http://lod.bco-dmo.org/id/dataset/964182 eng; USA utf8 dataset Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 2025-06-09 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Microbiome profiling of bacterioplankton communities on sponge excurrent water, coral exudate water, and surface reef water. 2025-06-17 publication 2025-06-17 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2025-06-20 publication https://doi.org/10.26008/1912/bco-dmo.964182.1 Amy Apprill Woods Hole Oceanographic Institution principalInvestigator Cole G. Easson Middle Tennessee State University principalInvestigator Cara L. Fiore Appalachian State University principalInvestigator Alicia M. Reigel Appalachian State University principalInvestigator Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. publisher Cite this dataset as: Fiore, C. L., Easson, C. G., Apprill, A., Reigel, A. M., Fortier, K., Moore, D. (2025) Microbiome profiling of bacterioplankton communities on sponge excurrent water, coral exudate water, and surface reef water. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-06-17 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.964182.1 [access date] Sponge Coral Picoplankton Incubation Experiment - NCBI Dataset Description: Methods and Sampling: &lt;p&gt;Seawater sampled from the incubation ‘soup’ or bottles was used for multiple nutrient analyses and DNA extraction.&amp;nbsp;&lt;/p&gt; &lt;p&gt;The rest of the seawater was filtered through an Omnipore 0.2 um filter using a peristaltic pump and acid and milliQ water rinsed Pharmed BP tubing and Teflon filter holders. The filter was stored at -80C until DNA extraction.&lt;/p&gt; &lt;p&gt;The NCBI dataset is the microbiome profiling data of the incubation experiment. These are the reads of 16S rRNA genes for each sample in the incubation experiment. Bottle incubations were set up as described in the methods for dataset 963872. The seawater from the bottles were filtered at T0 and at T48 and the filters were used for DNA extraction, &amp;nbsp;amplification of the v4 region of the 16S rRNA gene, and Illumina sequencing. Additional details available through the NCBI accession link.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924540 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924540 Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1923962 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1923962 completed Amy Apprill Woods Hole Oceanographic Institution 508-289-2649 Marine Chemistry and Geochemistry Department 266 Woods Hole Road, MS# 4 Woods Hole MA 02543 USA aapprill@whoi.edu pointOfContact Cole G. Easson Middle Tennessee State University 615-898-5822 1672 Greenland Drive SCI 2044 Murfreesboro TN 37132 USA Cole.Easson@mtsu.edu pointOfContact Cara L. Fiore Appalachian State University 828-262-7548 572 Rivers St Boone NC 28607 USA fiorec@appstate.edu pointOfContact Alicia M. Reigel Appalachian State University Lexington VA USA areigel@wlu.edu pointOfContact asNeeded Dataset Version: 1 Unknown Bioproject_Accession Biosample_accession Sample_Name SRA_run_ID SRA_run_link SPUID Organism Tax_ID library_ID SRA_study_ID SRA_title library_strategy library_source library_selection library_layout platform instrument_model design_description filetype filename filetype2 filename2 depth latitude longitude sample_date Illumina MiSeq theme None, User defined NCBI BioProject accession NCBI BioSample accession sample identification NCBI SRA run accession (SRR) external_link sample description taxon_code NCBI SRA study accession (SRP) seq_descrip instrument instrument model datatype file_name depth latitude longitude date featureType BCO-DMO Standard Parameters Automated DNA Sequencer instrument BCO-DMO Standard Instruments otherRestrictions otherRestrictions Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use. Collaborative Research: The Influence of Sponge Holobiont Metabolism on Coral Reef Dissolved Organic Matter and Reef Microorganisms https://osprey.bco-dmo.org/project/822468 Collaborative Research: The Influence of Sponge Holobiont Metabolism on Coral Reef Dissolved Organic Matter and Reef Microorganisms <p><em>NSF Award Abstract:</em><br /> The seawater around coral reefs is typically low in nutrients, yet coral reefs are teeming with life and are often compared to oases in a desert. Life exists in these 'marine deserts' in large part, due to symbiotic associations between single-celled microbes and invertebrates such as corals and sponges. The concentration and type of dissolved organic matter (DOM), a complex pool of organic nutrients such as amino acids, vitamins, and other diverse compounds, also affects the health of coral reefs. The composition of DOM on coral reefs is linked to both the composition of free-living microbes in the seawater and to the nutrition of filter-feeding organisms, such as corals and sponges. However, the factors that influence the composition of DOM on coral reefs and the consequences of how it changes are not well