Soil metagenomics in a changing environment: Assessing the impact of climate change on soil biodiversity at the molecular level, in a European experimental network

THIS IS AN EXCITING NEW PhD POSITION in the Centre of Biological Sciences, University of Southampton

Biology is currently undergoing a revolution with the introduction, over the last few years of second generation DNA sequencing technologies. These new technologies make it possible to sequence entire genomes for a few thousand rather than several million dollars. We can now, for the first time, sequence whole samples of soil and begin to unravel the complexity of diversity in contrasting plant and soil samples from different environments. Metagenomics undertakes brute-force sequencing of DNA samples obtained from uncultured and unpurified soil samples that is then linked to a bioinformatics analysis of what species are in the sample. Inferences are then made on abundance and relative importance of the different species. Here we will utilise the EXPEER network (a collaborative project funded by Europe, www.expeer.fr), where several ecosystem experiments are available to us that have already been subjected to long-term environmental manipulations including drought and increased soil temperature. Given the importance of forest ecosystems for the delivery of ecosystem services, including biodiversity, carbon and water regulation and wood production, we have chosen forests and drought as a first focus for this study. Drought is predicted to increase in frequency, particularly summer droughts, across most of Europe in future, including southern Britain and yet our understanding of the impacts of this on soil biodiversity has remained limited, largely because of the difficulties of culturing the organisms contributing to soil biota.
The aim of this PhD is to determine the impacts of long-term drought on the biodiversity of soil microbes and to test the hypothesis that DNA sequencing can be used to identify changes in the abundance and diversity of major taxa. We will investigate the idea that specialist rather than generalist taxa will increase in importance in conditions predicted for 2050. We will utilise the latest technologies in DNA sequencing in a highly novel approach, where virtually no data are available, to address this question. This will be achieved by field collections of soil and sequence analysis with our Italian collaborator.
This studentship provides the student with an outstanding training in DNA sequencing, new genomic technologies, new bioinformatic procedures for large datasets, metagenomic software alongside ecosystem sciences. The successful candidate will join a vibrant group with 5 post-doctoral researchers, six PhD students, working together on related RESEARCH. Travel to Italy for field work is an important part of this project, which also provides an outstanding opportunity for the candidate to be part of a network of excellence in EXPEER (www.expeer.fr), that includes the very vest European laboratories undertaking novel ecosystem science.