Engineering the Rhizosphere

Trends in Plant Science

Volumn 21, Issue 3, 2016, Pages 266-278

  Dessaux, Yves ^a   Grandclément, Catherine ^a   Faure, Denis ^a  

^a INSTITUTE FOR INTEGRATIVE BIOLOGY OF THE CELL I2BC   (France)

Author keywords

Exudation; Holobiont; Plant defense; Root; Soil amendment; Soil microbes

Indexed keywords

SOIL;

BOTANY; MICROBIOLOGY; MICROFLORA; PLANT; PROCEDURES; RHIZOSPHERE; SOIL;

BOTANY; MICROBIOTA; PLANTS; RHIZOSPHERE; SOIL; SOIL MICROBIOLOGY;

EID: 84959471941     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2016.01.002     Document Type: Review

References (150)

1. Hartmann A., et al. Plant-driven selection of microbes. Plant Soil 2008, 321:235-257.
2. Jones D.L., et al. Carbon flow in the rhizosphere: carbon trading at the soil-root interface. Plant Soil 2009, 321:5-33.
3. Buée M., et al. The rhizosphere zoo: an overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors. Plant Soil 2009, 321:189-212.
4. Philippot L., et al. Going back to the roots: the microbial ecology of the rhizosphere. Nat. Rev. Microbiol. 2013, 11:789-799.
5. O'Neill B., et al. Bacterial community composition in Brazilian anthrosols and adjacent soils characterized using culturing and molecular identification. Microb. Ecol. 2009, 58:23-35.
6. Beesley L., et al. A review of biochars' potential role in the remediation, revegetation and restoration of contaminated soils. Environ. Pollut. 2011, 159:3269-3282.
7. Ahmad M., et al. Biochar as a sorbent for contaminant management in soil and water: a review. Chemosphere 2014, 99:19-33.
8. 14C labeling. Soil Biol. Biochem. 2009, 41:210-219.
9. Yu L., et al. Effects of biochar application on soil methane emission at different soil moisture levels. Biol. Fertil. Soils 2012, 49:119-128.
10. Zimmerman A.R., et al. Positive and negative carbon mineralization priming effects among a variety of biochar-amended soils. Soil Biol. Biochem. 2011, 43:1169-1179.
11. Sidhu J.K., et al. Effect of silicon soil amendment on performance of sugarcane borer, Diatraea saccharalis (Lepidoptera: Crambidae) on rice. Bull. Entomol. Res. 2013, 103:656-664.
12. Yuliar, et al. Recent trends in control methods for bacterial wilt diseases caused by Ralstonia solanacearum. Microbes Environ. 2015, 30:1-11.
13. Singh R.P., et al. Land application of sewage sludge: physicochemical and microbial response. Rev. Environ. Contam. Toxicol. 2011, 214:41-61.
14. Shaheen S.M., et al. Opportunities and challenges in the use of coal fly ash for soil improvements - a review. J. Environ. Manage. 2014, 145:249-267.
15. Bradford S.A., et al. Reuse of concentrated animal feeding operation wastewater on agricultural lands. J. Environ. Qual. 2008, 37:S97-S115.
16. Singh R.P., et al. Biological responses of agricultural soils to fly-ash amendment. Reviews of Environmental Contamination and Toxicology 2014, 45-60. Springer International Publishing. D.M. Whitacre (Ed.).
17. Udikovic-Kolic N., et al. Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:15202-15207.
18. Barampuram S., Zhang Z.J. Recent advances in plant transformation. Methods Mol. Biol. 2011, 701:1-35.
19. Brunner I., Sperisen C. Aluminum exclusion and aluminum tolerance in woody plants. Front. Plant Sci. 2013, 4:172.
20. Kochian L.V. Plant adaptation to acid soils: the molecular basis for crop aluminum resistance. Annu. Rev. Plant Biol. 2015, 66:571-598.
21. Hoekenga O.A., et al. AtALMT1, which encodes a malate transporter, is identified as one of several genes critical for aluminum tolerance in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:9738-9743.
