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

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.

The project will provide essential data on methane cycling in soil, the factors controlling the sink strength of upland soils for methane and how this sink will respond to ongoing climate warming and land use change. It will develop molecular tools to investigate the physiology, activity, distribution and diversity of the key microorganisms (the upland soil cluster alpha, USCa) involved in this process and provide understanding of their response to environmental changes.

This research will have high impact because of the timely and urgent need of science and society, to better understand and predict the impacts of global climate change on environments worldwide. In particular because the uptake of methane by soils represents the largest and most effective biological sink for atmopsheric methane.

This research should benefit scientists worlwide, involved in research on terrestrial microbiology and global climate change, and will be of great interest to stakeholders involved in the environment and climate change (Defra, DECC, the MetOffice, IPCC, the Environment Agency). I will participate in end-user led meetings during the course of the project and engage with key individuals in the scientific community who are interested in integrating the data from this project in global flux models of methane and predictions concerning global climate change (Le Quere and Suntharalingum at UEA and Smith at Aberdeen). Discussions will als0 be initiated with Forest Research to advise government on important outcomes related to greenhouse gas emissions from natural forests and biomass plantations.

As outlined in more detail in the Pathways to Impact, there are other potential applications of this work. The possibility of exploiting new, high-affinity methane oxidation enzyme systems and methanotrophs during this reserach could also benefit biotechnology and industries. I will make contact with industries already exploiting methanotrophs in biotechnology and companies exploring new ways of removing low concentrations of methane from waste gases, e.g. in coal mines (UK Mining Industry). This would be followed up through meetings with the host institution's respective research and enterprise offices, which have expertise in biotechnology patents.

The results of this topical and globally relevant research involving: identification of microbial key players in the uptake of atmopsheric methane in upland soils, characterization of their physiology and nutritional requirements and investigation of the environmental factors controlling their global activity and distribution and their response to climate change and land use, will capture the public's attention. Therefore an attractive and informative web site is proposed, including e.g. video footage from field work and from work in the lab. The web site will be used to inform the public about the field of microbiology, methane and other atmospheric trace gases, and the connections to climate change, in an entertaining and easy to grasp way. School visits throughout the duration of the project are also proposed, as well as demonstrations in and outside the laboratory, to engage pupils and teachers in science, especially of environmental microbiology. Popular articles written for Microbiology Today, The Microbiologist, The New Scientist and Planet Earth will further publicise this work to the wider community.

The Applicant, together with the multidisciplinary collaborative team, has an excellent record of engaging with the public, e.g. via school visits and the popular scientific press and radio.

This approach will help to make the public more aware about the impacts of climate change and the role of microorganisms involved in biogeochemical cycles, and sensitize them to the environmental issues arising from global warming.