American Journal of Life Sciences

| Peer-Reviewed |

Isolation, Characterization and Identification of Endophytic Bacteria in Sugarcane (Saccharum spp. L.) Cultivated on Soils of the Dong Nai Province, Southeast of Vietnam

Received: Nov. 29, 2014    Accepted: Dec. 09, 2014    Published: Dec. 18, 2014
Views:       Downloads:

Share This Article

Abstract

Endophytic bacterial diversity in sugarcane plant cultivated on Latosols and Acrisols of the Eastern of South Vietnam was studied. Sugarcane plant samples were taken in four sites (districts/towns) (Xuanloc, Dinhquan, Vinhc uu and Trangbom) of Dong Nai province. Endophytic bacteria were isolated in LGI medium together with 16S rRNA gene fragments amplified from DNA using eubacterial universal primers (p515FPL and p13B). A total of 27 isolates were isolated on LGI medium and all of them have ability of nitrogen fixation and phosphate solubilization together with IAA biosynthesis but there were 10 isolates having the best characteristics. The sequences from selected endophytic bacteria (10 isolates) showed high degrees of similarity to those of the GenBank references strains (between 98% and 99%). All of them are Proteobacteria (gram-negative bacteria) and 3 isolates belonged to Alpha-proteobacteria (30%), 2 isolates were Beta-proteobacteria (20%), 5 isolates were Gamma-proteobacteria (50%). Based on Pi value (nucleotide diversity), Gamma-proteobacteria group had the highest theta values and Theta values (per sequence) from S of SNP for DNA polymorphism were calculated for each group and Gamma-proteobacteria group had the highest values in comparison of two groups. From these results showed that Enterobacter oryzae LT7, Achromobacter xylosoxidans T16, Achromobacter insolitus R15b and Pantoea agglomerans T12 revealed promising candidates with multiple beneficial characteristics and they have the potential for application as inoculants or bio-fertilizer adapted to poor latosols and acrisols because they are not only famous strains but also are safety strains for sustainable agriculture.

DOI 10.11648/j.ajls.20140206.16
Published in American Journal of Life Sciences ( Volume 2, Issue 6, December 2014 )
Page(s) 361-368
Creative Commons

This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.

Copyright

Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

Acrisols, 16S rRNA Gene Sequence, Latosols, the Eastern of the South Vietnam, Endophytic Bacteria, Sugarcane

