| [1] | Darrah PR (1993) The rhizosphere and plant nutrition: a quantitative approach. Plant Soil 155–156: 1–20. doi: 10.1007/bf00024980
|
| [2] | Hartmann A, Rothballer M, Schmid M (2008) Lorenz Hiltner, a pioneer in rhizosphere microbial ecology and soil bacteriology research. Plant Soil 312: 7–14. doi: 10.1007/s11104-007-9514-z
|
| [3] | Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic and human pathogenic microorganisms. FEMS Microbiol Rev 37: 634–663. doi: 10.1111/1574-6976.12028
|
| [4] | Berendsen RL, Pieterse CMJ, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17: 478–486. doi: 10.1016/j.tplants.2012.04.001
|
| [5] | Bloemberg GV, Lugtenberg BJJ (2001) Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Curr Opin Plant Biol 4: 343–350. doi: 10.1016/s1369-5266(00)00183-7
|
| [6] | Van der Ent S, Van Hulten M, Pozo MJ, Czechowski T, Udvardi MK, et al. (2009) Priming of plant innate immunity by rhizobacteria and beta-aminobutyric acid: differences and similarities in regulation. New Phytol 183: 419–431. doi: 10.1111/j.1469-8137.2009.02851.x
|
| [7] | Lugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63: 541–556. doi: 10.1146/annurev.micro.62.081307.162918
|
| [8] | Beneduzi A, Ambrosini A, Passaglia LMP (2012) Plant growth-promoting rhizobacteria (PGPR): Their potential as antagonists and biocontrol agents. Genet Mol Biol 35: 1044–1051. doi: 10.1590/s1415-47572012000600020
|
| [9] | Oger PM, Mansouri H, Nesme X, Dessaux Y (2004) Engineering root exudation of lotus toward the production of two novel carbon compounds leads to the selection of distinct microbial populations in the rhizosphere. Microb Ecol 47: 96–103. doi: 10.1007/s00248-003-2012-9
|
| [10] | Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57: 233–266. doi: 10.1146/annurev.arplant.57.032905.105159
|
| [11] | Haichar FZ, Marol C, Berge O, Rangel-Castro JI, Prosser JI, et al. (2008) Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2: 1221–1230. doi: 10.1038/ismej.2008.80
|
| [12] | Badri DV, Vivanco JM (2009) Regulation and function of root exudates. Plant Cell Environ 32: 666–681. doi: 10.1111/j.1365-3040.2009.01926.x
|
| [13] | Innes L, Hobbs PJ, Bardgett RD (2004) The impacts of individual plant species on rhizosphere microbial communities in soils of different fertility. Biol Fertil Soils 40: 7–13. doi: 10.1007/s00374-004-0748-0
|
| [14] | Batten KM, Scow KM, Davies KF, Harrison SP (2006) Two invasive plants alter soil microbial community composition in serpentine grasslands. Biol Invasions 8: 217–230. doi: 10.1007/s10530-004-3856-8
|
| [15] | 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. doi: 10.1007/s11104-007-9432-0
|
| [16] | Inceoglu O, Al-Soud Wa, Salles JF, Semenov AV, van Elsas JD (2011) Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing. PLoS One 6: e23321. doi: 10.1371/journal.pone.0023321
|
| [17] | Bakker MG, Manter DK, Sheflin AM, Weir TL, Vivanco JM (2012) Harnessing the rhizosphere microbiome through plant breeding and agricultural management. Plant Soil 360: 1–13. doi: 10.1007/s11104-012-1361-x
|
| [18] | DeAngelis KM, Brodie EL, DeSantis TZ, Andersen GL, Lindow SE, et al. (2009) Selective progressive response of soil microbial community to wild oat roots. ISME J 3: 168–178. doi: 10.1038/ismej.2008.103
|
| [19] | Bulgarelli D, Rott M, Schlaeppi K, Ver Loren van Themaat E, Ahmadinejad N, et al. (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488: 91–95. doi: 10.1038/nature11336
|
| [20] | Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, et al. (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488: 86–90. doi: 10.1038/nature11237
|
| [21] | Bodenhausen N, Horton MW, Bergelson J (2013) Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS One 8: e56329. doi: 10.1371/journal.pone.0056329
|
| [22] | Sugiyama A, Bakker MG, Badri DV, Manter DK, Vivanco JM (2013) Relationships between Arabidopsis genotype-specific biomass accumulation and associated soil microbial communities. Botany 91: 123–126. doi: 10.1139/cjb-2012-0217
|
| [23] | Chaparro JM, Badri DV, Vivanco JM (2013) Rhizosphere microbiome assemblage is affected by plant development. ISME J, in press.
