Determining the Composition of Resident and Transient Members of the Oyster Microbiome

Abstract

To better understand how complex microbial communities become assembled on eukaryotic hosts, it is essential to disentangle the balance between stochastic and deterministic processes that drive their assembly. Deterministic processes can create consistent patterns of microbiome membership that result in persistent resident communities, while stochastic processes can result in random fluctuation of microbiome members that are transient with regard to their association to the host. We sampled oyster reefs from six different populations across the east coast of the United States. At each site we collected gill tissues for microbial community analysis and additionally collected and shipped live oysters to Northeastern University where they were held in a common garden experiment. We then examined the microbiome shifts in gill tissues weekly for 6 weeks using 16S rRNA gene amplicon sequencing. We found a strong population-specific signal in the microbial community composition of field-sampled oysters. Surprisingly, the oysters sampled during the common garden experiment maintained compositionally distinct gill-associated microbial communities that reflected their wild population of origin, even after rearing them in a common garden for several weeks. This indicates that oyster gill-associated microbiota are predominantly composed of resident microbes specific to host population, rather than being a reflection of their immediate biotic and abiotic surroundings. However, certain bacterial taxa tended to appear more frequently on individuals from different populations than on individuals from the same population, indicating that there is a small portion of the gill microbiome that is transient and is readily exchanged with the environmental pool of microbes. Regardless, the majority of gill-associated microbes were resident members that were specific to each oyster population, suggesting that there are strong deterministic factors that govern a large portion of the gill microbiome. A small portion of the microbial communities, however, was transient and moved among oyster populations, indicating that stochastic assembly also contributes to the oyster gill microbiome. Our results are relevant to the oyster aquaculture industry and oyster conservation efforts because resident members of the oyster microbiome may represent microbes that are important to oyster health and some of these key members vary depending on oyster population.

Core Community Persistence Despite Dynamic Spatiotemporal Responses in the Associated Bacterial Communities of Farmed Pacific Oysters

“…We found clear structuring between sites that was evident in every sampling period. This is consistent with the spatial structuring observed in C. gigas [29] and Sydney Rock Oyster, Saccostrea glomerata [41] in Australian farms and the eastern oyster, Crassostrea virginica, across the east coast of the USA [42].…”

Host genomic variation shapes gut microbiome diversity in threespine stickleback fish

“…This degree of experimental control has been implemented more commonly for plant microbiome studies [56][57][58][59] , but it is logistically difficult for studies of free-living animal species. Because animal experiments with unrestricted co-housing require the tracking of individuals via marking or genotyping, a more convenient alternative has been to keep subjects with different genotypes physically separated but generally exposed to similar conditions 28,29,[60][61][62][63] . In contrast, we incorporated unrestricted co-housing in our current study, an approach taken in only a few other studies [64][65][66] .…”

Host genomic variation shapes gut microbiome diversity in threespine stickleback fish

“…This degree of experimental control has been implemented more commonly for plant microbiome studies [56][57][58][59] , but it is logistically difficult for studies of free-living animal species. Because animal experiments with unrestricted co-housing require the tracking of individuals via marking or genotyping, a more convenient alternative has been to keep subjects with different genotypes physically separated but generally exposed to similar conditions 28,29,[60][61][62][63] . In contrast, we incorporated unrestricted co-housing in our current study, an approach taken in only a few other studies [64][65][66] .…”