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Archives of Microbiology (v.194, #5)
Characterization of Deinococcus sahariens sp. nov., a radiation-resistant bacterium isolated from a Saharan hot spring by Hanene Bouraoui; Melek Ben Aissa; Feten Abbassi; Jean Pierre Touzel; Michael O’donohue; Mohamed Manai (pp. 315-322).
An ultraviolet-radiation-resistant, Gram-positive, orange-pigmented, thermophilic and strictly aerobic cocci was isolated from Saharan water hot spring in Tunisia. The newly isolated bacterium, designated HAN-23T, was identified based on polyphasic taxonomy including genotypic, phenotypic and chemotaxonomic characterization. Phylogenetic analysis based on 16S rRNA gene sequences placed this strain within Deinococcus genus. However, strain HAN-23T is different from recognized species of the genus Deinococcus, showing less than 94.0% similarity values to its closest relatives. The predominant cellular fatty acids determined by gas chromatography were iso-C15:0, iso-C17:0 and iso C17:1 ω9c. The major respiratory quinone was MK-8. The DNA G + C content was 66.9 mol%. DNA–DNA hybridization measurements revealed low DNA relatedness (6%) between the novel isolate and its closest neighbor, the type strain Deinococcus geothermalis DSM 11300. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain HAN-23T represents a novel species of the genus Deinococcus, for which the name Deinococcus sahariens sp. nov. is proposed, the type strain being HAN-23T (=DSM 18496T; LMG 23756T).
Keywords: Taxonomy; New species; Sahara; Hot spring; Deinococcus; UV resistance
Host responses of a marine bacterium, Roseobacter denitrificans OCh114, to phage infection by Yongyu Zhang; Fan Zhang; Jun Yang; Nianzhi Jiao (pp. 323-330).
RDJLΦ1 is a marine siphophage infecting Roseobacter denitrificans OCh114. In this study, host responses of R. denitrificans OCh114 to phage infection were investigated through in situ real-time atomic force microscopy (AFM) and proteomics approaches. As seen from the AFM observations, during phage infection processes, depression areas appeared on the host cell surface in a few minutes after infection and expanded in both diameter and depth over time and finally led to the collapse of host cells within 30 min. The two-dimensional polyacrylamide gel electrophoresis revealed significant changes in the proteomic composition of the host cells during infection. The expression of 91 proteins, including some involved in DNA transcription regulation and substrate transportation, was changed with at least twofold up- or downregulation as compared to the control without phage infection. This observed rapid lysis of host cells and the great changes in protein expression caused by phage infection added more perspectives to the documented important roles of viruses in mediating carbon cycling in the ocean.
Keywords: Roseobacter denitrificans OCh114; RDJLΦ1; Atomic force microscopy (AFM); Proteomics
Photosynthetic characteristics of marine aerobic anoxygenic phototrophic bacteria Roseobacter and Erythrobacter strains by Yuki Sato-Takabe; Koji Hamasaki; Koji Suzuki (pp. 331-341).
A coastal Roseobacter strain of marine aerobic anoxygenic phototrophic bacteria (AAnPB) was isolated and phylogenetically determined. The strain OBYS 0001 was characterized by its physiological and biochemical properties with reference to the Erythrobacter longus type strain NBRC 14126. When grown in batch cultures, the growth curves of the both strains were similar. Cellular bacteriochlorophyll a concentrations of the strains reached the maxima in the stationary growth conditions. In vivo fluorescence excitation/optical density spectra between 470 and 600 nm for OBYS 0001 represented higher values than NBRC 14126. Variable fluorescence measurements revealed that the functional absorption cross section (σ) of the bacterial photosynthetic complexes for OBYS 0001 was significantly higher than that for NBRC 14126 under green excitation. These results suggest that Roseobacter can capture green light more efficiently than Erythrobacter for photosynthesis. The photochemical quantum efficiencies (F v/F m) of the bacterial photosynthetic complexes for OBYS 0001 were consistently lower than those for NBRC 14126. A relationship between the growth rate and F v/F m was significant for OBYS 0001, but that was not found for NBRC 14126. These results suggested that F v/F m for AAnPB could not be used as a proxy of the growth rate which is consistent with their mostly heterotrophic characters.
