http://lod.bco-dmo.org/id/dataset/969228 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 2025-07-18 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Metagenome profiles of common emergent Caribbean sponges collected from temporary artificial reef in the Florida Keys, USA in Jan 2022 2025-07-18 publication 2025-07-18 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2025-09-23 publication https://doi.org/10.26008/1912/bco-dmo.969228.1 Amy Apprill Woods Hole Oceanographic Institution principalInvestigator Cole G. Easson Middle Tennessee State University principalInvestigator Cara L. Fiore 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: Zuniga, L., Easson, C. G., Apprill, A., Moore, D., Fiore, C. L. (2025) Metagenome profiles of common emergent Caribbean sponges collected from temporary artificial reef in the Florida Keys, USA in Jan 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-07-18 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.969228.1 [access date] Metagenome profiles of common emergent Caribbean sponges Dataset Description: Methods and Sampling: &lt;p&gt;Using day boats from a local boat rental company, sponge tissue (about 3-4 cm3) was collected from the sponge in situ (3 - 6 m depth, FL Keys, USA) and put in a sterile Whirl-Pak&amp;nbsp;bag with seawater. Bagged samples were stored on ice in the boat until return to the laboratory where they were removed from the water and stored in a cryovial (no buffer) at -80 degrees C. Total DNA was extracted from the sponge tissue and either host depleted ('hd' in sample name) using a QIAmp DNA microbiome kit or not host depleted (DNA extracted with the Qiagen powersoil powerlyser kit) before use in metagenome sequencing. Metagenome library preparation was completed with TruSeq DNA PCR-Free LP Illumina prep kit and sent to Azenta Life Sciences for sequencing. DNA sequencing was performed on an Ilumina HiSeq 4000 using 150 nucleotide length reads with paired end sequencing.&amp;nbsp;&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 asNeeded Dataset Version: 1 Unknown Accession_Number Sample_Name Organism Sample_Preparation Collection_Date Latitude Longitude Illumina HiSeq 4000 theme None, User defined NCBI BioSample accession sample identification No BCO-DMO term date latitude longitude 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 biota oceans -81.40871111 -81.369452 24.56200278 24.569055 2022-01-07 2022-01-13 Caribbean Sea 0 BCO-DMO catalogue of parameters from Metagenome profiles of common emergent Caribbean sponges collected from temporary artificial reef in the Florida Keys, USA in Jan 2022 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/969836.rdf Name: Accession_Number Units: unitless Description: <p>NCBI Biosample accession number</p> http://lod.bco-dmo.org/id/dataset-parameter/969837.rdf Name: Sample_Name Units: unitless Description: <p>Name of sample, unique identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/969838.rdf Name: Organism Units: unitless Description: <p>Type of organism utilized for experimentation</p> http://lod.bco-dmo.org/id/dataset-parameter/969839.rdf Name: Sample_Preparation Units: unitless Description: <p>DNA extracted with selection for prokaryotic DNA (QIAmp DNA microbiome kit) or total DNA (Qiagen powersoil powerlyser kit)</p> http://lod.bco-dmo.org/id/dataset-parameter/969840.rdf Name: Collection_Date Units: unitless Description: <p>Date of sample collection</p> http://lod.bco-dmo.org/id/dataset-parameter/969841.rdf Name: Latitude Units: decimal degrees Description: <p>Latitude of sample collection, positive is North</p> http://lod.bco-dmo.org/id/dataset-parameter/969842.rdf Name: Longitude Units: decimal degrees Description: <p>Longitude of sample collection, negative is South</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 2211 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/a5613b64-3f4c-4e3f-9b08-2d38abc77229/content download https://doi.org/10.26008/1912/bco-dmo.969228.1 download onLine dataset &lt;p&gt;Using day boats from a local boat rental company, sponge tissue (about 3-4 cm3) was collected from the sponge in situ (3 - 6 m depth, FL Keys, USA) and put in a sterile Whirl-Pak&amp;nbsp;bag with seawater. Bagged samples were stored on ice in the boat until return to the laboratory where they were removed from the water and stored in a cryovial (no buffer) at -80 degrees C. Total DNA was extracted from the sponge tissue and either host depleted ('hd' in sample name) using a QIAmp DNA microbiome kit or not host depleted (DNA extracted with the Qiagen powersoil powerlyser kit) before use in metagenome sequencing. Metagenome library preparation was completed with TruSeq DNA PCR-Free LP Illumina prep kit and sent to Azenta Life Sciences for sequencing. DNA sequencing was performed on an Ilumina HiSeq 4000 using 150 nucleotide length reads with paired end sequencing.&amp;nbsp;&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;Low quality reads and adapter sequences were removed from the raw demultiplexed data using fastp version 0.23.2 (Chen et al 2018). &amp;nbsp;Filtered short reads were assembled into longer nucleotide contiguous sequences (contigs) using SPAdes version 3.15.0 (Bankevich et al 2012). Gene prediction using the contigs was completed with Prodigal version 2.6.3 (Hyatt et al 2010). Functional annotation was completed with the KEGG GhostKoala server (Kanehisa et al 2016). &amp;nbsp;An in-house script “koala_sort.py” (Zuniga Acuna, n.d.) was used to filter out genes of interest for pathway specific analysis. Visualization of gene abundance was performed with the output of GhostKoala and sorted with the Koala_sort.py and visualized using R statistical software version 4.3.2 (R Core Team 2023).&amp;nbsp;&lt;/p&gt; Specified by the Principal Investigator(s) - Imported &quot;Caribbean Sponge Metagenome Accession Table.xlsx&quot; into BCO-DMO system - Split &quot;Coordinates&quot; parameter into Latitude and Longitude - Formatted the collection date in ISO 8601 format YYYY-MM - Renamed fields to remove spaces and replace with underscores - Exported file as &quot;969228_v1_metagenome_emergent_sponges.csv&quot; 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 HiSeq 4000 Illumina HiSeq 4000 PI Supplied Instrument Name: Illumina HiSeq 4000 PI Supplied Instrument Description:Metagenome library preparation was completed with TruSeq DNA PCR-Free LP Illumina prep kit and sent to Azenta Life Sciences for sequencing. DNA sequencing was performed on an Ilumina HiSeq 4000 using 150 nucleotide length reads with paired end sequencing.  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.