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Current Perspectives on Plant Growth-Promoting Rhizobacteria

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Abstract

The rhizosphere of plant species is an inimitable ecosystem that harbors an extensive range of microbes. Research in the wide areas of rhizosphere biotechnology highlighting new bioinoculants has received ample attention during recent past, and suitable expertises have been developed. However, the global recognition of such technologies by farmers is still overwhelmed with doubts owing to limited shelf-life and efficiency of the products which demonstrate discrepancies. This review illustrates plant growth-promoting rhizobacteria with detailed emphasis on nutrient acquisition and potential roles in conferring tolerance against abiotic stresses. The review demonstrates the recent research in the field of genomic and proteomic analysis, where systematic characterization of potentially effective rhizobacteria is being carried out by screening the extensive bacterial gene pool based on modern molecular tools. The review concludes by emphasizing the efforts made in the proteomics field which could compensate for understanding of prompt evolution in microbe-derived and plant-derived protein and metabolite substitute that activates vulnerability or resistance.

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References

  • Acebo-Guerrero Y, Hernández-Rodríguez A, Vandeputte O, Miguélez-Sierra Y, Heydrich-Pérez M, Ye L, El Jaziri M (2015) Characterization of Pseudomonas chlororaphis from Theobroma cacao L. rhizosphere with antagonistic activity against Phytophthora palmivora (Butler). J Appl Microbiol 119:1112–1126. doi:10.1111/jam.12910

    Article  CAS  PubMed  Google Scholar 

  • Afroz A, Zahur M, Zeeshan N, Komatsu S (2013) Plant-bacterium interactions analyzed by proteomics. Front Plant Sci 4:21

    Article  PubMed  PubMed Central  Google Scholar 

  • Ahemad M, Khan MS (2011) Toxicological assessment of selective pesticides towards plant growth promoting activities of phosphate solubilizing Pseudomonas aeruginosa. Acta Microbiol Immunol Hung 58:169–187

    Article  CAS  PubMed  Google Scholar 

  • Ahemad M, Khan MS (2012a) Effect of fungicides on plant growth promoting activities of phosphate solubilizing Pseudomonas putida isolated from mustard (Brassica compestris) rhizosphere. Chemosphere 86:945–950

    Article  CAS  PubMed  Google Scholar 

  • Ahemad M, Khan MS (2012b) Effects of pesticides on plant growth promoting traits of Mesorhizobium strain MRC4. J Saudi Soc Agric Sci 11:63–71

    CAS  Google Scholar 

  • Ahemad M, Kibret M (2014) Mechanisms and applications of plant growth promoting 386 rhizobacteria: current perspective. J King Saud Univ Sci 26:1–20

    Article  Google Scholar 

  • Ahmed E, Holmström SJ (2014) Siderophores in environmental research: roles and applications. Microbial Biotechnol 7(3):196–208

    Article  CAS  Google Scholar 

  • Aino M, Maekawa Y, Mayama S, Kato H (1997) Biocontrol of bacterial wilt of tomato by producing seedlings colonized with endophytic antagonistic pseudomonads. In: Ogoshi A, Kobayashi K, Homma Y, Kodama F, Kondo N, Akino S (eds) Plant growth-promoting Rhizobacteria—present status and future prospects. Faculty of agriculture. Hokkaido University, Sapporo, pp 120–123

    Google Scholar 

  • Andrade AE, Silva LP, Pereira JL, Noronha EF, Reis FB Jr, Bloch C Jr, Mehta A (2008) In vivo proteome analysis of Xanthomonas campestris pv. campestris in the interaction with the host plant Brassica oleracea. FEMS Microbiol Lett 281(2):167–174

    Article  CAS  PubMed  Google Scholar 

  • Antoun H, Beauchamp CJ, Goussard N, Chabot R, Lalande R (1998) Potential of Rhizobium and Bradyrhizobium species as plant growth promoting rhizobacteria on non-legumes: effects on radishes (Raphanus sativus L.). Plant Soil 204:57–67

    Article  CAS  Google Scholar 

  • Arora NK, Kang SC, Maheshwari DK (2001) Isolation of siderophore producing strains of Rhizobium meliloti and their biocontrol potential against Macrophomina phaseolina that causes charcoal rot of groundnut. Curr Sci 81:673–677

    Google Scholar 

  • Arshad M, Saleem M, Hussain S (2007) Perspectives of bacterial ACC deaminase in phytoremediation. Trends Biotechnol 25:356–362

    Article  CAS  PubMed  Google Scholar 

  • Ashraf M, Harris PJC (2013) Photosynthesis under stressful environments: an overview. Photosynthetica 51(2):163–190

    Article  CAS  Google Scholar 

  • Ashraf MA, Asif M, Zaheer A, Malik A, Ali Q, Rasool M (2013) Plant growth promoting rhizobacteria and sustainable agriculture: a review. Afr J Microbiol Res 7(9):704–709

    CAS  Google Scholar 

  • Baha N, Bekki A (2015) An approach of improving plant salt tolerance of Lucerne (Medicago sativa) grown under salt stress: use of Bio-inoculants. J Plant Growth Regul 34(1):169–182

    Article  CAS  Google Scholar 

  • Bakker P, Berendsen R, Doornbos R, Wintermans P, Pieterse C (2013) Rhizosphere revisited: root microbiomics. Front Plant Sci 165:1–7

    Google Scholar 

  • Barea JM, Richardson AE (2015) Phosphate mobilisation by soil microorganisms. In: Lugtenberg B (ed) Principles of plant-microbe interactions. Springer, Heidelberg, pp 225–234

    Google Scholar 

  • Barea JM, Pozo MJ, Azcon R, Azcón-Aguilar C (2013a) Microbial interactions in the rhizosphere. In: de Bruijn FJ (ed) Molecular microbial ecology of the rhizosphere, vol 1. Wiley, Hoboken, pp 29–44

    Chapter  Google Scholar 

  • Barea JM, Pozo MJ, López-Ráez JA, Aroca R, Ruíz-Lozano JM, Ferrol N, Azcón R, Azcón-Aguilar C (2013b) Arbuscular mycorrhizas and their significance in promoting soil-plant systems sustainability against environmental stresses. In: Rodelas B, González-López J (eds) Benefiial plant-microbial interactions: Ecology and applications. CRC Press, Boca Raton, pp 353–387

    Chapter  Google Scholar 

  • Bashan Y, de-Bashan LE, Prabhu SR, Hernandez JP (2014) Advances in plant growth-promoting bacterial inoculant technology: formulations and practical perspectives (1998–2013). Plant Soil 378:1–33

    Article  CAS  Google Scholar 

  • Bennett S (2004) Solexa Ltd. Pharmacogenomics 5:433–438

    Article  PubMed  Google Scholar 

  • Bhattacharyya PN, Jha DK (2012) Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture. World J Microbiol Biotechnol 28:1327–1350

    Article  CAS  PubMed  Google Scholar 

  • Bishnoi U, Polson SW, Sherrier DJ, Bais HP (2015) Draft genome sequence of a natural root isolate, Bacillus subtilis UD1022, a potential plant growth-promoting biocontrol agent. Genome Announc 3(4):e00696-15

    Article  PubMed  PubMed Central  Google Scholar 

  • Bishop PE, Jorerger RD (1990) Genetics and molecular biology of an alternative nitrogen fixation system. Plant Mol Biol 41:109–125

    CAS  Google Scholar 

  • Bloemberg GV, Lugtenberg BJJ (2001) Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Curr Opin Plant Biol 4:343–350

    Article  CAS  PubMed  Google Scholar 

  • Blom J, Rueckert C, Niu B, Wang Q, Borriss R (2012) The complete genome of Bacillus amyloliquefaciens subsp. plantarum CAU B946 contains a gene cluster for nonribosomal synthesis of iturin A. J Bacteriol 194(7):1845–1846

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boiero L, Perrig D, Masciarelli O, Penna C, Cassan F, Luna V (2007) Phytohormone production by three strains of Bradyrhizobium japonicum and possible physiological and technological implications. Appl Microbiol Biotech 74(4):874–880

