Skip to main content

Plant Rhizosphere Microbial Communities

  • Reference work entry
The Prokaryotes

Abstract

Plants have evolved in a microbial world. Thus, plant-microbe interactions may be inherent to plants’ adaptation to their environment. On the other hand, plants are the major source of organic nutrients in the soil, the driving force for microbial activity. The soil microflora interacts with plant roots and can even modulate the plant’s response to both biotic and abiotic stresses. Here, we describe the rhizosphere as an organized unit, composed of the root and its associated microbiome. This interaction occurs in the limited soil region directly influenced by the living plant root. The presence and activities of the root affect the surrounding soil chemically, physically, and biologically. Thus, numerous processes occur in parallel in the rhizosphere, creating a unique and active niche. The chemical processes involve passive and active deposition of a multitude of compounds, mostly labile organic matter from the plant root and sloughed-off plant cells and tissues. The deposits discharged from the roots into the surrounding soil include different amino acids and proteins, organic acids, carbohydrates and sugars, vitamins, and the mucilage, accounting for a large proportion of the plant’s fixed carbon. These, of course, are the driving force for alterations in the activity, function, abundance, composition and structure of the soil microbial community. The rhizosphere community will, in turn, affect root health and development.

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 599.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 549.99
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

  • Abou-Shanab RAI, van Berkum P, Angel JS (2007) Heavy metal resistance and genotypic analysis of metal resistance genes in Gram-positive and Gram-negative bacteria present in Ni-rich serpentine soil and in the rhizosphere of Alyssum murale. Chemospehre 68:360–367

    CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Ahrenholtz I, Harms K, De Vries J, Wackernagel W (2000) Increased killing of Bacillus subtilis on the hair roots of transgenic T4 lysozyme-producing potatoes. Appl Environ Microbiol 66:1862–1865

    PubMed  CAS  Google Scholar 

  • Alvey S, Yang CH, Buerkert A, Crowley DE (2003) Cereal/legume rotation effects on rhizosphere bacterial community structure in west African soils. Biol Fertil Soils 37:73–82

    Google Scholar 

  • Amann R, Lodwig W (2000) Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiol Rev 24:555–565

    PubMed  CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Aranda S, Montes-Borrego M, Jiménez-Díaz RM, Landa BB (2011) Microbial communities associated with the root system of wild olives (Olea europaea L. subsp. europaea var. sylvestris) are good reservoirs of bacteria with antagonistic potential against Verticillium dahlia. Plant Soil 343:329–345

    CAS  Google Scholar 

  • Artursson N, Finlay RD, Jansson JK (2006) Interactions between arbuscular mycorrhizal fungi and bacteria and their potential for stimulating plant growth. Environ Microbiol 8:1–10

    PubMed  CAS  Google Scholar 

  • Asanuma S, Tanaka H, Yatazawa M (1979) Rhizoplane microorganisms of rice seedlings as examined by scanning electron microscopy. Soil Sci Plant Nutr 25:539–551

    Google Scholar 

  • Ashoub AH, Amara MT (2010) Biocontrol activity of some bacterial genera against root-knot nematode, Meloidogyne incognita. J Am Sci 6:321–328

    Google Scholar 

  • Assmus B, Hutzler P, Kirchhof G, Amann, R, Lawrence JR, Hartmann A (1995) In situ localization of Azospirillum brasilense in the rhizosphere of wheat with fluorescently labeled, rRNA-targeted oligonucleotide probes and scanning confocal laser microscopy. Appl Environ Microbiol 61:1013–1019

    PubMed  CAS  Google Scholar 

  • Augustine DJ, Dijkstra FA, Hamilton EW, Morgan JA (2011) Rhizosphere interactions, carbon allocation, and nitrogen acquisition of two perennial North American grasses in response to defoliation and elevated atmospheric CO2. Oecologia 165:755–770

    PubMed  Google Scholar 

  • Avery LM, Lewis Smith RI, West HM (2003) Response of rhizosphere microbial communities associated with Antarctic hairgrass (Deschampsia antarctica) to UV radiation. Polar Biol 26:525–529

    Google Scholar 

  • Bacilio-Jiménez M, Aguilar-Flores S, del Valle MV, Pérez A, Zepeda A, Zenteno E (2001) Endophytic bacteria in rice seeds inhibit early colonization of roots by Azospirillum brasilense. Soil Biol Biochem 33:167–172

    Google Scholar 

  • Bardgett RD, Freeman C, Ostle N (2008) Microbial contributions to climate change through carbon cycle feedbacks. ISME J 2:805–814

    PubMed  CAS  Google Scholar 

  • Bardi DV, Quintana N, El Kassis EG, Kim KH, Choi YH, Sugiyama A, Verpoorte R, Martinoia E, Manter DK, Vivanco JM (2009) An ABC transporter mutation alters root exudation of phytochemicals that provoke an overhaul of natural soil microbiota. Plant Physiol 151:2006–2017

    Google Scholar 

  • Barret M, Morrissey JP, O’Gara F (2011) Functional genomics analysis of plant growth-promoting rhizobacterial traits involved in rhizosphere competence. Biol Fertil Soils 47:729–743

    CAS  Google Scholar 

  • Barriuso J, Ramos Solano B, Santamaría C, Gutiérez Mañero FJ (2008) Effect of inoculation with putative plant growth-promoting rhizobacteria isolated from Pinus spp. on Pinus pinea growth, mycorrhization and rhizosphere microbial communities. J Appl Microbiol 105:1289–1309

    Google Scholar 

  • Bashan Y, Levanony H, Whitmoyer RE (1991) Root surface colonization of non-cereal crop plants by pleomorphic Azospirillum brasilense Cd. J Gen Microbiol 137:187–196

    Google Scholar 

  • Bashan Y, Puente ME, Rodriguez-Mendoza MN, Toledo G, Holguin G, Ferrera-Cerrato R, Pedrin S (1995) Survival of Azospirillum brasilense in the bulk soil and rhizosphere of 23 soil types. Appl Environ Microbiol 61:1938–1945

    PubMed  CAS  Google Scholar 

  • Baudoin E, Benizri E, Guckert A (2002) Impact of growth stage on the bacterial community structure along maize roots, as determined by metabolic and genetic fingerprinting. Appl Soil Ecol 19:135–145

    Google Scholar 

  • Baumgrate S, Tebbe CC (2005) Field studies on the environmental fate of the Cry1Ab Bt-toxin produced by transgenic maize (MON810) and its effect on bacterial communities in the maize rhizosphere. Mol Ecol 14:2539–2551

    Google Scholar 

  • Becker A, Berges H, Krol E, Bruand C, Ruberg S, Capela D, Lauber E, Meilhoc E, Ampe F, de Bruijn FJ, Fourment J, Francez-Charlot A, Kahn D, Kuster H, Liebe C, Puhler A, Weidner S, Batut J (2004) Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions. Mol Plant-Microbe Interact 17:292–303

    PubMed  CAS  Google Scholar 

  • Belcom IN, Crowley DE (2009) Pyrene effects on rhizoplane bacterial communities. Int J Phytoremediat 11:609–622

    Google Scholar 

  • Bending GD, Poole EJ, Whipps JM, Read DJ (2002) Characterisation of bacteria from Pinus sylvestris-Suillus luteus mycorrhizas and their effects on root-fungus interactions and plant growth. FEMS Microbiol Ecol 39:219–227

    PubMed  CAS  Google Scholar 

  • Bending GD, Aspray TJ, Whipps JM (2006) Significance of microbial interactions in the mycorrhizosphere. Adv Appl Microbiol 60:97–131

    PubMed  CAS  Google Scholar 

  • Benitez MS, Tustas FB, Rotenberg D, Kleinhenz MD, Cardina J, Stinner D, Miller SA, McSpadden Gardene BB (2007) Multiple statistical approaches of community fingerprint data reveal bacterial populations associated with general disease suppression arising from the application of different organic field management strategies. Soil Biol Biochem 39:2289–2301

    CAS  Google Scholar 

  • Benizri E, Baudoin E, Guckert A (2001) Root colonization by inoculated plant growth-promoting rhizobacteria. Biocontrol Sci Techn 11:557–574

    Google Scholar 

  • Berg G, Roskot N, Steidle A, Eberl L, Zock A, Smalla K (2002) Plant-dependent genotypic and phenotypic diversity of antagonistic rhizobacteria isolated from different Verticullium host plants. Appl Environ Microbiol 68:3328–3338

    PubMed  CAS  Google Scholar 

  • Berg G, Krechel A, Ditz M, Sikora RA, Ulrich A, Hallmann J (2005) Endophytic and ectophytic potato-associated bacterial communities differ in structure and antagonistic function against plant pathogenic fungi. FEMS Microbiol Ecol 51:215–229

    PubMed  CAS  Google Scholar 

  • Berg G, Opelt K, Zachow C, Lottmann J, Götz M, Costa R, Smalla K (2006) The rhizosphere effect on bacteria antagonistic towards the pathogenic fungus Verticillium differs depending on plant species and site. FEMS Microbiol Ecol 56:250–261

    PubMed  CAS  Google Scholar 

  • Bergsma-Vlami M, Prins ME, Raaijmakers JM (2005) Influence of plant species on population dynamics, genotypic diversity and antibiotic production in the rhizosphere by indigenous Pseudomonas spp. FEMS Microbiol Ecol 52:59–69

    PubMed  CAS  Google Scholar 

  • Blatny JM, Ho J, Skogan G, Fykse EM, Aarskaug T, Waagen V (2011) Airborne Legionella bacteria from pulp waste treatment plant: aerosol particles characterized as aggregates and their potential hazard. Aerobiologia 27:147–162

    Google Scholar 

  • Bomberg M, Timonen S (2007) Distribution of Cren- and Euryarchaeota in Scots pine mycorrhizospheres and boreal forest humus. Microb Ecol 54:406–416

    PubMed  CAS  Google Scholar 

  • Bomberg M, Montonen L, Timonen S (2010) Anaerobic Eury- and Crenarchaeota inhabit ectomycorrhizas of boreal forest Scots pine. Eur J Soil Biol 46:356–364

    Google Scholar 

  • Bomberg M, Münster U, Pumpanen J, Ilvesniemi H, Heinonsalo J (2011) Archaeal communities in boreal forest tree rhizospheres respond to changing soil temperatures. Microb Ecol 62:205–217

    PubMed  Google Scholar 

  • Bowatte S, Asakawa S, Okada M, Kobayasi K, Kimura M (2007) Effect of elevated atmospheric CO2 concentration on ammonia oxidizing bacteria communities inhabiting in rice roots. Soil Sci Plant Nutr 53:32–39

    CAS  Google Scholar 

  • Bowen GD, Theodorou C (1979) Interactions between bacteria and ectomycorrhizal fungi. Soil Biol Biochem 11:119–126

    Google Scholar 

  • Brooks DD, Chan R, Starks ER, Grayston SJ, Jones MD (2011) Ectomycorrhizal hyphae structure components of the soil bacterial community for decreased phosphate production. FEMS Microbiol Ecol 76:245–255

    PubMed  CAS  Google Scholar 

  • Brusetti L, Francia P, Bertolini C, Pagliuca A, Borin S, Sorlini C, Abruzzese A, Sacchi G, Viti C, Giovannetti L, Giuntini E, Bazzicalupo M, Daffonchio D (2004) Bacterial communities associated with the rhizosphere of transgenic Bt 176 maize (Zea mays) and its non transgenic counterpart. Plant Soil 266:11–21

    CAS  Google Scholar 

  • Buddrus-Schiemann K, Schmid M, Schreiner K, Welzl G, Hartmann A (2010) Root colonization by Pseudomonas sp. DSMZ 13134 and impact on the indigenous rhizosphere bacterial community of barley. Microb Ecol 60:381–393

    PubMed  Google Scholar 

  • Cadillo-Quiroz H, Yavitt JB, Zinder SH, Thies JE (2010) Diversity and community structure of Archaea inhabiting the rhizoplane of two contrasting plants from and acidic bog. Microb Ecol 59:757–767

    PubMed  CAS  Google Scholar 

  • Çakmakçi R, Dönmez MF, Ertürk Y, Erat M, Haznedar A, Sekban R (2010) Diversity and metabolic potential of culturable bacteria from the rhizosphere of Turkish tea grown in acidic soils. Plant Soil 332:299–318

    Google Scholar 

  • Campbell R, Rovira AD (1973) The study of the rhizosphere by scanning electron microscopy. Soil Biol Biochem 5:747–752

    Google Scholar 

  • Castro-Sowinski S, Hersckovitz Y, Okon Y, Jurkevitch E (2007) Effects of inoculation with plant growth-promoting rhizobacteria on resident rhizosphere microorganisms. FEMS Microbiol Lett 276:1–11

