Skip to main content

Structure and Function of Rhizobiome

  • Chapter
  • First Online:
Plant Microbe Symbiosis

Abstract

Plant roots can select for certain microbial species from soil microbiome and interact with them. As a consequence, the structure (or composition) of root-associated microbiome (here after referred to as rhizobiome) is significantly different from that of soil microbiome. Although, it is widely accepted that rhizobiome positively influences plant growth and health, relatively less is known about its complete structure and function. High-resolution and large-scale studies are essential to unravel the structure and function of rhizobiome. Moreover, identification of “core rhizobiome” or “heritable rhizobiome” of different crop plants is a top priority for accelerating translational research toward improving crop productivity in an environmentally sustainable manner. Here, I summarize information about the structure and function of various rhizobiomes that is recently made available using culture-independent technologies. I also review the factors that regulate composition of rhizobiome. Specifically, I discuss the role of root exudates and plant immune system in shaping rhizobiome.

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

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Akiyama K, Matsuzaki K, Hayashi H (2005) Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi. Nature 435:824–827

    Article  CAS  PubMed  Google Scholar 

  • Badri DV, Vivanco JM (2009) Regulation and function of root exudates. Plant Cell Environ 32:666–681

    Article  CAS  PubMed  Google Scholar 

  • Badri DV, Loyola-Vargas VM, Du J, Stermitz FR, Broeckling CD, Iglesias-Andreu L, Vivanco JM (2008) Transcriptome analysis of Arabidopsis roots treated with signaling compounds: a focus on signal transduction, metabolic regulation and secretion. New Phytol 179:209–223

    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 20:642–650

    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 288:4502–4512

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Baetz U, Martinoia E (2014) Root exudates: the hidden part of plant defense. Trends Plant Sci 19:90–98

    Article  CAS  PubMed  Google Scholar 

  • Bai Y, Müller DB, Srinivas G, Garrido-Oter R, Potthoff E, Rott M, Dombrowski N, Münch PC, Spaepen S, Remus-Emsermann M, Hüttel B, McHardy AC, Vorholt JA, Schulze-Lefert P (2015) Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528:364–369

    Article  CAS  PubMed  Google Scholar 

  • Bais HP, Walker TS, Schweizer HP, Vivanco JM (2002) Root specific elicitation and antimicrobial activity of rosmarinic acid in hairy root cultures of sweet basil (Ocimum basilicum L.). Plant Physiol Biochem 40:983–995

    Article  CAS  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

    Article  CAS  PubMed  Google Scholar 

  • Barnett SJ, Roget DK, Ryder MH (2006) Suppression of Rhizoctonia solani AG-8 induced disease on wheat by the interaction between Pantoea, Exiguobacterium, and Microbacteria. Aust J Soil Res 44:331–342

    Article  Google Scholar 

  • Barriuso J, Solano BR (2008) Ecology, genetic diversity and screening strategies of plant growth promoting rhizobacteria (PGPR). J. Plant Nutrition:1–17. https://doi.org/10.1002/9783527621989

  • Battey NH, Blackbourn HD (1993) The control of exocitosis in plant cells. New Phytol 125:307–308

    Article  CAS  PubMed  Google Scholar 

  • Beauregard PB, Chai YR, Vlamakis H, Losick R, Kolter R (2013) Bacillus subtilis biofilm induction by plant polysaccharides. Proc Natl Acad Sci U S A 110:1621–1630

    Article  Google Scholar 

  • Benítez MS, Gardener BB (2009) Linking sequence to function in soil bacteria: sequence-directed isolation of novel bacteria contributing to soilborne plant disease suppression. Appl Environ Microbiol 75:915–924

    Article  CAS  PubMed  Google Scholar 

  • Berendsen R, Pieterse C, Bakker P (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486

    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 68:1–13

    Article  CAS  PubMed  Google Scholar 

  • Berg G, Grube M, Schloter M, Smalla K (2014) Unraveling the plant microbiome: looking back and future perspectives. Front Microbiol 5:148

    PubMed  PubMed Central  Google Scholar 

  • Bisseling T, Dangl JL, Schulze-Lefert P (2009) Next-generation communication. Science 324:691

    Article  CAS  PubMed  Google Scholar 

  • Bressan M, Roncato MA, Bellvert F, Comte G, Haichar FZ, Achouak W, Berge O (2009) Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots. ISME J 3:1243–1257

