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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_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 (external link) 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
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 (external link) 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_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 (external link) 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_747872.subset https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_747872 https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_747872.graph https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_747872/ public [Heterosigma akashiwo acclimation] - NCBI accessions of the harmful alga Heterosigma akashiwo (CCMP2393) grown under a range of CO2 concentrations from 200-1000 ppm (Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2) This dataset includes metadata associated with NCBI BioProject PRJNA377729 \\Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2\\ PRJNA377729: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA377729. The alga Heterosigma akashiwo was grown at CO2 levels from about 200 to 1000 ppm and then the DNA and RNA were sequenced.\n\ncdm_data_type = Other\nVARIABLES:\nsample_name (unitless)\nsample_title (unitless)\nbioproject_accession (unitless)\norganism (unitless)\nstrain (unitless)\nisolate (unitless)\nhost (unitless)\nisolation_source (unitless)\ntime (Collection Date, seconds since 1970-01-01T00:00:00Z)\ngeo_loc_name (unitless)\nsample_type (unitless)\nbiomaterial_provider (unitless)\ncollected_by (unitless)\ndepth (m)\nenv_biome (unitless)\ngenotype (unitless)\nlat_lon (Latitude, decimal degrees)\npassage_history (unitless)\nsamp_size (unitless)\ntemp_C (degrees Celsius)\nlight_level_umol_m2_s (micromol photons m-2 s-1)\nlight_dark_hr (hours)\nMedia (unitless)\nCO2_ppm (parts per million)\nAlkalinity (micromol per kilogram (umol/kg))\npH (Sea Water Ph Reported On Total Scale, unitless; pH scale)\n https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_747872/index.htmlTable https://www.bco-dmo.org/dataset/747872 (external link) https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_747872.rss https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_747872&showErrors=false&email= BCO-DMO bcodmo_dataset_747872
https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_658497.subset https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_658497 https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_658497.graph https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_658497/ public [Isolation culturing and sequencing of bacteria and viruses] - Isolation, culturing, and sequencing of bacteria and viruses collected in Canoe Cove, Nahant, MA during 2010 (Marine Bacterial Viruses project) (How can bacterial viruses succeed in the marine environment?) Isolation, culturing, and sequencing of bacteria and viruses collected in Canoe Cove, Nahant, MA during 2010 (Marine Bacterial Viruses project)\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nenv_biome (unitless)\ngeo_loc_name (unitless)\norganism_type (unitless)\ncollection_date (unitless)\nisolation_source (unitless)\nsample_name (unitless)\norganism (unitless)\nstrain (unitless)\nisolate (unitless)\nhost (unitless)\nlab_host (unitless)\nsample_type (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\ntemp (Temperature, degrees celsius)\nordinal_day_of_isolation (unitless)\ndescription (unitless)\n https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_658497_fgdc.xml https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_658497/index.htmlTable https://www.bco-dmo.org/dataset/658497 (external link) 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
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 (external link) 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_936069_v1 https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_936069_v1.graph https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_936069_v1/ public [Metagenome and metatranscriptome sequences from deep-sea hydrothermal vent microbial communities] - Metagenome and metatranscriptome sequences from deep-sea hydrothermal vent microbial communities collected on cruises AT42-22, TN405, and NA108 from May 2019 to Jun 2022 (Collaborative Research: Microbes need frenemies: unveiling microbial relationships with protists and viruses that support deep-sea hydrothermal vent food webs) This dataset is a collection of sample metadata, identified for all samples, and NCBI accession information for samples and sequence runs produced as part of the \"Microbes need frenemies\" project. This project examines trophic interactions among microbial eukaryotes, viruses, bacteria, and archaea at deep-sea hydrothermal vents using metagenomics and metatranscriptomics and characterizes these ecologically-significant interactions, such as mutualism, predator-prey, or virus-host. \n\nWe sequenced samples collected during the 2020 expedition AT42-22 to the Mid-Cayman Rise hydrothermal vent fields, as well as from the 2019 expedition NA108 to the Gorda Ridge and the 2022 expedition TN405 to the Axial seamount. Sequencing targeted archaea, bacteria, and viruses with metagenomics and microbial eukaryotes with metatranscriptomics. We plan to use these data to identify ecologically-significant interactions among protists, viruses, bacteria, and archaea, with a specific emphasis on microbial mortality via viral lysis and eukaryotic grazing. Archived samples were also included in the analysis.\n\ncdm_data_type = Other\nVARIABLES:\nSAMPLE_ID (unitless)\nSHORT_SAMPLE_ID (unitless)\nSAMPLE_NAME (unitless)\nLAB_NUM (unitless)\nCRUISE_ID (unitless)\nFIELD_REGION (unitless)\nYEAR (unitless)\nFIELD_YEAR (unitless)\nVENT (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nORIGIN_TYPE (unitless)\nORIGIN_DESCRIPTION (unitless)\nFRENEMIES_PROJ (unitless)\n... (11 more variables)\n https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_936069_v1_fgdc.xml https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_936069_v1_iso19115.xml https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_936069_v1/index.htmlTable https://www.bco-dmo.org/dataset/936069 (external link) https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_936069_v1.rss https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_936069_v1&showErrors=false&email= BCO-DMO bcodmo_dataset_936069_v1
