Skip to main content

Advertisement

SpringerLink
Log in

Characterisation of Pseudomonas spp. and Ochrobactrum sp. isolated from volcanic soil

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

Soil bacteria may have properties of plant growth promotion but not be sufficiently beneficial for plants under stress conditions. This challenge has led researchers to extend their searches into extreme environments for potential soil bacteria with multiple plant beneficial traits as well as abiotic stress tolerance abilities. In the current study, an attempt was made to evaluate soil bacteria from an extreme environment, volcano soils, based on plant growth promoting and abiotic stress mitigating characteristics. The screening led to the isolation of eight (NBRISH4, NBRISH6, NBRISH10, NBRISH11, NBRISH13, NBRISH14, NBRISH16 and NBRISH26) bacterial isolates capable of withstanding stresses, namely temperature (up to 45 °C), salt (up to 2 M NaCl) and drought (up to 60% Poly Ethylene Glycol 6000) in vitro. Further, the selected isolates were notable for their in vitro temporal performance with regards to survival (in terms of colony count), phosphate solubilisation, biofilm formation, auxin, alginate and exo-polysaccharide production abilities under abiotic stresses i.e. 40 °C temperature; 500 mM NaCl salt and drought (PEG) conditions. In vivo seed treatments of individual selected bacteria to maize plants resulted into significant enhancement in root and shoot length, root and shoot fresh and dry weight and number of leaves per plant. Overall, the plant growth promoting and abiotic stress tolerance ability was most evident for bacterial isolate NBRISH6 which was identified as an Ochrobactrum sp. using 16S rRNA based phylogenetic analysis.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Abiala MA, Odebode AC, Hsu SF, Blackwood CB (2015) Phytobeneficial properties of bacteria isolated from the rhizosphere of maize in southwestern Nigerian soils. Appl Environ Microbiol 81:4736–4743. doi:10.1128/AEM.00570-15

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Amaresan N, Kumar K, Sureshbabu K, Madhuri K (2014) Plant growth-promoting potential of bacteria isolated from active volcano sites of Barren Island, India. Lett Appl Microbiol 58:130–137. doi:10.1111/lam.12165

    Article  CAS  PubMed  Google Scholar 

  • Barea JM (2015) Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant-microbiome interactions. J Soil Sci Plant Nutr 15:261–282

    Google Scholar 

  • Bharucha U, Patel K, Trivedi UB (2013) Optimization of indole acetic acid production by Pseudomonas putida UB1 and its effect as plant growth-promoting rhizobacteria on mustard (Brassica nigra). Agric Res 2:215–221. doi:10.1007/s40003-013-0065-7

    Article  CAS  Google Scholar 

  • Bogino PC, Oliva MDLM, Sorroche FG, Giordano W (2013) The role of bacterial biofilms and surface components in plant-bacterial associations. Int J Mol Sci 14:15838–15859. doi:10.3390/ijms140815838

    Article  PubMed  PubMed Central  Google Scholar 

  • Brick JM, Bostock RM, Silversone SE (1991) Rapid in situ assay for indole acetic acid production by bacteria immobilized on nitrocellulose membrane. Appl Environ Microbiol 57:535–538

    Google Scholar 

  • Cardinale M, Ratering S, Suarez C, Montoya AMZ, Geissler-Plaum R, Schnell S (2015) Paradox of plant growth promotion potential of rhizobacteria and their actual promotion effect on growth of barley (Hordeum vulgare L.) under salt stress. Microbiol Res 181:22–32. doi:10.1016/j.micres.2015.08.002

    Article  CAS  PubMed  Google Scholar 

  • Cattelan AJ, Hartel PG, Furhmann JJ (1999) Screening for plant growth-promoting rhizobacteria to promote early soybean growth. Soil Sci Soc Am J 63:1670–1680. doi:10.2136/sssaj1999.6361670

    Article  CAS  Google Scholar 

  • Chakrabarty AM (1981) Microorganisms having multiple compatible degradative energy-generating plasmids and preparation thereof. US patent 4,259,444

  • Chaudhry V, Bhatia A, Bharti SK, Mishra SK, Chauhan PS, Mishra A, Sidhu OP, Nautiyal CS (2015) Metabolite profiling reveals abiotic stress tolerance in Tn5 mutant of Pseudomonas putida. PLoS ONE 10:e0113487. doi:10.1371/journal.pone.0113487

    Article  PubMed  PubMed Central  Google Scholar 

  • Chauhan PS, Nautiyal CS (2010) The purB gene controls rhizosphere colonization by Pantoea agglomerans. Lett Appl Microbiol 50:205–210. doi:10.1111/j.1472-765X.2009.02779

