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The identification and genetic diversity of endophytic bacteria isolated from selected crops

Published online by Cambridge University Press:  14 August 2018

M. Woźniak ,
A. Gałązka ,
J. Grządziel  and
M. Głodowska
M. Woźniak*
Affiliation:
Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation – State Research Institute, Czartoryskich Street 8, 24-100 Pulawy, Poland
A. Gałązka
Affiliation:
Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation – State Research Institute, Czartoryskich Street 8, 24-100 Pulawy, Poland
J. Grządziel
Affiliation:
Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation – State Research Institute, Czartoryskich Street 8, 24-100 Pulawy, Poland
M. Głodowska
Affiliation:
Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation – State Research Institute, Czartoryskich Street 8, 24-100 Pulawy, Poland
*
Author for correspondence: M. Woźniak, E-mail: mlyszcz@iung.pulawy.pl
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Abstract

A collection of 45 isolates was created based on bacteria isolated from maize, broad bean, wheat, rye and wild plants such as horsetail and burdock. The aim of the current study was to isolate the bacteria, and then identify and assess the degree of genomic diversity. The molecular identification of microsymbionts isolated from the endosphere (root and stem) of plants grown in agricultural soils was performed using 16S rRNA gene sequencing. To evaluate the genomic diversity between strains that occurred in multiple host plants, 18 bacterial isolates representing four species were subjected to denaturing gradient gel electrophoresis. The 16S rDNA analysis assigned all bacterial isolates to ten genera, from which Rhizobium was represented by 19 isolates, Delftia by 11, Agrobacterium by five, Stenotrophomonas by three, Brevundimonas by two and Novosphingobium, Variovorax, Collimonas, Achromobacter and Comamonas by only one isolate. Furthermore, the genomic diversity of the 11 isolates of Delftia sp. was assessed using the BOX – polymerase chain reaction (BOX-PCR) and enterobacterial repetitive intergenic consensus – PCR (ERIC-PCR) methods. Typing patterns and analysis using BOX-PCR and ERIC-PCR data demonstrated similarities among the tested isolates. In general, the results obtained with BOX-PCR and ERIC-PCR were in good agreement. However, a greater degree of differentiation patterns of the genomic DNA was obtained in the ERIC-PCR method.

Keywords

16S rRNA genebiodiversityendophytesPCR
Type
Crops and Soils Research Paper
Information
The Journal of Agricultural Science , Volume 156 , Issue 4 , May 2018 , pp. 547 - 556
Copyright
Copyright © Cambridge University Press 2018 