|
| [24] | Chaparro JM, Badri DV, Bakker MG, Sugiyama A, Manter DK, et al. (2013) Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. PLoS One 8: e55731. doi: 10.1371/journal.pone.0055731
|
| [25] | Mougel C, Offre P, Ranjard L, Corberand T, Gamalero E, et al. (2006) Dynamic of the genetic structure of bacterial and fungal communities at different developmental stages of Medicago truncatula Gaertn. cv. Jemalong line J5. New Phytol 170: 165–175. doi: 10.1111/j.1469-8137.2006.01650.x
|
| [26] | Houlden A, Timms-Wilson TM, Day MJ, Bailey MJ (2008) Influence of plant developmental stage on microbial community structure and activity in the rhizosphere of three field crops. FEMS Microbiol Ecol 65: 193–201. doi: 10.1111/j.1574-6941.2008.00535.x
|
| [27] | Xu YX, Wang GH, Jin J, Liu JJ, Zhang QY, et al. (2009) Bacterial communities in soybean rhizosphere in response to soil type, soybean genotype, and their growth stage. Soil Biol Biochem 41: 919–925. doi: 10.1016/j.soilbio.2008.10.027
|
| [28] | Micallef SA, Shiaris MP, Colon-Carmona A (2009) Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates. J Exp Bot 60: 1729–1742. doi: 10.1093/jxb/erp053
|
| [29] | Denison RF, Kiers ET (2011) Life histories of symbiotic rhizobia and mycorrhizal fungi. Curr Biol 21: R775–R785. doi: 10.1016/j.cub.2011.06.018
|
| [30] | Yokota K, Hayashi M (2011) Function and evolution of nodulation genes in legumes. Cell Mol Life Sci 68: 1341–1351. doi: 10.1007/s00018-011-0651-4
|
| [31] | Jie W, Liu X, Cai B (2013) Diversity of rhizosphere soil arbuscular mycorrhizal fungi in various soybean cultivars under different continuous cropping regimes. PLoS One 8: e72898. doi: 10.1371/journal.pone.0072898
|
| [32] | Inceoglu O, Salles JF, van Overbeek L, van Elsas JD (2010) Effects of plant genotype and growth stage on the betaproteobacterial communities associated with different potato cultivars in two fields. Appl Environ Microbiol 76: 3675–3684. doi: 10.1128/aem.00040-10
|
| [33] | Uroz S, Ioannidis P, Lengelle J, Cebron A, Morin E, et al. (2013) Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation. PLoS One 8: e55929. doi: 10.1371/journal.pone.0055929
|
| [34] | Badri DV, Quintana N, El Kassis EG, Kim HK, Choi YH, et al. (2009) An ABC transporter mutation alters root exudation of phytochemicals that provoke an overhaul of natural soil microbiota. Plant Physiol 151: 2006–2017. doi: 10.1104/pp.109.147462
|
| [35] | Manter DK, Delgado JA, Holm DG, Stong RA (2010) Pyrosequencing reveals a highly diverse and cultivar-specific bacterial endophyte community in potato roots. Microb Ecol 60: 157–166. doi: 10.1007/s00248-010-9658-x
|
| [36] | McKenzie VJ, Bowers RM, Fierer N, Knight R, Lauber CL (2012) Co-habiting amphibian species harbor unique skin bacterial communities in wild populations. ISME J 6: 588–596. doi: 10.1038/ismej.2011.129
|
| [37] | Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, et al. (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A 82: 6955–6959. doi: 10.1073/pnas.82.20.6955
|
| [38] | Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, et al. (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64: 795–799.
|
| [39] | Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing Mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537–7541. doi: 10.1128/aem.01541-09
|
| [40] | Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188–7196. doi: 10.1093/nar/gkm864
|
| [41] | Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194–2200. doi: 10.1093/bioinformatics/btr381
|
| [42] | Kodama Y, Shumway M (2012) Leinonen R; International Nucleotide Sequence Database Collaboration (2012) The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res 40: D54–D56. doi: 10.1093/nar/gkr854
|
| [43] | Sugiyama A, Vivanco JM, Jayanty SS, Manter DK (2010) Pyrosequencing assessment of soil microbial communities in organic and conventional potato farms. Plant Dis 94: 1329–1335. doi: 10.1094/pdis-02-10-0090
|
| [44] | Garland JL, Mills AL (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Appl Environ Microbiol 57: 2351–2359.
