Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
권호 표지
DOI QR코드

DOI QR Code

Diversity Analysis of Diazotrophic Bacteria Associated with the Roots of Tea (Camellia sinensis (L.) O. Kuntze)

  • Arvind, Gulati (Plant Pathology and Microbiology Laboratory, Hill Area Tea Science Division, Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research) ;
  • Sood, Swati (Plant Pathology and Microbiology Laboratory, Hill Area Tea Science Division, Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research) ;
  • Rahi, Praveen (Plant Pathology and Microbiology Laboratory, Hill Area Tea Science Division, Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research) ;
  • Thakur, Rishu (Plant Pathology and Microbiology Laboratory, Hill Area Tea Science Division, Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research) ;
  • Chauhan, Sunita (Plant Pathology and Microbiology Laboratory, Hill Area Tea Science Division, Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research) ;
  • Nee Chadha, Isha Chawla (Plant Pathology and Microbiology Laboratory, Hill Area Tea Science Division, Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research)
  • Received : 2010.12.16
  • Accepted : 2011.03.21
  • Published : 2011.06.28
Download PDF
⟨ Previous Next ⟩

Abstract

The diversity elucidation by amplified ribosomal DNA restriction analysis and 16S rDNA sequencing of 96 associative diazotrophs, isolated from the feeder roots of tea on enriched nitrogen-free semisolid media, revealed the predominance of Gram-positive over Gram-negative bacteria within the Kangra valley in Himachal Pradesh, India. The Gram-positive bacteria observed belong to two taxonomic groupings; Firmicutes, including the genera Bacillus and Paenibacillus; and Actinobacteria, represented by the genus Microbacterium. The Gram-negative bacteria included ${\alpha}$-Proteobacteria genera Brevundimonas, Rhizobium, and Mesorhizobium; ${\gamma}$-Proteobacteria genera Pseudomonas and Stenotrophomonas; and ${\beta}$-Proteobacteria genera Azospira, Burkholderia, Delftia, Herbaspirillum and Ralstonia. The low level of similarity of two isolates, with the type strains Paenibacillus xinjiangensis and Mesorhizobium albiziae, suggests the possibility of raising species novum. The bacterial strains of different phylogenetic groups exhibited distinct carbon-source utilization patterns and fatty acid methyl ester profiles. The strains differed in their nitrogenase activities with relatively high activity seen in the Gramnegative strains exhibiting the highest similarity to Azospira oryzae, Delftia lacustris and Herbaspirillum huttiense.

