http://lod.bco-dmo.org/id/dataset/954346 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 2025-02-25 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Microbiome data from sponges collected in 2013 and 2014 from reefs in Honduras, Belize, Panama and the Florida Keys. 2025-04-23 publication 2025-04-23 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2025-05-07 publication https://doi.org/10.26008/1912/bco-dmo.954346.1 David M. Baker University of Hong Kong principalInvestigator Cole G. Easson Middle Tennessee State University principalInvestigator Christopher J. Freeman College of Charleston principalInvestigator Kenan Matterson University of Alabama at Birmingham principalInvestigator Valerie J. Paul Smithsonian Marine Station principalInvestigator Robert W. Thacker Stony Brook 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: Freeman, C. J., Easson, C. G., Thacker, R. W., Matterson, K., Paul, V. J., Baker, D. M. (2025) Microbiome data from sponges collected in 2013 and 2014 from reefs in Honduras, Belize, Panama and the Florida Keys. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-04-23 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.954346.1 [access date] Microbiomes sponges 2013-2014 Dataset Description: Methods and Sampling: &lt;p&gt;Sponge collection:&amp;nbsp; Sponge species were collected from at least one site within four geographic regions spanning more than 15° of latitude (~1700 km) within the Caribbean Sea. Individual regions included the Bocas del Toro archipelago of Panama, the Miskito Cays of Honduras, the Mesoamerican barrier reef of Belize, and the Florida Keys. At each site, replicate small (3–5 ml) samples of dominant and conspicuous sponge species were collected by SCUBA using a dive knife and placed into individual bags containing seawater for transport back to the laboratory. Sponge samples always included a cross section with both inner and outer tissue regions to standardize collections and sample across the entire body of the sponge. Collections frequently included eight of the ten most dominant Caribbean species&amp;nbsp;and species previously designated as both HMA and LMA sponges. Samples were preserved, processed, and prepared for&amp;nbsp;&lt;em&gt;δ&lt;/em&gt;13C and&amp;nbsp;&lt;em&gt;δ&lt;/em&gt;15N analysis. Sponges were identified to species and, if necessary, identities were verified via tissue histology and spicule preparations. Replicate subsamples of each sponge species were also preserved in 95% EtOH in 5 ml cryovials and frozen at −20 °C for analyses of microbial community structure.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1929293 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1929293 completed David M. Baker University of Hong Kong The Swire Institute of Marine Science Kadoorie Biological Sciences Building, Pokfulam Road Hong Kong P.R. China dmbaker@hku.hk 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 Christopher J. Freeman College of Charleston 817-707-5840 66 George Street Department of Biology Charleston SC 29424 USA freemancj@cofc.edu pointOfContact Kenan Matterson University of Alabama at Birmingham kenanm@gmail.com pointOfContact Valerie J. Paul Smithsonian Marine Station 772-462-0982 701 Seaway Drive Fort Pierce FL 34949 USA paul@si.edu pointOfContact Robert W. Thacker Stony Brook University 631-632-9949 West 5510 FRK MEL LIB Stony Brook NY 11794 USA robert.thacker@stonybrook.edu pointOfContact asNeeded Dataset Version: 1 Unknown Bioproject Accession Region Dive_Site Lat Lon Collection_date File_id Sample_name Seq_count_post_proc Sponge_Species Read_direction Illumina MiSeq theme None, User defined NCBI BioProject accession NCBI BioSample accession region site latitude longitude date file_name sample identification count species scientific name (binomial) sample description 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: Investigations into microbially mediated ecological diversification in sponges https://osprey.bco-dmo.org/project/772220 Collaborative Research: Investigations into microbially mediated ecological diversification in sponges <p><em>NSF Award Abstract:</em><br /> Coral reefs represent a paradox because, despite their immense productivity and biodiversity, they are found in nutrient-poor habitats that are equivalent to "marine deserts." High biodiversity is often associated with a division of resources that allows many types of organisms to coexist with minimal competition. Indeed, unlike many other organisms on coral reefs, sponges are adapted to efficiently remove bacteria, phytoplankton, and dissolved organic matter from seawater by filter-feeding. 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. This research will combine manipulative field experiments with a novel combination of modern analytical tools to investigate both filter-feeding by sponge hosts and the metabolic pathways of their microbes. This work will advance our understanding of the ecological and evolutionary forces that have helped shape the species present on Caribbean coral reefs. Additionally, this project will support three early-career investigators and provide training opportunities for graduate and undergraduate students at Nova Southeastern University, Appalachian State University, Stony Brook University, and Smithsonian Marine Station. The investigators will also develop innovative outreach programs that expand existing platforms at their institutions to increase public engagement and scientific literacy.