Azoarcus halotolerans sp. nov., a novel member of Rhodocyclaceae isolated from activated sludge collected in Hong Kong

Members of the family Zoogloeaceae within the order Rhodocyclales 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 H1-1-2AT and ZN11-R3-1 affiliated to the family Zoogloeaceae were isolated from coastal wetland habitats. The 16S rRNA gene sequences of the two strains were 100% identical and had maximum similarity with Nitrogeniibacter mangrovi M9-3-2T 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 Nitrogeniibacter. The average nucleotide identity (ANI) value and digital DNA-DNA hybridization (dDDH) estimate between the two strains and N. mangrovi M9-3-2T were 78.5–78.7% and 21.4–21.6%, respectively, indicating that the two strains represent a novel species. The genomes of strain H1-1-2AT (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 N. mangrovi M9-3-2T 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 (C16:1ω7c and C16:1ω6c), C16:0, C12:0, and C10:0 3-OH. Based on genomic, phenotypic, and chemotaxonomic characterizations, strains H1-1-2AT and ZN11-R3-1 represent a novel species of the genus Nitrogeniibacter, for which the name Nitrogeniibacter aestuarii sp. nov. is proposed. The type strain is H1-1-2AT (=MCCC 1K04284T=KCTC 82672T), and additional strain is ZN11-R3-1 (=MCCC 1A17971=KCTC 82671). Additionally, phylogenomic analysis of the members of the family Zoogloeaceae 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, Parazoarcus gen. nov., Pseudazoarcus gen. nov., Pseudothauera gen. nov., and Cognatazoarcus gen. nov., were proposed. This study provided new insights to the taxonomy of the family Zoogloeaceae.

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“…The description is as for Azoarcus halotolerans ( Li et al, 2020 ). The type strain is HKLI-1 T (= KCTC 72659 T =CCTCC AB 2019312 T ).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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“…DNA-DNA hybridization (DDH) values were estimated online using formula 2 of the Genome-to-Genome Distance Calculator 2.1 (GGDC; http://ggdc.dsmz.de/ggdc.php) as described by Wang et al [12]. Orthologous average nucleotide identity (ANI) values were calculated online on the EZBioCloud sever ( www.ezbiocloud.net/tools/ani) as described by Li et al [13]. Average amino acid identity (AAI) values were calculated online by using the AAI calculator by the Kostas lab (http://enve-omics.ce.gatech.edu/aai/).…”

Section: Genomic Analysismentioning

confidence: 99%

Pseudaquidulcibacter saccharophilus gen. nov., sp. nov., a novel member of family Caulobacteraceae, isolated from a water purification facility with supplement of starch as a carbon source

Liu

Lin

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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During a survey of microbial communities in the influent (ambient water) and effluent of a water purification facility with aeration and supplement of starch as carbon source, a novel bacterial strain, designated SZ9T, was isolated from the effluent sample. Colonies of strain SZ9T were small (approximately 0.5–1.0 mm in diameter), creamy-white, circular, smooth, translucent and convex. Cells were facultative anaerobic, motile by means of a single polar flagellum, rod-shaped, multiplied by binary fission, Gram-stain-negative, oxidase-positive and catalase-negative. Growth occurred at 10–40 °C (optimum, 28 °C) and pH 5.5–8.0 (optimum, pH 7.5). The range of NaCl concentration for growth was 0–1.0 % (w/v), with an optimum of 0–0.5 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain SZ9T formed a lineage within the family Caulobacteraceae of the class Alphaproteobacteria and showed the highest 16S rRNA gene sequence similarities to Aquidulcibacter paucihalophilus TH1-2T (92.44%), followed by Vitreimonas flagellata SYSU XM001T (89.61 %), Asprobacter aquaticus DRW22-8T (89.49 %) and Hyphobacterium vulgare WM6T (89.49%). The predominant fatty acids (>10 % of the total fatty acids) of strain SZ9T was summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c), summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) and C16 : 0. The sole respiratory quinone was ubiquinone-10, and the major polar lipids were phosphatidylcholine and two unidentified glycolipids. The whole genome of strain SZ9T was 2 842 140 bp in size, including 2769 protein-coding genes, 37 tRNA genes and two rRNA genes, and the genomic G+C content was 41.4 mol%. The orthologous average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between strain SZ9T and other genera within the family Caulobacteraceae were 64.50–66.62 %, 46.96–54.17 % and 27.70–31.70 %, respectively. Therefore, based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, the isolated strain SZ9T could be distinguished from other genera, suggesting that it represents a novel species of a novel genus in the family Caulobacteraceae , for which the name Pseudaquidulcibacter saccharophilus gen. nov., sp. nov is proposed. The type strain is SZ9T (=CCTCC AB2021029T=KCTC 82788T).

