Hydrogenophaga temperata sp. nov., a betaproteobacterium isolated from compost in Korea

Kim, Yeon-Ju; Kim, Myung Kyum; Weon, Hang-Yeon; Kim, Ho-Bin; Yang, Deok‐Chun

doi:10.2323/jgam.56.419

Cited by 10 publications

(2 citation statements)

References 21 publications

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“…S5) revealed by CCA do not necessarily indicate that Hydrogenophaga is more strongly correlated with pH but, instead, that the community structure as a whole is somewhat correlated with pH. Hydrogenophaga can grow at pH values of up to 9.0 (35), but one study of alkaline shallow groundwaters in Lake Calumet, Chicago, IL (36), did show that Hydrogenophaga was active at pH 11.8, consistent with the presence of this genus in FG6, which has a pH of 10.7.…”

Section: Discussionmentioning

confidence: 94%

Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey

Neubeck

Sun

Müller

et al. 2017

Appl Environ Microbiol

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The surface waters at the ultramafic ophiolitic outcrop in Chimaera, Turkey, are characterized by high pH values and high metal levels due to the percolation of fluids through areas of active serpentinization. We describe the influence of the liquid chemistry, mineralogy, and H2 and CH4 levels on the bacterial community structure in a semidry, exposed, ultramafic environment. The bacterial and archaeal community structures were monitored using Illumina sequencing targeting the 16S rRNA gene. At all sampling points, four phyla, Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria, accounted for the majority of taxa. Members of the Chloroflexi phylum dominated low-diversity sites, whereas Proteobacteria dominated high-diversity sites. Methane, nitrogen, iron, and hydrogen oxidizers were detected as well as archaea and metal-resistant bacteria.IMPORTANCE Our study is a comprehensive microbial investigation of the Chimaera ophiolite. DNA has been extracted from 16 sites in the area and has been studied from microbial and geochemical points of view. We describe a microbial community structure that is dependent on terrestrial, serpentinization-driven abiotic H2, which is poorly studied due to the rarity of these environments on Earth.

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Section: Discussionmentioning

confidence: 94%

Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey

Neubeck

Sun

Müller

et al. 2017

Appl Environ Microbiol

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“…Members of the genus Hydrogenophaga are chemo-organotrophic or chemolithoautotrophic, use the oxidation of H 2 as an energy source and CO 2 as a carbon source (Willems et al 1989;Kämpfer et al 2005;Chung et al 2007;Yoon et al 2008;Kimura and Okabe 2013). The genus, at the time of writing the manuscript, comprised of nine recognized species (http://www.bacterio.net/hydrogenophaga.html), namely H. flava, H. palleronii, H. pseudoflava, H. taeniospiralis (Willems et al 1989), H. defluvii, H. atypica (Kämpfer et al 2005), H. bisanensis (Yoon et al 2008), H. caeni (Chung et al 2007) and H. intermedia (Contzen et al 2000) and four unrecognized species H. temperata (Kim et al 2010), H. electricum (Kimura and Okabe 2013), H. carboriunda (Reinauer et al 2014) and H. luteola (Du et al 2015). The main habitat of this genus seems to be compost soil, reed pond water, anodic biofilms, wastewater and activated sludge (Kim et al 2010;Kimura and Okabe 2013;Du et al 2015;Chung et al 2007;Yoon et al 2008;Kämpfer et al 2005).…”

Section: Introductionmentioning

confidence: 99%

Description of Hydrogenophaga laconesensis sp. nov. isolated from tube well water

2016

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A light cream color colony was isolated, using oligotrophic LB agar medium, from a water sample collected from a tube well and designated as HWB-10(T). Cells of strain HWB-10(T) were Gram-negative, motile rods, non-spore forming, positive for catalase, oxidase, nitrate reduction and esculin. The predominant fatty acids were C16:0, summed feature 4 (C16:1 ω7c/iso-C15:0 2-OH) and summed feature 7 (C18:1 ω7c, C18:1 ω9t and/or C18:1 ω12t), and the major ubiquinone was Q-8. NCBI-BLAST- and EzTaxon-based 16S rRNA gene sequence similarity search identified strain HWB-10(T) as a member of the genus Hydrogenophaga and H. atypica DSM 15342(T), H. defulvi DSM 15341(T), H. palleronii LMG2366(T) and H. taeniospiralis LMG7170(T) being the nearest phylogenetic species with a similarity (%) of 99.3, 99.1, 98.4 and 98.2, respectively, while the similarity was <98.0 % with other species of the genus. However, DNA-DNA similarities between HWB-10(T) and H. atypica DSM 15342(T) and H. defulvi DSM 15341(T) were 37.0 and 43.0 %, respectively, indicating that strain HWB-10(T) is a novel species. Further, the DNA fingerprinting, based on BOX-, ERIC-, (GTG)5- and REP-PCR amplifications, distinguished strain HWB-10(T) from its closest species, H. atypica DSM 15342(T) and H. defulvi DSM 15341(T) with similarity coefficients of 0.45 and 0.37, respectively, a value sufficient to establish the species status within the genus Hydrogenophaga. In addition, strain HWB-10(T) exhibited several phenotypic differences with its closely related species. Based on the above cumulative differentiating characteristics, strain HWB-10(T) was identified as a new species of the genus Hydrogenophaga and proposed as Hydrogenophaga laconesensis sp. nov. with strain HWB-10(T) (KTCC 42478(T) = LMG 28681(T)) as its type strain.

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Functional rigidity of a methane biofilter during the temporal microbial succession

Kim

Jeong

Cho

2013

Appl Microbiol Biotechnol

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Temporal microbial succession was investigated in relation to the performance of a methane biofilter. A laboratory-scale biofilter packed with perlite was operated for 108 days, without a deliberate biomass control. The system performance was stable over the period with a mean elimination capacity of 1,563 g m(-3) day(-1), despite a temporal deterioration (45-56 days). Ribosomal-tag pyrosequencing showed that bacterial communities at days 14-28 were distinct from those of days 68-108. The accumulation of nonviable substances strongly coincided with the community change (R (2) > 0.97). Rhodobacter, Hydrogenophaga, and Methylomonas were dominated in the earlier period, while Methylocaldum and Methylococcus were abundant in the later period. The methanotrophic proportion gradually increased to 41 %, and type I methanotrophs became predominant over time. However, community structure and methanotrophic population density stably retained over time, allowing the system to keep the similar performance. Therefore, the perlite biofilter system was functionally rigid against the temporal microbial succession.

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Hydrogenophaga temperata sp. nov., a betaproteobacterium isolated from compost in Korea

Cited by 10 publications

References 21 publications

Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey

Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey

Description of Hydrogenophaga laconesensis sp. nov. isolated from tube well water

Functional rigidity of a methane biofilter during the temporal microbial succession

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