Data Release
Prokaryotic Communities From Marine Biofilms Formed on Stainless Steel Plates in Coral Mesocosms – Raw and Processed Data
By Christina A. Kellogg,1 James S. Evans,1 and Julie J. Voelschow2
1 U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
2 Cherokee Nation System Solutions
Summary
The files in this data release 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.
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, please see the README file, README_Biofilm.txt, and metadata files.
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.
Data
| File Name and Description | Metadata (XML format) | Metadata (text format) | Download File |
|---|---|---|---|
| Biofilm_Raw_Data.zip Zip file containing raw sequencing data (FASTQ fastq.gz) and FGDC metadata (.txt and .xml) |
Biofilm_FGDC_metadata.xml | Biofilm_FGDC_metadata.txt | Biofilm_Raw_Data.zip (239.6 MB) |
| Biofilm_ASV_Table.zip Zip file containing tabulations of amplicon sequence variants (ASVs), their DNA sequences, their taxonomic identification, and abundance (number of sequence reads) for each of the samples and controls (.csv, .txt, .xlsx), and FGDC metadata (.txt and .xml) |
Same as above | Same as above | Biofilm_ASV_Table.zip (1.3 MB) |
| Supplemental information | |||
| Biofilm_MIMARKS.zip MIMARKS-compliant sampling metadata (.csv, .txt, .xlsx) |
Not applicable | Not applicable | Biofilm_MIMARKS.zip (19 KB) |
| Biofilm_SRA_metadata.zip Laboratory process metadata (.csv, .txt, .xlsx) |
Not applicable | Not applicable | Biofilm_SRA_metadata.zip (53 KB) |
| README_Biofilm.txt Readme file explaining data (.txt) |
Not applicable | Not applicable | README_Biofilm.txt (6 KB) |
Figure 1. Samples were created at the Smithsonian Marine Station, in Fort Pierce, Florida.
Suggested Citation
Kellogg, C.A., Evans, J.S., and Voelschow, J.J., 2022, Prokaryotic communities from marine biofilms formed on stainless steel plates in coral mesocosms – raw and processed data, U.S. Geological Survey data release., https://doi.org/10.5066/P9T6NW4V.