Diversity and niche partitioning of nitrite-oxidizing bacteria

Nitrite-oxidizing bacteria (NOB) are a phylogenetically diverse functional group with representatives in multiple genera and phyla within the bacterial domain. Despite this diversity, NOB commonly are difficult to grow in the laboratory, making it hard to identify them and study their biological traits. We have discovered several new NOB species and lineages, which are widely distributed and functionally important in various natural and engineered ecosystems.

Interestingly, different NOB often coexist within the same microbial communities, a phenomenon likely explained by ecological niche partitioning. Our research addresses the biological mechanisms that sustain such complex and stable NOB communities, and the factors driving shifts in NOB populations in dynamic environments.

Selected publications on this topic:

• Mueller AJ, Daebeler A, Herbold CW, Kirkegaard RH, Daims H. 2023. Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the Nitrospirales. ISME J. 17: 2123-2133 https://doi.org/10.1038/s41396-023-01518-6
• Mueller AJ, Jung MY, Strachan CR, Herbold CW, Kirkegaard RH, Wagner M, Daims H. 2021. Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting. ISME J. 15: 732-745 https://doi.org/10.1038/s41396-020-00809-6
• Kitzinger K, Koch H, Lücker S, Sedlacek CJ, Herbold C, Schwarz J, Daebeler A, Mueller AJ, Lukumbuzya M, Romano S, Leisch N, Karst SM, Kirkegaard R, Albertsen M, Nielsen PH, Wagner M, Daims H. 2018. Characterization of the first "Candidatus Nitrotoga" isolate reveals metabolic versatility and separate evolution of widespread nitrite-oxidizing bacteria. mBio 9: e01186-18 https://doi.org/10.1128/mbio.01186-18
• Gruber-Dorninger C, Pester M, Kitzinger K, Savio DF, Loy A, Rattei T, Wagner M, Daims H. 2015. Functionally relevant diversity of closely related Nitrospira in activated sludge. ISME J. 9: 643-655 https://doi.org/10.1038/ismej.2014.156
• Sorokin DY, Lücker S, Vejmelkova D, Kostrikina NA, Kleerebezem R, Rijpstra WIC, Sinninghe Damsté JS, Le Paslier D, Muyzer G, Wagner M, van Loosdrecht MCM, Daims H. 2012. Nitrification expanded: Discovery, physiology, and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi. ISME J. 6:2245-2256 https://doi.org/10.1038/ismej.2012.70