22. Liu J., et al. Aluminum-activated citrate and malate transporters from the MATE and ALMT families function independently to confer Arabidopsis aluminum tolerance. Plant J. 2009, 57:389-399.
23. Ma J.F., et al. Aluminium tolerance in plants and the complexing role of organic acids. Trends Plant Sci. 2001, 6:273-278.
24. Silva I.R., et al. Responses of eucalypt species to aluminum: the possible involvement of low molecular weight organic acids in the Al tolerance mechanism. Tree Physiol. 2004, 24:1267-1277.
25. Ryan P.R., et al. Rhizosphere engineering and management for sustainable agriculture. Plant Soil 2009, 321:363-383.
26. +-pyrophosphatase. Plant Biotechnol. J. 2007, 5:735-745.
27. Deng W., et al. Overexpression of Citrus junos mitochondrial citrate synthase gene in Nicotiana benthamiana confers aluminum tolerance. Planta 2009, 230:355-365.
28. Rascio N., Navari-Izzo F. Heavy metal hyperaccumulating plants: how and why do they do it? And what makes them so interesting?. Plant Sci. 2011, 180:169-181.
29. Simmons R.W., et al. Towards practical cadmium phytoextraction with Noccaea caerulescens. Int. J. Phytoremediation 2015, 17:191-199.
30. Losfeld G., et al. Mining in New Caledonia: environmental stakes and restoration opportunities. Environ. Sci. Pollut. Res. 2015, 22:5592-5607.
31. Janssen J., et al. Phytoremediation of metal contaminated soil using willow: exploiting plant-associated bacteria to improve biomass production and metal uptake. Int. J. Phytoremediation 2015, 17:1123-1136.
32. van der Ent A., et al. Hyperaccumulators of metal and metalloid trace elements: facts and fiction. Plant Soil 2012, 362:319-334.
33. van der Ent A., et al. Agromining: farming for metals in the future?. Environ. Sci. Technol. 2015, 49:4773-4780.
34. Clemens S. Zn and Fe biofortification: the right chemical environment for human bioavailability. Plant Sci. Int. J. Exp. Plant Biol. 2014, 225:52-57.
35. Tako E., et al. High bioavailablilty iron maize (Zea mays L.) developed through molecular breeding provides more absorbable iron in vitro (Caco-2 model) and in vivo (Gallus gallus). Nutr. J. 2013, 12:3.
36. Johnson A.A.T., et al. Constitutive overexpression of the OsNAS gene family reveals single-gene strategies for effective iron- and zinc-biofortification of rice endosperm. PLoS ONE 2011, 6:e24476.
37. Blancquaert D., et al. Present and future of folate biofortification of crop plants. J. Exp. Bot. 2014, 65:895-906.
38. Pinto E., Ferreira I.M. Cation transporters/channels in plants: tools for nutrient biofortification. J. Plant Physiol. 2015, 179:64-82.
39. Potrykus I. From the concept of totipotency to biofortified cereals. Annu. Rev. Plant Biol. 2015, 66:1-22.
40. Kikuchi A., et al. Review of recent transgenic studies on abiotic stress tolerance and future molecular breeding in potato. Breed. Sci. 2015, 65:85-102.
41. McKersie B. Planning for food security in a changing climate. J. Exp. Bot. 2015, 66:3435-3450.
42. Kuijken R.C.P., et al. Root phenotyping: from component trait in the lab to breeding. J. Exp. Bot. 2015, 66:5389-5401.
43. Jung J.K.H., McCouch S. Getting to the roots of it: genetic and hormonal control of root architecture. Front. Plant Sci. 2013, 4:186.
44. Zamioudis C., et al. Unraveling root developmental programs initiated by beneficial Pseudomonas spp. bacteria. Plant Physiol. 2013, 162:304-318.
