- Illumina-based analysis of bacterial diversity related to halophytes Salicornia europaea and Sueada aralocaspica
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Ying-wu Shi , Kai Lou , Chun Li , Lei Wang , Zhen-yong Zhao , Shuai Zhao , Chang-yan Tian
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J. Microbiol. 2015;53(10):678-685. Published online October 2, 2015
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DOI: https://doi.org/10.1007/s12275-015-5080-x
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 Abstract
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We used Illumina-based 16S rRNA V3 amplicon pyrosequencing
to investigate the community structure of soil bacteria
from the rhizosphere surrounding Salicornia europaea, and
endophytic bacteria living in Salicornia europaea plants and
Sueada aralocaspica seeds growing at the Fukang Desert
Ecosystem Observation and Experimental Station (FDEOES)
in Xinjiang Province, China, using an Illumina genome analyzer.
A total of 89.23 M effective sequences of the 16S rRNA
gene V3 region were obtained from the two halophyte species.
These sequences revealed a number of operational taxonomic
units (OTUs) in the halophytes. There were between
22–2,206 OTUs in the halophyte plant sample, at the 3%
cutoff level, and a sequencing depth of 30,000 sequences.
We identified 25 different phyla, 39 classes and 141 genera
from the resulting 134,435 sequences. The most dominant
phylum in all the samples was Proteobacteria (41.61%–99.26%;
average, 43.30%). The other large phyla were Firmicutes (0%–
7.19%; average, 1.15%), Bacteroidetes (0%–1.64%; average,
0.44%) and Actinobacteria (0%–0.46%; average, 0.24%). This
result
suggested that the diversity of bacteria is abundant in
the rhizosphere soil, while the diversity of bacteria was poor
within Salicornia europaea plant samples. To the extent of
our knowledge, this study is the first to characterize and
compare the endophytic bacteria found within different halophytic
plant species roots using PCR-based Illumina pyrosequencing
method
.
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- Oceanobacillus manasiensis sp. nov., a Moderately Halophilic Bacterium Isolated from the Salt Lakes of Xinjiang, China
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Lei Wang , Wen-Yan Liu , Zhi-Jing Gu , San-Feng Chen , Su-Sheng Yang
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J. Microbiol. 2010;48(3):312-317. Published online June 23, 2010
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DOI: https://doi.org/10.1007/s12275-010-0135-5
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Abstract
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Three Gram reaction positive, rod-shaped, moderately motile halophilic bacterial strains, designated YD3-56T, YD16, and YH29, were isolated from the sediments of Manasi and Aiding salt lakes in the Xinjiang region of China, respectively. The strains grew optimally at 30-37°C, pH 8-11, in the presence of 5-10% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains were closely related to members of the genus Oceanobacillus, exhibiting 99.1-99.2% similarity to O. kapialis KCTC 13177T, 99.2-99.3% to O. picturae KCTC 3821T, and 94.2-96% sequence similarity to other described Oceanobacillus species. SDS-PAGE of whole cell proteins preparations demonstrated that the strains exhibited high similarity to each other, but distinguished from O. kapialis KCTC 13177T and O. picturae KCTC 3821T (75%). DNA-DNA hybridization revealed that the similarity between the representative strain YD3-56T and O. kapialis KCTC 13177T was 35.3%, and the similarity between YD3-56T and O. picturae KCTC 3821T was 22.3%. Chemotaxonomic analysis of the strains showed menaquinone-7 was the predominant respiratory quinine. Major cellular fatty acids were anteiso-C15:0 and anteiso-C17:0. The polar lipid pattern for strain YD3-56T predominantly contained phosphatidylcholine, and trace to moderate amounts of phosphatidyl ethanolamine
and hydroxy-phosphatidyl ethanolamine. The diamino acid in murein was meso-diaminopimelic acid. The DNA G+C content of the strains was 39.7-40.1 mol%. On the basis of these results, the three strains should be classified as a novel species of the genus Oceanobacillus, for which the name Oceanobacillus manasiensis sp.
nov. has been proposed, with the type strain as YD3-56T (=CGMCC 1.9105T =NBRC 105903T).
