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Association of white clover (Trifolium repens L.) with rhizobia of sv. trifolii belonging to three genomic species in alkaline soils in North and East China

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Abstract

Aims

Rhizobia associated with white clover (Trifolium repens) grown in alkaline soils of China have never been investigated. This is the first survey to report of their genetic and biogeographical diversity.

Methods

Nodule bacteria were isolated from white clover grown in alkaline soils (pH 8.18–8.99) in North and East China and were characterized by multilocus sequence analysis (MLSA) of the housekeeping genes (atpD, recA, and glnII), and phylogenies of 16S rRNA gene and symbiotic genes nodC and nifH. The biogeographic distribution of rhizobial species was analyzed in relation to the soil factors.

Results

A total of 83 new strains could be affiliated to Rhizobium that shared 100 % sequence similarity of 16S rRNA gene with R. leguminosarum, R. acidisoli, R. anhuiense, R. indigoferae, R. sophorae, and R. laguerreae. Three genospecies were further distinguished based on the housekeeping gene analysis among these new strains: R. anhuiense, R. leguminosarum, and a hypothetical novel Rhizobium genospecies. Highly conserved symbiotic genes corresponding to those of symbiovar trifolii in R. leguminosarum were observed among all the new strains. Unique rhizobial communities associated with white clover were detected in the tested alkaline soils, and soil characteristics such as pH and nutrient levels were estimated as the determinant factors.

Conclusions

White clover established symbiosis with three Rhizobium genospecies harboring similar symbiotic genes in alkaline soils in China. Biogeographic pattern exists in clover rhizobia that was determined by the soil pH and nutrient levels.

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References

  • AFNOR (2005) Soil quality, determination of pH. NF ISO 10390. AFNOR, Paris

    Google Scholar 

  • Appunu C, Sasirekha N, Prabavathy VR, Nair S (2009) A significant proportion of indigenous rhizobia from India associated with soybean (Glycine max L.) distinctly belong to Bradyrhizobium and Ensifer genera. Biol Fert Soils 46:57–63

    Article  Google Scholar 

  • Braak CT, Smilauer P (2002) CANOCO reference manual and CanoDraw for Windows user’s guide: sofware for canonical community ordination (version 4.5). Section on Permutation Methods Microcomputer Power, Ithaca, Newyork.

  • Duodu S, Carlsson G, Huss-Danell K, Svenning MM (2007) Large genotypic variation but small variation in N2 fixation among rhizobia nodulating red clover in soils of northern Scandinavia. J Appl Microbiol 102:1625–1635

    Article  CAS  PubMed  Google Scholar 

  • Han L, Wang E, Han T, Liu J, Sui X, Chen W, Chen W (2009) Unique community structure and biogeography of soybean rhizobia in the saline-alkaline soils of Xinjiang, China. Plant Soil 324:291–305

    Article  CAS  Google Scholar 

  • Hill TC, Walsh KA, Harris JA, Moffett BF (2003) Using ecological diversity measures with bacterial communities. FEMS Microbiol Ecol 43:1–11

    Article  CAS  PubMed  Google Scholar 

  • Jordan DC (1984) Family III. Rhizobiaceae Conn 1938, 321AL. In: Krieg NR, Holt JG (eds) Bergey’s manual of systematic bacteriology. Williams & Wilkins, Baltimore

    Google Scholar 

  • Kumar N, Lad G, Giuntini E, Kaye M, Udomwong P, Shamsani N, Young J, Bailly X (2014) Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Open Biol 5:140133

    Article  Google Scholar 

  • Laguerre G, Mavingui P, Allard MR, Charnay MP, Louvrier P, Mazurier SI, Rigottier-Gois L, Amarger N (1996) Typing of rhizobia by PCR DNA fingerprinting and PCR-restriction fragment length polymorphism analysis of chromosomal and symbiotic gene regions: application to Rhizobium leguminosarum and its different biovars. Appl Environ Microbiol 62:2029–2036

    CAS  PubMed  PubMed Central  Google Scholar 

  • Laguerre G, Nour SM, Macheret V, Sanjuan J, Drouin P, Amarger N (2001) Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. Microbiol (England) 147:981–993

    CAS  Google Scholar 

  • Lan R, Reeves PR (2000) Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol 8:396–401

