\nCollection_Date (unitless)\nYear (unitless)\nMonth (unitless)\nGenus (unitless)\nBest_Taxonomic_ID (unitless)\nAlanine (parts per thousand)\nGlycine (parts per thousand)\nThreonine (parts per thousand)\nSerine (parts per thousand)\nValine (parts per thousand)\nLeucine (parts per thousand)\nIsoleucine (parts per thousand)\nProline (parts per thousand)\n... (21 more variables)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_917239_v1/index.htmlTable | https://www.bco-dmo.org/dataset/917239
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_917239_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_917239_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_917239_v1 | |||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_775451.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_775451 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_775451.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_775451/ | public | [Sponge holobiont accessions and metadata] - NCBI accessions and metadata associated with Caribbean sponge metagenomes collected from Curacao, Belize, Cayman Islands and St. Croix, 2009 and 2017-2018 (Collaborative Research: Dimensions: Evolutionary Ecology of Sponges and Their Microbiome Drives Sponge Diversity on Coral Reefs) | NCBI accessions and metadata associated with Caribbean sponge metagenomes collected from Curacao, Belize, Cayman Islands and St. Croix, 2009 and 2017-2018.\n\ncdm_data_type = Other\nVARIABLES:\nBioProject (Bio Project, unitless)\nBioSample (Bio Sample, unitless)\nSample_name (unitless)\nsample_type (unitless)\nhost (unitless)\ncollection_date (unitless)\ngeographic_location (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nsource_material_identifiers (unitless)\ndepth_ (Depth, feet seawater (fsw) or meters)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_775451_fgdc.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_775451/index.htmlTable | https://www.bco-dmo.org/dataset/775451
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_775451.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_775451&showErrors=false&email= | BCO-DMO | bcodmo_dataset_775451 | |||
| log in | [Surface Sedimentary Black Carbon Concentrations and Carbon Isotopes Values] - Surface Sedimentary Black Carbon Concentrations, Flux, and Carbon Isotopes Values from the R.V. Endeavor EN651 in the Equatorial Atlantic Ocean from March 2020 (Concentrations and source assessment of black carbon across tropical Atlantic air and sediment) | Surface sediments (0-1 cm) were obtained from the equatorial Atlantic Ocean and isolated for black carbon using the chemothermal oxidation at 375°C method (CTO 375). Multicores were taken aboard the R.V. Endeavor (EN651) from March 1st through March 15th, 2020, using a multi corer MC-800. Sediment samples were collected from 12 multicore stations along a west-to-east transect of the equatorial Atlantic centered on about 5˚N. Sediment deposition environments included the Amazon Submarine Fan, a series of sites across the Mid-Atlantic Ridge, and sites on the Sierra Leone Rise and adjacent Sierra Leone Basin. See Figure 1 in the EN651 cruise report (Lohmann 2020) for an illustration of coring site locations.\n\nBackground information taken from the EN651 cruise report (Lohmann 2020)\n\nBlack carbon (BC) is a highly graphitized incomplete combustion byproduct that could be a sink for fixed carbon, especially when deposited to pelagic sediments (Kuhlbusch 1998). There is a general assumption that rivers deliver most or all BC to the ocean (Coppola et al. 2018; Elmquist et al. 2008; Kuhlbusch 1998; Masiello and Druffel 2001; Mitra et al. 2014, 2002; Suman et al. 1997). Yet the effects and fluxes of BC are not well constrained in general circulation models. For example, few BC flux measurements are available in remote ocean sediments due to the expense and difficulty of obtaining samples. The formation of BC during incomplete combustion results in a fraction of carbon not being available for the biological pump and deep ocean respiration. Once deposited to the ocean, BC is buried in sediments and can account for significant fractions of the organic matter preserved in sediments. Hence, our results would contribute towards accounting for some of the ‘missing' terrestrial OC in sediments, as all BC is landmass derived (Hedges et al. 1997).\n\ncdm_data_type = Other\nVARIABLES:\nName (unitless)\nCruise_ID (unitless)\nSite_ID (unitless)\nCoring_Attempt (unitless)\nCore_Letter (unitless)\nCollection_Date (unitless)\n... (13 more variables)\n | BCO-DMO | bcodmo_dataset_935435_v1 | ||||||||||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_719420.