INTRODUCTION

Soil is heterogeneous in nearly all respects and contains a huge diversity of micro-organisms. The availability of carbon and other energy sources, mineral nutrients and water varies considerably over space and time, as does temperature. Adaptations to nutrient poverty including oligotrophy and zymogeny (upsurge in growth when nutrients are available) are common. The water films essential for microbial life in soil are discontinuous, and only clay particles have the necessary charges to hold water against the pull of gravity. Clay-coated soil particles cluster together to form aggregates, and these aggregates or clusters of aggregates with their adjacent water form the microhabitats in which bacteria function (Stotzky, 1997). The result of the discrete microhabitats in soil is that microbial population dynamics and interactions are very different from those in well-mixed substrates such as some aquatic environments. Soil is also a reservoir for pesticides and other chemical and microbiological inputs from slurry application, all of which will have a selective impact on the indigenous bacteria.

Bacterial evolutionary histories are difficult to untangle. Different scales of evolution occur simultaneously, from events possible over a few generations (chromosomal rearrangement, gene deletion and acquisition of genes via horizontal transfer) to the eon-scale generative evolution which creates diversity from which the novel functional genes of the future will be selected. In the age of genomics we are developing the tools to study the ecology of microbes in soil.