Environmental genomics of anaerobic ammonium oxidizing bacteria and Nitrospira-like bacteria
Application of the full-cycle rRNA approach has revealed that in many ecosystems previously not recognized bacteria catalyze key steps of the biogeochemical nitrogen cycle. For example, uncultured members of the phylum Nitrospirae are important nitrite oxidizers in many natural habitats and in wastewater treatment plants. These novel nitrite oxidizers are members of a unique bacterial phylum, which harbors also other highly interesting bacteria like the thermophilic sulfate reducers of the genus Thermodesulfovibrio and the acidophilic iron oxidizers of the genus Leptospirillum. In addition, anaerobic ammonium oxidation (Anammox) is mediated by novel, uncultured, deep branching members of the Planctomycetales, which are of significant biotechnological interest.
The goal of this project is to sequence large genome fragments or even the entire genome of a Nitrospira-like nitrite oxidizer and of an Anammox organism. For this purpose, high molecular weight DNA was extracted from enrichments of the respective organisms, purified by pulsed field gel electrophoresis, and partially digested. DNA fragments were cloned into bacterial artificial chromosomes (BAC). In total, approx. 9,000 BAC clones from the enrichment of the Anammox and 4,500 BAC clones from the Nitrospira-enrichment were obtained (insert size ranging from 30 to 200 kb) and both ends of each BAC insert were sequenced. In addition, encompassing shotgun libraries containing more than 100,000 clones were constructed and sequenced for both organisms. Large contigs were assembled. Subsequently, two approaches were applied to identify contigs of the target organisms. BACs carrying the 16S rRNA gene of the target organism were identified by membrane hybridization with suitable gene probes. In addition, peptide sequences of a key enzyme and a cytochrome of Anammox (determined by separate proteome analysis of the enrichment) were used to identify Anammox contigs by sequence homology searches. Genomic data will provide new insight into the biology of the elusive Nitrospira-like bacteria and Anammox organisms.
This study is undertaken in collaboration with  Mike Jetten (University of Nijmegen, The Netherlands), Jean Weissenbach and Denis LePaslier (Genoscope, Evry, France), and Eva Spieck (University of Hamburg, Germany).
Please follow this link for a general introduction on nitrifying bacteria.
Investigated by: Holger Daims
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