With 85% of the global oyster reefs destroyed, there is an urgent need for large
scale restoration to benefit from the ecosystem services provided by biogenic
oyster reefs and their associated biodiversity, including microorganisms that
drive marine biogeochemical cycles. This experiment established a baseline for
the monitoring of the bacterial and archaeal community associated with wild oysters,
using samples from their immediate environment of the Voordelta, with cohabiting Crassostreagigas and Ostreaedulis, Duikplaats with only C.gigas attached to rocks, and
the Dansk Skaldyrcentre, with no onsite oysters. The microbial profiling was carried
out through DNA analysis of samples collected from the surfaces of oyster
shells and their substrate, the sediment and seawater. Following 16S rRNA
amplicon sequencing and bioinformatics, alpha indices implied high species
abundance and diversity in sediment but low abundance in seawater. As expected,
Proteobacteria, Bacteroidetes, Firmicutes and Thaumarchaeota dominated the top
20 OTUs. In the Voordelta, OTUs related to Colwellia, Shewanella and Psychrobium differentiated the oysters collected from a reef with
those attached to rocks. Duikplaats were distinct for sulfur-oxidizers Sulfurimonas and sulfate-reducers from
the Sva 0081 sediment group. Archaea were found mainly in sediments and the
oyster associated microbiome, with greater abundance at the reef site, consisting mostly of Thaumarchaeota from the
family Nitrosopumilaceae. The oyster
free site displayed archaea in sediments only, and algal bloom indicator
microorganisms from the Rhodobacteraceae, Flavobacteriaceae family and genus [Polaribacter]huanghezhanensis, in addition to the ascidian symbiotic partner, Synechococcus.
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