</p> <p>Marine sponges have been widely successful in their expansion across ecological niches in the Caribbean, with biomass often exceeding that of reef-building corals and high species diversity. However, whether this success is linked to efficient heterotrophic filter-feeding on organic carbon in the water column or to their evolutionary investment in microbial symbionts is yet to be fully elucidated. Microbial symbionts expand the metabolic capabilities of host sponges, supplementing heterotrophic feeding with inorganic carbon and nitrogen, mediating the assimilation of dissolved organic matter, and facilitating recycling of host-derived nitrogen. Despite these benefits, microbial symbiont communities are widely divergent across coexisting sponge species and there is substantial variation in host reliance on symbiont-derived carbon and nitrogen among host sponges; therefore, these associations likely mediate the ecological diversification of coexisting sponge species. The goal of this project is to test this transformative hypothesis by adopting an integrative approach to assess the individual components of holobiont metabolism (i.e., microbial symbionts and sponge host) in ten of the most common sponge species in the Caribbean. The investigators will isolate autotrophic and heterotrophic metabolic pathways and explore potential links between microbial symbiont community composition and the assimilation of particulate and dissolved organic matter (POM and DOM) from seawater. This project will elucidate whether Caribbean sponge species are on similar or divergent evolutionary trajectories, and will provide information that is critical for our understanding of how conditions in the Caribbean basin have shaped the evolution of benthic organisms.</p> Ecological Diversification in Sponges largerWorkCitation project eng; USA oceans -88.113819 -81.442467 9.243206 24.578192 2013-05-01 2014-05-31 Caribbean coast of Panama 0 BCO-DMO catalogue of parameters from Microbiome data from sponges collected in 2013 and 2014 from reefs in Honduras, Belize, Panama and the Florida Keys. 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/954368.rdf Name: Bioproject Units: unitless Description: <p>Bioproject NCBI accession number</p> http://lod.bco-dmo.org/id/dataset-parameter/954369.rdf Name: Accession Units: unitless Description: <p>Biosample NCBI accession number</p> http://lod.bco-dmo.org/id/dataset-parameter/954370.rdf Name: Region Units: unitless Description: <p>Broad region of the Caribbean where samples were collected (by country: Panama, Belize, Honduras, or Florida Keys)</p> http://lod.bco-dmo.org/id/dataset-parameter/954371.rdf Name: Dive_Site Units: unitless Description: <p>Specific site within each region</p> http://lod.bco-dmo.org/id/dataset-parameter/954372.rdf Name: Lat Units: decimal degrees Description: <p>GPS latitude, south is negative</p> http://lod.bco-dmo.org/id/dataset-parameter/954373.rdf Name: Lon Units: decimal degrees Description: <p>GPS longitude, west is negative</p> http://lod.bco-dmo.org/id/dataset-parameter/954374.rdf Name: Collection_date Units: unitless Description: <p>Collection date</p> http://lod.bco-dmo.org/id/dataset-parameter/954375.rdf Name: File_id Units: unitless Description: <p>File name for barcoding data</p> http://lod.bco-dmo.org/id/dataset-parameter/954376.rdf Name: Sample_name Units: unitless Description: <p>Sample name for barcoding data</p> http://lod.bco-dmo.org/id/dataset-parameter/954377.rdf Name: Seq_count_post_proc Units: number Description: <p>Number of sequences</p> http://lod.bco-dmo.org/id/dataset-parameter/954378.rdf Name: Sponge_Species Units: unitless Description: <p>Scientific name for each sponge species; also includes seawater for water microbiome samples</p> http://lod.bco-dmo.org/id/dataset-parameter/954379.rdf Name: Read_direction Units: unitless Description: <p>Primer read direction (forward or reverse)</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 90596 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/22a9fc15-9eed-464e-a8db-f08574e8a6d7/content download https://doi.org/10.26008/1912/bco-dmo.954346.1 download onLine dataset &lt;p&gt;Sponge collection:&amp;nbsp; Sponge species were collected from at least one site within four geographic regions spanning more than 15° of latitude (~1700 km) within the Caribbean Sea. Individual regions included the Bocas del Toro archipelago of Panama, the Miskito Cays of Honduras, the Mesoamerican barrier reef of Belize, and the Florida Keys. At each site, replicate small (3–5 ml) samples of dominant and conspicuous sponge species were collected by SCUBA using a dive knife and placed into individual bags containing seawater for transport back to the laboratory. Sponge samples always included a cross section with both inner and outer tissue regions to standardize collections and sample across the entire body of the sponge. Collections frequently included eight of the ten most dominant Caribbean species&amp;nbsp;and species previously designated as both HMA and LMA sponges. Samples were preserved, processed, and prepared for&amp;nbsp;&lt;em&gt;δ&lt;/em&gt;13C and&amp;nbsp;&lt;em&gt;δ&lt;/em&gt;15N analysis. Sponges were identified to species and, if necessary, identities were verified via tissue histology and spicule preparations. Replicate subsamples of each sponge species were also preserved in 95% EtOH in 5 ml cryovials and frozen at −20 °C for analyses of microbial community structure.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;Analyses of microbiomes: We surveyed the microbiomes within 294 individuals of the 14 most dominant sponge species from our isotope surveys within the Caribbean. Sponge sampling was most comprehensive within sites in the Bocas del Toro archipelago of Panama (10–13 species within each site) and on Wonderland Reef in the Florida Keys (12 species). Sponges from sites within three regions (Belize and North and South sites in Honduras were pooled to provide a regional assessment of microbiome structure across species. &amp;nbsp;In short, polymerase chain reaction was performed on extracted total genomic DNA following the 16S Illumina Amplicon protocol of the Earth Microbiome project (earthmicrobiome.org) and with barcoded 16S rRNA primers (515F and 806R); sequencing on an Illumina MiSeq resulted in paired-end 250 base pair amplicons.&amp;nbsp;&lt;/p&gt; &lt;p&gt;Bioinformatics processing was conducted in R using the DADA2 pipeline&amp;nbsp;and taxonomic assignments of amplicon sequence variants (ASVs) were carried out using the Silva database release 128. Prior to analysis, singleton reads were removed and ASV abundance was transformed to relative abundance.&lt;/p&gt; Specified by the Principal Investigator(s) * converted date to ISO format * Adjusted field names to comply with database requirements * Added bioproject number 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 PI Supplied Instrument Description:Microbiome sequencing was carried out on an 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.