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“…Overexpression of PEP-CTERM A protein (PepA) could circumvent the requirement of PrsK and PrsR for floc-formation [19]. We had also demonstrated that one of the four RpoN paralogues, RpoN1, regulated the floc formation but not exopolysaccharide biosynthesis in a floc-forming Aquincola tertiaricarbonis RN12 strain [18] and Azoarcus halotolerans [21]. The synthesized exopolysaccharide chains were not tightly bound to the bulk of cell aggregates but were released into the cultivation broth.…”

Section: Introductionmentioning

confidence: 99%

Cellulose-mediated floc formation by the activated sludge bacterium Shinella zoogloeoides ATCC 19623

et al. 2022

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Background Bacterial floc formation plays a central role in the activated sludge (AS) process. The formation of AS flocs has long been known to require exopolysaccharide biosynthesis. We had demonstrated that both expolysaccharides and PEP-CTERM (a short C-terminal domain includes a near-invariant motif Pro-Glu-Pro (PEP)) proteins were required for floc-forming in Zoogloea resiniphila MMB, a dominant AS bacterium. However, the PEP-CTERM proteins are not encoded in the genome of AS bacterium Shinella zoogloeoides ATCC 19623 (formerly known as Zoogloea ramigera I-16-M) and other sequenced AS bacteria strains. The mechanism underlying floc formation of Shinella and related AS bacteria remained largely unclear. Results In this study, we have sequenced and annotated the complete genome of S. zoogloeoides ATCC 19623 (aka I-16-M), previously isolated in USA and treated as the neotype for the AS floc-forming bacterium Zoogloea ramigera I-16-M, and another AS strain XJ20 isolated in China. Mariner transposon mutagenesis had been conducted to isolate floc-forming-deficient mutants in the strain ATCC 19623 as previously performed by using Tn5 transposon three decades ago. The transposon insertional sites of multiple mutants were mapped to the gene cluster for bacterial cellulose synthesis (bcs) and secretion, and the role played by these genes in floc-formation had been further confirmed by genetic complementation. Interestingly, the restriction map of this bcs locus-flanking region was highly similar to that of the previously identified DNA fragment required for floc-formation in 1980s. Cellulase treatment abolished the floc-forming phenotype of S. zoogloeoides ATCC 19623 but not that of Z. resiniphila MMB strain. The FTIR spectral analyses revealed that the samples extracted from S. zoogloeoides ATCC 19623 were cellulose polymer. Conclusion Our results indicated that we have largely reproduced and completed the unfinished pioneering work on AS floc-formation mechanism, demonstrating that the floc-formation and flocculating capability of Shinella were mediated by extracellular cellulose polymers.

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Azoarcus halotolerans sp. nov., a novel member of Rhodocyclaceae isolated from activated sludge collected in Hong Kong

Cited by 9 publications

References 33 publications

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

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

Pseudaquidulcibacter saccharophilus gen. nov., sp. nov., a novel member of family Caulobacteraceae, isolated from a water purification facility with supplement of starch as a carbon source

Cellulose-mediated floc formation by the activated sludge bacterium Shinella zoogloeoides ATCC 19623

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