Title |
Illumina-based analysis of bacterial diversity related to halophytes Salicornia europaea and Sueada aralocaspica |
Author |
Ying-wu Shi1, Kai Lou1, Chun Li1, Lei Wang2, Zhen-yong Zhao2, Shuai Zhao2, and Chang-yan Tian2* |
Address |
1Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, P. R. China, 2State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, P. R. China |
Bibliography |
Journal of Microbiology, 53(10),678-685, 2015,
|
DOI |
10.1007/s12275-015-5080-x
|
Key Words |
halophyte, endophytic bacteria, diversity, Illumina,
16S rRNA gene |
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. |