Keywords

References

  1. Adhikari, T. B., C. M. Joseph, G. P. Yang, D. A. Phillips, and L. M. Nelson. 2001. Evaluation of bacteria isolated from rice for plant growth promotion and biological control of seedling disease of rice. Can. J. Microbiol. 47: 916-924. https://doi.org/10.1139/w01-097
  2. Albino, U., D. P. Saridakis, M. C. Ferreira, M. Hungria, P. Vinuesa, and G. Andrade. 2006. High diversity of diazotrophic bacteria associated with the carnivorous plant Drosera villosa var. villosa growing in oligotrophic habitats in Brazil. Plant Soil 287: 199-207. https://doi.org/10.1007/s11104-006-9066-7
  3. Andrade, G., E. Esteban, L. Velascol, J. L. Maria, and E. J. Bedmar. 1997. Isolation and identification of $N_2$-fixing microorganisms from the rhizosphere of Capparis spinosa (L.). Plant Soil 197: 19-23. https://doi.org/10.1023/A:1004211909641
  4. Bae, H. S., B. A. Rash, F. A. Rainey, M. Fernanda Nobre, I. Tiago, M. S. da Costa, and W. M. Moe. 2007. Description of Azospira restricta sp. nov., a nitrogen-fixing bacterium isolated from groundwater. Int. J. Syst. Evol. Microbiol. 57: 1521-1526. https://doi.org/10.1099/ijs.0.64965-0
  5. Baldani, V. L. D. and J. Doebereiner. 1980. Host-plant specificity in the infection of cereals with Azospirillum spp. Soil Biol. Biochem. 12: 433-439. https://doi.org/10.1016/0038-0717(80)90021-8
  6. Basile, F., K. J. Voorhees, and T. L. Hadfield. 1995. Microorganism Gram-type differentiation based on pyrolysis-mass spectrometry of bacterial fatty acid methyl ester extracts. Appl. Environ. Microbiol. 61: 1534-1539.
  7. Beauchamp, C. J., G. Levesque, D. Prevost, and F. P. Chalifour. 2006. Isolation of free-living dinitrogen-fixing bacteria and their activity in compost containing de-inking paper sludge. Bioresour. Technol. 97: 1002-1011. https://doi.org/10.1016/j.biortech.2005.04.041
  8. Bhattacharjee, R. B., A. Singh, and S. N. Mukhopadhyay. 2008. Use of nitrogen-fixing bacteria as biofertilizer for non-legumes: Prospects and challenges. Appl. Microbiol. Biotechnol. 80: 199-209. https://doi.org/10.1007/s00253-008-1567-2
  9. Bradford, M. M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72: 248- 254. https://doi.org/10.1016/0003-2697(76)90527-3
  10. Chowdhury, S. P., M. Schmid, A. Hartmann, and A. K. Tripathi. 2007. Identification of diazotrophs in the culturable bacterial community associated with roots of Lasiurus sindicus, a perennial grass of Thar desert, India. Microb. Ecol. 54: 82- 90. https://doi.org/10.1007/s00248-006-9174-1
  11. Ding, L. and A. Yokota. 2004. Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. Int. J. Syst. Evol. Microbiol. 54: 2223-2230. https://doi.org/10.1099/ijs.0.02975-0
  12. Ding, Y., J. Wang, Y. Liu, and S. Chen. 2005. Isolation and identification of nitrogen-fixing bacilli from plant rhizospheres in Beijing region. J. Appl. Microbiol. 99: 1271-1281. https://doi.org/10.1111/j.1365-2672.2005.02738.x
  13. Dutta, D. and R. Gachhui. 2006. Novel nitrogen-fixing Acetobacter nitrogenifigens sp. nov., isolated from Kombucha tea. Int. J. Syst. Evol. Microbiol. 56: 1899-1903. https://doi.org/10.1099/ijs.0.64101-0
  14. Eckford, R., F. D. Cook, D. Saul, J. Aislabie, and J. Foght. 2002. Free-living heterotrophic nitrogen-fixing bacteria isolated from fuel-contaminated Antarctic soil. Appl. Environ. Microbiol. 68: 5181-5185. https://doi.org/10.1128/AEM.68.10.5181-5185.2002
  15. Elmerich, C. and W. E. Newton. 2007. Associative and Endophytic Nitrogen-fixing Bacteria and Cyanobacterial Associations. Springer Verlag.
  16. Estrada-De Los Santos, P., R. Bustillos-Cristales, and J. Cabellaro-Mellado. 2001. Burkholderia, a genus rich in plantassociated nitrogen fixers with wide environmental and geographic distribution. Appl. Environ. Microbiol. 67: 2790-2798. https://doi.org/10.1128/AEM.67.6.2790-2798.2001
  17. Gardener, B. B. M. 2004. Ecology of Bacillus and Paenibacillus spp. in agricultural systems. Phytopathology 94: 1252-1258. https://doi.org/10.1094/PHYTO.2004.94.11.1252
  18. Guerlava, P., V. Izac, and J. L. Tholozan. 1998. Comparison of different methods of cell lysis and protein measurements in Clostridium perfringens: Application to the cell volume determination. Curr. Microbiol. 36: 131-135. https://doi.org/10.1007/PL00006756
  19. Han, J., L. Sun, X. Dong, Z. Cai, X. Sun, H. Yang, Y. Wang, and W. Song. 2005. Characterization of a novel plant growthpromoting bacteria strain Delftia tsuruhatensis HR4 both as a diazotroph and a potential biocontrol agent against various plant pathogens. Syst. Appl. Microbiol. 28: 66-76. https://doi.org/10.1016/j.syapm.2004.09.003
