基于高通量测序分析盐角草根部内生细菌多样性及动态规律

Endophytic bacterial diversity and dynamics in root of Salicornia europaea estimated via high throughput sequencing

摘要:

[目的] 探讨盐角草根部内生细菌群落多样性特征,揭示内生细菌群落结构在宿主关键发育期动态变化规律。[方法] 通过罗氏454高通量测序获得内生细菌16S rRNA片段,然后进行生物信息分析。[结果] 共获得20363条16S rRNA基因序列。各样品中可操作分类单元 (operational taxonomic units,OTUs)在552-941之间。根部内生细菌群落主要包括4个门,其中Proteobacteri门占主导地位,其余依次是Firmicutes,Actinobacteria,Bacteroidetes。在Proteobacteria门中,Gammaproteobacteria是第一大纲,其后是Betaproteobacteria纲。宿主5个发育时期共同拥有7个细菌属,包括Azomonas,Serratia,Pantoea,Serpens,Pseudomonas,Halomonas,Kushneria。整体上看,Gammaproteobacteria纲在宿主5个发育时期呈现增长趋势。优势菌属在5个发育期存在差异,分别为Delftia,Kushneria,Serratia,Pantoea,Erwinia。所有文库总共含2108个特异OTUs, 共同拥有5个相同OTUs。花期OTUs数量最多,结种期内生细菌多样性降低。在宿主的5个发育时期中,土壤pH、月均温和土壤盐含量这3个环境因子组成的集合对其内生细菌群落变化具有显著影响。[结论] 盐角草内生细菌群落多样性丰富,宿主发育期决定了内生细菌群落结构。

Abstract:

[Objective] This study aimed to describe the composition of the endophytic bacterial communities in Salicornia europaea root, and to examine how endophytic bacteria vary across host growth periods. [Methods] PCRbased Roche FLX 454 pyrosequencing was applied to reveal the diversity and succession of endophytic bacteria. [Results] A total of 20363 partial 16S rRNA gene sequences were obtained. These sequences revealed huge amount of operational taxonomic units (OTUs), that is, 552-941 OTUs in a root sample. Endophytes in roots mainly comprised four phyla, among which Proteobacteria was the most represented, followed by Firmicutes, Actinobacteria, and Bacteroidetes. Gammaproteobacteria was the most abundant class of Proteobacteria, followed by Betaproteobacteria of this phylum. Genus Azomonas, Serratia, Pantoea, Serpens, Pseudomonas, Halomonas, and Kushneria were shared by all growth stages. Gammaproteobacteria increased during the five stages. The dominant bacterial genera during five periods were related to Delftia, Kushneria, Serratia, Pantoea, Erwinia, respectively. Five libraries contained 2108 unique OTUs with 5 OTUs in common. The greatest number of OTUs was detected during flowering stage. Endophytic bacteria diversity was reduced during fruiting stage. A combination of soil pH, average monthly temperature and soil salt concentration has significant effects on the endophytic bacterial community structure during the five stages. [Conclusion] As a whole, the diversity of endophytic bacteria was high inroot of Salicornia europaea. The distribution of endophytic bacteria showed obvious dynamic changes, and the host growth stages determined the endophytic bacterial community.