ABSTRACT
Acknowledgments ......................................................................................... 77
References ..................................................................................................... 77
We learned in Chapter 2 that the high-throughput methods for DNA
sequencing have now catalogued the composition of several hundreds of
bacterial genomes, including those of many soil bacteria [1]. Comparative
analysis of these genomes has revealed that horizontal gene transfer (HGT)
processes are major contributors to bacterial genome composition, diversity
and dynamics [2,3]. This observation is in contrast with the long-standing
views that assume that HGT between bacteria occurs only sporadically and is
of marginal importance to bacterial evolution, as compared to random
mutational processes. For instance, recent multi-locus sequence typing
(MLST) methods provide evidence that single-basepair changes in the
genomes of the bacteria Escherichia coli, Neisseria sp. and Streptococcus
sp. are equally-or more-likely to arise by recombination than by mutation
[4-7]. In soil settings, HGT is well known to contribute to the exchange of
genetic material [8]. HGT events are often identified retrospectively and are
then tentatively explained within the prevailing paradigms of gene flow,
genetic drift and natural selection. Nevertheless, it should be pointed out that
the factors that ultimately determine the gene and genome composition of
bacterial populations are only rudimentarily understood. Hence, our current
knowledge is still insufficient for establishing criteria that can a priori identify
the DNA compositions and gene pools that benefit the survival of specific
bacterial populations or of larger bacterial communities in nature. Thus, the
knowledge gaps in respect of the genetic diversity present in bacterial
communities in soil, the spatial and temporal variability of natural selection,
and the stochastic component of gene acquisition, bacterial survival and
dispersal, all lead to our current inability to accurately predict when, where,
how and at which rate genes flow and establish in natural bacterial
communities. Nevertheless, this chapter will examine our current under-
standing of the importance of HGT as an adaptive mechanism that can
genetically shape soil bacterial communities and will attempt to pinpoint
strategies for future research.
