Hydrogenophaga crassostreae sp. nov., isolated from a Pacific oyster

Baek, Chaeyun; Kim, Eunji; Shin, Su Kyoung; Choi, Sung-Mi; Yi, Hana

doi:10.1099/ijsem.0.002244

Cited by 14 publications

(8 citation statements)

References 17 publications

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“…Species of Hydrogenophaga are positive for oxidase activity and show variable activity for catalase [1]. The main cellular fatty acids are C 16 : 0 and C 16 : 1 ω7 c and/or C 16 : 1 ω6 c [3–5]. The DNA G+C content ranges from 61.3 to 69.9 mol% [5, 6] and the predominant quinone system is ubiquinone-8 (Q-8) [1].…”

Section: Full-textmentioning

confidence: 99%

“…The main cellular fatty acids are C 16 : 0 and C 16 : 1 ω7c and/or C 16 : 1 ω6c [3][4][5]. The DNA G+C content ranges from 61.3 to 69.9 mol% [5,6] and the predominant quinone system is ubiquinone-8 (Q-8) [1]. At the time of writing, 15 species of the genus Hydrogenophaga have been validly described, which were isolated from diverse habitats, such as wastewater [7][8][9], activated sludge [2][3][4][5][6][7][8][9], soil [1,10], freshwater ecosystems [3,4,11] or even pacific oyster [5].…”

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confidence: 99%

“…The DNA G+C content ranges from 61.3 to 69.9 mol% [5,6] and the predominant quinone system is ubiquinone-8 (Q-8) [1]. At the time of writing, 15 species of the genus Hydrogenophaga have been validly described, which were isolated from diverse habitats, such as wastewater [7][8][9], activated sludge [2][3][4][5][6][7][8][9], soil [1,10], freshwater ecosystems [3,4,11] or even pacific oyster [5]. Additionally, members of the genus Hydrogenophaga can be key benzene-degrading bacteria in petroleum hydrocarbon contaminated subsurface environments [12].…”

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confidence: 99%

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Hydrogenophaga aromaticivorans sp. nov., isolated from a para-xylene-degrading enrichment culture, capable of degrading benzene, meta- and para-xylene

Banerjee

Táncsics

Tóth

et al. 2019

International Journal of Systematic and Evolutionary Microbiology

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A benzene, para- and meta-xylene-degrading Gram-stain-negative, aerobic, yellow-pigmented bacterium, designated as D2P1T, was isolated from a para-xylene-degrading enrichment culture. Phylogenetic analyses based on 16S rRNA genes showed that D2P1T shares a distinct phyletic lineage within the genus Hydrogenophaga and shows highest 16S rRNA gene sequence similarity to Hydrogenophaga taeniospiralis NBRC 102512T (99.2 %) and Hydrogenophaga palleronii NBRC 102513T (98.3 %). The draft genome sequence of D2P1T is 5.63 Mb long and the genomic DNA G+C content is 65.5 %. Orthologous average nucleotide identity (OrthoANI) and digital DNA–DNA hybridization (dDDH) analyses confirmed low genomic relatedness to its closest relatives (OrthoANI <86 %; dDDH <30 %). D2P1T contains ubiquinone 8 (Q-8) as the only respiratory quinone and phospholipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol as major polar lipids. The main whole-cell fatty acids of D2P1T are summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The polyphasic taxonomic results indicated that strain D2P1T represents a novel species of the genus Hydrogenophaga , for which the name Hydrogenophaga aromaticivorans sp. nov. is proposed. The type strain is D2P1T (=LMG 31780T=NCAIM B 02655T).

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Hydrogenophaga aromaticivorans sp. nov., isolated from a para-xylene-degrading enrichment culture, capable of degrading benzene, meta- and para-xylene

Banerjee

Táncsics

Tóth

et al. 2019

International Journal of Systematic and Evolutionary Microbiology

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“…Strain H7 was classified as a member of the Hydrogenophaga genus. Many members of this genus are chemoautotrophs, with the ability to oxidize hydrogen as an energy source (Baek et al, 2017). Analyzing the genome of strain H7, several hydrogenase and CO 2 fixing enzymes are found, which indicates that strain H7 may be also the chemoautotroph with hydrogen gas.…”

