Analytical precision and repeatability of respiratory quinones for quantitative study of microbial community structure in environmental samples

Hu, Hong-Ying; Lim, Byung-Ran; Goto, Naohiro; Fujie, Koich

doi:10.1016/s0167-7012(01)00286-x

Cited by 119 publications

(63 citation statements)

References 11 publications

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“…In the DGGE band profile, f ki and f kj are the fractions of the k DGGE bands intensity for the i and j samples, respectively. Values p0.1 of dissimilarity of quinones are not recognized as different quinone profiles (97% statistical reliability; Hu et al, 2001). Cluster analysis was performed with the StatPartner program (O-Ha Inc., Tokyo, Japan) based on the distance matrix, and a dendrogram was constructed using the between-groups linkage method.…”

Section: Dgge Analysis and Sequencing Analysis Of Dgge Bandsmentioning

confidence: 99%

Increase in Alphaproteobacteria in association with a polychaete, Capitella sp. I, in the organically enriched sediment

et al. 2011

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We conducted bioremediation experiments on the organically enriched sediment on the sea floor just below a fish farm, introducing artificially mass-cultured colonies of deposit-feeding polychaete, Capitella sp. I. To clarify the association between the Capitella and bacteria on the efficient decomposition of the organic matter in the sediment in the experiments, we tried to identify the bacteria that increased in the microbial community in the sediment with dense patches of the Capitella. The relationship between TOC and quinone content of the sediment as an indicator of the bacterial abundance was not clear, while a significant positive correlation was found between Capitella biomass and quinone content of the sediment. In particular, ubiquinone-10, which is present in members of the class Alphaproteobacteria, increased in the sediment with dense patches of the Capitella. We performed denaturing gradient gel electrophoresis (DGGE) analyses to identify the alphaproteobacterial species in the sediment with dense patches of the worm, using two DGGE fragments obtained from the sediment samples and one fragment from the worm body. The sequences of these DGGE fragments were closely related to the specific members of the Roseobacter clade. In the associated system with the Capitella and the bacteria in the organically enriched sediment, the decomposition of the organic matter may proceed rapidly. It is very likely that the Capitella works as a promoter of bacteria in the organically enriched sediment, and feeds the increased bacteria as one of the main foods, while the bacteria decompose the organic matter in the sediment with the assistance of the Capitella.

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Section: Dgge Analysis and Sequencing Analysis Of Dgge Bandsmentioning

confidence: 99%

Increase in Alphaproteobacteria in association with a polychaete, Capitella sp. I, in the organically enriched sediment

et al. 2011

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“…Susceptibility to antibiotics was examined as described by Nedashkovskaya et al ( , 2005b with results recorded after incubation at 30 uC for up to 3 days. Gram-staining and other phenotypic characteristics were determined according to the method described by Gerhardt et al (1994).Menaquinones were extracted from lyophilized cells and determined using the procedures reported by AkagawaMatsushita et al (1992) and Hu et al (2001). Biomass for the quantitative fatty acid analysis was prepared by collecting growth from shake flasks of LB medium that had been incubated for 2 days at 30 uC.…”

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confidence: 99%

“…Menaquinones were extracted from lyophilized cells and determined using the procedures reported by AkagawaMatsushita et al (1992) and Hu et al (2001). Biomass for the quantitative fatty acid analysis was prepared by collecting growth from shake flasks of LB medium that had been incubated for 2 days at 30 uC.…”

