title: Illumina-based analysis of bacterial diversity related to halophytes Salicornia europaea and Sueada aralocaspica.
abstract: 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.
authors.affiliation: Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang, 830091, P. R. China.
authors.forename: Ying-wu
authors.initials: YW
authors.lastname: Shi
authors.affiliation: Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang, 830091, P. R. China.
authors.forename: Kai
authors.initials: K
authors.lastname: Lou
authors.affiliation: Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang, 830091, P. R. China.
authors.forename: Chun
authors.initials: C
authors.lastname: Li
authors.affiliation: State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, 830011, P.R. China.
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, 830011, P.R. China.
authors.forename: Zhen-yong
authors.initials: ZY
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, 830011, P.R. China.
authors.forename: Shuai
authors.initials: S
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, 830011, P.R. China. tianchy@ms.xjb.ac.cn.
authors.forename: Chang-yan
authors.initials: CY
authors.lastname: Tian
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000302:isolation & purification*; D044822:Biodiversity; D019663:Chenopodiaceae / Q000382:microbiology*; D002681:China; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology; D012336:RNA, Ribosomal, 16S / Q000032:analysis / Q000235:genetics; D058441:Rhizosphere; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA gene; Illumina; diversity; endophytic bacteria; halophyte