Biodiversity Science ›› 2011, Vol. 19 ›› Issue (4): 485-493.doi: 10.3724/SP.J.1003.2011.09232

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Genetic diversity in rhizosphere soil microbes detected with SRAP markers

Chunnan Li1, 2, Hairui Cui1*, Weibo Wang1   

  1. 1Institute of Nuclear-Agricultural Sciences/Key Laboratory of Nuclear Agricultural Sciences, Ministry of Agriculture, Zhejiang University, Hangzhou 310029

    2Institute of Horticulture, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024
  • Received:2010-09-20 Revised:2011-01-30 Online:2011-07-29
  • Hairui Cui E-mail:hrcui@zju.edu.cn

We have attempted to use the SRAP (sequence-related amplified polymorphism) markers, a new molecular technology, to study genetic diversity in soil microbes. We sampled rhizosphere soil microbes from 20 plant species and employed 22 SRAP primer combinations. A total of 237 scorable fragments were identi-fied, of which 221 (93.2%) were polymorphic loci. The average percentage of polymorphic loci (PPL), po-lymorphism information content (PIC), allele haplotype (Ah), and expected heterozygosity (He) for each primer combination were 93.78%, 0.94, 18.05 and 0.92, respectively. Our results revealed rich genetic diver-sity in rhizosphere soil microbes and the high ability of SRAP to resolve samples based on their genetic basis. Differences in genetic distance for rice rhizosphere microbes between two locations, and that among four different developmental stages were both significant at 0.01 level, but the difference was not significant be-tween two varieties. Shannon diversity indices indicated that the genetic diversity of rhizosphere soil mi-crobes was lowest in rice and highest in lettuce. The rhizosphere soil microbes from 20 plant species could be clustered into three groups at the 0.454 (GD) level based on UPGMA, in which the first group was from rice, while the second group was from celery planted in plastic green house, and the third group was from 18 other plant species cultivated in dry lands. Our results suggest that SRAP is an efficient method for analyzing the genetic diversity in rhizosphere soil microbes.

Key words: scleractinian coral, species diversity, coral associated species

Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in-situ detection of individual microbial-cells without cultivation. Microbiological Reviews , 59, 143–169.

Bi JT (毕江涛), He DH (贺达汉) (2009) Research advances in effects of plant on soil microbial diversity. Chinese Agricultural Science Bulletin (中国农学通报), 25, 244–250. (in Chinese with English abstract)

Borneman J, Triplett EW (1997) Molecular microbial diversity in soils from Eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Applied and Environmental Microbiology, 63, 2647–2653.

Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic-linkage map in man using restriction fragment length polymorphisms. The American Journal of Human Genetics, 32, 314–331.

Carelli M, Gnocchi S, Fancelli S, Mengoni A, Paffetti D, Scotti C, Bazzicalupo M (2000) Genetic diversity and dynamics of sinorhizobium meliloti populations nodulating different alfalfa cultivars in Italian soils. Applied and Environmental Microbiology, 66, 4785–4789.

Chen J (陈静), Hu XH (胡晓辉), Miao HR (苗华荣),Cui FG (崔凤高), Yu SL (禹山林) (2008) Genome DNA extracted with CTAB method and its use for SSR and SRAP. Journal of Peanut Science (花生学报), 37, 29–31. (in Chinese with English abstract)

Chen XY (陈旭玉), Zhou YK (周亚奎), Yu XM (余贤美), Zheng FC (郑服丛) (2008) An affection method for DNA extraction from soil microorganisms. Chinese Agricultural Science Bulletin (中国农学通报), 24, 33–36. (in Chinese with English abstract)

Cho JC, Tiedje JM (2001) Bacterial species determination from DNA–DNA hybridization by using genome fragments and DNA microarrays. Applied and Environmental Microbiology, 67, 3677–3682.