References
[1] N. Thaweenut, Y. Hachisuka, S. Ando, S. Yanagisawa and T. Yoneyama, “Two season’ study on nifH gene expression and nitrogen fixation by diazotrophic endophytes in sugarcane (Saccharum spp. hybrids): expression of nifH genes similar to those of rhizobia,” Plant Soil, vol. 338, pp. 435-449, 2011.
[2] J. Dobereiner, “Biological nitrogen fixation in the tropics: social and economic contributions,” Soil Biol. Biochem,., vol. 29, pp.771-774, 1997.
[3] J.L. Baldani, V.M. Reis, V.L.D. Baldani and J. Dobereiner, “A brief story of nitrogen fixation in sugarcane – reasons for success in Brasil,” Funct. Plant. Biol., vol.29, pp.417-423, 2002.
[4] R.M. Boddey, S. Urguillar, B.J.R. Reis, and V. Reis,”Endophytic nitrogen fixation in sugarcane: present knowledge and future applications,” Plant Soil., vol. 252, pp: 139-149, 2003.
[5] V.A. Cavalcante and J. Dobereiner, “A new acid tolerant nitrogen fixing bacterium associated with sugarcane,” Plant Soil, vol. 108, pp.23-31, 1988.
[6] F.L.Olivares, E.K.James, J.I.Baldani and J. Dobereiner,“Infection of molted stripe disease susceptible and resistant varieties of sugarcane by the endophytic diazotroph Herbaspirillum, New Phytologist., vol. 135, pp.723-737, 1997.
[7] F.G. Loiret, E. Ortega, D. Kleiner, P. Ortega-rodes, R. Rodes, and Z. Dong, “A putative new endophytic nitrogen-fixing bacterium Pantoea sp. from sugarcane,” J. Appl. Microbiol., vol.97, pp.504-511, 2004.
[8] V.M. Reis, S.P. Estrada-de Los Santos, S. Tenorio-Salgodo, J. Vogel, M. Stoffels, S. Guyon, P. Mavigui, V.L. Baldani, M. Schmid, J.I. Baldani, J. Balandreau, A. Hartmann and J. Caballero-Mellado,” Burkholderia tropica sp. nov., a novel nitrogen-fixing, plant-associated bacterium,” Int. J. Syst. Evol. Microbiol., vol. 54, pp:2155-2162, 2004.
[9] J. Callero-Mellado, L. Martinez-Aguillar, G. Paredes-Valdes, and P. Estrada-de Los Santos,”Burkholderia unamae sp. nov., and N2-fixing rhizopheric and endophytic species,” Int. J. Syst. Evol. Microbiol., vol. 54, pp:1165-1172, 2004.
[10] L. Perin, L. Martinez-Aguillar, R. Castro-Gonzalez, P. Estrada-de Los Santos, T. Cabellos-Avelar, H.V. Guedes, V.M. Reis, J. Caballero-Mellado,”Diazotrophic Burkholderia species associated with field-grown maize and sugarcane,” Appl. Environ. Microbiol., vol. 72, pp:3103-3110, 2006.
[11] M. Rosenblueth and E. Martínez-Romero, “Bacterial endophytes and their interactions with hosts,” Molecular Plant-Microbe Interactions., vol. 19, pp.827-837,2006.
[12] P. Gyaneshwar, E.K. James, N. Mathan, P.M. Reddy, B. Reinhold-Hurek and J.K. Ladha,”Endophytic colonization of rice by a diazotrophic strain of Serratia marcescens,” J. Bacteriol., vol.183, pp: 2634-2645, 2001.
[13] N. Weyens, D. van der Lelie, T. Artois, K. Smeets, S. Taghavi, L. Newman, R. Carleer, J. Vangrontsveld,”Bioaugmentation with engineered endophytic bacteria improves contaminant fate in phytoremediation,” Environ. Sci. Technol., vol. 43, pp: 9413-9418, 2009.
