Enhancing Management Tools: Molecular Genetic Tracking to Target Microbial Pollution Sources in South Florida Coral Reefs, Year 1 - CRCP project #1114

Both coastal inlets and treated wastewater outfalls are recognized as major pathways for microbial contaminants from Land-Based Sources of Pollution (LBSP) to enter Florida's Southeastern coastal marine ecosystems, including an area containing reef tracks with an estimated annual economic value in excess of $3.88 Billion. These LBSP discharges can contain a variety of microbial contaminants including fecal indicator bacteria, fecal host marker bacteria, and pathogens to both human health and coral ecosystem health. The study reported here presents the first year of data from a two-year CRCP project (Project #1114), as part of the broader NOAA Florida Area Coastal Environment (FACE) research program and is established as the first preliminary pilot study for the broader NOAA Coral Genomic Observatory Network (CGON). This project is studying prevalence of fecal indicator bacteria, molecular microbial source tracking markers for fecal contaminants, selected pathogenic bacteria, as well as characterizing the bacterial, algal, and fungal communities of coastal inlet discharges, oceanic wastewater discharges, coral reef waters, and of actual coral tissue from 4 sentinel reefs in this study area offshore of Miami-Dade and Broward Counties in Florida. The data files referred to here that are archived at CORIS and at AOML, and linked to this year 1 metadata file include: (1) an excel spreadsheet file of the sample inventory log listing samples from year 1 with the dates, locations, sample types, unique filter ID # for extractions, processing status, and which samples have been sequenced; (2) an excel spreadsheet file for the viable enterococci data from the year 1 samples giving live enterococci counts in cfu/100mL water per EPA method 1600 for water samples from coastal inlets, wastewater outfalls, wastewater effluent, and coastal waters from sentinel reef sites; (3) an excel spreadsheet file showing data for year 1 water samples and selected year 1 coral tissue samples showing molecular microbial source tracking qPCR results for total enterococci, for Bacteroidales fecal markers specifically associated with cow, dog, and human hosts, and qPCR data for Human Polyoma Virus and for Pepper Mottled Mild Virus (both viral human fecal markers), and a summary of microfluidic qPCR analysis for specific food-borne and water-borne pathogen genes in selected water and coral tissue samples; (4) an excel spreadsheet showing nutrient and physical data and metadata for water samples, including GPS locations of water samples, dates, times, CTD cast numbers, depth, temperature, salinity, conductivity, density, CDOM, turbidity, oxygen saturation, and nutrients (N+N, TKN, TP, Chlorophyll), also includes embedded google earth map images showing sample sites; (5) an excel spreadsheet showing the physical data, observations, and metadata from divers diving computer for the coral benthic observations, including site GPS location, time, date, depth, temperature, and coral biometric observations, also includes embedded map images of coral/algal observation sites, and embedded charts of coral bleaching; (6) a powerpoint file showing a summary of the sequencing and metagenomic bioinformatics data, including summary of sequencing and bioinformatics analysis methods, rarefaction plots, heat maps of most prevalent phyla, heat maps of most prevalent families, PCoA plots comparing populations of coastal inlets, wastewater outfalls, and coral reefs, PCoA plots for populations of coral tissues, and preliminary conclusions so far for year 1 data. The actual Illumina Sequence data for each sample is archived at the National Center for Biotechnology Information (NCBI) as Bioproject # 292127 (see link above). This bioproject sequence data is scheduled to be available to the public on May 31, 2016. Until this time, access to the sequence files is password protected. If you require access to these files before this date, please contact the project PI, Dr. Christopher Sinigalliano (email: christopher.sinigalliano@noaa.gov).

                                            {
  "fn": "National Oceanic and Atmospheric Administration, Office of Oceanic and Atmospheric Research, Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystem Division, Molecular and Environmental Microbiology Program",
  "@type": "vcard:Contact",
  "hasEmail": "mailto:christopher.sinigalliano@noaa.gov"
}
                                        

                                            [
  {
    "@type": "dcat:Distribution",
    "accessURL": "http://www.coral.noaa.gov/collaborations/microbiology.html",
    "describedByType": "application/octet-steam"
  }
]
                                        

                                            [
  "CoRIS_Metadata",
  "Enhancing Management Tools: Molecular Genetic Tracking to Target Microbial Pollution Sources in South Florida Coral Reefs",
  "1114",
  "Genetic Data Sets > metagenomic analysis",
  "Genetic Data Sets > PCR/QPCR detection and measurements",
  "Numeric Data Sets > Water Quality",
  "EARTH SCIENCE > Biosphere > Zoology > Corals",
  "EARTH SCIENCE > Oceans > Marine Biology > Coral Communities",
  "EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Diseases",
  "EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology",
  "EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > Biodiversity",
  "EARTH SCIENCE > Biosphere > Aquatic Habitat > Reef Habitat",
  "EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment",
  "EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Benthos Analysis",
  "EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Microbiology",
  "EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Molecular Genetic Analysis > Quantitative Polymerase Chain Reaction",
  "EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Molecular Genetic Analysis > Microbial Source Tracking",
  "EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Molecular Genetic Analysis > DNA/RNA Sequencing",
  "EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Molecular Genetic Analysis > Metagenomic Analysis",
  "EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Molecular Genetic Analysis > Coral Genomic Observatory Network (CGON)",
  "EARTH SCIENCE > Biosphere > Microbiota",
  "EARTH SCIENCE > Biosphere > Microbiota > Microbiome",
  "EARTH SCIENCE > Oceans > Marine Biology > Coral > Halobiont",
  "United States",
  "Florida",
  "East Coast",
  "Southeast",
  "Miami-Dade",
  "Broward",
  "Gulfstream",
  "OCEAN BASIN > Atlantic Ocean > North Atlantic Ocean > Florida Reef Tract > Broward County (26N080W0006)",
  "COUNTRY/TERRITORY > United States of America > Florida > Broward County > Broward County (26N080W0006)",
  "OCEAN BASIN > Atlantic Ocean > North Atlantic Ocean > Miami-Dade County (25N080W0038)",
  "COUNTRY/TERRITORY > United States of America > Florida > Miami-Dade County (25N080W0038)"
]
                                        

                                            []
                                        

                                            {
  "name": "NOAA/OAR/AOML",
  "@type": "org:Organization"
}