Skip to main content

Microbial Ecology at Rhizosphere: Bioengineering and Future Prospective

  • Chapter
  • First Online:
Plant-Microbe Interaction: An Approach to Sustainable Agriculture

Abstract

Rhizosphere, the interface between soil and plant roots, is a chemically complex environment which supports the development and growth of diverse microbial communities. Studies in rhizosphere science have undoubtedly improved our ability to steer the knowledge into technological applications in agricultural industry, ecological engineering, and nature restoration. In this chapter we provide a holistic perception of rhizosphere functioning with a highlight on the ecological drivers that promote colonization of coherent functional groups of microorganisms influencing plant life through several direct and indirect mechanisms. We also discuss how the activities of the indigenous microbes from rhizosphere may be exploited toward developing profitable techniques or methods in sustainable agriculture, biotechnology, and environmental management. In this context, we emphasize on the need for high degree of innovation and active collaboration between basic research and technology development wings for the best use of the knowledge in order to meet the increasing global demand for food, fiber, and bioenergy.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 249.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abbas HK, Zablotowicz RM, Weaver MA, Shier WT, Bruns HA, Bellaloui N, Accinelli C, Abel CA (2013) Implications of Bt traits on mycotoxin contamination in maize: overview and recent experimental results in southern United States. J Agric Food Chem 61(48):11759–11770. doi:10.1021/jf400754g

    Article  CAS  PubMed  Google Scholar 

  • Abhilash PC, Jamil S, Singh N (2009) Transgenic plants for enhanced biodegradation and phytoremediation of organic xenobiotics. Biotechnol Adv 27(4):474–488. doi:10.1016/j.biotechadv.2009.04.002S0734-9750(09)00052-4 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Adenle AA (2011) Response to issues on GM agriculture in Africa: are transgenic crops safe? BMC Res Notes 4:388. doi:10.1186/1756-0500-4-3881756-0500-4-388 [pii]

    Article  PubMed  PubMed Central  Google Scholar 

  • Ajilogba CF, Babalola OO (2013) Integrated management strategies for tomato Fusarium wilt. Biocontrol Sci 18(3):117–127. doi:DN/JST.JSTAGE/bio/18.117 [pii]

    Article  PubMed  Google Scholar 

  • Ali JG, Alborn HT, Stelinski LL (2010) Subterranean herbivore-induced volatiles released by citrus roots upon feeding by Diaprepes abbreviatus recruit entomopathogenic nematodes. J Chem Ecol 36(4):361–368. doi:10.1007/s10886-010-9773-7

    Article  CAS  PubMed  Google Scholar 

  • Alsanius BW, Hultberg M, Englund JE (2002) Effect of lacZY-marking of the 2,4-diacetyl-phloroglucinol producing Pseudomonas fluorescens-strain 5-2/4 on its physiological performance and root colonization ability. Microbiol Res 157(1):39–45

    Article  CAS  PubMed  Google Scholar 

  • Apine OA, Jadhav JP (2011) Optimization of medium for indole-3-acetic acid production using Pantoea agglomerans strain PVM. J Appl Microbiol 110(5):1235–1244. doi:10.1111/j.1365-2672.2011.04976.x

    Article  CAS  PubMed  Google Scholar 

  • Araus JL, Li J, Parry MA, Wang J (2014) Phenotyping and other breeding approaches for a New Green Revolution. J Integr Plant Biol 56(5):422–424. doi:10.1111/jipb.12202

    Article  PubMed  Google Scholar 

  • Arazi T, Sunkar R, Kaplan B, Fromm H (1999) A tobacco plasma membrane calmodulin-binding transporter confers Ni2+ tolerance and Pb2+ hypersensitivity in transgenic plants. Plant J 20(2):171–182. doi:tpj588 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Arias MS, Pena-Cabriales JJ, Alarcon A, Maldonado Vega M (2015) Enhanced Pb absorption by Hordeum vulgare L. and Helianthus annuus L. plants inoculated with an arbuscular mycorrhizal fungi consortium. Int J Phytoremediation 17(1–6):405–413. doi:10.1080/15226514.2014.898023

    Article  CAS  PubMed  Google Scholar 

  • Arora K, Sharma S, Monti A (2015) Bio-remediation of Pb and Cd polluted soils by switchgrass: a case study in India. Int J Phytoremediation. doi:10.1080/15226514.2015.1131232

    Google Scholar 

  • Arruda P (2012) Genetically modified sugarcane for bioenergy generation. Curr Opin Biotechnol 23(3):315–322. doi:10.1016/j.copbio.2011.10.012

    Article  CAS  PubMed  Google Scholar 

  • Babikova Z, Gilbert L, Bruce TJ, Birkett M, Caulfield JC, Woodcock C, Pickett JA, Johnson D (2013) Underground signals carried through common mycelial networks warn neighbouring plants of aphid attack. Ecol Lett 16(7):835–843. doi:10.1111/ele.12115

    Article  PubMed  CAS  Google Scholar 

  • Badri DV, Vivanco JM (2009) Regulation and function of root exudates. Plant Cell Environ 32(6):666–681. doi:10.1111/j.1365-3040.2008.01926.xPCE1926 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Badri DV, Weir TL, van der Lelie D, Vivanco JM (2009) Rhizosphere chemical dialogues: plant-microbe interactions. Curr Opin Biotechnol 20(6):642–650. doi:10.1016/j.copbio.2009.09.014 S0958-1669(09)00128-1 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Badri DV, Chaparro JM, Zhang R, Shen Q, Vivanco JM (2013) Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome. J Biol Chem 288(7):4502–4512. doi:10.1074/jbc.M112.433300M112.433300 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bagyaraj DJ, Rangaswami G (2005) Microorganisms in soil. In: Agricultural microbiology, 2nd edn. Prentice Hall of India Private Limited, New Delhi, p 254

    Google Scholar 

  • Bais HP, Park SW, Weir TL, Callaway RM, Vivanco JM (2004) How plants communicate using the underground information superhighway. Trends Plant Sci 9(1):26–32. doi:10.1016/j.tplants.2003.11.008 S1360-1385(03)00302-9 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57:233–266. doi:10.1146/annurev.arplant.57.032905.105159

    Article  CAS  PubMed  Google Scholar 

  • Balseiro-Romero M, Kidd PS, Monterroso C (2014) Influence of plant root exudates on the mobility of fuel volatile compounds in contaminated soils. Int J Phytoremediation 16(7–12):824–839. doi:10.1080/15226514.2013.856851

    Article  CAS  PubMed  Google Scholar 

  • Banerjee A, Chisti Y, Banerjee UC (2004) Streptokinase – a clinically useful thrombolytic agent. Biotechnol Adv 22(4):287–307. doi:S0734975003001678 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Barrada A, Montane MH, Robaglia C, Menand B (2015) Spatial regulation of root growth: placing the plant TOR pathway in a developmental perspective. Int J Mol Sci 16(8):19671–19697. doi:10.3390/ijms160819671 ijms160819671 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bawa AS, Anilakumar KR (2013) Genetically modified foods: safety, risks and public concerns-a review. J Food Sci Technol 50(6):1035–1046. doi:10.1007/s13197-012-0899-1 899 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Bekkara F, Jay M, Viricel MR, Rome S (1998) Distribution of phenolic compounds within seed and seedlings of two Vicia faba cvs differing in their see tannin content and study of their seed and root phenolic exudations. Plant Soil 203:27–36

    Article  Google Scholar 

  • Bell TH, Cloutier-Hurteau B, Al-Otaibi F, Turmel MC, Yergeau E, Courchesne F, St-Arnaud M (2015) Early rhizosphere microbiome composition is related to the growth and Zn uptake of willows introduced to a former landfill. Environ Microbiol 17(8):3025–3038. doi:10.1111/1462-2920.12900

    Article  CAS  PubMed  Google Scholar 

  • Bennett AE, Bever JD (2007) Mycorrhizal species differentially alter plant growth and response to herbivory. Ecology 88(1):210–218

    Article  PubMed  Google Scholar 

  • Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17(8):478–486. doi:10.1016/j.tplants.2012.04.001 S1360-1385(12)00079-9 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Berg G, Smalla K (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68(1):1–13. doi:10.1111/j.1574-6941.2009.00654.x FEM654 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Bertsch J, Muller V (2015) Bioenergetic constraints for conversion of syngas to biofuels in acetogenic bacteria. Biotechnol Biofuels 8:210. doi:10.1186/s13068-015-0393-x 393 [pii]

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bhardwaj D, Ansari MW, Sahoo RK, Tuteja N (2014) Biofertilizers function as key player in sustainable agriculture by improving soil fertility, plant tolerance and crop productivity. Microb Cell Fact 13:66. doi:10.1186/1475-2859-13-66 1475-2859-13-66 [pii]