    Article  CAS  PubMed  Google Scholar 

  • Chien A, Edgar DB, Trela JM (1976) Deoxyribonucleic acid polymerase from the extreme thermophile Thermus acquaticus. J Bacteriol 127:1550–1557

    CAS  PubMed  PubMed Central  Google Scholar 

  • Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ (2009) Leifsonia kribbensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 59:18–21. doi:10.1099/ijs.0.001925-0

    Article  CAS  PubMed  Google Scholar 

  • Fiske CH, Subbarow Y (1925) The colorimetric determination of phosphorus. J Biol Chem 66:375–400

    CAS  Google Scholar 

  • Gadhave KR, Hourston JE, Gange AC (2016) Developing soil microbial inoculants for pest management: can one have too much of a good thing? J Chem Ecol 42:348–356. doi:10.1007/s10886-016-0689-8

    Article  CAS  PubMed  Google Scholar 

  • Gao Y-Z, Liu H, Chao H-J, Zhou N-Y (2016) Constitutive expression of a Nag-like dioxygenase gene through an internal promoter in the 2-chloronitrobenzene catabolism gene cluster of Pseudomonas stutzeri ZWLR2-1. Appl Environ Microbiol 82:3461–3470. doi:10.1128/AEM.00197-16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gopalakrishnan S, Sathya A, Vijayabharathi R, Varshney RK, Gowda CLL, Krishnamurthy L (2015) Plant growth promoting rhizobia: challenges and opportunities. 3 Biotech 5:355–377. doi:10.1007/s13205-014-0241

    Article  Google Scholar 

  • Gupta G, Parihar SS, Ahirwar NK, Snehi SK, Singh V (2015) Plant growth promoting rhizobacteria (PGPR): current and future prospects for development of sustainable agriculture. J Microb Biochem Technol 7:96–102. doi:10.4172/1948-5948.1000188

    Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Hayat R, Ali S, Amara U, Khalid R, Ahmed I (2010) Soil beneficial bacteria and their role in plant growth promotion: a review. Ann Microbiol 60:579–598. doi:10.1007/s13213-010-0117-1

    Article  Google Scholar 

  • Khan N, Mishra A, Chauhan PS, Sharma YK, Nautiyal CS (2012) Paenibacillus lentimorbus enhances growth of chickpea (Cicer arietinum L.) in chromium-amended soil. Antonie Van Leeuwenhoek 101:453–459. doi:10.1007/s10482-011-9637-3

    Article  CAS  PubMed  Google Scholar 

  • Khare E, Arora NK (2010) Effect of indole-3-acetic acid (IAA) produced by Pseudomonas aeruginosa in suppression of charcoal rot disease of chickpea. Curr Microbiol 61:64–68. doi:10.1007/s00284-009-9577-6

    Article  CAS  PubMed  Google Scholar 

  • Kloepper JW, Beauchamp CJ (1992) A review of issues related to measuring of plant roots by bacteria. Can J Microbiol 38:1219–1232. doi:10.1139/m92-202

    Article  Google Scholar 

  • Laditi MA, Nwoke OC, Jemo M, Abaidoo RC, Ogunjobi AA (2012) Evaluation of microbial inoculants as biofertilizers for the improvement of growth and yield of soybean and maize crops in savanna soils. Afr J Agric Res 7:405–413. doi:10.5897/AJAR11.904

    Article  Google Scholar 

  • Mei GY, Yan XX, Turak A, Luo ZQ, Zhang LQ (2010) AidH, an alpha/beta-hydrolase fold family member from an Ochrobactrum sp. strain, is a novel N-acylhomoserine lactonase. Appl Environ Microbiol 76:4933–4942. doi:10.1128/AEM.00477-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meintanis C, Chalkou KI, Kormas KA, Karagouni AD (2006) Biodegradation of crude oil by thermophilic bacteria isolated from a volcano island. Biodegradation 17:3–9. doi:10.1007/s10532-005-6495-6

    Article  CAS  Google Scholar 

  • Meng X, Yan D, Long X, Wang C, Liu Z, Rengel Z (2014) Colonization by endophytic Ochrobactrum anthropi Mn1 promotes growth of Jerusalem artichoke. Microb Biotechnol 7:601–610. doi:10.1111/1751-7915.12145

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meyer JM, Abdallah MA (1978) The florescent pigment of Pseudomonas fluorescens biosynthesis, purification and physical-chemical properties. J Gen Microbiol 107:319–328. doi:10.1099/00221287-107-2-319

