Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi
Top Cited Papers
Open Access
- 5 July 2012
- journal article
- research article
- Published by Oxford University Press (OUP) in The ISME Journal
- Vol. 6 (12), 2245-2256
- https://doi.org/10.1038/ismej.2012.70
Abstract
Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, a major process of the biogeochemical nitrogen cycle, but the recognized diversity of this guild is surprisingly low and only two bacterial phyla contain known NOB. Here, we report on the discovery of a chemolithoautotrophic nitrite oxidizer that belongs to the widespread phylum Chloroflexi not previously known to contain any nitrifying organism. This organism, named Nitrolancetus hollandicus, was isolated from a nitrifying reactor. Its tolerance to a broad temperature range (25–63 °C) and low affinity for nitrite (Ks=1 mM), a complex layered cell envelope that stains Gram positive, and uncommon membrane lipids composed of 1,2-diols distinguish N. hollandicus from all other known nitrite oxidizers. N. hollandicus grows on nitrite and CO2, and is able to use formate as a source of energy and carbon. Genome sequencing and analysis of N. hollandicus revealed the presence of all genes required for CO2 fixation by the Calvin cycle and a nitrite oxidoreductase (NXR) similar to the NXR forms of the proteobacterial nitrite oxidizers, Nitrobacter and Nitrococcus. Comparative genomic analysis of the nxr loci unexpectedly indicated functionally important lateral gene transfer events between Nitrolancetus and other NOB carrying a cytoplasmic NXR, suggesting that horizontal transfer of the NXR module was a major driver for the spread of the capability to gain energy from nitrite oxidation during bacterial evolution. The surprising discovery of N. hollandicus significantly extends the known diversity of nitrifying organisms and likely will have implications for future research on nitrification in natural and engineered ecosystems.Keywords
This publication has 65 references indexed in Scilit:
- Ecological Aspects of the Distribution of Different Autotrophic CO 2 Fixation PathwaysApplied and Environmental Microbiology, 2011
- Cell envelope architecture in the Chloroflexi: a shifting frontline in a phylogenetic turf warEnvironmental Microbiology, 2010
- MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogeniesBMC Genomics, 2010
- A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteriaProceedings of the National Academy of Sciences of the United States of America, 2010
- Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseumPLOS ONE, 2009
- Nitrifier genomics and evolution of the nitrogen cycleFEMS Microbiology Letters, 2008
- Occurrence, Classification, and Biological Function of Hydrogenases: An OverviewChemical Reviews, 2007
- Sponge-Associated Microorganisms: Evolution, Ecology, and Biotechnological PotentialMicrobiology and Molecular Biology Reviews, 2007
- Archaeal nitrification in the oceanProceedings of the National Academy of Sciences of the United States of America, 2006
- daime, a novel image analysis program for microbial ecology and biofilm researchEnvironmental Microbiology, 2005