    Article  PubMed  PubMed Central  Google Scholar 

  • Bhargava A, Carmona FF, Bhargava M, Srivastava S (2012) Approaches for enhanced phytoextraction of heavy metals. J Environ Manage 105:103–120. doi:10.1016/j.jenvman.2012.04.002 S0301-4797(12)00183-1 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Bhattacharyya PN, Jha DK (2012) Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture. World J Microbiol Biotechnol 28(4):1327–1350. doi:10.1007/s11274-011-0979-9

    Article  CAS  PubMed  Google Scholar 

  • Bisht S, Pandey P, Aggarwal H et al (2014) Utilization of endophytic strain Bacillus sp. SBER3 for biodegradation of polyaromatic hydrocarbons (PAH) in soil model system. Eur J Soil Biol 60:67–76

    Article  CAS  Google Scholar 

  • Bisht S, Pandey P, Bhargava B, Sharma S, Kumar V, Sharma KD (2015) Bioremediation of polyaromatic hydrocarbons (PAHs) using rhizosphere technology. Braz J Microbiol 46(1):7–21. doi:10.1590/S1517-838246120131354 1517-8382-bjm-46-01-0007 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blanco CA (2012) Heliothis virescens and Bt cotton in the United States. GM Crops Food 3(3):201–212. doi:10.4161/gmcr.21439 21439 [pii]

    Article  PubMed  Google Scholar 

  • Blossfeld S, Suessmilch S, Le Marie CA, Kuhn AJ (2011) Exploration of key rhizosphere parameters in plant-MFCs. Commun Agric Appl Biol Sci 76(2):7–9

    PubMed  Google Scholar 

  • Bonito G, Reynolds H, Robeson MS 2nd, Nelson J, Hodkinson BP, Tuskan G, Schadt CW, Vilgalys R (2014) Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants. Mol Ecol 23(13):3356–3370. doi:10.1111/mec.12821

    Article  PubMed  Google Scholar 

  • Bravin MN, Tentscher P, Rose J, Hinsinger P (2009) Rhizosphere pH gradient controls copper availability in a strongly acidic soil. Environ Sci Technol 43(15):5686–5691

    Article  CAS  PubMed  Google Scholar 

  • Bulgarelli D, Rott M, Schlaeppi K, Ver Loren van Themaat E, Ahmadinejad N, Assenza F, Rauf P, Huettel B, Reinhardt R, Schmelzer E, Peplies J, Gloeckner FO, Amann R, Eickhorst T, Schulze-Lefert P (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488(7409):91–95. doi:10.1038/nature11336 nature11336 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Bulgarelli D, Schlaeppi K, Spaepen S, Ver Loren van Themaat E, Schulze-Lefert P (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838. doi:10.1146/annurev-arplant-050312-120106

    Article  CAS  PubMed  Google Scholar 

  • Bulluck LR, Ristaino JB (2002) Effect of synthetic and organic soil fertility amendments on southern blight, soil microbial communities, and yield of processing tomatoes. Phytopathology 92(2):181–189. doi:10.1094/PHYTO.2002.92.2.181

    Article  CAS  PubMed  Google Scholar 

  • Cabral L, Soares CR, Giachini AJ, Siqueira JO (2015) Arbuscular mycorrhizal fungi in phytoremediation of contaminated areas by trace elements: mechanisms and major benefits of their applications. World J Microbiol Biotechnol 31(11):1655–1664. doi:10.1007/s11274-015-1918-y [pii]

    Article  CAS  PubMed  Google Scholar 

  • Campbell MA, Fitzgerald HA, Ronald PC (2002) Engineering pathogen resistance in crop plants. Transgenic Res 11(6):599–613

    Article  CAS  PubMed  Google Scholar 

  • Cezard C, Farvacques N, Sonnet P (2015) Chemistry and biology of pyoverdines, Pseudomonas primary siderophores. Curr Med Chem 22(2):165–186. doi:CMC-EPUB-62749 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Chan WF, Li H, Wu FY, Wu SC, Wong MH (2013) Arsenic uptake in upland rice inoculated with a combination or single arbuscular mycorrhizal fungi. J Hazard Mater 262:1116–1122. doi:10.1016/j.jhazmat.2012.08.020 S0304-3894(12)00826-6 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Chaudhry Q, Blom-Zandstra M, Gupta S, Joner EJ (2005) Utilising the synergy between plants and rhizosphere microorganisms to enhance breakdown of organic pollutants in the environment. Environ Sci Pollut Res Int 12(1):34–48

    Article  CAS  PubMed  Google Scholar 

  • Chen Y, Wang Y, Wu W, Lin Q, Xue S (2006) Impacts of chelate-assisted phytoremediation on microbial community composition in the rhizosphere of a copper accumulator and non-accumulator. Sci Total Environ 356(1–3):247–255. doi:10.1016/j.scitotenv.2005.04.028 S0048-9697(05)00245-7 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Clemens S, Palmgren MG, Kramer U (2002) A long way ahead: understanding and engineering plant metal accumulation. Trends Plant Sci 7(7):309–315. doi:S1360-1385(02)02295-1 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Costa R, Gotz M, Mrotzek N, Lottmann J, Berg G, Smalla K (2006) Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds. FEMS Microbiol Ecol 56(2):236–249. doi:10.1111/j.1574-6941.2005.00026.x FEM026 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Cowgill SE, Wright C, Atkinson HJ (2002) Transgenic potatoes with enhanced levels of nematode resistance do not have altered susceptibility to nontarget aphids. Mol Ecol 11(4):821–827. doi:1482 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Crosa JH, Walsh CT (2002) Genetics and assembly line enzymology of siderophore biosynthesis in bacteria. Microbiol Mol Biol Rev 66(2):223–249

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Curlango-Rivera G, Huskey DA, Mostafa A, Kessler JO, Xiong Z, Hawes MC (2013) Intraspecies variation in cotton border cell production: rhizosphere microbiome implications. Am J Bot 100(9):1706–1712. doi:10.3732/ajb.1200607 ajb.1200607 [pii]

    Article  PubMed  Google Scholar 

  • Davison J, Opik M, Zobel M, Vasar M, Metsis M, Moora M (2012) Communities of arbuscular mycorrhizal fungi detected in forest soil are spatially heterogeneous but do not vary throughout the growing season. PLoS One 7(8), e41938. doi:10.1371/journal.pone.0041938 PONE-D-12-12295 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Melo RW, Schneider J, de Souza CE, Sousa SC, Guimaraes GL, de Souza MF (2014) Phytoprotective effect of arbuscular mycorrhizal fungi species against arsenic toxicity in tropical leguminous species. Int J Phytoremediation 16(7–12):840–858. doi:10.1080/15226514.2013.856852

    PubMed  Google Scholar 

  • De Souza AP, Alvim Kamei CL, Torres AF, Pattathil S, Hahn MG, Trindade LM, Buckeridge MS (2015) How cell wall complexity influences saccharification efficiency in Miscanthus sinensis. J Exp Bot 66(14):4351–4365. doi:10.1093/jxb/erv183 erv183 [pii]

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • De Vos D, Vissenberg K, Broeckhove J, Beemster GT (2014) Putting theory to the test: which regulatory mechanisms can drive realistic growth of a root? PLoS Comput Biol 10(10), e1003910. doi:10.1371/journal.pcbi.1003910 PCOMPBIOL-D-13-02201 [pii]

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Delhaize E, Gruber BD, Ryan PR (2007) The roles of organic anion permeases in aluminium resistance and mineral nutrition. FEBS Lett 581(12):2255–2262. doi:10.1016/j.febslet.2007.03.057 S0014-5793(07)00311-0 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Dessaux Y, Grandclement C, Faure D (2016) Engineering the rhizosphere. Trends Plant Sci 21(3):266–278. doi:10.1016/j.tplants.2016.01.002 S1360-1385(16)00003-0 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Dhankher OP, Li Y, Rosen BP, Shi J, Salt D, Senecoff JF, Sashti NA, Meagher RB (2002) Engineering tolerance and hyperaccumulation of arsenic in plants by combining arsenate reductase and gamma-glutamylcysteine synthetase expression. Nat Biotechnol 20(11):1140–1145. doi:10.1038/nbt747 nbt747 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Diagne N, Arumugam K, Ngom M, Nambiar-Veetil M, Franche C, Narayanan KK, Laplaze L (2013) Use of Frankia and Actinorhizal plants for degraded lands reclamation. Biomed Res Int 2013:948258. doi:10.1155/2013/948258

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dong YH, Wang LH, Xu JL, Zhang HB, Zhang XF, Zhang LH (2001) Quenching quorum-sensing-dependent bacterial infection by an N-acyl homoserine lactonase. Nature 411(6839):813–817. doi:10.1038/35081101

