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Diverse culturable diazotrophic endophytic bacteria from Poaceae plants show cross-colonization and plant growth promotion in wheat

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Abstract

Background and aims

Diazotrophic endophytic bacteria colonizing cereal plants have a tremendous scope to increase crop yields by supporting low input sustainable agricultural demands of nitrogen. Present work was aimed at studying diversity and functional attributes of nitrogen fixing bacterial endophytes from cereal plants.

Methods

Diazotrophic endophytic bacteria from cereal plants were enriched on nitrogen-free medium and their diversity analyzed by PCR-denaturing gradient gel electrophoresis. Evaluation of plant growth promoting traits of individual isolates and their effect on wheat plants was carried out in plant-soil system.

Results

DGGE analysis and band sequencing showed diazotrophic community to be similar in different plant parts but different than total endophytes. Thirty-one nitrogen fixing endophytic bacteria affiliated to Actinobacteria, Proteobacteria and Firmicutes representing 14 genera were isolated, where Arthrobacter, Rhizobium, and Bacillus spp. were more cosmopolitan. Cross-colonization of the endophytes monitored by green fluorescent protein tagging showed that they are not plant specific. All the bacterial isolates showed presence of nifH gene, siderophore production whereas 81% and 48% isolates showed IAA and P-solubilization, respectively. Biocontrol activity was seen only in Streptomyces spp. which inhibited the growth of Rhizoctonia solani. Pot experiments conducted with wheat plant inoculations showed good growth promotion and correlated with IAA and siderophore production by the isolates.

Conclusion

Diverse endophytic nitrogen fixing bacteria colonize cereal plants non-specifically and possess other plant beneficial traits which help in plant growth promotion.

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References

  • Ahmad F, Ahmad I, Khan MS (2008) Screening of free-living rhizospheric bacteria for their multiple plant growth promoting activities. Microbiol Res 163:173–181

    Article  CAS  PubMed  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  • Andreote FD, da Rocha UN, Araújo WL, Azevedo JL, van Overbeek LS (2010) Effect of bacterial inoculation, plant genotype and developmental stage on root-associated and endophytic bacterial communities in potato (Solanum tuberosum). Antonie Van Leeuwenhoek 97:389–399

    Article  PubMed  PubMed Central  Google Scholar 

  • Araujo WL, Marcon J, Maccheroni W, van Elsas JD, van Vuurde JW, Azevedo JL (2002) Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants. Appl Environ Microbiol 68:4906–4914

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arnon DI (1949) Copper enzymes in isolated chloroplasts. Polyphenoloxidase in Beta vulgaris. Plant Physiol 24:1–15

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chanway CP, Shishido M, Nairn J, Jungwirth S, Markham J, Xiao G, Holl FB (2000) Endophytic colonization and field responses of hybrid spruce seedlings after inoculation with plant growth-promoting rhizobacteria. For Ecol Manag 133:81–88

    Article  Google Scholar 

  • Chaturvedi R, Archana G (2012) Novel 16S rRNA based PCR method targeting Deinococcus spp. and its application to assess the diversity of deinococcal populations in environmental samples. J Microbiol Methods 90:197–205

    Article  CAS  PubMed  Google Scholar 

  • Cheng HP, Walker GC (1998) Succinoglycan is required for initiation and elongation of infection threads during nodulation of alfalfa by Rhizobium meliloti. J Bacteriol 180:5183–5191

    CAS  PubMed  PubMed Central  Google Scholar 

  • Compant S, Clément C, Sessitsch A (2010) Plant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biol Biochem 42:669–678

    Article  CAS  Google Scholar 

  • Döbereiner J, Baldani VLD, Reis VM (1995) Endophytic occurrence of diazotrophic bacteria in non-leguminous crops. In: Fendrik I, del Gallo M, Vanderleyden J, de Zamaroczy M (eds) Azospirillum VI and related microorganisms. Springer, Berlin, pp 3–14

    Chapter  Google Scholar 

  • Ferrando L, Scavino AF (2015) Strong shift in the diazotrophic endophytic bacterial community inhabiting rice (Oryza sativa) plants after flooding. FEMS Microbiol Ecol 91:fiv104