[14] L.H. Ba, “Vietnam Soil Resource,” Education Publishing House, Vietnam, 2009.
[15] L.H.A. Thi, “Sugarcane Report 2012,” (Vietnamese). Ministry of Agriculture and Rural Development Vietanam, January, 2013.
[16] N. Tejera, C. Lluch, M.V. Martinez-Toledo and J. Gonzalez-Lopez,”Isolation and characterization of Azotobacter and Azospirillum strains from the sugarcane rhizosphere,” Plant Soil., vol. 270, pp:223-232, 2005.
[17] A. Oak, “A reevaluation of nitrogen assimilation in roots,”BioSci., vol. 42, pp.103-111, 1992.
[18] C. Taule, C. Mareque, C. Barlocco, F. Hackembruch, V.M. Reis, M. Sicardi and F. Battistoni,”The contribution of nitrogen fixation to sugarcane (Saccharum officinarum L.), and the identification and characterization of part of the associated diazotrophic bacterial commnunity,” Plant Soil., vol. 356, pp:35-46, 2012.
[19] M. Park, C. Kim, J. Yang, H. Lee, W. Shin, S. Kim and T. Sa, “Isolation and characterization of diazotrophic growth promoting bacteria from Gram rhizosphere of agricultural crops of Korea,” Microbiological Research, vol 160, pp. 127-133, 2005.
[20] C.S. Nautiyal, “An efficient microbiological growth medium for screening phosphate-solubilizing microorganisms,” FEMS Microbiology Letters, vol. 170, pp.256-270, 1999.
[21] S.A. Gordon and R.P. Weber., “Colometric estimation of indolacetic acid,” Plant Physiol., vol 26, pp.192-195, 1951.
[22] B. Neumann, A. Pospiech, and H.U. Schairrer, “Rapid isolation of genomic DNA from Gram-negative,” Trends Gent., vol. 8, pp. 332-333, 1992.
[23] D.A. Relman, T.M. Schmidt, E.P. MacDermontt, and S. Falkow, “Identification of the uncultured bacillus of Whipple’s disease,” N. Engl. J. Med., vol. 327, pp.293-301, 1992.
[24] D.A. Relman, J.S. Loutit, T.M. Schmidt, S. Falkow, and L.S. Tompkin, “The agent of bacillary angiomatosis. An approach to the identification of uncultuted pathogens,” N. Engl. J. Med., vol.323, pp.1573-1580, 1990.
[25] K.D. Zinniel, P. Lambercht, N.B. Harris, Z. Feng, D. Kuczmarshki, P. Higley, C.A. Ishimaru, A. Arunakumari, R.G. Barletta, and A.K. Vidaver, “Isolation and charcaterization of endophytic bacteria from agronomic crops and prairie plants,” Appl. Environ. Microbiol., vol. 68, pp. 2198-2208, 2002.
[26] K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar, “MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likehood, Evolutionary Distance and Maximum Parsimony Methods,” Mol. Biol. Evol., vol. 28, pp. 2731-2739,2011.
[27] M.K. Halushka, J.B. Fan, K. Bentley, L. Hsie, N. Shen, A. Weder, R. Cooper, R. Lipshutz, and A. Charavarti, “Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homestasis,” Nat. Genet., vol. 22(3), pp. 239-247,1999.
[28] O.B. Weber, V.L.D. Baldani, K.R.S. Teixeira, G. Kirchof, J.I. Baldani, and J. Dobereiner, “Isolation and characterization of diazotrophic bacteria from banana and pineapple plants,” Plant and Soil., vol 210, pp. 103-113, 1999.
[29] N.T.Thu Ha, H.T. Toan, C.N.Điep, “Isolation anf characrterization of endophytic bacteria in several forage grass cultivars,” J. Biotechnology., vol. 7(2), pp.241-250, 2009.