    Article  CAS  PubMed  Google Scholar 

  • Doty SL, Shang TQ, Wilson AM, Tangen J, Westergreen AD, Newman LA, Strand SE, Gordon MP (2000) Enhanced metabolism of halogenated hydrocarbons in transgenic plants containing mammalian cytochrome P450 2E1. Proc Natl Acad Sci U S A 97(12):6287–6291. doi:97/12/6287 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duca D, Lorv J, Patten CL, Rose D, Glick BR (2014) Indole-3-acetic acid in plant-microbe interactions. Antonie Van Leeuwenhoek 106(1):85–125. doi:10.1007/s10482-013-0095-y

    Article  CAS  PubMed  Google Scholar 

  • Dunfield KE, Germida JJ (2003) Seasonal changes in the rhizosphere microbial communities associated with field-grown genetically modified canola (Brassica napus). Appl Environ Microbiol 69(12):7310–7318

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dutta S, Morang P, Kumar SN, Dileep Kumar BS (2014) Two rhizobacterial strains, individually and in interactions with Rhizobium sp., enhance fusarial wilt control, growth, and yield in pigeon pea. J Microbiol 52(9):778–784. doi:10.1007/s12275-014-3496-3

    Google Scholar 

  • Eapen S, D’Souza SF (2005) Prospects of genetic engineering of plants for phytoremediation of toxic metals. Biotechnol Adv 23(2):97–114. doi:10.1016/j.biotechadv.2004.10.001 S0734-9750(04)00094-1 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Egamberdieva D, Kamilova F, Validov S, Gafurova L, Kucharova Z, Lugtenberg B (2008) High incidence of plant growth-stimulating bacteria associated with the rhizosphere of wheat grown on salinated soil in Uzbekistan. Environ Microbiol 10(1):1–9. doi:10.1111/j.1462-2920.2007.01424.x, EMI1424 [pii]

    CAS  PubMed  Google Scholar 

  • Ehlers RU (2003) Entomopathogenic nematodes in the European biocontrol market. Commun Agric Appl Biol Sci 68(4 Pt A):3–16

    CAS  PubMed  Google Scholar 

  • Ellouze W, Hamel C, Vujanovic V, Gan Y, Bouzid S, St-Arnaud M (2013) Chickpea genotypes shape the soil microbiome and affect the establishment of the subsequent durum wheat crop in the semi arid North American Great Plains. Soil Biol Biochem 63:129–141. doi:10.1016/j.soilbio.2013.04.001

    Article  CAS  Google Scholar 

  • Evans KM, Gatehouse JA, Lindsay WP, Shi J, Tommey AM, Robinson NJ (1992) Expression of the pea metallothionein-like gene PsMTA in Escherichia coli and Arabidopsis thaliana and analysis of trace metal ion accumulation: implications for PsMTA function. Plant Mol Biol 20(6):1019–1028

    Article  CAS  PubMed  Google Scholar 

  • Fahey C, Winter K, Slot M, Kitajima K (2016) Influence of arbuscular mycorrhizal colonization on whole-plant respiration and thermal acclimation of tropical tree seedlings. Ecol Evol 6(3):859–870. doi:10.1002/ece3.1952 ECE31952 [pii]

    Article  PubMed  PubMed Central  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. doi:10.1007/s10886-013-0317-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Farrar K, Bryant D, Cope-Selby N (2014) Understanding and engineering beneficial plant-microbe interactions: plant growth promotion in energy crops. Plant Biotechnol J 12(9):1193–1206. doi:10.1111/pbi.12279

    Article  PubMed  PubMed Central  Google Scholar 

  • Ferguson BJ, Mathesius U (2014) Phytohormone regulation of legume-rhizobia interactions. J Chem Ecol 40(7):770–790. doi:10.1007/s10886-014-0472-7

    Article  CAS  PubMed  Google Scholar 

  • Firmin S, Labidi S, Fontaine J, Laruelle F, Tisserant B, Nsanganwimana F, Pourrut B, Dalpe Y, Grandmougin A, Douay F, Shirali P, Verdin A, Lounes-Hadj Sahraoui A (2015) Arbuscular mycorrhizal fungal inoculation protects Miscanthus x giganteus against trace element toxicity in a highly metal-contaminated site. Sci Total Environ 527–528:91–99. doi:10.1016/j.scitotenv.2015.04.116 S0048-9697(15)30050-4 [pii]

    Article  PubMed  CAS  Google Scholar 

  • Fraley RT, Rogers SG, Horsch RB, Sanders PR, Flick JS, Adams SP, Bittner ML, Brand LA, Fink CL, Fry JS, Galluppi GR, Goldberg SB, Hoffmann NL, Woo SC (1983) Expression of bacterial genes in plant cells. Proc Natl Acad Sci U S A 80(15):4803–4807

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fray RG, Throup JP, Daykin M, Wallace A, Williams P, Stewart GS, Grierson D (1999) Plants genetically modified to produce N-acylhomoserine lactones communicate with bacteria. Nat Biotechnol 17(10):1017–1020. doi:10.1038/13717

    Article  CAS  PubMed  Google Scholar 

  • French CE, Rosser SJ, Davies GJ, Nicklin S, Bruce NC (1999) Biodegradation of explosives by transgenic plants expressing pentaerythritol tetranitrate reductase. Nat Biotechnol 17(5):491–494. doi:10.1038/8673

    Article  CAS  PubMed  Google Scholar 

  • Furtado A, Lupoi JS, Hoang NV, Healey A, Singh S, Simmons BA, Henry RJ (2014) Modifying plants for biofuel and biomaterial production. Plant Biotechnol J 12(9):1246–1258. doi:10.1111/pbi.12300

    Article  CAS  PubMed  Google Scholar 

  • Gevaudant F, Duby G, von Stedingk E, Zhao R, Morsomme P, Boutry M (2007) Expression of a constitutively activated plasma membrane H+−ATPase alters plant development and increases salt tolerance. Plant Physiol 144(4):1763–1776. doi:pp.107.103762 [pii] 10.1104/pp.107.103762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ghosh R, Barman S, Mukherjee R, Mandal NC (2016) Role of phosphate solubilizing Burkholderia spp. for successful colonization and growth promotion of Lycopodium cernuum L. (Lycopodiaceae) in lateritic belt of Birbhum district of West Bengal, India. Microbiol Res 183:80–91. doi:10.1016/j.micres.2015.11.011 S0944-5013(15)30033-1 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Gisbert C, Ros R, De Haro A, Walker DJ, Pilar Bernal M, Serrano R, Navarro-Avino J (2003) A plant genetically modified that accumulates Pb is especially promising for phytoremediation. Biochem Biophys Res Commun 303(2):440–445. doi:S0006291X03003498 [pii]

    Article  CAS  PubMed  Google Scholar 

  • GM Approval Databse-ISAAA.org (2016) http://www.isaaa.org. Accessed 5 Apr 2016

  • Gordon DM, Ryder MH, Heinrich K, Murphy PJ (1996) An experimental test of the rhizopine concept in Rhizobium meliloti. Appl Environ Microbiol 62(11):3991–3996

    CAS  PubMed  PubMed Central  Google Scholar 

  • Goto F, Yoshihara T, Shigemoto N, Toki S, Takaiwa F (1999) Iron fortification of rice seed by the soybean ferritin gene. Nat Biotechnol 17(3):282–286. doi:10.1038/7029

    Article  CAS  PubMed  Google Scholar 

  • Gregory PJ, Atkinson CJ, Bengough AG, Else MA, Fernandez-Fernandez F, Harrison RJ, Schmidt S (2013) Contributions of roots and rootstocks to sustainable, intensified crop production. J Exp Bot 64(5):1209–1222. doi:10.1093/jxb/ers385 ers385 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Gtari M, Ghodhbane-Gtari F, Nouioui I, Beauchemin N, Tisa LS (2012) Phylogenetic perspectives of nitrogen-fixing Actinobacteria. Arch Microbiol 194(1):3–11. doi:10.1007/s00203-011-0733-6

    Article  CAS  PubMed  Google Scholar 

  • Guerinot ML (1994) Microbial iron transport. Annu Rev Microbiol 48:743–772. doi:10.1146/annurev.mi.48.100194.003523

    Article  CAS  PubMed  Google Scholar 

  • Gupta S, Sharma P, Dev K, Sourirajan A (2016) Halophilic bacteria of Lunsu produce an array of industrially important enzymes with salt tolerant activity. Biochem Res Int 2016:9237418. doi:10.1155/2016/9237418

    PubMed  PubMed Central  Google Scholar 

  • Gurung N, Ray S, Bose S, Rai V (2013) A broader view: microbial enzymes and their relevance in industries, medicine, and beyond. Biomed Res Int 2013:329121. doi:10.1155/2013/329121