    Article  CAS  Google Scholar 

  • Bolan N, Kunhikrishnan A, Thangarajan R, Kumpiene J, Park J, Makino T, Kirkham MB, Scheckel K (2014) Remediation of heavy metal (loid)s contaminated soils—to mobilize or to immobilize. J Hazard Mater 266:141–166

    Article  CAS  PubMed  Google Scholar 

  • Brown SD, Utturkar SM, Klingeman DM, Johnson CM, Martin SL, Land ML, Pelletier DA (2012) Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides. J Bacteriol 194(21):5991–5993

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Browne P, Barret M, Morrissey JP, O’Gara F (2013) Molecular-based strategies to exploit the inorganic phosphate-solubilization ability of Pseudomonas in sustainable agriculture. In: de Bruijn FJ (ed) Molecular microbial ecology of the rhizosphere, vol 2. Wiley, Hoboken, pp 615–628

    Chapter  Google Scholar 

  • Bruto M, Prigent-Combaret C, Muller D, Moënne-Loccoz Y (2014) Analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related Proteobacteria. Sci Rep 4:6261

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Buensanteai N, Athinuwat D, Chatnaparat T, Yuen GY, Prathuangwong S (2008) Extracellular proteome of Bacillus amyloliquefaciens KPS46 and Its effect on enhanced growth promotion and induced resistance against bacterial pustule on soybean plant. Kasetsart J Nat Sci 42:13–26

    Google Scholar 

  • Calderón CE, Ramos C, de Vicente A, Cazorla FM (2015) Comparative genomic analysis of Pseudomonas chlororaphis PCL1606 reveals new insight into antifungal compounds involved in biocontrol. Mol Plant 28(3):249–260

    Google Scholar 

  • Camerini S, Senatore B, Lonardo E, Imperlini E, Bianco C, Moschetti G, Rotino GL, Campion B, Defez R (2008) Introduction of a novel pathway for IAA biosynthesis to rhizobia alters vetch root nodule development. Arch Microbiol 190:67–77

    Article  CAS  PubMed  Google Scholar 

  • Carvalhais LC, Dennis PG, Tyson GW, Schenk PM (2013) Rhizosphere metatranscriptomics: challenges and opportunities. In: de Bruijn FJ (ed) Molecular microbial ecology of the rhizosphere, vol 2. Wiley, Hoboken, pp 1137–1144

    Chapter  Google Scholar 

  • Cattelan AJ, Hartel PG, Fuhrmann JJ (1999) Screening for plant growth—promoting rhizobacteria to promote early soybean growth. Soil Sci Soc Am J 63(6):1670–1680

    Article  CAS  Google Scholar 

  • Chabot R, Beauchamp CJ, Kloepper JW, Antoun H (1998) Effect of phosphorus on root colonization and growth promotion of maize by bioluminescent mutants of phosphate-solubilizing Rhizobium leguminosarum biovar phaseoli. Soil Biol Biochem 30(12):1615–1618

    Article  Google Scholar 

  • Chakraborty S, Salekdeh GH, Yang P, Woo SH, Chin CF, Gehring C, Komatsu S (2015) Proteomics of important food crops in the Asia Oceania Region: current status and future perspectives. J Prot Res 14(7):2723–2744

    Article  CAS  Google Scholar 

  • Chen XH, Koumoutsi A, Scholz R et al (2007) Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotech 25(9):1007–1014

    Article  CAS  Google Scholar 

  • Chen Y, Shen X, Peng H, Hu H, Wang W, Zhang X (2015) Comparative genomic analysis and phenazine production of Pseudomonas chlororaphis, a plant growth-promoting rhizobacterium. Geno Data 4:33–42

    Article  Google Scholar 

  • Chernin L, Chet I (2002) Microbial enzymes in biocontrol of plant pathogens and pests. In: Burns RG, Dick RP (eds) Enzymes in the environment: activity, ecology, and applications. Marcel Dekker, New York, pp 171–225

    Google Scholar 

  • Chin-A-Woeng TF, Bloemberg GV, Van der Bij AJ, Van der Drift KM, Schripsema J, Kroon B, de Bruijn FJ (1998) Biocontrol by phenazine-1-carboxamide-producing Pseudomonas chlororaphis PCL1391 of tomato root rot caused by Fusarium oxysporum f. sp. radicis-lycopersici. Mol Plant 11(11):1069–1077

    CAS  Google Scholar 

  • Cohen AC, Bottini R, Pontin M, Berli FJ, Moreno D, Boccanlandro H, Piccoli PN (2015) Azospirillum brasilense ameliorates the response of Arabidopsis thaliana to drought mainly via enhancement of ABA levels. Physiol Plant 153(1):79–90

    Article  CAS  PubMed  Google Scholar 

  • Compant S, Duffy B, Nowak J, Clément C, Barka EA (2005) Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl Environ Microbiol 71(9):4951–4959

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Crowley DE, Kraemer SM (2007) Function of siderophores in the plant rhizosphere. In: Pinton R, Varanini Z, Nannipieri P (eds) The rhizosphere, biochemistry and organic substances at the soil-plant interface. CRC Press, Boca Raton, pp 73–109

    Google Scholar 

  • Daniels R, Vanderleyden J, Michiels J (2004) Quorum sensing and swarming migration in 448 bacteria. FEMS Microbiol Rev 28:261–289

    Article  CAS  PubMed  Google Scholar 

  • Daval S, Lebreton L, Gazengel K, Boutin M, Guillerm-Erckelboudt AY, Sarniguet A (2011) The biocontrol bacterium Pseudomonas fluorescens Pf29Arp strain affects the pathogenesis-related gene expression of the take-all fungus Gaeumannomyces graminis var. tritici on wheat roots. Mol Plant Path 12(9):839–854

    Article  CAS  Google Scholar 

  • De Maayer P, Chan WY, Rubagotti E, Venter SN, Toth IK, Birch PR, Coutinho TA (2014) Analysis of the Pantoea ananatis pan-genome reveals factors underlying its ability to colonize and interact with plant, insect and vertebrate hosts. BMC Genom 15(1):404

    Article  CAS  Google Scholar 

  • de Souza JT, Raaijmakers JM (2003) Polymorphisms within the PrnD and PltC genes from pyrrolnitrin and pyoluteorin-producing Pseudomonas and Burkholderia spp. FEMS Microbiol Ecol 43:21–34

    Article  PubMed  Google Scholar 

  • Decoin V, Barbey C, Bergeau D, Latour X, Feuilloley MG, Orange N, Merieau A (2014) A type VI secretion system is involved in Pseudomonas fluorescens bacterial competition. PLoS One 9(2):89411

    Article  CAS  Google Scholar 

  • Deslandes L, Rivas S (2012) Catch me if you can: bacterial effectors and plant targets. Trend Plant Sci 17:644–655

    Article  CAS  Google Scholar 

  • Donaldson JR, Shields-Menard S, Barnard JM, Revellame E, Hall JI, Lawrence A, French WT (2014) Characterization of the novel Enterobacter cloacae strain JD6301 and a genetically modified variant capable of producing extracellular lipids. Agricul Food Analyt Bacteriol 4:212–223

    Google Scholar 

  • Dosselaere F, Vanderleyden J (2001) A metabolic node in action: chorismate-utilizing enzymes in microorganisms. Crit Rev Microbiol 27:75–131

    Article  CAS  PubMed  Google Scholar 

  • Duffy BK, Défago G (1997) Zinc improves biocontrol of Fusarium crown and root rot of tomato by Pseudomonas fluorescens and represses the production of pathogen metabolites inhibitory to bacterial antibiotic biosynthesis. Phytopath 87(12):1250–1257

    Article  CAS  Google Scholar 

  • Duffy BK, Défago G (1999) Environmental factors modulating antibiotic and siderophore biosynthesis by Pseudomonas fluorescens biocontrol strains. Appl Environ Microbio 65(6):2429–2438

    CAS  Google Scholar 

  • Duffy BK, Défago G (2000) Controlling instability in gacS-gacA regulatory genes during inoculant production of Pseudomonas fluorescens biocontrol strains. Appl Environ Microbiol 66(8):3142–3150

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duffy BK, Défago G (2004) Potential role of pathogen signaling in multitrophic plant-microbe interactions involved in disease protection. Appl Environ Microbiol 70(3):1836–1842