understood. Recent work suggests that sponges could have a significant impact on the composition of reef dissolved organic nutrients, depending on sponge species due to differences in filtration capacity and in their symbiotic microbial communities. This project characterizes how diverse sponge species process DOM on coral reefs and determines the impacts of this processing on the free-living microbial community. Seawater is collected from sponges (pre- and post- sponge filtration) on coral reefs in the relatively pristine region of Curacao, and incubation experiments measure the impact of sponge filtration on the growth of the free-living microbial community. The organic nutrients of seawater samples are analyzed using cutting-edge techniques to distinguish the types of nutrients that are processed by sponges. The incubation experiments, using free-living microbes collected from the coral reef, quantify the impact of sponge filtration on the growth and composition of this community. This project provides fundamental understanding of how sponges contribute to the base of the coral reef food web. As the human-driven impacts continue to alter the composition of organisms on reefs, this understanding is necessary to predict changes to reef microbial food webs and is thus essential for scientists, reef managers, and policy decision makers. This project trains undergraduate students and a postdoctoral scholar and contributes to undergraduate and K-12 education through development of sponge-centric lessons that focus on local U.S. east coast aquatic environments as well as coral reef ecosystems.</p> <p>Sponges vary in their capacity to filter seawater and in their associated microbial communities, leading to diverse metabolic strategies that often coexist in one habitat. While it is well-established that sponges are important in processing dissolved organic matter (DOM), an important reservoir of reduced carbon compounds, and transferring this energy to benthic food webs, there has been limited work to understand the consequences of sponge processing on the composition of coral reef DOM and on pelagic food webs. Specifically, while studies have shown that exudates of corals and algae select for specific groups of picoplankton (autotrophic and heterotrophic, respectively), similar data for sponges are required to understand the multiple factors that shape the composition of DOM and of the picoplankton community on coral reefs. Thus, this project is aimed at addressing a major knowledge gap of the role of sponge-derived DOM (sponge exometabolome) in coral reef biogeochemistry. An in situ sampling design targeting prominent Caribbean sponges and picoplankton incubation experiments is coupled to address both the composition of sponge exometabolomes and delineate shifts in the picoplankton community derived from sponge exometabolomes. Molecular-level changes to seawater DOM by sponge processing and the impact of these changes on the overall coral reef DOM profile is assessed with two DOM analysis techniques: a commonly used fluorometry technique (fDOM analysis) and with high-resolution mass spectrometry (LC-MS/MS). Additionally, microbiome and functional gene profiling, growth metrics, and nutrient analyses are employed to assess changes in the picoplankton community in response to sponge exometabolomes. Advanced data analysis techniques then synthesize data generated by each approach to provide novel insight on a poorly uncharacterized biogeochemical pathway on coral reefs. The work outlined here represents entirely novel information on the impact of sponge metabolism on the composition of DOM, sheds light on biologically important molecules involved in benthic-pelagic coupling, and importantly, generates data using standardized methods, thus facilitating comparison to previous and future DOM datasets.</p> <p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p> Sponge Holobiont DOM largerWorkCitation project eng; USA oceans -81.40871111 -81.40871111 24.562002777778 24.562002777778 2022-01-06 2022-01-08 Caribbean Sea 0 BCO-DMO catalogue of parameters from Microbiome profiling of bacterioplankton communities on sponge excurrent water, coral exudate water, and surface reef water. Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact http://lod.bco-dmo.org/id/dataset-parameter/964295.rdf Name: Bioproject_Accession Units: unitless Description: <p>NCBI Bioproject accession ID</p> http://lod.bco-dmo.org/id/dataset-parameter/964296.rdf Name: Biosample_accession Units: unitless Description: <p>NCBI Biosample accession ID</p> http://lod.bco-dmo.org/id/dataset-parameter/964297.rdf Name: Sample_Name Units: unitless Description: <p>Submitter sample name</p> http://lod.bco-dmo.org/id/dataset-parameter/964298.rdf Name: SRA_run_ID Units: unitless Description: <p>NCBI SRA run accession ID</p> http://lod.bco-dmo.org/id/dataset-parameter/964299.rdf Name: SRA_run_link Units: unitless Description: <p>Link to SRA data on