-Nitrosospira sp. Nsp65 -

FIGURE 13.5 16S rRNA-based phylogenetic tree of the betaproteobacterial ammonia oxidizers. The tree includes only those oxidizers that have been demonstrated to represent different genospecies (DNA-DNA similarity <60%) and for which 16S rRNA gene sequences longer than 1000 nucleotides are available. Strains with DNA-DNA similarity >60% are in parentheses after the respective species name. Described species are depicted in bold. Scale bar represents 10% estimated sequence divergence (from Koops et al., 2003).

Worth noting too is the fact that these techniques do not normally provide quantitative information about the abundance and activity of different species in situ. Quantitative PCR and newer techniques based on membrane or in situ hybridization in concert with rRNA-targeted probes (e.g., fluorescence in situ hybridization or FISH, as used in aquatic and wastewater treatment studies; Juretschko et al., 1998) can directly relate community structure with activity and the spatial distribution of targeted organisms. Recent work (e.g., Prosser and Embley, 2002) has shown how these techniques can be used to discover nitrifier community change in response to changes in ecosystem management and land use.

Nitrite-oxidizing bacteria appear in a broader array of phylogenetic groupings than do the ammonia oxidizers, but only the genera Nitrobacter and Nitrospira (Freitag et al., 2005) have been detected in soil; the distribution of the other nitrite-oxidizing genera (Nitrosococcus and Nitrospina) is not fully known. Members of Nitrobacter form an exclusive and highly related cluster in the Alphaproteobac-teria (Fig. 13.4). Pairwise evolutionary distance estimates are less than 1%, indicating little genetic diversity within the group (Fig. 13.5), a finding supported by 16S rRNA sequence comparisons (Teske et al., 1994). The other nitrite-oxidizing genera are in the delta (Nitrospina and Nitrospira) and gamma (Nitrosococcus) subclasses of the Proteobacteria.

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