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Chapter 3 : Diversity and Environmental Distribution of Ammonia-Oxidizing Bacteria
Category: Environmental Microbiology
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This chapter discusses archaeal ammonia oxidation and anaerobic ammonia oxidation processes that have important roles in the global nitrogen cycle. It reviews the diversity, distribution, and biogeography of a subset of the ammonia-oxidizing prokaryotes, the aerobic chemolithotrophic ammonia-oxidizing bacteria (AOB). The terrestrial AOB are generally restricted to the Betaproteobacteria, while the marine organisms are found both in the Betaproteobacteria and the Gammaproteobacteria. Phylogeny inference based on the current data set does not support that all nitrosomonads are more closely related to each other than to members of the Nitrosospira lineage; especially problematic is the placement of Nitrosomonas cryotolerans and Nitrosomonas sp. Stable clusters based on 16S rRNA phylogeny are problematic within Nitrosospira because of the overall high levels of identity of the 16S rRNA (>97%). Soils are often dominated by Nitrosospira spp., while marine and freshwater systems often have mixtures of the genera of AOB present. During secondary succession, microbial communities develop on the soils that are often depleted in the number and diversity of microorganisms. In marine habitats, Nitrosococcus, Nitrosomonas, and Nitrosospira coexist with ammonia-oxidizing archaea; their relative contributions and diversity are only beginning to be delineated. The functional cohort of AOB, ammonia-oxidizing archaea, and the nitrite-oxidizing prokaryotes will persist as important model organisms for linking the process of nitrification to microbial diversity and biogeography.
Two 16S ribosomal RNA guide trees for the clusters of beta-proteobacterial (top) and gamma-proteobacterial (bottom) AOB based on high-quality sequences (>1,200 bp) from isolates. Sequence data retrieval and analysis was preformed with RDP version 10 database functions ( Cole et al., 2009 ). Several Nitrosococcus 16S rRNA gene sequences were from ongoing genomic sequencing projects (M. G. Klotz, personal communication). The scale is substitution per site. Strain selection and cluster designations are based on those of Purkhold et al. (2000 , 2003 ), Kowalchuk and Stephen (2001) , and Ward and O’Mullan (2002) .
Pairwise comparisons of 493 16S rRNA gene sequences of Nitrosospira spp. for genetic distance (percentage of divergence) and geographic distance (m) between sources. Sequence data retrieval and analysis was performed with RDP version 10 database functions ( Cole et al., 2009 ). Geographic distances calculated in ArcGIS (version 9.1; Environmental Systems Research Institute, Redlands, CA) were transformed into four categories, as displayed. Statistical analysis on the untransformed geographic and sequence distance matrices was performed with the Mantel r test (Ade4 version 1.4-11 ( Dray and Dufour, 2007 ) and indicated that DNA distance increased as geographic distance increased (r = 0.22, p = 0.001).
Outline of the taxonomy of chemolithotrophic AOB for selected pure culture isolates and strains a