Microbes and the global carbon cycle research projects
Adaptive evolution of anaerobic methanotrophic (ANME) archaea mediating methane oxidation in freshwater environments
Dr. Simon McIlroy
Methane is a greenhouse gas 28 times more potent than carbon dioxide. Anaerobic oxidation of methane (AOM) is a key biological process estimated to mitigate the release of up to 90% of methane into the atmosphere in some environments, making it a critical consideration for climate change models. This process is mediated by phylogenetically diverse lineages of anaerobic methanotrophic (ANME) archaea. The overall aim of this work will be to uncover the metabolic diversity of the Methanoperedenaceae and to understand the evolutionary mechanisms responsible for these adaptations.This project will integrate multi-omic approaches with novel visualisation techniques and bioinformatic analyses to increase our understanding of the archaeal family Methanoperedenaceae. More specifically, it will help us increase the genomic representation and identify the metabolic diversity of the family, gain insight into the evolutionary processes shaping metabolic capabilities of the family, and elucidate the importance of these microorganisms to global biogeochemical cycles and the Earth’s climate.
The proposed research will help to identify important links between the global climate and the metabolic activities of specific microorganisms. Increased global temperatures have already had substantial impacts on freshwater and marine ecosystems in Australia, negatively affecting agricultural production, tourism and human health. Our ability to minimise the impact of climate change will depend on accurate predictive models. Such models require an understanding of the microorganisms involved in methane cycling in the environment.
Understanding the ecology of microorganisms and phages involved in the consumption of short-chain hydrocarbons
Ms. Beatriz Delgado Corrales
The aim of the project is to analyse the microbial and viral community composition and dynamics of alkane rich environments, with an emphasis on environments where propane is consumed. We are using metagenomics and transcriptomics to recover and analyse bacteria and the bacteriophages that infect them using data from a bioreactor fed with propane and nitrate. The community structures will also then be visualised using a new fluorescence in situ hybridisation technique called GenomeFISH. So far, we have recovered a new species of Symbiobacteria that may be capable of anaerobic propane oxidation, along with multiple other Patescibacteria in the same bioreactor. This group of bacteria have small genomes and lack biosynthetic capacities; thus, it is a possibility that they are symbionts of the Symbiobacteria. Some phages that infect Patescibacteria have also been recovered, which might play a role in the community dynamics. Understanding mechanisms involved in the consumption and production of hydrocarbons might lead to the discovery of new microorganisms or enzymes that help us mitigate the effects of anthropogenic climate change and pollution in our ecosystems.
Parasite or symbiont: Investigation of the relationship between Patescibacteria and Goldbacteria
Ms. Eilish McMaster
The Tyson lab are involved in a longitudinal metagenomic study of a thawing permafrost in Stordalen, Sweden. Their previous work found a strong correlation in the relative abundances of a Patescibacteria and Goldbacteria representative in the metagenomic data across the mire. Patescibacteria have been hypothesised to be parasites but have not previously been observed interacting with other bacteria. The aim of this project is to characterise the relationship between the two representatives in Stordalen mire and to determine whether it is parasitic or commensal. The relationship between the Patescibacteria and Goldbacteria representatives is being investigated using existing metagenomic sequence data (Illumina and NovaSeq short reads). This project will focus on metabolic analysis, coevolution analysis, and compositional data analysis.
So far, the metabolism of both potential symbionts has been reconstructed and coevolution analysis has confirmed their evolutionary histories are significantly correlated. Phylum trees have been reconstructed for Goldbacteria and Patescibacteria, >18 de novo genomes have been assembled for each representative, and the representatives have been confirmed to be proportional across 406 samples from Stordalen mire. Further analyses will focus on what genes are enriched in these species and expand upon the coevolution analyses. Observation of a Patescibacteria interaction with other bacteria would be novel and contribute to our understanding of this diverse and ubiquitous phylum.
Identifying emergent ecosystem responses through genes-to-ecosystems integration at Stordalen Mire
Prof. Gene Tyson and Dr. Ben Woodcroft
Soils in the permafrost region hold twice as much carbon as the atmosphere does – almost 1,600 billion tonnes – and permafrost thaw induced by climate change makes this carbon available for microbial degradation. Despite having major implications for human health, prediction of the magnitude of carbon loss as carbon dioxide (CO2) or methane (CH4) is hampered by our limited knowledge of microbial metabolism of organic matter in these environments. Genome-centric meta-omic analysis of microbial communities provides the necessary information to examine how specific lineages transform organic matter during permafrost thaw. Stordalen Mire in northern Sweden has been subject to a decade of intense molecular and biogeochemical study, and almost 50 years of climate and vegetation research providing a unique opportunity to examine how microbial communities are changing alongside our climate.
Led by Prof Tyson and Dr Woodcroft, the overall aim of this project is to use integrated meta-omic approaches to examine how individual microbial community members and entire communities assemble, adapt and acclimatise to changing environmental conditions. Ultimately, this work will help to identify important links between the global climate and dynamics of microbial communities.
This work will be part of a recently awarded global EMERGE program funded by the American National Science Foundation. The goal of EMERGE is to create models to help predict ecosystem response to climate change, and this project will generate critical knowledge for these models using a ‘genes-to-ecosystems-to-genes' approach.