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eastman AW, Weselowski B, Nathoo N, Yuan ZC (2014) Complete genome sequence of Paenibacillus polymyxa CR1, a plant growth-promoting bacterium isolated from the corn rhizosphere exhibiting potential for biocontrol, biomass degradation, and biofuel production. Genome Announc 2(1):e01218-13

    Article  PubMed  PubMed Central  Google Scholar 

  • Egamberdiyeva D (2007) The effect of plant growth promoting bacteria on growth and nutrient uptake of maize in two different soils. Appl Soil Ecol 36:184–189

    Article  Google Scholar 

  • Eid J, Fehr A, Gray J et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138

    Article  CAS  PubMed  Google Scholar 

  • Farag MA, Zhang H, Ryu CM (2013) Dynamic chemical communication between plants and bacteria through airborne signals: induced resistance by bacterial volatiles. J Chem Ecol 39(7):1007–1018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Figueiredo MVB, Burity HA, Martinez CR, Chanway CP (2008) Alleviation of water stress effects in common bean (Phaseolus vulgaris L.) by co-inoculation Paenibacillus x Rhizobium tropici. Applied Soil Ecol 40:182–188

    Article  Google Scholar 

  • Figueiredo MDVB, Seldin L, de Araujo FF, Mariano RDLR (2011) Plant growth promoting rhizobacteria: fundamentals and applications. In: Maheshwari DK (ed) Plant growth and health promoting bacteria. Springer, Berlin, pp 21–43

    Google Scholar 

  • Frankowski J, Lorito M, Scala F, Schmidt R, Berg G, Bahl H (2001) Purification and properties of two chitinolytic enzymes of Serratia plymuthica HRO-C48. Arch Microbiol 176:421–426

    Article  CAS  PubMed  Google Scholar 

  • Fu Q, Liu C, Ding N, Lin Y, Guo B (2010) Ameliorative effects of inoculation with the plant growth-promoting rhizobacterium Pseudomonas sp. DW1 on growth of eggplant (Solanum melongena L.) seedlings under salt stress. Agric Water Manag 97(12):1994–2000

    Article  Google Scholar 

  • Gadd GM (2010) Metals, minerals and microbes: geomicrobiology and 473 bioremediation. Microbiology 156:609–643

    Article  CAS  PubMed  Google Scholar 

  • Garcion C, Lamotte O, Métraux JP (2007) Mechanisms of defense to pathogens: biochemistry and physiology. In: Walters DR, Newton AC, Lyon GD (eds) Induced resistance for plant defence. Blackwell Publishing, Oxford, pp 109–132

    Chapter  Google Scholar 

  • Ghignone S, Salvioli A, Anca I, Lumini E, Ortu G, Petiti L, Bonfante P (2012) The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions. ISME J 6(1):136–145

    Article  CAS  PubMed  Google Scholar 

  • Ghosh UD, Saha C, Maiti M, Lahiri S, Ghosh S, Seal A, Mitra Ghosh M (2014) Root associated iron oxidizing bacteria increase phosphate nutrition and influence root to shoot partitioning of iron in tolerant plant Typha angustifolia. Plant Soil 381(1–2):279–295

    Article  CAS  Google Scholar 

  • Glaeser SP, Imani J, Alabid I, Guo H, Kumar N, Kämpfer P, Hartmann A (2015) Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica. ISME J. doi:10.1038/ismej.2015.163

    PubMed  Google Scholar 

  • Glick BR (2010) Using soil bacteria to facilitate phytoremediation. Biotechnol Adv 28:367–374

    Article  CAS  PubMed  Google Scholar 

  • Glick BR (2012) Plant growth-promoting bacteria: Mechanisms and applications. Scientifica (Cairo) 1–15

  • Glick BR (2015) Biocontrol mechanisms. In: Glick BR (ed) Beneficial plant-bacterial interactions. Springer, Heidelberg, pp 123–157

    Google Scholar 

  • Glick BR, Patten CL, Holguin G, Penrose GM (1999) Biochemical and genetic mechanisms used by plant growth promoting bacteria. Imperial College Press, London

    Book  Google Scholar 

  • Glick BR, Cheng Z, Czarny J, Duan J (2007) Promotion of plant growth by ACC deaminase-producing soil bacteria. Eur J Plant Pathol 119:329–339

    Article  CAS  Google Scholar 

  • Guo JK, Ding YZ, Feng RW, Wang RG et al (2015) Burkholderia metalliresistens sp. nov., a multiple metal-resistant and phosphate-solubilising species isolated from heavy metal-polluted soil in Southeast China. Antonie van Leeuwenhoek 107(6):1591–1598

    Article  CAS  PubMed  Google Scholar 

  • Haas D, Keel C (2003) Regulation of antibiotic production in root-colonizing Pseudomonas spp. and relevance for biological control of plant disease. Annu Rev Phytopathol 41:117–153

    Article  CAS  PubMed  Google Scholar 

  • Han J, Sun L, Dong X, Cai Z, Sun X, Yang H, Song W (2005) Characterization of a novel plant growth-promoting bacteria strain Delftia tsuruhatensis HR4 both as a diazotroph and a potential biocontrol agent against various plant pathogens. Syst Appl MicrobioL 28(1):66–76

    Article  CAS  PubMed  Google Scholar 

  • Hao K, He P, Blom J, Rueckert C, Mao Z, Wu Y, Borriss R (2012a) The genome of plant growth-promoting Bacillus amyloliquefaciens subsp. plantarum strain YAU B9601-Y2 contains a gene cluster for mersacidin synthesis. J Bacteriol 194(12):3264–3265

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hao X, Xie P, Johnstone L, Miller SJ, Rensing C, Wei G (2012b) Genome sequence and mutational analysis of plant-growth-promoting bacterium Agrobacterium tumefaciens CCNWGS0286 isolated from a zinc-lead mine tailing. Appl Environ Microbiol 78:5384–5394

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Heidari M, Golpayegani A (2012) Effects of water stress and inoculation with plant growth promoting rhizobacteria (PGPR) on antioxidant status and photosynthetic pigments in basil (Ocimum basilicum L.). J Sau Soc of Agric Sci 11(1):57–61

    Google Scholar 

  • Henry G, Thonart P, Ongena M (2012) PAMPs, MAMPs, DAMPs and others: an update on the diversity of plant immunity elicitors. Biotechnol Agron Soc Environ 16:257–268

    Google Scholar 

  • Hiltner L (1904) Über neue Erfahrung und Problems auf dem Gebiet der Bodenbakteriologie und unter besonderer Berücksichtigung der Gründüngung und Brache. Ara Dtsch Landwirt Gellschaft 98:59–78

    Google Scholar 

  • Hossain MJ, Ran C, Liu K, Ryu CM, Rasmussen-Ivey CR, Williams MA, Liles MR (2015) Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum. Front Plant Sci 6:631

    PubMed  PubMed Central  Google Scholar 

  • Hou Q, Wang C, Guo H, Xia Z, Ye J, Liu K, Ding Y (2015) Draft genome sequence of Delftia tsuruhatensis MTQ3, a strain of plant growth-promoting rhizobacterium with antimicrobial activity. Genome Announc 3(4):e00822-15

    Article  PubMed  PubMed Central  Google Scholar 

  • Hu D, Li X, Chang Y, He H, Zhang C, Jia N, Wang Z (2012) Genome sequence of Streptomyces sp. strain TOR3209, a rhizosphere microecology regulator isolated from tomato rhizosphere. J Bacteriol 194(6):1627

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang E, Yousef AE (2012) Draft genome sequence of Paenibacillus polymyxa OSY-DF, which coproduces a lantibiotic, paenibacillin, and polymyxin E1. J Bacteriol 194(17):4739–4740

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Indiragandhi P, Anandham R, Madhaiyan M, Sa TM (2008) Characterization of plant growth-promoting traits of bacteria isolated from larval guts of diamondback moth Plutella xylostella (Lepidoptera: Plutellidae). Curr Microbiol 56:327–333

