http://lod.bco-dmo.org/id/dataset/906740 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 2023-08-24 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Microbiome dynamics of coral reef and cleanerfish from ecological surveys, in situ manipulations, and laboratory experiments conducted from 2020-2021 2023-08-30 publication 2023-08-30 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2023-10-25 publication https://doi.org/10.26008/1912/bco-dmo.906740.1 Amy Apprill Woods Hole Oceanographic Institution principalInvestigator Paul C. Sikkel University of Miami principalInvestigator Anya L. Brown Woods Hole Oceanographic Institution 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: Apprill, A., Sikkel, P. C., Brown, A. L. (2023) Microbiome dynamics of coral reef and cleanerfish from ecological surveys, in situ manipulations, and laboratory experiments conducted from 2020-2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-08-30 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.906740.1 [access date] Microbiome dynamics of coral reef and cleanerfish Dataset Description: Methods and Sampling: &lt;p&gt;Coral reef cleaning stations were identified for survey at locations&amp;nbsp;in Marathon, Florida (USA), St. Croix (US Virgin Islands), and Puerto Rico. SCUBA divers and snorkelers performed site surveys and fish observations at cleaning sites. All molecular samples were stored at -80 degrees Celsius or liquid nitrogen dry shipped until DNA extraction.&lt;/p&gt; &lt;p&gt;After observation, cleanerfish and damselfish were captured using individual hand nets and transferred to individual sealed plastic bags. Immediately upon capture, fish were taken to the lab and swabbed on both sides of the body with tubed sterile cotton swabs. Sampling was performed using gloves, and nets were submerged in a 30% bleach solution and rinsed with fresh water prior to each use.&lt;/p&gt; &lt;p&gt;At select coral cleaning stations, sterile clay hexagon tiles were deployed 1 meter above coral heads to develop biofilms. After 6-7 days, the tiles were recovered with minimal handling into Whirlpak bags and transported to the laboratory. The coral heads were also sampled for their mucus, and water was collected in 60-milliliter (mL) syringes from within 30 centimeters of the coral heads. Sterile swabs were used to collect samples from the tiles and coral mucus, and stored in 1.5 mL microcentrifuge tubes.&lt;/p&gt; &lt;p&gt;From select locations, water samples to examine macronutrients were collected from each station into acid-washed polypropylene bottles, frozen, and analyzed with a continuous segmented flow system at Oregon State University to resolve nitrate, nitrite, ammonium, phosphate, and silicate. Water for non-purgeable organic carbon (TOC) and organic nitrogen was collected from the stations into combusted, borosilicate EPA vials and acidified using 75 mL phosphoric acid. Samples were analyzed using a Shimadzu TOC-VCSH total organic carbon analyzer equipped with a TNM-1 module at Woods Hole Oceanographic Institution. To quantify abundances of Prochlorococcus, Synechococcus, picoeukaryotes, and unpigmented (heterotrophic) microorganisms, water (1.4 mL) was collected at the stations, preserved using paraformaldehyde, and frozen in liquid nitrogen vapors.&lt;/p&gt; &lt;p&gt;DNA extractions were performed on swabs of coral, damselfish, and cleanerfish mucus; swabs of tiles; and water filters. DNeasy PowerBiofilm DNA extraction kits (Qiagen, Germantown, MD, USA) were used with a modified protocol for the swab samples. Lysing reagents were added directly to the sample vial with the swab, vortexed, then the swab was re-oriented in the tube so it was cotton-side-up and was spun for 1 minute at 13,000 g to release the liquid absorbed by the swab. The liquid from the swab and the lysing reagents were added to the bead tube, and the manufacturer instructions were followed for the rest of the protocol. For water filters, the filter and lysing reagents were added directly to the bead tube, and then the manufacturer protocols were followed. DNA extraction controls (sterile hydroflock swabs, unused 0.22-micrometer (μm) filters, and unused bead tubes) were completed following the steps above.