http://lod.bco-dmo.org/id/dataset/953999
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
2025-02-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
16S microbiome metadata collected from shallow artificial reef sponges and seawater in the Florida Keys, USA from Apr 2021 to Aug 2021
2025-02-21
publication
2025-02-21
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-03-19
publication
https://doi.org/10.26008/1912/bco-dmo.953999.1
Cole G. Easson
Middle Tennessee State University
principalInvestigator
Cara L. Fiore
Appalachian State University
principalInvestigator
Christopher J. Freeman
College of Charleston
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: Easson, C. G., Freeman, C. J., Fiore, C. L., Thacker, R. W. (2025) 16S microbiome metadata collected from shallow artificial reef sponges and seawater in the Florida Keys, USA from Apr 2021 to Aug 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-02-21 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.953999.1 [access date]
16S microbiome data for artificial reef sponges and seawater Dataset Description: Methods and Sampling: <p><strong>Location</strong><br />
Samples were collected on shallow reefs (&lt;10m) in the Florida Keys, USA. The temporary artificial reef was constructed adjacent to patch reefs within the Looe Key special preservation area. At the conclusion of the experiment, the reef was completely dismantled.&nbsp;The environment was well mixed by wave action within minimal tidal influence.</p>
<p><strong>Collection and Analysis</strong></p>
<p>Seawater samples were collected via VacuSIP and filtered through 0.2 µm membranes with a peristaltic pump to collect samples of ambient microbes. Total genomic DNA was extracted from cross sections of sponge tissue (~0.25 grams) and ½ of seawater filter membranes using Qiagen PowerSoil Powerlyzer extraction kit and following the manufacturers protocol. After DNA extraction, polymerase chain reaction (PCR) was performed following the 16S Illumina Amplicon protocol of the Earth Microbiome project (<span style="font-family:helvetica,arial,sans-serif; font-size:14.4px">Caporaso, 2018)&nbsp;</span>with barcoded 16S rRNA primers (515F and 806R; (Apprill et al. 2015, Parada et al. 2016) and PCR products were cleaned using AMPure beads (Beckman Coulter). DNA concentration in cleaned products was measured using a Qubit fluorometer (Qubit). The concentration of each sample was diluted to 4 nM and then all samples were pooled in equal volumes. Pooled samples were then sequenced on an Illumina MiSeq platform following standard Illumina protocols for sample preparation and loading except that custom sequencing primers from the EMP protocol were used. A 500 cycle V2 chemistry MiSeq kit was used during sequencing, which yielded paired-end 250 base pair (bp) amplicons.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1915949 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1915949
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756799 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756799
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
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756114 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756114
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756249 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756249
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756171 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756171
onGoing
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
Christopher J. Freeman
College of Charleston
817-707-5840
66 George Street Department of Biology
Charleston
SC
29424
USA
freemancj@cofc.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
collection_date
latitude
longitude
accession
sample_name
species_ab
sample_type
organism
AphiaID
LSID
isolation_source
geo_loc_name
data_day
seq_attempt
Illumina MiSeq
Qubit
Vortex
Thermal cycler
theme
None, User defined
date
latitude
longitude
NCBI BioSample accession
sample identification
species scientific name (binomial)
sample description
taxon_code
Life Science Identifier (LSID)
region
days
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Qubit fluorometer
Shaker
Thermal Cycler
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
biota
oceans
-81.423
-81.369
24.538
24.576
2021-04-01
2021-08-31
Caribbean coast of Panama
0
BCO-DMO catalogue of parameters from 16S microbiome metadata collected from shallow artificial reef sponges and seawater in the Florida Keys, USA from Apr 2021 to Aug 2021
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/954125.rdf
Name: collection_date
Units: unitless
Description: <p>Date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/954126.rdf
Name: latitude
Units: Decimal Degrees
Description: <p>Latitude of sample collection; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/954127.rdf
Name: longitude
Units: Decimal Degrees
Description: <p>Longitude of sample collection; west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/954128.rdf
Name: accession
Units: unitless
Description: <p>NCBI BioSample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/954129.rdf
Name: sample_name
Units: unitless
Description: <p>Sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/954130.rdf
Name: species_ab
Units: unitless
Description: <p>Species abbreviation of sponge ajacent to the sampler</p>
http://lod.bco-dmo.org/id/dataset-parameter/954131.rdf
