Comparison of preservation and extraction methods on five taxonomically disparate coral microbiomes
All animals are host to a multitude of microorganisms that are essential to the animal’s health. Host-associated microbes have been shown to defend against potential pathogens, provide essential nutrients, interact with the host’s immune system, and even regulate mood. However, it can be difficult to preserve and obtain nucleic acids from some host-associated microbiomes, making studying their microbial communities challenging. Corals are an example of this, in part due to their potentially remote, underwater locations, their thick surface mucopolysaccharide layer, and various inherent molecular inhibitors. This study examined three different preservatives (RNAlater, DNA/RNA Shield, and liquid nitrogen) and two extraction methods (the Qiagen PowerBiofilm kit and the Promega Maxwell RBC kit with modifications) to determine if there was an optimum combination for examining the coral microbiome. These methods were employed across taxonomically diverse coral species, including deep-sea/shallow, stony/soft, and zooxanthellate/azooxanthellate: Lophelia pertusa, Paragorgia johnsoni, Montastraea cavernosa, Porites astreoides, and Stephanocoenia intersepta. Although significant differences were found between preservative types and extraction methods, these differences were subtle, and varied in nature from coral species to coral species. Significant differences between coral species were far more profound than those detected between preservative or extraction method. We suggest that the preservative types presented here and extraction methods using a bead-beating step provide enough consistency to compare coral microbiomes across various studies, as long as subtle differences in microbial communities are attributed to dissimilar methodologies. Additionally, the inclusion of internal controls such as a mock community and extraction blanks can help provide context regarding data quality, improving downstream analyses.
Citation Information
Publication Year | 2021 |
---|---|
Title | Comparison of preservation and extraction methods on five taxonomically disparate coral microbiomes |
DOI | 10.3389/fmars.2021.684161 |
Authors | Zoe A. Pratte, Christina A. Kellogg |
Publication Type | Article |
Publication Subtype | Journal Article |
Series Title | Frontiers in Marine Science |
Index ID | 70221762 |
Record Source | USGS Publications Warehouse |
USGS Organization | St. Petersburg Coastal and Marine Science Center |
Related Content
Coral Microbiome Preservation and Extraction Method Comparison-Raw Data
Related Content
- Data
Coral Microbiome Preservation and Extraction Method Comparison-Raw Data
The files in this data release are the raw 16S rRNA gene amplicon DNA sequence files from 90 samples of tropical and cold-water corals, as well as sequence files from a mock community and extraction blanks for the kits used for DNA extraction. The tropical coral samples (three species) were collected under permit FKNMS-2017-064 (Kellogg) in March 2018 from a nursery in the Florida Keys National Ma - Connect