Bastian M, Heymann S, Jacomy M (2009) Gephi: an open source software for exploring and manipulating networks. Third international AAAI conference on weblogs and social media.
Google Scholar
Benjamini Y, Hochberg YJ, Jot Rsss B. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B. 1995;57:289–300.
Berendsen RL, Pieterse CM, Bakker PA. The rhizosphere microbiome and plant health. Trends Plant Sci. 2012;17:478–86.
Article
CAS
PubMed
Google Scholar
Berendsen RL, Vismans G, Yu K, Song Y, de Jonge R, Burgman WP, Burmolle M, Herschend J, Bakker P, Pieterse CMJ. Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME J. 2018;12:1496–507. https://doi.org/10.1038/s41396-018-0093-1.
Article
CAS
PubMed
PubMed Central
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. mBio. 2010;7:335–6. https://doi.org/10.1038/nmeth.f.303.
Carrion VJ, Cordovez V, Tyc O, Etalo DW, de Bruijn I, de Jager VCL, Medema MH, Eberl L, Raaijmakers JM. Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils. ISME J. 2018;12:2307–21. https://doi.org/10.1038/s41396-018-0186-x.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chuberre C, Plancot B, Driouich A, Moore JP, Bardor M, Gugi B, Vicre M. Plant immunity is compartmentalized and specialized in roots. Front Plant Sci. 2018;9:1692. https://doi.org/10.3389/fpls.2018.01692.
Article
PubMed
PubMed Central
Google Scholar
Claesson MJ, O'Sullivan O, Wang Q, Nikkilä J, Marchesi JR, Smidt H, de Vos WM, Ross RP, O'Toole PW. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One. 2009;4:e6669. https://doi.org/10.1371/journal.pone.0006669.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cross ML. Microbes versus microbes: immune signals generated by probiotic lactobacilli and their role in protection against microbial pathogens. FEMS Immunology & Medical Microbiology. 2002;34:245–53.
Article
CAS
Google Scholar
Deng Y, Jiang Y-H, Yang Y, He Z, Luo F, Zhou JJBB. Mol Ecol Netw Analyses. 2012;13:113. https://doi.org/10.1186/1471-2105-13-113.
Article
Google Scholar
Dennis KL, Wang Y, Blatner NR, Wang S, Saadalla A, Trudeau E, Roers A, Weaver CT, Lee JJ, Gilbert JA, Chang EB, Khazaie K. Adenomatous polyps are driven by microbe-instigated focal inflammation and are controlled by IL-10–producing T cells. Cancer Res. 2013. https://doi.org/10.1158/0008-5472.can-13-1511.
Finkel OM, Castrillo G, Herrera Paredes S, Salas Gonzalez I, Dangl JL. Understanding and exploiting plant beneficial microbes. Curr Opin Plant Biol. 2017;38:155–63. https://doi.org/10.1016/j.pbi.2017.04.018.
Article
PubMed
PubMed Central
Google Scholar
Flores-Rentería D, Rincón A, Valladares F, Curiel Yuste J. Agricultural matrix affects differently the alpha and beta structural and functional diversity of soil microbial communities in a fragmented Mediterranean holm oak forest. Soil Biol Biochem. 2016;92:79–90. https://doi.org/10.1016/j.soilbio.2015.09.015.
Article
CAS
Google Scholar
Fu L, Ruan Y, Tao C, Li R, Shen Q. Continous application of bioorganic fertilizer induced resilient culturable bacteria community associated with banana Fusarium wilt suppression. Sci Rep. 2016;6:27731. https://doi.org/10.1038/srep27731.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gu Y, Wei Z, Wang X, Friman V-P, Huang J, Wang X, Mei X, Xu Y, Shen Q, Jousset A. Pathogen invasion indirectly changes the composition of soil microbiome via shifts in root exudation profile. Biol Fertil Soils. 2016;52:997–1005. https://doi.org/10.1007/s00374-016-1136-2.
Article
CAS
Google Scholar
Hanemian M, Barlet X, Sorin C, Yadeta KA, Keller H, Favery B, Simon R, Thomma BP, Hartmann C, Crespi M, Marco Y, Tremousaygue D, Deslandes L. Arabidopsis CLAVATA1 and CLAVATA2 receptors contribute to Ralstonia solanacearum pathogenicity through a miR169-dependent pathway. New Phytologist. 2016;211:502–15. https://doi.org/10.1111/nph.13913.
