Towards the biogeography of British soil microorganisms

PhD ThesisSoils are complex and highly variable ecosystems within which a multitude of diverse microbial populations can be found. Here the effects of co-correlating environmental variables and spatial separation upon the diversity and community structure of two microbial kingdoms is investigated using several molecular based community assessment methods. Using an optimised nucleic acid extraction procedure, suitable for landscape scale surveys of microbial biogeography, large scale bacterial and fungal targeted terminal restriction fragment length polymorphism (t-RFLP) analysis was undertaken on soils collected as part of the Countryside Survey 2007 to show that populations of both kingdoms are structured, in part, by variability in environmental and edaphic conditions as well as spatial separation. In the case of soil bacteria, pH was identified as the most important environmental variable, although computed models suggest that many other environmental variables also play strong roles. Fungal systems have weaker relationships with environmental variability and stronger spatial relationships, although dominant plant species and soil pH were shown to significantly affect community structure. However, comparing results generated from different genes with different taxonomic resolutions hinders accurate comparisons between divergent microbial kingdoms. Pyrosequencing analysis was undertaken on 15 geographically isolated soil samples forming a natural pH gradient to address the changes in bacterial and fungal populations at great sequencing depth and at taxonomic resolutions closer to the species level. Again, in both cases, members of these kingdoms responded to differences in soil pH and the above ground plant community. A number of bacterial and fungal taxa were found to be responsible for the changes in community structure and diversity noted in the t-RFLP based experiments and are proposed as candidates for indicators of soil pH. In summary soil bacterial and fungal populations are structured according to complex laws relating to co-correlating environmental and spatial variables. This leads to the hypothesis that microbial communities are structured in similar ways to terrestrial macro organisms, and thus ecological theories derived from observations of larger animals may be investigated within the microbial world.NERC and CE