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_719420 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_719420.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_719420/ | public | [Survival and size] - Survival, length, and growth responses of M. menidia offspring from different females exposed to contrasting CO2 environments. (Collaborative research: Understanding the effects of acidification and hypoxia within and across generations in a coastal marine fish) | Wild-caught M.\\u00a0menidia\\u00a0adults were spawned to test whether offspring\nfrom different mothers differ in their average survival and size responses to\nelevated CO2\\u00a0conditions.\\u00a0The experiment quantified three related\nsurvival and three size traits for each replicate, female, and\nCO2\\u00a0treatment: embryo survival (fertilization to 1\\u00a0dph), larval\nsurvival (1 to 16\\u00a0dph), and overall survival (fertilization to\n16\\u00a0dph); and size (SL) at hatch (1\\u00a0dph), SL at 16\\u00a0dph, and\nlarval growth rate\\u00a0(GR = (SL16dph\\u00a0\\u2013 SL1dph)/15).\n \nThese data are\\u00a0associated with the corresponding paper:\n \n[Snyder, J.T.*, Murray, C.S.*, and Baumann, H. (2017) Potential for maternal\neffects on offspring CO2-sensitivities in a coastal marine fish. Journal of\nExperimental Marine Biology and Ecology (in\npress).](\\\\https://doi.org/10.1016/j.jembe.2017.11.002\\\\)\n \nOther datasets related to this paper:\n \n[Fatty acid profiles of M. menidia females and their unfertilized\neggs.](\\\\https://www.bco-dmo.org/dataset/719379\\\\)\n\ncdm_data_type = Other\nVARIABLES:\nSpecies (unitless)\nCollection_site (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nCollection_date (unitless)\nFemale (unitless)\nTotal_length (centimeters)\npH (Sea Water Ph Reported On Total Scale, NIST units)\n... (8 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_719420_fgdc.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_719420/index.htmlTable | https://www.bco-dmo.org/dataset/719420
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_719420.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_719420&showErrors=false&email= | BCO-DMO | bcodmo_dataset_719420 | |||
| 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_783679.subset | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_783679 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_783679.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_783679/ | public | [Tidal study of seawater microbial communities] - Flow cytometry and nutrient analyses data from a tidal study over 48 hours of mangrove, seagrass, and seawater from the US Virgin Islands in July of 2017 (Signature exometabolomes of Caribbean corals and influences on reef picoplankton) | Data from a tidal study over 48 hours of mangrove, seagrass, and seawater from the US Virgin Islands in 2017. These data include tidal height, depth, temperature, salinity, Prochlorococcus counts, Synechococcus counts, Picoeukaryote abundances, nutrient concentrations at accession numbers for sequences at The National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA).\n\ncdm_data_type = Other\nVARIABLES:\nSample_ID (unitless)\nNCBI_BioProject_accession_number (NCBI Bio Project Accession Number, unitless)\nNCBI_BioSample_accession_number (NCBI Bio Sample Accession Number, unitless)\nSample_type (unitless)\nSequencing_Strategy (unitless)\nSequencing_Instrument_model (unitless)\nSequencing_strategy (unitless)\nSite_Name (unitless)\nBiome (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nCollection_Date (unitless)\nCollection_Time (unitless)\ntime (ISO Date Time UTC, seconds since 1970-01-01T00:00:00Z)\nTide (unitless)\nTide_Height (Sea Surface Height, meters (m))\nTime_elapsed_between_tide_timepoint_and_collection (Sea Surface Height, minutes)\ndepth (Collection Depth, m)\nSite_Depth (meters (m))\nTemperature (degrees Celsius (ºC))\nSalinity (Sea Water Practical Salinity, Practical Salinity Units (PSU))\nProchlorococcus (cells per milliliter (cells/ml))\nSynechococcus (cells per milliliter (cells/ml))\n... (7 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_783679_fgdc.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_783679/index.htmlTable | https://www.bco-dmo.org/dataset/783679
