Functional soil microbiome: Belowground solutions to an aboveground problem

Plant Physiology

Volumn 166, Issue 2, 2014, Pages 689-700

  Lakshmanan, Venkatachalam ^a   Selvaraj, Gopinath ^a   Bais, Harsh P ^a  

^a UNIVERSITY OF DELAWARE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; MAIZE; MICROBIOLOGY; MICROFLORA;

ARABIDOPSIS; MICROBIOTA; SOIL MICROBIOLOGY; ZEA MAYS;

EID: 84907766394     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.114.245811     Document Type: Article

References (145)

1. Ali B, Sabri AN, Ljung K, Hasnain S (2009) Auxin production by plant associated bacteria: impact on endogenous IAA content and growth of Triticum aestivum L. Lett Appl Microbiol 48: 542-547
2. Amann RI, Ludwig W, Schleifer K-H (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143-169
3. Badri DV, Chaparro JM, Zhang R, Shen Q, Vivanco JM (2013a) Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome. J Biol Chem 288: 4502-4512
4. Badri DV, Quintana N, El Kassis EG, Kim HK, Choi YH, Sugiyama A, Verpoorte R, Martinoia E, Manter DK, Vivanco JM (2009a) An ABC transporter mutation alters root exudation of phytochemicals that provoke an overhaul of natural soil microbiota. Plant Physiol 151: 2006-2017
5. Badri DV, Vivanco JM (2009) Regulation and function of root exudates. Plant Cell Environ 32: 666-681
6. Badri DV, Weir TL, van der Lelie D, Vivanco JM (2009b) Rhizosphere chemical dialogues: plant-microbe interactions. Curr Opin Biotechnol 20: 642-650
7. Badri DV, Zolla G, Bakker MG, Manter DK, Vivanco JM (2013b) Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behavior. New Phytol 198: 264-273
8. 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
9. 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
10. 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
11. 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
12. Beattie GA, Lindow SE (1995) The secret life of foliar bacterial pathogens on leaves. Annu Rev Phytopathol 33: 145-172
13. Beneduzi A, Peres D, Vargas LK, Bodanese-Zanettini MH, Passaglia LMP (2008) Evaluation of genetic diversity and plant growth promoting activities of nitrogen-fixing bacilli isolated from rice fields in South Brazil. Appl Soil Ecol 39: 311-320
14. Berendsen RL, Pieterse CMJ, Bakker PAHM (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17: 478-486
15. Berg G, Smalla K (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68: 1-13
16. Berlec A (2012) Novel techniques and findings in the study of plant microbiota: search for plant probiotics. Plant Sci 193-194: 96-102
17. Bever JD (2003) Soil community feedback and the coexistence of competitors: conceptual frameworks and empirical tests. New Phytol 157: 465-473
18. Bever JD, Platt TG, Morton ER (2012) Microbial population and community dynamics on plant roots and their feedbacks on plant communities. Annu Rev Microbiol 66: 265-283
19. Bhardwaj D, Ansari MW, Sahoo RK, Tuteja N (2014) Biofertilizers function as key player in sustainable agriculture by improving soil fertility, plant tolerance and crop productivity. Microb Cell Fact 13: 66-76
20. Bhattacharyya PN, Jha DK (2012) Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture. World J Microbiol Biotechnol 28: 1327-1350
21. Bressan M, Roncato MA, Bellvert F, Comte G, Haichar FZ, Achouak W, Berge O (2009) Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots. ISME J 3: 1243-1257
22. Broeckling CD, Broz AK, Bergelson J, Manter DK, Vivanco JM (2008) Root exudates regulate soil fungal community composition and diversity. Appl Environ Microbiol 74: 738-744