    PubMed  CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Cavalca L, Zanchi R, Corsini A, Colombo M, Romagnoli C, Canzi E, Andreoni V (2010) Arsenic-resistant bacteria associated with roots of the wild Cirsium arvense (L.) plant from an arsenic polluted soil, and screening of potential plant growth-promoting characteristics. Sys Appl Microbiol 33:154–164

    CAS  Google Scholar 

  • Cavalo-Bado LA, Petch G, Parsons NR, Morgan JAW, Pettitt TR, Whipps JM (2006) Microbial community responses associated with the development of oomycete plant pathogens on tomato roots in soilless growing systems. J Appl Micrbiol 100:1194–1207

    Google Scholar 

  • Chauhan PS, Chaudhry V, Mishra S, Nautiyal CS (2011) Uncultured bacterial diversity in tropical maize (Zea mays L.) rhizosphere. J Basic Microbiol 51:15–32

    PubMed  CAS  Google Scholar 

  • Chelius MK, Triplett EW (2001) The diversity of Archaea and Bacteria in association with the roots of Zea mays L. Microb Ecol 41:252–263

    PubMed  CAS  Google Scholar 

  • Cheng W, Zhang Q, Coleman DC, Carroll CR, Hoffman CA (1996) Is available carbon limiting microbial respiration in the rhizosphere? Soil Biol. Biochem 28:1283–1288

    CAS  Google Scholar 

  • Cheng Y, Howieson JG, O’Hara GW, Watkin ELJ, Souche G, Jaillard B, Hinsinger P (2004) Proton release by roots of Medicago murex and Medicago sativa growing in acidic conditions, an implication for rhizosphere pH changes and nodulation at low pH. Soil Biol Biochem 36:1357–1365

    CAS  Google Scholar 

  • Chiarini L, Bevivino A, Dalmastri C, Nacamulli C, Tabacchioni S (1998) Influence of plant development, cultivar and soil type on microbial colonization of maize roots. Appl Soil Ecol 8:11–18

    Google Scholar 

  • Chin-A-Woeng TFC, de Priester W, van der Bij AJ, Lugtenberg BJJ (1997) Description of the colonization of a gnotobiotic tomato rhizosphere by Pseudomonas fluorescens biocontrol strain WCS365, using scanning electron microscopy. Mol Plant Microbe Interact 1:79–86

    Google Scholar 

  • Chow ML, Radomski CC, McDermott JM, Davis J, Axelrood PE (2002) Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source. FEMS Microbiol Ecol 42:347–357

    PubMed  CAS  Google Scholar 

  • Chowdhury SP, Schmid M, Hartmann A, Tripathi AK (2009) Diversity of 16S-rRNA and nifH genes derived from rhizosphere soil and roots of an endemic drought tolerant grass, Lasiurus sindicus. Eur J Soil Biol 45:114–122

    CAS  Google Scholar 

  • Chu H, Lin X, Fujii T, Morimoto S, Yagi K, Hu J, Zhang J (2007) Soil bacterial biomass, dehydrogenase activity, bacterial community structure in response to long-term fertilizer management. Soil Biol Biochem 39:2971–2976

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Compant S, van der Heijden MGA, Sessitsch A (2010b) Climate change effects on beneficial plant-microorganism interactions. FEMS Microbiol Ecol 73:197–214

    PubMed  CAS  Google Scholar 

  • Conrad R, Erkel C, Liesack W (2006) Rice cluster I methanogenes, an important group of Archaea producing greenhouse gas in soil. Curr Opin Biotech 17:262–267

    PubMed  CAS  Google Scholar 

  • Conrad R, Klose M, Noll M, Kemnitz D (2008) Soil type links microbial colonization of rice roots to methane emission. Glob Change Biol 14:657–669

    Google Scholar 

  • Costa R, Gomes NCM, Peixoto RS, Rumjanek N, Berg G, Mendoça-Hagler LCS, Smalla K (2006) Diversity and antagonistic potential of Pseudomonas spp. associated to the rhizosphere of maize grown in a subtropical organic farm. Soil Biol. Biochem 38:2434–2447

    CAS  Google Scholar 

  • Dandurand LM, Schotzko DJ, Knudsen GR (1997) Spatial patterns of rhizoplane population of Pseudomonas fluorescens. Appl Environ Microbiol 63:3211–3217

    PubMed  CAS  Google Scholar 

  • da Rocha UN, van Elsas JD, van Overbeek LS (2010) Real-time PCR detection of Holophagae (Acidobacteria) and Verrucomicrobia subdivisión 1 groups in bulk and leek (Alium porrum) rhizosphere soils. J Microbiol Meth 83:141–148

    Google Scholar 

  • De Brito Alvarez MA, Gagné S, Antoun H (1995) Effect of compost on rhizosphere microflora of the tomato and on the incidence of plant growth-promoting rhizobacteria. Appl Environ Microbiol 61:194–199

    Google Scholar 

  • De Graaff MA, Van Kessel C, Six J (2009) Rhizodeposition-induced decomposition increases N availability to wild and cultivated wheat genotypes under elevated CO2. Soil Biol Biochem 41:1094–1103

    Google Scholar 

  • de la Fuente JM, Ramírez-Rodríguez V, Cabrera-Ponce JL, Herrera-Estrella L (1997) Aluminum tolerance in transgenic plants by alteration of citrate synthesis. Science 276:1566–1568

    PubMed  Google Scholar 

  • De Leij FAAM, Whipps JM, Lynch JM (1993) The use of colony development for the characterization of bacterial communities in soil and on roots. Microb Ecol 24:81–97

    Google Scholar 

  • De Leij FAAM, Sutton EJ, Whipps JM, Fenlon JS, Lynch JM (1995) Impact of field release of genetically modified Pseudomonas fluorescens on indigenous microbial populations of what. Appl Environ Microbiol 61:3443–3453

    PubMed  Google Scholar 

  • de Souza JT, Weller DM, Raaijmakers JM (2003) Frequency, diversity, and activity of 2,4-diacetylphloroglucinol-producing fluorescent Pseudomonas spp. in Dutch take-all decline soils. Phytopathology 93:54–63

    PubMed  Google Scholar 

  • De Vries J, Harms K, Broer I, Kriete G, Mahn A, Düring K, Wackernagel W (1999) The bacteriolytic activity in transgenic potatoes expressing a chimeric T4 lysozyme gene and the effect of T4 lysozyme on soil- and phytopathogenic bacteria. Sys Appl Microbiol 22:280–286

    Google Scholar 

  • DeAngelis KM, Brodie EK, DeSantis TZ, Andersen GL, Lindow SE, Firestone MK (2009) Selective progressive response of soil microbial community to wild oat roots. ISME J 3:168–1780

    PubMed  CAS  Google Scholar 

  • Deiglmayr K, Philippot L, Hartwig UA, Kandeler E (2004) Structure and activity of the nitrate-reducing community in the rhizosphere of Lolium perenne and Trifolium repens under long-term elevated atmospheric CO2. FEMS Microbiol Ecol 49:445–454

    PubMed  CAS  Google Scholar 

  • Dekkers LC, Mulders IHM, Phoelich CC, Chin-A-Woeng TFC, Wijfjes AHM, Lugtenberg BJJ (2000) The sss colonization gene of the tomato-Fusarium oxysporum f. sp. radicis-lycopersici biocontrol strain Pseudomonas fluorescens WCS365 can improve root colonization of other wild-type Pseudomonas spp. bacteria. Mol. Plant-Microbe Interact 13:1177–1183

    CAS  Google Scholar 

  • Dell’Amico E, Cavalca L, Andreoni V (2005) Analysis of rhizobacterial communities in perennial Graminaceae from polluted water meadow soil, and screening of metal-resistant, potentially plant growth-promoting bacteria. FEMS Microbiol Ecol 52:153–162

    PubMed  Google Scholar 

  • Denef K, Bubenheim H, Lenhart K, Vermeulen J, van Cleemput O, Boeckx P, Müller C (2007) Community shifts and carbon translocation within metabolically-active rhizosphere microorganisms in grasslands under elevated CO2. Biogeosciences 4:769–779

    CAS  Google Scholar 

  • Díaz S, Grime JP, Harris J, McPherson E (1993) Evidence of a feedback mechanism limiting plant response to elevated carbon dioxide. Nature 364:616–617

    Google Scholar 

  • Dohrmann AB, Tebbe CC (2005) Effect of elevated tropospheric ozone on the structure of bacterial communities inhabiting the rhizosphere of herbaceous plants native to Germany. Appl Environ Microbiol 71:7750–7758

    PubMed  CAS  Google Scholar 

  • Domanski G, Kuzyakov Y, Siniakina SV, Stahr K (2001) Carbon flows in the rhizosphere of rygrass (Lolium perenne). J Plant Nutr Soil Sci 164:381–387

    CAS  Google Scholar 

  • Donachie SP, Foster JS, Brown MV (2007) Culture clash: challenging the dogma of microbial diversity. ISME J 1:97–102

    PubMed  Google Scholar 

  • Donate-Correa J, León-Barrios M, Pérez-Galdona R (2004) Screening for plant growth-promoting rhizobacteria in Chamaecytisus proliferus (tagasaste), a forage tree-shrub legume endemic to the Canary Islands. Plant Soil 266:261–272

    CAS  Google Scholar 

  • Dorodnikov M, Blagodatskaya E, Blagodatsky S, Marhan S, Fangmeier A, Kuzyakov Y (2009) Stimulation of microbial extracellular enzyme activities by elevated CO2 depends on soil aggregate size. Glob Change Biol 15:1603–1614

    Google Scholar 

  • Drigo B, Kowalchuk GA, Yergeau E, Bezemer TM, Boschker HS, van Veen JA (2007) Impact of elevated carbon dioxide on the rhizosphere communities of Carex arenaria and Festuca rubra. Glob Change Biol 13:2396–2410

    Google Scholar 

  • Drigo B, Kowalchuk GA, van Veen JA (2008) Climate change goes underground: effects of elevated atmospheric CO2 on microbial community structure and activities in the rhizosphere. Biol Fert Soils 44:667–679

    Google Scholar 

  • Drigo B, van Veen JA, Kowalchuk GA (2009) Specific rhizosphere bacterial and fungal groups respond differently to elevated atmospheric CO2. ISME J 3:1204–1217

    PubMed  CAS  Google Scholar 

  • Duineveld BM, Van Veen JA (1999) The number of bacteria in the rhizosphere during plant development: relating colony-forming units to different reference units. Biol Fert Soils 28:285–291

    Google Scholar 

  • Dunbar J, Takala S, Barns SM, Davis JA, Kuske CR (1999) Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol 65:1662–1669

    PubMed  CAS  Google Scholar 

  • Dunbar J, Barns SM, Ticknor LO, Kuske CR (2002) Empirical and theoretical bacterial diversity in four Arizona soils. Appl Environ Microbiol 68:3035–3045

    PubMed  CAS  Google Scholar 

  • Dunfield KE, Germida JJ (2001) Diversity of bacterial communities in the rhizosphere and root interior of field-grown genetically modified Brassica napus. FEMS Microbiol Ecol 38:1–9

    CAS  Google Scholar 

  • Dutta S, Podile AR (2010) Plant growth promoting rhizobacteria (PGPR): the bugs to debug the root zone. Crit Rev Microbiol 36:232–244

    PubMed  Google Scholar 

  • Egamberdleva D, Kamllova F, Valldov 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 10:1–9

    Google Scholar 

  • El-Tarabily KA, Soliman MH, Nassar AH, Al-Hassani HA, Sivasithamparam K, McKenna F, Hardi GESJ (2000) Biological control of Sclerotinia minor using a chitinolytic bacterium and actinomycetes. Plant Pathol 49:573–583

    Google Scholar 

  • Enwell K, Philippot L, Hallin S (2005) Activity and composition of denitrifying bacterial community respond differentially to long-term fertilization. Appl Environ Microbiol 71:8335–8343

    Google Scholar 

  • Esperschütz J, Gattinger A, Mäder P, Shloter M, Fließbach A (2007) Response of soil microbial biomass and community structure to conventional and organic farming systems under identical crop rotations. FEMS Microbiol Ecol 61:26–37

    PubMed  Google Scholar 

  • Esperschütz J, Pritsch K, Gattinger A, Welzl G, Haesler F, Buegger F, Winkler JB, Munch JC, Schloter M (2009) Influence of chronic ozone stress on carbon translocation pattern into rhizosphere microbial communities of beech trees (Fagus sylvatica L.) during a growing season. Plant Soil 323:85–95

    Google Scholar 

  • Fan F, Zhang F, Lu Y (2011) Linking plant identity and interspecific competition to soil nitrogen cycling through ammonia oxidizer communities. Soil Biol Biochem 43:46–54

