Bacterial community composition of flocculent matter under a salmonid aquaculture site in Newfoundland, Canada

Abstract

Aquaculture has become a rapidly growing industry: over the past 3 decades, commercial production has steadily increased, and further expansion seems likely. However, the rise of aquaculture has been accompanied by concerns, especially regarding environmental sustainability. Substrates located under aquaculture sites receive large influxes of organic matter that can subsequently create anoxic conditions and thereby impact existing benthic communities. Shifts in the relative abundance of specific groups of bacteria could prove to be important indicators of impact and remediation. Here, we investigated bacterial community composition via 16S rRNA gene sequencing on isolated DNA from flocculent matter samples and associated bacterial mats under a hard-bottom aquaculture site in Newfoundland, Canada. We describe the heterogeneous community present in the flocculent matter, characterized by high relative abundances of the genera Spirochaeta (12%), Prolixibacter (5.6%) and Marinifilum (4.6%). Bacterial mats were not composed of Beggiatoa as often hypothesized, but instead were dominated by the genera Spirochaeta (15%), Prevotella (21%), Meniscus (11%) and Odoribacter (20%). Our findings provide insights into the bacterial composition of flocculent matter deposited on hard substrates and undergoing degradation, and point to 3 unexpected bacterial genera as potential indicators of organic enrichment.