23. Bulgarelli D, Rott M, Schlaeppi K, Ver Loren, van Themaat E, Ahmadinejad N, Assenza F, Rauf P, Huettel B, Reinhardt R, Schmelzer E, et al (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488: 91-95
24. Carvalhais LC, Dennis PG, Badri DV, Tyson GW, Vivanco JM, Schenk PM (2013) Activation of the jasmonic acid plant defence pathway alters the composition of rhizosphere bacterial communities. PLoS ONE 8: e56457
25. Chaparro JM, Badri DV, Bakker MG, Sugiyama A, Manter DK, Vivanco JM (2013) Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. PLoS ONE 8: e55731
26. Chaparro JM, Badri DV, Vivanco JM (2014) Rhizosphere microbiome assemblage is affected by plant development. ISME J 8: 790-803
27. Chaparro JM, Sheflin AM, Manter DK, Vivanco JM (2012) Manipulating the soil microbiome to increase soil health and plant fertility. Biol Fertil Soils 48: 489-499
28. Dangl JL, Jones JD (2001) Plant pathogens and integrated defence responses to infection. Nature 411: 826-833
29. Dennis PG, Miller AJ, Hirsch PR (2010) Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities? FEMS Microbiol Ecol 72: 313-327
30. De Vos M, Van Zaanen W, Koornneef A, Korzelius JP, Dicke M, Van Loon LC, Pieterse CMJ (2006) Herbivore-induced resistance against microbial pathogens in Arabidopsis. Plant Physiol 142: 352-363
31. de Weert S, Vermeiren H, Mulders IHM, Kuiper I, Hendrickx N, Bloemberg GV, Vanderleyden J, De Mot R, Lugtenberg BJJ (2002) Flagella-driven chemotaxis towards exudate components is an important trait for tomato root colonization by Pseudomonas fluorescens. Mol Plant Microbe Interact 15: 1173-1180
32. Dini-Andreote F, van Elsas JD (2013) Back to the basics: the need for ecophysiological insights to enhance our understanding of microbial behavior in the rhizosphere. Plant Soil 373: 1-15
33. Doornbos RF, van Loon LC, Bakker PAHM (2012) Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere: a review. Agron Sustain Dev 32: 227-243
34. East R (2013) Microbiome: soil science comes to life. Nature 501: S18-S19
35. Fang C, Zhuang Y, Xu T, Li Y, Li Y, Lin W (2013) Changes in rice allelopathy and rhizosphere microflora by inhibiting rice phenylalanine ammonia-lyase gene expression. J Chem Ecol 39: 204-212
36. Fitzsimons MS, Miller RM (2010) The importance of soil microorganisms for maintaining diverse plant communities in tallgrass prairie. Am J Bot 97: 1937-1943
37. Forchetti G, Masciarelli O, Alemano S, Alvarez D, Abdala G (2007) Endophytic bacteria in sunflower (Helianthus annuus L.): isolation, characterization, and production of jasmonates and abscisic acid in culture medium. Appl Microbiol Biotechnol 76: 1145-1152
38. Friedrich MW (2006) Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes. Curr Opin Biotechnol 17: 59-66
39. Gamalero E, Berta G, Glick BR (2009) The use of microorganisms to facilitate the growth of plants in saline soils. In MS Khan, A Zaidi, J Musarrat, eds, Microbial Strategies for Crop Improvement. Springer, Berlin, pp 1-22
40. Garbeva P, van Veen JA, van Elsas JD (2004) Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol 42: 243-270
41. Glazebrook J (2005) Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annu Rev Phytopathol 43: 205-227
42. Glick BR (1995) The enhancement of plant growth by free-living bacteria. Can J Microbiol 41: 109-117
43. Gupta VV (2012) Beneficial microorganisms for sustainable agriculture. Microbiol Australia 3: 113-115
44. Haichar FZ, Marol C, Berge O, Rangel-Castro JI, Prosser JI, Balesdent J, Heulin T, Achouak W (2008) Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2: 1221-1230