[30] R.P. Ryan, K. Germanie, A. Franks, D. J. Ryan and D.N. Dowling, “Bacterial endophytes: recent developments and applications,” FEMS Microbiol. Lett., vol. 278, pp.1-9, 2008.
[31] S.C. Verma, J.K. Ladha and A.K. Tripathi, “Evaluation of plant growth promoting and colonization ability of endophytic diazotrophs from deep water rice,” J. Biotechnol., vol. 91, pp.127-141, 2001.
[32] S, Wakelin, R. Warren, P. Harvey and M. Ryder, “Phosphate solubilization by Penicillium spp. closely associated with wheat roots,” Bio. Fert. Soils, vol. 40, pp.36-43, 2004.
[33] S. Lee, M. Flores-Encarnation, M. Contreras-Zentella, L. Garcia-Flores, J.E. Escamilla and C. Kennedy, “Indole-3-acetic acid biosynthesis is deficient in Gluconacetobacter diazotrophicus strains with mutations in cychrome C biogenesis genes,” J. Bacteriol., vol. 186, pp.5384-5391, 2004.
[34] D.Y. Kobayashi, and J.D. Palumbo, “Bacterial Endophytes and Their Effects on Plants and Uses in Agricultulture,” C.W. Bacon and J.F. White. Eds, Marcel Dekker, New York, 2000.
[35] C. Lodewyckx, J. Vangronsveld, F. Porteous, E.R.B. Moore, S. Taghavi, M. Mezgeay and D. van der Lelie, “Endophytic Bacteria and Their Potential Applications,” Critical Reviews in Plant Sciences, vol. 21 (6), pp. 583-602, 2002.
[36] A. Montanez, A.R. Blanco, C.Barlocco, M. Beracochea, and M. Sicardi, “Characterization of cultivable putative endophytic plant growth promoting bacteria associated with maize cultivars (Zea mays L.) and their inoculation effects in vitro,” Applied Soil Ecology, vol.58, pp.21-28, 2012.
[37] G.A. Watterson, “On the number of segregation sites in general models without recobination,” Theor. Pop. Biol., vol. 7, pp.256-276, 1975.
[38] J. Rozas, and R. Rozas, “DnaSP version 4.1: an integrated program for molecular population genetics and molecular evolution analysis,” Bioinformatics, vol. 15, pp. 174-175, 2005.
[39] J.I. Baldani, V.L.D. Baldani, L. Seldin and J. Dobereiner,”Characterization of Herbaspirillum seropedicae gen. nov. sp. nov., a root-associated nitrogen-fixing bacterium,” Int. J. Syst. Bacteriol., vol. 36, pp: 86-93, 1986.
[40] F.B. Reis Junior, L.G. Silva, V.M. Reis and J. Dobereiner,”Occurrence of diazotrophic bacteria in different sugarcane genetypes,” Pesp. Agropec. Bras., vol. 35, pp:985-994,2000.
[41] A.Suman, A.K. Shasany, M. Singh and H.N. Shani,”Molecular assessment of diversity among endophytic diazotrophs isolated from subtropical Indian sugarcane,” World J. Microbiol. Biotechnol,, vol.17, pp:39-45, 2001.
[42] G.S.Magnani, C.M. Didonet, L.M.Cruz, C.F.Picheth, F.O.Pedrosa, and E.M.,”Diversity of endophytic bacteria in Brazilian sugarcane,” Genetics and Molecular Research, vol.9(1),pp:250-258, 2010.
[43] K.U.Zakria, T. Ogawa, A. Yamamoto, Y. Saeki and S. Akao,”Influence of inoculation technique on the endophytic colonization of rice by Pantoea sp. isolated from sweet potato and by Enterobacter sp. isolated from sugarcane Muhammad,” Soil Sci. Plant. Nutr., vol. 54, pp:224-236, 2008.