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2022955 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2022955 Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2023420 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2023420 Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2204963 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2204963 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 Paul C. Sikkel University of Miami 270-293-5489 4600 Rickenbacker Causeway Miami FL 33149-1031 USA pcs75@miami.edu pointOfContact Anya L. Brown Woods Hole Oceanographic Institution 605 Hutchison Drive Davis CA USA anybrown@ucdavis.edu pointOfContact asNeeded Dataset Version: 1 Unknown BioProject_accession BioSample_accession sample_name SRA_accession collection_date geo_loc_name host lat lon isolation_source host_common_name host_disease host_condition host_coral_cleaner_goby_pretreatment host_coral_reef_id location_survey_date location_mean_total_species FCM_Pro_mL FCM_Syn_mL FCM_Peuk_mL FCM_Hbac_mL NPOC_uM TN_uM phosphate nitrate_nitrite silicate NO2 ammonium nitrate Illumina MiSeq Altra flow cytometer (Beckman Coulter) SCUBA Shimadzu TOC-VCSH total organic carbon analyzer equipped with a TNM-1 module theme None, User defined NCBI BioProject accession NCBI BioSample accession sample identification accession number date site taxon latitude longitude sample description treatment number abundance particulate organic Carbon (POC) total organic Nitrogen phosphate nitrate plus nitrite Silicate, Si(OH)4, silicic acid Nitrite Ammonium Nitrate featureType BCO-DMO Standard Parameters Automated DNA Sequencer Flow Cytometer Self-Contained Underwater Breathing Apparatus Shimadzu Total Organic Carbon Analyzer TOC-VCPH 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: Cleaning stations as hubs for the maintenance and recovery of microbial diversity on coral reefs. https://osprey.bco-dmo.org/project/870348 Collaborative Research: Cleaning stations as hubs for the maintenance and recovery of microbial diversity on coral reefs. <p>NSF Award Abstract:</p> <p>Biodiversity in the ocean is influenced by interactions between disparate organisms which ultimately shape population, community, and ecosystem dynamics. Symbiotic interactions involving subsets of species can have disproportionate impacts on communities, reaching well beyond each interacting species. 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. These highly used territories are viewed both as “clinics of the sea”, where parasitized and sickly fish seek the service of cleaners, but also as potential “garbage dumps”, where unnecessary parasites and other microorganisms are removed. This project seeks to understand the role of cleaning symbiosis transferring microbes in coral reef environments. This research supports training for U.S. graduate students and for undergraduates from Arkansas State University, a primarily undergraduate institution that includes a large population of first-generation college students. These students participate in field site research and have opportunities to visit the Woods Hole Oceanographic Institution for broader exposure to ocean science and more specific laboratory training. The project strengthens international collaboration and further builds on the existing relationships between the team of scientists and resource managers, local divers, fishers, and boat operators, as well as K-12 schools and environmental education programs, and will therefore contribute to local economies. Outreach efforts include a film highlighting this research and publicly accessible narratives shared through press releases and an on-line magazine.</p> <p>While the benefits of cleaning to reef ecosystem health have been extensively studied, the cleaning costs for cleaner species and the role of cleaning stations as potential sinks for microbial diversity and possibly even pathogens have never been assessed. Here, the researchers utilize the unique features of cleaning stations to understand transfer of bacterial and archaeal symbionts amongst fish and within coral reef environment. The study capitalizes on cleanerfish access to multiple variety of hosts or clients within stations to address new questions about how cleanerfish act as vectors to transfer microorganisms between hosts on a reef and if and how these microorganisms may play a broader functional role in reef resilience. Specifically, the project addresses the following hypotheses: 1) Cleanerfishes serve as keystone regulators of microbial communities, enhancing microbial community diversity and transferring key microbial species between clients, and 2) Cleanerfishes are a particularly important contributor to reef resilience, facilitating recovery of the microbiome following disturbance. The research team uses an integrative interdisciplinary approach involving field and laboratory observations and experiments, and molecular-based tools. The core research team includes experts in cleaning mutualisms, fish behavior, coral reef ecology, and microbial ecology. The proposed project aims to link behavior of individual organisms with ecosystem-level process.