NCBI</p> http://lod.bco-dmo.org/id/dataset-parameter/964300.rdf Name: SPUID Units: unitless Description: <p>SPUID (Submitter Provided Unique Identifier), a unique identifier assigned by the submitter to a sample in the NCBI BioSample database</p> http://lod.bco-dmo.org/id/dataset-parameter/964301.rdf Name: Organism Units: unitless Description: <p>Biological entity</p> http://lod.bco-dmo.org/id/dataset-parameter/964302.rdf Name: Tax_ID Units: unitless Description: <p>Unique numerical identifier assigned by unique numerical identifier assigned by the NCBI Taxonomy database to each organism or taxonase to each organism or taxon</p> http://lod.bco-dmo.org/id/dataset-parameter/964303.rdf Name: library_ID Units: unitless Description: <p>Unique identifier for the sequencing library (can be the sample name repeated).</p> http://lod.bco-dmo.org/id/dataset-parameter/964304.rdf Name: SRA_study_ID Units: unitless Description: <p>NCBI study accession ID</p> http://lod.bco-dmo.org/id/dataset-parameter/964305.rdf Name: SRA_title Units: unitless Description: <p>Title of SRA run</p> http://lod.bco-dmo.org/id/dataset-parameter/964306.rdf Name: library_strategy Units: unitless Description: <p>Sequencing library strategy</p> http://lod.bco-dmo.org/id/dataset-parameter/964307.rdf Name: library_source Units: unitless Description: <p>Source of sequencing library</p> http://lod.bco-dmo.org/id/dataset-parameter/964308.rdf Name: library_selection Units: unitless Description: <p>Selection used for sequencing library</p> http://lod.bco-dmo.org/id/dataset-parameter/964309.rdf Name: library_layout Units: unitless Description: <p>single or paired end sequencing reads</p> http://lod.bco-dmo.org/id/dataset-parameter/964310.rdf Name: platform Units: unitless Description: <p>Sequencing platform manufacturer</p> http://lod.bco-dmo.org/id/dataset-parameter/964311.rdf Name: instrument_model Units: unitless Description: <p>Sequencer model</p> http://lod.bco-dmo.org/id/dataset-parameter/964312.rdf Name: design_description Units: unitless Description: <p>Description explaining how this library was prepared and sequenced</p> http://lod.bco-dmo.org/id/dataset-parameter/964313.rdf Name: filetype Units: unitless Description: <p>File type</p> http://lod.bco-dmo.org/id/dataset-parameter/964314.rdf Name: filename Units: unitless Description: <p>Forward reads file name</p> http://lod.bco-dmo.org/id/dataset-parameter/964315.rdf Name: filetype2 Units: unitless Description: <p>File type</p> http://lod.bco-dmo.org/id/dataset-parameter/964316.rdf Name: filename2 Units: unitless Description: <p>Reverse reads file name</p> http://lod.bco-dmo.org/id/dataset-parameter/964317.rdf Name: depth Units: meters (m) Description: <p>Sampling depth</p> http://lod.bco-dmo.org/id/dataset-parameter/964318.rdf Name: latitude Units: decimal degrees Description: <p>Sampling latitude, south is negative</p> http://lod.bco-dmo.org/id/dataset-parameter/964319.rdf Name: longitude Units: decimal degrees Description: <p>Sampling longitude, west is negative</p> http://lod.bco-dmo.org/id/dataset-parameter/965377.rdf Name: sample_date Units: unknown Description: <p>Sample date</p> GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 55452 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/ea63230d-cf1e-49d9-b071-21475154bec1/content download https://doi.org/10.26008/1912/bco-dmo.964182.1 download onLine dataset &lt;p&gt;Seawater sampled from the incubation ‘soup’ or bottles was used for multiple nutrient analyses and DNA extraction.&amp;nbsp;&lt;/p&gt; &lt;p&gt;The rest of the seawater was filtered through an Omnipore 0.2 um filter using a peristaltic pump and acid and milliQ water rinsed Pharmed BP tubing and Teflon filter holders. The filter was stored at -80C until DNA extraction.&lt;/p&gt; &lt;p&gt;The NCBI dataset is the microbiome profiling data of the incubation experiment. These are the reads of 16S rRNA genes for each sample in the incubation experiment. Bottle incubations were set up as described in the methods for dataset 963872. The seawater from the bottles were filtered at T0 and at T48 and the filters were used for DNA extraction, &amp;nbsp;amplification of the v4 region of the 16S rRNA gene, and Illumina sequencing. Additional details available through the NCBI accession link.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;DNA from the Omnipore filters was extracted using a commercial kit and the 16S rRNA gene was amplified using the modified earth microbiome primer set for the V4 region&amp;nbsp;(515F and 806R, Apprill et al. 2015). PCRs were sent to Middle Tennessee State University for library construction and sequencing on an Illumina MiSeq, producing FASTQ files as output.&lt;/p&gt; Specified by the Principal Investigator(s) *Added sampling date to dataset Specified by BCO-DMO Data Managers asNeeded 7.x-1.1 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact Illumina MiSeq Illumina MiSeq PI Supplied Instrument Name: Illumina MiSeq Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.