Journal article

Publication year: 2016

Pages: 1383-1399

Journal: The ISME Journal: Multidisciplinary Journal of Microbial Ecology

Volume number: 10

Issue number: 6

ISSN: 1751-7362

eISSN: 1751-7370

Open access status: Hybrid

DOI Link: https://doi.org/10.1038/ismej.2015.214

Publisher: Oxford University Press

Abstract: 
Nitrite-oxidizing bacteria (NOB) of the genus Nitrospina have exclusively been found in marine environments. In the brine-seawater interface layer of Atlantis II Deep (Red Sea), Nitrospina-like bacteria constitute up to one-third of the bacterial 16S ribosomal RNA (rRNA) gene sequences. This is much higher compared with that reported in other marine habitats (similar to 10% of all bacteria), and was unexpected because no NOB culture has been observed to grow above 4.0% salinity, presumably due to the low net energy gained from their metabolism that is insufficient for both growth and osmoregulation. Using phylogenetics, single-cell genomics and metagenomic fragment recruitment approaches, we document here that these Nitrospina-like bacteria, designated as Candidatus Nitromaritima RS, are not only highly diverged from the type species Nitrospina gracilis (pairwise genome identity of 69%) but are also ubiquitous in the deeper, highly saline interface layers (up to 11.2% salinity) with temperatures of up to 52 degrees C. Comparative pan-genome analyses revealed that less than half of the predicted proteome of Ca. Nitromaritima RS is shared with N. gracilis. Interestingly, the capacity for nitrite oxidation is also conserved in both genomes. Although both lack acidic proteomes synonymous with extreme halophiles, the pangenome of Ca. Nitromaritima RS specifically encodes enzymes with osmoregulatory and thermoprotective roles (i.e., ectoine/hydroxyectoine biosynthesis) and of thermodynamic importance (i.e., nitrate and nitrite reductases). Ca. Nitromaritima RS also possesses many hallmark traits of microaerophiles and high-affinity NOB. The abundance of the uncultured Ca. Nitromaritima lineage in marine oxyclines suggests their unrecognized ecological significance in deoxygenated areas of the global ocean.

Harvard Citation style: Ngugi, D., Blom, J., Stepanauskas, R. and Stingl, U. (2016) Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines, The ISME Journal: Multidisciplinary Journal of Microbial Ecology, 10(6), pp. 1383-1399. https://doi.org/10.1038/ismej.2015.214

APA Citation style: Ngugi, D., Blom, J., Stepanauskas, R., & Stingl, U. (2016). Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. 10(6), 1383-1399. https://doi.org/10.1038/ismej.2015.214