    Article  CAS  PubMed  Google Scholar 

  • Jacobs JM, Babujee L, Meng F, Milling A, Allen C (2012) The in planta transcriptome of Ralstonia solanacearum: conserved physiological and virulence strategies during bacterial wilt of tomato. MBio 3:e00114-12

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • James P (1997) Protein identification in the post-genome era: the rapid rise of proteomics. Qua Rev Biophysic 30(4):279–331

    Article  CAS  Google Scholar 

  • Jeong H, Park SY, Chung WH, Kim SH, Kim N, Park SH, Kim JF (2011) Draft genome sequence of the Paenibacillus polymyxa type strain (ATCC 842T), a plant growth-promoting bacterium. J Bacteriol 193(18):5026–5027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jha Y, Subramanian RB (2014) PGPR regulate caspase-like activity, programmed cell death, and antioxidant enzyme activity in paddy under salinity. Physiol Mol Biol Plant 20(2):201–207

    Article  CAS  Google Scholar 

  • Jing YX, Yan JL, He HD, Yang DJ, Xiao L, Zhong T, Yuan M, Cai XD, Li SB (2014) Characterization of bacteria in the rhizosphere soils of polygonum pubescens and their potential in promoting growth and Cd, Pb, Zn uptake by Brassica napus. Int J Phytoremed 16:321–333

    Article  CAS  Google Scholar 

  • Jones JD, Dang JL (2006) The plant immune system. Nature 444:323–329

    Article  CAS  PubMed  Google Scholar 

  • Kamilova F, Validov S, Azarova T, Mulders I, Lugtenberg B (2005) Enrichment for enhanced competitive plant root tip colonizers selects for a new class of biocontrol bacteria. Environ Microbiol 7(11):1809–1817

    Article  CAS  PubMed  Google Scholar 

  • Kandasamy S, Loganathan K, Muthuraj R, Duraisamy S, Seetharaman S, Thiruvengadam R, Ramasamy S (2009) Understanding the molecular basis of plant growth promotional effect of Pseudomonas fluorescens on rice through protein profiling. Prot Sci 7(1):47

    Article  CAS  Google Scholar 

  • Kang BG, Kim WT, Yun HS, Chang SC (2010) Use of plant growth-promoting rhizobacteria to control stress responses of plant roots. Plant Biotechnol Rep 4(3):179–183

    Article  Google Scholar 

  • Kang Y, Shen M, Wang H, Zhao Q (2015) Complete genome sequence of Bacillus pumilus strain WP8, an efficient plant growth-promoting rhizobacterium. Genome Announc 3(1):e01452-14

    Article  PubMed Central  PubMed  Google Scholar 

  • Kaur G, Reddy MS (2014) Influence of P-solubilizing bacteria on crop yield and soil fertility at multilocational sites. Eur J Soil Biol 61:35–40

    Article  CAS  Google Scholar 

  • Khalid A, Akhtar MJ, Mahmood MH, Arshad M (2006) Effect of substrate-dependent microbial ethylene production on plant growth. Microbiology 75:231–236

    Article  CAS  Google Scholar 

  • Khan MS, Zaidi A, Wani PA (2006) Role of phosphate-solubilizing microorganisms in sustainable agriculture—a review. Agron Sustain Dev 27:29–43

    Article  Google Scholar 

  • Khan MS, Zaidi A, Wani PA, Oves M (2009) Role of plant growth promoting rhizobacteria in the remediation of metal contaminated soils. Environ Chem Lett 7:1–19

    Article  CAS  Google Scholar 

  • Khodair TA, Galal GF, El-Tayeb TS (2008) Effect of inoculating wheat seedlings with exopolysaccharide-producing bacteria in saline soil. J Appl Sci Res 4:2065–2070

    Google Scholar 

  • Kim J, Rees D (1994) Nitrogenase and biological nitrogen fixation. Biochemistry 33:389–397

    Article  CAS  PubMed  Google Scholar 

  • Kim KY, Jordan D, McDonald GA (1998) Enterobacter agglomerans, phosphate solubilizing bacteria, and microbial activity in soil: effect of carbon sources. Soil Biol Biochem 30(8):995–1003

    Article  CAS  Google Scholar 

  • Kim BS, Moon SS, Hwang BK (1999) Isolation, identification and antifungal activity of a macrolide antibiotic, oligomycin A, produced by Streptomyces libani. Can J Bot 77:850–858

    CAS  Google Scholar 

  • Kim JF, Jeong H, Park SY, Kim SB, Park YK, Choi SK, Park SH (2010) Genome sequence of the polymyxin-producing plant-probiotic rhizobacterium Paenibacillus polymyxa E681. J Bacteriol 192(22):6103–6104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim HJ, Park JY, Han SH, Lee JH, Rong X, Gardener BBM, Kim YC (2011) Draft genome sequence of the biocontrol bacterium Chromobacterium sp. strain C-61. J Bacteriol 193(23):6803–6804

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim BK, Chung JH, Kim SY, Jeong H, Kang SG, Kwon SK, Kim JF (2012) Genome sequence of the leaf-colonizing bacterium Bacillus sp. strain 5B6, isolated from a cherry tree. J Bacteriol 194(14):3758–3759

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kimura N, Yamazoe A, Hosoyama A, Hirose J, Watanabe T, Suenaga H, Fujihara H, Futagami T, Goto M, Furukawa K (2015) Draft genome sequence of Pseudomonas abietaniphila KF717 (NBRC 110669), isolated from biphenyl-contaminated soil in Japan. Genome Announc 3(2):e00059-15

    Article  PubMed  PubMed Central  Google Scholar 

  • Kloepper JW, Beauchamp CJ (1992) A review of issues related to measuring colonization of plant roots by bacteria. Can J Microbiol 38(12):1219–1232

    Article  Google Scholar 

  • Kloepper JW, Schroth MN (1981) Plant growth-promoting rhizobacteria and plant growth under gnotobiotic conditions. Phytopathol 71:642–644

    Article  Google Scholar 

  • Kloepper JW, Ryu CM, Zhang S (2004) Induced systemic resistance and promotion of plant growth by Bacillus spp. Phytopathol 94:1259–1266

    Article  CAS  Google Scholar 

  • Kloepper JW, Gutierrez-Estrada A, McInroy JA (2007) Photoperiod regulates elicitation of growth promotion but not induced resistance by plant growth-promoting rhizobacteria. Can J Microbio 53(2):159–167

    Article  CAS  Google Scholar 

  • Koberl M, White RA, Erschen S, El-Arabi TF, Jansson JK, Berg G (2015) Draft genome sequence of Paenibacillus polymyxa strain Mc5Re-14, an antagonistic root endophyte of Matricaria chamomilla. Genome Announc 3(4):e00861-15

    Article  PubMed  PubMed Central  Google Scholar 

  • Kohler J, Hernández JA, Caravaca F, Roldán A (2009) Induction of antioxidant enzymes is involved in the greater effectiveness of a PGPR versus AM fungi with respect to increasing the tolerance of lettuce to severe salt stress. Environ Exp Bot 65(2):245–252

    Article  CAS  Google Scholar 

  • Kohler C, Lourenço RF, Bernhardt J, Albrecht D, Schüler J, Hecker M, Gomes SL (2015) A comprehensive genomic, transcriptomic and proteomic analysis of a hyperosmotic stress sensitive α-proteobacterium. BMC Microbiol 15(1):71

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kojic M, Degrassi G, Venturi V (1999) Cloning and characterization of the rpoS gene from the plant growth-promoting Pseudomonas putida WCS358: RpoS is not involved in siderophore and homoserine lactone production. Biochem Biophys Acta 1489:413–420

    CAS  PubMed  Google Scholar 

  • Kumar V, Behl RK, Narula N (2001) Establishment of phosphate solubilizing strains of Azotobacter chroococcum in the rhizosphere and their effect on wheat cultivars under greenhouse conditions. Microbiol Res 156:87–93

    Article  CAS  PubMed  Google Scholar 

  • Lee SY, Kim BY, Ahn JH, Song J, Seol YJ, Kim WG, Weon HY (2012) Draft genome sequence of the biocontrol bacterium Bacillus amyloliquefaciens strain M27. J Bacteriol 194(24):6934–6935