    Article  CAS  PubMed  Google Scholar 

  • Liu XY, Wang ET, Li Y, Chen WX (2007) Diverse bacteria isolated from root nodules of Trifolium, Crotalaria and Mimosa grown in the subtropical regions of China. Arch Microbiol 188:1–14

    Article  CAS  PubMed  Google Scholar 

  • Man CX, Wang H, Chen WF, Sui XH, Wang ET, Chen WX (2008) Diverse rhizobia associated with soybean grown in the subtropical and tropical regions of China. Plant Soil 310:77–87

    Article  CAS  Google Scholar 

  • Marek-Kozaczuk M, Leszcz A, Wielbo J, Wdowiak-Wróbel S, Skorupska A (2013) Rhizobium pisi sv. trifolii K3.22 harboring nod genes of the Rhizobium leguminosarum sv. trifolii cluster. Syst Appl Microbiol 36:252–258

    Article  CAS  PubMed  Google Scholar 

  • Martens M, Dawyndt P, Coopman R, Gillis M, De Vos P, Willems A (2008) Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). Int J Syst Evol Microbiol 58:200–214

    Article  CAS  PubMed  Google Scholar 

  • Mauchline TH, Hayat R, Roberts R, Powers SJ, Hirsch PR (2014) Assessment of core and accessory genetic variation in Rhizobium leguminosarum symbiovar trifolii strains from diverse locations and host plants using PCR-based methods. Lett Appl Microbiol 59:238–246

    Article  CAS  PubMed  Google Scholar 

  • Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 76:5269–5273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Olsen SR (1954) Estimation of available phosphorus in soils by extraction with sodium bicarbonate. USDA, Washington, DC

    Google Scholar 

  • Ormeño-Orrillo E, Servín-Garcidueñas LE, Rogel MA, González V, Peralta H, Mora J, Julio Martínez-Romero J, Martínez-Romero E (2015) Taxonomy of rhizobia and agrobacteria from the Rhizobiaceae family in light of genomics. Syst Appl Microbiol 38:287–291

    Article  PubMed  Google Scholar 

  • Ramirez-Bahena MH, Velazquez E, Fernandez-Santos F, Peix A, Martinez-Molina E, Mateos PF (2009) Phenotypic, genotypic, and symbiotic diversities in strains nodulating clover in different soils in Spain. Can J Microbiol 55:1207–1216

    Article  CAS  PubMed  Google Scholar 

  • Rivas R, Laranjo M, Mateos PF, Oliveira S, Martinez-Molina E, Velazquez E (2007) Strains of Mesorhizobium amorphae and Mesorhizobium tianshanense, carrying symbiotic genes of common chickpea endosymbiotic species, constitute a novel biovar (ciceri) capable of nodulating Cicer arietinum. Lett Appl Microbiol 44:412–418

    Article  CAS  PubMed  Google Scholar 

  • Rogel MA, Ormeno-Orrillo E, Martinez Romero E (2011) Symbiovars in rhizobia reflect bacterial adaptation to legumes. Syst Appl Microbiol 34:96–104

    Article  PubMed  Google Scholar 

  • Seguin P, Graham PH, Sheaffer CC, Ehlke NJ, Russelle MP (2001) Genetic diversity of rhizobia nodulating Trifolium ambiguum in North America. Can J Microbiol 47:81–85

    Article  CAS  PubMed  Google Scholar 

  • Shamseldin A, Moawad H, Abd El-Rahim WM, Sadowsky MJ (2014) Near-full length sequencing of 16S rDNA and RFLP indicates that Rhizobium etli is the dominant species nodulating Egyptian winter Berseem clover (Trifolium alexandrinum L.). Syst Appl Microbiol 37:121–128

    Article  CAS  PubMed  Google Scholar 

  • Simonis AD (1996) Effect of temperature on extraction of phosphorus and potassium from soils by various extracting solutions. Commun Soil Sci Plant Anal 27:665–684

    Article  CAS  Google Scholar 

  • Sullivan JT, Ronson CW (1998) Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. Proc Natl Acad Sci U S A 95:5145–5149

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Terefework Z, Kaijalainen S, Lindstrom K (2001) AFLP fingerprinting as a tool to study the genetic diversity of Rhizobium galegae isolated from Galega orientalis and Galega officinalis. J Biotechnol 91:169–180