    Article  CAS  PubMed  Google Scholar 

  • Brigham LA, Michaels PJ, Flores HE (1999) Cell-specific production and antimicrobial activity of naphthoquinones in roots of Lithospermum erythrorhizon. Plant Physiol 119:417–428

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brodie EL, Desantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL, Hazen TC, Richardson PM, Herman DJ, Tokunaga TK, Wan JM, Firestone MK (2006) Application of a high density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72:6288–6298

    Article  CAS  PubMed  PubMed Central  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 488:91–95

    Article  CAS  PubMed  Google Scholar 

  • Bulgarelli D, Garrido-Oter R, Münch PC, Weiman A, Dröge J, Pan Y, McHardy AC, Schulze-Lefert P (2015) Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17(3):392–403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cai T, Cai W, Zhang J, Zheng H, Tsou AM, Xiao L, Zhong Z, Zhu J (2009) Host legume-exuded antimetabolites optimize the symbiotic rhizosphere. Mol Microbiol 73:507–517

    Article  CAS  PubMed  Google Scholar 

  • Callaway RM, Aschehoug ET (2000) Invasive plants versus their new and old neighbors: a mechanism for exotic invasion. Science 90:521–523

    Article  Google Scholar 

  • Chaparro J, Sheflin A, Manter D, Vivanco J (2012) Manipulating the soil microbiome to increase soil health and plant fertility. Biol Fertil Soils 48:489–499

    Article  Google Scholar 

  • Chaparro JM, Badri DV, Vivanco JM (2014) Rhizosphere microbiome assemblage is affected by plant development. ISME J 8:790–803

    Article  CAS  PubMed  Google Scholar 

  • Chen Y, Cao S, Chai Y, Clardy J, Kolter R, Guo JH, Losick R (2012) A Bacillus subtilis sensor kinase involved in triggering biofilm formation on the roots of tomato plants. Mol Microbiol 85(3):418–430

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Czarnota MA, Paul RN, Weston LA, Duke SO (2003) Anatomy of sorgoleone-secreting root hairs of Sorghum species. Int J Plant Sci 164:861–866

    Article  Google Scholar 

  • Dakora FD, Phillips DA (2002) Root exudates as mediators of mineral acquisition in low-nutrient environments. Plant Soil 245:35–47

    Article  CAS  Google Scholar 

  • De Angelis KM, Brodie EL, De Santis TZ, Andersen GL, Lindow SE, Firestone MK (2009) Selective progressive response of soil microbial community to wild oat roots. ISME J 3:168–178

    Article  CAS  Google Scholar 

  • de Souza RS, Okura VK, Armanhi JS, Jorrín B, Lozano N, da Silva MJ, González-Guerrero M, de Araújo LM, Verza NC, Bagheri HC, Imperial J, Arruda P (2016) Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome. Sci Rep 6:28774

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Weert S, Vermeiren H, Mulders IHM, Kuiper I, Hendrickx N, Bloemberg GV, Vanderleyden J, De Mot R, Lugtenberg BJJ (2002) Flagella-driven chemotaxis towards exudate components is an important trait for tomato root colonization by Pseudomonas fluorescens. Mol Plant-Microbe Interact 15:1173–1180

    Article  PubMed  Google Scholar 

  • Demoling F, Figueroa D, Baath E (2007) Comparison of factors limiting bacterial growth in different soils. Soil Biol Biochem 39:2485–2495

    Article  CAS  Google Scholar 

  • Duijff BJ, Recorbet G, Bakker PAHM, Loper JE, Lemanceau P (1999) Microbial antagonism at the root level is involved in the suppression of Fusarium wilt by the combination of nonpathogenic Fusarium oxysporum Fo47 and Pseudomonas putida WCS358. Phytopathology 89:1073–1079

    Article  CAS  PubMed  Google Scholar 

  • Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V (2015) Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci U S A 112:911–920

    Article  CAS  Google Scholar 

  • Flores HE, Vivanco JM, Loyola-Vargas VM (1999) “Radicle” biochemistry: the biology of root-specific metabolism. Trends Plant Sci 4:220–226

    Article  CAS  PubMed  Google Scholar 

  • Gilbert JA, Jannson JK, Knight R (2014) The Earth microbiome project: successes and aspirations. BMC Biol 12:69

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Glick BR (2005) Modulation of plant ethylene levels by the bacterial enzyme ACC deaminase. FEMS Microbiol Lett 251:1–7