Section: Discussionmentioning

confidence: 99%

Simultaneous 3-/4-Hydroxybenzoates Biodegradation and Arsenite Oxidation by Hydrogenophaga sp. H7

et al. 2019

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Aromatic compounds and arsenic (As) often coexist in the environment. As(III)-oxidizing bacteria can oxidize the more toxic As(III) into the less toxic As(V), and As(V) is easily removed. Microorganisms with the ability to degrade aromatic compounds and oxidize arsenite [As(III)] may have strong potential to remediate co-contaminated water. In this study, a Gram-negative bacterium Hydrogenophaga sp. H7 was shown to simultaneously degrade 3-hydroxybenzoate (3-HBA) or 4-HBA (3-/4-HBA) and oxidize arsenite [As(III)] to arsenate [As(V)] during culture. Notably, the addition of As(III) enhanced the degradation rates of 3-/4-HBA, while the addition of 3-/4-HBA resulted in a slight delay in As(III) oxidation. Use of a 1% bacterial culture in combination with FeCl 3 could completely degrade 250 mg/L 3-HBA or 4-HBA and remove 400 μM As(III) from simulated lake water within 28 h. Genomic analysis revealed the presence of As(III) oxidation/resistance genes and two putative 3-/4-HBA degradation pathways (the protocatechuate 4,5-dioxygenase degradation pathway and the catechol 2,3-dioxygenase degradation pathway). Comparative proteomics suggested that strain H7 degraded 4-HBA via the protocatechuate 4,5-dioxygenase degradation pathway in the absence of As(III); however, 4-HBA could be degraded via the catechol 2,3-dioxygenase degradation pathway in the presence of As(III). In the presence of As(III), more NADH was produced by the catechol 2,3-dioxygenase degradation pathway and/or by As(III) oxidation, which explained the enhancement of bacterial 4-HBA degradation in the presence of As(III). In addition, the key gene dmpB , which encodes catechol 2,3-dioxygenase in the catechol 2,3-dioxygenase degradation pathway, was knocked out, which resulted in the disappearance of As(III)-enhanced bacterial 4-HBA degradation from the dmpB mutant strain, which further confirmed that As(III) enhancement of 4-HBA degradation was due to the utilization of the catechol 2,3-dioxygenase pathway. These discoveries indicate that Hydrogenophaga sp. H7 has promise for the application to the removal of aromatic compounds and As co-contamination and reveal the relationship between As oxidation and aromatic compound degradation.

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“…Hydrogenophaga palleronii DSM 63 T[11,40,41]; 7, Macromonas bipunctata DSM 12705 T[6]. +, Positive; −, negative; w, weak positive; nt, not tested or not available in the literature…”

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Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov., Serpentinimonas barnesii sp. nov. and Serpentinimonas maccroryi sp. nov., hyperalkaliphilic and facultative autotrophic bacteria isolated from terrestrial serpentinizing springs

Bird

Kuenen

Osburn

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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Three highly alkaliphilic bacterial strains designated as A1T, H1T and B1T were isolated from two highly alkaline springs at The Cedars, a terrestrial serpentinizing site. Cells from all strains were motile, Gram-negative and rod-shaped. Strains A1T, H1T and B1T were mesophilic (optimum, 30 °C), highly alkaliphilic (optimum, pH 11) and facultatively autotrophic. Major cellular fatty acids were saturated and monounsaturated hexadecenoic and octadecanoic acids. The genome size of strains A1T, H1T and B1T was 2 574 013, 2 475 906 and 2 623 236 bp, and the G+C content was 66.0, 66.2 and 66.1 mol%, respectively. Analysis of the 16S rRNA genes showed the highest similarity to the genera Malikia (95.1–96.4 %), Macromonas (93.0–93.6 %) and Hydrogenophaga (93.0–96.6 %) in the family Comamonadaceae . Phylogenetic analysis based on 16S rRNA gene and phylogenomic analysis based on core gene sequences revealed that the isolated strains diverged from the related species, forming a distinct branch. Average amino acid identity values of strains A1T, H1T and B1T against the genomes of related members in this family were below 67 %, which is below the suggested threshold for genera boundaries. Average nucleotide identity by blast values and digital DNA–DNA hybridization among the three strains were below 92.0 and 46.6 % respectively, which are below the suggested thresholds for species boundaries. Based on phylogenetic, genomic and phenotypic characterization, we propose Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov. (type strain A1T=NBRC 111848T=DSM 103917T), Serpentinimonas barnesii sp. nov. (type strain H1T= NBRC 111849T=DSM 103920T) and Serpentinimonas maccroryi sp. nov. (type strain B1T=NBRC 111850T=DSM 103919T) belonging to the family Comamonadaceae . We have designated Serpentinimonas raichei the type species for the genus because it is the dominant species in The Cedars springs.

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Hydrogenophaga crassostreae sp. nov., isolated from a Pacific oyster

Cited by 14 publications

References 17 publications

Hydrogenophaga aromaticivorans sp. nov., isolated from a para-xylene-degrading enrichment culture, capable of degrading benzene, meta- and para-xylene

Hydrogenophaga aromaticivorans sp. nov., isolated from a para-xylene-degrading enrichment culture, capable of degrading benzene, meta- and para-xylene

Simultaneous 3-/4-Hydroxybenzoates Biodegradation and Arsenite Oxidation by Hydrogenophaga sp. H7

Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov., Serpentinimonas barnesii sp. nov. and Serpentinimonas maccroryi sp. nov., hyperalkaliphilic and facultative autotrophic bacteria isolated from terrestrial serpentinizing springs

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