Article
CAS
PubMed
Google Scholar
Huang X-F, Chaparro JM, Reardon KF, Zhang R, Shen Q, Vivanco JM. Rhizosphere interactions: root exudates, microbes, and microbial communities. Botany. 2014;92:267–75.
Article
Google Scholar
Jiang J, Yu M, Hou R, Li L, Ren X, Jiao C, Yang L, Xu H. Changes in the soil microbial community are associated with the occurrence of Panax quinquefolius L. root rot diseases. 2019;438(1):143-56.
Kolton M, Graber ER, Tsehansky L, Elad Y, Cytryn E. Biochar-stimulated plant performance is strongly linked to microbial diversity and metabolic potential in the rhizosphere. New Phytol. 2017;213:1393–404.
Article
CAS
PubMed
Google Scholar
Kyselková M, Kopecký J, Frapolli M, Défago G, Ságová-Marečková M, Grundmann GL, Moënne-Loccoz Y. Comparison of rhizobacterial community composition in soil suppressive or conducive to tobacco black root rot disease. ISME J. 2009;3:1127.
Article
PubMed
Google Scholar
Larousse M, Rancurel C, Syska C, Palero F, Etienne C, Industri B, Nesme X, Bardin M, Galiana E. Tomato root microbiota and Phytophthora parasitica-associated disease. Microbiome. 2017;5:56. https://doi.org/10.1186/s40168-017-0273-7.
Article
PubMed
PubMed Central
Google Scholar
Li M, Song J, Ma Q, Kong D, Zhou Y, Jiang X, Parales R, Ruan Z, Zhang Q. Insight into the characteristics and new mechanism of nicosulfuron biodegradation by a Pseudomonas sp. LAM1902. J Agric Food Chem. 2020;68:826–37.
Article
CAS
PubMed
Google Scholar
Liu X, Zhang S, Jiang Q, Bai Y, Shen G, Li S, Ding W. Using community analysis to explore bacterial indicators for disease suppression of tobacco bacterial wilt. Sci Rep. 2016;6:36773.
Article
CAS
PubMed
PubMed Central
Google Scholar
Locey KJ, Lennon JT. Scaling laws predict global microbial diversity. Proc Natl Acad Sci. 2016;113:5970–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ma J, Ibekwe AM, Yang CH, Crowley DE. Bacterial diversity and composition in major fresh produce growing soils affected by physiochemical properties and geographic locations. Sci Total Environ. 2016;563-564:199–209. https://doi.org/10.1016/j.scitotenv.2016.04.122.
Article
CAS
PubMed
Google Scholar
Massalha H, Korenblum E, Tholl D, Aharoni A. Small molecules below-ground: the role of specialized metabolites in the rhizosphere. Plant J. 2017;90:788–807. https://doi.org/10.1111/tpj.13543.
Article
CAS
PubMed
Google Scholar
Mendes LW, Mendes R, Raaijmakers JM, Tsai SM. Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean. ISME J. 2018;12:3038–42. https://doi.org/10.1038/s41396-018-0234-6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mendes R, Garbeva P, Raaijmakers JM. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev. 2013;37:634–63.
Article
CAS
PubMed
Google Scholar
Mendes R, Raaijmakers JM. Cross-kingdom similarities in microbiome functions. ISME J. 2015;9:1905.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mommer L, Kirkegaard J, van Ruijven J. Root-root interactions: towards a Rhizosphere framework. Trends Plant Sci. 2016;21:209–17. https://doi.org/10.1016/j.tplants.2016.01.009.
Article
CAS
PubMed
Google Scholar
Peyraud R, Cottret L, Marmiesse L, Genin S. Control of primary metabolism by a virulence regulatory network promotes robustness in a plant pathogen. Nat Commun. 2018;9:418. https://doi.org/10.1038/s41467-017-02660-4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Philippot L, Raaijmakers JM, Lemanceau P, Van Der Putten WH. Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol. 2013;11:789. https://doi.org/10.1038/nrmicro3109.
