AUTHOR=Huang Zhaobin , Liu Renju , Chen Fenghua , Lai Qiliang , Oren Aharon , Shao Zongze 

TITLE=Nitrogeniibacter aestuarii sp. nov., a Novel Nitrogen-Fixing Bacterium Affiliated to the Family Zoogloeaceae and Phylogeny of the Family Zoogloeaceae Revisited

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.755908

DOI=10.3389/fmicb.2021.755908

ISSN=1664-302X

ABSTRACT=<p>Members of the family <italic>Zoogloeaceae</italic> within the order <italic>Rhodocyclales</italic> are found to play vital roles in terrestrial and aquatic ecosystems by participating in biofloc formation in activated sludge, polycyclic aromatic hydrocarbon degradation, and nitrogen metabolism, such as denitrification and nitrogen fixation. Here, two bacterial strains designated H1-1-2A<sup>T</sup> and ZN11-R3-1 affiliated to the family <italic>Zoogloeaceae</italic> were isolated from coastal wetland habitats. The 16S rRNA gene sequences of the two strains were 100% identical and had maximum similarity with <italic>Nitrogeniibacter mangrovi</italic> M9-3-2<sup>T</sup> of 98.4% and ≤94.5% with other species. Phylogenetic analysis suggested that the two strains belonged to a single species and formed a novel monophyletic branch affiliated to the genus <italic>Nitrogeniibacter</italic>. The average nucleotide identity (ANI) value and digital DNA-DNA hybridization (dDDH) estimate between the two strains and <italic>N. mangrovi</italic> M9-3-2<sup>T</sup> were 78.5–78.7% and 21.4–21.6%, respectively, indicating that the two strains represent a novel species. The genomes of strain H1-1-2A<sup>T</sup> (complete genome) and ZN11-R3-1 (draft genome) were 4.7Mbp in length encoding ~4,360 functional genes. The DNA G+C content was 62.7%. Nitrogen fixation genes were found in the two strains, which were responsible for the growth on nitrogen-free medium, whereas denitrification genes found in <italic>N. mangrovi</italic> M9-3-2<sup>T</sup> were absent in the two strains. The respiratory quinone was ubiquinone-8. The major polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and aminophospholipid. The major fatty acids were summed feature 3 (C<sub>16:1</sub><italic>ω</italic>7<italic>c</italic> and C<sub>16:1</sub><italic>ω</italic>6<italic>c</italic>), C<sub>16:0</sub>, C<sub>12:0</sub>, and C<sub>10:0</sub> 3-OH. Based on genomic, phenotypic, and chemotaxonomic characterizations, strains H1-1-2A<sup>T</sup> and ZN11-R3-1 represent a novel species of the genus <italic>Nitrogeniibacter</italic>, for which the name <italic>Nitrogeniibacter aestuarii</italic> sp. nov. is proposed. The type strain is H1-1-2A<sup>T</sup> (=MCCC 1K04284<sup>T</sup>=KCTC 82672<sup>T</sup>), and additional strain is ZN11-R3-1 (=MCCC 1A17971=KCTC 82671). Additionally, phylogenomic analysis of the members of the family <italic>Zoogloeaceae</italic> including type strains and uncultivated bacteria was performed, using the Genome Taxonomic Database toolkit (GTDB-Tk). Combined with the 16S rRNA gene phylogeny, four novel genera, <italic>Parazoarcus</italic> gen. nov., <italic>Pseudazoarcus</italic> gen. nov., <italic>Pseudothauera</italic> gen. nov., and <italic>Cognatazoarcus</italic> gen. nov., were proposed. This study provided new insights to the taxonomy of the family <italic>Zoogloeaceae</italic>.</p>