    CAS  Google Scholar 

  • Faye A, Krasova-Wade T, Thiao M, Thioulouse J, Neyra M, Prin Y, Galiana A, Ndoye I, Dreyfus B, Duponnois R (2009) Controlled ectomycorrhization of an exotic legume tree species Acacia holoseriacea affects the structure of root nodule bacteria community and their symbiotic effectiveness on Faidherbia albida, a native Sahelian Acacia. Soil Biol Biochem 41:1245–1252

    CAS  Google Scholar 

  • Felici C, Vettori L, Giraldi E, Forino LMC, Toffanin A, Tagliasacchi AM, Nuti M (2008) Single and co-inoculation of Bacillus subtilis and Azospirillum brasilense on Lycopersicon esculentum: effects on plant growth and rhizosphere microbial community. Appl Soil Ecol 40:260–270

    Google Scholar 

  • Ferrero MA, Menoyo E, Lugo MA, Negritto MA, Farías ME, Anton AM, Siñeriz F (2010) Molecular characterization and in situ detection of bacterial communities associated with rhizosphere soil of high altitude native Poaceae from the Andean Puna region. J Arid Environ 74:1177–1185

    Google Scholar 

  • Ferris R, Taylor G (1993) Contrasting effects of elevated CO2 on the root and shoot growth of four native herbs commonly found in chalk grassland. New Phytol 125:855–866

    Google Scholar 

  • Fierer N, Breitbart M, Nulton J, Salomon P, Lozupone C, Jones R, Robeson M, Edwards RE, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB (2007) Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of Bacteria, Archaea, Fungi and Viruses in soil. Appl Environ Microbiol 73:7059–7066

    PubMed  CAS  Google Scholar 

  • Filion M, Hamelin RC, Bernier L, St-Arnaud M (2004) Molecular profiling of rhizosphere microbial communities associated with healthy and diseased black spruce (Picea mariana) seedlings grown in a nursery. Appl Environ Microbiol 70:3541–3551

    PubMed  CAS  Google Scholar 

  • Folman LB, Postma J, Van Veen JA (2001) Ecophysiological characterization of rhizosphere bacterial communities at different root locations and plant developmental stages of cucumber grown on rockwool. Microb Ecol 42:586–597

    PubMed  CAS  Google Scholar 

  • Foster RC (1986) The ultrastructure of the rhizoplane and rhizosphere. Annu Rev Phytopathol 24:211–234

    Google Scholar 

  • Foster RC, Bowen GD (1982) Plant surfaces and bacterial growth: the rhizosphere and rhizoplane. In: Mount MS, Lacy GH (eds) Phytopathogenic prokaryotes. Academic, New York, pp 159–185

    Google Scholar 

  • Frenzel P, Bosse U (1996) Methyl fluoride, an inhibitor of methane oxidation and methane production. FEMS Microbiol Ecol 21:25–36

    CAS  Google Scholar 

  • Frey-Klett P, Chavatte M, Clausse ML, Courrier S, Le Roux C, Raaijmakers JM, Martinotti MG, Pierrat JC, Garbaye J (2005) Ectomycorrhizal symbiosis affects functional diversity of rhizosphere fluorescent Pseudomonads. New Phytol 165:317–328

    PubMed  Google Scholar 

  • Frey-Klett P, Garbaye J, Tarkka M (2007) The mycorrhiza helper bacteria revisited. New Phytol 176:22–36

    PubMed  CAS  Google Scholar 

  • Fürnkranz M, Müller H, Berg G (2009) Characterization of plant growth promoting bacteria from crops in Bolivia. J Plant Dis Protect 4:149–155

    Google Scholar 

  • Gans J, Wolinsky M, Dunbar J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:1387–1390

    PubMed  CAS  Google Scholar 

  • Gantner S, Schmid M, Dürr C, Schuhegger R, Steidle A, Hutzler P, Langebartels C, Eberl L, Hartmann A, Dazzo FB (2006) In situ quantification of the spatial scale of calling distances and population density-independent N-acylhomoserine lactone-mediated communication by rhizobacteria colonized on plant roots. FEMS Microbiol Ecol 56:188–194

    PubMed  CAS  Google Scholar 

  • Gao Y, Yang Y, Ling W, Kong W, Zhu X (2011) Gradient distribution of root exudates and polycyclic aromatic hydrocarbons in rhizosphere soil. Soil Sci Soc Am J 75:1694–1703

    CAS  Google Scholar 

  • Garbeva P, van Veen JA, van Elsas JD (2004) Assessment of the diversity, and antagonism towards Rhizoctonia solani AG3, of Pseudomonas species in soil from different agricultural regimes. FEMS Microbiol Ecol 47:51–64

    PubMed  CAS  Google Scholar 

  • Garbeva P, van Elsas JD, van Veen JA (2008) Rhizosphere microbial community and its response to plant species and soil history. Plant Soil 302:19–32

    CAS  Google Scholar 

  • Gardner T, Acosta-Martinez V, Senwo Z, Dowd SE (2011) Soil rhizosphere microbial communities and enzyme activities under organic farming in Alabama. Diversity 3:308–328

    CAS  Google Scholar 

  • Germida JJ, Siciliano SD, de Freitas R, Seib AM (1998) Diversity of root-associated bacteria with field-grown canola (Brassica napus L.) and wheat (Triticum aestivum L.). FEMS Microbiol Ecol 26:43–50

    CAS  Google Scholar 

  • Giovannoni S, Stingl U (2007) The importance of culturing bacterioplancton in the ‘omics’ age. Nat Rev Microbiol 5:820–826

    PubMed  CAS  Google Scholar 

  • Gomes NCM, Heuer H, Schönfeld J, Costa R, Mendoça-Halger L, Smalla K (2001) Bacterial diversity of the rhizosphere of maize (Zea mays) grown in tropical soil studied by temperature gradient gel electrophoresis. Plant Soil 232:167–180

    CAS  Google Scholar 

  • Gomes NCM, Cleary DFR, Pinto NF, Egas C, Almeida A, Cunha A, Mendonça-Hagler LCS, Smalla K (2010) Taking root: Enduring effect of rhizosphere bacteiral colonization in mangroves. PLoS One 5:e14065

    PubMed  Google Scholar 

  • Gottel NR, Castro HF, Kerley M, Yang Z, Pelletier DA, Podar M, Karpinets T, Uberbacher E, Tuskan GA, Vilgalys R, Doktycz MJ, Schadt CW (2011) Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides roots across contrasting soil types. Appl Environ Microbiol 77:5934–5944

    PubMed  CAS  Google Scholar 

  • Gransee A, Wittenmayer L (2000) Qualitative and quantitative analysis of water-soluble root exudates in relation to plant species and development. J Plant Nutr Soil Sci 163:381–385

    CAS  Google Scholar 

  • Grayston SJ, Campbel CD, Lutze JL, Gifford RM (1998a) Impact of elevated CO2 on the metabolic diversity of microbial communities in N-limited grass swards. Plant Soil 203:289–300

    CAS  Google Scholar 

  • Grayston SJ, Wang S, Campbell CD, Edwards AC (1998b) Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol Biochem 30:369–378

    CAS  Google Scholar 

  • Green SJ, Inbar E, Michel FC Jr, Hadar Y, Minz D (2006) Succession of bacterial communities during early plant development: transition from seed to root and effect of compost amendment. Appl Environ Microbiol 72:3975–3983

    PubMed  CAS  Google Scholar 

  • Green SJ, Michel FC Jr, Hadar Y, Minz D (2007) Contrasting patterns of seed and root colonization by bacteria from the genus Chrysobacterium and from the family Oxalobacteraceae. ISME J 1:291–299

    PubMed  CAS  Google Scholar 

  • Gremion F, Chatzinotas A, Harms H (2003) Comparative 16S rDNA and 16S rRNA sequence analysis indicates that Actinobacteria might be a dominant part of the metabolically active bacteria in heavy metal contaminated bulk and rhizosphere soil. Environ Microbiol 5:896–907

    PubMed  CAS  Google Scholar 

  • Griffiths BS, Ritz K, Ebblewhite N, Paterson E, Killham K (1998) Ryegrass rhizosphere microbial community structure under elevated carbon dioxide concentrations, with observations on wheat rhizosphere. Soil Biol Biochem 30:315–321

    CAS  Google Scholar 

  • Griffiths BS, Geoghegan IE, Robertson WM (2000) Testing genetically engineered potato, producing lectins GNA and Con A, on non-target soil organisms and processes. J Appl Ecol 37:159–170

    Google Scholar 

  • Griffiths BS, Caul S, Thompson J, Birch ANE, Cortet J, Andersen MN, Krogh PH (2007) Microbial and microfaunal community structure in cropping systems with genetically modified plants. Pedobiologia 51:195–206

    Google Scholar 

  • Grosskopf R, Stubner S, Liesack W (1998) Novel Euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl Environ Microbiol 64:4983–4989

    CAS  Google Scholar 

  • Gschwendtner S, Reichmann M, Müller M, Radl V, Munch JC, Schloter M (2010a) Abundance of bacterial genes encoding for proteases and chitinases in the rhizosphere of three different potato cultivars. Biol Fertil Soils 46:649–652

    CAS  Google Scholar 

  • Gschwendtner S, Reichmann M, Müller M, Radl V, Munch JC, Schloter M (2010b) Effects of genetically modified amylopectin-accumulating potato plants on the abundance of beneficial and pathogenic microorganisms in the rhizosphere. Plant Soil 335:413–422

    CAS  Google Scholar 

  • Gschwendtner S, Esperschütz J, Buegger F, Reichmann M, Müller M, Munch JC, Schloter M (2011) Effects of genetically modified starch metabolism in potato plants on photosynthate fluxes into the rhizosphere and on microbial degraders of root exudates. FEMS Microbiol Ecol 76:564–575

    PubMed  CAS  Google Scholar 

  • Guerrero-Molina MF, Einik BC, Pedraza RO (2011) More than rhizosphere colonization of strawberry plants by Azospirillum brasilense. Appl Soil Ecol. doi:10.1016/j.apsoil.2011.10.011

    Google Scholar 

  • Gyamfi S, Pfeifer U, Stierschneider M, Sessitisch A (2002) Effects of transgenic glufosinate-tolerant oilseed rape (Brassica napus) and the associated herbicide application on eubacteiral and Pseudomonas communities in the rhizosphere. FEMS Microbiol Ecol 14:181–190

    Google Scholar 

  • Haase S, Philippot L, Neumann G, Marhan S, Kandeler E (2008) Local response of bacterial densities and enzyme activities to elevated atmospheric CO2 and different N supply in the rhizosphere of Phaseolus vulgaris L. Soil Biol Biochem 40:1225–1234

    CAS  Google Scholar 

  • Hallmann J, Rodŕiguez-Kábana R, Kloepper JW (1999) Chitin-mediated changes in bacterial communities of the soil, rhizosphere and within roots of cotton in relation to nematode control. Soil Biol Biochem 31:551–560

    CAS  Google Scholar 

  • Han J, Song Y, Liu Z, Hu Y (2011) Culturable bacterial community analysis in the rot domains of two varieties of tree peony (Paeonia ostii). FEMS Microbiol Lett 322:15–24

    PubMed  CAS  Google Scholar 

  • Hansen M, Kragelund L, Nybroe O, Sørensen J (1997) Early colonization of barley roots by Pseudomonas fluorescens studies by immonofluorescence technique and confocal laser scanning microscopy. FEMS Microbiol Ecol 23:353–360

    CAS  Google Scholar 

  • Hart MM, Powell JR, Gulden RH, Dunfield KE, Pauls KP, Swanton CJ, Klironomos JN, Antunes PM, Koch AM, Trevors JT (2009) Separating the effect of crop from herbicide on soil microbial communities in glyphosate-resistant corn. Pedobiologia 52:253–262

    CAS  Google Scholar 

  • Hashimoto-Yasuda T, Ikenaga M, Asakawa S, Kim HY, Okada M, Kobayashi K, Kimura M (2005) Effect of free-air CO2 enrichment (FACE) on methanogenic Archaeal communities inhabiting rice roots in a Japanese rice field. Soil Sci Plant Nutr 51:91–100

    CAS  Google Scholar 

  • Hayat R, Ali S, Amara U, Khalid R, Ahmad I (2010) Soil beneficial bacteria and their role in plant growth promotion: a review. Ann Microbiol 60:579–598

    Google Scholar 

  • He Z, Xu M, Deng Y, Kang S, Kellogg L, van Nostrand JD, Hobbie SE, Reich PB, Zhou J (2010) Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecol Lett 13:564–575

    PubMed  Google Scholar 

  • Herrmann M, Saunders AM, Schramm A (2008) Archaea dominate the ammonia-oxidizing community in the rhizosphere of the freshwater macrophyte Littorella uniflora. Appl Environ Microbiol 74:3279–3283

