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

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.