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lefort F, Calmin G, Pelleteret P, Farinelli L, Osteras M, Crovadore J (2014) Whole-genome shotgun sequence of Bacillus amyloliquefaciens strain UASWS BA1, a bacterium antagonistic to plant pathogenic fungi. Genome Announc 2(1):e00016-14

    Article  PubMed  PubMed Central  Google Scholar 

  • Lekberg Y, Koide RT (2014) Integrating physiological, community, and evolutionary perspectives on the arbuscular mycorrhizal symbiosis. Botanty 92:241–251

    Article  CAS  Google Scholar 

  • Li S, Yang D, Qiu M, Shao J, Guo R, Shen B, Shen Q (2014) Complete genome sequence of Paenibacillus polymyxa SQR-21, a plant growth-promoting rhizobacterium with antifungal activity and rhizosphere colonization ability. Genome Announc 2(2):e00281-14

    Article  PubMed  PubMed Central  Google Scholar 

  • Liang S, Jin D, Wang X, Fan H, Bai Z (2015) Draft genome sequence of Paenibacillus polymyxa EBL06, a plant growth-promoting bacterium isolated from wheat phyllosphere. Genome Announc 3(3):00414–00415

    Article  Google Scholar 

  • Lim JH, Kim SD (2013) Induction of drought stress resistance by multi-functional PGPR Bacillus licheniformis K11 in Pepper. Plant Pathol J 29(2):201

    Article  PubMed  PubMed Central  Google Scholar 

  • Lim HS, Kim YS, Kim SD (1991) Pseudomonas stutzeri YPL-1 genetic transformation and antifungal mechanism against Fusarium solani, an agent of plant root rot. Appl Environ Microbiol 57:510–516

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu WY, Wong CF, Chung KMK, Jiang JW, Leung FCC (2013) Comparative genome analysis of Enterobacter cloacae. PLoS One 8:1–15

    Google Scholar 

  • Loper JE, Henkels MD (1999) Utilization of Heterologous siderophores enhances levels of iron available to Pseudomonas putida in the rhizosphere. Appl Environ Microbiol 65(12):5357–5363

    CAS  PubMed Central  PubMed  Google Scholar 

  • Loper JE, Kobayashi DY, Paulsen IT (2007) The genomic sequence of Pseudomonas fluorescens Pf-5: insights into biological control. Phytopathology 97(2):233–238

    Article  CAS  PubMed  Google Scholar 

  • Loper JE, Hassan KA, Mavrodi DV, Davis EW et al (2012) Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Gen 8:1002784

    Article  CAS  Google Scholar 

  • Lubeck PS, Hansen M, Sorensen J (2000) Simultaneous detection of the establishment of seed-inoculated Pseudomonas fluorescens strain Dr54 and native soil bacteria on sugar beet root surfaces using fluorescence antibody and in situ hybridization techniques. FEMS Microbiol Ecol 33:11–19

    Article  CAS  PubMed  Google Scholar 

  • Lugtenberg B (2015) Life of microbes in the rhizosphere. In: Lugtenberg B (ed) Principles of plant-microbe interactions. Springer, Heidelberg, pp 7–15

    Google Scholar 

  • Lugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63:541–556

    Article  CAS  PubMed  Google Scholar 

  • Lugtenberg BJJ, Dekkers L, Bloemberg GV (2001) Molecular determinants of rhizosphere colonization by Pseudomonas. Annu Rev Phytopathol 39:461–490

    Article  CAS  PubMed  Google Scholar 

  • Ma M, Wang C, Ding Y, Li L, Shen D, Jiang X et al (2011) Complete genome sequence of Paenibacillus polymyxa SC2, a strain of plant growth-promoting rhizobacterium with broad-spectrum antimicrobial activity. J Bacteriol 193(1):311–312

    Article  CAS  PubMed  Google Scholar 

  • Maffei ME, Arimura GI, Mithofer A (2012) Natural elicitors, effectors and modulators of plant responses. Nat Prod Rep 29(11):1288–1303

    Article  CAS  PubMed  Google Scholar 

  • Magno-Perez C, Martinez-Garcia PM, Hierrezuelo J, Rodriquez-Palenzuela P, Arrebola E, Ramos C, Romero DF (2015) Comparative genomics within the Bacillus genus reveal the singularities of two robust Bacillus amyloliquefaciens biocontrol strains. Mol Plant 28(10):1102–1116

    Google Scholar 

  • Manzoor S, Niazi A, Bejai S, Meijer J, Bongcam-Rudloff E (2013) Genome sequence of a plant-associated bacterium, Bacillus amyloliquefaciens strain UCMB5036. Gen Announc 1(2):e00111–e00113

    Google Scholar 

  • Marchi M, Boutin M, Gazengel K, Rispe C, Gauthier JP, Guillerm-Erckelboudt AY, Lebreton L, Barret M, Daval S, Sarniguet A (2013) Genomic analysis of the biocontrol strain Pseudomonas fluorescens Pf29Arp with evidence of T3SS and T6SS gene expression on plant roots. Environ Microbiol Rep 5:393–403

    Article  CAS  PubMed  Google Scholar 

  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Volkmer GA (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057):376–380

    CAS  PubMed Central  PubMed  Google Scholar 

  • Mathimaran N, Srivastava R, Wiemken A, Sharma AK, Boller T (2012) Genome sequences of two plant growth-promoting fluorescent Pseudomonas strains, R62 and R81. J Bacteriol 194(12):3272–3273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matilla MA, Pizarro-Tobias P, Roca A, Fernández M, Duque E, Molina L, Ramos JL (2011) Complete genome of the plant growth-promoting rhizobacterium Pseudomonas putida BIRD-1. J Bacteriol 193(5):1290

    Article  CAS  PubMed  Google Scholar 

  • Mayak S, Tirosh T, Glick BR (2004) Plant growth-promoting bacteria that confer resistance to water stress in tomatoes and peppers. Plant Sci 166:525

    Article  CAS  Google Scholar 

  • McKenzie RH, Roberts TL (1990) Soil and fertilizers phosphorus update. In: Proceedings of Alberta soil science workshop proceedings, Edmonton, Alberta. p 84–104 Feb 20–22

  • Merino E, Jensen RA, Yanofsky C (2008) Evolution of bacterial trp operons and their regulation. Curr Opin Microbiol 11:78–86

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Molina L, Constantinescu F, Reimmann C, Duffy C, Defago G (2003) Degradation of pathogen quorum-sensing molecules by soil bacteria: a preventive and curative biological control mechanism. FEMS Microbiol Ecol 45:71–81

    Article  CAS  PubMed  Google Scholar 

  • Montor-Antonio JJ, Sachman-Ruiz B, Lozano L, Del Moral S (2015) Draft genome sequence of Bacillus amyloliquefaciens JJC33M, isolated from sugarcane soils in the Papaloapan region, Mexico. Genome Announce 3(1):e01519-14

    Article  Google Scholar 

  • Nadeem SM, Zahir ZA, Naveed M, Arshad M (2007) Preliminary investigations on inducing salt tolerance in maize through inoculation with rhizobacteria containing ACC deaminase activity. Can J Microbiol 53:1141–1149

    Article  CAS  PubMed  Google Scholar 

  • Nadeem SM, Zahir ZA, Naveed M, Arshad M (2009) Rhizobacteria containing ACC-deaminase confer salt tolerance in maize grown on salt-affected fields. Can J Microbiol 55:1302–1309

    Article  CAS  PubMed  Google Scholar 

  • Neilands JB (1995) Siderophores: structure and function of microbial iron transport compounds. J Biol Chem 270:26723–26726

    Article  CAS  PubMed  Google Scholar 

  • Neubauer U, Nowack B, Furrer G, Schulin R (2000) Heavy metal sorption on clay minerals affected by the siderophore desferrioxamine B. Environ Sci Technol 34(13):2749–2755

    Article  CAS  Google Scholar 

  • Newman MA, Sundelin T, Nielsen JT, Erbs G (2013) MAMP (microbe associated molecular pattern) triggered immunity in plants. Front Plant Sci 4:139

    Article  PubMed  PubMed Central  Google Scholar 

  • Newton JA, Fray RG (2004) Integration of environmental and host-derived signals with quorum sensing during plant–microbe interactions. Cell Microbiol 6(3):213–224