    PubMed  CAS  Google Scholar 

  • Herschkovitz Y, Lerner A, Davidov Y, Okon Y, Jurkevitch E (2005a) Azospirillum brasilense does not affect population structure of specific rhizobacteiral communities of inoculated maize (Zea mays). Environ Microbiol 7:1847–1852

    PubMed  CAS  Google Scholar 

  • Herschkovitz Y, Lerner A, Davidov Y, Rothballer M, Hartmann A, Okon Y, Jurkevitch E (2005b) Inoculation with the plant-growth-promoting rhizobacterium Azospirillum brasilense causes little disturbance in the rhizosphere and rhizoplane of maize (Zea mays). Microb Ecol 50:277–288

    PubMed  CAS  Google Scholar 

  • Heuer H, Kroppenstedt RM, Lottmann J, Berg G, Smalla K (2002) Effects of T4 lysozyme release from transgenic potato roots on bacterial rhizosphere communities are negligible relative to natural factors. Appl Environ Microbiol 68:1325–1335

    PubMed  CAS  Google Scholar 

  • Hinsinger P (2001) Bioavailability of soil inorganic P in the rhizosphere as affected by root-induced chemical changes: a review. Plant Soil 237:173–195

    CAS  Google Scholar 

  • Hinsinger P, Bengough AG, Vetterlein D, Young IM (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance. Plant Soil 321:117–152

    CAS  Google Scholar 

  • Högberg P, Read DJ (2006) Towards a more plant physiological perspective on soil ecology. Trends Ecol Evol 21:548–554

    PubMed  Google Scholar 

  • Högberg P, Högberg MN, Göttlicher SG, Beston NR, Keel SG, Metcalfe DB, Campbell C, Schindlbacher A, Hurry V, Lundmark T, Linder S, Näsholm T (2008) High temporal resolution tracing of photosynthate carbon from the tree canopy to forest soil microorganisms. New Phytol 177:220–228

    PubMed  Google Scholar 

  • Hood MA, van Dijk KV, Nelson EB (1998) Factors affecting attachment of Enterobacter cloacae to germinating cotton seed. Microb Ecol 36:101–110

    PubMed  Google Scholar 

  • Hütsch BW, Augustin J, Merbach W (2002) Plant rhizodeposition- an important source for carbon turnover in soils. J Plant Nutr Soil Sci 165:397–407

    Google Scholar 

  • Ibekwe AM, Grieve CM (2004) Changes in developing plant microbial community structure as affected by contaminated water. FEMS Microbiol Ecol 48:239–248

    PubMed  CAS  Google Scholar 

  • Ibekwe AM, Poss JA, Grattan SR, Grieve CM, Suarez D (2010) Bacterial diversity in cucumber (Cucumis sativus) rhizosphere in response to salinity, soil pH, and carbon. Soil Biol Biochem 42:567–575

    CAS  Google Scholar 

  • Idris R, Trifonova R, Puschenreiter M, Wenzel WW, Sessitsch A (2004) Bacterial communities associated with flowering plants of the Ni hyperaccumulator Thlaspi goesingense. Appl Environ Microbiol 70:2667–2677

    PubMed  CAS  Google Scholar 

  • Idris A, Labuschagne N, Korsten L (2009) Efficacy of rhizobacteria for growth promotion in sorghum under greenhouse conditions and selected modes of action studies. J Agri Sci 147:17–30

    CAS  Google Scholar 

  • Ikeda S, Okubo T, Takeda N, Banba M, Sasaki K, Imaizumi-Anraku H, Fujihara S, Ohwaki Y, Ohshima K, Fukuta Y, Eda S, Mitsui H, Hattori M, Sato T, Shinano T, Minamisawa K (2011) The genotype of the calcium/calmodulin-dependent protein kinase dene (CCaMK) determines bacterial community diversity in rice roots under paddy and upland field conditions. Appl Environ Microbiol 77:4399–4405

    PubMed  CAS  Google Scholar 

  • Inbar E, Green SJ, Hadar Y, Minz D (2005) Competing factors of compost concentration and proximity to root affect the distribution of Streptomycetes. Microb Ecol 50:73–81

    PubMed  Google Scholar 

  • Inceoğlu Ö, Abu Al-Soud W, Falcã Salles J, Semanov AV, van Elsas JD (2011) Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing. PLoS One 6:e23321

    PubMed  Google Scholar 

  • Insunza V, Alström S, Eriksson KB (2002) Root bacteria from nematicidal plants and their biocontrol potential against trichodorid nematodes in potato. Plant Soil 241:271–278

    CAS  Google Scholar 

  • Jack ALH, Rangarajan A, Culman SW, Sooksa-Nguan T, Thies JE (2011) Choice of organic amendments in tomato transplants has lasting effects on bacterial rhizosphere communities and crop performance in the field. Appl Soil Ecol 48:94–101

    Google Scholar 

  • Jenkins MB, Franzluebbers AJ, Humayoun SB (2006) Assessing short-term responses of prokaryotic communities in bulk and rhizosphere soils to tall fescue endophyte infection. Plant Soil 289:309–320

    CAS  Google Scholar 

  • Ji X, Lu G, Gai Y, Gao H, Lu B, Kong L, Mu Z (2010) Colonization of Morus alba L. by the plant-growth-promoting and antagonistic bacterium Burkholderia cepacia strain Lu10-1. BMC Microbiol 10:243

    PubMed  Google Scholar 

  • Jones DL, Hodge A, Kuzyakov Y (2004) Plant and mycorrhizal regulation of rhizodeposition. New Phytol 163:459–480

    CAS  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

    CAS  Google Scholar 

  • Jossi M, Fromin N, Tarnawski S, Kohler F, Gillet F, Aragno M, Hamelin J (2006) How elevated pCO2 modifies total and metabolically active bacterial communities in the rhizosphere of two perennial grasses grown under field conditions. FEMS Microbiol Ecol 55:339–350

    PubMed  CAS  Google Scholar 

  • Jung S, Park S, Kim D, Kim SB (2008) Denaturing gradient gel electrophoresis analysis of bacterial community profiles in the rhizosphere of cry1AC-carrying Brassica rapa subsp. pekinensis. J Microbiol 46:12–15

    PubMed  CAS  Google Scholar 

  • Kaiser O, Pühler A, Selbitschka W (2001) Phylogenetic analysis of microbial diversity in the rhizoplane of oilseed rape (Brassica napus cv. Westar) employing cultivation-dependent and cultivation-independent approaches. Microb Ecol 42:136–149

    PubMed  CAS  Google Scholar 

  • Kao-Kniffin J, Balser TC (2007) Elevated CO2 differentially alters belowground plant and soil microbial community structure in reed canary grass-invaded experimental wetlands. Soil Biol Biochem 39:517–525

    CAS  Google Scholar 

  • Kao-Kniffin J, Freyre DS, Balser TC (2010) Methane dynamics across wetland plant species. Aquat Bot 93:107–113

    CAS  Google Scholar 

  • Kao-Kniffin J, Freyer DS, Balser TC (2011) Increased methane emissions from an invasive wetland plant under elevated carbon dioxide levels. Appl Soil Ecol 48:309–312

    Google Scholar 

  • Karpouzas DG, Karatasas A, Spiridaki E, Rousidou C, Bekris F, Omirou M, Ehaliotis C, Papadopoulpus KK (2011) Impact of a beneficial and a pathogenic Fusarium strain on the fingerprinting-based structure of microbial communities in tomato (Lycopersicon esculentum Milll.) rhizosphere. Eur. J. Soil Biol 47:400–408

    Google Scholar 

  • Khamna S, Yokota A, Lumyong S (2009) Actinomycetes isolated from medicinal plant rhizosphere soils: diversity and screening of antifungal compounds, indole-3-acetic acid and siderophore production. World J Microb Biot 25:649–655

    CAS  Google Scholar 

  • Kielak A, Pijl AS, van Veen JA, Kowalchuk GA (2008) Differences in vegetation composition and plant species identity lead to only minor changes in soil-borne microbial communities in a former arable field. FEMS Microbiol Ecol 63:372–382

    PubMed  CAS  Google Scholar 

  • Kiely PD, Haynes JM, Higgins CH, Franks A, Mark GL, Morrissey JP, O’Gara F (2006) Exploiting new systems-based strategies to elucidate plant-bacterial interactions in the rhizosphere. Microb Ecol 51:257–266

    PubMed  CAS  Google Scholar 

  • Kleineidam K, Košmrlj K, Kublik S, Palmer I, Pfab H, Ruser R, Fiedler S, Schloter M (2011) Influence of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on ammonia-oxidizing bacteria and archaea in rhizosphere and bulk soil. Chemosphere 84:182–186

    PubMed  CAS  Google Scholar 

  • Klironomos JN, Rilling MC, Allen MF (1996) Below-ground microbial and microfaunal responses to Artemisia tridentata grown under elevated atmospheric CO2. Funct Ecol 10:527–534

    Google Scholar 

  • Kloepper JW, Rodríguez-Kábana R, McInory JA, Young RW (1992) Rhizosphere bacteria antagonistic to soybean cyct (Heteroera glycines) and root-knot (Meloidogyne incognita) nematodes: identification by fatty acid analysis and frequency of biological control activity. Plant Soil 139:75–84

    CAS  Google Scholar 

  • Kluepfel DA, McInnis TM, Zehr EI (1993) Involvement of root-colonizing bacteria in peach orchard soils suppressive of the nematode Criconemella xenoplax. Phytopathology 83:1240–1245

    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

    PubMed  CAS  Google Scholar 

  • Köberl M, Müller H, Ramadan EM, Berg G (2011) Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health. PLoS One 6:e24452

    PubMed  Google Scholar 

  • Kohler J, Knapp BA, Waldhuber S, Caravaca F, Roldán A, Insam H (2010) Effects of elevated CO2, water stress, and inoculation with Glomus intraradices or Pseudomonas nemdocina of lettuce dry matter and rhizosphere microbial and functional diversity under growth chamber conditions. J Soils Sediment 10:1585–1597

    CAS  Google Scholar 

  • Kolton M, Meller Harel Y, Pasternak Z, Graber ER, Elad Y, Cytryn E (2011) Impact of biochar application to soil on the root-associated bacterial community structure of fully developed greenhouse pepper plants. Appl Environ Microbiol 77:4924–4930

    PubMed  CAS  Google Scholar 

  • Kowalchuk GA, Yergean E, Leveau JHJ, Sessitch A, Bailey M (2010) Plant associated microbial communities. In: Liu WT, Jansson JK (eds) Environmental molecular biology. Caister Academic Press, Norfolk, pp 131–148

    Google Scholar 

  • Kozdrój J, Trevors JT, van Elsas JD (2004) Influence of introduced potential biocontrol agents on maize seedling growth and bacterial community structure in the rhizosphere. Soil Biol Biochem 36:1775–1784

    Google Scholar 

  • Krechel A, Faupel A, Hallmann J, Ulrich A, Berg G (2002) Potato-associated bacteria and their antagonistic potential towards plant-pathogenic fungi and the plant-parasitic nematode Meloidogyne incognita (Kofoid & White) Chitwood. Can J Microbiol 48:772–786

    PubMed  CAS  Google Scholar 

  • Kremer RJ, Means NE (2009) Glyphosate and glyphosate-resistant crop interactions with rhizosphere microorganisms. Eur J Agron 31:153–161

    CAS  Google Scholar 

  • Krüger M, Frenzel P, Kemnitz D, Conrad R (2005) Activity, structure and dynamics of the methanogenic archaeal community in a flooded Italian rice field. FEMS Microbiol Ecol 51:323–331

    PubMed  Google Scholar 

  • Kuske CR, Barns SM, Busch JD (1997) Diverse uncultivated bacterial groups form soils of the arid southwestern United States that are present in many geographic regions. Appl Environ Microbiol 63:3614–3621

    PubMed  CAS  Google Scholar 

  • Kuzyakov Y, Domanski G (2000) Carbon input by plants into the soil. Review. J Plant Nutr Soil Sci 163:421–431

    CAS  Google Scholar 

  • Kuzyakov Y, Domanski G (2002) Model for rhizodeposition and CO2 efflux from planted soil and its validation by 14C pulse labeling of ryegrass. Pant Soil 239:87–102

    CAS  Google Scholar 

  • Kuzyakov Y, Raskatov A, Kaupenjohann M (2003) Turnover and distribution of root exudates of Zea mays. Plant Soil 254:317–327

    CAS  Google Scholar 

  • La Scola B, Birtles RJ, Mallet MN, Raoult D (1998) Massilia timonae gen. nov., sp. nov., isolated from blood of an immunocompromised patient with cerebellar lesions. J Clin Microbiol 36:2847–2852