  • Garbeva P, van Overbeek LS, van Vuurde JWL, van Elsas JD (2001) Analysis of endophytic bacterial communities of potato by plating and denaturing gradient gel electrophoresis (DGGE) of 16S rRNA based PCR fragments. Microb Ecol 41:369–383

    Article  CAS  PubMed  Google Scholar 

  • Glick BR (2014) Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol Res 169:30–39

    Article  CAS  PubMed  Google Scholar 

  • 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 64:252–261

    Article  Google Scholar 

  • Gyaneshwar P, James EK, Mathan N, Reddy PM, Reinhold-Hurek B, Ladha JK (2001) Endophytic colonization of rice by a diazotrophic strain of Serratia marcescens. J Bacteriol 183:2634–2645

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gyaneshwar P, Parekh LJ, Archana G, Poole PS, Collins MD, Hutson RA, Kumar GN (1999) Involvement of a phosphate starvation inducible glucose dehydrogenase in soil phosphate solubilization by Enterobacter asburiae. FEMS Microbiol Lett 171:223–229

    Article  CAS  Google Scholar 

  • Hammer Ø, Harper DAT, Ryan PD (2001) Past: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:1–9

    Google Scholar 

  • Holt JG, Krieg NR, Sneath PHA, Staley JT, Williams ST (1994) Bergey’s Manual of determinate bacteriology, 9th edn. Williams and Wilkins, Baltimore

    Google Scholar 

  • Iniguez AL, Dong Y, Triplett EW (2004) Nitrogen fixation in wheat provided by Klebsiella pneumoniae 342. Mol Plant-Microbe Interact 17:1078–1085

    Article  CAS  PubMed  Google Scholar 

  • Jimtha JC, Smitha PV, Anisha C, Deepthi T, Meekha G, Radhakrishnan EK, Remakanthan A (2014) Isolation of endophytic bacteria from embryogenic suspension culture of banana and assessment of their plant growth promoting properties. Plant Cell Tissue Organ Cult 118:57–66

    Article  Google Scholar 

  • Kang SH, Cho HS, Cheong H, Ryu CM, Kim JF, Park SH (2007) Two bacterial entophytes eliciting both plant growth promotion and plant defense on pepper (Capsicum annuum L.) J Microbiol Biotechnol 17:96–103

    CAS  PubMed  Google Scholar 

  • Kembhavi AA, Kulkarni A, Pant A (1993) Salt-tolerant and thermostable alkaline protease from Bacillus subtilis NCIM no.64. Appl Biochem Biotechnol 38:83–92

    Article  CAS  PubMed  Google Scholar 

  • Khan A, Geetha R, Akolkar A, Pandya A, Archana G, Desai AJ (2006) Differential cross-utilization of heterologous siderophores by nodule bacteria of Cajanus cajan and its possible role in growth under iron-limited conditions. Appl Soil Ecol 34:19–26

    Article  Google Scholar 

  • Khan AL, Waqas M, Kang SM, Al-Harrasi A, Hussain J, Al-Rawahi A, Lee IJ (2014) Bacterial endophyte Sphingomonas sp. LK11 produces gibberellins and IAA and promotes tomato plant growth. J Microbiol 52:689–695

    Article  CAS  PubMed  Google Scholar 

  • Khatri BP, Bhattarai T, Shrestha S, Maharjan J (2015) Alkaline thermostable pectinase enzyme from Aspergillus niger strain MCAS2 isolated from Manaslu conservation area, Gorkha, Nepal. SpringerPlus 4:488

    Article  PubMed  PubMed Central  Google Scholar 

  • Kuklinsky-Sobral J, Araujo WL, Mendes R, Geraldi IO, Pizzirani-Kleiner AA, Azevedo JL (2004) Isolation and characterization of soybean-associated bacteria and their potential for plant growth promotion. Environ Microbiol 6:1244–1251

    Article  CAS  PubMed  Google Scholar 

  • Larran S, Perello A, Simon MR, Moreno V (2002) Isolation and analysis of endophytic microorganisms in wheat (Triticum aestivum L.) leaves. World J Microbiol Biotechnol 18:683–686

