The files in this data release (doi:10.5066/P9T6NW4V) 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, CnH100B, Pstr4B, Pstr10B, and seawaterB) derived from biofilms on stainless steel plates (316 grade) formed in mesocosms containing diseased corals (stony coral tissue loss disease, n = 10), healthy corals (n = 4), or no coral (n = 1). Also included are the sequence files from a mock community, and two reagent blanks. Corals (Colpophyllia natans and Pseudodiploria strigosa) were collected between January 2019 and March 2021, from various locations throughout the Florida Keys. Plates were added to mesocosm buckets containing ultraviolet (UV)-sterilized, 0.2 micrometer (μm)-filtered seawater and either diseased (n = 10), healthy (n = 4), or no coral (n = 1) at the Smithsonian Marine Station in Fort Pierce, Florida (FL) on March 25, 2021. Plates were removed on March 28, 2021, and placed in individual sterile whirlpaks with RNAlater for future processing. 

Evans, J.S., Paul, V.J., and Kellogg, C.A., 2022, Biofilms as potential reservoirs of stony coral tissue loss disease: Frontiers in Marine Science, v. 9, art. 1009407, https://doi.org/10.3389/fmars.2022.1009407.

Extraction of DNA from the samples and blanks occurred in April 2021 at the Coral Microbial Ecology Laboratory in St. Petersburg, FL using the QIAGEN DNeasy PowerBiofilm Kit. Library preparation and DNA sequencing were conducted on May 13, 2021, by the Michigan State University RTSF Genomics Core (East Lansing, Michigan) using primers 515F: GTGCCAGCMGCCGCGGTAA and 806R: GGACTACHVGGGTWTCTAAT to target the V4 variable region of the 16S rRNA gene on a MiSeq sequencing system with v2 chemistry to obtain paired-end 250-bp (base pair) reads. The raw data files associated with this data release have also been submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject number PRJNA828575.
For more information, you may contact Christina Kellogg at the USGS St. Petersburg Coastal and Marine Science Center, 600 4th Street South, St. Petersburg, Florida, USA, 33710; Telephone: (727) 502-8128; Email: ckellogg@usgs.gov.

The file labeled "Biofilm_Raw_data.zip" contains 28 raw 16S rRNA gene sequence files from the biofilm samples, two KitBlank extraction control sequence files, two mock sequence files, two PBS blank sequence files, two filtered seawater sequence files, and an md5.txt file (designed to test the downloaded files for errors), as well as links accessing online FastQC reports for each file. The data consist of two compressed FASTQ sequence files (paired end forward and reverse reads) per sample (n= 14), and two compressed FASTQ sequence files per control (n= 4).

The files labeled "Biofilm_SRA_metadata.zip" and "Biofilm_MIMARKS.zip" contain metadata files (.csv, .txt, .xlsx) that are SRA and MIMARKS (minimum information about a marker sequence) compliant, based on standards developed by the Genomic Standards Consortium for reporting marker gene sequences (Yilmaz and others, 2011, Nature Biotechnology 29:415-420, doi:10.1038/nbt.1823). The column headers in these metadata files are defined below. An entry of "NA" is defined as "not applicable" and an entry of "ND" is defined as "not determined".

sample_name: a name that you choose for the sample that is concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique.

sample_number: Numeric identifier.

sample_title: Title of sample.

bioproject_accession: The accession number of the BioProject(s) to which the BioSample belongs. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345.

organism: The most descriptive organism name for this sample (to the species, if possible).

collection_date: The date on which the sample was collected. 

env_broad_scale: Terms that identify the major environment type(s) where your sample was collected. 

env_local_scale: Terms that identify environmental entities having causal influences upon the entity at time of sampling.

env_medium: Terms that identify the material displaced by the entity at time of sampling. Recommend subclasses of environmental material.

geo_loc_name: Geographical origin of the sample. Colon used to separate the country or ocean from more detailed information about the location, e.g. "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps"

lat_lon: The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", e.g., 38.98 N 77.11 W

samp_collect_device: Method or device employed for collecting sample.

samp_mat_process: Processing applied to the sample during or after isolation.

samp_store_loc: Name of location where sample was stored.

samp_store_temp: Temperature at which the sample was stored in degrees Celsius.

description: Description of the sample.

contact_name: Primary contact name.

contact_email: Primary contact email.

The file labeled "Biofilm_ASV_Table.zip" contains tabulations of amplicon sequence variants (ASVs), their DNA sequences, their taxonomic identification, and abundance for each sample and controls. The ASV table was produced using QIIME2 (Bolyen and others, 2019, Nature Biotechnology 37:852-857, doi: 10.1038/s41587-019-0209-9). The column headers in the Biofilm_ASV_Table data files (.csv, .txt, .xlsx) are defined as follows:

ASV: amplicon sequence variant, unique identifier generated by QIIME2.

Sequence: DNA sequence.

Taxon: Taxonomy of the DNA sequence, identified to the most specific level.

CnD16B: sample name

CnD17B: sample name

CnD18B: sample name

CnD19B: sample name

CnD21B: sample name

CnD22B: sample name

CnD23B: sample name

CnD24B: sample name

CnD25B: sample name

CnH100B: sample name

CnH101B: sample name

kitblankB: sample name

ourmockB: sample name

PBS2contB: sample name

PsD5B: sample name

Pstr10B: sample name

Pstr4B: sample name

seawaterB: sample name