    PubMed  Google Scholar 

  • Laheurte F, Berthelin J (1988) Effect of a phosphate solubilizing bacteria on maize growth and root exudation over four levels of labile phosphorus. Plant Soil 105:11–17

    CAS  Google Scholar 

  • Larigauderie A, Reynolds JF, Strain BR (1994) Root response to CO2 enrichment and nitrogen supply in loblolly pine. Plant Soil 165:21–32

    CAS  Google Scholar 

  • Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111–5120

    PubMed  CAS  Google Scholar 

  • Lee SH, Ka JO, Cho JC (2008) Members of the phylum Acidobacteria are dominant and metabolically active in rhizosphere soil. FEMS Microbiol Ecol 285:263–269

    CAS  Google Scholar 

  • Lehmann-Richter S, Großkopf R, Liesack W, Frenzel P, Conrad R (1999) Methanogenic archaea and CO2-dependent methanogenesis on washed rice roots. Environ Microbiol 1:159–166

    PubMed  CAS  Google Scholar 

  • Leninger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806–809

    Google Scholar 

  • Lerner A, Hersckovitz Y, Baudoin E, Nazaret S, Moenne-Loccoz Y, Okon Y, Jurkevitch E (2006) Effect of Azospirillum brasilense inoculation on rhizobacterial communities analyzed by denaturing gradient gel electrophoresis and automated ribosomal intergenic spacer analysis. Soil Biol Biochem 38:1212–1218

    CAS  Google Scholar 

  • Lewis JD, Ward JK, Tissue DT (2010) Phosphorus supply drives nonlinear responses of cottonwood (Populus deltoids) to increases in CO2 concentration from glacial to future concentrations. New Phytol 187:438–448

    PubMed  CAS  Google Scholar 

  • Liljeroth E, van Veen JA, Miller HJ (1990) Assimilate translocation to the rhizosphere of two wheat lines and subsequent utilization by rhizosphere microorganisms at two soil nitrogen concentrations. Soil Biol Biochem 22:1015–1021

    CAS  Google Scholar 

  • Lin Q, Zhao HM, Chen YX (2007) Effects of 2,4-dichlorophenol, pentachlorophenol and vegetation on microbial characteristics in a heavy metal polluted soil. J Environ Sci Heal B 42:551–557

    CAS  Google Scholar 

  • Lindquist D, Murrill D, Burran WP, Winans G, Janda MJ, Probert W (2003) Characteristics of Massilia timonae and Massilia timonae-like isolates from human patients, with an emended description of the species. J Clin Microbiol 41:192–196

    PubMed  CAS  Google Scholar 

  • Lioussanne L, Perreault F, Jolicoeur M, St-Arnaud M (2010) The bacterial community of tomato rhizosphere is modified by inoculation with arbuscular mycrorrhizal fungi but unaffected by soil enrichment with mycorrhizal root exudates or inoculation with Phytophthora nicotianae. Soil Biol Biochem 42:473–483

    CAS  Google Scholar 

  • Liu X, Zhao H, Chen S (2006) Colonization of maize and rice plants by strain Bacillus megaterium C4. Curr Microbiol 52:186–190

    PubMed  CAS  Google Scholar 

  • Liu W, Lu HH, Wu W, Wei QK, Chen YX, Thies JE (2008) Transgenic Bt rice does not affect enzyme activities and microbial composition in the rhizosphere during crop development. Soil Biol Biochem 40:475–486

    CAS  Google Scholar 

  • Lopes MS, Foyer CH (2012) The impact of high CO2 on plant abiotic stress tolerance. In: Slafer GA, Araus JL (eds) Crop stress management and global climate change. CABI, Wallingford, pp 85–100

    Google Scholar 

  • Lottmann J, Heuer H, Smalla K, Berg G (1999) Influence of transgenic T4-lysozyme-producing potato plants on potentially beneficial plant-associated bacteria. FEMS Microbiol Ecol 29:365–377

    CAS  Google Scholar 

  • Lottmann J, Heuer H, de Vries J, Mahn A, Düring K, Wackernagel W, Smalla K, Berg G (2000) Establishment of introduced antagonistic bacteria in the rhizosphere of transgenic potatoes and their effect on the bacterial community. FEMS Microbiol Ecol 33:41–49

    PubMed  Google Scholar 

  • Lu Y, Conrad R (2005) In situ isotope probing of methanogenic Archaea in the rice rhizosphere. Science 309:1088–1090

    PubMed  CAS  Google Scholar 

  • Lu Y, Lueders T, Friedrich MW, Conrad R (2005) Detecting active methanogenic populations on rice roots using stable isotope probing. Environ Microbiol 7:326–336

    PubMed  CAS  Google Scholar 

  • Lu Y, Wolf-Rainer A, Conrad R (2007) Spatial variation of active microbiota in the rice rhizosphere revealed by in situ stable isotope probing of phospholipid fatty acids. Environ Microbiol 9:474–481

    PubMed  CAS  Google Scholar 

  • Lübeck PS, Hansen M, Sørensen J (2000) Simultaneous detection of the establishment of seed-inoculated Pseudomonas fluorescens strain DR54 and native soil bacteria on sugar beet root surfaces using fluorescence antibody and in situ hybridization technique. FEMS Microbiol Ecol 33:11–19

    PubMed  Google Scholar 

  • Lucas-García JA, Domenech J, Santamaría C, Camacho M, Daza A, Gutierrez Mañero FJ (2004) Growth of forest plants (pine and holm-oak) inoculated with rhizobacteria: relationship with microbial community structure and biological activity of its rhizosphere. Environ Exp Bot 52:239–251

    Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Mahaffee WE, Kloepper JW (1997) Temporal changes in the bacterial communities of soil, rhizosphere, and endorhiza associated with field-grown cucumber (Cucumis sativus L.). Microb Ecol 34:210–223

    PubMed  Google Scholar 

  • Malik KA, Bilal R, Mehnaz S, Rasul G, Mirza MS, Ali S (1997) Association of nitrogen-fixing, plant-growth-promoting rhizobacteria (PGPR) with kallar grass and rice. Plant Soil 194:37–44

    CAS  Google Scholar 

  • Maloney PE, van Bruggen AHC, Hu S (1997) Bacterial community structure in relation to the carbon environments in lettuce and tomato rhizospheres and in bulk soil. Microb Ecol 34:109–117

    PubMed  CAS  Google Scholar 

  • Manter DK, Delgado JA, Holm DG, Stong RA (2010) Pyrosequencing reveals a highly divers and cultivar-specific bacterial endophyte community in potato roots. Microb Ecol 60:157–166

    PubMed  Google Scholar 

  • Mariley L, Aragno M (1999) Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots. Appl Soil Ecol 13:127–136

    Google Scholar 

  • Marilley L, Vogt G, Blanc M, Aragno M (1998) Bacterial diversity in the bulk soil and rhizosphere fractions of Lolium perenne and Trifolium repens as revealed by PCR restriction analysis of 16S rRNA. Plant Soil 198:219–224

    CAS  Google Scholar 

  • Marilley L, Hartwig UA, Aragno M (1999) Influence of an elevated atmospheric CO2 content on soil and rhizosphere bacterial communities beneath Lolium perenne and Trifolium repens under field conditions. Microb Ecol 38:39–49

    PubMed  CAS  Google Scholar 

  • Marschner P, Baumann K (2003) Changes in bacterial community structure induced by mycorrhizal colonization in split-root maize. Plant Soil 251:279–289

    CAS  Google Scholar 

  • Marschner P, Timonen S (2005) Interactions between plant species and mycorrhizal colonization on the bacterial community composition in the rhizosphere. Appl Soil Ecol 28:23–36

    Google Scholar 

  • Marschner P, Crowley DE, Lieberei R (2001a) Arbuscular mycorrhizal infection changes the bacterial 16S rDNA community composition in the rhizosphere of maize. Mycorrhiza 11:297–302

    CAS  Google Scholar 

  • Marschner P, Yang CH, Lieberei R, Crowley DE (2001b) Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol Biochem 33:1437–1445

    CAS  Google Scholar 

  • Marschnner P, Neumann G, Kania A, Wiskopf L, Lieberei R (2002) Spatial and temporal dynamics of the microbial community structure in the rhizosphere of cluster roots of white lupin (Lupinus albus L.). Plant Soil 246:167–174

    Google Scholar 

  • Marschner P, Crowley D, Yang CH (2004) Development of specific rhizosphere bacterial communities in relation to plant species, nutrition and soil type. Plant Soil 261:199–208

    CAS  Google Scholar 

  • Martin JK, Foster RC (1985) A model system for studying the biochemistry and biology of the root-soil interface. Soil Biol Biochem 17:261–269

    CAS  Google Scholar 

  • Mary B, Fresneau C, Morel JL, Mariotti A (1993) C and N cycling during decomposition of root mucilage, roots and glucose in soil. Soil Biol Biochem 25:1005–1014

    CAS  Google Scholar 

  • Matilla MA, Espinosa-Urgel M, Rodrígez-Herva JJ, Ramos JL, Ramos-González MI (2007) Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere. Genome Biol 8:R179

    PubMed  Google Scholar 

  • Mazzola M, Gu YH (2002) Wheat genotype-specific induction of soil microbial communities suppressive to disease incited by Rhizoctonia solani anastomosis group (AG)-5 and AG-8. Phytopathology 92:1300–1307

    PubMed  Google Scholar 

  • Meharg AA, Killham K (1995) Loss of exudates from the roots of perennial ryegrass inoculated with a range of micro-organisms. Plant Soil 170:345–349

    CAS  Google Scholar 

  • Mendes R, Pizzirani-Kleiner AA, Araujo WL, Raaijmakers JM (2007) Diversity of cultivated endophytic bacteria from sugarcane: genetic and biochemical characterization of Burkholderia cepacia complex isolates. Appl Environ Microbiol 73:7259–7267

    PubMed  CAS  Google Scholar 

  • Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JHM, Piceno YM, DeSantis TZ, Andersen GL, Bakker PAHM, Raaijmakers JM (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 331:1097–1100

    Google Scholar 

  • Miethling R, Wieland G, Backhous H, Tebbe CC (2000) Variation of microbial rhizosphere communities in response to crop species, soil origin, and inoculation with Sinorhizobium meliloti L33. Mircob Ecol 41:43–56

    Google Scholar 

  • Miller SCM, LiPuma JJ, Parke JL (2002) Culture-based and non-growth-dependent detection of the Burkholderia cepacia complex in soil environments. Appl Environ Microbiol 68:3750–3758

    PubMed  CAS  Google Scholar 

  • Mishra A, Chauhan PS, Chaudhry V, Tripathi M, Nautiyal CS (2011) Rhizosphere competent Pantoea agglomerans enhances maize (Zea mays) and chickpea (Cicer arietinum L.) growth, without altering the rhizosphere functional diversity. A Van Leeuw J Microb 100:405–413

    Google Scholar 

  • Mogge B, Loferer C, Agerer R, Hutzler P, Hartmann A (2000) Bacteiral community structure and colonization patterns of Fagus sylvatica L. ectomycorrhizospheres as determined by fluorescence in situ hybridization and confocal laser scanning microscopy. Mycorrhiza 9:271–278

    Google Scholar 

  • Montealegre CM, Van Kessel C, Blumenthal JM, Hur HG, Hartwig UA, Sadowsky MJ (2000) Elevated atmospheric CO2 alters microbial population structure in a pasture ecosystem. Glob Change Biol 6:475–482

    Google Scholar 

  • Montealegre CM, van Kessel C, Russelle MP, Sadowsky MJ (2002) Changes in microbial activity and composition in a pasture ecosystem exposed to elevated atmospheric carbon dioxide. Plant Soil 243:197–207

    CAS  Google Scholar 

  • Morgan JA, Mosier AR, Milchunas DG, LeCain DR, Nelson JA, Parton WJ (2004) CO2 enhances productivity, alters species composition, and reduces digestibility of shortgrass steppe vegetation. Ecol Appl 14:208–219

    Google Scholar 

  • Nagy ML, Pérez A, Garcia-Pichel F (2005) The prokaryotic diversity of biological soil crusts in the Sonoran Desert (Organ Pipe Cactus National Monument, AZ). FEMS Microbiol Ecol 54:233–245

    PubMed  CAS  Google Scholar 

  • Navarro-Noya YE, Jan-Roblero J, González-Chávez MDC, Hernández-Gama R, Hernández-Rodrígez C (2010) Bacterial communities associated with the rhizosphere of pioneer plants (Bahia xylopoda and Viguiera linearis) growing on heavy metals-contaminated soils. A Van Leeuw J Microb 97:335–349

    CAS  Google Scholar 

  • Nelson DM, Cann IKO, Mackie RI (2010) Response of Archaeal communities in the rhizosphere of maize and soybean to elevated atmospheric CO2 concentrations. PLoS One 5:e15897