    Article  CAS  PubMed  Google Scholar 

  • Tesfaye M, Holl FB (1999) Rhizobium strains that nodulate Trifolium semipilosum Fres. are phylogenetically distinct. Plant Soil 207:147–154

    Article  Google Scholar 

  • Vincent JM (1970) A manual for the practical study of root nodule bacteria. International Biological Programme (By) Blackwell Scientific, Oxford

    Google Scholar 

  • Vinuesa P, Silva C, Lorite MJ, Izaguirre-Mayoral ML, Bedmar EJ, Martinez-Romero E (2005a) Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands. Syst Appl Microbiol 28:702–716

    Article  CAS  PubMed  Google Scholar 

  • Vinuesa P, Silva C, Werner D, Martínez-Romero E (2005b) Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. Mol Phylogenet Evol 34:29–54

    Article  CAS  PubMed  Google Scholar 

  • Wang E, Van Berkum P, Sui X, Beyene D, Chen W, Martínez-Romero E (1999) Diversity of rhizobia associated with Amorpha fruticosa isolated from Chinese soils and description of Mesorhizobium amorphae sp. nov. Int J Syst Bacteriol 49:51–65

    Article  PubMed  Google Scholar 

  • Wei G, Chen W, Zhu W, Chen C, Young JPW, Bontemps C (2009) Invasive Robinia pseudoacacia in China is nodulated by Mesorhizobium and Sinorhizobium species that share similar nodulation genes with native American symbionts. FEMS Microbiol Ecol 68:320–328

    Article  CAS  PubMed  Google Scholar 

  • Wernegreen JJ, Riley MA (1999) Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: a case for the genetic coherence of rhizobial lineages. Mol Biol Evol 16:98–113

    Article  CAS  PubMed  Google Scholar 

  • Zhang YM, Li Y Jr, Chen WF, Wang ET, Tian CF, Li QQ, Zhang YZ, Sui XH, Chen WX (2011) Biodiversity and biogeography of rhizobia associated with soybean plants grown in the North China Plain. Appl Environ Microbiol 77:6331–6342

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang J, Lou K, Jin X, Mao P, Wang E, Tian C, Sui X, Chen W, Chen W (2012) Distinctive Mesorhizobium populations associated with Cicer arietinum L. in alkaline soils of Xinjiang, China. Plant Soil 353:123–134

    Article  CAS  Google Scholar 

  • Zhang YJ, Zheng WT, Everall I, Young JP, Zhang XX, Tian CF, Sui XH, Wang ET, Chen WX (2015) Rhizobium anhuiense sp. nov. isolated from effective nodules of Vicia faba and Pisum sativum. Int J Syst Evol Microbiol 65:2960–2967

Download references

Acknowledgments

This work was financed by the National Natural Science Foundation of China (Project No. 31400008) and the Scientific Research Funds of Zhengzhou University of Light Industry (Project No. 2014bsjj006). ETW is financially supported by grants SIP20150597 authorized by Instituto Politécnico Nacional, Mexico. Thanks to JunWei Zhang from Ruzhou and Xianchao Yang from Shanghai for assistance in the soil sampling.

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Authors and Affiliations

  1. Department of Bioengineering and Biotechnology, College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, Henan, People’s Republic of China

    Jun Jie Zhang, Xiao Yan Jing & Pei Xin He

  2. Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, Zhengzhou, 450002, Henan Province, P. R. China

    Jun Jie Zhang & Chuang Ma

  3. IRD, Lab Symbioses Trop & Mediterraneennes, F-34398, Montpellier 5, France

    Philippe de Lajudie

  4. Department of Environmental Engineering, College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, Henan Province, P. R. China

    Chuang Ma

  5. State Key Laboratory of Microbial Technology, College of Life Science, Shandong University, Jinan, 250100, Shandong Province, People’s Republic of China

    Raghvendra Pratap Singh

  6. College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing, 100193, People’s Republic of China

    Wen Feng Chen

  7. Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México, D. F. 11340, México

    En Tao Wang

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  1. Jun Jie Zhang
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Correspondence to Jun Jie Zhang.

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Zhang, J.J., Jing, X.Y., de Lajudie, P. et al. Association of white clover (Trifolium repens L.) with rhizobia of sv. trifolii belonging to three genomic species in alkaline soils in North and East China. Plant Soil 407, 417–427 (2016). https://doi.org/10.1007/s11104-016-2899-9

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