http://lod.bco-dmo.org/id/dataset/858459 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 2021-08-13 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) 16S V4 rRNA gene tag sequences from reef seawater samples collected in the Florida Keys and the U.S. Virgin Islands in 2019-2020 2021-08-13 publication 2021-08-13 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2021-08-24 publication https://doi.org/10.26008/1912/bco-dmo.858459.1 Amy Apprill Woods Hole Oceanographic Institution principalInvestigator Lei Ma 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., Ma, L. (2021) 16S V4 rRNA gene tag sequences from reef seawater samples collected in the Florida Keys and the U.S. Virgin Islands in 2019-2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-08-13 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.858459.1 [access date] 16S V4 rRNA gene tag sequences from reef seawater Dataset Description: Methods and Sampling: &lt;p&gt;Samples were collected in two reef systems, the Florida Reef Tract in June of 2019 and off the southern coast of St. Thomas in the U.S. Virgin Islands in Februrary of 2020. See Supplemental File, &quot;&lt;a href=&quot;https://datadocs.bco-dmo.org/docs/305/Quantitative_coral_microbiomes/data_docs/sampling_locations.csv&quot; target=&quot;_blank&quot;&gt;sampling_locations.csv&lt;/a&gt;&quot; for latitude, longitude, depth, and dates of each sampling location. A total of 3 reef sites at each reef system&amp;nbsp;were sampled. At each reef site, three 10 meter transects were taken by laying down a 10 meter weighted line that was marked every meter. Water samples were taken by a diver using a 60 or 100 mL syringe positioned approximately 5 mm above the benthos at each meter line. The transects were laid haphazardly, but did not intersect with each other. Because of inclement conditions, only 1 transect was collected at Site 73, rather than the intended 3. To capture the seawater microbial community, 60 mL of the seawater was filtered through a 0.22 µm Supor filter (25 mm; Pall Corporation). Filters were placed in 2 mL cryovials, flash frozen in a liquid nitrogen dry shipper, and processed upon return to Woods Hole, MA.&lt;/p&gt; &lt;p&gt;DNA was extracted from the filters using the DNEasy PowerBiofilm Kit (Qiagen) according to manufacturer protocols. Seven DNA extraction controls, consisting of unused 0.22 µm filter, were processed alongside samples. Primers 515F (Parada et al. 2016) and 806R (Apprill et al. 2015) containing Nextera adapter sequences were used to amplify the V4 region of the small subunit rRNA gene in bacteria and archaea.&lt;/p&gt; &lt;p&gt;PCR reactions contained 14.75 µL molecular grade water, 5 µL GoTaq Flexi 5X buffer (Promega Corporation), 2.5 µL of 25 mM MgCl2, 1 µL of 10 mM dNTPs, 1 µL of 10 mM forward and reverse primers, 0.5 µL GoTaq DNA polymerase (Promega). Three PCR controls consisting of 1 µL of PCR-grade water was also included, as well as microbial genomic DNA from a Human Microbiome Project mock community (BEI Resources, NIAID, NIH as part of the Human Microbiome Project: Genomic DNA from Microbial Mock Community B (Even, Low Concentration), v5.1L, for 16S RNA Gene Sequencing, HM-782D). The first stage PCR conditions were: 28 cycles (95°C 20s, 55°C 20s, 72°C 5 min) with a 2 minute 95°C hot start and 10 min 72°C final elongation. PCR products were screened for quality using gel electrophoresis and purified using the MinElute PCR purification kit (Qiagen). PCR products were then barcoded using the Nextera XT Index Kit v2 primers (Illumina) using the following conditions: 8 cycles (95°C 30s, 55°C 30s, 72°C 30s) with 3 minute 95° hot start and 5 minute 72°C final elongation. Barcoded products were purified as above and concentrations of the purified products were assessed using the HS dsDNA assay on the Qubit 2.0 fluorometer (ThermoFisher Scientific). Products were diluted with Tris HCl to 5 nM before being pooled randomly into two libraries. The libraries were diluted to a final loading concentration of 50 pM with a 5% spike-in of 50 pM PhiX. The libraries were then sequenced on the iSeq 100 System (Illumina).