  20. Han, W., S. J. Kemmitt, and P. C. Brookes. 2007. Soil microbial biomass and activity in Chinese tea gardens of varying stand age and productivity. Biochemistry 39: 1468-1478.
  21. Hardy, R. W. F., R. D. Holsten, E. K. Jackson, and R. C. Burns. 1968. The acetylene-ethylene assay for $N_2$ fixation: Laboratory and field evaluation. Plant Physiol. 43: 1185-1207. https://doi.org/10.1104/pp.43.8.1185
  22. Hejnar, P., Z. Chmela, and M. Rypka. 2002. Fatty acid analysis of Stenotrophomonas maltophilia clinical strains showing different susceptibility to antibiotics at 30 and $37{^{\circ}C}$. Folia Microbiol. 47: 742-746. https://doi.org/10.1007/BF02818682
  23. Kennedy, I. R., A. T. M. A. Choudhury, and M. L. Keeskes. 2004. Non-symbiotic bacterial diazotrophs in crop farming systems: Can their potential for plant growth promotion be better exploited? Soil Biol. Biochem. 36: 1229-1244. https://doi.org/10.1016/j.soilbio.2004.04.006
  24. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120. https://doi.org/10.1007/BF01731581
  25. Ladha, J. K. and P. M. Reddy. 2000. Steps for nitrogen-fixation in rice, pp. 359. In J. K. Ladha and P. M. Reddy (eds.). "The quest for nitrogen fixation in rice" Proceedings of the Third Working Group Meeting on Assessing Opportunities for Nitrogen Fixation in Rice, Makai City (Philippines).
  26. Lugtenberg, B. J. J. and L. C. Dekkers. 1999. What makes Pseudomonas bacteria rhizosphere competent? Environ. Microbiol. 1: 9-13. https://doi.org/10.1046/j.1462-2920.1999.00005.x
  27. Martensson, L., B. Deiz, I. Wartianen, Z. Weiwen, El-S. Rehab, and R. Ulla. 2009. Diazotrophic diversity, nifH gene expression and nitrogenase activity in a rice paddy field in Fujian, China. Plant Soil 325: 207-218. https://doi.org/10.1007/s11104-009-9970-8
  28. Martinez, L., J. Caballero-Mellado, J. Orozco, and E. Martinez- Romero. 2003. Diazotrophic bacteria associated with banana (Musa spp.). Plant Soil 257: 35-47. https://doi.org/10.1023/A:1026283311770
  29. Martinez-Romero, E. and J. Caballero-Mellado. 1996. Rhizobium phylogenies and bacterial genetic diversity. Crit. Rev. Plant Sci. 15: 113-140. https://doi.org/10.1080/07352689.1996.10393183
  30. Matiru, V. N. and F. D. Dakora. 2004. Potential use of rhizobial bacteria as promoters of plant growth for increased yield in landraces of African cereal crops. Afr. J. Biotechnol. 3: 1-7. https://doi.org/10.5897/AJB2004.000-2002
  31. Mehboob, I., M. Naveed, and A. Zahir. 2009. Rhizobial association with non-legumes: Mechanisms and applications. Crit. Rev. Plant Sci. 28: 432-456. https://doi.org/10.1080/07352680903187753
  32. Montanez, A., C. Abreu, P. R. Gill, G. Hardarson, and M. Sicardi. 2009. Biological nitrogen fixation in maize (Zea mays L.) by $^{15}__N$ isotope-dilution and identification of associative culturable diazotrophs. Biol. Fertil. Soils 45: 253-263. https://doi.org/10.1007/s00374-008-0322-2
  33. Naher, U. A., O. Radziah, Z. H. Shamsiddin, M. S. Halimi, and M. Razi. 2009. Isolation of diazotrophs from different soils of Tanjong Karang rice growing area in Malaysia. Int. J. Agric. Biol. 11: 547-552.
  34. Natsvaladze, M. Y., L. K. Nitse, and S. N. Sakharova. 1992. Free-living and associative diazotrophs in the rhizocoenosis of tea. Izvestia Timiryazevskoi Sel' sokhozyaistvennoi Akademii 2: 95-102.
  35. Ndifon, W., J. B. Plotkin, and J. Dushoff. 2009. On the accessibility of adaptive phenotypes of a bacterial metabolic network. PLoS Comput. Biol. 5: 1-11.
  36. O'Donnell, A. G., M. Seasman, A. Macrae, I. Waite, and J. T. Davies. 2001. Plants and fertilisers as drivers of change in microbial community structure and function in soils Plant Soil 232: 135-145. https://doi.org/10.1023/A:1010394221729
  37. Oh, K., T. Kato, Z. P. Li, and F. Y. Li. 2006. Environmental problems from tea cultivation in Japan and a control measure using calcium cyanamide. Pedosphere 16: 770-777. https://doi.org/10.1016/S1002-0160(06)60113-6
  38. Okano, K., K. Chutani, and K. Matsuo. 1997. Suitable level of nitrogen fertilizer for tea (Camellia sinensis L.) plants in relation to growth, photosynthesis, nitrogen uptake and accumulation of free amino acids. Jpn. J. Crop Sci. 66: 279-287. https://doi.org/10.1626/jcs.66.279
  39. Pandey, A. and L. M. S. Palni. 1996. The rhizosphere effect of tea on soil microbes in a Himalayan monsoonal location. Biol. Fertil. Soils 21: 131-137. https://doi.org/10.1007/BF00335924
  40. Pandey, A. and L. M. S. Palni. 1997. Bacillus species: The dominant bacteria of the rhizosphere of established tea bushes. Microbiol. Res. 152: 359-365. https://doi.org/10.1016/S0944-5013(97)80052-3