    Article  CAS  PubMed  Google Scholar 

  • Nia SH, Zarea MJ, Rejali F, Varma A (2012) Yield and yield components of wheat as affected by salinity and inoculation with Azospirillum strains from saline or non-saline soil. J Saudi Soc Agric Sci 11:113–121

    Google Scholar 

  • Niazi A (2014) Genome-wide analyses of Bacillus amyloliquefaciens strains provide insights into their beneficial role on plants. Thesis submitted to Swedish University of Agricultural Sciences, Uppsala

  • Niazi A, Manzoor S, Asari S, Bejai S, Meijer J, Bongcam-Rudloff E (2014) Genome analysis of Bacillus amyloliquefaciens subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management. PLoS One 9(8):e104651

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nielsen TH, Sorensen J (2003) Production of cyclic lipopeptides by Pseudomonas fluorescens strains in bulk soil and in the sugar beet rhizosphere. Appl Environ Microbiol 69:861–868

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Niu B, Rueckert C, Blom J, Wang Q, Borriss R (2011) The genome of the plant growth-promoting rhizobacterium Paenibacillus polymyxa M-1 contains nine sites dedicated to nonribosoml synthesis of lipopeptides and polyketides. J Bacteriol 193(20):5862–5863

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Olivares J, Bedmar EJ, Sanjuan J (2013) Biological nitrogen fiation in the context of global change. Mol Plant 26:486–494

    CAS  Google Scholar 

  • Ovadis M, Liu X, Gavriel S, Ismailov Z, Chet I, Chernin L (2004) The global regulator genes from biocontrol strain Serratia plymuthica IC1270: cloning, sequencing, and functional studies. J Bacteriol 186:4986–4993

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pan HQ, Hu JC (2015) Draft genome sequence of the novel strain Pseudomonas sp. 10B238 with potential ability to produce antibiotics from deep-sea sediment. Marine Genom 23:55–57

    Article  Google Scholar 

  • Park JY, Han SH, Lee JH, Han YS, Lee YS, Rong X, Kim YC (2011) Draft genome sequence of the biocontrol bacterium Pseudomonas putida B001, an oligotrophic bacterium that induces systemic resistance to plant diseases. J Bacteriol 193(23):6795–6796

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parray JA, Kamili AN, Reshi ZA, Hamid R, Qadri RA (2013) Screening of beneficial properties of rhizobacteria isolated from Saffron (Crocus sativus L.) rhizosphere. Afr J Microbiol Res 7(23):2905–2910

    CAS  Google Scholar 

  • Parray JA, Kamili AN, Reshi ZA, Qadri RA, Jan S (2015) Interaction of rhizobacterial strains for growth improvement of Crocus sativus L. under tissue culture conditions. Plant Cell Tiss Organ Cul 121(2):325–334

    Article  CAS  Google Scholar 

  • Patten CL, Glick BR (1996) Bacterial biosynthesis of indole-3- acetic acid. Can J Microbiol 42:207–220

    Article  CAS  PubMed  Google Scholar 

  • Paul D, Nair S (2008) Stress adaptations in a plant growth promoting rhizobacterium (PGPR) with increasing salinity in the coastal agricultural soils. J Basic Microbiol 48(5):378

    Article  CAS  PubMed  Google Scholar 

  • Paul D, Dineshkumar N, Nair S (2006) Proteomics of a plant growth-promoting rhizobacterium, Pseudomonas fluorescens MSP-393, subjected to salt shock. World J Microbiol Biotechnol 22(Suppl 4):369–374

    Article  CAS  Google Scholar 

  • Pavel VL, Sobariu DL, Fertu IDT, Statescu F, Gavrilescu M (2013) Symbiosis in the environment biomanagement of soils contaminated with heavy metals. Europ J Sci Theol 9:211–224

    Google Scholar 

  • Picard C, Di Cello F, Ventura M, Fani R, Guckert A (2000) Frequency and biodiversity of 2,4-diacetylphloroglucinol-producing bacteria isolated from the maize rhizosphere at different stages of plant growth. Appl Environ Microbiol 66:948–955

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pii Y, Mimmo T, Tomasi N, Terzano R, Cesco S, Crecchio C (2015) Microbial interactions in the rhizosphere: beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process- a review. Biol Fertil Soil 51:403–415

    Article  CAS  Google Scholar 

  • Qurashi AW, Sabri AN (2012) Bacterial exopolysaccharide and biofilm formation stimulate chickpea growth and soil aggregation under salt stress. Braz J Microbiol 11:83–91

    Google Scholar 

  • Raaijmakers JM, Vlami M, de Souza JT (2002) Antibiotic production by bacterial biocontrol agents. Antonie Leeuwenhoek 81:537–547

    Article  CAS  PubMed  Google Scholar 

  • Rajkumar M, Ae N, Prasad MNV, Freitas H (2010) Potential of siderophore-producing bacteria for improving heavy metal phytoextraction. Trends Biotechnol 28:142–149

    Article  CAS  PubMed  Google Scholar 

  • Rajkumar M, Sandhya S, Prasad MNV, Freitas H (2012) Perspectives of plant-associated microbes in heavy metal phytoremediation. Biotechnol Adv 30:1562–1574

    Article  CAS  PubMed  Google Scholar 

  • Ramadoss D, Lakkineni VK, Bose P, Ali S, Annapurna K (2013) Mitigation of salt stress in wheat seedlings by halotolerant bacteria isolated from saline habitats. Springer Plus 2(6):1–7

    Google Scholar 

  • Ravel J, Cornelis P (2003) Genomics of pyoverdine-mediated iron uptake in pseudomonads. Trends Microbiol 11:195–200

    Article  CAS  PubMed  Google Scholar 

  • Redondo-Nieto M, Barret M, Morrisey JP, Germaine K, Martínez-Granero F, Barahona E, Rivilla R (2012) Genome sequence of the biocontrol strain Pseudomonas fluorescens F113. J Bacteriol 194(5):1273–1274

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rojas A, Holguin G, Glick BR, Bashan Y (2001) Synergism between Phyllobacterium sp. (N2-fixer) and Bacillus licheniformis (P-solubilizer), both from a semiarid mangrove rhizosphere. FEMS Microbiol Ecol 35(2):181–187

    Article  CAS  PubMed  Google Scholar 

  • Rong X, Gurel FB, Meulia T, Gardener BBM (2012) Draft genome sequences of the Pseudomonas fluorescens biocontrol strains Wayne1R and Wood1R. J Bacteriol 194(3):724–725

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roquigny R, Arseneault T, Gadkar VJ, Novinscak A, Joly DL, Filion M (2015) Complete genome sequence of biocontrol strain Pseudomonas fluorescens LBUM223. Genom Announc 3(3):e00443-15

    Article  Google Scholar 

  • Rusk N (2011) Torrents of sequence. Nat Meth 8:44

    Google Scholar 

  • Saleem M, Arshad M, Hussain S, Bhatti AS (2007) Perspective of plant growth promoting rhizobacteria (PGPR) containing ACC deaminase in stress agriculture. J Indian Microbiol Biotechnol 34:635–648

    Article  CAS  Google Scholar 

  • Saleh SS, Glick BR (2001) Involvement of gacS and rpoS in enhancement of the plant growth-promoting capabilities of Enterobacter cloacae CAL2 and Pseudomonas putida UW4. Can J Microbiol 47:698–705

    Article  CAS  PubMed  Google Scholar 

  • Salvioli A, Ghignone S, Novero M, Navazio L, Bagnaresi P, Bonfante P (2015) Symbiosis with an endobacterium increases the fitness of a mycorrhizal fungus, raising its bioenergetic potential. ISME J 10(1):130–144

    Article  PubMed  CAS  Google Scholar 

  • Sandhya V, Grover M, Reddy G, Venkateswarlu B (2009) Alleviation of drought stress effects in sunflower seedlings by the exopolysaccharides producing Pseudomonas putida strain GAP-P45. Biol Fertil Soil 46(1):17–26

    Article  CAS  Google Scholar 

  • Santner A, Calderon-Villalobos LIA, Estelle M (2009) Plant hormones are versatile chemical regulators of plant growth. Nat Chem Biol 5:301–307