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References

Ambawade, MS and Pathade, GR (2015) Production of indole acetic acid (IAA) by Stenotrophomonas maltophilia BE25 isolated from roots of banana (Musa spp). International Journal of Science and Research 4, 2644–2650.Google Scholar
Bers, K, Sniegowski, K, Albers, P, Breugelmans, P, Hendrickx, L, De Mot, R and Springael, D (2011) A molecular toolbox to estimate the number and diversity of Variovorax in the environment: application in soils treated with the phenylurea herbicide linuron. FEMS Microbiology Ecology 76, 14–25.Google Scholar
Boon, N, Goris, J, De Vos, P, Verstraete, W and Top, EM (2001) Genetic diversity among 3-chloroaniline-and aniline-degrading strains of the comamonadaceae. Applied and Environmental Microbiology 67, 1107–1115.Google Scholar
Brooke, JS (2012) Stenotrophomonas maltophilia: an emerging global opportunistic pathogen. Clinical Microbiology Reviews 25, 2–41.Google Scholar
De Bruijn, FJ (1992) Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Applied and Environmental Microbiology 58, 2180–2187.Google Scholar
De Oliveira, VM, Coutinho, HLC, Sobral, BWS, Guimaraes, CT, Van Elsas, JD and Manfio, GP (1999) Discrimination of Rhizobium tropici and R. leguminosarum strains by PCR-specific amplification of 16S–23S rDNA spacer region fragments and denaturing gradient gel electrophoresis (DGGE). Letters in Applied Microbiology 28, 137–141.Google Scholar
De Oliveira Costa, LE, de Queiroz, MV, Borges, AC, de Moraes, CA and de Araújo, EF (2012) Isolation and characterization of endophytic bacteria isolated from the leaves of the common bean (Phaseolus vulgaris). Brazilian Journal of Microbiology 43, 1562–1575.Google Scholar
Deshwal, VK, Pandey, P, Kang, SC and Maheshwari, DK (2003) Rhizobia as a biological control agent against soil borne plant pathogenic fungi. Indian Journal of Experimental Biology 41, 1160–1164.Google Scholar
Dice, LR (1945) Measures of the amount of ecologic association between species. Ecology 26, 297–302.Google Scholar
Frąc, M and Jezierska-Tys, S (2010) Różnorodność mikroorganizmów środowiska glebowego. Postępy Mikrobiologii 40, 47–58.Google Scholar
Gaiero, JR, McCall, CA, Thompson, KA, Day, NJ, Best, AS and Dunfield, KE (2013) Inside the root microbiome: bacterial root endophytes and plant growth promotion. American Journal of Botany 100, 1738–1750.Google Scholar
Gałązka, A, Gawryjołek, K, Grządziel, J, Frąc, M and Księżak, J (2017) Microbial community diversity and the interaction of soil under maize growth in different cultivation techniques. Plant Soil and Environment 63, 264–270.Google Scholar
Gao, J, Terefework, Z, Chen, W and Lindström, K (2001) Genetic diversity of rhizobia isolated from Astragalus adsurgens growing in different geographical regions of China. Journal of Biotechnology 91, 155–168.Google Scholar
Gnat, S, Małek, W, Oleńska, E, Trościańczyk, A, Wdowiak-Wróbel, S, Kalita, M and Wójcik, M (2015) Insight into the genomic diversity and relationship of Astragalus glycyphyllos symbionts by RAPD, ERIC-PCR, and AFLP fingerprinting. Journal of Applied Genetics 56, 551–554.Google Scholar
Grządziel, J and Gałązka, A (2018) Microplot long-term experiment reveals strong soil type influence on bacteria composition and its functional diversity. Applied Soil Ecology 124, 117–123.Google Scholar
Gupta, RM, Kale, PS, Rathi, ML and Jadhav, NN (2015) Isolation, characterization and identification of endophytic bacteria by 16S rRNA partial sequencing technique from roots and leaves of Prosopis cineraria plant. Asian Journal of Plant Science and Research 5, 36–43.Google Scholar
Han, JI, Choi, HK, Lee, SW, Orwin, PM, Kim, J, LaRoe, SL, Kim, TG, O'Neil, J, Leadbetter, JR, Lee, SY, Hur, CG, Spain, JC, Ovchinnikova, G, Goodwin, L and Han, C (2011) Complete genome sequence of the metabolically versatile plant growth-promoting endophyte Variovorax paradoxus S110. Journal of Bacteriology 193, 1183–1190.Google Scholar
Handelsman, J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews 68, 669–685.Google Scholar
Hollender, J, Dreyer, U, Kornberger, L, Kämpfer, P and Dott, W (2002) Selective enrichment and characterization of a phosphorus-removing bacterial consortium from activated sludge. Applied Microbiology and Biotechnology 58, 106–111.Google Scholar
James, DW, Suslow, TV and Steinback, KE (1985) Relationship between rapid, firm adhesion and long-term colonization of roots by bacteria. Applied and Environmental Microbiology 50, 392–397.Google Scholar
Jha, P and Kumar, A (2009) Characterization of novel plant growth promoting endophytic bacterium Achromobacter xylosoxidans from wheat plant. Microbial Ecology 58, 179–188.Google Scholar
Katara, J, Deshmukh, R, Singh, NK and Kaur, S (2012) Molecular typing of native Bacillus thuringiensis isolates from diverse habitats in India using REP-PCR and ERIC-PCR analysis. Journal of General and Applied Microbiology 58, 83–94.Google Scholar
Kawamura, I, Yagi, T, Hatakeyama, K, Hasegawa, Y, Ohkura, T, Ohkusu, K, Takahashi, Y and Kojima, S (2011) Recurrent vascular catheter-related bacteremia caused by Delftia acidovorans with different antimicrobial susceptibility profiles. Journal of Infection and Chemotherapy 17, 111–113.Google Scholar
