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Microbial Ecology

, Volume 77, Issue 3, pp 676–688 | Cite as

Diversity and Tissue Preference of Osmotolerant Bacterial Endophytes Associated with Pearl Millet Genotypes Having Differential Drought Susceptibilities

  • B. S. Manjunatha
  • Sangeeta PaulEmail author
  • Chetana Aggarwal
  • S. Bandeppa
  • V. Govindasamy
  • Ajinath S. Dukare
  • Maheshwar S. Rathi
  • C. T. Satyavathi
  • K. Annapurna
Plant Microbe Interactions

Abstract

Genetic and functional diversity of osmotolerant bacterial endophytes colonizing the root, stem, and leaf tissues of pearl millet genotypes differing in their drought susceptibility was assessed. Two genotypes of pearl millet, viz., the drought tolerant genotype TT-1 and the drought susceptible genotype PPMI-69, were used in the present study. Diazotrophs were found to be the predominant colonizers, followed by the Gram positive bacteria in most of the tissues of both the genotypes. Higher proportion of bacterial endophytes obtained from the drought tolerant genotype was found to be osmotolerant. Results of 16S rRNA gene-ARDRA analysis grouped 50 of the highly osmotolerant isolates into 16 clusters, out of which nine clusters had only one isolate each, indicating their uniqueness. One cluster had 21 isolates and remaining clusters were represented by isolates ranging from two to four. The representative isolates from each cluster were identified, and Bacillus was found to be the most prevalent osmotolerant genera with many different species. Other endophytic bacteria belonged to Pseudomonas sp., Stenotrophomonas sp., and Macrococcus caseolyticus. High phylogenetic diversity was observed in the roots of the drought tolerant genotype while different tissues of the drought susceptible genotype showed less diversity. Isolates of Bacillus axarquiensis were present in all the tissues of both the genotypes of pearl millet. However, most of the other endophytic bacteria showed tissue/genotype specificity. With the exception of B. axarquiensis and B. thuringiensis, rest all the species of Bacillus were found colonizing only the drought-tolerant genotype; while M. caseolyticus colonized all the tissues of only the drought susceptible genotype. There was high incidence of IAA producers and low incidence of ACC deaminase producers among the isolates from the root tissues of the drought-tolerant genotype while reverse was the case for the drought-susceptible genotype. Thus, host played an important role in the selection of endophytes based on both phylogenetic and functional traits.

Keywords

Diversity Osmotolerant Genotype specificity Tissue specificity Bacillus sp. Functional characterization 

Notes

Acknowledgements

First author is thankful to the Indian Agricultural Research Institute, New Delhi, for providing the infrastructure facilities to carry out the research.

Funding Information

The first author is also thankful to the Indian Council of Agricultural Research for financial support in the form of fellowship.

Supplementary material

248_2018_1257_MOESM1_ESM.docx (12 kb)
Suppl. Fig 1 (DOCX 12 kb)
248_2018_1257_MOESM2_ESM.docx (12 kb)
Suppl. Table 1 (DOCX 12 kb)

