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& Bowman, 2001; Labrenz & Hirsch, 2001). The current study attempts to describe the
phenetic relationships between numerous bacteria from a suite of lakes in relation to cold
adaptation. The following sections describe the molecular methods used to assess
bacterial biodiversity and biogeography.
1.6.1 -
Bacterial biodiversity
Biodiversity is the irreducible complexity of life. Staley and Gosink (1999) refer
to it as the variety and abundance of life forms that live on Earth. Biodiversity is the
diversity of units of life, the basic unit being the species. However, it is also measured as
intraspecific genetic variability and by the richness of evolutionary lineages at high
taxonomic levels (Staley & Gosink, 1999). Bacterial biodiversity is one of the most
challenging aspects of microbiology. Traditionally, microbial diversity has been assessed
using phenetic characterisation of a pure culture by determination of physiology and
morphology (Priest & Austin, 1995) and by the use of biochemical tests, serotyping and
enzymatic products (Jayarao et al., 1992a). This approach is limited because of its
inability to determine inter-species evolutionary relatedness (Staley & Gosink, 1999) and
since traditional culturing techniques are not capable of isolating all bacteria from an
environmental sample, there results a massive under-estimation of diversity in natural
habitats (Staley & Gosink, 1999). Within the past twenty years there has been a gradual
shift towards using molecular techniques to identify bacterial strains, which has
revolutionised our concept of microbial ecology (Olsen et al., 1986; Pace et al., 1986).
Woese (1987) pioneered the use of the RNA from the small ribosomal subunit, 16s or 18s
rRNA. This allowed not only a phylogenetic tree to be produced to show bacterial
evolutionary relatedness, but also provided a basis for revolutionising phenetic
identification (Priest & Austin, 1995). Environmental monitoring has been dramatically
improved with the use of direct nucleic acid assessment from environmental samples
without prior culturing (van Elsas et al., 2000). Woese (1987) described 12 divisions
within the Eubacteria based on the analysis of cultivated organisms, but with the use of
culture-independent phylogenetic surveys of environmental microbial communities the
number of identifiable bacterial divisions has increased three fold to 36 (Pace, 1997;
Hugenholtz et al., 1998). There are a number of areas which have been significantly
stimulated by the introduction and development of nucleic acid approaches:
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