Microbes, contaminants, and molecular biomonitoring: Structural and functional sediment community responses to multiple stressors

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Copyright: Birrer, Simone
The development of coastal areas often results in the introduction of a suite of contaminants to these highly productive systems. Contaminants accumulate in soft sedimentary environments where they may affect resident microorganisms responsible for driving major biogeochemical cycles and providing a range of ecosystem services. The cumulative effects of multiple contaminants can impact both the structure and function of microbial communities. These cumulative effects are not yet well understood, however they have potential repercussions at local, regional and global scales. Microbes are inherently difficult to study as the majority cannot be cultured in the laboratory. Modern molecular techniques enable the study of microbes at a genetic level. Targeted gene sequencing and meta-omics provide snapshots of community structure and function. However, their application as biomonitoring tools is still in its infancy. In this thesis, I investigate targeted sequencing for ecosystem health assessment and assess metatranscriptomics as a new biomonitoring tool. I use experiments and surveys to test the value of molecular techniques in informing ecosystem-wide consequences of structural and functional changes. Targeted sequencing revealed that bacterial communities are more sensitive to multiple disturbances than eukaryotes (traditionally used for biomonitoring) and are potentially better indicators of ecosystem change. Metatranscriptomics proved to be a sensitive, reliable and replicable tool, which provided rapid, ecologically relevant, information. Sediment communities exposed to metals and organic enrichment had significantly altered gene expression profiles that may reflect accumulation of toxic compounds and increased production of greenhouse gases. Surveys revealed that sediment communities impacted by legacy contaminants had reduced primary productivity and greater potential for community fracturing, which itself may lead to lower productivity and lower remediation capacity. Molecular approaches generated information that could revolutionise biomonitoring approaches. However, the lack of extensive genetic reference libraries and complex data processing requirements continue to pose challenges to the routine adoption of these techniques. My research highlights the power of molecular approaches for assessing ecosystem health and the consequences of urban contaminants on community structure and function.
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Birrer, Simone
Johnston, Emma
Dafforn, Katherine
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PhD Doctorate
UNSW Faculty
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