    Article  CAS  Google Scholar 

  • Mishra S, Mishra A, Chauhan PS, Mishra SK, Kumari M, Niranjan A, Nautiyal CS (2012) Pseudomonas putida NBRIC19 dihydrolipoamide succinyltransferase (SucB) gene controls degradation of toxic allelochemicals produced by Parthenium hysterophorus. J Appl Microbiol 112:793–808. doi:10.1111/j.1365-2672.2012.05256

    Article  CAS  PubMed  Google Scholar 

  • Nautiyal CS (1997) A method for selection and characterization of rhizosphere-competent bacteria of chickpea. Curr Microbiol 34:12–17. doi:10.1007/s002849900136

    Article  CAS  PubMed  Google Scholar 

  • Nautiyal CS (1999) An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS Microbiol Lett 170:265–270. doi:10.1111/j.1574-6968.1999.tb13383

    Article  CAS  PubMed  Google Scholar 

  • Nishiyama M, Watanabe Y, Marumoto T (1998) Bacterial 16S rDNA sequences in immature volcanic ash soil on volcanoes Mt. Sakurajima and Mt. Fugen in Japan determined by PCR amplification. Soil Sci Plant Nutr 44:711–715. doi:10.1080/00380768.1998.10414498

    Article  Google Scholar 

  • Ortega-González DK, Cristiani-Urbina E, Flores-Ortíz CM, Cruz-Maya JA, Cancino-Díaz JC, Jan-Roblero J (2015) Evaluation of the removal of pyrene and fluoranthene by Ochrobactrum anthropi Fusarium sp. and their coculture. Appl Biochem Biotechnol 175:1123–1138. doi:10.1007/s12010-014-1336

    Article  PubMed  Google Scholar 

  • Oteino N, Lally RD, Kiwanuka S, Lloyd A, Ryan D, Germaine KJ, Dowling DN (2015) Plant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates. Front Microbiol 6:745. doi:10.3389/fmicb.2015.00745

    Article  PubMed  PubMed Central  Google Scholar 

  • Penrose DM, Glick BR (2003) Methods for isolating and characterizing ACC deaminase-containing plant growth-promoting rhizobacteria. Physiol Plant 118:10–15. doi:10.1034/j.1399-3054.2003.00086

    Article  CAS  PubMed  Google Scholar 

  • Podile AR, Vukanti RVNR, Sravani A, Kalam S, Dutta S, Durgeshwar P, Rao VP (2013) Root colonization and quorum sensing are the driving forces of plant growth promoting rhizobacteria (PGPR) for growth promotion. Proc Natl Acad Sci, India, Sect B Biol 80:407–413. doi:10.16943/ptinsa/2014/v80i2/55117

    Article  Google Scholar 

  • Qurashi AW, Sabri AN (2012) Bacterial exopolysaccharide and biofilm formation stimulate chickpea growth and soil aggregation under salt stress. Braz J Microbiol 43:1183–1191. doi:10.1590/S1517-838220120003000046

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Redmile-Gordon MA, Brookes PC, Evershed RP, Goulding KWT, Hirsch PR (2014) Measuring the soil-microbial interface: extraction of extracellular polymeric substances (EPS) from soil biofilms. Soil Biol Biochem 72:163–171. doi:10.1016/j.soilbio.2014.01.025

    Article  CAS  Google Scholar 

  • Requena N, Jimenez I, Toro M, Barea JM (1997) Interactions between plant-growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi and Rhizobium spp. in the rhizosphere of Anthyllis cytisoides, a model legume for revegetation in mediterranean semi-arid ecosystems. New Phytol 136:667–677. doi:10.1046/j.1469-8137.1997.00786

    Article  Google Scholar 

  • Rodriguez RJ, Henson J, Van Volkenburgh E, Hoy M, Wright L, Beckwith F, Kim Y-O, Redman RS (2008) Stress tolerance in plants via habitat-adapted symbiosis. ISME J 2:404–416. doi:10.1038/ismej.2007.106

    Article  PubMed  Google Scholar 

  • Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491. doi:10.1126/science.2448875

    Article  CAS  PubMed  Google Scholar 

  • Seufferheld MJ, Alvarez HM, Farias ME (2008) Role of polyphosphates in microbial adaptation to extreme environments. Appl Environ Microbiol 74:5867–5874. doi:10.1128/AEM.00501-08

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shrivastava P, Kumar R (2015) Soil salinity: a serious environmental issue and plant promoting bacteria as one of the tools for its alleviation. Saudi J Biol Sci 22:123–131. doi:10.1016/j.sjbs.2014.12.001