</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> Cleanerfish microbiomes largerWorkCitation project eng; USA oceans -80.8137 -64.8109 17.7734 24.8261 2020-11-17 2021-11-16 Eastern Caribbean 0 BCO-DMO catalogue of parameters from Microbiome dynamics of coral reef and cleanerfish from ecological surveys, in situ manipulations, and laboratory experiments conducted from 2020-2021 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/907425.rdf Name: BioProject_accession Units: unitless Description: <p>SRA BioProject Accession number</p> http://lod.bco-dmo.org/id/dataset-parameter/907426.rdf Name: BioSample_accession Units: unitless Description: <p>SRA BioSample Accession number</p> http://lod.bco-dmo.org/id/dataset-parameter/907427.rdf Name: sample_name Units: unitless Description: <p>Sample name</p> http://lod.bco-dmo.org/id/dataset-parameter/907428.rdf Name: SRA_accession Units: unitless Description: <p>SRA Data Accession number</p> http://lod.bco-dmo.org/id/dataset-parameter/907429.rdf Name: collection_date Units: unitless Description: <p>Collection date</p> http://lod.bco-dmo.org/id/dataset-parameter/907430.rdf Name: geo_loc_name Units: unitless Description: <p>Geographical location, in State: Location</p> http://lod.bco-dmo.org/id/dataset-parameter/907431.rdf Name: host Units: unitless Description: <p>Host organism scientific name</p> http://lod.bco-dmo.org/id/dataset-parameter/907432.rdf Name: lat Units: decimal degrees Description: <p>Station latitude, south is negative</p> http://lod.bco-dmo.org/id/dataset-parameter/907433.rdf Name: lon Units: decimal degrees Description: <p>Station longitude, west is negative</p> http://lod.bco-dmo.org/id/dataset-parameter/907434.rdf Name: isolation_source Units: unitless Description: <p>Sample isolation</p> http://lod.bco-dmo.org/id/dataset-parameter/907435.rdf Name: host_common_name Units: unitless Description: <p>Host organism common name</p> http://lod.bco-dmo.org/id/dataset-parameter/907436.rdf Name: host_disease Units: unitless Description: <p>Host disease state</p> http://lod.bco-dmo.org/id/dataset-parameter/907437.rdf Name: host_condition Units: unitless Description: <p>Host condition</p> http://lod.bco-dmo.org/id/dataset-parameter/907438.rdf Name: host_coral_cleaner_goby_pretreatment Units: unitless Description: <p>Whether host coral was pre-treated</p> http://lod.bco-dmo.org/id/dataset-parameter/907439.rdf Name: host_coral_reef_id Units: unitless Description: <p>Host coral site ID</p> http://lod.bco-dmo.org/id/dataset-parameter/907440.rdf Name: location_survey_date Units: unitless Description: <p>Survey date</p> http://lod.bco-dmo.org/id/dataset-parameter/907441.rdf Name: location_mean_total_species Units: unitless Description: <p>Survey mean number of species present</p> http://lod.bco-dmo.org/id/dataset-parameter/907442.rdf Name: FCM_Pro_mL Units: cells per milliliter (cells/mL) Description: <p>Abundance of prochlorococcus</p> http://lod.bco-dmo.org/id/dataset-parameter/907443.rdf Name: FCM_Syn_mL Units: cells per milliliter (cells/mL) Description: <p>Abundance of synechococcus</p> http://lod.bco-dmo.org/id/dataset-parameter/907444.rdf Name: FCM_Peuk_mL Units: cells per milliliter (cells/mL) Description: <p>Abundance of picoeukaryotes</p> http://lod.bco-dmo.org/id/dataset-parameter/907445.rdf Name: FCM_Hbac_mL Units: cells per milliliter (cells/mL) Description: <p>Abundance of heterotrophic bacteria</p> http://lod.bco-dmo.org/id/dataset-parameter/907446.rdf Name: NPOC_uM Units: micromolar (uM) Description: <p>Particulate organic carbon</p> http://lod.bco-dmo.org/id/dataset-parameter/907447.rdf Name: TN_uM Units: micromolar (uM) Description: <p>Total organic nitrogen</p> http://lod.bco-dmo.org/id/dataset-parameter/907448.rdf Name: phosphate Units: micromolar (uM) Description: <p>Phosphate</p> http://lod.bco-dmo.org/id/dataset-parameter/907449.rdf Name: nitrate_nitrite Units: micromolar (uM) Description: <p>Nitrate+nitrite</p> http://lod.bco-dmo.org/id/dataset-parameter/907450.rdf Name: silicate Units: micromolar (uM) Description: <p>silicate</p> http://lod.bco-dmo.org/id/dataset-parameter/907451.rdf Name: NO2 Units: micromolar (uM) Description: <p>NO2</p> http://lod.bco-dmo.org/id/dataset-parameter/907452.rdf Name: ammonium Units: micromolar (uM) Description: <p>ammonium</p> http://lod.bco-dmo.org/id/dataset-parameter/907453.rdf Name: nitrate Units: micromolar (uM) Description: <p>Nitrate</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 125607 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/21500789-0540-42af-9275-3f36f2c068df/content download https://doi.org/10.26008/1912/bco-dmo.906740.1 download onLine dataset &lt;p&gt;Coral reef cleaning stations were identified for survey at locations&amp;nbsp;in Marathon, Florida (USA), St. Croix (US Virgin Islands), and Puerto Rico. SCUBA divers and snorkelers performed site surveys and fish observations at cleaning sites. All molecular samples were stored at -80 degrees Celsius or liquid nitrogen dry shipped until DNA extraction.