45. Heintz C, Mair W (2014) You are what you host: microbiome modulation of the aging process. Cell 156: 408-411
46. Higa T, Parr JF (1994) Beneficial and Effective Microorganisms for a Sustainable Agriculture and Environment. International Nature Farming Research Center, Atami, Japan
47. Hirano SS, Upper CD (2000) Bacteria in the leaf ecosystem with emphasis on Pseudomonas syringae: a pathogen, ice nucleus, and epiphyte. Microbiol Mol Biol Rev 64: 624-653
48. Horiuchi J, Prithiviraj B, Bais HP, Kimball BA, Vivanco JM (2005) Soil nematodes mediate positive interactions between legume plants and rhizobium bacteria. Planta 222: 848-857
49. Horrigan L, Lawrence RS, Walker P (2002) How sustainable agriculture can address the environmental and human health harms of industrial agriculture. Environ Health Perspect 110: 445-456
50. 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
51. Huang XF, Chaparro JM, Reardon KF, Zhang R, Shen Q, Vivanco JM (2014) Rhizosphere interactions: root exudates, microbes, and microbial communities. Botany 92: 267-275
52. Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180: 4765-4774
53. Ikeda S, Okubo T, Takeda N, Banba M, Sasaki K, Imaizumi-Anraku H, Fujihara S, Ohwaki Y, Ohshima K, Fukuta Y, et al (2011) The genotype of the calcium/calmodulin-dependent protein kinase gene (CCaMK) determines bacterial community diversity in rice roots under paddy and upland field conditions. Appl Environ Microbiol 77: 4399-4405
54. Jain V, Nainawatee HS (2002) Plant flavonoids: signals to legume nodulation and soil microorganisms. J Plant Biochem Biotechnol 11: 1-10
55. Jetiyanon K, Kloepper JW (2002) Mixtures of plant growth-promoting rhizobacteria for induction of systemic resistance against multiple plant diseases. Biol Control 24: 285-291
56. Johansson JF, Paul LR, Finlay RD (2004) Microbial interactions in the mycorrhizosphere and their significance for sustainable agriculture. FEMS Microbiol Ecol 48: 1-13
57. Jones DL, Nguyen C, Finlay RD (2009) Carbon flow in the rhizosphere: carbon trading at the soil-root interface. Plant Soil 321: 5-33
58. Keiblinger KM, Wilhartitz IC, Schneider T, Roschitzki B, Schmid E, Eberl L, Riedel K, Zechmeister-Boltenstern S (2012) Soil metaproteomics: comparative evaluation of protein extraction protocols. Soil Biol Biochem 54: 14-24
59. Klironomos JN (2002) Feedback with soil biota contributes to plant rarity and invasiveness in communities. Nature 417: 67-70
60. Kloepper JW, Ryu CM, Zhang S (2004) Induced systemic resistance and promotion of plant growth by Bacillus spp. Phytopathology 94: 1259-1266
61. Kloepper JW, Schroth MN (1978) Plant growth-promoting rhizobacteria inradish. In Station de pathologie vegetale et phyto-bacteriologie (ed.), Proceedings of the 4th International Conference on Plant Pathogenic Bacteria, vol 2. Gilbert-Clarey, Tours, France, pp 879-882
62. Knief C, Delmotte N, Chaffron S, Stark M, Innerebner G, Wassmann R, von Mering C, Vorholt JA (2012) Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J 6: 1378-1390
63. Kniskern JM, Traw MB, Bergelson J (2007) Salicylic acid and jasmonic acid signaling defense pathways reduce natural bacterial diversity on Arabidopsis thaliana. Mol Plant Microbe Interact 20: 1512-1522
64. Kolmeder CA, de Vos WM (2014) Metaproteomics of our microbiome: developing insight in function and activity in man and model systems. J Proteomics 97: 3-16