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confidence: 99%

Pontibacter akesuensis sp. nov., isolated from a desert soil in China

Zhou

Wang

Liu

et al. 2007

International Journal of Systematic and Evolutionary Microbiology

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A Gram-negative, non-motile, rod-shaped bacterium, designated strain AKS 1 T , was isolated from a desert soil sample collected from Akesu, XinJiang Province, China. A taxonomic study, including phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics, was performed on the novel isolate. The predominant menaquinone of strain AKS 1 T was MK-7. The major fatty acids included i-C 15 : 0 , ai-C 17 : 1 B/i-C 17 : 1 I and i-C 17 : 0 3-OH. The G+C content of the DNA was 51.4 mol%. Based on the results of phenotypic and genotypic characteristics, strain AKS 1 T should be assigned as representing a novel species of the genus Pontibacter, for which the name Pontibacter akesuensis is proposed. The type strain is AKS 1 T (=KCTC 12758 T =CCTCC AB 206086 T ).The genus Pontibacter belongs to the phylum Bacteroidetes and was first described by Nedashkovskaya et al. (2005b) based on a single isolate from an unidentified sea anemone. The main characteristics of members of the phylum Bacteroidetes include the ability to move by gliding (many lack motility), a rod-shaped or ring-shaped morphology, possession of Gram-negative cell walls and pigmentation. The majority of the members of the phylum Bacteroidetes have been isolated from seawater, sediment or algae. Some marine bacteria of the phylum Bacteroidetes possess menaquinone 7 (MK-7) as their main respiratory quinone (Bowman et al., 2003; Brettar et al., 2004a, b; Nedashkovskaya et al., , 2004 Nedashkovskaya et al., , 2005aRaj & Maloy, 1990;Van Trappen et al., 2004;Yi & Chun, 2004;Yoon et al., 2004Yoon et al., , 2005a. The present investigation was designed to establish the taxonomic position of a novel isolate that formed a common clade with the genus Pontibacter within the phylum Bacteroidetes. Although the novel isolate has some properties characteristic of the phylum Bacteroidetes, it also has many special properties that are distinct from other members of the phylum. Genotypic and phenotypic data show that the strain represents a novel species of the genus Pontibacter.Strain AKS 1 T was isolated from a desert soil sample collected from Akesu, XinJiang Province, north-west China, by using the traditional dilution plating method. LB agar (Sambrook & Russell, 2002) was used for selective isolation and cultures were incubated at 30 uC for 1 week. The novel strain was maintained on LB agar slants at 4 u C and as glycerol suspensions (20 %, v/v) at 280 uC. Biomass for molecular systematic and chemotaxonomic studies was obtained after incubation in LB at 30 uC for 2 days in shake flasks (about 150 r.p.m.), with the pH adjusted to pH 7.8 using NaOH.Cell morphology of the novel isolate was observed by light microscopy (BH2; Olympus) and by transmission electron microscopy (H-7650; Hitachi) after 24 h growth on LB medium. Acid production from carbohydrates was tested using the media and methods described by Gordon et al. (1974). Sole carbon and sole carbon/nitrogen source utilization was investigated using the Biolog GN2 Microplate system (Nedashkovsk...

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“…Cellular fatty acid composition was tested (Sasser, 1990) using the Microbial Identifi cation System (MIDI, Inc., USA). Respiratory quinones were extracted from lyophilized cells and the samples were purifi ed and analyzed by reverse-phase high performance liquid chromatography (HPLC) using the procedures reported by Hu et al (2001). Genomic DNA was prepared for the base composition following the procedures of Marmur (1961).…”

Section: Methodsmentioning

confidence: 99%

Azospirillum palatum sp. nov., isolated from forest soil in Zhejiang province, China

Zhou

Wei

Wang

et al. 2009

J. Gen. Appl. Microbiol.

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Analytical precision and repeatability of respiratory quinones for quantitative study of microbial community structure in environmental samples

Cited by 119 publications

References 11 publications

Increase in Alphaproteobacteria in association with a polychaete, Capitella sp. I, in the organically enriched sediment

Increase in Alphaproteobacteria in association with a polychaete, Capitella sp. I, in the organically enriched sediment

Pontibacter akesuensis sp. nov., isolated from a desert soil in China

Azospirillum palatum sp. nov., isolated from forest soil in Zhejiang province, China

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