Fu HT (傅洪拓), Qiao H (乔慧), Yao JH (姚建华), Gong YS (龚永生), Wu Y (吴滟), Jiang SF (蒋速飞), Xiong YW (熊贻伟) (2010) Genetic diversity in five Macrobrachium hainanense populations using SRAP markers, Biodiversity Science (生物多样性), 18, 145–149. (in Chinese with English abstract)

Head IM, Saunders JR, Pickup RW (1998) Microbial evolution, diversity and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microbial Ecology, 35, 1–21.

Hubert C, Shen Y, Voordouw G (1999) Composition of toluene-degrading microbial communities from soil at different concentrations of toluene. Applied and Environmental Microbiology, 65, 3064–3070.

Kirk JL, Beaudette LA, Hart M, Moutoglis P, Klironomos JN, Lee H, Trevors JT (2004) Methods of studying soil microbial diversity. Journal of Microbiological Methods, 58, 169–188.

Lee DH, Zo YG, Kim SJ (1996) Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism. Applied and Environmental Microbiology, 62, 3112–3120.

Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theoretical and Applied Genetics, 103, 455–461.

Li Y (李严), Zhang CQ (张春庆) (2005) A molecular marker—SRAP technique optimization and application analysis, Chinese Agricultural Science Bulletin (中国农学通报), 21, 108–112.(in Chinese with English abstract)

Liu LW (柳李旺), Gong YQ (龚义勤), Huang H (黄浩), Zhu XW (朱献文) (2004) Novel molecular marker systems—SRAP and TRAP and their application, Hereditas (遗传), 26, 777–781. (in Chinese with English abstract)

Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Applied and Environmental Microbiology, 63, 4516–4522.

Muyzer G (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Current Opinion in Microbiology, 2, 317–322.

Muyzer G, Dewaal EC, Uitterlinden AG (1993) Profiling of complex microbial-populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16S ribosomal-RNA. Applied and Environmental Microbiology, 59, 695–700.

Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences, USA, 76, 569–573.

Osborn AM, Moore ERB, Timmis KN (2000) An evaluation of terminal restriction fragment length polymorphisms (T-RFLP) analysis for the study of microbial community structure and dynamics. Environmental Microbiology, 2, 39–50.

Ren M (任民), Jia XH (贾兴华), Jiang CH (蒋彩虹), Yang AG (杨爱国), Wang RJ (王日新) (2008) Comparison study of Bassam and Sanguinetti silver staining in the detecting of SRAP and TRAP, Biotechnology Bulletin (生物技术通报), 1, 113–116. (in Chinese with English abstract)

Terefework Z, Kaijalainen S, Lindstr?m K (2001) AFLP fingerprinting as a tool to study the genetic diversity of Rhizobium galegae isolated from Galega orientalis and Galega officianlis. Journal of Biotechnology, 91, 169–180.

Willems A, Doignon-Bourcier F, Coopman R, Hoste B, de Lajudie P, Gillis M (2000) AFLP fingerprint analysis of Bradyrhizobium strains isolated from Faidherbia albida and Aeschynommene species. Systematic and Applied Microbiology, 23, 137–147.

Xia X, Bollinger J, Ogram A (1995) Molecular genetic analysis of the response of three soil microbial communities to the application of 2, 4-D. Molecular Ecology, 4, 17–28.

Zhang JE (章家恩), Liu WG (刘文高), Hu G (胡刚) (2002) The relationship between quantity index of soil microorganisms and soil fertility of different land use systems. Soil and Enviromental Sciences (土壤与环境), 11, 140–143. (in Chinese with English abstract)

Zhao X (赵雪), Xie H (谢华), Ma RC (马荣才) (2007) New functional molecular markers for plants in the functional genomics Era. China Biotechnology (中国生物工程杂志), 27(8), 104–110. (in Chinese with English abstract)

Zhou J (周桔), Lei T (雷霆) (2007) Review and prospects on methodology and affecting factors of soil microbial diversity. Biodiversity Science (生物多样性), 15, 306–311. (in Chinese with English abstract)
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