https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_756997.subset https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_756997 https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_756997.graph https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_756997/ public [Microbial community composition of the Cinder Cones Cold Seep] - Microbial community composition from 16s V4 region amplicon sequencing of the methane Seep at the Cinder Cones Cold Seep site, Nov 2016 (EAGER: Elucidating the Antarctic Methane Cycle at the Cinder Cones Reducing Habitat) This dataset includes microbial community composition from 16s V4 region amplicon sequencing on 151 marine sediment community samples collected from the Cinder Cones Cold Seep site [-77.8, 166.666] in the Ross Sea region, Antarctica in November 2016. Data are uploaded to the NCBI Sequence Read Archive under submission SUB2655615 [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA387720] with a subset of the data from that archive originating from this project.\n\ncdm_data_type = Other\nVARIABLES:\naccession (unitless)\nsample_name (unitless)\norganism (unitless)\nhost (unitless)\ntime (Collection Date, seconds since 1970-01-01T00:00:00Z)\ngeo_loc_name (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nReplicate (unitless)\nSediment_Depth_cm (centimeters)\nHabitat (unitless)\n https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_756997_fgdc.xml https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_756997/index.htmlTable https://www.bco-dmo.org/dataset/756997 (external link) https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_756997.rss https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_756997&showErrors=false&email= BCO-DMO bcodmo_dataset_756997
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 (external link) 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 (external link) https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_926299_v1.rss https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_926299_v1&showErrors=false&email= BCO-DMO bcodmo_dataset_926299_v1
log in [Microorganisms associated with pyrosomes] - High-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry of pyrosome-associated microorganisms compared to seawater sampled during a Pyrosoma atlanticum bloom in the Northern California Current System in July 2018. (Collaborative Research: Comparative feeding by gelatinous grazers on microbial prey) Pyrosomes are widely distributed pelagic tunicates that have the potential to reshape marine food webs when they bloom. However, their grazing preferences and interactions with the background microbial community are poorly understood. The diversity, relative abundance, and taxonomy of pyrosome-associated microorganisms were compared to seawater during a Pyrosoma atlanticum bloom in the Northern California Current System using high-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry.\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nbiosample_accession (unitless)\nsample_name (unitless)\nsra_sample_accession (unitless)\nsample_accession_title (unitless)\norganism_name (unitless)\norganism_taxonomy_id (unitless)\norganism_taxonomy_name (unitless)\nkeywords (unitless)\nbiosample_package (unitless)\ncollection_date (unitless)\nenv_broad_scale (unitless)\nenv_local_scale (unitless)\nenv_medium (unitless)\ngeo_loc_name (unitless)\nhost (unitless)\nlatitude (Sampling_lat, degrees_north)\nlongitude (Sampling_lon, degrees_east)\ndepth (m)\nhost_length (centimeter (cm))\nsource_material_id (unitless)\nstatus (unitless)\n... (20 more variables)\n BCO-DMO bcodmo_dataset_926093_v1
log in [Northern California Current Microorganisms] - 16S rRNA gene of microorganisms sampled along the Newport Hydrographic (NH) and Trinidad Head (TR) lines, in OR and CA in 2018 and 2019 (Collaborative Research: Comparative feeding by gelatinous grazers on microbial prey) The Northern California Current ecosystem is a productive system which supports major fisheries. To determine how the microbial community responds to variable upwelling, we examined the 16S rRNA gene of microorganisms from two size fractions, 0.2-1.6µm and greater than 1.6µm along the Newport Hydrographic (NH) and Trinidad Head (TR) lines, in OR and CA.\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nbiosample_accession (unitless)\nmessage (unitless)\nsample_name (unitless)\norganism (unitless)\ncollection_date (unitless)\ndepth (m)\nenv_broad_scale (unitless)\nenv_local_scale (unitless)\nenv_medium (unitless)\ngeo_loc_name (unitless)\nlatitude (Sampling_lat, degrees_north)\nlongitude (Sampling_lon, degrees_east)\nsize_frac (unitless)\nsra_run_accession (unitless)\nsra_study_accession (unitless)\nobject_status (unitless)\nlibrary_ID (unitless)\ntitle (unitless)\nlibrary_strategy (unitless)\nlibrary_source (unitless)\nlibrary_selection (unitless)\nlibrary_layout (unitless)\nplatform (unitless)\n... (5 more variables)\n BCO-DMO bcodmo_dataset_926850_v1
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_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 (external link) 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_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 (external link) 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

 
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