[44] R.J. Rennie, J.R. De Freitas, A.P. Ruschel and P.B. Vose, “Isolation and identification of N2-fixing bacteria associated with sugarcane (Saccharum sp.,” Can. J. Microbiol., vol. 28, pp:462-467, 1982.
[45] A.B. Torres, et al.,”Diversity of endophytic enterobacteria associated with different host plants,” J. Microbiol., vol. 46, pp:373-379, 2008.
[46] M. Rossignol, A. Basset, O. Espeli, and F. Bocard, “NKBOR, a miniTn-10-based transposon for random insertion in the chromosome of Gram-negative bacteria and the rapid recovery of sequences flanking the insertion sites in Escherichia coli,” Res. Microbiol., vol.152, pp:481-485, 2001.
[47] C.A. Asis and C.A. Adachi,”Isolation of endophytic diazotroph Pantoea agglomerans and nondiazotroph Enterobacter asburiae from sweetpotato stem in Japan,” Lett. Appl. Microbiol., vol. 38, pp:19-23, 2004.
[48] S. Ruppel, C. Hecht-Buchholz, R. Remus, U. Artmann and R. Schmeizer, “Settlement of the diazotrophic, phytoeffective bacterial strain Pantoea agglomerans on and within winter wheat:an investagation using ELISA and transmission electron microscoly,” Plant Soil., vol. 145, pp:261-273, 1992.
[49] W.L. Ararujo, W. Maccheroni, C. Aguilar-Vidoso, P.A.V. Baroso, H.O. Saridakis, and J.L. Azevedo,”Variability and interaction between endophytic bacteria and fungi isolated from leaf tissues of citrus rootstocks,” Can. J. Microbiol., vol.47, pp:229-236, 2001.
[50] M. Ongena, et al.,”Systematic induction of phytoalexins in cucumber in response to treatments with fluorescent pseudomonads,” Plant Pathol., vol.49, pp:523-530, 2000.
[51] T.F. Hsich, H.C. huang, and R.S.Erickson, “Biological control of bacterial wilt of bean using a bacterial endophyte, Pantoea agglomerans,” J. Phytopathol., vol. 153, pp:608-614, 2005.
[52] S.C. Verma, A. Singh, S.P. Chowdhury and A.K. Tripathi, “Endophytic colonization ability of two deep-water rice endophytes, Pantoea sp. and Ochrobactrum sp. using green fluorescent protein reporter,” Biotechnol. Lett., vol. 26, pp:425-429, 2004.
[53] M.A. Malboobi et al.,”Solubilization of organic and inorganic phosphates by three highly efficient soil bacterial isolates,” World J. Microbiol., vol. 25, pp:1471-1477, 2009.
[54] W. Zimmer, B. Hundeshagen, and E. Niederau,”Demonstration of the indopyruvate decarboxylase gene homologous in different auxin producing species of the Enterobacteriaceae,” Can. J. Microbiol., vol. 40, pp:1072-1076,1994.
[55] M.C. Quecine, W.L. Araujo, P.B. Rosetto, A. Ferreira, S. Tsui, P.T. Lacava, M. Moudin, J.L. Azevedo, and A.A.Pizzirani-Kleiner,”Sugarcane Growth Promotion by the Endophytic Bacterium Pantoea agglomerans 33.1,” Appl. Environ. Microbiol., 78(21), pp:7511-7518, 2012.
[56] P. Jha and A. Kumar,”Characterization of Novel Plant Growth Promoting Endophytic Bacterium Achromobacter xylosoxidans from Wheat Plant,” Microb. Ecol., vol. 58, pp:179-188, 2009.
Cite This Article
  • APA Style