References

  1. 1.
    Agler MT, Ruhe J, Kroll S, Morhenn C, Kim S-T, Weigel D, Kemen EM (2016) Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biol 14(1):e1002352Google Scholar
  2. 2.
    Atlas RM (2010) Handbook of microbiological media 4th edn. CRC Press, Washington D.CGoogle Scholar
  3. 3.
    Bandeppa, Paul S, Kandpal BK (2015) Evaluation of osmotolerant rhizobacteria for alleviation of water deficit stress in mustard. Green Farm Int J 6(2):590–593–593Google Scholar
  4. 4.
    Chowdhury EK, Jeon J, Rim SO, Park Y-H, Lee SK, Bae H (2017) Composition, diversity and bioactivity of culturable bacterial endophytes in mountain-cultivated ginseng in Korea. Sci Rep 7(1):10098.  https://doi.org/10.1038/s41598-017-10280-7 Google Scholar
  5. 5.
    da Silva DAF, Cotta SR, Vollú RE, de Jurelevicius DA, Marques JM, Marriel IE, Seldin L (2014) Endophytic microbial community in two transgenic maize genotypes and in their near-isogenic non-transgenic maize genotype. BMC Microbiol 14:332.  https://doi.org/10.1186/s12866-014-0332-1 Google Scholar
  6. 6.
    Gaiero JR, McCall CA, Thompson KA, Day NJ, Best AS, Dunfield KE (2013) Inside the root microbiome: bacterial root endophytes and plant growth promotion. Am J Bot 100(9):1738–1750Google Scholar
  7. 7.
    Glick BR (2012) Plant growth-promoting bacteria: mechanisms and applications. Scientifica 2012:1–15.  https://doi.org/10.6064/2012/963401 Google Scholar
  8. 8.
    Gould WD, Hagedorn C, Bardinelli TR, Zablotowicz RM (1985) New selective media for enumeration and recovery of fluorescent pseudomonads from various habitats. Appl Environ Microbiol 49(1):28–32Google Scholar
  9. 9.
    Govindasamy V, Raina SK, George P, Kumar M, Rane J, Minhas PS, Vittal KPR (2017) Functional and phylogenetic diversity of cultivable rhizobacterial endophytes of sorghum [Sorghum bicolor (L.) Moench]. Antonie Van Leeuwenhoek 110(7):925–943Google Scholar
  10. 10.
    Gupta G, Panwar J, Jha PN (2013) Natural occurrence of Pseudomonas aeruginosa, a dominant cultivable diazotrophic endophytic bacterium colonizing Pennisetum glaucum (L.) R.Br. Appl Soil Ecol 64:252–261Google Scholar
  11. 11.
    Hagedorn C, Holt JG (1975) A nutritional and taxonomic survey of Arthrobacter soil isolates. Can J Microbiol 21(3):353–361Google Scholar
  12. 12.
    Hallmann J, Quadt-Hallman A, Mahaffee WF, Kloepper JW (1997) Bacterial endophytes in agricultural crops. Can J Microbiol 43(10):895–914Google Scholar
  13. 13.
    Hameed A, Yeh M-W, Hsieh Y-T, Chung W-C, Lo C-T, Young L-S (2015) Diversity and functional characterization of bacterial endophytes dwelling in various rice (Oryza sativa L.) tissues, and their seed-borne dissemination into rhizosphere under gnotobiotic P-stress. Plant Soil 394(1–2):177–197Google Scholar
  14. 14.
    Hardoim PR, Andreote FD, Reinhold-Hurek B, Sessitsch A, Van Overbeek LS, van Elsas JD (2011) Rice root-associated bacteria: insights into community structures across 10 cultivars. FEMS Microbiol Ecol 77(1):154–164Google Scholar
  15. 15.
    Hardoim PR, Hardoim CCP, van Overbeek LS, van Elsas JD (2012) Dynamics of seed-borne rice endophytes on early plant growth stages. PLoS One 7:e30438.  https://doi.org/10.1371/journal.pone.0030438 Google Scholar
  16. 16.
    Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring M, Sessitsch A (2015) The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev 79(3):293–320Google Scholar
  17. 17.
    Hartmann A, Singh M, Klingmüller W (1983) Isolation and characterization of Azospirillum mutants excreting high amounts of indoleacetic acid. Can J Microbiol 29(8):916–923Google Scholar
  18. 18.
    Jackson ML (1967) Soil chemical analysis. Prentice Hall of India, Pvt. Ltd., New DelhiGoogle Scholar
  19. 19.
    James EK, Gyaneshwar P, Mathan N, Barraquio WL, Reddy PM, Iannetta PP, Olivares FL, Ladha JK (2002) Infection and colonization of rice seedlings by the plant growth-promoting bacterium Herbaspirillum seropedicae Z67. Mol Plant-Microbe Interact 15(9):894–906Google Scholar