Keywords: Aerobic anoxygenic phototrophic bacteria; Roseobacter ; Erythrobacter ; Variable fluorescence; Absorption; Excitation spectrum
Erratum to: Photosynthetic characteristics of marine aerobic anoxygenic phototrophic bacteria Roseobacter and Erythrobacter strains
by Yuki Sato-Takabe; Koji Hamasaki; Koji Suzuki (pp. 343-343).
The Paenibacillus polymyxa species is abundant among hydrogen-producing facultative anaerobic bacteria in Lake Averno sediment by Sadhana Lal; Stefano Romano; Luigi Chiarini; Antonella Signorini; Silvia Tabacchioni (pp. 345-351).
Lake Averno sediment was used to isolate the facultative anaerobic bacteria having the potential for H2 production. Twenty-five out of 35 isolates recovered from the sediment sample produced hydrogen under anaerobic conditions from glucose with yields ranging from 0.1 to 0.49 mol H2/mol glucose. Identification based on 16S rRNA gene sequence analysis revealed that most of them belong to the Firmicutes group, with a prevalence of the Paenibacillus polymyxa species. Seven distinct genomic fingerprints among the 11 P. polymyxa isolates were obtained using the random amplified polymorphic DNA (RAPD) technique. Glucose fermentation by P. polymyxa isolates was investigated. Glucose was totally consumed after 3 days of fermentation. The fermentation products were hydrogen (0.18–0.47 mol H2/mol glucose), ethanol (0.1–0.5 mol ethanol/mol glucose), and 2,3-butanediol (0.1 mol 2,3-butanediol/mol glucose). Lower amounts of acetic, butyric, formic, lactic, and propionic acids were detected. All metabolic data concerning P. polymyxa isolates were analyzed by cluster analysis to reveal similarities and/or differences with clustering based on RAPD profiles. Despite the high metabolic similarity among almost all P. paenibacillus isolates, results of cluster analyses of metabolic and genetic data do not match completely.
Keywords: Paenibacillus polymyxa ; Lake sediment; Hydrogen; 2,3-Butanediol; Ethanol
Diversity and abundance of the rumen and fecal methanogens in Altay sheep native to Xinjiang and the influence of diversity on methane emissions by C. Liu; Z. P. Zhu; Y. F. Liu; T. J. Guo; H. M. Dong (pp. 353-361).
This study aims to investigate the influence of diet roughage proportion on the methanogenic communities from the rumen and fecal samples in Altay local sheep native to Xinjiang and better understand the association of methanogenic diversity or abundance with methane emissions of the ruminants. In this study, the high roughage diet was found to cause more methane emissions for either maintenance or ad-lib group, but the total methanogenic abundance was not influenced by roughage proportion and showed no significant difference between groups. Furthermore, the denaturing gradient gel electrophoresis was conducted to reveal the difference in methanogenic diversity. Phylogenetic analysis showed that the sequences obtained were divided into three groups, affiliated to the genus of Methanobrevibacter, Methanocorpusculum and an unidentified methanogenic-like group. Of these sequences, the predominant diversity from the genus of Methanobrevibacter and the unidentified methanogenic-like archaeons in the rumen was found to be significantly induced by the high roughage diet, implying that the variation of diversity at the species or strain level might have an effect on methane emissions from the rumen. Further analysis showed that five methangenic sequences from the rumen were possibly associated with the differential methane emissions.
Keywords: Methanogenic diversity; Rumen; Fecal samples; DGGE
Colistin A and colistin B among inhibitory substances of Paenibacillus polymyxa JB05-01-1 by Karim Naghmouchi; Riadh Hammami; Ismail Fliss; Ron Teather; John Baah; Djamel Drider (pp. 363-370).
