AUTHOR=Fujitani Hirotsugu , Momiuchi Kengo , Ishii Kento , Nomachi Manami , Kikuchi Shuta , Ushiki Norisuke , Sekiguchi Yuji , Tsuneda Satoshi 

TITLE=Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated From a Drinking Water Treatment Plant

JOURNAL=Frontiers in Microbiology

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2020.545190

DOI=10.3389/fmicb.2020.545190

ISSN=1664-302X

ABSTRACT=<p>Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, which is an important process of the biogeochemical nitrogen cycle and is exploited extensively as a biological nitrogen removal process. Members of the genus <italic>Nitrospira</italic> are often identified as the dominant NOB in a diverse range of natural and artificial environments. Additionally, a number of studies examining the distribution, abundance, and characterization of complete ammonia oxidation (comammox) <italic>Nitrospira</italic> support the ecological importance of the genus <italic>Nitrospira</italic>. However, niche differentiation between nitrite-oxidizing <italic>Nitrospira</italic> and comammox <italic>Nitrospira</italic> remains unknown due to a lack of pure cultures. In this study, we report the isolation, physiology, and genome of a novel nitrite-oxidizing <italic>Nitrospira</italic> strain isolated from a fixed-bed column at a drinking water treatment plant. Continuous feeding of ammonia led to the enrichment of <italic>Nitrospira</italic>-like cells, as well as members of ammonia-oxidizing genus <italic>Nitrosomonas</italic>. Subsequently, a microcolony sorting technique was used to isolate a novel nitrite-oxidizing <italic>Nitrospira</italic> strain. Sequences of strains showing the growth of microcolonies in microtiter plates were checked. Consequently, the most abundant operational taxonomic unit (OTU) exhibited high sequence similarity with <italic>Nitrospira japonica</italic> (98%) at the 16S rRNA gene level. The two other <italic>Nitrospira</italic> OTUs shared over 99% sequence similarities with <italic>N. japonica</italic> and <italic>Nitrospira</italic> sp. strain GC86. Only one strain identified as <italic>Nitrospira</italic> was successfully subcultivated and designated as <italic>Nitrospira</italic> sp. strain KM1 with high sequence similarity with <italic>N. japonica</italic> (98%). The half saturation constant for nitrite and the maximum nitrite oxidation rate of strain KM1 were orders of magnitude lower than the published data of other known <italic>Nitrospira</italic> strains; moreover, strain KM1 was more sensitive to free ammonia compared with previously isolated <italic>Nitrospira</italic> strains. Therefore, the new <italic>Nitrospira</italic> strain appears to be better adapted to oligotrophic environments compared with other known non-marine nitrite oxidizers. The complete genome of strain KM1 was 4,509,223 bp in length and contained 4,318 predicted coding sequences. Average nucleotide identities between strain KM1 and known cultured <italic>Nitrospira</italic> genome sequences are 76.7–78.4%, suggesting at least species-level novelty of the strain in the <italic>Nitrospira</italic> lineage II. These findings broaden knowledge of the ecophysiological diversity of nitrite-oxidizing <italic>Nitrospira</italic>.</p>