Evolution of thaumarchaeotal metabolism under contrasting oxygen conditions

Lead Research Organisation: University of Aberdeen
Department Name: Inst of Biological and Environmental Sci

Abstract

Many of the important ecological processes essential for life on earth and for the sustainability of our environment are performed by microbes (the bacteria and archaea) that are astonishingly abundant and diverse on the planet. Their functional diversity has arisen through many millions of years of adaptation to environmental change. Despite the contribution of microbial activity to global nutrient cycles and environmental stability, our inability to grow most microbes in the laboratory has severely limited our understanding of the ways in which they adapt to change and evolve. Recent technological innovations remove this limitation and allow us to study adaptation in microbes. The first innovation is the ability to sequence genomes of microscopic single cells extracted from the environment, allowing identification of genetic changes involved in adaptation and inference of how genomes have changed through deep evolutionary time. The second is the use of this genetic information to improve our ability to cultivate microbes, enabling physiological studies.

This project aims to use these cutting-edge technological advances to answer key questions about the mechanisms that generate this vast microbial functional diversity in nature, one of the greatest and most exciting challenges in biology. It will focus on a microbial group, the Thaumarchaeota, which are very diverse and abundant and have enormous environmental and economic impacts because of their role in oxidising ammonia fertilisers (resulting in greenhouse gas production and annual loss of >$70 billion of nitrogen fertilisers). As not all Thaumarchaeota perform ammonia oxidation, it is important to understand the distribution and activity of other Thaumarchaeota in the environment. This project will therefore address important environmental concerns about soil security and environmental change.

In this project, soil will be incubated at varying oxygen concentrations to determine the Thaumarchaeota that are active under different conditions. Novel thaumarchaeotal genomes will be extracted from soils with different oxygen preferences using a cutting-edge technology, single-cell genomics, which enables sequencing of the genome of individual microscopic cells. This will establish the genetic basis for the differences in these oxygen preferences. We will compare these new genomes with those previously available to trace the evolutionary origin of the genes and metabolic pathways implicated. We will test our evolutionary inferences using physiological studies of laboratory cultures, using novel techniques and genomic information, to isolate organisms never previously grown in the laboratory. Finally, the relative abundance and activity of these groups will be assessed in several ecosystems to determine their ecological relevance.

The project will address the crucial and exciting scientific and technological challenge of understanding the processes leading to the enormous functional diversity of microbes in terrestrial ecosystems, and will have broad environmental and socio-economic impact. It will increase our ability to predict the impact of environmental change on microbial diversity and ecosystem functions and will ensure better management of soil by facilitating the development of improved strategies for fertilisation utilisation and reduced greenhouse gas production. As the microbes studied in this proposal are unexplored, limited current information is available but their role in biogeochemical cycles and potential involvement in plant-microbe interactions is likely, offering novel scope of environmental and ecosystem understanding. Through various events, the scientific findings of this project will be disseminated to the public of all ages and to governing bodies and policy makers to communicate the importance of understanding adaptation in the face of environmental change and the need for better management of natural capital for ecosystem services.

Planned Impact

The proposed research project will directly benefit (i) academic and applied researchers, (ii) the biotechnology companies, (iii) policy makers, environmental agencies and government, and (iv) members of the general public.

(i) Research sector:

The aim of this proposal is to bring together innovative concepts and cutting-edge methodologies to understand the functional and evolutionary mechanisms driving functional diversification within a single microbial phylum, the Thaumarchaeota. Necessarily, the study will focus on a single phylum but the technology to be developed and applied, and the mechanistic understanding and concepts arising from the study will be applicable to other archaeal and bacterial phyla of importance in terrestrial and other natural environments. It will impact on our fundamental knowledge of the general integrated ecological-evolutionary-functional mechanisms of adaptation and diversification that generate high functional diversity in nature. In addition to the immediate archaeal research community, this research will therefore benefit those interested in biochemistry, genomics, population genetics, phylogeny, ecology and evolution of microorganisms, including those performing important ecosystem functions.

Comparison of the physiological and evolutionary mechanisms of adaptation in Thaumarchaeota with those in other archaea, bacteria and eukaryotes will advance broader aspects of ecological and evolutionary theory and release of genomic data associated with this project will be useful for many researchers interested, for example, in microbial physiological pathways or in the diversification of early life on Earth.

A major element of the proposed project is the use of microbial single cell sequencing technology and whole genome application, which is still in its infancy.Its establishment, including development of procedures and methodologies, will benefit those who wish to exploit this technology for other organisms, be it for academic research, or retrieval of novel genomic content for discovery of novel gene products for industrial use.

(ii) Biotechnology partners:

This project has the potential to contribute to biotechnology applications as it will identify novel enzymatic activities and metabolic pathways. Several meetings will be organised with different biotechnological companies (including Syngenta, Bayer) and with Bristol's new BrisSynBio synthetic biology centre, to evaluate the use of these novel microbial activities for biotechnology.

(iii) Policy holder agencies and governments:

Almost nothing is currently known about the contribution of non-ammonia-oxidising Thaumarchaeota to environmentally important processes and this research will provide novel, fundamental insights into their contribution to terrestrial carbon and nitrogen cycling. This work will therefore be potentially relevant to those concerned with pollution of natural ecosystems (e.g. nitrous oxide emissions or other sources).Beneficiaries therefore include those agencies concerned with legislation, nitrous oxide emissions and climate change. The discovery of novel sources of microbial pollution and relevance for the ecosystem stability will be directly communicated to governing bodies in Scotland, UK and EU through quarterly news bulletin. These actions will guide future regulatory and legislative decisions in land and fertilizer management.

(iv) General public:

Members of the general public will also benefit from the research through environmental, political and industrial decisions, and information will be disseminated through public lectures and scientific workshops to inform about the power of novel genomics technologies to understand ecosystem biodiversity and to enhance scientific interest in schoolchildren.

Publications

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Title Genome separation by ultracentrifugation on Cesium Chloride 
Description We separate the microbial DNA based on their GC% using ultracentrifugation on Cesium Chloride. This is used to selectively enrich DNA in the genomic content of interest fro genome sequencing. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? No  
Impact none as yet 
 
Description Terrestrial thaumarchaeotal genomes 
Organisation University of Warwick
Country United Kingdom 
Sector Academic/University 
PI Contribution We analyse the phylogenetic classification of several assembled thaumarchaeotal genomes provided by our collaborator and we currently analyse potential metabolic pathways for the novel lineages.
Collaborator Contribution Our partner (Christopher Quince) provided us several assembled thaumarchaeotal genomes.
Impact None yet.
Start Year 2018
 
Description School microbial workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact My research team provided a full afternoon of various activities related to microbiology. This included stalls on DNA extraction, DNA structure, microbial microscopy and creative microbial building. The children greatly appreciated the event and the school reported a fantastic interest in these kinds of events.
Year(s) Of Engagement Activity 2018