Single cell genomics and characterisation of the atmospheric methane oxidizing clade USC alpha and their response to climate change

点击翻译按钮获取中文摘要

Methane is a very potent greenhouse gas, at least 20 times more effective than carbon dioxide. It has a current atmospheric concentration of about 1.8 ppmv. The largest biogenic sources of atmospheric methane include natural wetlands, rice agriculture, livestock, landfills, termites and oceans. The most important biological sinks for methane in the biosphere are upland soils, especially forest soils which show the greatest methane oxidation consumption capability of any soil ecosystem. Methane from the atmosphere (ie at very low concentrations) is taken up by a specific group of microorganisms in those soils. The bacterial "upland soil cluster alpha" clade (USCa clade) in forest soils, which has been previously detected solely by cultivation-independent molecular biological techniques, is assumed to represent the methanotrophic bacteria adapted to the trace level of atmospheric methane which play an essential part in the removal of methane from the atmosphere. We know from studying the cycles of climatically important gases such as methane that microbial consumption is an extremely important process which is greatly influenced by climate change. Global warming and land use change will have a significant impact on the microorganisms in forest soil by changing the environmental and soil conditions (e.g. increased temperature, changing water content, increased methane and carbon dioxide concentration, deforestation and nitrogen fertilization due to agricultural use).However, since bacteria of the USCa clade have not be isolated and grown in culture in the laboratory, little is known about the about the identity, the physiology, biochemistry and metabolic capabilities of these microorganisms and how they respond to changes in the environment ie how their activities are regulated in response to environmental change.Using powerful molecular biology-based techniques, I therefore aim to investigate the identity and abilities of the USCa by sorting single cells of this clade from soil and looking at the DNA of the cells, the genome. Most bacteria and archaea look alike, so we frequently use DNA and RNA sequences to study their roles and activity in nature. I will use the genome information which contains how a microorganism works (the metabolic blueprint of the microorganism) and what it needs in terms of nutrients, to enrich and isolate bacteria of the USCa clade from soils that have high activities in oxidising methane at atmospheric concentrations. The purification of the enzyme responsible for the high-affinity methane oxidation activity from bacteria of the USCa clade will give us significant insight into the regulation of its methane oxidation activity. Additionally, I will apply tools developed by myself and collaborators to analyse total DNA and RNA of soil samples and enrichments, termed metagenomics and metatranscriptomics, respectively. This will further enable us to determine how the USCa bacteria will react to rising temperatures and changes in land use. The use of state-of-the-art techniques will allow me to identify the atmospheric methane oxidizing USCa bacteria in forest soil, and to determine how their activity is controlled and influenced by a changing climate and changes in land use (e.g. deforestation and changes in agricultural practice). In addition, this information will be used to survey for the presence of USCa bacteria in different geographical locations and to look at the long-term effect of different environments on the evolution of these microorganisms.The results of this project will provide robust mechanistic data with which to predict the impact of climate change and land use on health and functioning of the global sink strength for atmospheric methane in forest/upland soils.