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Cold-water coral microbiomes (Acanthogorgia spp. Desmophyllum dianthus, and Lophelia pertusa) from the Gulf of Mexico and Atlantic Ocean off the southeast coast of the United States: raw sequencing data
The files provided in this U.S. Geological Survey (USGS) data release (Kellogg and Voelschow, 2021) are the raw DNA sequence files referenced in the associated journal article (Kellogg and Pratte, 2021) entitled, “Unexpected diversity of Endozoicomonas in deep-sea corals.”. This dataset, PRJNA699458_16S-V3V4_raw_data_1.zip, represents the 16S rRNA gene amplicon surveys of 28 samples of deep-sea corals, including Acanthogorgia aspera (n=5), Acanthogorgia spissa (n=4), Desmophyllum dianthus (n=7), and ... |
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Cold-water coral microbiomes (Anthothela spp.) from Baltimore and Norfolk Canyons: raw and processed data
The files included in this data release are the raw and processed deoxyribonucleic acid (DNA) sequence files referenced in the journal article by Lawler and others (2016) entitled “Coral-Associated Bacterial Diversity is Conserved Across Two Deep-Sea Anthothela Species”. They represent a 16S rRNA gene amplicon survey of cold-water corals (Anthothela spp.) microbiomes completed using Roche 454 pyrosequencing with titanium reagents. The samples used in this study were collected from cold-water corals ... |
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Digital Polymerase Chain Reaction (dPCR) Data from the Sediment-Bound Contaminant Resiliency and Response Strategy Pilot Study, Northeastern United States, 2015
Due to the recognized proliferation and spread of antibiotic resistance genes by anthropogenic use of antibiotics for human, agriculture and aquaculture purposes, antibiotic resistance genes have been defined as an emerging contaminant (Laxminarayan and others, 2013; Rodriguez-Rojas and others, 2013; Niu and others, 2016). The presence and spread of these genes in non-clinical and non-agricultural environments has created the need for background investigations to enhance our understanding of the magnitude ... |
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Functional gene microarray data from cold-water corals (Acanthogorgia spp., Desmophyllum dianthus, Desmophyllum pertusum, and Enallopsammia profunda) from the Atlantic Ocean off the Southeast Coast of the United States–Raw Data and Sample Site Information
The files in this data release (Kellogg and Voelschow, 2023) contain normalized microarray probe intensity values from GeoChip 5.0S microarrays referenced in the journal article entitled “Functional gene composition and metabolic potential of deep-sea coral-associated microbial communities” by Pratte and others (2023). The GeoChip 5.0S microarrays, provided by Glomics Inc., contain 57,498 oligonucleotide probes that target 383 microbial (archaeal, bacterial, and fungal) genes and cover 151,797 coding ... |
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Microbial and environmental dataset from Crocker Reef, Florida Keys, 2014-2015
Crocker Reef was the site of an integrated reefscape characterization effort focused on calcification and related biogeochemical processes as part of the USGS Coral Reef Ecosystem Study (CREST) project. This effort included two intensive seasonal sampling trips to capture summer (July 8 to 17, 2014) and winter (January 29 to February 5, 2015) conditions. This data release represents water column microbial and environmental data collected for use as metadata in future publications examining reef metabolic ... |
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Presence/absence Quantitative Polymerase Chain Reaction (qPCR) Data from the Sediment-Bound Contaminant Resiliency and Response Strategy Pilot Study, Northeastern United States, 2015
Due to the recognized proliferation and spread of antibiotic resistance genes by anthropogenic use of antibiotics for human, agriculture and aquaculture purposes, antibiotic resistance genes have been defined as an emerging contaminant (Laxminarayan and others, 2013; Rodriguez-Rojas and others, 2013; Niu and others, 2016). The presence and spread of these genes in non-clinical and non-agricultural environments has created the need for background investigations to enhance our understanding of the magnitude ... |
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Prokaryotic Communities From Marine Biofilms Formed on Stainless Steel Plates in Coral Mesocosms – Raw and Processed Data
The files in this data release (Kellogg and others, 2022) are those referenced in the journal article by Evans and others (2022) entitled “Biofilms as Potential Reservoirs of Stony Coral Tissue Loss Disease.” They contain an amplicon sequence variant (ASV) table and the raw 16S ribosomal ribonucleic acid (rRNA) gene amplicon deoxyribonucleic acid (DNA) sequence files from 15 microbial communities (sample names: CnD16B, CnD17B, CnD18B, CnD19B, CnD21B, CnD22B, CnD23B, CnD24B, CnD25B, PsD5B, CnH101B, ... |
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Prokaryotic Communities Shed by Diseased and Healthy Corals (Diploria labyrinthiformis, Pseudodiploria strigosa, Montastraea cavernosa, Colpophyllia natans, and Orbicella faveolata) into Filtered Seawater Mesocosms – Raw and Processed Data
The files in this data release (Kellogg and others, 2023) are those referenced in the journal article by Evans and others (2023) entitled “Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD).” They contain an amplicon sequence variant (ASV) table and the raw 16S rRNA gene amplicon files from fifty-six 0.22-micrometer (µm) pore size filters, as well as six reagent blanks, three mock communities, and a 0.22-µm-filtered ultraviolet (UV)-treated ... |
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Raw sequencing and amplicon sequence variant data from bacterial communities shed by Montastraea cavernosa coral fragments into filtered seawater mesocosms
The files provided in this U.S. Geological Survey (USGS) data release (Kellogg and others, 2021) include an amplicon sequence variant (ASV) table and the raw 16S rRNA gene amplicon files from six microbial communities (Mcav17, Mcav18, McH-101, McH-103, McD-57, and McD-58) derived from mesocosms consisting of filtered seawater in which either healthy or diseased (stony coral tissue loss disease) fragments of Montastraea cavernosa had been incubated, as well as sequence files of a mock community and ... |
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Southeast Florida and Florida Keys Antibiotic Resistance Study
The prevalence of antibiotic resistance genes in microbial communities from sewage wastewater streams and from offshore marine sediments in the vicinity of sewage wastewater outfalls in Southeast Florida was investigated from June 2018 to March 2019. Sediment and wastewater samples were analyzed for 15 different antibiotic resistant gene targets via polymerase chain reaction (PCR) presence/absence assays in Southeast Florida coral reef environments. Data collected from five sites (Broward North Wastewater ... |
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Testing Treatments Against Parasitic Scuticociliate (Philaster apodigitiformis) that Causes Mass Mortality Among Sea Urchins (Diadema antillarum) - Results
The information contained in this data release are the results observed and collected during an experiment that tested the efficacy of nine compounds (2’4’ dihydroxychalcone, bithionol sulfoxide, carnidazole, furaltadone, plumbagin, oxyclozanide, quinacrine, tomatine, and toltrazuril), previously found to be effective against the parasitic ciliate family Philasteridae (Iglesias and others, 2002; Sueiro and others, 2022). One commercially available product (Kordon Ich Attack) was also tested, however was ... |
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