    Article  CAS  PubMed  Google Scholar 

  • Gutierrez-Manero FJ, Ramos-Solano B, Probanza A, Mehouachi J, Tadeo FR, Talon M (2001) The plant-growth-promoting rhizobacteria Bacillus pumilus and Bacillus licheniformis produce high amounts of physiologically active gibberellins. Physiol Plant 111:206–211

    Article  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Haichar FZ, Marol C, Berge O, Rangel-Castro JI, Prosser JI, Balesdent J, Heulin T, Achouak W (2008) Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2:1221–1230

    Article  CAS  PubMed  Google Scholar 

  • Haney CH, Samuel BS, Bush J, Ausubel FM (2015) Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nat Plants 1(6):15051

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hardoim PR, Hardoim CCP, van Overbeek LS, van Elsas JD (2012) Dynamics of seed-borne rice endophytes on early plant growth stages. PLoS One 7(2):e30438

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hawkes CV, DeAngelis KM, Firestone MK (2007) Root interactions with soil microbial communities and processes. In: Cardon Z, Whitbeck J (eds) The rhizosphere. Elsevier, New York

    Google Scholar 

  • Heijnen CE, Page S, Vanelsas JD (1995) Metabolic activity of Flavobacterium strain P25 during starvation and after introduction into bulk soil and the rhizosphere of wheat. FEMS Microbiol Ecol 18:129–138

    Article  CAS  Google Scholar 

  • Hein JW, Wolfe GV, Blee KA (2008) Comparison of rhizosphere bacterial communities in Arabidopsis thaliana mutants for systemic acquired resistance. Microb Ecol 55:333–343

    Article  CAS  PubMed  Google Scholar 

  • Iijima M, Griffiths B, Bengouch AG (2000) Sloughing of cap cells and carbon exudation from maize seedling roots in compacted sand. New Phytol 145:477–482

    Article  PubMed  Google Scholar 

  • James EK (2000) Nitrogen fixation in endophytic and associative symbiosis. Field Crop Res 65:197–209

    Article  Google Scholar 

  • Jones DL, Nguyen C, Finlay RD (2009) Carbon flow in the rhizosphere: carbon trading at the soil-root interface. Plant Soil 321:5–33

    Article  CAS  Google Scholar 

  • Jung WJ, Park RD, Mabood F, Souleimanov A, Smith D (2011) Effects of Pseudomonas aureofaciens 63-28 on defense responses in soybean plants infected by Rhizoctonia solani. J Microbiol Biotechnol 21:379–386

    CAS  PubMed  Google Scholar 

  • Kang SM, Joo GJ, Hamayun M, Na CI, Shin DH, Kim HY, Hong JK, Lee IJ (2009) Gibberellin production and phosphate solubilization by newly isolated strain of Acinetobacter calcoaceticus and its effect on plant growth. Biotechnol Lett 31:277–281

    Article  CAS  PubMed  Google Scholar 

  • Knee EM, Gong FC, Gao M, Teplitski M, Jones AR, Foxworthy A, Mort AJ, Bauer WD (2001) Root mucilage from pea and its utilization by rhizosphere bacteria as a sole carbon source. Mol Plant-Microbe Interact 14:775–784

    Article  CAS  PubMed  Google Scholar 

  • Kwak MJ, Kong HG, Choi K, Kwon SK, Song JY, Lee J, Lee PA, Choi SY, Seo M, Lee HJ, Jung EJ, Park H, Roy N, Kim H, Lee MM, Rubin EM, Lee SW, Kim JF (2018) Rhizosphere microbiome structure alters to enable wilt resistance in tomato. Nat Biotechnol 36:1100–1109

    Article  CAS  Google Scholar 

  • Lanoue A, Burlat V, Henkes GJ, Koch I, Schurr U, Röse US (2010) De novo biosynthesis of defense root exudates in response to Fusarium attack in barley. New Phytol 185:577–588

    Article  CAS  PubMed  Google Scholar 

  • Lebeis SL, Rott M, Dangl JL, Schulze-Lefert P (2012) Culturing a plant microbiome community at the cross-rhodes. New Phytol 196:341–344

    Article  PubMed  Google Scholar 

  • Lebeis SL, Herrera Paredes S, Lundberg DS, Breakfield N, Gehring J, McDonald M, Malfatti S, Glavina del Rio T, Jones CD, Tringe SG, Dangl JL (2015) Plant microbiome: salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 349:860–864

    Article  CAS  PubMed  Google Scholar 

  • Li J, Ovakim DH, Charles TC, Glick BR (2000) An ACC deaminase minus mutant of Enterobacter cloacae UW4 no longer promotes root elongation. Curr Microbiol 41:101–105