    Article  PubMed  PubMed Central  CAS  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. doi:10.1146/annurev.phyto.41.052002.095656 052002.095656 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Hannink NK, Subramanian M, Rosser SJ, Basran A, Murray JA, Shanks JV, Bruce NC (2007) Enhanced transformation of tnt by tobacco plants expressing a bacterial nitroreductase. Int J Phytoremediation 9(5):385–401. doi:10.1080/15226510701603916

    Article  CAS  PubMed  Google Scholar 

  • Hardtke CS, Dorcey E, Osmont KS, Sibout R (2007) Phytohormone collaboration: zooming in on auxin-brassinosteroid interactions. Trends Cell Biol 17(10):485–492. doi:10.1016/j.tcb.2007.08.003 S0962-8924(07)00191-2 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Harvey PJ, Campanella BF, Castro PM, Harms H, Lichtfouse E, Schaffner AR, Smrcek S, Werck-Reichhart D (2002) Phytoremediation of polyaromatic hydrocarbons, anilines and phenols. Environ Sci Pollut Res Int 9(1):29–47

    Article  CAS  PubMed  Google Scholar 

  • Hashem A, Abd Allah EF, Alqarawi AA, Egamberdieva D (2016) Bioremediation of adverse impact of cadmium toxicity on Cassia italica Mill by arbuscular mycorrhizal fungi. Saudi J Biol Sci 23(1):39–47. doi:10.1016/j.sjbs.2015.11.007 S1319-562X(15)00277-6 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Hill K, Porco S, Lobet G, Zappala S, Mooney S, Draye X, Bennett MJ (2013) Root systems biology: integrative modeling across scales, from gene regulatory networks to the rhizosphere. Plant Physiol 163(4):1487–1503. doi:10.1104/pp.113.227215 pp.113.227215 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hiltner L (1904) U¨ ber neuere Erfahrungen und Probleme auf dem Gebiete der Bodenbakteriologie unterbessonderer Ber ¨ ucksichtigung der Gr¨undung und Brache. Arb Dtsch Landwirtsch Ges Berl 98:59–78

    Google Scholar 

  • Hiltpold I, Turlings TC (2012) Manipulation of chemically mediated interactions in agricultural soils to enhance the control of crop pests and to improve crop yield. J Chem Ecol 38(6):641–650. doi:10.1007/s10886-012-0131-9

    Article  CAS  PubMed  Google Scholar 

  • Hiltpold I, Jaffuel G, Turlings TC (2015) The dual effects of root-cap exudates on nematodes: from quiescence in plant-parasitic nematodes to frenzy in entomopathogenic nematodes. J Exp Bot 66(2):603–611. doi:10.1093/jxb/eru345 eru345 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Hirschi KD, Korenkov VD, Wilganowski NL, Wagner GJ (2000) Expression of arabidopsis CAX2 in tobacco. Altered metal accumulation and increased manganese tolerance. Plant Physiol 124(1):125–133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Honeycutt CW (1998) Crop rotation impacts on potato protein. Plant Foods Hum Nutr 52(4):279–291

    Article  CAS  PubMed  Google Scholar 

  • Hopkins F, Gonzalez-Meler MA, Flower CE, Lynch DJ, Czimczik C, Tang J, Subke JA (2013) Ecosystem-level controls on root-rhizosphere respiration. New Phytol 199(2):339–351

    Article  CAS  PubMed  Google Scholar 

  • Hua H, Luo H, Bai Y, Wang K, Niu C, Huang H, Shi P, Wang C, Yang P, Yao B (2014) A thermostable glucoamylase from Bispora sp. MEY-1 with stability over a broad pH range and significant starch hydrolysis capacity. PLoS One 9(11), e113581. doi:10.1371/journal.pone.0113581 PONE-D-14-31239 [pii]

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Huang RH, Yang HL, Huang W, Lu YM, Chen K (2015) Effects of Funneliformis mosseae on endogenous hormones and photosynthesis of Sorghum haipense under Cs stress. Ying Yong Sheng Tai Xue Bao 26(7):2146–2150

    CAS  PubMed  Google Scholar 

  • Hughes M, Donnelly C, Crozier A, Wheeler CT (1999) Effects of the exposure of roots Almus glutinosa to light on flavonoid and nodulation. Can J Bot 77:1311–1315

    CAS  Google Scholar 

  • Hwang KY, Song HK, Chang C, Lee J, Lee SY, Kim KK, Choe S, Sweet RM, Suh SW (1997) Crystal structure of thermostable alpha-amylase from Bacillus licheniformis refined at 1.7 A resolution. Mol Cells 7(2):251–258

    CAS  PubMed  Google Scholar 

  • Ibanez S, Talano M, Ontanon O, Suman J, Medina MI, Macek T, Agostini E (2015) Transgenic plants and hairy roots: exploiting the potential of plant species to remediate contaminants. N Biotechnol. doi:S1871-6784(15)00267-8 [pii] 10.1016/j.nbt.2015.11.008

  • Jeong JS, Kim YS, Baek KH, Jung H, Ha SH, Do Choi Y, Kim M, Reuzeau C, Kim JK (2010) Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. Plant Physiol 153(1):185–197. doi:10.1104/pp.110.154773 pp.110.154773 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jia H, Fan Y, Feng X, Li C (2014) Enhancing stress-resistance for efficient microbial biotransformations by synthetic biology. Front Bioeng Biotechnol 2:44. doi:10.3389/fbioe.2014.00044

    Article  PubMed  PubMed Central  Google Scholar 

  • Jones AG (2008) A theoretical quantitative genetic study of negative ecological interactions and extinction times in changing environments. BMC Evol Biol 8:119. doi:10.1186/1471-2148-8-1191471-2148-8-119[pii]

    Article  PubMed  PubMed Central  Google Scholar 

  • Kabouw P, van Dam NM, van der Putten WH, Biere A (2012) How genetic modification of roots affects rhizosphere processes and plant performance. J Exp Bot 63(9):3475–3483. doi:10.1093/jxb/err399 err399 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Kenney E, Eleftherianos I (2016) Entomopathogenic and plant pathogenic nematodes as opposing forces in agriculture. Int J Parasitol 46(1):13–19. doi:10.1016/j.ijpara.2015.09.005 S0020-7519(15)00260-X [pii]

    Article  PubMed  Google Scholar 

  • Kent AD, Triplett EW (2002) Microbial communities and their interactions in soil and rhizosphere ecosystems. Annu Rev Microbiol 56:211–236. doi:10.1146/annurev.micro.56.012302.161120 012302.161120 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Khan AG (2006) Mycorrhizoremediation–an enhanced form of phytoremediation. J Zhejiang Univ Sci B 7(7):503–514. doi:10.1631/jzus.2006.B0503

    Article  PubMed  PubMed Central  Google Scholar 

  • Khan MI, Trivellini A, Fatma M, Masood A, Francini A, Iqbal N, Ferrante A, Khan NA (2015) Role of ethylene in responses of plants to nitrogen availability. Front Plant Sci 6:927. doi:10.3389/fpls.2015.00927

    CAS  PubMed  PubMed Central  Google Scholar 

  • Khorassani R, Hettwer U, Ratzinger A, Steingrobe B, Karlovsky P, Claassen N (2011) Citramalic acid and salicylic acid in sugar beet root exudates solubilize soil phosphorus. BMC Plant Biol 11:121. doi:10.1186/1471-2229-11-121 1471-2229-11-121 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kikulwe EM, Wesseler J, Falck-Zepeda J (2011) Attitudes, perceptions, and trust. Insights from a consumer survey regarding genetically modified banana in Uganda. Appetite 57(2):401–413. doi:10.1016/j.appet.2011.06.001 S0195-6663(11)00483-1 [pii]

    Article  PubMed  Google Scholar 

  • Kisiel A, Kepczynska E (2016) Medicago truncatula Gaertn. as a model for understanding the mechanism of growth promotion by bacteria from rhizosphere and nodules of alfalfa. Planta. doi:10.1007/s00425-016-2469-7 10.1007/s00425-016-2469-7 [pii]

  • Klironomos JN (2002) Feedback with soil biota contributes to plant rarity and invasiveness in communities. Nature 417(6884):67–70. doi:10.1038/417067a 417067a [pii]

    Article  CAS  PubMed  Google Scholar 

  • Kohli A, Leech M, Vain P, Laurie DA, Christou P (1998) Transgene organization in rice engineered through direct DNA transfer supports a two-phase integration mechanism mediated by the establishment of integration hot spots. Proc Natl Acad Sci U S A 95(12):7203–7208

