Phenotypic characterization of Astragalus glycyphyllos symbionts and their phylogeny based on the 16S rDNA sequences and RFLP of 16S rRNA gene

Antonie van Leeuwenhoek - Tập 105 - Trang 1033-1048 - 2014
Sebastian Gnat1, Magdalena Wójcik2, Sylwia Wdowiak-Wróbel2, Michał Kalita2, Aneta Ptaszyńska3, Wanda Małek2
1Department of Veterinary Microbiology, University of Life Sciences, Lublin, Poland
2Department of Genetics and Microbiology, University of Maria Curie-Skłodowska, Lublin, Poland
3Department of Botany and Mycology, University of Maria Curie-Skłodowska, Lublin, Poland

Tóm tắt

In this study, the nitrogen fixing Astragalus glycyphyllos symbionts were characterized by phenotypic properties, restriction fragment length polymorphism (RFLP), and sequences of 16S rDNA. The generation time of A. glycyphyllos rhizobia in yeast extract mannitol medium was in the range 4–6 h. The studied isolates exhibited a low resistance to antibiotics, a moderate tolerance to NaCl, assimilated di- and trisaccharides, and produced acid in medium containing mannitol as a sole carbon source. In the cluster analysis, based on 86 phenotypic properties of A. glycyphyllos symbionts and the reference rhizobia, examined isolates and the genus Mesorhizobium strains were placed on a single branch, clearly distinct from other lineages of rhizobial genera. By the comparative analysis of 16S rRNA gene sequences and 16S rDNA–RFLP, A. glycyphyllos nodulators were also identified as the members of the genus Mesorhizobium. On the 16S rDNA sequence phylogram, the representatives of A. glycyphyllos nodule isolates formed a robust, monophyletic cluster together with the Mesorhizobium species at 16S rDNA sequence similarity of these bacteria between 95 and 99 %. Similarly, the cluster analysis of the combined RFLP–16S rDNA patterns, obtained with seven restriction endonucleases, showed that A. glycyphyllos rhizobia are closely related to the genus Mesorhizobium bacteria. The taxonomic approaches used in this paper allowed us to classify the studied bacteria into the genus Mesorhizobium.