    Article  CAS  PubMed  Google Scholar 

  • Schenk PM, Carvalhais LC, Kazan K (2012) Unraveling plant-microbe interactions: can multi-species transcriptomics help? Trend Biotechnol 30(3):177–184

    Article  CAS  Google Scholar 

  • Schmidt W (1999) Mechanisms and regulation of reduction-based iron uptake in plants. New Phytol 141:1–26

    Article  CAS  Google Scholar 

  • Sessitsch A, Coenye T, Sturz AV, Vandamme P, Ait Barka E, Salles JF, van Elsas JF, Faure D, Reiter B, Glick BR, Wang-Pruski G, Nowak J (2005) Burkholderia phytofirmans sp. nov., a novel plantassociated bacterium with plant beneficial properties. Int J Syst Evol Microbiol 55:1187–1192

    Article  CAS  PubMed  Google Scholar 

  • Seul K, Park S, Ryu C, Lee Y, Ghim S (2007) Proteome analysis of Paenibacillus polymyxa E681 affected by barley. J Microbiol Biotechnol 17(6):934

    CAS  PubMed  Google Scholar 

  • Shaharoona B, Arshad M, Khalid A (2007a) Differential response of etiolated pea seedlings to inoculation with rhizobacteria capable of utilizing 1-aminocyclopropane-1-carboxylate or L-methionine. J Microbiol 45:15–20

    CAS  PubMed  Google Scholar 

  • Shaharoona B, Jamro GM, Zahir ZA, Arshad M, Memon KS (2007b) Effectiveness of various Pseudomonas spp. and Burkholderia caryophylli containing ACC-deaminase for improving growth and yield of wheat (Triticum aestivum L.). J Microbiol Biotechnol 17:1300–1307

    CAS  PubMed  Google Scholar 

  • Shaharoona B, Naveed M, Arshad M, Zahir ZA (2008) Fertilizer-dependent efficiency of Pseudomonads for improving growth, yield, and nutrient use efficiency of wheat (Triticum aestivum L.). Appl Microbiol Biotechnol 79:147–155

    Article  CAS  PubMed  Google Scholar 

  • Shanker AK, Maheswari M, Yadav SK, Desai S, Bhanu D, Attal NB, Venkateswarlu B (2014) Drought stress responses in crops. Funct Integ Genom 14(1):11–22

    Article  CAS  Google Scholar 

  • Shao J, Li S, Zhang N, Cui X, Zhou X, Zhang G, Zhang R (2015) Analysis and cloning of the synthetic pathway of the phytohormone indole-3-acetic acid in the plant-beneficial Bacillus amyloliquefaciens SQR9. Microb Cell factor 14(1):130

    Article  CAS  Google Scholar 

  • Sharma A, Johri BN, Sharma AK, Glick BR (2003) Plant growth-promoting bacterium Pseudomonas sp. strain GRP3 influences iron acquisition in mung bean (Vigna radiata L. Wilzeck). Soil Biol Biochem 35:887–894

    Article  CAS  Google Scholar 

  • Shen X, Hu H, Peng H, Wang W, Zhang X (2013) Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas. BMC Genom 14(1):1

    Article  CAS  Google Scholar 

  • Shin SH, Kim S, Kim JY, Song HY, Cho SJ, Lee KI, Yang KS (2012) Genome sequence of Paenibacillus terrae HPL-003, a xylanase-producing bacterium isolated from soil found in forest residue. J Bacteriol 194(5):1266

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shoresh M, Harman GE (2010) Differential expression of maize chitinases in the presence or absence of Trichoderma harzianum strain T22 and indications of a novel exo-endo-heterodimeric chitinase activity. BMC Plant Biol 10(1):136

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Singh S, Kapoor KK (1999) Inoculation with phosphate-solubilizing microorganisms and a vesicular-arbuscular mycorrhizal fungus improves dry matter yield and nutrient uptake by wheat grown in a sandy soil. Bio Fert Soil 28(2):139–144

    Article  CAS  Google Scholar 

  • Singh PP, Shin YC, Park CS, Chung YR (1999) Biological control of Fusarium wilt of cucumber by chitinolytic bacteria. Phytopath 89:92–99

    Article  CAS  Google Scholar 

  • Smith KP, Handelsman J, Goodman RM (1999) Genetic basis in plants for interactions with disease-suppressive bacteria. Proc Natl Acad Sci USA 96:4786–4790

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song JY, Kim HA, Kim JS, Kim SY, Jeong H, Kang SG et al (2012) Genome sequence of the plant growth-promoting rhizobacterium Bacillus sp. strain JS. J Bacteriol 194(14):3760–3761

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spaepen S, Vanderleyden J (2011) Auxin and plant-microbe interactions. Cold Spring Harb Perspect Biol 3(4):a001438

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Spaepen S, Vanderleyden J, Remans R (2007) Indole- 3-acetic acid in microbial and microorganism-plant signaling. FEMS Microbiol Rev 31:425–448

    Article  CAS  PubMed  Google Scholar 

  • Sturz AV, Christie BR, Matheson BG, Arsenault WJ, Buchanan NA (1999) Endophytic communities in the periderm of potato tubers and their potential to improve resistance to soil-borne plant pathogens. Plant Pathol 48:360–369

    Article  Google Scholar 

  • Suarez C, Cardinale M, Ratering S, Steffens D, Jung S, Montoya AMZ, Schnell S (2015) Plant growth-promoting effects of Hartmannibacter diazotrophicus on summer barley (Hordeum vulgare L.) under salt stress. Appl Soil Ecol 95:23–30

    Article  Google Scholar 

  • Taghavi S, Garafola C, Monchy S, Newman L, Hoffman A, Weyens N, Barac T, Vangronsveld J, van der Lelie D (2009) Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees. App Environ Microbiol 75:748–757

    Article  CAS  Google Scholar 

  • Taghavi S, van der Lelie D, Hoffman A, Zhang Y-B, Walla MD et al (2010) Genome sequence of the plant growth promoting endophytic bacterium Enterobacter sp. 638. PLoS Genet 6(5):e1000943

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tangahu BV, Sheikh Abdullah SR, Basri H, Idris M, Anuar N, Mukhlisin M (2011) A review on heavy metals (As, Pb, and Hg) uptake by plants through phytoremediation. Int J Chem Eng. Article ID 939161

  • Ting ASY (2015) Microbial cells dead or alive: prospect, potential and innovations for heavy metal removal. In: Chandra R (ed) Advances in biodegradation and bioremediation of industrial waste. CRC Press, Boca Raton, pp 31–66

    Chapter  Google Scholar 

  • Tong YJ, Ji XJ, Liu LG, Shen MQ, Huang H (2013) Genome sequence of Paenibacillus polymyxa ATCC 12321, a promising strain for optically active (R, R)-2, 3-butanediol production. Genome Announc 1(4):e00572-13

    Article  PubMed  PubMed Central  Google Scholar 

  • Toyoda H, Utsumi R (1991) Method for the prevention of Fusarium diseases and microorganisms used for the same. U.S. Patent No. 4,988,586

  • Trippe K, McPhail K, Armstrong D, Azevedo M, Banowetz G (2013) Pseudomonas fluorescens SBW25 produces furanomycin, a non-proteinogenic amino acid with selective antimicrobial properties. BMC Microbiol 13:111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Udaondo Z, Molina L, Segura A, Duque E, Ramos JL (2015) Analysis of the core genome and pangenome of Pseudomonas putida. Environ Microbiol 15:780–794

    Google Scholar 

  • Ullah A, Heng S, Munis MFH, Fahad S, Yang X (2015a) Phytoremediation of heavy metals assisted by plant growth promoting (PGP) bacteria: a review. Environ Exp Bot 117:28–40

    Article  CAS  Google Scholar 

  • Ullah A, Mushtaq H, Ali H, Munis MFH, Javed MT, Chaudhary HJ (2015b) Diazotrophs- assisted phytoremediation of heavy metals: a novel approach. Environ Sci Pollut Res 22:2505–2514