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Koller R, Robin C, Bonkowski M, Ruess L, Scheu S (2013a) Litter quality as driving factor for plant nutrition via grazing of protozoa on soil microorganisms. FEMS Microbiol Ecol 85(2):241–250. doi:10.1111/1574-6941.12113

    Article  CAS  PubMed  Google Scholar 

  • Koller R, Rodriguez A, Robin C, Scheu S, Bonkowski M (2013b) Protozoa enhance foraging efficiency of arbuscular mycorrhizal fungi for mineral nitrogen from organic matter in soil to the benefit of host plants. New Phytol 199(1):203–211. doi:10.1111/nph.12249

    Article  CAS  PubMed  Google Scholar 

  • Konsoula Z, Liakopoulou-Kyriakides M (2007) Co-production of alpha-amylase and beta-galactosidase by Bacillus subtilis in complex organic substrates. Bioresour Technol 98(1):150–157. doi:10.1016/j.biortech.2005.11.001 S0960-8524(05)00525-0 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Koyama H, Kawamura A, Kihara T, Hara T, Takita E, Shibata D (2000) Overexpression of mitochondrial citrate synthase in Arabidopsis thaliana improved growth on a phosphorus-limited soil. Plant Cell Physiol 41(9):1030–1037

    Article  CAS  PubMed  Google Scholar 

  • Kuiper I, Bloemberg GV, Lugtenberg BJ (2001) Selection of a plant-bacterium pair as a novel tool for rhizostimulation of polycyclic aromatic hydrocarbon-degrading bacteria. Mol Plant Microbe Interact 14(10):1197–1205. doi:10.1094/MPMI.2001.14.10.1197

    Article  CAS  PubMed  Google Scholar 

  • Kuiper I, Lagendijk EL, Bloemberg GV, Lugtenberg BJ (2004) Rhizoremediation: a beneficial plant-microbe interaction. Mol Plant Microbe Interact 17(1):6–15. doi:10.1094/MPMI.2004.17.1.6

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Karan R, Kapoor S, Singh SP, Khare SK (2012) Screening and isolation of halophilic bacteria producing industrially important enzymes. Braz J Microbiol 43(4):1595–1603. doi:10.1590/S1517-838220120004000044 S1517-838220120004000044 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kwak YS, Weller DM (2013) Take-all of wheat and natural disease suppression: a review. Plant Pathol J 29(2):125–135. doi:10.5423/PPJ.SI.07.2012.0112 ppj-29-125 [pii]

    Article  PubMed  PubMed Central  Google Scholar 

  • Labidi S, Jeddi FB, Tisserant B, Yousfi M, Sanaa M, Dalpé Y, Sahraoui AL (2015) Field application of mycorrhizal bio-inoculants affects the mineral uptake of a forage legume (Hedysarum coronarium L.) on a highly calcareous soil. Mycorrhiza 25(4):297–309. doi:10.1007/s00572-014-0609-0

    Article  CAS  PubMed  Google Scholar 

  • Lacey LA, Grzywacz D, Shapiro-Ilan DI, Frutos R, Brownbridge M, Goettel MS (2015) Insect pathogens as biological control agents: back to the future. J Invertebr Pathol 132:1–41. doi:10.1016/j.jip.2015.07.009 S0022-2011(15)00134-2 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Lai MC, Lan EI (2015) Advances in metabolic engineering of Cyanobacteria for photosynthetic biochemical production. Metabolites 5(4):636–658. doi:10.3390/metabo5040636 metabo5040636 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lakshmanan V, Selvaraj G, Bais HP (2014) Functional soil microbiome: belowground solutions to an aboveground problem. Plant Physiol 166(2):689–700. doi:10.1104/pp.114.245811 pp.114.245811 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leaungvutiviroj C, Ruangphisarn P, Hansanimitkul P, Shinkawa H, Sasaki K (2010) Development of a new biofertilizer with a high capacity for N2 fixation, phosphate and potassium solubilization and auxin production. Biosci Biotechnol Biochem 74(5):1098–101. doi:10.1271/bbb.90898[pii]

    Article  CAS  PubMed  Google Scholar 

  • Lee EH, Eo JK, Ka KH, Eom AH (2013) Diversity of arbuscular mycorrhizal fungi and their roles in ecosystems. Mycobiology 41(3):121–125. doi:10.5941/MYCO.2013.41.3.121

    Article  PubMed  PubMed Central  Google Scholar 

  • Lenoir I, Fontaine J, Lounes-Hadj Sahraoui A (2016) Arbuscular mycorrhizal fungal responses to abiotic stresses: a review. Phytochemistry 123:4–15. doi:10.1016/j.phytochem.2016.01.002 S0031-9422(16)30002-4 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Li RX, Cai F, Pang G, Shen QR, Li R, Chen W (2015) Solubilisation of phosphate and micronutrients by Trichoderma harzianum and its relationship with the promotion of tomato plant growth. PLoS One 10(6), e0130081. doi:10.1371/journal.pone.0130081 PONE-D-15-00619 [pii]

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lim SL, Wu TY, Lim PN, Shak KP (2015) The use of vermicompost in organic farming: overview, effects on soil and economics. J Sci Food Agric 95(6):1143–1156. doi:10.1002/jsfa.6849

    Article  CAS  PubMed  Google Scholar 

  • Lojkova L, Vranova V, Rejsek K, Formanek P (2014) Natural occurrence of enantiomers of organic compounds versus phytoremediations: should research on phytoremediations be revisited? A mini-review. Chirality 26(1):1–20. doi:10.1002/chir.22255

    Article  CAS  PubMed  Google Scholar 

  • Lu YF, Lu M, Peng F, Wan Y, Liao MH (2014) Remediation of polychlorinated biphenyl-contaminated soil by using a combination of ryegrass, arbuscular mycorrhizal fungi and earthworms. Chemosphere 106:44–50. doi:10.1016/j.chemosphere.2013.12.089 S0045-6535(14)00026-5 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Magalhaes JV, Liu J, Guimaraes CT, Lana UG, Alves VM, Wang YH, Schaffert RE, Hoekenga OA, Pineros MA, Shaff JE, Klein PE, Carneiro NP, Coelho CM, Trick HN, Kochian LV (2007) A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sorghum. Nat Genet 39(9):1156–1161. doi:10.1038/ng2074 ng2074 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Mark G, Morrissey JP, Higgins P, O’Gara F (2006) Molecular-based strategies to exploit Pseudomonas biocontrol strains for environmental biotechnology applications. FEMS Microbiol Ecol 56(2):167–177. doi:10.1111/j.1574-6941.2006.00056.x FEM056 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Marsalek B, Simek M (1992) Abscisic acid and its synthetic analog in relation to growth and nitrogenase activity of Azotobacter chroococcum and Nostoc muscorum. Folia Microbiol (Praha) 37(2):159–160

    Article  CAS  Google Scholar 

  • Marschner H (1995) Mineral nutrition of higher plants, 2nd edn. Academic, London

    Google Scholar 

  • Mayak S, Tirosh T, Glick BR (2004) Plant growth-promoting bacteria confer resistance in tomato plants to salt stress. Plant Physiol Biochem 42(6):565–572. doi:10.1016/j.plaphy.2004.05.009 S0981-9428(04)00076-2 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Mazzola M (2002) Mechanisms of natural soil suppressiveness to soilborne diseases. Antonie Van Leeuwenhoek 81(1–4):557–564

    Article  CAS  PubMed  Google Scholar 

  • Mazzola M (2007) Manipulation of rhizosphere bacterial communities to induce suppressive soils. J Nematol 39(3):213–220

    PubMed  PubMed Central  Google Scholar 

  • Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JH, Piceno YM, DeSantis TZ, Andersen GL, Bakker PA, Raaijmakers JM (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332(6033):1097–1100. doi:10.1126/science.1203980.science.1203980 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37(5):634–663. doi:10.1111/1574-6976.12028

    Article  CAS  PubMed  Google Scholar 

  • Micallef SA, Channer S, Shiaris MP, Colon-Carmona A (2009) Plant age and genotype impact the progression of bacterial community succession in the Arabidopsis rhizosphere. Plant Signal Behav 4(8):777–780. doi:10.1093/jxb/erp053 9229 [pii]

    Article  PubMed  PubMed Central  Google Scholar 

  • Mishra V, Gupta A, Kaur P, Singh S, Singh N, Gehlot P, Singh J (2015) Synergistic effects of Arbuscular mycorrhizal fungi and plant growth promoting rhizobacteria in bioremediation of iron contaminated soils. Int J Phytoremediation. doi:10.1080/15226514.2015.1131231

    Google Scholar 

  • Montes-Borrego M, Metsis M, Landa BB (2014) Arbuscular mycorrhizal fungi associated with the olive crop across the Andalusian landscape: factors driving community differentiation. PLoS One 9(5), e96397. doi:10.1371/journal.pone.0096397 PONE-D-13-49105 [pii]