    Article  CAS  Google Scholar 

  • Liu X, Jia J, Atkinson S, Cámara M, Gao K, Li H, Cao J (2010) Biocontrol potential of an endophytic Serratia sp. G3 and its mode of action. World J Microbiol Biotechnol 26:1465–1471

    Article  Google Scholar 

  • Lorck H (1948) Production of hydrocyanic acid by bacteria. Physiol Plant 1:142–146

    Article  CAS  Google Scholar 

  • 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 22:175–185

    Article  Google Scholar 

  • Nagpure A, Gupta RK (2013) Purification and characterization of an extracellular chitinase from antagonistic Streptomyces violaceusniger. J Basic Microbiol 53:429–439

    Article  CAS  PubMed  Google Scholar 

  • Ogut M, Er F, Kandemir N (2010) Phosphate solubilization potentials of soil Acinetobacter strains. Biol Fertil Soils 46:707–715

    Article  CAS  Google Scholar 

  • Pillai P, Archana G (2008) Hide depilation and feather disintegration studies with keratinolytic serine protease from a novel Bacillus subtilis isolate. Appl Microbiol Biotechnol 78:643–650

    Article  CAS  PubMed  Google Scholar 

  • Poly F, Monrozier L, Bally R (2001) Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Res Microbiol 152:95–103

    Article  CAS  PubMed  Google Scholar 

  • Prakamhang J, Minamisawa K, Teamtaisong K, Boonkerd N, Teaumroong N (2009) The communities of endophytic diazotrophic bacteria in cultivated rice (Oryza sativa L.) App soil ecol 42:141–149

    Article  Google Scholar 

  • Rangjaroen C, Rerkasem B, Teaumroong N, Sungthong R, Lumyong S (2014) Comparative study of endophytic and endophytic diazotrophic bacterial communities across rice landraces grown in the highlands of northern Thailand. Arch Microbiol 196:35–49

    Article  CAS  PubMed  Google Scholar 

  • Román-Ponce B, Ramos-Garza J, Vásquez-Murrieta MS, Rivera-Orduña FN, Chen WF, Yan J, Wang ET (2016) Cultivable endophytic bacteria from heavy metal(loid)-tolerant plants. Arch Microbiol 198:941–956

    Article  PubMed  Google Scholar 

  • Saha S, Roy RN, Sen SK, Ray AK (2006) Characterization of cellulase-producing bacteria from the digestive tract of tilapia, Oreochromis mossambica (Peters) and grass carp, Ctenopharyngodon idella (Valenciennes). Aquac Res 37:380–388

    Article  CAS  Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning: a laboratory Manual, 3rd edn. Cold Springs Harbor, Cold Springs Harbor Laboratory Press

    Google Scholar 

  • Seghers D, Wittebolle L, Top EM, Verstraete W, Siciliano SD (2004) Impact of agricultural practices on the Zea mays L. endophytic community. Appl Environ Microbiol 70:1475–1482

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sessitsch A, Hardoim P, Döring J, Weilharter A, Krause A, Woyke T, Hurek T (2012) Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol Plant-Microbe Interact 25:28–36

    Article  CAS  PubMed  Google Scholar 

  • Sharaff M, Archana G (2015) Assessment of microbial communities in mung bean (Vigna radiata) rhizosphere upon exposure to phytotoxic levels of copper. J Basic Microbiol 55:1299–1307

    Article  CAS  PubMed  Google Scholar 

  • Sharaff M, Archana G (2016) Copper-induced modifications in early symbiotic signaling factors of Ensifer (Sinorhizobium)–Medicago interactions. Arch Microbiol 198:701–709

    Article  CAS  PubMed  Google Scholar 

  • Sharma V, Kumar V, Archana G, Kumar GN (2005) Substrate specificity of glucose dehydrogenase (GDH) of Enterobacter asburiae PSI3 and rock phosphate solubilization with GDH substrates as C sources. Can J Microbiol 51:477–482

