Abstract:
This chapter is devoted to application of whole genome sequence comparisons in taxonomy.
Driven by the rapid progress in sequencing technologies, “low budget” bacterial genomes
become increasingly available in a nearly unlimited number. During finalizing this chapter,
completed genomes representing 1,604 bacterial and 85 archaeal species were present in the
public data bank (http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi) reflecting the
enormous progress made within sequencing microbial genomes in the last years. With the
advent of next generation sequencing, whole genome sequence comparisons will be more and
more important for taxonomy, especially valuable in elucidating relationship of groups of
closely related bacterial strains which might form a single taxon, a subspecies or just an
ecovar within a given species. The aim of this chapter is to hand out a tool set for applying
genomics to the interested taxonomist. Using these tools might prove as being useful
especially in refining groups of closely related strains, which are not resolved by their 16S
rRNA sequence. Here, we will exemplify this approach by selecting a specific group of plant
– associated Bacillus amyloliquefaciens strains with plant growth promoting properties. In
recent years, those strains were increasingly applied as biological substitutes of
agrochemicals, mainly used as biofertilizer and for biocontrol of phytopathogenic
microorganisms, and nematodes (Chen et al., 2007).