&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1938147 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1938147 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 Lei Ma Woods Hole Oceanographic Institution 266 Woods Hole Rd. MS#4 Woods Hole MA 02543 USA lma@whoi.edu pointOfContact asNeeded Dataset Version: 1 Unknown BioProject Sample_Name SRA_Run_ID SRA_run_link SRA_Study SRA_Sample geo_loc_name isolation_source lat lon Assay_Type Platform Instrument LibraryLayout LibrarySelection LibrarySource Organism samp_collect_device samp_mat_process reef_system site substrate_class transect distance Sample_or_Control collection_date unique_ID iSeq 100 System (Illumina) Qubit 2.0 fluorometer (ThermoFisher Scientific) diver and syringe PCR theme None, User defined NCBI BioProject accession sample identification NCBI SRA run accession (SRR) external_link NCBI SRA study accession (SRP) NCBI SRA Sample accession (SRS) site sample description latitude longitude experiment type instrument sampling_method site description transect track length sample type date featureType BCO-DMO Standard Parameters Automated DNA Sequencer Fluorometer Manual Biota Sampler 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. EAGER: Collaborative Research: Quantifying coral microbiome dynamics under change https://osprey.bco-dmo.org/project/822475 EAGER: Collaborative Research: Quantifying coral microbiome dynamics under change <p><em>NSF Award Abstract:</em><br /> Corals are the architectural base of reefs, one of the most biodiverse and ecologically complex ocean ecosystems that also provide substantial economic resources to coastal communities. Unfortunately, recent episodes of widespread bleaching and disease have reduced coral populations and contributed to declines in reef ecosystems. There is speculation that the coral microbiome, including a community of bacteria and archaea, may provide added resistance and resilience to corals facing pathogens and warmer ocean conditions. However, there are no quantitatively methods available to track specific microbial lineages within coral microbiomes, thus limiting the ability to examine these concepts. This research will improve capabilities to quantitatively measure and track specific microbial lineages within the coral microbiome. Coral reefs are one of the most globally threatened ecosystems in the ocean. The project will provide methodological advancements that will enhance understanding about the response of coral microbiomes to warming, disease and environmental-related disturbance. These efforts will help provide a necessary knowledge framework for scientists, reef managers and decision makers who are urgently exploring solutions to prevent the further decline of coral reef ecosystems. The team will communicate project findings broadly through publicly accessible narratives shared through press releases and an online magazine. This project will promote data sharing and collaboration amongst coral microbiome scientists, through a data sharing and visualization portal. The project will train undergraduate and graduate students and will be led by two female PIs (one Hispanic).</p> <p>This research has the potential to transform our current ability to quantify ecological changes within coral microbiomes and to understand and predict how coral-associated microbes may be able to contribute to the resilience and resistance of corals to warming, disease and environmental change related stressors on reefs. This project will contribute methodological and resource contributions that will advance knowledge and studies of coral microbiomes as well as other host-microbiome systems. Specifically, the team plans to develop and test two types of controls, 1) spike-in microbial cells and 2) a coral microbiome specific mock community. These methods will be used to address the following hypothesis: improved quantitative descriptions of coral microbiome dynamics in relation to relevant scenarios of change are obtained using spike-in controls and coral-specific mock communities. To address this, the investigators will develop endogenous spike-in controls of bacteria and archaea to track microbial load or abundance within samples and construct a coral microbiome mock community to optimize PCR, sequencing and data analysis. These methods will first be optimized in a replicated experimental manner across healthy, nonstressed and ecologically and phylogenetically diverse coral species. Next, optimized methods will be applied to coral samples from experiments, which are expected to show changes in microbiome dynamics over time. These experiments include scenarios of thermal stress, reef environmental change, and disease development. These experiments will take place in Little Cayman, a location with reefs with contrasting temperature and other environmental properties, as well as the U.S. Virgin Islands, a site of a recent coral disease outbreak.