The microbiome of seafloor sediments near oyster communities on intertidal shorelines in coastal Alabama were compared to sludge sediments collected on a fiberglass catchment beneath submerged oyster aquaculture equipment. The top 1 cm of shoreline sediments from three coastal Alabama sites (Mobile Bay, Portersville Bay and Bayou LaBatre) spanning different levels of salinity and National Shellfish Sanitation Program classifications (conditionally approved and prohibited) were sampled with a sterile spoon during intertidal exposure on November 8, 2021. Shoreline sediments from these three areas primarily consisted of coarse sand whereas the sediment sample collected from the fiberglass deck of a submersible oyster aquaculture vessel (Shellevator) positioned ~100m offshore from the Portersville Bay shoreline site had a sludge-like consistency likely from the droppings of feces and pseudo-feces that had accumulated on a flat fiberglass deck.
The purified metacommunity DNA from triplicate samples at each location was subjected to high-throughput amplicon sequencing (HTS) targeting the V4 region of the 16S rRNA gene using an Illumina MiSeq platform with 250 bp paired-end kits. The resulting HTS datasets were demultiplexed into FASTQ files, quality-checked, and denoised with DADA2 to generate amplicon sequence variants (ASVs). Data were then rarefied, and taxonomic identifications were assigned using the Silva database. All bioinformatics analyses were conducted using tools and commands available in Quantitative Insights into Microbial Ecology (QIIME2; v2022.2).
The three most prevalent bacterial genera identified in the Portersville Bay sludge sample were 10-fold higher than any of the shoreline sediment samples and >100-fold more abundant than in the Portersville Bay shoreline site (Anaerococcus: 10.86%/0.1%), (Tyzzerella: 7.48%/0.0%) and (Clostridioides: 4.51%/0.07%). Genes associated with carbohydrate, lipid and amino acid metabolism generally occurred at a higher frequency than in the Portersville Bay sludge sample than in the three shoreline sediment samples.
The microbiome of sludge from oyster secretions and excretions is readily distinguishable from than seafloor sediments associated with natural oyster communities. Examination of the sludge microbiome may provide insight into the oyster community health status analogous to early identification of community public health threats like COVID 19 by sampling sewage treatment plant influents. This approach could be implemented to identify the cause and/or provide an early signal for the onset of Sudden Unusual Mortality Syndrome that has plagued oyster in coastal Alabama and other locations in recent years.