Nitrifying microorganisms occur across a wide temperature range from 4 to 84 °C and previous studies in geothermal systems revealed their activity under extreme conditions. Archaea were detected to be responsible for the first step of nitrification, but it is still a challenging issue to clarify the identity of heat-tolerant nitrite oxidizers. In a long-term cultivation approach, we inoculated mineral media containing ammonium and nitrite as substrates with biofilms and sediments of two hot springs in Yellowstone National Park (USA). The nitrifying consortia obtained at 70 °C consisted mostly of novel Chloroflexi as revealed by metagenomic sequencing. Among these, two deep-branching novel Chloroflexi were identified as putative nitrite-oxidizing bacteria (NOB) by the presence of nitrite oxidoreductase encoding genes in their genomes. Stoichiometric oxidation of nitrite to nitrate occurred under lithoautotrophic conditions, but was stimulated by organic matter. Both NOB candidates survived long periods of starvation and the more abundant one formed miniaturized cells and was heat resistant. This detection of novel thermophilic NOB exemplifies our still incomplete knowledge of nitrification, and indicates that nitrite oxidation might be an ancient and wide-spread form of energy conservation.

Studies in microbial ecology focus on identifying field dominant microbial populations using culture-independent tools, whereas minor populations are often ignored. we characterized the cyanobacterial populations from the Tikehau Atoll lagoon, Tuamotu Archipelago, which responded to standard culturing media. The cultivation approach recruited cryptic cyanobacterial taxa, which were not observed in the studied mats, as revealed by microscopic comparison. Twelve strains belonging to the unicellular genera (Aphanothece nägeli, Chlorogloea Wille and Cyanocystis borzi) and the filamentous cyanobacteria with narrow filaments (Leptolyngbya anagnostidis et komárek, Phormidium küzing ex gomont and Pseudanabaena lauterborn) dominated the cultures. The genera Cyanocystis and Chlorogloea were genotypically characterized for the first time. Four strains assigned to Phormidium showed 100% identity using 16S rRNA sequences but additional gene analyses as well as phenotypic distinctions suggest finer differentiation within this group. Eight cyanobacterial strains out of twelve fixed dinitrogen with rates ranging from 3.3 up to 15.8 nmoles N 2 µg -1 chl-a h -1 and their nitrogen fixation ability was further confirmed by molecular detection of nifH gene. Nine strains possessed phycoerythrin, and two performed complementary chromatic adaptation. The present study documented the existence of an autochthonous subdominant cyanobacterial assemblage with variable physiological features that may enable them to replace dominant species in the microbial mats of Tikehau Atoll lagoon. These minor populations may be ecologically important, particularily in case of environmental disturbances.