Genomic indicators of nitrogen cycling processes in sediments of Port Phillip Bay

Submission note: A thesis submitted in total fulfilment of the requirements for the degree of Doctor of Philosophy to the Department of Animal, Plant and Soil Sciences, School of Life Sciences, College of Sciences, Health and Engineering, La Trobe University, Bundoora, Victoria.

Thesis with publications.

Port Phillip Bay (PPB), Victoria, Australia is a shallow, semi-enclosed embayment with a slow exchange rate to the open ocean. Due to these physical factors, the system is at risk of nutrient enrichment, yet due to the removal of nitrogen (N) by the sediment microbial community, water column primary productivity remains nitrogen limited. A combination of molecular measures (qPCR/RTqPCR, 16S rRNA, metatranscriptomics) was used in conjunction with benthic flux denitrification efficiency (DE percent) and sediment chemistry to assess changes in the structure and function of the sediment microbial community in PPB. Sediment was collected from three locations that vary in their proximity to nutrient inputs: Hobsons Bay (HB) and Long Reef (LR) are adjacent to the two main sources of nitrogen inflows into PPB and the centre of PPB (CPPB) is distant from coastal inputs. The objectives of this research were to investigate microbial N-cycling within the sediments of PPB, identify the physicochemical drivers which select for spatial and temporal differences in microbial N-cycling pathways, assess the composition and stability of the sediment microbial community in relation to changes in the DE percent , generate a metatranscriptomic assembly for the sediments of PPB and determine if site-based differences exist between community-wide gene expression profiles. In summary, the application of multiple molecular approaches has identified that the sediments of PPB harbour spatially and functionally complex microbial communities. The microbial community composition, the dominant N-cycling processes and the relationship between these genes and the sediment environment as well as the dominant community transcript profiles are spatially unique. The differences in the microbial community composition and dominant microbial functions between HB and CPPB suggest that these sediment environments are distinct microbial environments which explains why the DE percent behaves uniquely between these locations. The influence of season was not identified within the microbial community of CPPB sediments. Whereas, the composition and function of the sediment microbial community in HB responds to seasonal differences between Spring and Summer. This thesis has identified several potential indicator microbial taxa and functions associated with the sediment nitrogen-cycle that could be further developed as biomarkers for whole ecosystem monitoring of N-cycling in coastal sediments.