45. Galland M., et al. The ethylene pathway contributes to root hair elongation induced by the beneficial bacteria Phyllobacterium brassicacearum STM196. Plant Sci. 2012, 190:74-81.
46. Splivallo R., et al. Truffles regulate plant root morphogenesis via the production of auxin and ethylene. Plant Physiol. 2009, 150:2018-2029.
47. Gutiérrez-Luna F.M., et al. Plant growth-promoting rhizobacteria modulate root-system architecture in Arabidopsis thaliana through volatile organic compound emission. Symbiosis 2010, 51:75-83.
48. Uga Y., et al. Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nat. Genet. 2013, 45:1097-1102.
49. Jeong J.S., et al. Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. Plant Physiol. 2010, 153:185-197.
50. Redillas M.C.F.R., et al. The overexpression of OsNAC9 alters the root architecture of rice plants enhancing drought resistance and grain yield under field conditions. Plant Biotechnol. J. 2012, 10:792-805.
51. Lu G., et al. OsPIN5b modulates rice (Oryza sativa) plant architecture and yield by changing auxin homeostasis, transport and distribution. Plant J. 2015, 83:913-925.
52. Lebeis S.L., et al. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 2015, 349:860-864.
53. De Vleesschauwer D., et al. Pseudomonas fluorescens WCS374r-induced systemic resistance in rice against Magnaporthe oryzae is based on pseudobactin-mediated priming for a salicylic acid-repressible multifaceted defense response. Plant Physiol. 2008, 148:1996-2012.
54. Pieterse C.M., et al. Induced systemic resistance by beneficial microbes. Annu. Rev. Phytopathol. 2014, 52:347-375.
55. Shah J., et al. Signaling by small metabolites in systemic acquired resistance. Plant J. 2014, 79:645-658.
56. Lorito M., et al. Genes from mycoparasitic fungi as a source for improving plant resistance to fungal pathogens. Proc. Natl. Acad. Sci. U.S.A. 1998, 95:7860-7865.
57. Volpi C., et al. The ectopic expression of a pectin methyl esterase inhibitor increases pectin methyl esterification and limits fungal diseases in wheat. Mol. Plant-Microbe Interact. 2011, 24:1012-1019.
58. Pogorelko G., et al. Arabidopsis and Brachypodium distachyon transgenic plants expressing Aspergillus nidulans acetylesterases have decreased degree of polysaccharide acetylation and increased resistance to pathogens. Plant Physiol. 2013, 162:9-23.
59. Sanford J.C., Johnston S. The concept of parasite-derived resistance. Deriving resistance genes from the parasites our genome. J. Theor. Biol. 1985, 113:395-405.
60. Malnoë P., et al. Small-scale field tests with transgenic potato, cv. Bintje, to test resistance to primary and secondary infections with potato virus Y. Plant Mol. Biol. 1994, 25:963-975.
61. Golemboski D.B., et al. Plants transformed with a tobacco mosaic virus nonstructural gene sequence are resistant to the virus. Proc. Natl. Acad. Sci. U.S.A. 1990, 87:6311-6315.
62. Lapidot M., et al. A dysfunctional movement protein of tobacco mosaic virus that partially modifies the plasmodesmata and limits virus spread in transgenic plants. Plant J. 1993, 4:959-970.
63. Nicaise V. Crop immunity against viruses: outcomes and future challenges. Front. Plant Sci. 2014, 5:660.
64. Cillo F., et al. Analysis of mechanisms involved in the cucumber mosaic virus satellite RNA-mediated transgenic resistance in tomato plants. Mol. Plant-Microbe Interact. 2004, 17:98-108.
65. Waterhouse P.M., et al. Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc. Natl. Acad. Sci. U.S.A. 1998, 95:13959-13964.
66. Maliogka V.I., et al. Control of viruses infecting grapevine. Adv. Virus Res. 2015, 91:175-227.