&lt;/p&gt; &lt;p&gt;After observation, cleanerfish and damselfish were captured using individual hand nets and transferred to individual sealed plastic bags. Immediately upon capture, fish were taken to the lab and swabbed on both sides of the body with tubed sterile cotton swabs. Sampling was performed using gloves, and nets were submerged in a 30% bleach solution and rinsed with fresh water prior to each use.&lt;/p&gt; &lt;p&gt;At select coral cleaning stations, sterile clay hexagon tiles were deployed 1 meter above coral heads to develop biofilms. After 6-7 days, the tiles were recovered with minimal handling into Whirlpak bags and transported to the laboratory. The coral heads were also sampled for their mucus, and water was collected in 60-milliliter (mL) syringes from within 30 centimeters of the coral heads. Sterile swabs were used to collect samples from the tiles and coral mucus, and stored in 1.5 mL microcentrifuge tubes.&lt;/p&gt; &lt;p&gt;From select locations, water samples to examine macronutrients were collected from each station into acid-washed polypropylene bottles, frozen, and analyzed with a continuous segmented flow system at Oregon State University to resolve nitrate, nitrite, ammonium, phosphate, and silicate. Water for non-purgeable organic carbon (TOC) and organic nitrogen was collected from the stations into combusted, borosilicate EPA vials and acidified using 75 mL phosphoric acid. Samples were analyzed using a Shimadzu TOC-VCSH total organic carbon analyzer equipped with a TNM-1 module at Woods Hole Oceanographic Institution. To quantify abundances of Prochlorococcus, Synechococcus, picoeukaryotes, and unpigmented (heterotrophic) microorganisms, water (1.4 mL) was collected at the stations, preserved using paraformaldehyde, and frozen in liquid nitrogen vapors.&lt;/p&gt; &lt;p&gt;DNA extractions were performed on swabs of coral, damselfish, and cleanerfish mucus; swabs of tiles; and water filters. DNeasy PowerBiofilm DNA extraction kits (Qiagen, Germantown, MD, USA) were used with a modified protocol for the swab samples. Lysing reagents were added directly to the sample vial with the swab, vortexed, then the swab was re-oriented in the tube so it was cotton-side-up and was spun for 1 minute at 13,000 g to release the liquid absorbed by the swab. The liquid from the swab and the lysing reagents were added to the bead tube, and the manufacturer instructions were followed for the rest of the protocol. For water filters, the filter and lysing reagents were added directly to the bead tube, and then the manufacturer protocols were followed. DNA extraction controls (sterile hydroflock swabs, unused 0.22-micrometer (μm) filters, and unused bead tubes) were completed following the steps above.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;FlowJo software (Tree Star, Inc.) was used for flow cytometry.&lt;/p&gt; Specified by the Principal Investigator(s) - Imported original file &quot;bco-dmo_submission.xlsx&quot; into the BCO-DMO system. - Separated latitude and longitude values into separate columns where they were combined. - Saved the final file as &quot;906740_v1_sequence_sample_information.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 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. Altra flow cytometer (Beckman Coulter) Altra flow cytometer (Beckman Coulter) PI Supplied Instrument Name: Altra flow cytometer (Beckman Coulter) Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells. (from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/ SCUBA SCUBA PI Supplied Instrument Name: SCUBA Instrument Name: Self-Contained Underwater Breathing Apparatus Instrument Short Name:SCUBA Instrument Description: The self-contained underwater breathing apparatus or scuba diving system is the result of technological developments and innovations that began almost 300 years ago. Scuba diving is the most extensively used system for breathing underwater by recreational divers throughout the world and in various forms is also widely used to perform underwater work for military, scientific, and commercial purposes. Reference: https://oceanexplorer.noaa.gov/technology/technical/technical.html Shimadzu TOC-VCSH total organic carbon analyzer equipped with a TNM-1 module Shimadzu TOC-VCSH total organic carbon analyzer equipped with a TNM-1 module PI Supplied Instrument Name: Shimadzu TOC-VCSH total organic carbon analyzer equipped with a TNM-1 module Instrument Name: Shimadzu Total Organic Carbon Analyzer TOC-VCPH Instrument Short Name:TOC-VCPH Instrument Description: The Shimadzu Total Organic Carbon Analyzer TOC-VCPH is a PC-controlled, total organic carbon analyzer (high-sensitivity model), designed to measure total carbon (TC), inorganic carbon (IC), total organic carbon (TOC), and non-purgeable organic carbon (NPOC); an optional accessory enables the measurement of particulate organic carbon (POC) and total nitrogen (TN) as well. The instrument uses the 680 degrees Celsius combustion catalytic oxidation method to analyze aqueous samples, and optionally solid and gas samples.