Oral Presentation Australian Microbial Ecology 2022

Exploring microbial community dynamics and their ecological functions in a subtropical estuary - bay ecosystem (#29)

Apoorva Prabhu 1 , Simon J McIlroy 2 , Matthew DeMaere 3 , Christian Rinke 1
  1. Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia
  2. Centre for Microbiome Research, Queensland University of Technology, Brisbane, Queensland, Australia
  3. University of Technology Sydney, Sydney, New South Wales, Australia

Tropical and subtropical river systems account for nearly 69% of Australia's estuaries, play an important role in promoting primary productivity, and provide valuable ecosystem services, such as transportation and removal of organic matter to the oceans via river discharge1. Estuaries host microbes from multiple biomes (freshwater, terrestrial and marine) producing unique, thriving communities that exploit these variable physico-chemical gradients2,3. The Brisbane River is the largest tidal estuary in subtropical South East Queensland and characterised by high nutrient inputs from urban runoff, which are eventually discharged in the saline Moreton Bay.

There is limited genomic information on microbial players in the Brisbane River estuary since previous field monitoring approaches relied exclusively on 16S rRNA gene surveys4. In this study, we applied a spatio-temporal sampling strategy combining genome-resolved metagenomics and physico-chemical measurements to elucidate microbial community structure, phylogeny and function across three sites in the estuary - bay ecosystem.

We recovered 2,459 dereplicated MAGs (>50% completeness and <10% contamination) from 22 bacterial and 4 archaeal phyla including some lineages rarely seen in brackish estuaries. We identified sharp contrasts in community structure and functions across the three sites and seasons, indicating strong habitat preferences by microbes in the bay and brackish estuary waters. These environments provide unique niches for subgroups of marine lineages such as SAR11, SAR324, SAR86, Flavobacteraceae, Rhodobacteraceae suggesting that, these taxa have adapted to a wide salinity range. Microbial players in biogeochemical processes (carbon, nitrogen and sulphur cycling) also differed considerably between sites, indicating their contribution to nutrient cycling in the surface water microbiome. In addition, we identified patterns in microbial community responses to anthropogenic stressors such as the spread of antimicrobial resistance genes, abundance of potential pathogenic microbes, viral load, and plastic degrading genes.

In summary, our work provides an in-depth analysis of the brackish water microbiome and their importance in the context of their adaptation and evolutionary strategies to the dynamic conditions in the ecosystem.

 

  1. Bucher, D. & Saenger, P. An Inventory of Australian Estuaries and Enclosed Marine Waters: An Overview of Results. Aust. Geogr. Stud. 29, 370–381 (1991).
  2. CSIRO PUBLISHING | Marine and Freshwater Research. https://www.publish.csiro.au/mf/MF00084.
  3. Bauer, J. E. et al. The changing carbon cycle of the coastal ocean. Nature 504, 61–70 (2013).
  4. Beale, D. J. et al. A Community Multi-Omics Approach towards the Assessment of Surface Water Quality in an Urban River System. Int. J. Environ. Res. Public. Health 14, 303 (2017).