    Article  CAS  PubMed  Google Scholar 

  • Locey KJ, Lennon JT (2016) Scaling laws predict global microbial diversity. Proc Natl Acad Sci U S A 113:5970–5975

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matilla MA, Ramos JL, Bakker PAHM, Doornbos R, Badri DV, Vivanco JM, Ramos-González MI (2010) Pseudomonas putida KT2440 causes induced systemic resistance and changes in Arabidopsis root exudation. Environ Microbiol Rep 2:381–388

    Article  CAS  PubMed  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 332:1097–1100

    Article  CAS  PubMed  Google Scholar 

  • Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Neal AL, Ahmad S, Gordon-Weeks R, Ton J (2012) Benzoxazinoids in root exudates of maize attract Pseudomonas putida to the Rhizosphere. PLoS One 7(4):e35498

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nguyen C (2003) Rhizodeposition of organic C by plants: mechanisms and controls. Agronomie 23:375–396

    Article  CAS  Google Scholar 

  • Niu B, Paulson JN, Zheng X, Kolter R (2017) Simplified and representative bacterial community of maize roots. Proc Natl Acad Sci U S A 114:2450–2459

    Article  CAS  Google Scholar 

  • Nosengo N (2003) Fertilized to death. Nature 425:894–895

    Article  CAS  PubMed  Google Scholar 

  • O’Brien FJM, Dumont MG, Webb JS, Poppy GM (2018) Rhizosphere bacterial communities differ according to fertilizer regimes and cabbage (Brassica oleracea var. capitata L.) harvest time, but not aphid herbivory. Front Microbiol 9:1620

    Article  PubMed  PubMed Central  Google Scholar 

  • Osborn AM, Moore ERB, Timmis KN (2000) An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol 2:39–50

    Article  CAS  PubMed  Google Scholar 

  • Park WJ, Hochholdinger F, Gierl A (2004) Release of the benzoxazinoids defense molecules during lateral- and crown root emergence in Zea mays. J Plant Physiol 161:981–985

    Article  CAS  PubMed  Google Scholar 

  • Pérez-Montaño F, Jiménez-Guerrero I, Contreras Sánchez-Matamoros R, López-Baena FJ, Ollero FJ, Rodríguez-Carvajal MA, Bellogín RA, Espuny MR (2013) Rice and bean AHL-mimic quorum-sensing signals specifically interfere with the capacity to form biofilms by plant-associated bacteria. Res Microbiol 164:749–760

    Article  CAS  PubMed  Google Scholar 

  • Peters NK, Frost JW, Long SR (1986) A plant flavone, luteolin, induces expression of Rhizobium meliloti nodulation genes. Science 233:977–980

    Article  CAS  PubMed  Google Scholar 

  • Philippot L, Hallin S, Borjesson G, Baggs EM (2009) Biochemical cycling in the rhizosphere having an impact on global change. Plant Soil 321:61–81

    Article  CAS  Google Scholar 

  • Pinto AJ, Raskin L (2012) PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One 7(8):e43093

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Podile AR, Kishore K (2007) Plant growth-promoting rhizobacteria. In: Plant associated bacteria. Springer, Dordrecht, pp 195–230

    Google Scholar 

  • Poole P, Ramachandran V, Terpolilli J (2018) Rhizobia: from saprophytes to endosymbionts. Nat Rev Microbiol 16:291–303

    Article  CAS  PubMed  Google Scholar 

  • Prasad R, Kumar M, Varma A (2015) Role of PGPR in soil fertility and plant health. In: Egamberdieva D, Shrivastava S, Varma A (eds) Plant Growth-Promoting Rhizobacteria (PGPR) and medicinal plants. Springer, Cham, pp 247–260

    Chapter  Google Scholar 

  • Raaijmakers JM, Weller DM (1998) Natural plant protection by 2,4-diacetylphloroglucinol-producing Pseudomonas spp. in take-all decline soils. Mol Plant-Microbe Interact 11:144–152

    Article  CAS  Google Scholar 

  • Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394

    Article  CAS  PubMed  Google Scholar 

  • Reay DS (2004) Fertiliser ‘solution’ could turn local problem global. Nature 427:485

    Article  CAS  PubMed  Google Scholar 

  • Redmond JW, Batley M, Djordjevic MA, Innes RW, Kuempel PL, Rolfe BG (1986) Flavones induce expression of nodulation genes in Rhizobium. Nature 323:632–635