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Montesinos-Navarro A, Segarra-Moragues JG, Valiente-Banuet A, Verdu M (2012) Plant facilitation occurs between species differing in their associated arbuscular mycorrhizal fungi. New Phytol 196(3):835–844. doi:10.1111/j.1469-8137.2012.04290.x

    Article  CAS  PubMed  Google Scholar 

  • Mougel C, Offre P, Ranjard L, Corberand T, Gamalero E, Robin C, Lemanceau P (2006) Dynamic of the genetic structure of bacterial and fungal communities at different developmental stages of Medicago truncatula Gaertn. cv. Jemalong line J5. New Phytol 170(1):165–175. doi:10.1111/j.1469-8137.2006.01650.x NPH1650 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Nakaya M, Tsukaya H, Murakami N, Kato M (2002) Brassinosteroids control the proliferation of leaf cells of Arabidopsis thaliana. Plant Cell Physiol 43(2):239–244

    Article  CAS  PubMed  Google Scholar 

  • Narasimhan K, Basheer C, Bajic VB, Swarup S (2003) Enhancement of plant-microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls. Plant Physiol 132(1):146–153. doi:10.1104/pp.102.016295

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Neilands JB (1995) Siderophores: structure and function of microbial iron transport compounds. J Biol Chem 270(45):26723–26726

    Article  CAS  PubMed  Google Scholar 

  • Newman LA, Reynolds CM (2004) Phytodegradation of organic compounds. Curr Opin Biotechnol 15(3):225–230. doi:10.1016/j.copbio.2004.04.006 S0958166904000588 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Nunan N, Daniell TJ, Singh BK, Papert A, McNicol JW, Prosser JI (2005) Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques. Appl Environ Microbiol 71(11):6784–6792. doi:71/11/6784 [pii] 10.1128/AEM.71.11.6784-6792.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oger P, Petit A, Dessaux Y (1997) Genetically engineered plants producing opines alter their biological environment. Nat Biotechnol 15(4):369–372. doi:10.1038/nbt0497-369

    Article  CAS  PubMed  Google Scholar 

  • Onofre-Lemus J, Hernandez-Lucas I, Girard L, Caballero-Mellado J (2009) ACC (1-aminocyclopropane-1-carboxylate) deaminase activity, a widespread trait in Burkholderia species, and its growth-promoting effect on tomato plants. Appl Environ Microbiol 75(20):6581–6590. doi:10.1128/AEM.01240-09 AEM.01240-09 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Owen SM, Clark S, Pompe M, Semple KT (2007) Biogenic volatile organic compounds as potential carbon sources for microbial communities in soil from the rhizosphere of Populus tremula. FEMS Microbiol Lett 268(1):34–39. doi:10.1111/j.1574-6968.2006.00602.x FML602 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Paulin MM, Novinscak A, St-Arnaud M, Goyer C, DeCoste NJ, Prive JP, Owen J, Filion M (2009) Transcriptional activity of antifungal metabolite-encoding genes phlD and hcnBC in Pseudomonas spp. using qRT-PCR. FEMS Microbiol Ecol 68(2):212–222. doi:10.1111/j.1574-6941.2009.00669.x FEM669 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Pence NS, Larsen PB, Ebbs SD, Letham DL, Lasat MM, Garvin DF, Eide D, Kochian LV (2000) The molecular physiology of heavy metal transport in the Zn/Cd hyperaccumulator Thlaspi caerulescens. Proc Natl Acad Sci U S A 97(9):4956–4960, 97/9/4956 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Perez-Alfocea F, Ghanem ME, Gomez-Cadenas A, Dodd IC (2011) Omics of root-to-shoot signaling under salt stress and water deficit. OMICS 15(12):893–901. doi:10.1089/omi.2011.0092

    Article  CAS  PubMed  Google Scholar 

  • Perez-Montano F, Alias-Villegas C, Bellogin RA, del Cerro P, Espuny MR, Jimenez-Guerrero I, Lopez-Baena FJ, Ollero FJ, Cubo T (2014) Plant growth promotion in cereal and leguminous agricultural important plants: from microorganism capacities to crop production. Microbiol Res 169(5–6):325–336. doi:10.1016/j.micres.2013.09.011 S0944-5013(13)00164-X [pii]

    Article  CAS  PubMed  Google Scholar 

  • Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH (2013) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11(11):789–799. doi:10.1038/nrmicro3109 mnrmicro3109 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Pilon-Smits E (2005) Phytoremediation. Annu Rev Plant Biol 56:15–39. doi:10.1146/annurev.arplant.56.032604.144214

    Article  CAS  PubMed  Google Scholar 

  • Pilon-Smits EA, Hwang S, Mel Lytle C, Zhu Y, Tai JC, Bravo RC, Chen Y, Leustek T, Terry N (1999) Overexpression of ATP sulfurylase in indian mustard leads to increased selenate uptake, reduction, and tolerance. Plant Physiol 119(1):123–132

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ping L, Boland W (2004) Signals from the underground: bacterial volatiles promote growth in Arabidopsis. Trends Plant Sci 9(6):263–266. doi:10.1016/j.tplants.2004.04.008 S1360-1385(04)00105-0 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Plett D, Safwat G, Gilliham M, Skrumsager Moller I, Roy S, Shirley N, Jacobs A, Johnson A, Tester M (2010) Improved salinity tolerance of rice through cell type-specific expression of AtHKT1;1. PLoS One 5(9), e12571. doi:10.1371/journal.pone.0012571

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Porras-Soriano A, Soriano-Martin ML, Porras-Piedra A, Azcon R (2009) Arbuscular mycorrhizal fungi increased growth, nutrient uptake and tolerance to salinity in olive trees under nursery conditions. J Plant Physiol 166(13):1350–1359. doi:10.1016/j.jplph.2009.02.010 S0176-1617(09)00080-7 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Powell PE, Szaniszlo PJ, Reid CP (1983) Confirmation of occurrence of hydroxamate siderophores in soil by a novel Escherichia coli bioassay. Appl Environ Microbiol 46(5):1080–1083

    CAS  PubMed  PubMed Central  Google Scholar 

  • Quiza L, St-Arnaud M, Yergeau E (2015) Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering. Front Plant Sci 6:507. doi:10.3389/fpls.2015.00507

    Article  PubMed  PubMed Central  Google Scholar 

  • Rasmann S, Kollner TG, Degenhardt J, Hiltpold I, Toepfer S, Kuhlmann U, Gershenzon J, Turlings TC (2005) Recruitment of entomopathogenic nematodes by insect-damaged maize roots. Nature 434(7034):732–737. doi:nature03451 [pii] 10.1038/nature03451

    Article  CAS  PubMed  Google Scholar 

  • Rengel Z, Marschner P (2005) Nutrient availability and management in the rhizosphere: exploiting genotypic differences. New Phytol 168(2):305–312. doi:10.1111/j.1469-8137.2005.01558.x NPH1558 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Reynolds HL, Smith AA, Farmer JR (2014) Think globally, research locally: paradigms and place in agroecological research. Am J Bot 101(10):1631–1639. doi:10.3732/ajb.1400146 ajb.1400146 [pii]

    Article  PubMed  Google Scholar 

  • Rillig MC, Mummey DL (2006) Mycorrhizas and soil structure. New Phytol 171(1):41–53. doi:10.1111/j.1469-8137.2006.01750.x NPH1750 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Rivoal J, Hanson AD (1994) Metabolic control of anaerobic glycolysis overexpression of lactate dehydrogenase in transgenic tomato roots supports the Davies-Roberts hypothesis and points to a critical role for lactate secretion. Plant Physiol 106:1179–1185

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rogers EE, Eide DJ, Guerinot ML (2000) Altered selectivity in an Arabidopsis metal transporter. Proc Natl Acad Sci U S A 97(22):12356–12360. doi:10.1073/pnas.210214197 210214197 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roose T, Schnepf A (2008) Mathematical models of plant-soil interaction. Philos Trans A Math Phys Eng Sci 366(1885):4597–4611. doi:10.1098/rsta.2008.0198 2RT9X62Q81L87186 [pii]

    Article  PubMed  Google Scholar 

  • Rugh CL, Wilde HD, Stack NM, Thompson DM, Summers AO, Meagher RB (1996) Mercuric ion reduction and resistance in transgenic Arabidopsis thaliana plants expressing a modified bacterial merA gene. Proc Natl Acad Sci U S A 93(8):3182–3187

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ryan P, Dessaux Y, Thomashow L, Weller D (2009) Rhizosphere engineering and management for sustainable agriculture. Plant Soil 321:363–383. doi:10.1007/s11104-009-0001-6

