This dataset is the raw Luminex antibody responses to six common waterborne pathogens reported in MFI (Median Fluorescence Intensity) units. This dataset is associated with the following publication: Augustine , S., T. Eason , K. Simmons, C. Curioso, S. Griffin , M. Ramudit, and T. Plunkett. Developing a Salivary Antibody Multiplex Immunoassay to Measure Human Exposure to Environmental Pathogens. Journal of Visualized Experiments. JoVE, Somerville, MA, USA, 115: e54415, (2016).

The data contained in this worksheet provides the Median Fluorescence Intensity (MFI) readings for the Boquerón Beach, Puerto Rico saliva samples collected on Day 1 of the study and used to assess immunoprevalence of the beachgoers to the pathogens in the multiplex immunoassay. This dataset is associated with the following publication: Augustine, S., K. Simmons, T. Eason, C. Curioso, S. Griffin, T. Wade, A. Dufour, S. Fout, A. Grimm, K. Oshima, E. Sams, M. See, and L. Wymer. Immunoprevalence to Six Waterborne Pathogens in Beachgoers at Boquerón Beach, Puerto Rico: Application of a Microsphere-Based Salivary Antibody Multiplex Immunoassay. Frontiers in Public Health. Frontiers, Lausanne, SWITZERLAND, 5(84): 1-11, (2017).

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 processes via metagenomes derived from water samples and fine-scale temporal and spatial carbonate chemistry measurements. Microbial data are total bacterial counts per milliliter seawater, total viral counts per milliliter of seawater, and plate counts using Thiosulfate Citrate Bile Salts Sucrose (TCBS) agar of Vibrio (bacteria) per milliliter of seawater. Environmental data are water temperature, salinity, dissolved oxygen, and pH.

Three replicate Montipora colonies displaying areas of apparently healthy coral tissue and black areas with obvious diseased lesions were sampled from a small reef flat area in Nelly Bay, Magnetic Island, Australia. 'Healthy' samples were collected from normally pigmented areas of a coral colony separated by >5 cm from an observed lesion. 'Diseased' samples were collected from the boundary margin of healthy and diseased skeleton and tissue of black lesions. A permanent photographic monitoring site was established in the area in early January 2002.Samples were prepared in media designed for the isolation and enumeration of heterotrophic marine bacteria and Vibrio organisms respectively. Bacteria obtained from this study were designated: MA-HC1 and MA-HC2 for isolates obtained from healthy coral (HC) samples and MA-DC1 to MA-DC4 for isolates cultured from diseased coral (DC) samples, both grown on marine agar (MA) medium; and TCBS-DC1 to TCBS DC-4 for isolates cultured from diseased coral (DC) samples grown on TCBS growth medium.DNA was extracted from cultured isolates using the propriety reagent GeneReleaser and from coral samples using a modified UREA extraction buffer protocol. Universal bacterial primers 27F and 1492R, were used for amplification of 16S rRNA genes. PCR products were checked on a 1% agarose gel with bands of appropriate size either sequenced (bacterial isolates) or cloned (DNA extracted from corals). Duplicate PCR reactions were performed on DNA extracted from each coral sample and the products from the replicated reactions pooled.Amplified rDNA restriction analysis (ARDRA) was performed to analyse the diversity of clones within each of the healthy coral and disease coral libraries constructed.The diversity of clone libraries was further investigated by rarefaction analysis calculations. Other indices and models were used to analyse the variation of microbial diversity within clone libraries, with three different categories of measurement calculated with the EstimateS software package: Richness indices, Evenness indices, and Abundance models.Sequences of clones representing the OTU groupings generated were designated: HC-OTU1 to HC-OTU12 for clones from the healthy coral (HC) sample clone library, DC-OTU1 to DC-OTU12 for clones from the diseased coral (DC) sample clone library. Sequences were checked for chimera formation with the CHECK_CHIMERA software of the Ribosomal Database Project. Sequence data generated was analysed with the ARB software package. Tree topology was evaluated by reconstructing phylogenies using evolutionary distance (Jukes and Cantor model), maximum parsimony (ARB and DNAPARS) and maximum likelihood (ARB and fastDNAml) analyses of the aligned near full-length sequences extracted from the GenBank database. To report the results of culture-based andmolecular microbial analysis of both healthy and diseased coral tissue from Montipora corals at Magnetic Island undergoing atramentous necrosis and compare those data with 16S rDNA sequences from diseased lesions reported previously. The nucleotide sequence data appears in the GenBank database under the accession numbers: AY529868, AY529869, AY529870, AY529871, AY529872, AY529873, AY529874, AY529875, AY529876, AY529877, AY529878, AY529879, AY529880, AY529881, AY529882, AY529883, AY529884, AY529885, AY529886, AY529887, AY529888, AY529889, AY529890, AY529891, AY529892, AY529893, AY529894, AY529895, AY529896, AY529897, AY529898, AY529899, AY529900.

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 Lophelia pertusa [Desmophyllum pertusum] (n=12), plus a kit extraction control blank. The sequencing targeted the V3-V4 variable region (primers 341F/806R) and was completed using an Illumina MiSeq sequencing system with version 2 chemistry to obtain paired-end reads.

Amplicon sequence variants from enrichment cultures and non-enriched water samples generated with primer sets targeting the V4 region of the 16SrRNA “This research dataset has been reviewed in accordance with U.S. Environmental Protection Agency (U.S. EPA), Office of Research and Development, and approved for release. Mention of brand names or vendors does not constitute an endorsement of products or services by the U.S. EPA.”

Amplicon sequence variants from enrichment cultures and non-enriched water samples generated with primer sets targeting the V4 region of the 16SrRNA. “This research dataset has been reviewed in accordance with U.S. Environmental Protection Agency (U.S. EPA), Office of Research and Development, and approved for release. Mention of brand names or vendors does not constitute an endorsement of products or services by the U.S. EPA.”

,This repository contains data supporting the publication, "Detection of viral, bacterial, and protozoan pathogens and microbial source tracking markers in paired large- and small-volume water samples." The dataset comprises qPCR concentrations of microbial targets in paired large volume and small volume samples from field studies and laboratory recovery experiments, as described in the main publication.,"Field studies.csv" contains sample data and target concentrations for three field studies, two in groundwater and one in surface water. In the "Groundwater - Private wells (n = 138)" study, large volume samples taken by dead-end ultrafiltration were compared to small volume grab samples. In the remaining two studies, large volume dead-end ultrafiltration and small volume samples were collected synchronously to remove the effect of spatial/temporal heterogeneity during collection. Only the 15 qPCR assays with detections and common to all studies are included. Geographic information is not included to protect the privacy of study participants.,"Recovery data.csv" contains laboratory data for large volume and small volume method recovery of three microbial targets (a bacterium, a virus, and a protozoan) at varying initial concentrations.,"Storage data.csv" contains laboratory data for microbial target decay during storage prior to processing. Liquid small volume samples and large volume ultrafilters were stored at 4 C to simulate normal sample storage and transport conditions. Concentrations of three microbial targets (a bacterium, a virus, and a protozoan) were determined for storage times from 0 to 96 hours.,Descriptive data for all microbial targets is provided in "Target data.csv". An explanation of variables (with units) for all data files can found in "Key to variables.csv".,

This data set includes information pertaining to 300 bivalve mollusk tissue samples collected from mollusk specimens from waters in eastern Maryland on the Delmarva Peninsula. Data includes source location, species, morphometric data, and IAV matrix gene detection status for the bivalve samples collected and analyzed in the associated study.