Tài liệu tham khảo

Allen ON, Allen EK (1981) The Leguminosae, a source book of characteristics, uses, and nodulation. University of Wisconsin Press, Madison Balachandar D, Raja P, Kumar K, Sundaram SP (2007) Non-rhizobial nodulation in legumes. Biotechnol Mol Biol Rev 2:049–057 Cowan ST, Steel KJ (1965) Manual for the identification of medical bacteria. University Press, Cambridge Cubo MT, Buendia-Claveria AM, Beringer JE, Ruiz-sainz J (1998) Melanin production by Rhizobium strains. Appl Environ Microbiol 54:1812–1817 Elkan GH (1992) Taxonomy of the rhizobia. Can J Microbiol 38:446–450 Garrity GM, Winters M, Kuo AW, Searles DB (2002) Taxonomic outline of the prokaryotes Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York Graham PH, Sadowsky MJ, Keiser HH et al (1991) Proposed minimal standards for the description of new genera and species of root and stem-nodulating bacteria. Int J Syst Bacteriol 41:582–587 Haag AF, Markus FF, Arnold MFF, Myka KK, Kerscher B, Dall’Angelo S, Matteo Zanda M, Mergaert PP, Gail P, Ferguson GP (2013) Molecular insights into bacteroid development during Rhizobium–legume symbiosis. FEMS Microbiol Rev 37:364–383 Hofer AW (1941) A characterization of Bacterium radiobacter (Beijerinck and Van Delden) Löhnis. J Bacteriol 41:193–224 Jarvis BDW, van Berkum P, Chen WX, Nour SM, Fernandez MP, Cleyet-Marel JC, Gillis M (1997) Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium ciceri, Rhizobium mediterraneum, and Rhizobium tianshanense to Mesorhizobium gen. nov. Int J Syst Bacteriol 47:895–898 Kalita M, Małek W (2004) Phenotypic and genomic characteristics of rhizobia isolated from Genista tinctoria root nodules. Syst Appl Microbiol 27:707–715 Kalita M, Małek W (2010) Genista tinctoria microsymbionts from Poland are new members of Bradyrhizobium japonicum bv. genistearum. Syst Appl Microbiol 33:252–259 Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120 Madhaiyan M, Poonguzhali S (2014) Methylobacterium pseudosasae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the bamboo phyllosphere. Antonie Van Leeuwenhoek 105:367–376 Małek W, Sajnaga E (1999) Current taxonomy of the rhizobia. Acta Microbiol Pol 48:109–122 Mierzwa B, Wdowiak-Wróbel S, Małek W (2009) Phenotypic, genomic and phylogenetic characteristics of rhizobia isolated from root nodules of Robinia pseudoacacia (black locust) growing in Poland and Japan. Arch Microbiol 191:697–710 Mierzwa B, Wdowiak-Wróbel S, Małek W (2010) Robinia pseudoacacia in Poland and Japan is nodulated by Mesorhizobium amorphae strains. Antonie Van Leeuwenhoek 97:351–361 Minamisawa K, Fukai K (1991) Production of indole-3-acetic acid by Bradyrhizobium japonicum: a correlation with genotype grouping and rhizobiotoxin production. Plant Cell Physiol 32:1–9 Nei M, Li WH (1979) Mathematical model for studying genetic variations in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:52–69 Parte AC (2014) LPSN—list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42:D613–D616. doi:10.1093/nar/gkt1111 Perret X, Staehelin C, Broughton WJ (2000) Molecular basis of symbiotic Promiscuity. Microbiol Mol Biol Rev 64:180–201 Pitcher DG, Saunders NA, Owen RJ (1989) Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8:151–156 Posada D, Crondall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818 Rossellό-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67 Safronova VI, Kimeklis A, Chizhevskaya EP, Belimov AA, Andronov EE, Pinaev AG, Pukhaev AR, Popov KP, Tikhonovich IP (2014) Genetic diversity of rhizobia isolated from nodules of the relic species Vavilovia formosa (Stev.) Fed. Antonie Van Leeuwenhoek 105:389–399 Sawada H, Kuykendall LD, Young JM (2003) Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. J Gen Appl Microbiol 49:155–179 Shamseldin A, Moawad H, Abd El-Rahim WM, Sadowsky MJ (2013) 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. doi:10.1016/j.syapm.2013.08.002 Sherwood MT (1970) Improved synthetic medium for the growth of Rhizobium. J Appl Bacteriol 33:708–713 Sikora S, Redžepović S (2003) Genotypic characterization of indigenous soybean rhizobia by PCR-RFLP of 16S rDNA, rep-PCR and RAPD analysis. Food Technol Biotechnol 41:61–67 Smibert RM, Krieg N (1981) Systematics: general characterization. In: Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA, Krieg NR, Phillips GB (eds) Manual of methods for general bacteriology. American Society for Microbiology, Washington, DC, pp 409–443 Sneath PA, Sokal R (1973) Principles of numerical taxonomy. Freeman and Co., San Francisco Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA:DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. IJSB 4(4):846–849 Swofford DL (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol Biol Evol 24(8):1596–1599 Toolarood SA, Alikhani HA, Asadi-Rahmani H, Salehi Gh, Khavazi K, Poorbabaee AA, Lindström K (2012) Molecular diversity of rhizobia isolated from root nodules of alfalfa evaluated by analysis of IGS and 16S rRNA. Ann Biol Res 3(5):2058–2063 Van Berkum P, Eardly BD (1998) Molecular evolutionary systematics of the Rhizobiaceae. In: Spaink H, Kondorosi A, Hooykass PIJ (eds) The Rhizobiaceae. Kluwer Academic Publishers, Dordrecht, pp 1–24 Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swing J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438 Vinay O, Bhupendra P, Kiran S (2013) 16S rDNA–RFLP analysis of phylogenetic tree of Rhizobium bacteria. Microbiology 12(3):474–476 Vincent J (1970) A manual for the practical study of root nodule bacteria. Blackwell Scientific Publication Ltd., Oxford Vinuesa P, Silva C, Lorite J, Izaguirre-Mayoral ML, Bedmar EJ, Martinez-Romero E (2005) 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 Wang ET, van Berkum P, Sui XH, Beyene D, Chen WX (1999) Diversity of rhizobia associated with Amorpha fruticosa isolated from Chinese soils and description of Mesorhizobium amorphae sp. nov. IJSB 49:51–65 Wang FQ, Wang ET, Liu J, Chen Q, Sui XH, Chen WF, Chen WX (2007) Mesorhizobium albiziae sp. nov., a novel bacterium that nodulates Albizia kalkora in a subtropical region of China. IJSEM 57:1192–1197 Wdowiak-Wróbel S, Małek W (2000) Numerical analysis of Astragalus cicer microsymbionts. Curr Microbiol 41:142–148 Wdowiak-Wróbel S, Małek W (2010) Following phylogenetic tracks of Astragalus cicer microsymbionts. Antonie Van Leeuwenhoek 97:21–34 Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703 Willems A (2006) The taxonomy of rhizobia: an overview. Plant Soil 287:3–14 Willems A, Collins MD (1993) Phylogenetic analysis of rhizobia and agrobacteria based on 16S rRNA gene sequences. Int J Syst Bacterial 43:305–313 Wolde-meskel E, Terefework Z, Frosteġard A, Lingstram K (2005) Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia. Int J Syst Evol Microbiol 55:1439–1452