  41. Pandey, A., L. M. S. Palni, and N. Coulomb. 1997. Antifungal activity of bacteria isolated from rhizosphere of established tea bushes. Microb. Ecol. 152: 105-112.
  42. Park, M., C. Kin, J. Yang, H. Lee, W. Shin, S. Kim, and. T. Sa. 2005. Isolation and characterization of diazotrophic growth promoting bacteria from rhizosphere of agricultural crops of Korea. Microbiol. Res. 160: 127-133. https://doi.org/10.1016/j.micres.2004.10.003
  43. Prakamhang, J., K. Minamisawa, K. Teamtaisong, N. Boonkerd, and N. Teaumroong. 2009. The communities of endophytic diazotrophic bacteria in cultivated rice (Oryza sativa L.). Appl. Soil Ecol. 42: 141-149. https://doi.org/10.1016/j.apsoil.2009.02.008
  44. Rodriguez Caceres, E. A. 1982. Improved medium for isolation of Azospirillum spp. Appl. Environ. Microbiol. 44: 990-991.
  45. Roesch, L. F. W., F. A. O. Camargo, F. M. Bento, and E. W. Triplett. 2008. Biodiversity of diazotrophic bacteria within the soil, root and stem of field-grown maize. Plant Soil 302: 91- 104. https://doi.org/10.1007/s11104-007-9458-3
  46. Rozycki, H., H. Dahm, E. Strzelcyk, and C. Y. Li. 1999. Diazotrophic bacteria in root free soil in the root of pine (Pinus sylvestris L.) and oak (Quercus robur L.). Appl. Soil Ecol. 12: 239-250. https://doi.org/10.1016/S0929-1393(99)00008-6
  47. Sachdev, D., V. Agarwal, P. Verma, Y. Shouche, P. Dhakephalkar, and B. Chopade. 2009. Assessment of microbial biota associated with rhizosphere of wheat (Triticum aestivum) during flowering stage and their plant growth promoting traits. Internet J. Microbiol. Accessible http://www.ispub.com/journal/the_internet_ journal_of_microbiology/volume_7_number_2_26.
  48. Saikia, S. P. and V. Jain. 2007. Biological nitrogen fixation with non-legumes: An achievable target or a dogma? Curr. Sci. 92: 317-322.
  49. Saleena, L. M., S. Rangarajan, and S. Nair. 2002. Diversity of Azospirillum strains isolated from rice plants grown in saline and nonsaline sites of coastal agricultural ecosystems. Microb. Ecol. 44: 271-277. https://doi.org/10.1007/s00248-002-2019-7
  50. Saravanakumar, D., C. Vijayakumar, N. Kumar, and R. Samiyappan. 2007. PGPR-induced defense responses in the tea plant against blister blight disease. Crop Prot. 26: 556-565. https://doi.org/10.1016/j.cropro.2006.05.007
  51. Sarita, S., U. B. Priefer, J. Prell, and P. K. Sharma. 2008. Diversity of nifH gene amplified from rhizosphere soil DNA. Curr. Sci. 94: 109-115.
  52. Sasser, M. 1990. Tracking a Strain Using the Microbial Identification System. Technical Note 102. MIS, Newark, DE.
  53. Sato, A., T. Watanabe, Y. Unno, E. Purnomo, M. Osaki, and T. Shinano. 2009. Analysis of diversity of diazotrophic bacteria associated with the rhizosphere of a tropical arbor, Melastoma malabathricum L. Microbes Environ. 24: 81-87. https://doi.org/10.1264/jsme2.ME08565
  54. Sharma, D. K., S. Thakur, and K. L. Sharma. 2005. Effect of method, time and levels of phosphorous application on yield and quality of tea (Camellia sinensis). Indian J. Agron. 50: 324-326.
  55. Soares, R. A., L. F. R. Roesch, G. Zanatta, F. A. O. Camargo, and L. M. P. Passaglia. 2006. Occurrence and distribution of nitrogen fixing bacterial community associated with oat (Avena sativa) assessed by molecular and microbiological techniques. Appl. Soil Ecol. 33: 221-234. https://doi.org/10.1016/j.apsoil.2006.01.001
  56. Sood, A., S. Sharma, V. Kumar, and R. L. Thakur. 2007. Antagonism of dominant bacteria in tea rhizosphere of Indian Himalayan regions. J. Appl. Sci. Environ. Manage. 11: 63-66.
  57. Sud, R. G. and A. Baru. 2000. Seasonal variations in theaflavins, thearubigins, total colour and brightness of Kangra orthodox tea (Camellia sinensis (L.) O. Kuntze) in Himachal Pradesh. J. Sci. Food Agric. 80: 1291-1299. https://doi.org/10.1002/1097-0010(200007)80:9<1291::AID-JSFA633>3.0.CO;2-K
  58. Tan, Z. and B. Reinhold-Hurek. 2000. Dechlorosoma suillum Achenbach et al. 2001 is a later subjective synonym of Azospira oryzae Reinhold-Hurek and Hurek 2000. Int. J. Syst. Evol. Microbiol. 53: 1139-1142.
  59. Van de Peer, Y. and R. de Watcher. 1994. TREECON for Windows: A software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Appl. Biosci. 10: 569-570.
  60. Weisburg, W. G., S. M. Barns, D. A. Pelletier, and D. J. Lane. 1991. 16S Ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173: 697-703.
  61. Zhang, G. X., G. X. Peng, E. T. Wang, H. Yan, H. Y. Qing, W. Zhang, X. Lou, H. Wu, and Z. Y. Tan. 2008. Diverse endophytic nitrogen-fixing bacteria isolated from wild rice Oryza rufipogon and description of Phytobacter diazotrophicus gen. nov. sp. nov. Arch. Microbiol. 189: 431-439. https://doi.org/10.1007/s00203-007-0333-7