    Article  CAS  Google Scholar 

  • Savka MA, Dessaux Y, Oger P, Rossbach S (2002) Engineering bacterial competitiveness and persistence in the phytosphere. Mol Plant Microbe Interact 15(9):866–874. doi:10.1094/MPMI.2002.15.9.866

    Article  CAS  PubMed  Google Scholar 

  • Schachtman DP, Shin R (2007) Nutrient sensing and signaling: NPKS. Annu Rev Plant Biol 58:47–69. doi:10.1146/annurev.arplant.58.032806.103750

    Article  CAS  PubMed  Google Scholar 

  • Schouteden N, De Waele D, Panis B, Vos CM (2015) Arbuscular mycorrhizal fungi for the biocontrol of plant-parasitic nematodes: a review of the mechanisms involved. Front Microbiol 6:1280. doi:10.3389/fmicb.2015.01280

    Article  PubMed  PubMed Central  Google Scholar 

  • Schultze M, Kondorosi A (1998) Regulation of symbiotic root nodule development. Annu Rev Genet 32:33–57. doi:10.1146/annurev.genet.32.1.33

    Article  CAS  PubMed  Google Scholar 

  • Shapira R, Ordentlich A, Chet I, Oppenheim AB (1989) Control of plant diseases by chitinase expressed from cloned DNA in Escherichia coli. Phytopathology 79:1246–1249

    Article  CAS  Google Scholar 

  • Sharma SB, Sayyed RZ, Trivedi MH, Gobi TA (2013) Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils. SpringerPlus 2:587. doi:10.1186/2193-1801-2-587 1439 [pii]

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shaw LJ, Morris P, Hooker JE (2006) Perception and modification of plant flavonoid signals by rhizosphere microorganisms. Environ Microbiol 8(11):1867–1880. doi:10.1111/j.1462-2920.2006.01141.x EMI1141 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Shrivastava P, Kumar R (2015) Soil salinity: a serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation. Saudi J Biol Sci 22(2):123–131. doi:10.1016/j.sjbs.2014.12.001 S1319-562X(14)00171-5 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Silva JP, Mussatto SI, Roberto IC (2010) The influence of initial xylose concentration, agitation, and aeration on ethanol production by Pichia stipitis from rice straw hemicellulosic hydrolysate. Appl Biochem Biotechnol 162(5):1306–1315. doi:10.1007/s12010-009-8867-6

    Article  CAS  PubMed  Google Scholar 

  • Singh S, Grover A, Nasim M (2016) Biofuel potential of plants transformed genetically with NAC family genes. Front Plant Sci 7:22. doi:10.3389/fpls.2016.00022

    PubMed  PubMed Central  Google Scholar 

  • Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, Roskot N, Heuer H, Berg G (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67(10):4742–4751

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sokarda Slavić M, Pesic M, Vujcic Z, Bozic N (2016) Overcoming hydrolysis of raw corn starch under industrial conditions with Bacillus licheniformis ATCC 9945a alpha-amylase. Appl Microbiol Biotechnol 100(6):2709–2719. doi:10.1007/s00253-015-7101-4 10.1007/s00253-015-7101-4 [pii]

  • Spaepen S, Versees W, Gocke D, Pohl M, Steyaert J, Vanderleyden J (2007) Characterization of phenylpyruvate decarboxylase, involved in auxin production of Azospirillum brasilense. J Bacteriol 189(21):7626–7633. doi:10.1128/JB.00830-07 JB.00830-07 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spiers AS, Wade HE (1976) Bacterial glutaminase in treatment of acute leukaemia. Br Med J 1(6021):1317–1319

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Taghavi S, Barac T, Greenberg B, Borremans B, Vangronsveld J, van der Lelie D (2005) Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene. Appl Environ Microbiol 71(12):8500–8505. doi:71/12/8500 [pii] 10.1128/AEM.71.12.8500-8505.2005

  • Tesfaye M, Temple SJ, Allan DL, Vance CP, Samac DA (2001) Overexpression of malate dehydrogenase in transgenic alfalfa enhances organic acid synthesis and confers tolerance to aluminum. Plant Physiol 127(4):1836–1844

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thomas JC, Davies EC, Malick FK, Endreszl C, Williams CR, Abbas M, Petrella S, Swisher K, Perron M, Edwards R, Osenkowski P, Urbanczyk N, Wiesend WN, Murray KS (2003) Yeast metallothionein in transgenic tobacco promotes copper uptake from contaminated soils. Biotechnol Prog 19(2):273–280. doi:10.1021/bp025623q

    Article  CAS  PubMed  Google Scholar 

  • Timms-Wilson TM, Ellis RJ, Renwick A, Rhodes DJ, Mavrodi DV, Weller DM, Thomashow LS, Bailey MJ (2000) Chromosomal insertion of phenazine-1-carboxylic acid biosynthetic pathway enhances efficacy of damping-off disease control by Pseudomonas fluorescens. Mol Plant Microbe Interact 13(12):1293–1300. doi:10.1094/MPMI.2000.13.12.1293

    Article  CAS  PubMed  Google Scholar 

  • Timmusk S, Wagner EG (1999) The plant-growth-promoting rhizobacterium Paenibacillus polymyxa induces changes in Arabidopsis thaliana gene expression: a possible connection between biotic and abiotic stress responses. Mol Plant Microbe Interact 12(11):951–959. doi:10.1094/MPMI.1999.12.11.951

    Article  CAS  PubMed  Google Scholar 

  • Tisserant E, Malbreil M, Kuo A, Kohler A, Symeonidi A, Balestrini R, Charron P, Duensing N, Frei dit Frey N, Gianinazzi-Pearson V, Gilbert LB, Handa Y, Herr JR, Hijri M, Koul R, Kawaguchi M, Krajinski F, Lammers PJ, Masclaux FG, Murat C, Morin E, Ndikumana S, Pagni M, Petitpierre D, Requena N, Rosikiewicz P, Riley R, Saito K, San Clemente H, Shapiro H, van Tuinen D, Becard G, Bonfante P, Paszkowski U, Shachar-Hill YY, Tuskan GA, Young JP, Sanders IR, Henrissat B, Rensing SA, Grigoriev IV, Corradi N, Roux C, Martin F (2013) Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Natl Acad Sci U S A 110(50):20117–20122. doi:10.1073/pnas.1313452110 1313452110 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trabelsi D, Mhamdi R (2013) Microbial inoculants and their impact on soil microbial communities: a review. Biomed Res Int 2013:863240. doi:10.1155/2013/863240

    Article  PubMed  PubMed Central  Google Scholar 

  • Underkofler LA, Barton RR, Rennert SS (1958) Production of microbial enzymes and their applications. Appl Microbiol 6(3):212–221

    CAS  PubMed  PubMed Central  Google Scholar 

  • van Dam NM, Bouwmeester HJ (2016) Metabolomics in the rhizosphere: tapping into belowground chemical communication. Trends Plant Sci 21(3):256–265. doi:10.1016/j.tplants.2016.01.008 S1360-1385(16)00009-1 [pii]

    Article  PubMed  CAS  Google Scholar 

  • van der Heijden MG, Streitwolf-Engel R, Riedl R, Siegrist S, Neudecker A, Ineichen K, Boller T, Wiemken A, Sanders IR (2006) The mycorrhizal contribution to plant productivity, plant nutrition and soil structure in experimental grassland. New Phytol 172(4):739–752. doi:10.1111/j.1469-8137.2006.01862.x NPH1862 [pii]

    Article  PubMed  Google Scholar 

  • van der Zaal BJ, Neuteboom LW, Pinas JE, Chardonnens AN, Schat H, Verkleij JA, Hooykaas PJ (1999) Overexpression of a novel Arabidopsis gene related to putative zinc-transporter genes from animals can lead to enhanced zinc resistance and accumulation. Plant Physiol 119(3):1047–1055

    Article  PubMed  PubMed Central  Google Scholar 

  • Vivas A, Voros I, Biro B, Campos E, Barea JM, Azcon R (2003) Symbiotic efficiency of autochthonous arbuscular mycorrhizal fungus (G. mosseae) and Brevibacillus sp. isolated from cadmium polluted soil under increasing cadmium levels. Environ Pollut 126(2):179–189, S0269749103003001957 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Walder F, Boller T, Wiemken A, Courty PE (2016) Regulation of plants’ phosphate uptake in common mycorrhizal networks: role of intraradical fungal phosphate transporters. Plant Signal Behav 11(2), e1131372. doi:10.1080/15592324.2015.1131372

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Walker TS, Bais HP, Deziel E, Schweizer HP, Rahme LG, Fall R, Vivanco JM (2004) Pseudomonas aeruginosa-plant root interactions. Pathogenicity, biofilm formation, and root exudation. Plant Physiol 134(1):320–331. doi:10.1104/pp.103.027888 pp.103.027888 [pii]

