Macquarie University
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The distribution and function of microbes in Eastern Australian coal seams

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posted on 2022-03-28, 17:04 authored by Silas Harry Watts Vick
Coal is a sedimentary rock containing fossilised organic matter derived from ancient plant material which has been sequestered underground in subsurface coal seams. From a microbial perspective, coal seams represent a type of subsurface oasis containing all the essential components required for life: water, warmth and abundant carbon in the form of fossilised organic material. In coal beds microbes work in complex syntrophic associations to degrade complex, recalcitrant fossilised organic matter to methane. This process mobilises fossilised carbon in the geosphere to the biosphere and contributes to global carbon cycles. Additionally, the methane often accumulates and represents a valuable energy resource with a potential lower carbon intensity when compared to coal. Despite the environmental and economic importance of this process, little is known about the microbial ecology microbial communities in coal seam. The current body of work aimed to investigate the microbial ecology of coal seam microbial communities with a focus on microbial distributions at the fine and global scales and the functional roles of individual bacterial taxa in coal seams. A range of approaches and techniques have been undertaken in this body of work to interrogate these questions. A 16S rRNA dataset of coal seam microbial operational taxonomic units (OTUs) was constructed from a large set of eastern Australian formation water amplicon surveys and published studies. This dataset facilitates global comparisons of coal seam taxa and identified a number of taxa with global distributions as well as others with more endemic distributions. A study of ecological succession and physical niche partitioning for microbial communities from three eastern Australian coal basins was performed and traditional ecological theories used hypothesise microbial roles. This study identified that coal seams harbour distinctly different coal degrading microbial communities attached to the coal surface and living planktonically in associated formation waters, supporting previous suggestions that some microbial taxa may preferentially attach to coal surfaces. Multiple modes of attachment were also identified and biofilm formation was observed as an attachment mechanism used by the high methane yielding Surat Basin coal seam community. A study whereby geochemical fractionation of coal organics was coupled with enrichment culture microcosms was performed in an effort to identify the biodegradable components of coal and the specific taxa tied to these biodegradation phenotypes. This study identified 81 taxa implicated in the degradation of specific classes of coal organics with proliferating taxa being identified on all organic fractions. Of particular note, this study also identified the kerogen fraction, generally thought to be the most recalcitrant, as the coal fraction from which the most biogenic methane was produced. A finding which may explain why coal degrading microbial communities in oil reservoirs differ so significantly from those seen in coal seams. Classical isolation of microbes into axenic culture was also pursued in the current body of work in an attempt to definitively elucidate catabolic roles for the curious facultatively aerobic microbes found in strictly anaerobic coal seam microbial communities. This isolation effort resulted in the generation of thirteen axenic bacterial isolates which were subsequently interrogated with genomic sequencing and catabolic phenotyping. Results of this analysis suggest that these aerobic taxa typically have roles involved in biomass recycling with many harbouring diverse catabolic potentials which likely facilitate a lifestyle as a subsurface generalist rather than coal seam endemic. Comparative genomic analysis of coal associated Stappia indica genomes with highly phylogenetically related marine and freshwater S. indica genomes revealed a suite of genes associated with the subsurface coal seam environment. These genes were enriched in processes including: viral defence, secondary metabolite production, the Calvin cycle, polyamine metabolism and polypeptide membrane uptake transporters. This finding provides an insight into some of the environmental and evolutionary pressures experienced by microbes in subsurface coal seam environments.


Table of Contents

Chapter 1. General introduction -- Chapter 2. The coal seam Mmcrobiome (CSMB) reference set, a lingua franca for the microbial coal-to-methane community -- Chapter 3. Microbial communities deploy divergent strategies for degrading coal in the deep subsurface -- Chapter 4. Who eats what? Unravelling microbial conversion of coal to methane -- Chapter 5. Genomes of subsurface coal seam microbes show catabolic flexibility and roles in biomass recycling -- Chapter 6. Comparative genomics of Stappia isolates from coal seam formation waters reveals a functionally distinct clade within the phylogenetically cohesive Stappia indica species -- Chapter 7. General discussion.


Bibliography: pages 285-321 Empirical thesis.

Awarding Institution

Macquarie University

Degree Type

Thesis PhD


PhD, Macquarie University, Faculty of Science and Engineering, Department of Molecular Sciences

Department, Centre or School

Department of Molecular Sciences

Year of Award


Principal Supervisor

Ian T. Paulsen

Additional Supervisor 1

Sasha Tetu

Additional Supervisor 2

David Midgley


Copyright Silas Harry Watts Vick 2018. Copyright disclaimer:






1 online resource (xxi, 234 pages) illustrations (some colour)

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