Environmental influences shaping microbial communities in a low oxygen, highly stratified marine embayment

Microbial communities in the marine environment drive biogeochemical and nutrient cycles. However, microbial composition and therefore their role in ecosystems is likely to be strongly influenced by the environment. Here, we examined Macquarie Harbour, a highly stratified system on the west coast of Tasmania, Australia, to determine environmental factors driving microbial diversity. Water was sampled along spatial and environmental gradients to examine the structure and composition of the microbial communities, using high-throughput sequencing. The spatial distribution of the communities was found to be homogenous throughout the harbour’s surface, although it differed from riverine and oceanic samples. In contrast, the distribution and composition of microbial communities varied with depth-related changes in salinity and oxygen. Prokaryotes associated with riverine and brackish waters dominated the oxic surface waters. Phytoplankton metabolite-related bacteria and nitrite oxidizers were abundant at the halocline, whereas microbes linked to the consumption of organic matter, nitrogen and sulphur metabolization inhabited the hypoxic bottom waters and may be acting as major players in oxygen consumption throughout the harbour’s water column. This study provides valuable insights into microbial community ecology in a semi-enclosed and highly stratified environment and will improve our knowledge on how bacterial and archaeal distribution may be influenced by a changing environment.