65. Krzyzanowska D, Obuchowski M, Bikowski M, Rychlowski M, Jafra S (2012) Colonization of potato rhizosphere by GFP-tagged Bacillus subtilis MB73/2, Pseudomonas sp. P482 and Ochrobactrum sp. A44 shown on large sections of roots using enrichment sample preparation and confocal laser scanning microscopy. Sensors (Basel) 12: 17608-17619
66. Kutschera U (2007) Plant-associated methylobacteria as co-evolved phytosymbionts: a hypothesis. Plant Signal Behav 2: 74-78
67. Lakshmanan V, Bais HP (2013) Factors other than root secreted malic acid that contributes toward Bacillus subtilis FB17 colonization on Arabidopsis roots. Plant Signal Behav 8: e27277
68. Lakshmanan V, Kitto SL, Caplan JL, Hsueh YH, Kearns DB, Wu YS, Bais HP (2012) Microbe-associated molecular patterns-triggered root responses mediate beneficial rhizobacterial recruitment in Arabidopsis. Plant Physiol 160: 1642-1661
69. Lankau RA (2011) Conflicts in maintaining biodiversity at multiple scales. Mol Ecol 20: 2035-2037
70. Larson JL, Siemann E (1998) Legumes may be symbiont-limited during old-field succession. Am Midl Nat 140: 90-95
71. Lau JA, Lennon JT (2011) Evolutionary ecology of plant-microbe interactions: soil microbial structure alters selection on plant traits. New Phytol 192: 215-224
72. Lavelle P, Spain AV (2001) Soil Ecology. Kluwer, Dordrecht, The Netherlands
73. Lee B, Lee S, Ryu CM (2012) Foliar aphid feeding recruits rhizosphere bacteria and primes plant immunity against pathogenic and non-pathogenic bacteria in pepper. Ann Bot (Lond) 110: 281-290
74. Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (2006) Archaea predominate among ammoniaoxidizing prokaryotes in soils. Nature 442: 806-809
75. Lindow SE, Brandl MT (2003) Microbiology of the phyllosphere. Appl Environ Microbiol 69: 1875-1883
76. Liu Y, Zhang N, Qiu M, Feng H, Vivanco JM, Shen Q, Zhang R (2014) Enhanced rhizosphere colonization of beneficial Bacillus amyloliquefaciens SQR9 by pathogen infection. FEMS Microbiol Lett 353: 49-56
77. Long SR (1989) Rhizobium-legume nodulation: life together in the underground. Cell 56: 203-214
78. López-Bucio J, de La Vega OM, Guevara-García A, Herrera-Estrella L (2000) Enhanced phosphorus uptake in transgenic tobacco plants that overproduce citrate. Nat Biotechnol 18: 450-453
79. Lugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63: 541-556
80. Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, del Rio TG, et al (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488: 86-90
81. Marques JM, da Silva TF, Vollu RE, Blank AF, Ding GC, Seldin L, Smalla K (2014) Plant age and genotype affect the bacterial community composition in the tuber rhizosphere of field-grown sweet potato plants. FEMS Microbiol Ecol 88: 424-435
82. Marschner P, Neumann G, Kania A, Weiskopf 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
83. Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JHM, Piceno YM, DeSantis TZ, Andersen GL, Bakker PAHM, et al (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 332: 1097-1100
84. Micallef SA, Channer S, Shiaris MP, Colón-Carmona A (2009) Plant age and genotype impact the progression of bacterial community succession in the Arabidopsis rhizosphere. Plant Signal Behav 4: 777-780
85. Minz D, Ofek M, Hadar Y (2013) Plant rhizosphere microbial communities. In EF DeLong, S Lory, E Stackebrandt, F Thompson, eds, The Prokaryotes: Prokaryotic Communities and Ecophysiology. Springer-Verlag, Berlin, pp 57-84
86. Mishra PK, Mishra S, Selvakumar G, Kundub S, Gupta HS (2009) Enhanced soybean (Glycine max L.) plant growth and nodulation by Bradyrhizobium japonicum-SB1 in presence of Bacillus thuringiensis-KR1. Acta Agric Scand B Soil Plant Sci 59: 189-196