Article
CAS
PubMed
Google Scholar
Pieterse CM, Zamioudis C, Berendsen RL, Weller DM, Van Wees SC, Bakker PA. Induced systemic resistance by beneficial microbes. Annu Rev Phytopathol. 2014;52:347–75. https://doi.org/10.1146/annurev-phyto-082712-102340.
Article
CAS
PubMed
Google Scholar
Raza W, Ling N, Yang L, Huang Q, Shen Q. Response of tomato wilt pathogen Ralstonia solanacearum to the volatile organic compounds produced by a biocontrol strain Bacillus amyloliquefaciens SQR-9. Sci Rep. 2016;6:24856. https://doi.org/10.1038/srep24856.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rudrappa T, Czymmek KJ, Pare PW, Bais HP. Root-secreted malic acid recruits beneficial soil bacteria. Plant Physiol. 2008;148:1547–56. https://doi.org/10.1104/pp.108.127613.
Article
CAS
PubMed
PubMed Central
Google Scholar
Scholer A, Jacquiod S, Vestergaard G, Schulz S, Schloter M. Analysis of soil microbial communities based on amplicon sequencing of marker genes. Biology and Fertility of Soils. 2017;53(5):485-89.
Schönfeld J, Heuer H, Van Elsas J, Smalla K. Specific and sensitive detection of Ralstonia solanacearum in soil on the basis of PCR amplification of fliC fragments. Appl Environ Microbiol. 2003;69:7248–56.
Article
PubMed
PubMed Central
Google Scholar
Scharf BE, Hynes MF, Alexandre GM. Chemotaxis signaling systems in model beneficial plant-bacteria associations. Plant Mol Biol. 2016;90:549–59. https://doi.org/10.1007/s11103-016-0432-4.
Article
CAS
PubMed
Google Scholar
Shi S, Nuccio EE, Shi ZJ, He Z, Zhou J, Firestone MK. The interconnected rhizosphere: high network complexity dominates rhizosphere assemblages. Ecol Lett. 2016;19:926–36. https://doi.org/10.1111/ele.12630.
Article
PubMed
Google Scholar
Thomashow LS, Kwak YS, Weller DM. Root-associated microbes in sustainable agriculture: models, Metabolites and Mechanisms. Pest Manag Sci. 2019. https://doi.org/10.1002/ps.5406.
Venturi V, Keel C. Signaling in the Rhizosphere. Trends Plant Sci. 2016;21:187–98. https://doi.org/10.1016/j.tplants.2016.01.005.
Article
CAS
PubMed
Google Scholar
Vestergaard G, Schulz S, Scholer A, Schloter M. Making big data smart—how to use metagenomics to understand soil quality. Biology and Fertility of Soils. 2017;53(5):479-84.
Wei Z, Hu J, Gu Y, Yin S, Xu Y, Jousset A, Shen Q, Friman VP. Ralstonia solanacearum pathogen disrupts bacterial rhizosphere microbiome during an invasion. Soil Biol Biochem. 2018a;118:8–17. https://doi.org/10.1016/j.soilbio.2017.11.012..
Article
CAS
Google Scholar
Wei Z, Yang T, Friman VP, Xu Y, Shen Q, Jousset A. Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health. Nat Commun. 2015;6:8413. https://doi.org/10.1038/ncomms9413.
Article
CAS
PubMed
Google Scholar
Yuan J, Ruan Y, Wang B, Zhang J, Waseem R, Huang Q, Shen Q. Plant growth-promoting rhizobacteria strain Bacillus amyloliquefaciens NJN-6-enriched bio-organic fertilizer suppressed Fusarium wilt and promoted the growth of banana plants. J Agric Food Chem. 2013;61:3774–80. https://doi.org/10.1021/jf400038z.
Article
CAS
PubMed
Google Scholar
Yuan J, Wu Y, Zhao M, Wen T, Huang Q, Shen Q. Effect of phenolic acids from banana root exudates on root colonization and pathogen suppressive properties of Bacillus amyloliquefaciens NJN-6. Biol Control. 2018a;125:131–7. https://doi.org/10.1016/j.biocontrol.2018.05.016.