    Article  CAS  PubMed  Google Scholar 

  • Singh RB (2013) Climate change and abiotic stress management in India. In: Tuteja N, Gill SS (eds) Climate change and plant abiotic stress tolerance, vol 1. Wiley, Weinheim, pp 57–77. doi:10.1002/9783527675265.ch03

    Chapter  Google Scholar 

  • Singh BN, Singh HB, Singh A, Singh BR, Mishra A, Nautiyal CS (2012) Lagerstroemia speciosa fruit extract modulates quorum sensing-controlled virulence factor production and biofilm formation in Pseudomonas aeruginosa. Microbiol 158:529–538. doi:10.1099/mic.0.052985-0

    Article  CAS  Google Scholar 

  • Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology, 3rd edn. ASM Press, Washington DC, pp 607–654

    Google Scholar 

  • Srivastava S, Yadav A, Seem K, Mishra S, Chaudhary V, Nautiyal CS (2008) Effect of high temperature on Pseudomonas putida NBRI10987 biofilm formation and expression of stress sigma factor RpoS. Curr Microbiol 56:453–457. doi:10.1007/s00284-008-9105-0

    Article  CAS  PubMed  Google Scholar 

  • Srivastava S, Chaudhry V, Mishra A, Chauhan PS, Rehman A, Yadav A, Tuteja N, Nautiyal CS (2012) Gene expression profiling through microarray analysis in Arabidopsis thaliana colonized by Pseudomonas putida MTCC5279, a plant growth promoting rhizobacterium. Plant Signal Behav 7:235–245. doi:10.4161/psb.18957

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 101:11030–11035. doi:10.1073/pnas.0404206101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. doi:10.1093/molbev/msr121

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Titus S, Gasnkar N, Srivastava KB, Karande AA (1995) Exopolymer production by a fouling marine bacterium Pseudomonas alcaligenes. Indian J Mar Sci 24:45–48

    CAS  Google Scholar 

  • Venkadesaperumal G, Amaresan N, Kumar K (2014) Plant growth promoting capability and genetic diversity of bacteria isolated from mud volcano and lime cave of Andaman and Nicobar Islands. Braz J Microbiol 45:1271–1281. doi:10.1590/S1517-83822014000400018

    Article  CAS  PubMed  Google Scholar 

  • World Economic Forum (2011) Realizing a new vision for agriculture: a roadmap for stakeholders. World Economic Forum, Davos

    Google Scholar 

  • Yadav AN, Verma P, Kumar M, Pal KK, Dey R, Gupta A, Padaria JC, Gujar GT, Kumar S, Suman A, Prasanna R, Saxena AK (2015) Diversity and phylogenetic profiling of niche-specific Bacilli from extreme environments of India. Ann Microbiol 65:611–629. doi:10.1007/s13213-014-0897-9

    Article  Google Scholar 

  • Zhu H-H, Yao Q, Sun X-T, Hu Y-L (2007) Colonization, ALP activity and plant growth promotion of native and exotic arbuscular mycorrhizal fungi at low pH. Soil Biol Biochem 39:942–950. doi:10.1016/j.soilbio.2006.11.006

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The study was conducted using the operating funds of the network project Plant Microbe and Soil Interactions (PMSI) (BSC-0117) funded by Council of Scientific and Industrial Research, New Delhi, India. Authors are thankful to the Director, CSIR-NBRI, Lucknow for providing necessary resources to conduct this study.

Author information

Authors and Affiliations

  1. Division of Plant Microbe Interactions, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226 001, India

    Shashank Kumar Mishra, Mohammad Haneef Khan, Sankalp Misra, Vijay Kant Dixit, Praveen Khare, Suchi Srivastava & Puneet Singh Chauhan

Authors
  1. Shashank Kumar Mishra
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mohammad Haneef Khan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sankalp Misra
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Vijay Kant Dixit
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Praveen Khare
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Suchi Srivastava
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Puneet Singh Chauhan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Puneet Singh Chauhan.

Electronic supplementary material

Below is the link to the electronic supplementary material.

10482_2016_796_MOESM1_ESM.docx

Supplementary material 1 (DOCX 120 kb) Supplementary data associated with this article can be found in Figure S1–S3, and Table S1

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Mishra, S.K., Khan, M.H., Misra, S. et al. Characterisation of Pseudomonas spp. and Ochrobactrum sp. isolated from volcanic soil. Antonie van Leeuwenhoek 110, 253–270 (2017). https://doi.org/10.1007/s10482-016-0796-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-016-0796-0

Keywords

Search

Navigation