67. Soler N., et al. Transformation of Mexican lime with an intron-hairpin construct expressing untranslatable versions of the genes coding for the three silencing suppressors of Citrus tristeza virus confers complete resistance to the virus. Plant Biotechnol. J. 2012, 10:597-608.
68. Shekhawat U.K.S., et al. Transgenic banana plants expressing small interfering RNAs targeted against viral replication initiation gene display high-level resistance to banana bunchy top virus infection. J. Gen. Virol. 2012, 93:1804-1813.
69. Karasev A.V., Gray S.M. Continuous and emerging challenges of potato virus Y in potato. Annu. Rev. Phytopathol. 2013, 51:571-586.
70. Azad A.K., et al. Gene technology for papaya ringspot virus disease management. ScientificWorldJournal 2014, 2014:768038.
71. Prins M., et al. Strategies for antiviral resistance in transgenic plants. Mol. Plant Pathol. 2008, 9:73-83.
72. Gómez P., et al. Genetic resistance for the sustainable control of plant virus diseases: breeding, mechanisms and durability. Eur. J. Plant Pathol. 2009, 125:1-22.
73. Galvez L.C., et al. Engineered plant virus resistance. Plant Sci. 2014, 228:11-25.
74. Forsyth A., et al. Genetic dissection of basal resistance to Pseudomonas syringae pv. phaseolicola in accessions of Arabidopsis. Mol. Plant-Microbe Interact. 2010, 23:1545-1552.
75. Thapa S.P., et al. Identification of QTLs controlling resistance to Pseudomonas syringae pv. tomato race 1 strains from the wild tomato, Solanum habrochaites LA1777. Theor. Appl. Genet. 2015, 128:681-692.
76. Luo Y., et al. Marker-assisted breeding of Indonesia local rice variety Siputeh for semi-dwarf phonotype, good grain quality and disease resistance to bacterial blight. Rice 2014, 7:33.
77. Kim S.M., et al. Identification and fine-mapping of a new resistance gene, Xa40, conferring resistance to bacterial blight races in rice (Oryza sativa L.). Theor. Appl. Genet. 2015, 128:1933-1943.
78. Huet G. Breeding for resistances to Ralstonia solanacearum. Front. Plant Sci. 2014, 5:715.
79. Zipfel C., et al. Bacterial disease resistance in Arabidopsis through flagellin perception. Nature 2004, 428:764-767.
80. Boller T., Felix G. A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. Annu. Rev. Plant Biol. 2009, 60:379-406.
81. Huang P-Y., Zimmerli L. Enhancing crop innate immunity: new promising trends. Front. Plant Sci. 2014, 5:624.
82. Zipfel C. Plant pattern-recognition receptors. Trends Immunol. 2014, 35:345-351.
83. Cunnac S., et al. Pseudomonas syringae type III secretion system effectors: repertoires in search of functions. Curr. Opin. Microbiol. 2009, 12:53-60.
84. Dou D., Zhou J-M. Phytopathogen effectors subverting host immunity: different foes, similar battleground. Cell Host Microbe 2012, 12:484-495.
85. Cui H., et al. Pseudomonas syringae effector protein AvrB perturbs Arabidopsis hormone signaling by activating MAP kinase 4. Cell Host Microbe 2010, 7:164-175.
86. Hurley B., et al. Proteomics of effector-triggered immunity (ETI) in plants. Virulence 2014, 5:752-760.
87. Piquerez S.J.M., et al. Improving crop disease resistance: lessons from research on Arabidopsis and tomato. Front. Plant Sci. 2014, 5:671.
88. Trdá L., et al. Perception of pathogenic or beneficial bacteria and their evasion of host immunity: pattern recognition receptors in the frontline. Front. Plant Sci. 2015, 6:219.
89. Dangl J.L., et al. Pivoting the plant immune system from dissection to deployment. Science 2013, 341:746-751.