Article
CAS
Google Scholar
Yuan J, Zhao J, Wen T, Zhao M, Li R, Goossens P, Huang Q, Bai Y, Vivanco JM, Kowalchuk GA, Berendsen RL, Shen Q. Root exudates drive the soil-borne legacy of aboveground pathogen infection. Microbiome. 2018b;6:156. https://doi.org/10.1186/s40168-018-0537-x.
Article
PubMed
PubMed Central
Google Scholar
Zhalnina K, Louie KB, Hao Z, Mansoori N, da Rocha UN, Shi S, Cho H, Zhao H, Karaoz U, Northen TR, Firestone MK. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol. 2018;3:470. https://doi.org/10.1038/s41564-018-0129-3.
Article
CAS
PubMed
Google Scholar
Zhao M, Yuan J, Shen Z, Dong M, Liu H, Wen T, Li R, Shen Q. Predominance of soil vs root effect in rhizosphere microbiota reassembly. FEMS Microbiol Ecol. 2019;95. https://doi.org/10.1093/femsec/fiz139.
Zhou J, Deng Y, Luo F, He Z, Tu Q, XJM Z. Functional molecular ecological networks. 2010;1:e00169–10.
Hayward AC. Biology and Epidemiology of Bacterial Wilt Caused by Pseudomonas Solanacearum. Ann Rev Phytopathol. 1991;29(1):65-87. https://doi.org/10.1146/annurev.py.29.090191.000433.
Article
CAS
Google Scholar
Jiang G, Wei Z, Xu J, Chen H, Zhang Y, She X, Macho AP, Ding W, Liao B. Bacterial wilt in China: history, current status, and future perspectives. Front Plant Sci. 2017;8. https://doi.org/10.3389/Fpls.2017.01549.
Yabuuchi E, Kosako Y, Yano I, Hotta H, Nishiuchi Y. Transfer of two burkholderia and an alcaligenes species to Ralstonia gen. Nov.: proposal of Ralstonia pickettii (ralston, palleroni and doudoroff 1973) comb. Nov., Ralstonia solanacearum (smith 1896) comb. Nov. and Ralstonia eutropha (davis 1969) comb. Nov. Microbiol Immunol. 1995;39:897–904.
Article
CAS
PubMed
Google Scholar
Dalsing BL, Truchon AN, Gonzalez-Orta ET, Milling AS, Allen C. Ralstonia solanacearum uses inorganic nitrogen metabolism for virulence, ATP production, and detoxification in the oxygen-limited host xylem environment. Mbio 2015;6. https://doi.org/10.1128/mBio.02471-14.
Huang Q, Allen C. Polygalacturonases are required for rapid colonization and full virulence of Ralstonia solanacearum on tomato plants. Physiol Mol Plant Pathol. 2000;57:77–83. https://doi.org/10.1006/pmpp.2000.0283.
Article
CAS
Google Scholar
Saile E, McGarvey JA, Schell MA, Denny TP. Role of extracellular polysaccharide and endoglucanase in root invasion and colonization of tomato plants by Ralstonia solanacearum. Phytopathology 1997;87:1264–1271. https://doi.org/10.1094/Phyto.1997.87.12.1264.
Article
CAS
PubMed
Google Scholar
Denny TP, Baek SR. Genetic-evidence that extracellular polysaccharide is a virulence factor of pseudomonas-solanacearum. Mol Plant Microbe Interact 1991;4:198–206. https://doi.org/10.1094/Mpmi-4-198.
Article
CAS
Google Scholar
Genin S, Denny TP. Pathogenomics of the Ralstonia solanacearum species complex. Ann Rev Phytopathol. 2012;50:67–89. https://doi.org/10.1146/annurev-phyto-081211-173000.
Article
CAS
Google Scholar
Paulson J, Stine O, Bravo H, Pop M, et al. Differential abundance analysis for microbial marker-gene surveys. Nat Methods 2013;10:1200–1202. https://doi.org/10.1038/nmeth.2658.
Article
CAS
PubMed
PubMed Central
Google Scholar
Worley B, Powers R. Multivariate Analysis in Metabolomics. Curr Metabolomics. 2013;1(1):92–107.
CAS
PubMed
PubMed Central
Google Scholar