Microbial Ecology

, Volume 55, Issue 3, pp 415–424 | Cite as

Endophytic Bacterial Diversity in Rice (Oryza sativa L.) Roots Estimated by 16S rDNA Sequence Analysis

  • Lei Sun
  • Fubin Qiu
  • Xiaoxia Zhang
  • Xin Dai
  • Xiuzhu Dong
  • Wei Song
Original Article


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.


Clone Library Rice Root Terminal Restriction Fragment Length Polymorphism Endophytic Bacterium Uncultured Bacterium 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was supported by the National Natural Science Foundation of China (Project No. 30370032 and 30170035), the Education Ministry Foundation of China (Project No. 20060028001), and the Natural Science Foundation of Hebei (Project No.2004000106).


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Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  1. 1.College of Life SciencesCapital Normal UniversityBeijingPeople’s Republic of China
  2. 2.Institute of MicrobiologyChinese Academy of SciencesBeijingPeople’s Republic of China
  3. 3.College of Life SciencesHebei UniversityBaodingPeople’s Republic of China

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