87. Moe LA (2013) Amino acids in the rhizosphere: from plants to microbes. Am J Bot 100: 1692-1705
88. Mougel C, Offre P, Ranjard L, Corberand T, Gamalero E, Robin C, Lemanceau P (2006) Dynamic of the genetic structure of bacterial and fungal communities at different developmental stages of Medicago truncatula Gaertn. cv. Jemalong line J5. New Phytol 170: 165-175
89. Mullis KB, Erlich HA, Arnheim N, Horn GT, Saiki RK, Scharf SJ July 28, 1987. Process for amplifying, detecting, and/or-cloning nucleic acid sequences. US Patent Application No. US4683195 A
90. Muyzer G (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2: 317-322
91. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695-700
92. Nannipieri P, Ascher J, Ceccherini MT, Landi L, Pietramellara G, Renella G (2003) Microbial diversity and soil functions. Eur J Soil Sci 54: 655-670
93. Narula N, Deubel A, Gans W, Behl RK, Merbach W (2006) Paranodules and colonization of wheat roots by phytohormone producing bacteria in soil. Plant Soil Environ 52: 119-129
94. Neal AL, Ahmad S, Gordon-Weeks R, Ton J (2012) Benzoxazinoids in root exudates of maize attract Pseudomonas putida to the rhizosphere. PLoS ONE 7: e35498
95. Ortíz-Castro R, Martínez-Trujillo M, López-Bucio J (2008) N-Acyl-L-homoserine lactones: a class of bacterial quorum-sensing signals alter post-embryonic root development in Arabidopsis thaliana. Plant Cell Environ 31: 1497-1509
96. Paungfoo-Lonhienne C, Rentsch D, Robatzek S, Webb RI, Sagulenko E, Näsholm T, Schmidt S, Lonhienne TGA (2010) Turning the table: plants consume microbes as a source of nutrients. PLoS ONE 5: e11915
97. Peiffer JA, Ley RE (2013) Exploring the maize rhizosphere microbiome in the field: a glimpse into a highly complex system. Commun Integr Biol 6: e25177
98. Peiffer JA, Spor A, Koren O, Jin Z, Tringe SG, Dangl JL, Buckler ES, Ley RE (2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci USA 110: 6548-6553
99. Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH (2013) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11: 789-799
100. Pieterse CMJ, Van der Does D, Zamioudis C, Leon-Reyes A, Van Wees SC (2012) Hormonal modulation of plant immunity. Annu Rev Cell Dev Biol 28: 489-521
101. Pieterse CMJ, Van Pelt JA, Van Wees SCM, Ton J, Léon-Kloosterziel KM, Keurentjes JJB, Verhagen BWM, Knoester M, Van der Sluis I, Bakker PAHM, et al (2001) Rhizobacteria-mediated induced systemic resistance: triggering, signalling and expression. Eur J Plant Pathol 107: 51-61
102. Pieterse CMJ, van Pelt JA, Verhagen BWM, Ton J, van Wees SCM, Leon-Kloosterziel KM, van Loon LC (2003) Induced systemic resistance by plant growth-promoting rhizobacteria. Symbiosis 35: 39-54
103. Pineda A, Zheng SJ, van Loon JJA, Pieterse CMJ, Dicke M (2010) Helping plants to deal with insects: the role of beneficial soil-borne microbes. Trends Plant Sci 15: 507-514
104. Pozo MJ, Van Der Ent S, Van Loon LC, Pieterse CMJ (2008) Transcription factor MYC2 is involved in priming for enhanced defense during rhizobacteria-induced systemic resistance in Arabidopsis thaliana. New Phytol 180: 511-523
105. Raaijmakers JM, Paulitz TC, Steinberg C, Alabouvette C, Moënne-Loccoz Y (2009) The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil 321: 341-361
106. Ramamoorthy V, Viswanathan R, Raguchander T, Prakasam V, Samiyappan R (2001) Induction of systemic resistance by plant growth promoting rhizobacteria in crop plants against pests and diseases. Crop Prot 20: 1-11