</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> Quantitative coral microbiomes largerWorkCitation project eng; USA oceans -82.828323 -64.980451 18.316767 25.38634 2019-06-07 2020-02-12 Little Cayman 0 BCO-DMO catalogue of parameters from 16S V4 rRNA gene tag sequences from reef seawater samples collected in the Florida Keys and the U.S. Virgin Islands in 2019-2020 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/858475.rdf Name: BioProject Units: unitless Description: <p>NCBI BioProject number</p> http://lod.bco-dmo.org/id/dataset-parameter/858476.rdf Name: Sample_Name Units: unitless Description: <p>Sample identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/858477.rdf Name: SRA_Run_ID Units: unitless Description: <p>SRA run ID</p> http://lod.bco-dmo.org/id/dataset-parameter/858478.rdf Name: SRA_run_link Units: unitless Description: <p>SRA run link</p> http://lod.bco-dmo.org/id/dataset-parameter/858479.rdf Name: SRA_Study Units: unitless Description: <p>SRA study ID</p> http://lod.bco-dmo.org/id/dataset-parameter/858480.rdf Name: SRA_Sample Units: unitless Description: <p>SRA sample</p> http://lod.bco-dmo.org/id/dataset-parameter/858481.rdf Name: geo_loc_name Units: unitless Description: <p>Geolocation name</p> http://lod.bco-dmo.org/id/dataset-parameter/858482.rdf Name: isolation_source Units: unitless Description: <p>Description of source of sample</p> http://lod.bco-dmo.org/id/dataset-parameter/858483.rdf Name: lat Units: unitless Description: <p>Latitude of sample collection</p> http://lod.bco-dmo.org/id/dataset-parameter/858484.rdf Name: lon Units: unitless Description: <p>Longitude of sample collection</p> http://lod.bco-dmo.org/id/dataset-parameter/858485.rdf Name: Assay_Type Units: unitless Description: <p>Assay type</p> http://lod.bco-dmo.org/id/dataset-parameter/858486.rdf Name: Platform Units: unitless Description: <p>Instrument platform</p> http://lod.bco-dmo.org/id/dataset-parameter/858487.rdf Name: Instrument Units: unitless Description: <p>Instrument</p> http://lod.bco-dmo.org/id/dataset-parameter/858488.rdf Name: LibraryLayout Units: unitless Description: <p>Description of library layout</p> http://lod.bco-dmo.org/id/dataset-parameter/858489.rdf Name: LibrarySelection Units: unitless Description: <p>Library selection</p> http://lod.bco-dmo.org/id/dataset-parameter/858490.rdf Name: LibrarySource Units: unitless Description: <p>Library source</p> http://lod.bco-dmo.org/id/dataset-parameter/858491.rdf Name: Organism Units: unitless Description: <p>Organism descriptoin</p> http://lod.bco-dmo.org/id/dataset-parameter/858492.rdf Name: samp_collect_device Units: unitless Description: <p>Sample collection device</p> http://lod.bco-dmo.org/id/dataset-parameter/858493.rdf Name: samp_mat_process Units: unitless Description: <p>Sample extraction process</p> http://lod.bco-dmo.org/id/dataset-parameter/858494.rdf Name: reef_system Units: unitless Description: <p>Reef system: FLA = Florida Keys; STT = St. Thomas</p> http://lod.bco-dmo.org/id/dataset-parameter/858495.rdf Name: site Units: unitless Description: <p>Site identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/858496.rdf Name: substrate_class Units: unitless Description: <p>Description of substrate</p> http://lod.bco-dmo.org/id/dataset-parameter/858497.rdf Name: transect Units: unitless Description: <p>Transect number</p> http://lod.bco-dmo.org/id/dataset-parameter/858498.rdf Name: distance Units: meters Description: <p>Distance along transect</p> http://lod.bco-dmo.org/id/dataset-parameter/858499.rdf Name: Sample_or_Control Units: unitless Description: <p>Indicates if the sample is a control</p> http://lod.bco-dmo.org/id/dataset-parameter/858500.rdf Name: collection_date Units: unitless Description: <p>Date of sample collection; format: YYYY-MM-DD</p> http://lod.bco-dmo.org/id/dataset-parameter/858501.rdf Name: unique_ID Units: unitless Description: <p>Unique ID for each row</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 65096 https://darchive.mblwhoilibrary.org/bitstream/1912/27471/1/dataset-858459_16s-v4-rrna-gene-tag-sequences-reef-seawater__v1.tsv download https://doi.org/10.26008/1912/bco-dmo.858459.1 download onLine dataset &lt;p&gt;Samples were collected in two reef systems, the Florida Reef Tract in June of 2019 and off the southern coast of St. Thomas in the U.S. Virgin Islands in Februrary of 2020. See Supplemental File, &quot;&lt;a href=&quot;https://datadocs.bco-dmo.org/docs/305/Quantitative_coral_microbiomes/data_docs/sampling_locations.csv&quot; target=&quot;_blank&quot;&gt;sampling_locations.csv&lt;/a&gt;&quot; for