The phylogeny of autotrophic ammonia-oxidizing bacteria as determined by analysis of 16S ribosomal RNA gene sequences

Abstract

Partial sequences of the 16s ribosomal RNA genes of eleven autotrophic ammonia-oxidizing bacteria were determined by PCR amplification from small amounts of heat-lysed biomass followed by direct sequencing of PCR products. The sequences were aligned with those of representative Proteobacteria and phylogenetic trees inferred using both parsimony and distance matrix methods. This confirmed that the autotrophic ammonia-oxidizers comprise two major lines of descent within the Proteobacteria. Nitrosomonas spp., Nitrosococcus mobilis, and strains of Nitrosovibrio, Nitrosospira and Nitrosolobus were located in the beta-subdivision. The recovery of Nitrosococcus oceanus strains as a deep branch in the gamma-subdivision supported the RNA catalogue data which had indicated that the genus Nitrosococcus is polyphyletic. The autotrophic ammonia-oxidizing bacteria of the beta-Proteobacteria formed a coherent group which is interpreted as representing a single family. Within this clade, the genera Nitrosovibrio, Nitrosospira and Nitrosolobus exhibited very high levels of homology in their 16s ribosomal RNA gene sequences and can be accommodated within a single genus. Separation of these genera is currently based entirely on gross morphological differences and these can now be considered more appropriate for the identification of species within this group. It is therefore proposed that Nitrosolobus, Nitrosovibrio and Nitrosospira strains be reclassified in a single genus for which the name Nitrosospira has priority.

Effects of aboveground grazing on coupling among nitrifier activity, abundance and community structure

“…Dominance of the AOB community by Nitrosospira has already been reported for soil environments (for example, Kowalchuk et al, 2000;Wheatley et al, 2003). Although the various Nitrosopira phylogenetic clusters have been shown to sometimes yield unstable tree topologies (Head et al, 1993;Purkhold et al, 2000), the assignation of the AOB clones to particular clusters in our study was found to be reliable, that is robust when comparing the assignation obtained with the three different treeing algorithms. The only exception was cluster 2 that was differentiated from cluster 3b only with the maximum likelihood method, but only eight sequences were affiliated to this 'cluster 2'.…”

Biological nitrogen removal with nitrification and denitrification via nitrite pathway

“…On one hand, the close physical association is useful for energetic reasons: NOB are able to efficiently intercept the nitrite Head et al 1993;Teske et al 1994). The bacterial genera responsible for the oxidation of ammonia and nitrite are presumed to be predominantly the genera Nitrosomonas and Nitrobacter, both of which are chemolithoautotrophic members of the class Proteobacteria (Wheaton et al 1994).…”

Bacteria, not archaea, restore nitrification in a zinc-contaminated soil

“…Until recently, ammonia oxidation has been considered to be entirely mediated through activities of ammonia-oxidizing bacteria (AOB; Kowalchuk and Stephen, 2001). Cultivation-dependent (Head et al, 1993), and subsequently cultivation-independent studies (Stephen et al, 1996(Stephen et al, , 1998, had suggested that members of a distinct clade of b-proteobacteria were the primary biological agents of ammonia oxidation in soil. The narrow phylogenetic breadth of this group facilitated the design of primers to monitor AOB using both phylogenetic (rRNA) and functional gene (amoA encoding the a-subunit of the key enzyme ammonia monooxygenase) markers (Rotthauwe et al, 1997;Kowalchuk et al, 2000;Kowalchuk and Stephen, 2001).…”