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PMID: 17690836 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Endophytic bacterial diversity in rice (Oryza sativa L.) roots estimated by 16S rDNA sequence analysis.

Microbial ecology ·Vol. 55 ·No. 3 ·2008-04-00 ·Pages 415-24

Sun L, Qiu F, Zhang X, Dai X, Dong X, Song W

Abstract

The endophytic bacterial diversity in the roots of rice (Oryza sativa L.) growing in the agricultural experimental station in Hebei Province, China was analyzed by 16S rDNA cloning, amplified ribosomal DNA restriction analysis (ARDRA), and sequence homology comparison. To effectively exclude the interference of chloroplast DNA and mitochondrial DNA of rice, a pair of bacterial PCR primers (799f-1492r) was selected to specifically amplify bacterial 16S rDNA sequences directly from rice root tissues. Among 192 positive clones in the 16S rDNA library of endophytes, 52 OTUs (Operational Taxonomic Units) were identified based on the similarity of the ARDRA banding profiles. Sequence analysis revealed diverse phyla of bacteria in the 16S rDNA library, which consisted of alpha, beta, gamma, delta, and epsilon subclasses of the Proteobacteria, Cytophaga/Flexibacter/Bacteroides (CFB) phylum, low G+C gram-positive bacteria, Deinococcus-Thermus, Acidobacteria, and archaea. The dominant group was Betaproteobacteria (27.08% of the total clones), and the most dominant genus was Stenotrophomonas. More than 14.58% of the total clones showed high similarity to uncultured bacteria, suggesting that nonculturable bacteria were detected in rice endophytic bacterial community. To our knowledge, this is the first report that archaea has been identified as endophytes associated with rice by the culture-independent approach. The results suggest that the diversity of endophytic bacteria is abundant in rice roots.

MeSH Terms
Bacteria/classification,genetics,isolation & purification Bacterial Physiological Phenomena Biodiversity China DNA, Bacterial/genetics,isolation & purification DNA, Ribosomal/genetics,isolation & purification Gene Library Molecular Sequence Data Oryza/microbiology Phylogeny Plant Roots/microbiology,physiology Polymerase Chain Reaction Polymorphism, Restriction Fragment Length RNA, Ribosomal, 16S/genetics,isolation & purification Sequence Analysis, DNA/methods Soil Microbiology Symbiosis
Chemicals
DNA, Bacterial DNA, Ribosomal RNA, Ribosomal, 16S
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Sun Lei
College of Life Sciences, Capital Normal University, Beijing 100037, People's Republic of China.
Qiu Fubin
Zhang Xiaoxia
Dai Xin
Dong Xiuzhu
Song Wei
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Article Info
Journal
Microbial ecology
Abbr.
Microb Ecol
ISSN
0095-3628
DOI
10.1007/s00248-007-9287-1
Published
2008-04-00
Epub
2007-00-10
Pages
415-24
Language
English
Region
United States
NLM ID
7500663
Subset
IM
Databases
GENBANK
DQ340871, DQ340872, DQ340873, DQ340874, DQ340875, DQ340876, DQ340877, DQ340878, DQ340879, DQ340880, DQ340881, DQ340882, DQ340883, DQ340884, DQ340885, DQ340886, DQ340887, DQ340888, DQ340889, DQ340890, DQ340891, DQ340892, DQ340893, DQ340894, DQ340895, DQ340896, DQ340897, DQ340898, DQ340899, DQ340900, DQ340901, DQ340902, DQ340903, DQ340904, DQ340905, DQ340906, DQ340907, DQ340908, DQ340909, DQ340910, DQ340911, DQ340912, DQ340913, DQ340914, DQ340915, DQ340916, DQ340917, DQ340918, DQ340919, DQ340920, DQ340921, DQ340922, DQ340923
External Links
PubMed source DOI: 10.1007/s00248-007-9287-1 View journal details
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