latitude, longitude, depth, and dates of each sampling location. A total of 3 reef sites at each reef system&amp;nbsp;were sampled. At each reef site, three 10 meter transects were taken by laying down a 10 meter weighted line that was marked every meter. Water samples were taken by a diver using a 60 or 100 mL syringe positioned approximately 5 mm above the benthos at each meter line. The transects were laid haphazardly, but did not intersect with each other. Because of inclement conditions, only 1 transect was collected at Site 73, rather than the intended 3. To capture the seawater microbial community, 60 mL of the seawater was filtered through a 0.22 µm Supor filter (25 mm; Pall Corporation). Filters were placed in 2 mL cryovials, flash frozen in a liquid nitrogen dry shipper, and processed upon return to Woods Hole, MA.&lt;/p&gt; &lt;p&gt;DNA was extracted from the filters using the DNEasy PowerBiofilm Kit (Qiagen) according to manufacturer protocols. Seven DNA extraction controls, consisting of unused 0.22 µm filter, were processed alongside samples. Primers 515F (Parada et al. 2016) and 806R (Apprill et al. 2015) containing Nextera adapter sequences were used to amplify the V4 region of the small subunit rRNA gene in bacteria and archaea.&lt;/p&gt; &lt;p&gt;PCR reactions contained 14.75 µL molecular grade water, 5 µL GoTaq Flexi 5X buffer (Promega Corporation), 2.5 µL of 25 mM MgCl2, 1 µL of 10 mM dNTPs, 1 µL of 10 mM forward and reverse primers, 0.5 µL GoTaq DNA polymerase (Promega). Three PCR controls consisting of 1 µL of PCR-grade water was also included, as well as microbial genomic DNA from a Human Microbiome Project mock community (BEI Resources, NIAID, NIH as part of the Human Microbiome Project: Genomic DNA from Microbial Mock Community B (Even, Low Concentration), v5.1L, for 16S RNA Gene Sequencing, HM-782D). The first stage PCR conditions were: 28 cycles (95°C 20s, 55°C 20s, 72°C 5 min) with a 2 minute 95°C hot start and 10 min 72°C final elongation. PCR products were screened for quality using gel electrophoresis and purified using the MinElute PCR purification kit (Qiagen). PCR products were then barcoded using the Nextera XT Index Kit v2 primers (Illumina) using the following conditions: 8 cycles (95°C 30s, 55°C 30s, 72°C 30s) with 3 minute 95° hot start and 5 minute 72°C final elongation. Barcoded products were purified as above and concentrations of the purified products were assessed using the HS dsDNA assay on the Qubit 2.0 fluorometer (ThermoFisher Scientific). Products were diluted with Tris HCl to 5 nM before being pooled randomly into two libraries. The libraries were diluted to a final loading concentration of 50 pM with a 5% spike-in of 50 pM PhiX. The libraries were then sequenced on the iSeq 100 System (Illumina).&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;Sequences deposited on the NCBI database are raw sequence reads before primer trimming or any processing. Sequences&amp;nbsp;can be found in NCBI under&amp;nbsp;the bioproject PRJNA733652.&lt;/p&gt; &lt;p&gt;BCO-DMO Processing:&lt;br /&gt; - replaced 'NA' with 'nd' (no data);&lt;br /&gt; - changed date format to YYYY-MM-DD;&lt;br /&gt; - renamed 'SRA_runk_link' to 'SRA_run_link';&lt;br /&gt; - removed commas from geo_loc_name field.&lt;/p&gt; Specified by the Principal Investigator(s) 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 iSeq 100 System (Illumina) iSeq 100 System (Illumina) PI Supplied Instrument Name: iSeq 100 System (Illumina) 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 2.0 fluorometer (ThermoFisher Scientific) Qubit 2.0 fluorometer (ThermoFisher Scientific) PI Supplied Instrument Name: Qubit 2.0 fluorometer (ThermoFisher Scientific) Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/ diver and syringe diver and syringe PI Supplied Instrument Name: diver and syringe PI Supplied Instrument Description:Water samples were taken by a diver using a 60 or 100 mL syringe Instrument Name: Manual Biota Sampler Instrument Short Name:Manual Biota Sampler Instrument Description: "Manual Biota Sampler" indicates that a sample was collected in situ by a person, possibly using a hand-held collection device such as a jar, a net, or their hands. This term could also refer to a simple tool like a hammer, saw, or other hand-held tool. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/90/ PCR PCR PI Supplied Instrument Name: PCR 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)