|
| [45] | Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69: 1800–1809. doi: 10.1128/aem.69.3.1800-1809.2003
|
| [46] | Shentu JL, He ZL, Yang XE, Li TQ (2008) Microbial activity and community diversity in a variable charge soil as affected by cadmium exposure levels and time. J Zhejiang Univ Sci B 9: 250–260. doi: 10.1631/jzus.b0710630
|
| [47] | Fr？c M, Oszust K, Lipiec J (2012) Community level physiological profiles (CLPP), characterization and microbial activity of soil amended with dairy sewage sludge. Sensors (Basel) 12: 3253–3268. doi: 10.3390/s120303253
|
| [48] | Ofek M, Hadar Y, Minz D (2012) Ecology of root colonizing Massilia (Oxalobacteraceae). PLoS One 7: e40117. doi: 10.1371/journal.pone.0040117
|
| [49] | Uroz S, Buee 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. doi: 10.1111/j.1758-2229.2009.00117.x
|
| [50] | Sugiyama A, Yazaki K (2012) Root exudates of legume plants and their involvement in interactions with soil microbes. In: Vivanco JM, Baluska F, editors. Secretions and exudates in biological systems. Berlin Heidelberg: Springer. pp. 27–48.
|
| [51] | Ikeda S, Okubo T, Kaneko T, Inaba S, Maekawa T, et al. (2010) Community shifts of soybean stem-associated bacteria responding to different nodulation phenotypes and N levels. ISME J 4: 315–326. doi: 10.1038/ismej.2009.119
|
| [52] | Barbour WM, Hattermann DR, Stacey G (1991) Chemotaxis of Bradyrhizobium japonicum to soybean exudates. Appl Environ Microbiol 57: 2635–2639.
|
| [53] | Choudhary DK, Johri BN (2009) Interactions of Bacillus spp. and plants - with special reference to induced systemic resistance (ISR). Microbiol Res 164: 493–513. doi: 10.1016/j.micres.2008.08.007
|
| [54] | Govindasamy V, Senthilkumar M, Magheshwaran V, Kumar U, Bose P, et al.. (2011) Bacillus and Paenibacillus spp.: potential PGPR for sustainable agriculture. In: Maheshwari DK, editor. Plant growth and health promoting bacteria. Berlin Heidelberg: Springer. pp. 333–364.
|
| [55] | Kumar A, Prakash A, Johri BN (2011) Bacillus as PGPR in crop ecosystems. In: Maheshwari DK, editor. Bacteria in agrobiology: crop ecosystems. Berlin Heidelberg: Springer. pp. 37–59.
|
| [56] | Insunza V, Alstrom S, Eriksson KB (2002) Root bacteria from nematicidal plants and their biocontrol potential against trichodorid nematodes in potato. Plant Soil 241: 271–278.
|
| [57] | Richardson AE, Barea JM, McNeill AM, Prigent-Combaret C (2009) Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms. Plant Soil 321: 305–339. doi: 10.1007/s11104-009-9895-2
|
| [58] | de Souza R, Beneduzi A, Ambrosini A, da Costa PB, Meyer J, et al. (2013) The effect of plant growth-promoting rhizobacteria on the growth of rice (Oryza sativa L.) cropped in southern Brazilian fields. Plant Soil 366: 585–603. doi: 10.1007/s11104-012-1430-1
|
| [59] | Tsavkelova EA, Cherdyntseva TA, Klimova SY, Shestakov AI, Botina SG, et al. (2007) Orchid-associated bacteria produce indole-3-acetic acid, promote seed germination, and increase their microbial yield in response to exogenous auxin. Arch Microbiol 188: 655–664. doi: 10.1007/s00203-007-0286-x
|
| [60] | de Vasconcellos RLF, Cardoso EJBN (2009) Rhizospheric streptomycetes as potential biocontrol agents of Fusarium and Armillaria pine rot and as PGPR for Pinus taeda. Biocontrol 54: 807–816. doi: 10.1007/s10526-009-9226-9
|
| [61] | Buonaurio R, Stravato VM, Kosako Y, Fujiwara N, Naka T, et al. (2002) Sphingomonas melonis sp. nov., a novel pathogen that causes brown spots on yellow Spanish melon fruits. Int J Syst Evol Microbiol 52: 2081–2087. doi: 10.1099/ijs.0.02063-0
|
| [62] | Johnson EG, Sparks JP, Dzikovski B, Crane BR, Gibson DM, et al. (2008) Plant-pathogenic Streptomyces species produce nitric oxide synthase-derived nitric oxide in response to host signals. Chem Biol 15: 43–50. doi: 10.1016/j.chembiol.2007.11.014
|
| [63] | Seipke RF, Song L, Bicz J, Laskaris P, Yaxley AM, et al. (2011) The plant pathogen Streptomyces scabies 87–22 has a functional pyochelin biosynthetic pathway that is regulated by TetR- and AfsR-family proteins. Microbiology 157: 2681–2693. doi: 10.1099/mic.0.047977-0
|