Recently, we isolated and reported the antagonism of Paenibacillus polymyxa JB05-01-1 (P. polymyxa JB05-01-1) against Gram-negative bacteria. Here, we provide more insights and attribute the abovementioned antagonism to the production of colistins A and B, which were purified by Amberlite column exchange, C18 column hydrophobicity, superdex 75 16/60 gel filtration chromatography connected to fast protein liquid chromatography and identified by MALDI TOF/TOF, and manual nanospray analysis. The amount of colistin A and colistin B recovered from 500 ml of culture supernatant was about 0.05 mg. The specific activity and the average recovery of the eluted substances were 5,120 AU/mg and 1.1%, respectively. The minimal inhibitory concentrations of the purified colistins against Escherichia coli O157:H7 and Pseudomonas fluorescens LRC R73 were 0.13 and 0.62 μg/ml, respectively.
Keywords: Colistin; Paenibacillus polymyxa JB05-01-1; Antagonism; Escherichia coli
Rhizobium helanshanense sp. nov., a bacterium that nodulates Sphaerophysa salsula (Pall.) DC. in China by Wei Qin; Zhen Shan Deng; Lin Xu; Na Na Wang; Ge Hong Wei (pp. 371-378).
Studying rhizobia in the root nodules of Sphaerophysa salsula (Pall.) DC in the northwest of China, we obtained five strains classified as genus Rhizobium on the basis of their 16S rRNA gene sequences. The sequence similarity of strain CCNWQTX14T with the most related species was 99.0%. Further phylogenetic analysis of housekeeping genes (recA and atpD) suggested the five strains comprised a novel lineage within Rhizobium. The nifH and nodD gene sequences of CCNWQTX14T were phylogenetically closely related with those of Sinorhizobium kummerowiae and R. sphaerophysae, respectively. The five strains isolated from different places were also distinct from related Rhizobium species using ERIC fingerprint profiles. The DNA–DNA hybridization value was 41.8% between CCNWQTX14T and Rhizobium sphaerophysae CCNWGS0238T. Our novel strains were only able to form effective nodules on its original host Sphaerophysa salsula. Our data showed that the five Rhizobium strains formed a unique genomic species, for which a novel species Rhizobium helanshanense sp. nov. is proposed. The type strain is CCNWQTX14T (=ACCC 16237T =HAMBI 3083T).
Keywords: Polyphasic taxonomy; Phylogeny; Sphaerophysa salsula ; Rhizobia
Quorum sensing and alternative sigma factor RpoN regulate type VI secretion system I (T6SSVA1) in fish pathogen Vibrio alginolyticus by Lili Sheng; Dan Gu; Qiyao Wang; Qin Liu; Yuanxing Zhang (pp. 379-390).
Type VI secretion system (T6SS) is a highly conserved bacterial protein secretion system and is precisely regulated in Gram-negative pathogens. In Vibrio alginolyticus, an important fish pathogen, two complete T6SS gene clusters (T6SSVA1 and T6SSVA2) were identified. In this study, expression of a hemolysin coregulated protein (Hcp1), which is one of the hallmarks of T6SS, was found to be strictly regulated in this bacterium. We showed that the expression of Hcp1 was growth phase-dependent and the production of Hcp1 reached a maximum in the exponential phase. The expression of Hcp1 was positively and negatively regulated by quorum sensing regulators LuxO and LuxR, respectively. In addition, we observed that Hcp1 expression required the alternative sigma factor RpoN and the enhancer-binding protein VasH, which is encoded in T6SSVA1 gene cluster. Moreover, LuxR, RpoN, and VasH could positively regulate the expression of other T6SS genes. Taken together, we demonstrated that the expression of T6SS in V. alginolyticus was under the regulation of quorum sensing and alternative sigma factor.
Keywords: Vibrio alginolyticus ; T6SS; Quorum sensing; Hcp; RpoN