90. Suh J.P., et al. Development of breeding lines with three pyramided resistance genes that confer broad-spectrum bacterial blight resistance and their molecular analysis in rice. Rice 2013, 6:5.
91. Wang G.L., et al. The cloned gene, Xa21, confers resistance to multiple Xanthomonas oryzae pv. oryzae isolates in transgenic plants. Mol. Plant-Microbe Interact. 1996, 9:850-855.
92. Lacombe S., et al. Interfamily transfer of a plant pattern-recognition receptor confers broad-spectrum bacterial resistance. Nat. Biotechnol. 2010, 28:365-369.
93. Hao G., et al. Reduced susceptibility to Xanthomonas citri in transgenic citrus expressing the FLS2 receptor from Nicotiana benthamiana. Mol. Plant Microbe Interact. 2016, Published online January 5, 2016. 10.1094/MPMI-09-15-0211-R.
94. Großkinsky D.K., et al. Phytoalexin transgenics in crop protection - fairy tale with a happy end?. Plant Sci. 2012, 195:54-70.
95. Jeandet P., et al. Modulation of phytoalexin biosynthesis in engineered plants for disease resistance. Int. J. Mol. Sci. 2013, 14:14136-14170.
96. Ono E., et al. Essential role of the small GTPase Rac in disease resistance of rice. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:759-764.
97. Robert-Seilaniantz A., et al. The microRNA miR393 re-directs secondary metabolite biosynthesis away from camalexin and towards glucosinolates. Plant J. 2011, 67:218-231.
98. Siegrist M. Factors influencing public acceptance of innovative food technologies and products. Trends Food Sci. Technol. 2008, 19:603-608.
99. Kloepper J.W., Schroth M.N. Plant growth-promoting rhizobacteria on radishes. Proceedings of the 4th International Conference on Plant Pathogenic Bacteria (Vol. 2) 1978, 879-882. Gilbert-Clarey.
100. Tailor A.J., Joshi B.H. Harnessing plant growth promoting rhizobacteria beyond nature: a review. J. Plant Nutr. 2014, 37:1534-1571.
101. Chauhan H., et al. Novel plant growth promoting rhizobacteria - prospects and potential. Appl. Soil Ecol. 2015, 95:38-53.
102. Pii Y., et al. Microbial interactions in the rhizosphere: beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process. A review. Biol. Fertil. Soils 2015, 51:403-415.
103. Belimov A.a., et al. Rhizobacteria that produce auxins and contain 1-amino-cyclopropane-1-carboxylic acid deaminase decrease amino acid concentrations in the rhizosphere and improve growth and yield of well-watered and water-limited potato (Solanum tuberosum). Ann. Appl. Biol. 2015, 167:11-25.
104. Drogue B., et al. Which specificity in cooperation between phytostimulating rhizobacteria and plants?. Res. Microbiol. 2012, 163:500-510.
105. Saraf M., et al. Role of allelochemicals in plant growth promoting rhizobacteria for biocontrol of phytopathogens. Microbiol. Res. 2014, 169:18-29.
106. Raaijmakers J.M., et al. Utilization of heterologous siderophores and rhizosphere competence of fluorescent Pseudomonas spp. Can. J. Microbiol. 1995, 41:126-135.
107. van Dillewijn P., et al. Construction and environmental release of a Sinorhizobium meliloti strain genetically modified to be more competitive for alfalfa nodulation. Appl. Environ. Microbiol. 2001, 67:3860-3865.
108. Ma W., et al. Expression of an exogenous 1-aminocyclopropane-1-carboxylate deaminase gene in Sinorhizobium meliloti increases its ability to nodulate alfalfa. Appl. Environ. Microbiol. 2004, 70:5891-5897.
109. Suárez R., et al. Improvement of drought tolerance and grain yield in common bean by overexpressing trehalose-6-phosphate synthase in rhizobia. Mol. Plant-Microbe Interact. 2008, 21:958-966.
