Shi Ying-wu, Lou Kai, Li Chun, Wang Lei, Zhao Zhen-yong, Zhao Shuai, Tian Chang-yan
Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang, 830091, P. R. China.
State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, 830011, P.R. China.
J Microbiol. 2015 Oct;53(10):678-85. doi: 10.1007/s12275-015-5080-x. Epub 2015 Oct 2.
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.
我们使用基于Illumina的16S rRNA V3扩增子焦磷酸测序技术，利用Illumina基因组分析仪，对中国新疆阜康荒漠生态系统观测与实验站（FDEOES）生长的盐角草根际土壤细菌群落结构、盐角草植物内生细菌以及盐爪爪种子内生细菌进行了研究。从这两种盐生植物中总共获得了8923万个16S rRNA基因V3区域的有效序列。这些序列揭示了盐生植物中的一些操作分类单元（OTU）。在3%的截断水平和30000条序列的测序深度下，盐生植物样本中的OTU数量在22至2206个之间。我们从得到的134435条序列中鉴定出25个不同的门、39个纲和141个属。所有样本中最主要的门是变形菌门（41.61%-99.26%；平均为43.30%）。其他较大的门是厚壁菌门（0%-7.19%；平均为1.15%）、拟杆菌门（0%-1.64%；平均为0.44%）和放线菌门（0%-0.46%；平均为0.24%）。这一结果表明，根际土壤中细菌多样性丰富，而盐角草植物样本中的细菌多样性较差。据我们所知，本研究首次使用基于PCR的Illumina焦磷酸测序方法对不同盐生植物物种根内发现的内生细菌进行了表征和比较。