    PubMed  CAS  Google Scholar 

  • Newman EI, Bowen HJ (1974) Patterns of distribution of bacteria on root surfaces. Soil Biol Biochem 6:205–209

    Google Scholar 

  • Neumann G, Römheld V (2002) Root-induced changes in the availability of nutrients in the rhizosphere. In: Waisel Y, Eshel A, Kafkafi U (eds) Plant roots: the hidden half, 3rd edn. Marcel Dekker, New York, pp 617–650

    Google Scholar 

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

    CAS  Google Scholar 

  • Nguyen LM, Buttner MP, Cruz P, Smith SD, Robleto EA (2011) Effects of elevated atmospheric CO2 on the rhizosphere soil microbial communities in a Mojave Desert ecosystem. J Arid Enviro 75:917–925

    Google Scholar 

  • Nichols D (2007) Cultivation gives context to the microbial ecologist. FEMS Microbiol Ecol 60:351–357

    PubMed  CAS  Google Scholar 

  • Nicol GW, Glover LA, Prosser JI (2003) The impact of grassland management on archaeal community structure in upland pasture rhizosphere soil. Environ Microbiol 5:152–162

    PubMed  CAS  Google Scholar 

  • Normander B, Prosser JI (2000) Bacterial origin and community composition in the barley phytosphere as a function of habitat and presowing conditions. Appl Environ Microbiol 66:4372–4377

    PubMed  CAS  Google Scholar 

  • Ofek M, Ruppel S, Waisel Y (2007) Differences between bacterial associations with two root types of Vicia faba L. Plant Biosyst 141:352–362

    Google Scholar 

  • Ofek M, Hadar Y, Minz D (2009) Comparison of effects of compost amendment and single-strain inoculation on root bacterial communities of young cucumber seedlings. Appl Environ Microbiol 75:6441–6450

    PubMed  CAS  Google Scholar 

  • Ofek M, Hadar Y, Minz D (2011) Colonization of cucumber seeds by bacteria during germination. Environ Microbiol 13:2794–2807

    PubMed  Google Scholar 

  • Offre O, Pivato B, Siblot S, Gamalero E, Corberand T, Lemanceau P, Mougel C (2007) Identification of bacterial groups preferentially associated with mycorrhizal roots of Medicago truncatula. Appl Environ Microbiol 73:913–921

    PubMed  CAS  Google Scholar 

  • Oliveira CA, Alves VMC, Marriel IE, Gomes EA, Scotti MR, Carneiro NP, Guimarães CT, Schaffert RE, Sá NMH (2009) Phosphate solubilizing microorganisms isolated from rhizosphere of maize cultivated in an oxisol of the Brazilian Cerrado Biome. Soil Biol Biochem 41:1782–1787

    CAS  Google Scholar 

  • Olsson PA, Wallander H (1998) Interactions between ectomycorrhizal fungi and the bacterial community in soils amended with various primary minerals. FEMS Microbiol Ecol 27:195–205

    CAS  Google Scholar 

  • Ostle N, Whiteley AS, Bailey MJ, Sleep D, Ineson P, Manefield M (2003) Active microbial RNA turnover in a grassland soil estimated using a 13CO2 spike. Soil Biol Biochem 35:877–885

    CAS  Google Scholar 

  • Øvreås L, Torsvik V (1998) Microbial diversity and community structure in two different agricultural soil communities. Microb Ecol 36:303–315

    PubMed  Google Scholar 

  • Oyaizu-Masuchi Y, Komagata K (1988) Isolation of free-living nitrogen-fixing bacteria from the rhizosphere of rice. J Gen Appl Microbiol 34:127–164

    CAS  Google Scholar 

  • Pakarinen J, Hyvärinen A, Salkinoja-Salonen M, Laitinen S, Nevalainen A, Mäkelä MJ, Haahtela T, von Hertzen L (2008) Predominance of Gram-positive bacteria in house dust in the low-allergy risk Russian Karelia. Environ Microbiol 10:3317–3325

    PubMed  CAS  Google Scholar 

  • Paterson E, Rattray EAS, Killham K (1996) Effect of elevated atmospheric CO2 concentration on C-partitioning and rhizosphere C-flow for three plant species. Soil Biol Biochem 28:195–201

    CAS  Google Scholar 

  • Paterson E, Hall JM, Rattray EAS, Griffiths BS, Ritz K, Killham K (1997) Effect of elevated CO2 on rhizosphere carbon flow and soil microbial processes. Glob Change Biol 3:363–377

    Google Scholar 

  • Paterson E, Thornton B, Midwood AJ, Osborne SM, Millard P (2008) Atmopheric CO2 enrichment and nutrient additions to planted soil increases mineralization of soil organic matter, but do not alter microbial utilization of plant- and soil C-sources. Soil Biol Biochem 40:2434–2440

    CAS  Google Scholar 

  • Paungfoo-Lonhienne C, Lonhienne TGA, Rentsch D, Robinson N, Christie M, Webb RI, Hamage HK, Carroll BJ, Schenk PM, Schmidt S (2008) Plants can use protein as a nitrogen source without assistance from other organisms. P Natl Acad Sci USA 105:4524–4529

    CAS  Google Scholar 

  • Paungfoo-Lonhienne C, Lonhienne TGA, Mudge SR, Schenk PM, Christie M, Carroll BJ, Schmidt S (2010a) DNA is taken up by root hairs and pollen, and stimulates root and pollen tube growth. Plant Physiol 153:799–805

    PubMed  CAS  Google Scholar 

  • Paungfoo-Lonhienne C, Rentsch D, Robatzek S, Webb RI, Sagulenko E, Näsholm T, Schmidt S, Lonhienne TGA (2010b) Turning the table: plants consume microbes as a source of nutrients. PLoS One 5:e11915

    PubMed  Google Scholar 

  • Pedraza RO, Bellone CH, Carrizo de Bellone S, Boa Sorte PMR, Teixeira KRDS (2009) Azospirillum inoculation and nitrogen fertilization effect on grain yield and on the diversity of endophytic bacteria in the phyllosphere of rice rainfed crop. Eur J Soil Biol 45:36–43

    CAS  Google Scholar 

  • Pereira EIP, Chung H, Scow K, Sadowsky MJ, van Kessel C, Six J (2011) Soil nitrogen transformations under elevated atmospheric CO2 and O3 during the soybean growing season. Environ Pollut 159:401–407

    CAS  Google Scholar 

  • Philippot L, Kuffner M, Chèneby D, Depret G, Laguerre G, Martin-Laurent F (2006) Genetic structure and activity of the nitrate-reducers community in the rhizosphere of different cultivars of maize. Plant Soil 287:177–186

    CAS  Google Scholar 

  • Phillips RP (2007) Towards a rhizo-centric view of plant-microbial feedbacks under elevated atmospheric CO2. New Phytol 173:664–667

    PubMed  CAS  Google Scholar 

  • Phillips RP, Bernhardt ES, Schlesinger WH (2009) Elevated CO2 increases root exudation from loblolly pine (Pinus taeda) seedlings as an N-mediated response. Tree Physiol 29:1513–1523

    PubMed  CAS  Google Scholar 

  • Phillips RP, Finzi AC, Bernhardt ES (2011) Enhanced root exudation induces microbial feedbacks to N cycling in a pine forest under long-term CO2 fumigation. Ecol Lett 14:187–194

    PubMed  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Pisa G, Magnani GS, Weber H, Souza EM, Faoro H, Monteiro RA, Daros E, Baura V, Bespalhok JP, Pedrosa FO, Cruz LM (2011) Diversity of 16S rRNA genes from bacteria of sugarcane rhizosphere soil. Bra J Med Biol Res 44:1215–1221

    CAS  Google Scholar 

  • Poole EJ, Bending GD, Whipps JM, Read DJ (2001) Bacteria associated with Pinus sylvestris-Lactarius rufus ectomycorrhizas and their effects on mycorrhiza formation in vitro. New Phytol 151:743–751

    Google Scholar 

  • Poonguzhali S, Madhaiyan M, Yim WJ, Kim KA, Sa TM (2008) Colonization patterns of plant root and leaf surfaces visualized by use of green-fluorescent-marked strain of Methylobacterium suomiense and its persistence in rhizosphere. Appl Microbiol Biot 78:1033–1043

    CAS  Google Scholar 

  • Poplawski AB, Mårtensson L, Wartiainen I, Rasmussen U (2007) Archaeal diversity and community structure in a Swedish barley field: specificity of the EK510R/(EURY498) 16S rDNA primer. J Microbiol Meth 69:161–173

    CAS  Google Scholar 

  • Pregitzer KS, Zak DR, Maziasz J, DeForest J, Curtis PS, Lussenhop J (2000) Interactive effects of atmospheric CO2 and soil-N availability on fine roots of Populus tremuloides. Ecol Appl 10:18–33

    Google Scholar 

  • Probanza A, Mateos JL, Lucas García JA, de Felipe MR, Gutierrez-Mañero FJ (2001) Effect of inoculation with PGPR Bacillus and Pisolithus tinctorius on Pinus pinea L. growth, bacterial rhizosphere colonization, and mycorrhizal infection. Microb Ecol 41:140–148

    PubMed  CAS  Google Scholar 

  • Probanza A, Lucas-García JA, Ruiz Palomino M, Ramos B, Gutiérrez Mañero FJ (2002) Pinus pinea L. seedling growth and bacterial rhizosphere structure after inoculation with PGPR Bacillus (B. lichniformis CECT 5106 and B. pumilus CECT 5105). Appl. Soil Ecol 20:75–84

    Google Scholar 

  • Puente ME, Bashan Y, Li CY, Lebsky VK (2004) Microbial populations and activities in the rhizoplane of rock-weathering desert plants. I. Root colonization and weathering of igneous rocks. Plant Biol 6:629–642

    PubMed  CAS  Google Scholar 

  • Raaijmakers JM, Weller DM, Thomashow LS (1997) Frequency of antibiotic-producing Pseudomonas spp. in natural environments. Appl Environ Microbiol 63:881–887

    PubMed  CAS  Google Scholar 

  • Racke J, Sikora RA (1992) Isolation, formulation and antagonistic activity of rhizobacteria toward the potato cyct nematode Globodera pallida. Soil Biol Biochem 24:521–526

    Google Scholar 

  • Ramachandran VK, East AK, Karunakaran R, Downie JA, Poole PS (2011) Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics. Genome Biol 12:R106

    PubMed  CAS  Google Scholar 

  • Ramakrishnan B, Lueders T, Dunfield PF, Conrad R, Friedrich MW (2001) Archaeal community structures in rice soils from different geographical regions before and after initiation of methane production. FEMS Microbiol Ecol 37:175–186

    CAS  Google Scholar 

  • Ramos B, Lucas García JA, Probanza A, Domenech J, Gutierrez Mañero JF (2003) Influence of an indigenous European alder (Alnus glutinosa (L.) Gaertn) rhizobacterium (Bacillus pumilis) on the growth of alder and its rhizosphere microbial community structure in two soils. New For 25:149–159

    Google Scholar 

  • Rangel-Castro JI, Killham K, Ostle N, Nicol GW, Anderson IC, Scrimgeour CM, Ineson P, Meharg A, Prosser JI (2005a) Stable isotope probing analysis of the influence of liming on root exudates utilization by soil microorganisms. Environ Microbiol 7:828–838

    PubMed  CAS  Google Scholar 

  • Rangel-Castro JI, Prosser JI, Ostle N, Scrimgeour CM, Killham K, Meharg AA (2005b) Flux and turnover of fixed carbon in soil microbial biomass of limed and unlimed plots of an upland grassland ecosystem. Environ Microbiol 7:544–552

    PubMed  CAS  Google Scholar 

  • Rasche F, Hödl V, Poll C, Kandeler E, Gerzabek MH, van Elsas JD, Sessitsch A (2006) Rhizosphere bacteria affected by transgenic potatoes with antibacterial activities compared with the effects of soil, wild-type potatoes, vegetation stage and pathogen exposure. FEMS Microbiol Ecol 56:219–235

    PubMed  CAS  Google Scholar 

  • Rattray EAS, Paterson E, Killham K (1995) Characterisation of the dynamics of C-partitioning within Lolium perenne and to the rhizosphere microbial biomass using 14C pulse chase. Biol Fertil Soils 19:280–286

    Google Scholar 

  • Richardt W, Mascariña G, Padre B, Doll J (1997) Microbial communities of continuously cropped irrigated rice fields. Appl Environ Microbiol 63:233–238

    Google Scholar 

  • Riedewald F (2006) Bacterial adhesion to surfaces: the influence of surface roughness. PDA J Pharm Sci Technol 60:164–171