    Article  CAS  Google Scholar 

  • Upadhyay SK, Singh JS, Saxena AK, Singh DP (2011) Impact of PGPR inoculation on growth and antioxidant status of wheat under saline conditions. Plant Biol 14:605–611

    Article  PubMed  CAS  Google Scholar 

  • Validov SZ, Kamilova F, Lugtenberg BJ (2009) Pseudomonas putida strain PCL1760 controls tomato foot and root rot in stonewool under industrial conditions in a certified greenhouse. Biol Control 48(1):6–11

    Article  Google Scholar 

  • Vanderschuren H, Lentz E, Zainuddin I, Gruissem W (2013) Proteomics of model and crop plant species: status, current limitations and strategic advances for crop improvement. J Proteom 93:5–19

    Article  CAS  Google Scholar 

  • Vansuyt G, Robin A, Briat JF, Curie C, Lemanceau P (2007) Iron acquisition from Fe-pyoverdine by Arabidopsis thaliana. Mol Plant Microb Interact 20:441–447

    Article  CAS  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 Biotech 91(2):127–141

    Article  CAS  Google Scholar 

  • Vessey JK (2003) Plant growth-promoting rhizobacteria as biofertilizers. Plant Soil 255:571–586

    Article  CAS  Google Scholar 

  • Walker V, Couillerot O, Von Felten A, Bellvert F, Jansa J, Maurhofer M et al (2011) Variation of secondary metabolite levels in maize seedling roots induced by inoculation with Azospirillum, Pseudomonas and Glomus consortium under field conditions. Plant Soil 356:151–163

    Article  CAS  Google Scholar 

  • Walters D, Walsh D, Newton A, Lyon G (2005) Induced resistance for plant disease control: maximizing the efficacy of resistance elicitors. Phytopathology 95(12):1368–1373

    Article  CAS  PubMed  Google Scholar 

  • Walters DR, Ratsep J, Havis ND (2013) Controlling crop diseases using induced resistance: challenges for the future. J Exp Bot 64:1263–1280

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Brown HN, Crowley DE, Szaniszlo PJ (1993) Evidence for direct utilization of a siderophore, ferrioxamine B in axenically grown cucumber. Plant Cell Environ 16:579–585

    Article  CAS  Google Scholar 

  • Weilharter A, Mitter B, Shin MV, Chain PS, Nowak J, Sessitsch A (2011) Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN. J Bacteriol 193(13):3383–3384

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Werner D (2005) Production and biological nitrogen fixation of tropical legumes. In: Nitrogen fixation in agriculture, forestry, ecology, and the environment. Springer, pp 1–13

  • Whipps JM (2001) Microbial interactions and biocontrol in the rhizosphere. J Exp Bot 52(1):487–511

    Article  CAS  PubMed  Google Scholar 

  • Wiesel L, Newton AC, Elliott I (2014) Molecular effects of resistance elicitors from biological origin and their potential for crop protection. Front Plant Sci 5:655

    Article  PubMed  PubMed Central  Google Scholar 

  • Wisniewski-Dyé F, Vial L, Burdman S, Okon Y, Hartmann A (2015) Phenotypic variation in Azospirillum spp and other root-associated bacteria. In: De Bruijn FJ (ed) Biological nitrogen fixation. Wiley, Hoboken, pp 1047–1054

    Chapter  Google Scholar 

  • Xu Y, Wang A, Tao F, Su F, Tang H, Ma C, Xu P (2012) Genome sequence of Enterobacter cloacae subsp. dissolvens SDM, an efficient biomass-utilizing producer of platform chemical 2,3-butanediol. J Bacteriol 194(4):897–898

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yadav J, Verma JP, Jaiswal DK, Kumar A (2014) Evaluation of PGPR and different concentration of phosphorus level on plant growth, yield and nutrient content of rice (Oryza sativa). Ecol Eng 62:123–128

    Article  Google Scholar 

  • Yang J, Kloepper JW, Ryu CM (2009) Rhizosphere bacteria help plants tolerate abiotic stress. Trend Plant Sci 14(1):1–4

    Article  CAS  Google Scholar 

  • Yao L, Wu Z, Zheng Y, Kaleem I, Li C (2010) Growth promotion and protection against salt stress by Pseudomonas putida Rs-198 on cotton. Eur J Soil Biol 46:49–54

    Article  CAS  Google Scholar 

  • Yong X, Chen Y, Liu W, Xu L, Zhou J, Wang S, Chen P, Ouyang P, Zheng T (2014) Enhanced cadmium resistance and accumulation in Pseudomonas putida KT2440 expressing the phytochelatin synthase gene of Schizosaccharomyces po mbe. Lett Appl Microbiol 58:255–261

    Article  CAS  PubMed  Google Scholar 

  • Younesi O, Moradi A (2014) Effects of plant growth-promoting rhizobacterium (PGPR) and arbuscular mycorrhizal fungus (AMF) on antioxidant enzyme activities in salt-stressed bean (Phaseolus vulgaris L.). Agric 60(1):10–21

    CAS  Google Scholar 

  • Yue HT, Mo WP, Li C, Zheng YY, Li H (2007) The salt stress relief and growth promotion effect of Rs-5 on cotton. Plant Soil 297(1–2):139–145

    Article  CAS  Google Scholar 

  • Zahir ZA, Munir A, Asghar HN, Shaharoona B, Arshad M (2008) Effectiveness of rhizobacteria containing ACC-deaminase for growth promotion of pea (Pisum sativum) under drought conditions. J Microbiol Biotechnol 18:958–963

    CAS  PubMed  Google Scholar 

  • Zahir ZA, Ghani U, Naveed M, Nadeem SM, Asghar HN (2009) Comparative effectiveness of Pseudomonas and Serratia sp. containing ACC-deaminase for improving growth and yield of wheat (Triticum aestivum L.) under salt-stressed conditions. Arch Microbiol 191:415–424

    Article  CAS  PubMed  Google Scholar 

  • Zahran HH (2001) Rhizobia from wild legumes: diversity, taxonomy, ecology, nitrogen fixation and biotechnology. J Biotechnol 91:143–153

    Article  CAS  PubMed  Google Scholar 

  • Zaidi A, Khan MS, Ahemad M, Oves M (2009) Plant growth promotion by phosphate solubilizing bacteria. Acta Microbiol Immunol Hung 56:263–284

    Article  CAS  PubMed  Google Scholar 

  • Zhang L, Birch RG (1996) Biocontrol of sugar cane leaf scald disease by an isolate of Pantoea dispersa which detoxifies albicidin phytotoxins. Lett Appl Microbiol 22:132–136

    Article  CAS  Google Scholar 

  • Zhang H, Murzello C, Sun Y, Kim MS, Xie X, Jeter RM, Pare PW (2010) Choline and osmotic-stress tolerance induced in Arabidopsis by the soil microbe Bacillus subtilis (GB03). Mol Plant 23(8):1097–1104

    CAS  Google Scholar 

  • Zhao X, de Jong A, Zhou Z, Kuipers OP (2015) Complete genome sequence of Bacillus amyloliquefaciens strain BH072, isolated from honey. Genome Announc 3(2):e00098-15

    Article  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Center for Research and Development (CORD), University of Kashmir, Srinagar, Jammu and Kashmir, India

    Javid A. Parray & Azra N. Kamili

  2. ICAR- Central Institute of Temperate Horticulture, Rangreth, Srinagar, Jammu and Kashmir, India

    Sumira Jan

  3. Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India

    Raies A. Qadri

  4. Department of Microbiology and Biotechnology, Faculty of Biology and Soil Science, National University of Uzbekistan, Tashkent, Uzbekistan

    Dilfuza Egamberdieva

  5. Department of Botany, S.P. College, Srinagar, Jammu and Kashmir, India

    Parvaiz Ahmad

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  1. Javid A. Parray
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  2. Sumira Jan
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  4. Raies A. Qadri
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  5. Dilfuza Egamberdieva
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  6. Parvaiz Ahmad
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Correspondence to Parvaiz Ahmad.

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Parray, J.A., Jan, S., Kamili, A.N. et al. Current Perspectives on Plant Growth-Promoting Rhizobacteria. J Plant Growth Regul 35, 877–902 (2016). https://doi.org/10.1007/s00344-016-9583-4

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