Do trace gas oxidising bacteria help build soil on volcanic rock?

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BackgroundUnderstanding how soil establishes is crucial to be able to restore degraded soil. 80% of the world's soils are of volcanic origin, and these are among the most fertile. Volcanism is a primary process of land formation serving as model system to study soil formation. After lava solidifies, microbes colonise it by obtaining energy from light or from oxidation of chemicals. Previously, Hernandez examined the diversity of bacteria following a chrono-sequence path (i.e. soils of different ages) on Llaima volcano, Chile and discovered that a specific class of bacteria (Ktedonobacterales), dominated newly-formed soil1. Very little is known about Ktedonobacterales, but they contain genes encoding for enzymes that enable them to grow using H2 and CO gases2. Hernandez's work on volcanic soils, and that of others, has shown a dominance of CH4, H2 and CO-consuming microbes in the first decades of volcanic soil succession2,3,4,5,6. These trace gases in the atmosphere provide energy and carbon sources for bacteria that colonise volcanic rocks and convert these substrates into biomass and hence organic carbon, which in turn make a substantial contribution to soil formation on volcanic rocks.HypothesisThe overarching hypothesis is that CO-oxidising microorganisms, and their ability to consume other gases (e.g. H2), play a key role in producing organic matter that initiates soil formation. Objectives1) To determine the role of trace gases and the microbes that consume them in the development of volcanic soils. 2) To determine the metabolic pathways common to trace-gas metabolising microbes, particularly Ktedonobacterales, inhabiting volcanic soils.Work PackagesWP-1. Soil incubations and community profiling (years 0-1.5)The student will characterise the microbial community using cultivation-independent methods addressing the questions: i) Is CO-oxidation capacity greatest in early volcanic deposits? ii) What are the (other) important carbon and energy sources for the microbial community in early volcanic deposits? The student will join sampling campaigns in Chile, prepare microcosms incubations and learn interdisciplinary techniques including qPCR, gas-chromatography measurements, DNA shotgun sequencing and bioinformatics. Deliverables: 1) CO oxidation rates along successional gradients. 2) Identify bacteria and their functional guilds along succession, leading to publications in high quality microbial ecology journals.WP-2. Bacterial isolation and characterisation (years 0.8-3.0): The student will assess the potential of microbial communities in volcanic deposits, addressing the questions: i) Are Ktedonobacterales able to oxidise CO and H2? ii) Which other bacteria from these environments are able to oxidise CO? iii) How are other primary sources of carbon and energy processed? The PhD student will learn cultivation-dependent techniques including enrichment and isolation of bacteria, genome sequencing, gas-chromatography measurements, and bioinformatics. Deliverables: 1) Successful isolation of bacteria from volcanic soils and characterisation of isolates and gene expression networks. 2) Potential CO, H2 and CH4 oxidation rates and kinetic parameters in these isolates, leading to high quality publications in environmental microbiology journals.