110. Zhang X., et al. Enhancing plant disease suppression by Burkholderia vietnamiensis through chromosomal integration of Bacillus subtilis chitinase gene chi113. Biotechnol. Lett. 2012, 34:287-293.
111. Delgadillo J., et al. Improving legume nodulation and Cu rhizostabilization using a genetically modified rhizobia. Environ. Technol. 2015, 36:1237-1245.
112. Liu H., et al. Quorum sensing coordinates brute force and stealth modes of infection in the plant pathogen Pectobacterium atrosepticum. PLoS Pathol. 2008, 4:e1000093.
113. Raoul des Essarts, Y. (2015) Pathogénie de Dickeya dianthicola et Dickeya solani chez Solanum tuberosum, Développement et Evaluation de Stratégie de Lutte Biologique, PhD thesis, Université Paris Sud.
114. Põllumaa L., et al. Quorum sensing and expression of virulence in pectobacteria. Sensors 2012, 12:3327-3349.
115. Faure D., Dessaux Y. Quorum sensing as a target for developing control strategies for the plant pathogen Pectobacterium. New Perspectives and Approaches in Plant Growth-Promoting Rhizobacteria Research 2007, 353-365. Springer, Netherlands. P.A.H.M. Bakker (Ed.).
116. Dong Y-H., et al. Quenching quorum-sensing-dependent bacterial infection by an N-acyl homoserine lactonase. Nature 2001, 411:813-817.
117. Dong Y.H., et al. AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:3526-3531.
118. Uroz S., et al. Novel bacteria degrading N-acylhomoserine lactones and their use as quenchers of quorum-sensing-regulated functions of plant-pathogenic bacteria. Microbiology 2003, 149:1981-1989.
119. Kwasiborski A., et al. Transcriptome of the quorum-sensing signal-degrading Rhodococcus erythropolis responds differentially to virulent and avirulent Pectobacterium atrosepticum. Heredity 2015, 114:476-484.
120. Cirou A., et al. Growth promotion of quorum-quenching bacteria in the rhizosphere of Solanum tuberosum. Environ. Microbiol. 2007, 9:1511-1522.
121. Cirou A., et al. Gamma-caprolactone stimulates growth of quorum-quenching Rhodococcus populations in a large-scale hydroponic system for culturing Solanum tuberosum. Res. Microbiol. 2011, 162:945-950.
122. Cirou A., et al. Efficient biostimulation of native and introduced quorum-quenching Rhodococcus erythropolis populations is revealed by a combination of analytical chemistry, microbiology, and pyrosequencing. Appl. Environ. Microbiol. 2012, 78:481-492.
123. Barac T., et al. Engineered endophytic bacteria improve phytoremediation of water-soluble, volatile, organic pollutants. Nat. Biotechnol. 2004, 22:583-588.
124. Taghavi S., et al. Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene. Appl. Environ. Microbiol. 2005, 71:8500-8505.
125. Ramesh R., et al. Pseudomonads: major antagonistic endophytic bacteria to suppress bacterial wilt pathogen, Ralstonia solanacearum in the eggplant (Solanum melongena L.). World J. Microbiol. Biotechnol. 2009, 25:47-55.
126. Weyens N., et al. Phytoremediation: plant-endophyte partnerships take the challenge. Curr. Opin. Biotechnol. 2009, 20:248-254.
127. Gaiero J.R., et al. Inside the root microbiome: bacterial root endophytes and plant growth promotion. Am. J. Bot. 2013, 100:1738-1750.
128. Sessitsch A., et al. The role of plant-associated bacteria in the mobilization and phytoextraction of trace elements in contaminated soils. Soil Biol. Biochem. 2013, 60:182-194.
129. Savka M.A., et al. Engineering bacterial competitiveness and persistence in the phytosphere. Mol. Plant-Microbe Interact. 2002, 15:866-874.