    Article  CAS  Google Scholar 

  • Reinhold-Hurek B, Bünger W, Burbano CS, Sabale M, Hurek T (2015) Roots shaping their microbiome: global hotspots for microbial activity. Annu Rev Phytopathol 53:403–424

    Article  CAS  PubMed  Google Scholar 

  • Rodriguez H, Fraga R, Gonzalez T, Bashan Y (2006) Genetics of phosphate solubilization and its potential applications for improving plant growth-promoting bacteria. Plant Soil 287:15–21

    Article  CAS  Google Scholar 

  • Rolli E, Marasco R, Vigani G, Ettoumi B, Mapelli F, Deangelis ML, Gandolfi C, Casati E, Previtali F, Gerbino R, Pierotti Cei F, Borin S, Sorlini C, Zocchi G, Daffonchio D (2015) Improved plant resistance to drought is promoted by the root-associated microbiome as a water stress-dependent trait. Environ Microbiol 17:316–331

    Article  PubMed  Google Scholar 

  • Rosenberg K, Bertaux J, Krome K, Hartmann A, Scheu S, Bonkowski M (2009) Soil amoebae rapidly change bacterial community composition in the rhizosphere of Arabidopsis thaliana. ISME J 3:675–684

    Article  CAS  PubMed  Google Scholar 

  • Rudrappa T, Czymmek KJ, Pare PW, Bais HP (2008) Root-secreted malic acid recruits beneficial soil bacteria. Plant Physiol 148:1547–1556

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ryu CM, Farag MA, Hu CH, Reddy MS, Wei HX, Paré PW, Kloepper JW (2003) Bacterial volatiles promote growth in Arabidopsis. Proc Natl Acad Sci U S A 100:4927–4932

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sanders D, Bethke P (2000) Membrane transport. In: Buchanan BB, Gruisham W, Jones RL (eds) Biochemistry and molecular biology of plants. ASPP, Rockville, MD, pp 110–158

    Google Scholar 

  • Schlaeppi K, Dombrowski N, Oter RG, Ver Loren van Themaat E, Schulze-Lefert P (2014) Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc Natl Acad Sci U S A 111(2):585–592

    Article  CAS  PubMed  Google Scholar 

  • Semenov AM, van Bruggen AHC, Zelenev VV (1999) Moving waves of bacterial populations and total organic carbon along roots of wheat. Microb Ecol 37:116–128

    Article  CAS  PubMed  Google Scholar 

  • Shidore T, Dinse T, Öhrlein J, Becker A, Reinhold-Hurek B (2012) Transcriptomic analysis of responses to exudates reveal genes required for rhizosphere competence of the endophyte Azoarcus sp. strain BH72. Environ Microbiol 14:2775–2787

    Article  CAS  PubMed  Google Scholar 

  • Singh D, Raina TK, Kumar A, Singh J, Prasad R (2019) Plant microbiome: a reservoir of novel genes and metabolites. Plant Gene 18:100177. https://doi.org/10.1016/j.plgene.2019.100177

    Article  CAS  Google Scholar 

  • Strehmel N, Böttcher C, Schmidt S, Scheel D (2014) Profiling of secondary metabolites in root exudates of Arabidopsis thaliana. Phytochemistry 108:35–46

    Article  CAS  PubMed  Google Scholar 

  • Sugiyama A, Shitan N, Yazaki K (2007) Involvement of a soybean ATP-binding cassette-type transporter in the secretion of genistein, a signal flavanoid in legume–Rhizobium symbiosis. Plant Physiol 144:2000–2008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sugiyama A, Unno Y, Ui O, Yoshikawa E, Suzuki H, Minamisawa K, Yazaki K (2017) Assessment of bacterial communities of black soybean grown in fields. Commun Integr Biol 10(5–6):e1378290

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Svennerstam H, Ganeteg U, Bellini C, Nasholm T (2007) Comprehensive screening of Arabidopsis mutants suggests the lysine histidine transporter 1 to be involved in plant uptake of amino acids. Plant Physiol 143:1853–1860

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tett AJ, Turner TR, Poole PS (2012) Genomics and the rhizosphere. Wiley, New York

    Book  Google Scholar 

  • Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversity–magnitude, dynamics, and controlling factors. Science 296:1064–1066

