AUTHOR=Liu Guo-Hong , Yang Shang , Tang Rong , Xie Cheng-Jie , Zhou Shun-Gui 

TITLE=Genome Analysis and Description of Three Novel Diazotrophs Geomonas Species Isolated From Paddy Soils

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.801462

DOI=10.3389/fmicb.2021.801462

ISSN=1664-302X

ABSTRACT=<p>Five strictly anaerobic strains, designated RG2<sup>T</sup>, RG3, RG10<sup>T</sup>, RF4<sup>T</sup>, and RG29, were isolated from paddy soils in China. Strains RG2<sup>T</sup>, RF4<sup>T</sup>, RG10<sup>T</sup>, RG3, and RG29 grew at temperatures ranging 5–42°C and pH ranging 5.5–8.5. Strains RG2<sup>T</sup>, RF4<sup>T</sup>, RG3, and RG29 could tolerate NaCl up to 0–0.7% (w/v) while strain RG10<sup>T</sup> could tolerate NaCl up to 0–0.8% (w/v). The isolated strains showed the highest 16S rRNA gene sequence similarities to the type strains of <italic>Geomonas terrae</italic> Red111<sup>T</sup> and <italic>Geomonas paludis</italic> Red736<sup>T</sup>. In phylogenetic (based on 16S rRNA gene sequence) and phylogenomic trees, strains clustered with the members of the genus <italic>Geomonas.</italic> Menaquinone-8 was the predominant quinone present in all strains. The major fatty acid profiles of all strains were C<sub>15:1</sub> ω6<italic>c</italic>, C<sub>16:0</sub>, iso-C<sub>15:0</sub>, and Summed Feature 3. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the isolated strains and the closely related <italic>Geomonas</italic> species were lower than the cutoff value (ANI 95–96% and dDDH 70%) for prokaryotic species delineation. Based on physiological, biochemical, and chemotaxonomic properties, strains RG2<sup>T</sup>, RG10<sup>T</sup>, and RF4<sup>T</sup> could easily be differentiated with the members of the genus <italic>Geomonas</italic>. Additionally, all the isolated strains possessed <italic>nifHDK</italic> clusters and catalytic compartments of nitrogenase. Based on the above results, the isolated five strains represent three novel species of the genus <italic>Geomonas</italic>, for which the names <italic>Geomonas oryzisoli</italic> sp. nov., <italic>Geomonas subterranea</italic> sp. nov., and <italic>Geomonas nitrogeniifigens</italic> sp. nov. are proposed. The type strains are RG10<sup>T</sup> (= GDMCC1.2537<sup>T</sup> = KCTC 26318<sup>T</sup>), RG2<sup>T</sup> (= GDMCC1.2536<sup>T</sup> = KCTC 25317<sup>T</sup>), and RF4<sup>T</sup> (= GDMCC 1.2547<sup>T</sup> = KCTC 25316<sup>T</sup>).</p>