Knief, C, Delmotte, N and Vorholt, JA (2011) Bacterial adaptation to life in association with plants–A proteomic perspective from culture to in situ conditions. Proteomics 11, 3086–3105.Google Scholar
Kumar, V and Gera, R (2014) Isolation of a multi-trait plant growth promoting Brevundimonas sp. and its effect on the growth of Bt-cotton. 3 Biotech 4, 97–101.Google Scholar
Kumar, A, Kumar, A and Pratush, A (2014) Molecular diversity and functional variability of environmental isolates of Bacillus species. SpringerPlus 3, 312.Google Scholar
Lane, DJ (1991) 16S/23S rRNA sequencing. In Stackebrandt, E and Goodfellow, M (eds), Nucleic Acid Techniques in Bacterial Systematics. New York, NY, USA: John Wiley & Sons, pp. 115–147.Google Scholar
Li, JH, Wang, ET, Chen, WF and Chen, WX (2008) Genetic diversity and potential for promotion of plant growth detected in nodule endophytic bacteria of soybean grown in Heilongjiang province of China. Soil Biology and Biochemistry 40, 238–246.Google Scholar
Liaqat, F and Eltem, R (2016) Identification and characterization of endophytic bacteria isolated from in vitro cultures of peach and pear rootstocks. 3 Biotech 6, 120.Google Scholar
Lin, CW, Chiou, CS, Chang, YC and Yang, TC (2008) Comparison of pulsed-field gel electrophoresis and three rep-PCR methods for evaluating the genetic relatedness of Stenotrophomonas maltophilia isolates. Letters in Applied Microbiology 47, 393–398.Google Scholar
Lodewyckx, C, Vangronsveld, J, Porteous, F, Moore, ER, Taghavi, S, Mezgeay, M and van der Lelie, D (2002) Endophytic bacteria and their potential applications. Critical Reviews in Plant Sciences 21, 583–606.Google Scholar
Miliute, I, Buzaite, O, Baniulis, D and Stanys, V (2015) Bacterial endophytes in agricultural crops and their role in stress tolerance: a review. Zemdirbyste (Agriculture) 102, 465–478.Google Scholar
Müller, RH, Jorks, S, Kleinsteuber, S and Babel, W (1999) Comamonas acidovorans strain MC1: a new isolate capable of degrading the chiral herbicides dichlorprop and mecoprop and the herbicides 2, 4-D and MCPA. Microbiological Research 154, 241–246.Google Scholar
Muyzer, G and Smalla, K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek 73, 127–141.Google Scholar
Myers, RM, Maniatis, T and Lerman, LS (1987) Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods in Enzymology 155, 501–527.Google Scholar
Nakatsu, CH, Torsvik, V and Øvreås, L (2000) Soil community analysis using DGGE of 16S rDNA polymerase chain reaction products. Soil Science Society of America Journal 64, 1382–1388.Google Scholar
Narayan, KD, Pandey, SK and Das, SK (2010) Characterization of Comamonas thiooxidans sp. nov., and comparison of thiosulfate oxidation with Comamonas testosteroni and Comamonas composti. Current Microbiology 61, 248–253.Google Scholar
Niu, B, Paulson, JN, Zheng, X and R K (2017) Simplified and representative bacterial community of maize roots. Proceedings of the National Academy of Sciences USA 114, E2450–E2459.Google Scholar
Ogutcu, H, Adiguzel, A, Gulluce, M, Karadayi, M and Sahin, F (2009) Molecular characterization of Rhizobium strains isolated from wild chickpeas collected from high altitudes in Erzurum-Turkey. Romanian Biotechnological Letters 14, 4294–4300.Google Scholar
Otsu, Y, Matsuda, Y, Shimizu, H, Ueki, H, Mori, H, Fujiwara, K, Nakajima, T, Miwa, A, Nonomura, T, Sakuratani, Y, Tosa, Y, Mayama, S and Toyoda, H (2003) Biological control of phytophagous ladybird beetles Epilachna vigintioctopunctata (Col., Coccinellidae) by chitinolytic phylloplane bacteria Alcaligenes paradoxus entrapped in alginate beads. Journal of Applied Entomology 127, 441–446.Google Scholar
Puławska, J, Willems, A, De Meyer, SE and Süle, S (2012) Rhizobium nepotum sp. nov. isolated from tumors on different plant species. Systematic and Applied Microbiology 35, 215–220.Google Scholar
Robinson, RJ, Fraaije, BA, Clark, IM, Jackson, RW, Hirsch, PR and Mauchline, TH (2016) Endophytic bacterial community composition in wheat (Triticum aestivum) is determined by plant tissue type, developmental stage and soil nutrient availability. Plant and Soil 405, 381–396.Google Scholar
Santoyo, G, Moreno-Hagelsieb, G, del Carmen Orozco-Mosqueda, M and Glick, BR (2016) Plant growth-promoting bacterial endophytes. Microbiological Research 183, 92–99.Google Scholar
Senthilkumar, M, Anandham, R, Madhaiyan, M, Venkateswaran, V and Sa, T (2011) Endophytic bacteria: perspectives and applications in agricultural crop production. In Maheshwari, DK (ed.), Bacteria in Agrobiology: Crop Ecosystems. Berlin, Germany: Springer, pp. 61–96.Google Scholar
Sun, L, Qiu, F, Zhang, X, Dai, X, Dong, X and Song, W (2008) Endophytic bacterial diversity in rice (Oryza sativa L.) roots estimated by 16S rDNA sequence analysis. Microbial Ecology 55, 415–424.Google Scholar
Szilagyi-Zecchin, VJ, Ikeda, AC, Hungria, M, Adamoski, D, Kava-Cordeiro, V, Glienke, C and Galli-Terasawa, LV (2014) Identification and characterization of endophytic bacteria from corn (Zea mays L.) roots with biotechnological potential in agriculture. AMB Express 4, 26.Google Scholar
Versalovic, J, Schneider, M, De Bruijn, FJ and Lupski, JR (1994) Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods in Molecular and Cellular Biology 5, 25–40.Google Scholar
Wilson, D (1995) Endophyte: the evolution of a term, and clarification of its use and definition. Oikos 73, 274–276.Google Scholar