    Article  CAS  PubMed  Google Scholar 

  • Turner TR, James EK, Poole PS (2013a) The plant microbiome. Genome Biol 14:209

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Turner TR, Ramakrishnan K, Walshaw J, Heavens D, Alston M, Swarbreck D, Anne Osbourn A, Alastair Grant A, Philip S, Poole PS (2013b) Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants. ISME J 7:2248–2258

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Van Etten HD, Mansfield JW, Bailey JA, Farmer EE (1994) Two classes of plant antibiotics: phytoalexins versus “phytoanticipins”. Plant Cell 6:1191–1192

    Article  Google Scholar 

  • Van Spanning RJM, Delgado MJ, Richardson DJ (2005) The nitrogen cycle: denitrification and its relationship to N2 fixation. In: Werner D, Newton WE (eds) Nitrogen fixation in agriculture, forestry, ecology, and the environment. Springer, Dordrecht, pp 277–342

    Chapter  Google Scholar 

  • Vaughan MM, Wang Q, Webster FX, Kiemle D, Hong YJ, Tantillo DJ, Coates RM, Wray AT, Askew W, O’Donnell C, Tokuhisa JG, Tholl D (2013) Formation of the unusual semivolatile diterpene rhizathalene by the Arabidopsis class I Terpene synthase TPS08 in the root stele is involved in defense against belowground herbivory. Plant Cell 25:1108–1125

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Velazquez-Sepulveda I, Orozco-Mosqueda MC, Prieto-Barajas CM, Santoyo G (2012) Bacterial diversity associated with the rhizosphere of wheat plants (Triticum aestivum): toward a metagenomic analysis. Phyton Int J Exp Bot 81:81–87

    Google Scholar 

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

    Article  CAS  Google Scholar 

  • Vicré M, Santaella C, Blanchet S, Gateau A, Driouich A (2005) Root border-like cells of Arabidopsis. Microscopical characterization and role in the interaction with rhizobacteria. Plant Physiol 138:998–1008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vukovic’ R, Bauer N, Curković-Perica M (2013) Genetic elicitation by inducible expression of b-cryptogein stimulates secretion of phenolics from Coleus blumei hairy roots. Plant Sci 199–200:18–28

    Article  CAS  Google Scholar 

  • Wagner MR, Lundberg DS, del Rio TG, Tringe SG, Dangl JL, Mitchell-Olds T (2016) Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat Commun 7:12151

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Walters WA, Jin Z, Youngblut N, Wallace JG, Sutter J, Zhang W, González-Peña A, Peiffer J, Koren O, Shi Q, Knight R, del Rio TG, Tringe SG, Buckler ES, Dangl JL, Ley RE (2018) Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proc Natl Acad Sci U S A 115:7368–7373

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang QY, Dodd IC, Belimov AA, Jiang F (2016) Rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase growth and photosynthesis of pea plants under salt stress by limiting Na+ accumulation. Funct Plant Biol 43:161–172

    Article  CAS  PubMed  Google Scholar 

  • Weinert N, Piceno Y, Ding GC, Meincke R, Heuer H, Berg G, Schloter M, Andersen G, Smalla K (2011) PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. FEMS Microbiol Ecol 75:497–506

    Article  CAS  PubMed  Google Scholar 

  • Weller DM, Raaijmakers JM, McSpadden Gardener BB, Thomashow LS (2002) Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annu Rev Phytopathol 40:309–348

    Article  CAS  PubMed  Google Scholar 

  • Yin C, Hulbert SH, Schroeder KL, Mavrodi O, Mavrodi D, Dhingra A, Schillinger WF, Paulitz TC (2013) Role of bacterial communities in the natural suppression of Rhizoctonia solani bare patch disease of wheat (Triticum aestivum L.). Appl Environ Microbiol 79:7428–7438

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zamioudis C, Pieterse CMJ (2012) Modulation of host immunity by beneficial microbes. Mol Plant-Microbe Interact 25:139–150

    Article  CAS  PubMed  Google Scholar 

  • Zhang H, Sun Y, Xie X, Kim MS, Dowd SE, Paré PW (2009) A soil bacterium regulates plant acquisition of iron via deficiency-inducible mechanisms. Plant J 58:568–577

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Raja V. N. R. Vukanti .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Vukanti, R.V.N.R. (2020). Structure and Function of Rhizobiome. In: Varma, A., Tripathi, S., Prasad, R. (eds) Plant Microbe Symbiosis. Springer, Cham. https://doi.org/10.1007/978-3-030-36248-5_13

Download citation

Publish with us

Policies and ethics