107. Rejmanek M, Richardson DM (1996) What attributes make some plant species more invasive? Ecology 77: 1655-1661
108. Rincon-Florez VA, Carvalhais LC, Schenk PM (2013) Culture-independent molecular tools for soil and rhizosphere microbiology. Diversity 5: 581-612
109. Rosenblueth M, Martínez-Romero E (2006) Bacterial endophytes and their interactions with hosts. Mol Plant Microbe Interact 19: 827-837
110. Rosenzweig N, Bradeen JM, Tu ZJ, McKay SJ, Kinkel LL (2013) Rhizosphere bacterial communities associated with long-lived perennial prairie plants vary in diversity, composition, and structure. Can J Microbiol 59: 494-502
111. Rout ME, Southworth D (2013) The root microbiome influences scales from molecules to ecosystems: the unseen majority. Am J Bot 100: 1689-1691
112. Rudrappa T, Biedrzycki ML, Kunjeti SG, Donofrio NM, Czymmek KJ, Paré PW, Bais HP (2010) The rhizobacterial elicitor acetoin induces systemic resistance in Arabidopsis thaliana. Commun Integr Biol 3: 130-138
113. Rudrappa T, Czymmek KJ, Paré PW, Bais HP (2008) Root-secreted malic acid recruits beneficial soil bacteria. Plant Physiol 148: 1547-1556
114. Schlaeppi K, Dombrowski N, Oter RG, Ver Loren, van Themaat E, Schulze-Lefert P (2014) Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc Natl Acad Sci USA 111: 585-592
115. Schnitzer SA, Klironomos JN, Hillerislambers J, Kinkel LL, Reich PB, Xiao K, Rillig MC, Sikes BA, Callaway RM, Mangan SA, et al (2011) Soil microbes drive the classic plant diversity-productivity pattern. Ecology 92: 296-303
116. Shakya M, Gottel N, Castro H, Yang ZK, Gunter L, Labbé J, Muchero W, Bonito G, Vilgalys R, Tuskan G, et al (2013) A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees. PLoS ONE 8: e76382
117. Sharma SK, Ramesh A, Sharma MP, Joshi OP, Govaerts B, Steenwerth KL, Karlen DL (2010) Microbial community structure and diversity as indicators for evaluating soil quality. In E Lichtfouse, ed, Biodiversity, Biofuels, Agroforestry and Conservation Agriculture, Vol 5. Springer, Dordrecht, The Netherlands, pp 317-358
118. Shaw CH (1991) Swimming against the tide: chemotaxis in Agrobacterium. BioEssays 13: 25-29
119. Shi S, Richardson AE, O’Callaghan M, DeAngelis KM, Jones EE, Stewart A, Firestone MK, Condron LM (2011) Effects of selected root exudate components on soil bacterial communities. FEMS Microbiol Ecol 77: 600-610
120. Spence C, Alff E, Johnson C, Ramos C, Donofrio N, Sundaresan V, Bais H (2014) Natural rice rhizospheric microbes suppress rice blast infections. BMC Plant Biol 14: 130
121. Spence C, Bais H (2013) Probiotics for plants: rhizospheric microbiome and plant fitness. In FJ de Bruijn, ed, Molecular Microbial Ecology of the Rhizosphere: Vols 1 and 2. John Wiley & Sons, Hoboken, NJ, pp 713-721 doi: 10.1002/9781118297674.ch67
122. Tan S, Yang C, Mei X, Shen S, Raza W, Shen O, Xu Y (2013) The effect of organic acids from tomato root exudates on rhizosphere colonization of Bacillus amyloliquefaciens T5. Appl Soil Ecol 64: 15-22
123. Taulé C, Mareque C, Barlocco C, Hackembruch F, Reis VM, Sicardi M, Battistoni F (2012) The contribution of nitrogen fixation to sugarcane (Saccharum officinarum L.), and the identification and characterization of part of the associated diazotrophic bacterial community. Plant Soil 356: 35-49
124. Turner TR, James EK, Poole PS (2013a) The plant microbiome. Genome Biol 14: 209-219
125. Turner TR, Ramakrishnan K, Walshaw J, Heavens D, Alston M, Swarbreck D, Osbourn A, Grant A, Poole PS (2013b) Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants. ISME J 7: 2248-2258
