Although aquatic environments are well understood in terms of their impact on the Earth System, many of the organisms driving major biogeochemical cycles are poorly characterised, and this limits mechanistic understanding and reduces predictive capacity.

This project is an integrated consortium of microbiologists who will utilise post-genomics to investigate aquatic microbial assemblages that control biogeochemical cycles.

Project Background

The consortium exploits the strengths of the UK community of microbial ecologists, many of whom are already applying post-genomic approaches to environmental studies. We propose to exploit recent advances in genomics that allow access to all genes and proteins in microbial assemblages. The genome of interest is the metagenome of the community of organisms that interact to form a biogeochemical cycle. The project is built around three specific hypotheses and the study will provide answers to important, current environmental questions.

The hypotheses to be tested are:-

1. That microbes in the ocean exist in definable communities and that biogeochemical fluxes depend on microbial community structure.
2. That the oligotrophic ocean is ultimately limited by the availability of nitrogen and that the scale of nitrogen limitation is a function of interactions between microbes in the assemblage.
3. That marine microbial activity is a major source of atmospheric biogases, much of which involves anaerobic metabolism in an aerobic environment.

In addition, there are heuristic elements to the proposal. It is proposed to use the expertise of the consortium to make a significant contribution to understanding a largely ignored (until recently) and rapidly changing aspect of climate change that the pH of the ocean is decreasing as a result of the dissolution of anthropogenic CO2 from the atmosphere. The aim is to use genomics/transcriptomics/proteomics to investigate how the environment, and human influences on it, influences community structure and function. It is also anticipated that the project will lead to the development of microarrays that will form the basis for environmental research in the next decade.

The advances in genomics, transcriptomics and proteomics enable us to make rapid progress in testing these hypotheses. We will combine these approaches with stable isotope probing (SIP) to directly target specific biogeochemical pathways. The SIP procedure was developed by Professor Murrell's group at Warwick (who will lead a key activity of this consortium) and we propose to use the SIP approach with both DNA and RNA to investigate functional microbial biodiversity.

The sensitivity of both DNA-SIP and RNA-SIP has now been improved to the point that we are confident that we can link SIP to metagenomics. We intend to make extensive use of existing time-series samples. For example the water column of the English Channel (station L4) and sediments of the Colne estuary have extensive data sets, of biogeochemical parameters; linking these studies with microbial diversity will allow investigation of year-to-year and seasonal variability.

Biannual samples from the Atlantic Meridional Transect consortium programme (sampling the North and South Atlantic from the UK to the Southern Ocean) will allow us to extend the approach to a global scale. Additionally, all members of the consortium will participate in a manipulative mesocosm experiment to assess how microbial communities are likely to respond to the expected change of ocean pH in the coming century.

This project addresses the NERC priority area of the Earth's Life Support System, as highlighted in the NERC strategy document Science for a sustainable future; it is of particular relevance to climate change, biogeochemistry and biodiversity. This proposal is structured around hypothesis testing and heuristic observation and hypothesis induction — the postgenomic cycle of knowledge. The experiments will provide techniques and metagenomic environmental data that can be utilised by the whole UK community and will provide tools and approaches that will be used by microbial ecologists in the next decade.