  20. 20.
    Kaga H, Mano H, Tanaka F, Watanabe A, Kaneko S, Morisaki H (2009) Rice seeds as sources of endophytic bacteria. Microbes Environ 24(2):154–162Google Scholar
  21. 21.
    Kennedy IR, Choudhury ATMA, Kecskés ML (2004) Non-symbiotic bacterial diazotrophs in crop-farming systems: can their potential for plant growth promotion be better exploited? Soil Biol Biochem 36(8):1229–1244Google Scholar
  22. 22.
    Koomnok C, Teaumroong N, Rerkasem B, Lumyong S (2007) Diazotroph endophytic bacteria in cultivated and wild rice in Thailand. Sci Asia 33:429–435Google Scholar
  23. 23.
    Kumar A, Verma JP (2018) Does plant–microbe interaction confer stress tolerance in plants: a review? Microbiol Res 207:41–52Google Scholar
  24. 24.
    Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–175Google Scholar
  25. 25.
    Loaces I, Ferrando L, Scavino AF (2011) Dynamics, diversity and function of endophytic siderophore-producing bacteria in rice. Microb Ecol 61(3):606–618Google Scholar
  26. 26.
    Lodewyckx C, Vangronsveld J, Porteous F, Moore ERB, Taghavi S, Mezgeay M, van der Lelie D (2002) Endophytic bacteria and their potential applications. Crit Rev Plant Sci 21(6):583–606Google Scholar
  27. 27.
    Lowry OH, Rosebrough NJ, Farr AL, Randall RJ (1951) Protein measurement with Folin phenol reagent. J Biol Chem 193(1):265–275Google Scholar
  28. 28.
    Manjunatha BS, Paul S, Aggarwal C, Rathi MS (2016) Effect of osmotic stress on growth and plant growth promoting activities of osmotolerant endophytic bacteria from pearl millet. Environ Ecol 34(3B):1223–1228Google Scholar
  29. 29.
    Manjunatha BS, Asha AD, Nivetha N, Bandeppa, Govindasamy V, Rathi MS, Paul S (2017) Evaluation of endophytic bacteria for their influence on plant growth and seed germination under water stress conditions. Int J Curr Microbiol App Sci 6(11):4061–4067Google Scholar
  30. 30.
    Mano H, Tanaka F, Nakamura C, Kaga H, Morisaki H (2007) Culturable endophytic bacterial flora of the maturing leaves and roots of rice plants (Oryza sativa) cultivated in a paddy field. Microbes Environ 22(2):175–185Google Scholar
  31. 31.
    Manter DK, Delgado JA, Holm DG, Stong RA (2010) Pyrosequencing reveals a highly diverse and cultivar-specific bacterial endophyte community in potato roots. Microb Ecol 60(1):157–166Google Scholar
  32. 32.
    Misaghi IJ, Donndelinger CR (1990) Endophytic bacteria in symptom-free cotton plants. Phytopathology 80(9):808–811Google Scholar
  33. 33.
    Neal AL, Ahmad S, Gordon-Weeks R, Ton J (2012) Benzoxazinoids in root exudates of maize attract Pseudomonas putida to the rhizosphere. PLoS One 7:35498.  https://doi.org/10.1371/journal.pone.0035498 Google Scholar
  34. 34.
    Nei M, Li WH (1979) Mathematical model for studying genetic variations in terms of restriction endonucleases. Proc Natl Acad Sci U S A 76(10):5269–5273Google Scholar
  35. 35.
    Obeng E, Cebert E, Singh BP, Ward R, Nyochembeng LM, Mays DA (2012) Growth and grain yield of pearl millet (Pennisetum glaucum) genotypes at different levels of nitrogen fertilization in the southeastern United States. J Agric Sci 4(12):155–163Google Scholar
  36. 36.
    Okunishi S, Sako K, Mano H, Imamura A, Morisaki H (2005) Bacterial flora of endophytes in the maturing seed of cultivated rice (Oryza sativa). Microbes Environ 20(3):168–177Google Scholar
  37. 37.
    Paul S, Bandeppa, Aggarwal C, Thakur JK, Rathi MS, Khan MA (2014) Effect of salt on growth and plant growth promoting activities of Azotobacter chroococcum isolated from saline soils. Environ Ecol 32(4):1255–1259Google Scholar
  38. 38.
    Penrose DM, Glick BR (2003) Methods for isolating and characterizing ACC deaminase-containing plant growth-promoting rhizobacteria. Physiol Plant 118(1):10–15Google Scholar
  39. 39.