126. Uhlik O, Leewis MC, Strejcek M, Musilova L, Mackova M, Leigh MB, Macek T (2013) Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation. Biotechnol Adv 31: 154-165
127. Uren NC (2001) Types, amounts and possible functions of compounds released into the rhizosphere by soil-grown plants. In R Pinton, Z Varanini, P Nannipieri, eds, The Rhizosphere: Biochemistry and Organic Substances at the Soil-Plant Interface. Marcel Dekker, New York, pp 19-40
128. van der Heijden MGA, Bardgett RD, van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11: 296-310
129. van Loon LC, Bakker PAHM, Pieterse CMJ (1998) Systemic resistance induced by rhizosphere bacteria. Annu Rev Phytopathol 36: 453-483
130. van Loon LC, Rep M, Pieterse CMJ (2006) Significance of inducible defense-related proteins in infected plants. Annu Rev Phytopathol 44: 135-162
131. Van Oosten VR, Bodenhausen N, Reymond P, Van Pelt JA, Van Loon LC, Dicke M, Pieterse CMJ (2008) Differential effectiveness of microbially induced resistance against herbivorous insects in Arabidopsis. Mol Plant Microbe Interact 21: 919-930
132. Vessey JK (2003) Plant growth promoting rhizobacteria as biofertilizers. Plant Soil 255: 571-586
133. Wagg C, Jansa J, Schmid B, van der Heijden MG (2011) Belowground biodiversity effects of plant symbionts support aboveground productivity. Ecol Lett 14: 1001-1009
134. Walker TS, Bais HP, Grotewold E, Vivanco JM (2003) Root exudation and rhizosphere biology. Plant Physiol 132: 44-51
135. Weinert N, Piceno Y, Ding GC, Meincke R, Heuer H, Berg G, Schloter M, Andersen G, Smalla K (2011) PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. FEMS Microbiol Ecol 75: 497-506
136. White JF Jr, Crawford H, Torres MS, Mattera R, Irizarry I, Bergen M (2012) A proposed mechanism for nitrogen acquisition by grass seedlings through oxidation of symbiotic bacteria. Symbiosis 57: 161-171
137. White JF, Torres MS, Johnson H, Irizarry I, Tadych M (2014) A functional view of plant microbiomes: endosymbiotic systems that enhance plant growth and survival. In VC Verma, AC Gange, eds, Advances in Endophytic Research. Springer, Bangalore, India, pp 425-439
138. Whiteley AS, Manefield M, Lueders T (2006) Unlocking the ‘microbial black box’ using RNA-based stable isotope probing technologies. Curr Opin Biotechnol 17: 67-71
139. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74: 5088-5090
140. Wu F, Wang W, Ma Y, Liu Y, Ma X, An L, Feng H (2013) Prospect of beneficial microorganisms applied in potato cultivation for sustainable agriculture. Afr J Microbiol Res 7: 2150-2158
141. Yang JW, Yi HS, Lee B, Lee S, Ghim SY, Ryu CM (2011) Whitefly infestation of pepper plants elicits defence responses against bacterial pathogens in leaves and roots and changes the below-ground microflora. J Ecol 99: 46-56
142. Yergeau E, Sanschagrin S, Maynard C, St-Arnaud M, Greer CW (2014) Microbial expression profiles in the rhizosphere of willows depend on soil contamination. ISME J 8: 344-358
143. Zhou X, Wu F (2012) p-Coumaric acid influenced cucumber rhizosphere soil microbial communities and the growth of Fusarium oxysporum f.sp. cucumerinum Owen. PLoS ONE 7: e48288
144. Zhou X, Wu F (2013) Artificially applied vanillic acid changed soil microbial communities in the rhizosphere of cucumber (Cucumis sativus L.). Can J Soil Sci 93: 13-21
145. Zolla G, Badria DV, Bakker MG, Manter DK, Vivanco JM (2013) Soil microbiomes vary in their ability to confer drought tolerance to Arabidopsis. Appl Soil Ecol 68: 1-9