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Citations
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- Cloning and Characterization of a Na+/H+ Antiporter Gene of the Moderately Halophilic Bacterium Halobacillus aidingensis AD-6T
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Ya Jie Zou , Li Fu Yang , Lei Wang , Su Sheng Yang
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J. Microbiol. 2008;46(4):415-421. Published online August 31, 2008
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DOI: https://doi.org/10.1007/s12275-008-0009-2
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Abstract
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A gene encoding a Na+/H+ antiporter was obtained from the genome of Halobacillus aidingensis AD-6T, which was sequenced and designated as nhaH. The deduced amino acid sequence of the gene was 91% identical to the NhaH of H. dabanensis, and shared 54% identity with the NhaG of Bacillus subtilis. The cloned gene enable the Escherichia coli KNabc cell, which lack all of the major Na+/H+ antiporters, to grow in medium containing 0.2 M NaCl or 10 mM LiCl. The nhaH gene was predicted to encode a 43.5 kDa protein (403 amino acid residues) with 11 putative transmembrane regions. Everted membrane vesicles prepared from E. coli KNabc cells carrying NhaH exhibited Na+/H+ as well as Li+/H+ antiporter activity, which was pH-dependent with the highest activity at pH 8.0, and no K+ /H+ antiporter activity was detected. The deletion of hydrophilic C-terminal amino acid residues showed that the short C-terminal tail was vital for Na+/H+ antiporter activity.
- Cloning and Characterization of the Gene Cluster for Biosynthesis of Ectoine from Nesterenkonia halobia DSM 20541
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Bo Zhang , Xin Bao , Lei Wang , Su Sheng Yang
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J. Microbiol. 2008;46(3):309-318. Published online July 5, 2008
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DOI: https://doi.org/10.1007/s12275-008-0001-x
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54
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7
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Abstract
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The ectABC genes encoding the biosynthesis of ectoine were identified from Nesterenkonia halobia DSM 20541. The intergenic regions of the ectABC genes from N. halobia DSM 20541 were more loosely spaced than those that had been reported before. The amino acid sequence deduced from ectABC of the strain was highly homologous to the EctABC of Brevibacterium linens BL2 (EctA 50%, EctB 70%, and EctC 68% identities). The osmoprotection of ectABC was studied in the Escherichia coli KNabc and E. coli XL1-Blue. The results revealed that ectABC could shorten the lag phase and enhance the final OD600 of E. coli XL1-Blue in MM63 medium containing 0.68 M NaCl, and could initiate KNabc growth in 0.2 M NaCl. Ectoine was proven to be accumulated in E. coli KNabc/pGEM-Nect using HPLC-UV, and validated by LC-MSD-Trap-VL.
- Genetic Characterization of the Escherichia coli O66 Antigen and Functional Identification of its wzy Gene
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Jiansong Cheng , Bin Liu , David A. Bastin , Weiqing Han , Lei Wang , Lu Feng
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J. Microbiol. 2007;45(1):69-74.
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DOI: https://doi.org/2488 [pii]
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Abstract
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Escherichia coli is a clonal species, and occurs as both commensal and pathogenic strains, which are normally classified on the basis of their O, H, and K antigens. The O-antigen (O-specific polysaccharide), which consists of a series of oligosaccharide (O-unit) repeats, contributes major antigenic variability to the cell surface. The O-antigen gene cluster of E. coli O66 was sequenced in this study. The genes putatively responsible for the biosynthesis of dTDP-6-deoxy-L-talose and GDP-mannose, as well as those responsible for the transfer of sugars and for O-unit processing were identified based on their homology. The function of the wzy gene was confirmed by the results of a mutation test. Genes specific for E. coli O66 were identified via PCR screening against representatives of 186 E. coli and Shigella O type strains. The comparison of intergenic sequences located between galF and the O-antigen gene cluster in a range of E. coli and Shigella showed that this region may perform an important function in the homologous recombination of the O-antigen gene clusters.
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