Cited by

  1. Isolation and identification of diazotrophic bacteria from internal tissues ofPinus contortaandThuja plicata vol.42, pp.4, 2011, https://doi.org/10.1139/x2012-023
  2. Diazotrophic diversity in the rhizosphere of two exotic weed plants, Prosopis juliflora and Parthenium hysterophorus vol.28, pp.2, 2011, https://doi.org/10.1007/s11274-011-0853-9
  3. Analysis of unculturable bacterial communities in tea orchard soils based on nested PCR-DGGE vol.28, pp.5, 2011, https://doi.org/10.1007/s11274-011-0999-5
  4. Comparison among bacterial communities present in arenized and adjacent areas subjected to different soil management regimes vol.373, pp.1, 2011, https://doi.org/10.1007/s11104-013-1796-8
  5. Stenotrophomonas: a versatile diazotrophic bacteria from the rhizospheric soils of Western Himalayas and development of its liquid biofertilizer formulation vol.32, pp.1, 2019, https://doi.org/10.1007/s42535-019-00013-8
  6. Molecular Identification and Evaluation of Indigenous Bacterial Isolates for Their Plant Growth Promoting and Biological Control Activities against Fusarium Wilt Pathogen of Tomato vol.35, pp.2, 2011, https://doi.org/10.5423/ppj.oa.06.2018.0104
  7. Nitrogen-fixing bacteria and Oxalis - evidence for a vertically inherited bacterial symbiosis vol.19, pp.1, 2019, https://doi.org/10.1186/s12870-019-2049-7
  8. Divulging diazotrophic bacterial community structure in Kuwait desert ecosystems and their N 2 -fixation potential vol.14, pp.12, 2011, https://doi.org/10.1371/journal.pone.0220679
  9. Potential PGPR Properties of Cellulolytic, Nitrogen-Fixing, Phosphate-Solubilizing Bacteria in Rehabilitated Tropical Forest Soil vol.8, pp.3, 2011, https://doi.org/10.3390/microorganisms8030442
  10. Oak (Quercus robur) Associated Endophytic Paenibacillus sp. Promotes Poplar (Populus spp.) Root Growth In Vitro vol.9, pp.6, 2011, https://doi.org/10.3390/microorganisms9061151
  11. A rapid change in microbial communities of the shale gas drilling fluid from 3548 m depth to the above-ground storage tank vol.784, pp.None, 2011, https://doi.org/10.1016/j.scitotenv.2021.147009