  • Walton BT, Anderson TA (1990) Microbial degradation of trichloroethylene in the rhizosphere: potential application to biological remediation of waste sites. Appl Environ Microbiol 56(4):1012–1016

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang C, Knill E, Glick BR, Defago G (2000) Effect of transferring 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase genes into Pseudomonas fluorescens strain CHA0 and its gacA derivative CHA96 on their growth-promoting and disease-suppressive capacities. Can J Microbiol 46(10):898–907

    Article  CAS  PubMed  Google Scholar 

  • Wang P, Bi S, Wang S, Ding Q (2006) Variation of wheat root exudates under aluminum stress. J Agric Food Chem 54(26):10040–10046. doi:10.1021/jf061249o

    Article  CAS  PubMed  Google Scholar 

  • Wang D, Yang S, Tang F, Zhu H (2012) Symbiosis specificity in the legume: rhizobial mutualism. Cell Microbiol 14(3):334–342. doi:10.1111/j.1462-5822.2011.01736.x

    Article  PubMed  CAS  Google Scholar 

  • Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C, Qiu JL (2014) Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol 32(9):947–951. doi:10.1038/nbt.2969 nbt.2969 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Feng J, Jia W, Chang S, Li S, Li Y (2015) Lignin engineering through laccase modification: a promising field for energy plant improvement. Biotechnol Biofuels 15(8):145. doi:10.1186/s13068-015-0331-y

    Article  CAS  Google Scholar 

  • Wang J, Li Q, Mao X, Li A, Jing R (2016a) Wheat transcription factor TaAREB3 participates in drought and freezing tolerances in Arabidopsis. Int J Biol Sci 12(2):257–269. doi:10.7150/ijbs.13538 ijbsv12p0257 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang X, Wu D, Yang Q, Zeng J, Jin G, Chen ZH, Zhang G, Dai F (2016b) Identification of mild freezing shock response pathways in barley based on transcriptome profiling. Front Plant Sci 7:106. doi:10.3389/fpls.2016.00106

    PubMed  PubMed Central  Google Scholar 

  • Watt M, Evans JR (1999) Linking development and determinacy with organic acid efflux from proteoid roots of white lupin grown with low phosphorus and ambient or elevated atmospheric CO2 concentration. Plant Physiol 120(3):705–716

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wenke K, Kai M, Piechulla B (2010) Belowground volatiles facilitate interactions between plant roots and soil organisms. Planta 231(3):499–506. doi:10.1007/s00425-009-1076-2

    Article  CAS  PubMed  Google Scholar 

  • Wentzell AM, Kliebenstein DJ (2008) Genotype, age, tissue, and environment regulate the structural outcome of glucosinolate activation. Plant Physiol 147(1):415–428. doi:10.1104/pp.107.115279 pp.107.115279 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weyens N, Thijs S, Popek R, Witters N, Przybysz A, Espenshade J, Gawronska H, Vangronsveld J, Gawronski SW (2015) The role of plant-microbe interactions and their exploitation for phytoremediation of air pollutants. Int J Mol Sci 16(10):25576–25604. doi:10.3390/ijms161025576 ijms161025576 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xiao C, Janssens IA, Liu P, Zhou Z, Sun OJ (2007) Irrigation and enhanced soil carbon input effects on below-ground carbon cycling in semiarid temperate grasslands. New Phytol 174(4):835–846. doi:10.1111/j.1469-8137.2007.02054.x NPH2054 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Xun F, Xie B, Liu S, Guo C (2015) Effect of plant growth-promoting bacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) inoculation on oats in saline-alkali soil contaminated by petroleum to enhance phytoremediation. Environ Sci Pollut Res Int 22(1):598–608. doi:10.1007/s11356-014-3396-4

    Article  CAS  PubMed  Google Scholar 

  • Yang H, Knapp J, Koirala P, Rajagopal D, Peer WA, Silbart LK, Murphy A, Gaxiola RA (2007) Enhanced phosphorus nutrition in monocots and dicots over-expressing a phosphorus-responsive type I H+−pyrophosphatase. Plant Biotechnol J 5(6):735–745. doi:10.1111/j.1467-7652.2007.00281.x PBI281 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Yang J, Kloepper JW, Ryu CM (2009) Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci 14(1):1–4. doi:10.1016/j.tplants.2008.10.004 S1360-1385(08)00290-2 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Yang Z, Chen H, Tang W, Hua H, Lin Y (2011) Development and characterisation of transgenic rice expressing two Bacillus thuringiensis genes. Pest Manag Sci 67(4):414–422. doi:10.1002/ps.2079

    Article  CAS  PubMed  Google Scholar 

  • Yang Y, Liang Y, Ghosh A, Song Y, Chen H, Tang M (2015) Assessment of arbuscular mycorrhizal fungi status and heavy metal accumulation characteristics of tree species in a lead-zinc mine area: potential applications for phytoremediation. Environ Sci Pollut Res Int 22(17):13179–13193. doi:10.1007/s11356-015-4521-8

    Article  CAS  PubMed  Google Scholar 

  • Yergeau E, Sanschagrin S, Maynard C, St-Arnaud M, Greer CW (2014) Microbial expression profiles in the rhizosphere of willows depend on soil contamination. ISME J 8(2):344–358. doi:10.1038/ismej.2013.163 ismej2013163 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Zaitsev S, Spitzer D, Murciano JC, Ding BS, Tliba S, Kowalska MA, Marcos-Contreras OA, Kuo A, Stepanova V, Atkinson JP, Poncz M, Cines DB, Muzykantov VR (2010) Sustained thromboprophylaxis mediated by an RBC-targeted pro-urokinase zymogen activated at the site of clot formation. Blood 115(25):5241–5248. doi:10.1182/blood-2010-01-261610 blood-2010-01-261610 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang H, Kim MS, Sun Y, Dowd SE, Shi H, Pare PW (2008) Soil bacteria confer plant salt tolerance by tissue-specific regulation of the sodium transporter HKT1. Mol Plant Microbe Interact 21(6):737–744. doi:10.1094/MPMI-21-6-0737

    Article  PubMed  CAS  Google Scholar 

  • Zhang Y, Ruyter-Spira C, Bouwmeester HJ (2015a) Engineering the plant rhizosphere. Curr Opin Biotechnol 32:136–142. doi:10.1016/j.copbio.2014.12.006 S0958-1669(14)00221-3 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Zhang T, Chaturvedi V, Chaturvedi S (2015b) Novel Trichoderma polysporum strain for the biocontrol of Pseudogymnoascus destructans, the fungal etiologic agent of bat white nose syndrome. PLoS One 10(10), e0141316. doi:10.1371/journal.pone.0141316 PONE-D-14-51371 [pii]

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang F, Ge H, Guo N, Wang Y, Chen L, Ji X, Li C (2016) Biocontrol potential of Trichoderma harzianum isolate T-aloe against Sclerotinia sclerotiorum in soybean. Plant Physiol Biochem 100:64–74. doi:10.1016/j.plaphy.2015.12.017 S0981-9428(15)30195-9 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Zhu YG, Rosen BP (2009) Perspectives for genetic engineering for the phytoremediation of arsenic-contaminated environments: from imagination to reality? Curr Opin Biotechnol 20(2):220–224. doi:10.1016/j.copbio.2009.02.011 S0958-1669(09)00024-X [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu YL, Pilon-Smits EA, Tarun AS, Weber SU, Jouanin L, Terry N (1999) Cadmium tolerance and accumulation in Indian mustard is enhanced by overexpressing gamma-glutamylcysteine synthetase. Plant Physiol 121(4):1169–1178

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu JR, Zhou H, Pan YB, Lu X (2014) Genetic variability among the chloroplast genomes of sugarcane (Saccharum spp) and its wild progenitor species Saccharum spontaneum L. Genet Mol Res 13(2):3037–3047. doi:10.4238/2014.January.24.3 gmr3004 [pii]

    Article  PubMed  CAS  Google Scholar 

  • Zhuang X, Chen J, Shim H, Bai Z (2007) New advances in plant growth-promoting rhizobacteria for bioremediation. Environ Int 33(3):406–413. doi:10.1016/j.envint.2006.12.005 S0160-4120(07)00003-7 [pii]

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Sanghamitra Sengupta .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Nature Singapore Pte Ltd.

About this chapter

Cite this chapter

Haldar, S., Sengupta, S. (2016). Microbial Ecology at Rhizosphere: Bioengineering and Future Prospective. In: Choudhary, D., Varma, A., Tuteja, N. (eds) Plant-Microbe Interaction: An Approach to Sustainable Agriculture. Springer, Singapore. https://doi.org/10.1007/978-981-10-2854-0_4

Download citation

Publish with us

Policies and ethics