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_783679.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_783679&showErrors=false&email= | BCO-DMO | bcodmo_dataset_783679 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_907507_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_907507_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_907507_v1/ | public | [Tissue data from Keister et al. 2023] - Comparative analysis of tissue biomass and energy reserves of six coral species from nearshore and offshore reefs in Palau, Micronesia during March 2017 (Collaborative Research: Stability, flexibility, and functionality of thermally tolerant coral symbioses) | The nearshore reef habitats in Palau, Micronesia, serve as a representation of the challenges that coral populations may face in a future with warmer and more acidic oceans. Interestingly, corals inhabiting these nearshore habitats demonstrate a greater ability to withstand and recover from episodes of thermal stress compared to their offshore counterparts. In order to investigate the underlying physiological mechanisms behind this tolerance, we conducted a comparative analysis of six coral species found in both offshore and nearshore environments. Specifically, we examined parameters such as tissue biomass (ash-free dry weight cm−2), energy reserves (including protein, total lipid, and carbohydrate content), as well as several crucial lipid classes.\n\ncdm_data_type = Other\nVARIABLES:\nlatitude (degrees_north)\nlongitude (degrees_east)\nSampleID (unitless)\nSpecies (unitless)\nSite (unitless)\nCollection_Date (unitless)\nAFDW (grams)\nTotal_lipids (joules)\nSurface_Area (squared centimeters (cm^2))\nProtein (joules)\nCarbohydrate (joules)\nWAX (milligrams Ash Free Dry Weight per gram (mg AFDW/g))\nTAG (milligrams Ash Free Dry Weight per gram (mg AFDW/g))\nST (milligrams Ash Free Dry Weight per gram (mg AFDW/g))\nPhospholipids (milligrams Ash Free Dry Weight per gram (mg AFDW/g))\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_907507_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_907507_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_907507_v1/index.htmlTable | https://www.bco-dmo.org/dataset/907507
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_907507_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_907507_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_907507_v1 | |||
| 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 | |||
| log in | [Wild copepod pool-seq data] - Pool-seq data from wild populations of copepods in the North Sea from May 2014 (Evolutionary genomics of a copepod project) (Evolutionary Responses to Global Changes in Salinity and Temperature) | This dataset was generated from studies of wild populations of Eurytemora affinis (E. affinis). Copepod populations were collected from three locations in the North Sea using bongo nets with 100 micrometer (μm) mesh and stored in RNAlater. Sampling locations included two freshwater lakes and one brackish estuary. Individual copepods (100 individuals, 50:50 male:female) were pooled and their DNA was extracted. Paired-end whole-genome sequencing libraries were prepared using the Illumina Nextera DNA kit (Illumina, Inc.) and sequenced on three lanes of an Illumina HiSeq 2000 sequencer, generating an average of approximately 158 million paired-end (100 bp) reads per pool. These data have been deposited in the National Center for Biotechnology Information (NCBI) under BioProject number PRJNA923656.\n\ncdm_data_type = Other\nVARIABLES:\nLocation (unitless)\nCollection_Date (unitless)\nSample_Code (unitless)\nSample_Salinity (Practical salinity units (PSU))\nSample_Temperature (degrees Celsius)\nLatitude (degrees_north)\nLongitude (degrees_east)\nBioSample (unitless)\nSRA_Run (unitless)\n | BCO-DMO | bcodmo_dataset_897977_v1 | ||||||||||||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_931936_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_931936_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_931936_v1/ | public | [Winam Gulf Metagenomic Time Series] - Metagenomic Time Series of Winam Gulf, Lake Victoria from 2022-2023 (ASI Lake Victoria project) (IRES Track II: Advanced studies institute on water quality and harmful algal blooms in Lake Victoria) | Compared to the other \"Great Lakes\" (Laurentian Great Lakes of North America and Lake Baikal of Russia) the African Great Lakes have remained widely unstudied. This serves as a substantial research gap within the limnological literature given the African Great Lakes contribute approximately 25% of all global, accessible