    Pikovskaya RI (1948) Mobilization of phosphorus in soil connection with the vital activity of some microbial species. Microbiol 17:362–370Google Scholar
  40. 40.
    Qadri M, Rajput R, Abdin MZ, Vishwakarma RA, Riyaz-Ul-Hassan S (2014) Diversity, molecular phylogeny, and bioactive potential of fungal endophytes associated with the Himalayan blue pine (Pinus wallichiana). Microb Ecol 67(4):877–887Google Scholar
  41. 41.
    Rennie RJ (1981) A single medium for the isolation of acetylene-reducing (dinitrogen-fixing) bacteria from soils. Can J Microbiol 27(1):8–14Google Scholar
  42. 42.
    Rosenblueth M, Martínez-Romero E (2006) Bacterial endophytes and their interactions with hosts. Mol Plant-Microbe Interact 19(8):827–837Google Scholar
  43. 43.
    Sankar SM, Satyavathi CT, Singh SP, Singh MP, Bharadwaj C, Barthakur S (2014) Genetic diversity analysis for high temperature stress tolerance in pearl millet [Pennisetum glaucum (L.) R. Br.]. Indian J Plant Physiol 19(4):324–329Google Scholar
  44. 44.
    Santoyo G, Moreno-Hagelsieb G, Orozco-Mosqueda Mdel C, Glick BR (2016) Plant growth-promoting bacterial endophytes. Microbiol Res 183:92–99Google Scholar
  45. 45.
    Schwyn B, Neilands JB (1987) Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160(1):47–56Google Scholar
  46. 46.
    Singh RP, Shelke GM, Kumar A, Jha PN (2015) Biochemistry and genetics of ACC deaminase: a weapon to “stress ethylene” produced in plants. Front Microbiol 6:937.  https://doi.org/10.3389/frmicb.2015.00937 Google Scholar
  47. 47.
    Vacheron J, Desbrosses G, Bouffaud ML, Touraine B, Moënne-Loccoz Y, Muller D, Legendre L, Wisniewski-Dyé F, Prigent-Combaret C (2013) Plant growth-promoting rhizobacteria and root system functioning. Front Plant Sci 4:356.  https://doi.org/10.3389/fpls.2013.00356 Google Scholar
  48. 48.
    Valluru R, Davies WJ, Reynolds MP, Dodd IC (2016) Foliar abscisic acid-to-ethylene accumulation and response regulate shoot growth sensitivity to mild drought in wheat. Front Plant Sci 7:461.  https://doi.org/10.3389/fpls.2016.00461 Google Scholar
  49. 49.
    Wemheuer F, Kaiser K, Karlovsky P, Daniel R, Vidal S, Wemheuer B (2017) Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes. Sci Rep 7:40914.  https://doi.org/10.1038/srep40914 Google Scholar
  50. 50.
    Xia Y, Greissworth E, Mucci C, Williams MA, De Bolt S (2013) Characterization of culturable bacterial endophytes of switchgrass (Panicum virgatum L.) and their capacity to influence plant growth. GCB Bioenergy 5(6):674–682Google Scholar
  51. 51.
    Xia Y, DeBolt S, Dreyer J, Scott D, Williams MA (2015) Characterization of culturable bacterial endophytes and their capacity to promote plant growth from plants grown using organic or conventional practices. Front Plant Sci 6:490.  https://doi.org/10.3389/fpls.2015.00490 Google Scholar
  52. 52.
    Zinniel DK, Lambrecht P, Harris NB, Feng Z, Kiczmarski D, Higley P, Ishimaru CA, Arunakumari A, Barletta RG, Vidaver AK (2002) Isolation and characterization of endophytic colonizing bacteria from agronomic crops and prairie plants. Appl Environ Microbiol 68(5):2198–2208Google Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • B. S. Manjunatha
    • 1
  • Sangeeta Paul
    • 1
    Email author
  • Chetana Aggarwal
    • 2
  • S. Bandeppa
    • 3
  • V. Govindasamy
    • 1
  • Ajinath S. Dukare
    • 4
  • Maheshwar S. Rathi
    • 1
  • C. T. Satyavathi
    • 5
  • K. Annapurna
    • 1
  1. 1.Division of MicrobiologyICAR-Indian Agricultural Research InstituteNew DelhiIndia
  2. 2.ICAR-National Research Centre on Plant BiotechnologyNew DelhiIndia
  3. 3.Division of Soil ScienceICAR-Indian Institute of Rice ResearchHyderabadIndia
  4. 4.Division of Horticultural Crop ProcessingICAR-Central Institute of Post Harvest Engineering and TechnologyAboharIndia
  5. 5.ICAR-All India Coordinated Research Project on Pearl MilletJodhpurIndia

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