    PubMed  Google Scholar 

  • Rigamonte TA, Pylro VS, Daurte GF (2010) The role of mycorrhization helper bacteria in the establishment and action of ectomycorrhizae association. Bra J Microbiol 41:832–840

    Google Scholar 

  • Rillig MC, Scow KM, Kilonomos JN, Allen MF (1997) Microbial carbon-substrate utilization in the rhizosphere of Gutierrezia sorothrae grown in elevated atmospheric carbon dioxide. Soil Biol Biochem 29:1387–1394

    CAS  Google Scholar 

  • Rinan R, Nerg AM, Ahtoniemi P, Suokanerva H, Holopainen T, Kyrö E, Bååth E (2008) Plant-mediated effects of elevated ultraviolet-B radiation on peat microbial communities of a subarctic mire. Glob Change Biol 14:925–937

    Google Scholar 

  • Ringelberg DB, Stair JO, Almeida J, Norby RJ, O’Neill EG, White DC (1997) Consequences of rising atmospheric carbon dioxide levels for the belowground microbiota associated with white Oak. J Environ Qual 26:495–503

    CAS  Google Scholar 

  • Robleto EA, Borneman J, Triplett EW (1998) Effects of bacterial antibiotic production on rhizosphere microbial communities from a culture-independent perspective. Appl Environ Microbiol 64:5020–5022

    PubMed  CAS  Google Scholar 

  • Rodríguez-Díaz M, Rodelas-Gonzalés B, Pozo-Clemente C, Martínez-Toledo MV, González-López J (2008) A review on the taxonomy and possible screening traits of plant growth-promoting rhizobacteria. In: Pichtel AJ, Hayat S (eds) Plant-bacteria interactions: strategies and techniques to promote plant growth. Wiley-VCH, Weinheim, pp 55–80

    Google Scholar 

  • Roesch LFW, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, Kent AD, Daroub SH, Camargo FAO, Farmerie WG, Triplett EW (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290

    PubMed  CAS  Google Scholar 

  • Roesti D, Gaur R, Johri BN, Imfeld G, Sharma S, Kawaljeet K, Aragno M (2006) Plant growth stage, fertilizer management and bio-inoculation of arbuscular mycorrhizal fungi and plant growth promoting rhizobacteia affect the rhizobacterial community structure in rain-fed what fields. Soil Biol Biochem 38:1111–1120

    CAS  Google Scholar 

  • Rogers HH, Runion GB, Krupa SV (1994) Plant responses to atmospheric CO2 enrichment with emphasis on roots and the rhizosphere. Environ Pollut 83:155–189

    PubMed  CAS  Google Scholar 

  • Rondon MR, Goodman RM, Handelsman J (1999) The earth’s bounty: assessing and accessing soil microbial diversity. Trends Biotechnol 17:403–409

    PubMed  CAS  Google Scholar 

  • Rønn R, Gavito M, Larsen J, Jakobsen I, Frederiksen H, Christensen S (2002) Response of free-living soil protozoa and microorganisms to elevated atmospheric CO2 and presence of mycorrhiza. Soil Biol Biochem 34:923–932

    Google Scholar 

  • Ros M, Pascual JA, Garcia C, Mernandez MT, Insam H (2006) Hydrolase activities, microbial biomass and bacterial community in a soil after long-term amendment with different composts. Soil Biol Biochem 38:3443–3452

    CAS  Google Scholar 

  • Rosenberg E, Zilberg-Rosenberg I (2011) Symbiosis and development: the hologenome concept. Birth Defects Res 93:56–66

    CAS  Google Scholar 

  • Rosenberg E, Koren O, Reshef L, Efrony R, Zilberg-Rosenberg I (2007) The role of microorganisms in coral health, disease and evolution. Nat Rev Microbiol 5:355–362

    PubMed  CAS  Google Scholar 

  • Rovira AD (1965) Interactions between plant roots and soil microorganisms. Annu Rev Microbiol 19:241–266

    PubMed  CAS  Google Scholar 

  • Rovira AD, Campbell R (1974) Scanning electron microscopy of microorganisms on the roots of wheat. Microb Ecol 1:15–23

    Google Scholar 

  • Rovira AD, Campbell R (1975) A scanning electron microscope study of interaction between micro-organisms and Gaeumannomyces graminis (Syn. Ophiobolus graminis) on wheat roots. Microb Ecol 2:177–185

    Google Scholar 

  • Rovira AD, Newman EI, Bowen HJ, Campbell R (1974) Quantitative assessment of the rhizoplane microflora by direct microscopy. Soil Biol Biochem 6:211–216

    Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Ruffel S, Freixes S, Balzergue S, Tillard P, Jeudy C, Martin-Magniette ML, van der Merwe MJ, Kakar K, Gouzy J, Fernie AR, Udvardi M, Salon C, Gojon A, Lepetit M (2008) Systemic signaling of the plant nitrogen status triggers specific transcriptome responses depending on the nitrogen source in Medicago truncatula. Plant Physiol 146:2020–2035

    PubMed  CAS  Google Scholar 

  • Rui YK, Yi GX, Zhao J, Wang BM, Li ZH, Zhai ZX, He ZP, Li QX (2005) Changes of Bt toxin in the rhizosphere of transgenic Bt cotton and its influence on soil functional bacteria. World J Microbiol 21:1279–1284

    CAS  Google Scholar 

  • Ryan PR, Dessaux Y, Thomashow LS, Weller DM (2009) Rhizosphere engineering and management for sustainable agriculture. Plant Soil 321:363–383

    CAS  Google Scholar 

  • Salles JF, van Veen JA, van Elsas JD (2004) Multivariate analyses of Burkholderia species in soil: effect of crop and land use history. Appl Environ Microbiol 70:4012–4020

    PubMed  CAS  Google Scholar 

  • Sarathchandra SU, Bruch G, Cox NR (1997) Growth patterns of bacterial communities in the rhizoplane and rhizosphere of white clover (Trifolium repens L.) and perennial ryegrass (Lolium perenne L.) in long-term pasture. Appl. Soil Ecol 6:293–299

    Google Scholar 

  • Sato A, Watanabe T, Unno Y, Purnomo E, Osaki M, Shinano T (2009) Analysis of diversity of diazotrophic bacteria associated with the rhizosphere of a tropical arbor, Melastoma malabathricum L. Microbes Environ 24:81–870

    PubMed  Google Scholar 

  • Schallmach E, Minz D, Jurkevitch E (2000) Culture-independent detection of changes in root-associated bacterial populations of common bean (Phaseolus vulgaris L.) following nitrogen depletion. Microb Ecol 40:309–316

    PubMed  CAS  Google Scholar 

  • Scheid D, Stubner S, Conrad R (2003) Effects of nitrate- and sulfate-amendment on the methanogenic populations in rice root incubations. FEMS Microbiol Ecol 43:309–315

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Scheublin TR, Sanders IR, Keel C, van der Meer JR (2010) Characterisation of microbial communities colonizing the hyphal surface of arbuscular mycorrhizal fungi. ISME J 4:752–763

    PubMed  Google Scholar 

  • Schloss PD, Handelsman J (2006) Toward a census of bacteria in soil. PLoS Comp Biol 2:e92

    Google Scholar 

  • Schloter M, Winkler JB, Aneja M, Koch N, Fleischmann F, Pritsch K, Heller W, Stich S, Grams TEE, Göttlein A, Matyssek R, Munch JC (2005) Short term effects of ozone on the plant-rhizosphere-bulk soil system of young beech trees. Plant Biol 7:728–736

    PubMed  CAS  Google Scholar 

  • Schmalengerger A, Tebbe CC (2002) Bacterial community composition in the rhizosphere of a transgenic, herbicide-resistant maize (Zea mays) and comparison to its non-transtenic cultivar Bosphore. FEMS Microbiol Ecol 40:29–37

    Google Scholar 

  • Schmalenberger A, Tebbe CC (2003) Genetic profiling of noncultivated bacteria from the rhizosphere of sugar beet (Beta vulgaris) reveal field and annual variability but no effect of a transgenic herbicide resistance. Can J Microbiol 49:1–8

    PubMed  CAS  Google Scholar 

  • Schortemeyer M, Hartwig UA, Hendrey GR, Sadowsky MJ (1996) Microbial community changes in the rhizospheres of white clover and perennial ryegrass exposed to free air carbon dioxide enrichment (FACE). Soil Biol Biochem 28:1717–1724

    CAS  Google Scholar 

  • Schwieger F, Tebbe CC (2000) Effect of field inoculation with Sinorhizobium meliloti L33 on the composition of bacterial communities in the rhizosphere of a target plant (Medicago sativa) and a non-target plant (Chenopodium album) – Linking of 16S rRNA gene-based single-strand conformation polymorphism community profiles to the diversity of cultivated bacteria. Appl Environ Microbiol 66:3553–3565

    Google Scholar 

  • Scott JS, Knudsen GR (1999) Soil amendment effects of rape (Brassica napus) residues on pea rhizosphere bacteria. Soil Biol Biochem 31:1435–1441

    CAS  Google Scholar 

  • Senthilkumar M, Anandham R, Madhaiyan M, Venkateswaran V, Sa T (2011) Endophytic bacteria: perspectives and applications in Agricultural crop production. In: Maheshwari DK (ed) Bacteria in agrobiology: crop ecosystems. Springer, Berlin/Heidelberg, pp 61–96

    Google Scholar 

  • Sessitsch A, Kan FY, Pfeifer U (2003) Diversity and community structure of culturable Bacillus spp. populations in the rhizosphere of transgenic potatoes expressing the lytic peptide cecropin B. Appl. Soil Ecol 22:149–158

    Google Scholar 

  • Sessitsch A, Gyamfi S, Tscherko D, Gerzabek MH, Kabdeler E (2004) Activity of microorganisms in the rhizosphere of herbicide treated and untreated transgenic glufosinate-tolerant and wildtype oilseed rape grown in containment. Plant Soil 266:105–113

    CAS  Google Scholar 

  • Shanmugam V, Verma R, Rajkumar S, Naruka DS (2011) Bacterial diversity and soil enzyme activity in diseased and disease free apple rhizosphere soils. Ann Microbiol 61:765–772

    CAS  Google Scholar 

  • Shiomi Y, Mishitama M, Onizuka T, Marumoto T (1999) Comparison of bacterial community structures in the rhizoplane of tomato plants grown in soils suppressive and conducive towards bacterial wilt. Appl Environ Microbiol 65:3996–4001

    PubMed  CAS  Google Scholar 

  • Siciliano SD, Germida JJ (1999) Taxonomic diversity of bacteria associated with the roots of field-grown transgenic Brassica napus cv. Quest, compared to the non-transgenic B. napus cv. Excel and B. rapa cv. Parkland. FEMS Microbiol Ecol 29:263–272

    CAS  Google Scholar 

  • Simon HM, Dodsworth JA, Goodman RM (2000) Crenarchaeota colonize terrestrial plant roots. Environ Microbiol 2:495–505

    PubMed  CAS  Google Scholar 

  • Singh BK, Munro S, Potts JM, Millard P (2007) Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils. Appl Soil Ecol 36:147–155

    Google Scholar 

  • Sliwinski MK, Goodman RM (2004) Comparison of Crenarchaeal consortia inhabiting the rhizosphere of diverse terrestrial plants with those in bulk soil in native environments. Appl Environ Microbiol 70:1821–1826

    PubMed  CAS  Google Scholar 

  • Söderberg KH, Olsson PA, Bååth E (2002) Structure and activity of the bacterial community in the rhizosphere of different plant species and the effect of arbuscular mycorrhizal colonization. FEMS Microbiol Ecol 40:223–231

    PubMed  Google Scholar 

  • Solís-Domínguez AF, Valentín-Vargas A, Chorover J, Maier RM (2011) Effect of arbuscular mycorrhizal fungi on plant biomass and the rhizosphere microbial community structure of mesquite grown in acidic lead/zinc mine tailings. Sci Total Environ 409:1009–1016

    PubMed  Google Scholar 

  • Somenahally AC, Hollister EB, Loeppert RH, Yan W, Gentry TJ (2011) Microbial communities in rice rhizosphere altered by intermittent and continuous flooding in fields with long-term arsenic application. Soil Biol Biochem 43:1220–1228

    CAS  Google Scholar 

  • Stanfford WHL, Baker GC, Brown SA, Burton SG, Cowan DA (2005) Bacterial diversity in the rhizosphere of Proteaceae species. Environ Microbiol 7:1755–1768

    Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Teixeira LCRS, Peixoto RS, Cury JC, Sul WJ, Pellizari VH, Tiedge J, Rosado AS (2010) Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty bay, maritime Antartica. ISME J 4:989–1001

