Bacterial Community Dynamics in an Oyster Hatchery in Response to Probiotic Treatment

Abstract

Larval oysters in hatcheries are susceptible to diseases caused by bacterial pathogens, including Vibrio spp. Previous studies have shown that daily addition of the probiotic Bacillus pumilus RI06-95 to water in rearing tanks increases larval survival when challenged with the pathogen Vibrio coralliilyticus. We propose that the presence of probiotics causes shifts in bacterial community structure in rearing tanks, leading to a net decrease in the relative abundance of potential pathogens. During three trials spanning the 2012-2015 hatchery seasons, larvae, tank biofilm, and rearing water samples were collected from control and probiotic-treated tanks in an oyster hatchery over a 12-day period after spawning. Samples were analyzed by 16S rRNA sequencing of the V4 or V6 regions followed by taxonomic classification, in order to determine bacterial community structures. There were significant differences in bacterial composition over time and between sample types, but no major effect of probiotics on the structure and diversity of bacterial communities (phylum level, Bray-Curtis k = 2, 95% confidence). Probiotic treatment, however, led to a higher relative percent abundance of Oceanospirillales and Bacillus spp. in water and oyster larvae. In the water, an increase in Vibrio spp. diversity in the absence of a net increase in relative read abundance suggests a likely decrease in the abundance of specific pathogenic Vibrio spp., and therefore lower chances of a disease outbreak. Co-occurrence network analysis also suggests that probiotic treatment had a systemic effect on targeted members of the bacterial community, leading to a net decrease in potentially pathogenic species.

Mechanistic molecular responses of the giant clam Tridacna crocea to Vibrio coralliilyticus challenge

“…In recent years, the breeding of giant clams has attracted increasing attention worldwide. However, diseases caused by bacterial pathogens have been reported to result in losses in aquaculture populations of these commercially important shellfish [7]. Pathogenic vibrios can affect larval stages of cultured bivalves and are also involved in diseases of juveniles and adults [8].…”

Diversity and Function of the Eastern Oyster (Crassostrea virginica) Microbiome

“…Following functional inferences obtained from the metabolic reconstruction of the oyster Mollicutes MAG, emphasis was placed on the composition and diversity of Mollicutes across different oyster microbiomes obtained from this and other studies. A total of three additional datasets were identified from public databases, including the community profiling of gut samples from the adult eastern oyster [39], the profiling of adult eastern oyster biodeposits [40], and the profiling of eastern oyster larvae homogenate [27]. Raw data from these prior studies were downloaded and reanalyzed with a standardized pipeline to minimize potential inconsistencies caused by variation in computational procedures (Materials and Methods).…”

“…Relative abundance of a taxon was calculated through dividing the ASV counts of that taxon in a given sample by the total number of ASVs in the same sample. The raw reads from three previous eastern oyster microbiome studies were retrieved from the NCBI Sequence Read Archive (SRA) linked to the following BioProject accession numbers: PRJNA518081 [27], PRJNA504404 [40], and PRJNA386685 [39] and subjected to the same analyses as specified above. Based on metadata from the SRA, samples that were not from the eastern oyster (water, mussels, etc.)…”

“…Tissues that showed a significant difference between uninfected and P. marinus infected samples were marked: * p-value < 0.05. [39], larvae homogenate samples [27], and biodeposit samples [40]. Pairwise statistical significance was assessed with Tukey's Honest Significant Differences test.…”

“…hemolymph, gill, mantle, and gut) when compared with microbial communities of the surrounding seawater, suggesting potential host selections that lead to the enrichment of specific groups [20]. Multiple factors, including changes in environmental conditions [15,17,21,22], diet [23], infection [24][25][26], and the use of probiotics [27], have been shown to influence the composition of oyster microbiomes during certain life stages and among different tissue types. All these studies set the stage for further investigating the taxonomic composition and functional potentials of the oyster microbiomes across different tissues.…”