Name: sample_type
Units: unitless
Description: <p>Description of sample type: tissue, incurrent (In), or excurrent (Ex) water</p>
http://lod.bco-dmo.org/id/dataset-parameter/954132.rdf
Name: organism
Units: unitless
Description: <p>Organism that corresponds to tissue samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/954133.rdf
Name: AphiaID
Units: unitless
Description: <p>AphiaID of organism that corresponds to tissue samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/954134.rdf
Name: LSID
Units: unitless
Description: <p>LSID of organism that corresponds to tissue samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/954135.rdf
Name: isolation_source
Units: unitless
Description: <p>Type of source: environmental</p>
http://lod.bco-dmo.org/id/dataset-parameter/954136.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Geographic location of sample source</p>
http://lod.bco-dmo.org/id/dataset-parameter/954137.rdf
Name: data_day
Units: days
Description: <p>Unique collection day the sample was obtained (0-6)</p>
http://lod.bco-dmo.org/id/dataset-parameter/954138.rdf
Name: seq_attempt
Units: unitless
Description: <p>Number of times a sample had to be sequenced to obtain adequate data</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
19816
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/be9b9409-b24c-43c2-aa0c-c0f856219a0c/content
download
https://doi.org/10.26008/1912/bco-dmo.953999.1
download
onLine
dataset
<p><strong>Location</strong><br />
Samples were collected on shallow reefs (&lt;10m) in the Florida Keys, USA. The temporary artificial reef was constructed adjacent to patch reefs within the Looe Key special preservation area. At the conclusion of the experiment, the reef was completely dismantled.&nbsp;The environment was well mixed by wave action within minimal tidal influence.</p>
<p><strong>Collection and Analysis</strong></p>
<p>Seawater samples were collected via VacuSIP and filtered through 0.2 µm membranes with a peristaltic pump to collect samples of ambient microbes. Total genomic DNA was extracted from cross sections of sponge tissue (~0.25 grams) and ½ of seawater filter membranes using Qiagen PowerSoil Powerlyzer extraction kit and following the manufacturers protocol. After DNA extraction, polymerase chain reaction (PCR) was performed following the 16S Illumina Amplicon protocol of the Earth Microbiome project (<span style="font-family:helvetica,arial,sans-serif; font-size:14.4px">Caporaso, 2018)&nbsp;</span>with barcoded 16S rRNA primers (515F and 806R; (Apprill et al. 2015, Parada et al. 2016) and PCR products were cleaned using AMPure beads (Beckman Coulter). DNA concentration in cleaned products was measured using a Qubit fluorometer (Qubit). The concentration of each sample was diluted to 4 nM and then all samples were pooled in equal volumes. Pooled samples were then sequenced on an Illumina MiSeq platform following standard Illumina protocols for sample preparation and loading except that custom sequencing primers from the EMP protocol were used. A 500 cycle V2 chemistry MiSeq kit was used during sequencing, which yielded paired-end 250 base pair (bp) amplicons.</p>
Specified by the Principal Investigator(s)
<p>Sample barcodes were input into the MiSeq to demultiplex samples.&nbsp;No additional data processing was done to these samples.</p>
Specified by the Principal Investigator(s)
- Imported "PRJNA1179970_attributes_11_22.tsv" into the BCO-DMO System
- Removed columns without values
- Imported WoRMS report on all species included in the dataset as "easson_organisms_matched.txt" into the BCO-DMO System
- Join "easson_organisms_matched.txt" to "PRJNA1179970_attributes_11_22.tsv" on the species name, including the AphiaID and the LSID in the dataset
- Split the lat_lon field into Latitude and Longitude and removed the string components
- Convert West Long values to negative
- Exported file as "953999_v1_16s_reef_microbiome.csv"
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:Illumina MiSeq - sequencer used to generate sequence libraries from prepared samples 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.
Qubit
Qubit
PI Supplied Instrument Name: Qubit PI Supplied Instrument Description:Qubit - fluorometer used for quantitation of double-stranded DNA Instrument Name: Qubit fluorometer Instrument Short Name: Instrument Description: Benchtop fluorometer. The Invitrogen Qubit Fluorometer accurately and quickly measures the concentration of DNA, RNA, or protein in a single sample. It can also be used to assess RNA integrity and quality.
Manufactured by Invitrogen, Carlsbad, CA, USA (Invitrogen is one of several brands under the Thermo Fisher Scientific corporation.)
Vortex
Vortex
PI Supplied Instrument Name: Vortex PI Supplied Instrument Description:Vortex - standard laboratory vortex for mixing samples and extracting DNA Instrument Name: Shaker Instrument Short Name: Instrument Description: A Shaker is a piece of lab equipment used to mix, blend, or to agitate substances in tube(s) or flask(s) by shaking them, which is mainly used in the fields of chemistry and biology. A shaker contains an oscillating board which is used to place the flasks, beakers, test tubes, etc.
Thermal cycler
Thermal cycler
PI Supplied Instrument Name: Thermal cycler PI Supplied Instrument Description:Thermal cycler - Used for polymerase chain reaction Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)