    PubMed  Google Scholar 

  • Thies JE, Woomer PL, Singleton PW (1995) Enrichment of Bradyrhizobium spp. populations in soil due to cropping of the homologous host legume. Soil Biol. Biochem 27:633–636

    CAS  Google Scholar 

  • Timonen S, Jørgensen S, Haahtela K, Sen R (1998) Bacterial community structure at defined locations of Pinus sylvestris-Suillus bovinus and Pinus sylvestris-Paxillus involutus mycorrhizospheres in dry pine forest humus and nursery peat. Can J Microbiol 44:499–513

    CAS  Google Scholar 

  • Tiquia SM, Lloyd J, Herms DA, Hoitink HAJ, Michel FC Jr (2002) Effects of mulching and fertilization on soil nutrients, microbial activity and rhizosphere bacterial community structure determined by analysis of TRFLPs of PCR-amplified 16S rRNA genes. Appl Soil Ecol 21:31–48

    Google Scholar 

  • Tobita H, Uemura A, Kitao M, Kitaoka S, Maruyama Y, Utsugi H (2011) Effects of elevated atmospheric carbon dioxide, soil nutrients and water conditions on photosymthetic and growth responses of Alnus hirsute. FunctPlant Biol 38:702–710

    CAS  Google Scholar 

  • Toljander JF, Lindahl BD, Paul LR, Elfstrand M, Finlay RD (2007) Influence of arbuscular mycorrhizal mycelia exudates on soil bacterial growth and community structure. FEMS Microbiol Ecol 61:295–304

    PubMed  CAS  Google Scholar 

  • Toljander JF, Santos-González JC, Tehler A, Finlay RD (2008) Community analysis of arbuscular mycorrhizal fungi and bacteria in the maize mycorrhizosphere in a long-term fertilization trail. FEMS Microbiol Ecol 65:323–338

    PubMed  CAS  Google Scholar 

  • Torsvik V, Sørheim R, Goksøyr J (1996) Total bacterial diversity in soil and sediment communities- a review. J Ind Microbiol 17:170–178

    CAS  Google Scholar 

  • Treonis AM, Ostle NJ, Stott AW, Primrose R, Grayston SJ, Ineson P (2004) Identification of groups of metabolically-active rhizosphere microorganisms by stable isotope probing of PLFAs. Soil Biol Biochem 36:533–537

    CAS  Google Scholar 

  • Trivedi P, Duan Y, Wang N (2010) Huanglongbing, a systemic disease, restructures the bacterial community associated with citrus roots. Appl Environ Microbiol 76:3427–3436

    PubMed  CAS  Google Scholar 

  • Uren NC (2001) Types, amounts, and possible functions of compounds released into the rhizosphere by soil-grown plants. In: Pinton R, Varanini Z, Nannipieri P (eds) The rhizosphere. Marcel Dekker, New York, pp 19–40

    Google Scholar 

  • Uroz S, Buée M, Murat C, Frey-Klett P, Martin F (2010) Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ Microbiol Rep 2:281–288

    CAS  Google Scholar 

  • Van Elsas JD, Bersma FGH (2011) A review of molecular methods to study the microbiota of soil and the mycosphere. Eur J Soil Biol 47:77–87

    Google Scholar 

  • Van Elsas JD, Garbeva P, Salles J (2002) Effects of agronomical measures on the microbial diversity of soils as related to the suppression of soil-borne plant pathogens. Biodegradation 13:29–40

    PubMed  Google Scholar 

  • Van Overbeek L, van Elsas JD (2008) Effects of plant genotype and growth stage on the structure of bacterial communities associated with potato (Solanum tuberosum L.). FEMS Microbiol Ecol 64:283–296

    PubMed  Google Scholar 

  • Vandenkoornhuyse P, Mahé S, Ineson P, Staddon P, Ostle N, Cliquet JB, Francez AJ, Fitter AH, Young JPW (2007) Active root-inhabiting microbes identified by rapid incorporation of plant-drived carbon into RNA. Proc Natl Acad Sci USA 104:16970–16975

    PubMed  CAS  Google Scholar 

  • Vestergard M, Henry F, Rangel-Castro JI, Michelsen A, Prosser JI, Christensen S (2008) Rhizosphere bacterial community composition responds to arbuscular mycorrhiza, but not to reductions in microbial activity by foliar cutting. FEMS Microbiol Ecol 64:78–89

    Google Scholar 

  • Vázquez MM, Cesar S, Azcon R, Barea JM (2000) Interactions between arbuscular mycorrhizal fungi and other microbial inoculants (Azospirillum, Pseudomonas, Trichoderma) and their effects on microbial population and enzyme activities in the rhizosphere of maize plants. Appl Soil Ecol 15:261–272

    Google Scholar 

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

    CAS  Google Scholar 

  • Vetterlein D, Reinhold J (2004) Gradients in soil solution composition between bulk soil and rhizosphere- In situ measurement with changing soil water content. Plant Soil 258:307–317

    CAS  Google Scholar 

  • Waisel Y, Eshel A (2002) Functional diversity of various constituents of a single root system. In: Waisel Y, Eshel A, Kafkafi U (eds) plant roots: the hidden half, 3rd edn. Marcel Dekker, New York, pp 157–174

    Google Scholar 

  • Wamberg C, Christensen S, Jakobsen I, Müller AK, Sørensen SJ (2003) The mycorrhizal fungus (Glomus intraradices) affects microbial activity in the rhizosphere of pea plants (Pisum sativum). Soil Biol Biochem 35:1349–1357

    CAS  Google Scholar 

  • Wand SJE, Midgley GF, Jones MH, Curtis PS (1999) Responses of wild C4 and C3 grass (Poaceae) species to elevated atmospheric CO2 concentration: a meta-analytic test of current theories and perceptions. Glob Change Biol 5:723–741

    Google Scholar 

  • Wasaki J, Rothe A, Kania A, Neumann G, Römheld V, Shinano T, Osaki M, Kandeler E (2005) Root exudation, phosphorus acquisition and microbial diversity in the rhizosphere of white lupine as affected by phosphorus supply and atmospheric carbon dioxide concentration. J Environ Qual 34:2157–2166

    PubMed  CAS  Google Scholar 

  • Watt M, McCully ME, Canny MJ (1994) Formation and stabilization of rhizosheaths of Zea mays L. Plant Physiol 106:179–186

    PubMed  CAS  Google Scholar 

  • Watt M, McCully ME, Kirkegaard JA (2003) Soil strength and rate of root elongation alter the accumulation of Pseudomonas spp. and other bacteria in the rhizosphere of wheat. Funct Plant Biol 30:483–491

    Google Scholar 

  • Watt M, Hugenholtz P, White R, Vinall K (2006) Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH). Environ Microbiol 8:871–884

    PubMed  Google Scholar 

  • Weinert N, Piceno Y, Ding GC, Meincke R, Heuer H, Berg G, Schloter M, Andersen G, Smalla K (2008) PhyloChip hybridization uncovered an enourmous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. FEMS Microbiol Ecol 75:497–506

    Google Scholar 

  • Weinert N, Meincke R, Gottwald C, Heuer H, Gomes NCM, Schloter M, Berg G, Smalla K (2009) Rhizosphere communities of genetically modified zeaxanthin-accumulating potato plants and their parent cultivar differ less than those of different potato cultivars. Appl Environ Microbiol 75:3859–3865

    PubMed  CAS  Google Scholar 

  • Weinert N, Meincke R, Gottwald C, Radi V, Dong X, Schloter M, Berg G, Smalla K (2010) Effects of genetically modified potatoes with increased zeaxanthin content on the abundance and diversity of rhizobacteria with in vitro antagonistic activity do not exceed natural variability among cultivars. Plant Soil 326:437–452

    CAS  Google Scholar 

  • Weisskopf L, Fromin N, Tomasi N, Aragno M, Martinoia E (2005) Secretion activity of white lupin’s cluster roots influences bacterial abundance, function and community structure. Plant Soil 268:181–194

    CAS  Google Scholar 

  • Weisskopf L, Le Bayon RC, Kohler F, Page V, Jossi M, Gobat JM, Martinoia E, Aragno M (2008) Spatio-temporal dynamics of bacterial communities associated with two plant species differing in organic acid secretion: a one-year microcosm study on lupin and wheat. Soil Biol Biochem 40:1772–1780

    CAS  Google Scholar 

  • Weisskopf L, Heller S, Eberl L (2011) Burkholderia species are major inhabitants of white lupin cluster roots. Appl Environ Microbiol 77:7715–7720

    PubMed  CAS  Google Scholar 

  • Werker E, Kislev M (1978) Mucilage on the root surface and root hairs of Sorghum: heterogeneity in structure, manner of production and site of accumulation. Ann Bot 42:809–816

    Google Scholar 

  • Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583

    PubMed  CAS  Google Scholar 

  • Widmar F, Rasche F, Hartmann M, Fliessbach A (2006) Community structures and substrate utilization of bacteria in soils from organic and conventional farming systems of DOK long-term field experiment. Appl Soil Ecol 33:294–307

    Google Scholar 

  • Will C, Thürmer A, Wollherr A, Nacke H, Herold N, Schrumpf M, Gutknecht J, Wubet T, Buscot F, Daniel R (2010) Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes. Appl Environ Microbiol 76:6751–6759

    PubMed  CAS  Google Scholar 

  • Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088–5090

    PubMed  CAS  Google Scholar 

  • Wu WX, Liu W, Lu HH, Chen YX, Devare M, Thies J (2009a) Use of 13C labeling to assess carbon partitioning in transgenic and nontransgenic (parental) rice and their rhizosphere soil microbial communities. FEMS Microbiol Ecol 67:93–102

    PubMed  CAS  Google Scholar 

  • Wu L, Ma K, Li Q, Ke X, Lu Y (2009b) Composition of Archaeal community in a paddy field as affected by rice cultivar and N fertilizer. Microb Ecol 58:819–823

    PubMed  CAS  Google Scholar 

  • Yang CH, Crowley DE (2000) Rhizosphere microbial community structure in relation to root location and plant iron nutritional status. Appl Environ Microbiol 66:345–351

    PubMed  CAS  Google Scholar 

  • Yang CH, Crowley DE, Menge JA (2001) 16S rDNA fingerprinting of rhizosphere bacterial communities associated with healthy and Phytophthora infected avocado roots. FEMS Microbiol Ecol 35:129–136

    PubMed  CAS  Google Scholar 

  • Yang JH, Liu HX, Zhu GM, Pan YL, Xu LP, Guo JH (2008) Diversity analysis of antagonists from rice-associated bacteria and their application in biocontrol of rice diseases. J Appl Microbiol 104:91–104

    PubMed  CAS  Google Scholar 

  • Young IM, Crawford JW (2004) Interactions and self-organization in the soil-microbe complex. Science 304:1634–1637

    PubMed  CAS  Google Scholar 

  • Young IM, Crawford JW, Nunan N, Otten W, Spiers A (2008) Microbial distribution in soils: physics and scaling. Adv Agron 100:81–121

    Google Scholar 

  • Zachow C, Tilcher R, Berg G (2008) Sugar beet-associated bacterial and fungal communities show a high indigenous antagonistic potential against plant pathogens. Microb Ecol 55:119–129

    PubMed  Google Scholar 

  • Zak DR, Pregitzer KS, King JS, Holmes WE (2000) Elevated atmospheric CO2, fine roots and response of soil microorganisms: a review and hypothesis. New Phytol 147:201–222

    CAS  Google Scholar 

  • Zhang NN, Sun YM, Li L, Wang ET, Chen WX, Yuan HL (2010) Effects of intercropping and Rhizobium inoculation on yield and rhizosphere bacterial community of faba bean (Vicia faba L.). Biol Fertil Soils 46:625–639

    Google Scholar 

  • Zhang Y, Du BH, Jin ZG, Li ZH, Song HN, Ding YQ (2011a) Analysis of bacterial communities in rhizosphere soil of healthy and diseased cotton (Gossypium sp.) at different plant growth stages. Plant Soil 339:447–455

    CAS  Google Scholar 

  • Zhang YZ, Wang ET, Li M, Li QQ, Zhang YM, Zhao SJ, Jia XL, Zhang LH, Chen WF, Chen WX (2011b) Effects of rhizobial inoculation, cropping systems and growth stages on endophytic bacterial community of soybean roots. Plant Soil 347:147–161

    CAS  Google Scholar 

  • Zilber-Rosenberg I, Rosenberg E (2008) Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev 32:723–735

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Dror Minz .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this entry

Cite this entry

Minz, D., Ofek, M., Hadar, Y. (2013). Plant Rhizosphere Microbial Communities. In: Rosenberg, E., DeLong, E.F., Lory, S., Stackebrandt, E., Thompson, F. (eds) The Prokaryotes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30123-0_38

Download citation

Publish with us

Policies and ethics