title: Long-term rice and green manure rotation alters the endophytic bacterial communities of the rice root.
abstract: This study focuses on the effects of long-term rice rotated with milk vetch being as green manure on the composition of bacteria in rice roots. The endophytic bacterial communities in rice roots of the rice-rice-milk vetch (R-R-MV) and the rice-rice-winter fallow (R-R-WF) crop rotations with a 28-year research history were investigated using combined culture-dependent and culture-independent methods. It was found that the endophytic bacterial population in rice roots with the green manure was significantly higher than that of without it. There were 169 and 77 strains of endophytic bacteria that were isolated from rice roots of the R-R-MV and the R-R-WF, respectively. The 16S rRNA gene analysis shows that the 77 R-R-WF bacteria belong to 15 species of 14 genera while the other 169 R-R-MV bacteria belong to 21 species of 19 genera, in which Herbaspirillum and Cedecea were two mutually dominant populations and Burkholderia, Pseudomonas, Sphingomonas, and Pantoea accounted for large proportions of the endophytic bacteria in rice roots through R-R-MV rotation. The analysis of 16S rDNA clone libraries showed that the Shannon-Weaver diversity index of endophytic bacteria in R-R-MV approximates that in R-R-WF rotation, whereas the richness indexes of Chao 1 and ACE in R-R-MV rotation system were significantly higher than those in R-R-WF rotation. The diversity of endophytic bacteria was richer in R-R-MV. Both the culture-dependent and the culture-independent method revealed significant effect of long-term different tillage systems on the microbial community.
authors.affiliation: Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
authors.forename: Xiao-Xia
authors.initials: XX
authors.lastname: Zhang
authors.forename: Ju-Sheng
authors.initials: JS
authors.lastname: Gao
authors.forename: Yan-Hua
authors.initials: YH
authors.lastname: Cao
authors.forename: Xiao-Tong
authors.initials: XT
authors.lastname: Ma
authors.forename: Ji-Zheng
authors.initials: JZ
authors.lastname: He
mesh_terms: D000383:Agriculture; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D044822:Biodiversity; D060026:Endophytes / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D008372:Manure / Q000032:analysis*; D008969:Molecular Sequence Data; D012275:Oryza / Q000254:growth & development / Q000382:microbiology*; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology*; D013997:Time Factors
chemical_list: D008372:Manure
references.citation: Int J Syst Evol Microbiol. 2012 Mar;62(Pt 3):716-721
references.pmid: 22140171
references.citation: FEMS Microbiol Ecol. 2003 Jul 1;45(1):39-47
references.pmid: 19719605
references.citation: Appl Environ Microbiol. 2009 Dec;75(23):7537-41
references.pmid: 19801464
references.citation: EMBO Rep. 2004 Oct;5(10):922-6
references.pmid: 15459741
references.citation: Microb Ecol. 2008 Apr;55(3):415-24
references.pmid: 17690836
references.citation: Microb Ecol. 2001 Apr;41(3):252-263
references.pmid: 11391463
references.citation: FEMS Microbiol Ecol. 2003 Feb 1;43(1):1-11
references.pmid: 19719691
references.citation: Microb Ecol. 2001 Aug;42(2):136-149
references.pmid: 12024277
references.citation: Trends Microbiol. 2008 Oct;16(10):463-71
references.pmid: 18789693
references.citation: Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
references.pmid: 9396791
references.citation: Bioresour Technol. 2008 Apr;99(6):1758-67
references.pmid: 17512725
references.citation: Syst Appl Microbiol. 2003 Sep;26(3):445-52
references.pmid: 14529188
references.citation: Microb Ecol. 2001 Feb;41(4):369-383
references.pmid: 12032611
references.citation: Microbes Environ. 2008;23(2):109-17
references.pmid: 21558696
references.citation: J Microbiol Biotechnol. 2007 Jan;17(1):96-103
references.pmid: 18051359
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: Science. 2000 Sep 15;289(5486):1922-5
references.pmid: 10988070
references.citation: Appl Environ Microbiol. 2001 Nov;67(11):5285-93
references.pmid: 11679357
references.citation: PLoS One. 2010 May 26;5(5):e10834
references.pmid: 20520808