    Article  CAS  PubMed  Google Scholar 

  • Simon R, Priefer U, Pühler A (1983) A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram negative bacteria. Nature Biotechnol 1:784–791

    Article  CAS  Google Scholar 

  • Subrahmanyam G, Archana G, Chamyal LS (2011) Microbial activity and diversity in the late Pleistocene paleosols of alluvial Mahi River basin, Gujarat, western India. Curr Sci 101:202–209

    CAS  Google Scholar 

  • Sun L, Qiu F, Zhang X, Dai X, Dong X, Song W (2008) Endophytic bacterial diversity in rice (Oryza sativa L.) roots estimated by 16S rDNA sequence analysis. Microbial ecol 55:415–424

    Article  CAS  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tanaka K, Shimizu T, Zakria M, Njoloma J, Saeki Y, Sakai M, Akao S (2006) Incorporation of a DNA sequence encoding green fluorescent protein (GFP) into endophytic diazotroph from sugarcane and sweet potato and the colonizing ability of these bacteria in Brassica oleracea. Microbes Environ 21:122–128

    Article  Google Scholar 

  • Teather RM, Wood PJ (1982) Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol 43:777–780

    CAS  PubMed  PubMed Central  Google Scholar 

  • Thomas P, Swarna GK, Roy PK, Patil P (2008) Identification of culturable and originally non-culturable endophytic bacteria isolated from shoot tip cultures of banana cv. Grand Naine. Plant Cell Tissue Organ Cult 93:55–63

    Article  Google Scholar 

  • Tian F, Ding Y, Zhu H, Yao L, Du B (2009) Genetic diversity of siderophore-producing bacteria of tobacco rhizosphere. Braz J Microbiol 40:276–284

    Article  PubMed  PubMed Central  Google Scholar 

  • Verma SC, Ladha JK, Tripathi AK (2001) Evaluation of plant growth promoting and colonization ability of endophytic diazotrophs from deep water rice. J Biotechnol 91:127–141

    Article  CAS  PubMed  Google Scholar 

  • Villegas E, Ortega Martinez EI, Bauer R (1984) Chemical methods used at CIMMYT for determining protein quality in cereal grains. CIMMYT, Mexico

    Google Scholar 

  • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wemheuer F, Wemheuer B, Kretzschmar D, Pfeiffer B, Herzog S, Daniel R, Vidal S (2016) Impact of grassland management regimes on bacterial endophyte diversity differs with grass species. Lett Appl Microbiol 62:323–329

    Article  CAS  PubMed  Google Scholar 

  • Yanni YG, Rizk RY, Corich V, Squartini A, Ninke K, Philip-Hollingsworth S, Dazzo FB (1997) Natural endophytic association between Rhizobium leguminosarum bv. trifolii and rice roots and assessment of its potential to promote rice growth. Plant Soil 194:99–114

    Article  CAS  Google Scholar 

  • Zinniel DK, Lambrecht P, Harris NB, Feng Z, Kuczmarski D, Higley P, Vidaver AK (2002) Isolation and characterization of endophytic colonizing bacteria from agronomic crops and prairie plants. Appl Environ Microbiol 68:2198–2208

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

JKP is grateful to Department of Biotechnology, Government of India, for fellowship under DBT-MSUB-ILSPARE project. Authors acknowledge the support from Dr. Vikram Sarabhai Central Instrument Facility, The M.S. University of Baroda for confocal microscopy. We are grateful to Department of Biochemistry, Anand Agricultural University for providing their facility for estimating plant nitrogen content.

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  1. Department of Microbiology and Biotechnology Center, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 39002, India

    Janki K. Patel & G. Archana

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  1. Janki K. Patel
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  2. G. Archana
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Correspondence to G. Archana.

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Responsible Editor: Stéphane Compant.

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Patel, J.K., Archana, G. Diverse culturable diazotrophic endophytic bacteria from Poaceae plants show cross-colonization and plant growth promotion in wheat. Plant Soil 417, 99–116 (2017). https://doi.org/10.1007/s11104-017-3244-7

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  • DOI: https://doi.org/10.1007/s11104-017-3244-7

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