freshwater. Lake Victoria of the African Great Lakes is notable for its large size - serving as the second largest freshwater lake in the world by surface area. Yet, Lake Victoria is also known for the prolific year-long cyanobacterial blooms that occur throughout her waters such as the Winam Gulf. These blooms are fueled by intense agricultural and anthropogenic development much like other freshwater harmful algal blooms. However, unlike other freshwater blooms such as those occurring in Lake Erie and Lake Taihhu - these cyanobacterial blooms have remained widely uncharacterized (especially using molecular techniques). \n\nThe central study area is the Winam Gulf of Lake Victoria, Kenya. This is a relatively shallow, hypereutrophic system that has various rivers serving as nutrient loading sources (such as the Sondu River). This dataset also contains opportunistic samples collected from a variety of riverine systems and Lakes Simbi and Naivasha. \n\nHere, we present the biological, chemical and physical data corresponding to a two year metagenomic time series of the Winam Gulf, Lake Victoria. We further present the physiochemical data of eight outgroup samples including adjacent riverine systems and Lakes Simbi and Naivasha.\n\ncdm_data_type = Other\nVARIABLES:\nLibrary_ID (unitless)\nSite_Name (unitless)\nReplicate_id (unitless)\nSampleID (unitless)\nStudyID (unitless)\nSample_type (unitless)\nLake_or_river (unitless)\nlatitude (degrees_north)\n... (40 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_931936_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_931936_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_931936_v1/index.htmlTable | https://www.bco-dmo.org/dataset/931936
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_931936_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_931936_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_931936_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_926368_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_926368_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_926368_v1/ | public | [Zooplankton Acidification Lab Results] - Results from Calanus pacificus Acidification Laboratory Experiments from 2019-2020 (Zooplankton Swimming project) (Causes and consequences of hypoxia and pH impacts on zooplankton: Linking movement behavior to vertical distribution.) | We conducted laboratory experiments using stratified 1 m x 0.1 × 0.1 acrylic water columns to measure the effects of bottom water hypoxia and low pH on mortality, distribution, and swimming behaviors of the calanoid copepod Calanus pacificus. Calanus pacificus were collected from within Puget Sound, Washington, USA, between June and October of 2019 and 2020. Their behaviors and vertical distributions in response to either hypoxic or acidified bottom waters were observed in an array of 4 replicate columns. Swimming behavior was observed for 90 minutes using 5-megapixel IR USB cameras. Two front-facing cameras (‘bottom camera', ‘surface camera') recorded swimming in the X (left, right) and Z (up, down) directions. An upwards-facing ‘base camera' was added to each tank in 2020 to improve tracking and behavioral analysis of copepods near the bottom. Base cameras recorded the bottom 2 cm of each tank in the X and Y (front, back) directions. \n\nThe primary data file of this dataset contains collection and organism details for copepods used in acidification experiments (926368_v1_zooplankton_acidification_pH_experiment_overview.csv). This dataset also includes four Supplemental Files .csv files summarizing results from our acidification experiments (926368_v1_zooplankton_acidification_pH_chemistry.csv, 926368_v1_zooplankton_acidification_pH_moribundity.csv, 926368_v1_zooplankton_acidification_pH_mean_height.csv, 926368_v1_zooplankton_acidification_pH_speed.csv).\n\ncdm_data_type = Other\nVARIABLES:\nExperiment_Date (unitless)\nCollection_Date (unitless)\nSort_Date (unitless)\nCollector (unitless)\nCollection_Site (unitless)\nLifestage (unitless)\nSex (unitless)\nCollection_Lat (degrees_north)\nlongitude (Collection_long, degrees_east)\nExperiment_Type (unitless)\nCollection_Notes (unitless)\nExperiment_Notes (unitless)\n | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_926368_v1/index.htmlTable | https://www.bco-dmo.org/dataset/926368
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_926368_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_926368_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_926368_v1 |