    Hoang Minh Tam, Cao Ngoc Diep. (2014). Isolation, Characterization and Identification of Endophytic Bacteria in Sugarcane (Saccharum spp. L.) Cultivated on Soils of the Dong Nai Province, Southeast of Vietnam. American Journal of Life Sciences, 2(6), 361-368. https://doi.org/10.11648/j.ajls.20140206.16

    Copy | Download

    ACS Style

    Hoang Minh Tam; Cao Ngoc Diep. Isolation, Characterization and Identification of Endophytic Bacteria in Sugarcane (Saccharum spp. L.) Cultivated on Soils of the Dong Nai Province, Southeast of Vietnam. Am. J. Life Sci. 2014, 2(6), 361-368. doi: 10.11648/j.ajls.20140206.16

    Copy | Download

    AMA Style

    Hoang Minh Tam, Cao Ngoc Diep. Isolation, Characterization and Identification of Endophytic Bacteria in Sugarcane (Saccharum spp. L.) Cultivated on Soils of the Dong Nai Province, Southeast of Vietnam. Am J Life Sci. 2014;2(6):361-368. doi: 10.11648/j.ajls.20140206.16

    Copy | Download

  • @article{10.11648/j.ajls.20140206.16,
      author = {Hoang Minh Tam and Cao Ngoc Diep},
      title = {Isolation, Characterization and Identification of Endophytic Bacteria in Sugarcane (Saccharum spp. L.) Cultivated on Soils of the Dong Nai Province, Southeast of Vietnam},
      journal = {American Journal of Life Sciences},
      volume = {2},
      number = {6},
      pages = {361-368},
      doi = {10.11648/j.ajls.20140206.16},
      url = {https://doi.org/10.11648/j.ajls.20140206.16},
      eprint = {https://download.sciencepg.com/pdf/10.11648.j.ajls.20140206.16},
      abstract = {Endophytic bacterial diversity in sugarcane plant cultivated on Latosols and Acrisols of the Eastern of South Vietnam was studied. Sugarcane plant samples were taken in four sites (districts/towns) (Xuanloc, Dinhquan, Vinhc uu and Trangbom) of Dong Nai province. Endophytic bacteria were isolated in LGI medium together with 16S rRNA gene fragments amplified from DNA using eubacterial universal primers (p515FPL and p13B). A total of 27 isolates were isolated on LGI medium and all of them have ability of nitrogen fixation and phosphate solubilization together with IAA biosynthesis but there were 10 isolates having the best characteristics. The sequences from selected endophytic bacteria (10 isolates) showed high degrees of similarity to those of the GenBank references strains (between 98% and 99%). All of them are Proteobacteria (gram-negative bacteria) and 3 isolates belonged to Alpha-proteobacteria (30%), 2 isolates were Beta-proteobacteria (20%), 5 isolates were Gamma-proteobacteria (50%). Based on Pi value (nucleotide diversity), Gamma-proteobacteria group had the highest theta values and Theta values (per sequence) from S of SNP for DNA polymorphism were calculated for each group and Gamma-proteobacteria group had the highest values in comparison of two groups. From these results showed that Enterobacter oryzae LT7, Achromobacter xylosoxidans T16, Achromobacter insolitus R15b and Pantoea agglomerans T12 revealed promising candidates with multiple beneficial characteristics and they have the potential for application as inoculants or bio-fertilizer adapted to poor latosols and acrisols because they are not only famous strains but also are safety strains for sustainable agriculture.},
     year = {2014}
    }
    

    Copy | Download

  • TY  - JOUR
    T1  - Isolation, Characterization and Identification of Endophytic Bacteria in Sugarcane (Saccharum spp. L.) Cultivated on Soils of the Dong Nai Province, Southeast of Vietnam
    AU  - Hoang Minh Tam
    AU  - Cao Ngoc Diep
    Y1  - 2014/12/18
    PY  - 2014
    N1  - https://doi.org/10.11648/j.ajls.20140206.16
    DO  - 10.11648/j.ajls.20140206.16
    T2  - American Journal of Life Sciences
    JF  - American Journal of Life Sciences
    JO  - American Journal of Life Sciences
    SP  - 361
    EP  - 368
    PB  - Science Publishing Group
    SN  - 2328-5737
    UR  - https://doi.org/10.11648/j.ajls.20140206.16
    AB  - Endophytic bacterial diversity in sugarcane plant cultivated on Latosols and Acrisols of the Eastern of South Vietnam was studied. Sugarcane plant samples were taken in four sites (districts/towns) (Xuanloc, Dinhquan, Vinhc uu and Trangbom) of Dong Nai province. Endophytic bacteria were isolated in LGI medium together with 16S rRNA gene fragments amplified from DNA using eubacterial universal primers (p515FPL and p13B). A total of 27 isolates were isolated on LGI medium and all of them have ability of nitrogen fixation and phosphate solubilization together with IAA biosynthesis but there were 10 isolates having the best characteristics. The sequences from selected endophytic bacteria (10 isolates) showed high degrees of similarity to those of the GenBank references strains (between 98% and 99%). All of them are Proteobacteria (gram-negative bacteria) and 3 isolates belonged to Alpha-proteobacteria (30%), 2 isolates were Beta-proteobacteria (20%), 5 isolates were Gamma-proteobacteria (50%). Based on Pi value (nucleotide diversity), Gamma-proteobacteria group had the highest theta values and Theta values (per sequence) from S of SNP for DNA polymorphism were calculated for each group and Gamma-proteobacteria group had the highest values in comparison of two groups. From these results showed that Enterobacter oryzae LT7, Achromobacter xylosoxidans T16, Achromobacter insolitus R15b and Pantoea agglomerans T12 revealed promising candidates with multiple beneficial characteristics and they have the potential for application as inoculants or bio-fertilizer adapted to poor latosols and acrisols because they are not only famous strains but also are safety strains for sustainable agriculture.
    VL  - 2
    IS  - 6
    ER  - 

    Copy | Download

Author Information
  • Dept. Natural Science Teacher Training, Sai Gon University, HCM City, Vietnam

  • Dept. Microbiology Biotechnology, Biotechnology R&D Institute, Can Tho University, Can Tho City, Vietnam

  • Section