130. Savka M., et al. The 'biased rhizosphere' concept and advances in the omics era to study bacterial competitiveness and persistence in the phytosphere. Molecular Microbial Ecolology of the Rhizosphere 2013, Vol. 2:1147-1161. Wiley Blackwell.
131. Tempé J., Petit A. Opine utilization in Agrobacterium. Molecular Biology of Plant Tumors 1982, 451-459. Academic Press. G. Kalh (Ed.).
132. Dessaux Y., et al. Opines and opine-like molecules involved in plant-Rhizobiaceae interactions. The Rhizobiaceae 1998, 173-197. Springer, Netherlands. H.P. Spaink (Ed.).
133. Savka M.A., Farrand S.K. Modification of rhizobacterial populations by engineering bacterium utilization of a novel plant-produced resource. Nat. Biotechnol. 1997, 15:363-368.
134. Oger P., et al. Genetically engineered plants producing opines alter their biological environment. Nat. Biotechnol. 1997, 15:369-372.
135. Mansouri H., et al. Engineered rhizosphere: the trophic bias generated by opine-producing plants is independent of the opine type, the soil origin, and the plant species. Appl. Environ. Microbiol. 2002, 68:2562-2566.
136. Oger P.M., et al. 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. 2004, 47:96-103.
137. Mondy S., et al. An increasing opine carbon bias in artificial exudation systems and genetically modified plant rhizospheres leads to an increasing reshaping of bacterial populations. Mol. Ecol. 2014, 23:4846-4861.
138. Tempé J., et al. Presence of opine-like substances in alfalfa nodules. Comptes Rendus Académie Sci. Sér. III- Sci. Vie 1982, 295:413-416.
139. Murphy P.J., et al. Genes for the catabolism and synthesis of an opine-like compound in Rhizobium meliloti are closely linked and on the Sym plasmid. Proc. Natl. Acad. Sci. U.S.A. 1987, 84:493-497.
140. Lakshmanan V., et al. Microbe-associated molecular patterns-triggered root responses mediate beneficial rhizobacterial recruitment in Arabidopsis. Plant Physiol. 2012, 160:1642-1661.
141. Cai H., et al. Human-induced grassland degradation/restoration in the central Tibetan Plateau: the effects of ecological protection and restoration projects. Ecol. Eng. 2015, 83:112-119.
142. Molina L., et al. Degradation of pathogen quorum-sensing molecules by soil bacteria: a preventive and curative biological control mechanism. FEMS Microbiol. Ecol. 2003, 45:71-81.
143. Lundberg D.S., et al. Defining the core Arabidopsis thaliana root microbiome. Nature 2012, 488:86-90.
144. Zilber-Rosenberg I., Rosenberg E. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol. Rev. 2008, 32:723-735.
145. Rosenberg E., et al. The evolution of animals and plants via symbiosis with microorganisms. Environ. Microbiol. Rep. 2010, 2:500-506.
146. Vandenkoornhuyse P., et al. The importance of the microbiome of the plant holobiont. New Phytol. 2015, 206:1196-1206.
147. Pérez-Jaramillo J.E., et al. Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Mol. Biol. 2015, Published online June 18, 2015. 10.1007/s11103-015-0337-7.
148. Sangabriel-Conde W., et al. Native maize landraces from Los Tuxtlas, Mexico show varying mycorrhizal dependency for P uptake. Biol. Fertil. Soils 2014, 50:405-414.
149. Germida J.J., Siciliano S.D. Taxonomic diversity of bacteria associated with the roots of modern, recent and ancient wheat cultivars. Biol. Fertil. Soils 2001, 33:410-415.
150. Nogales A., et al. Can functional hologenomics aid tackling current challenges in plant breeding?. Brief Funct. Genomics 2015, Published online August 20, 2015. 10.1093/bfgp/elv030.