Leach JE, Tringe SG. Plant–microbiome interactions: from community assembly to plant health. Nat Rev Microbiol. 2020;18:607–21.
Google Scholar
Pii Y, Mimmo T, Tomasi N, Terzano R, Cesco S, Crecchio C. Microbial interactions in the rhizosphere: beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process. A Rev Biol Fertil Soils. 2015;51:403–21.
Google Scholar
Backer R, Rokem JS, Ilangumaran G, Lamont J, Praslickova D, Ricci E, et al. Plant growth-promoting rhizobacteria: context, mechanisms of action, and roadmap to commercialization of biostimulants for sustainable agriculture. Front Plant Sci. 2018;871:1473–89.
Google Scholar
Lugtenberg B, Kamilova F. Plant-growth-promoting rhizobacteria. Annu Rev Microbiol. 2009;63:541–56.
Google Scholar
Bhattacharyya PN, Jha DK. Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture. World J Microbiol Biotechnol. 2012;28:1327–50.
Google Scholar
Leach JE, Triplett LR, Argueso CT, Trivedi P. Communication in the phytobiome. Cell. 2017;169:587–96.
Google Scholar
Vorholt JA, Vogel C, Carlström CI, Müller DB. Establishing causality: opportunities of synthetic communities for plant microbiome research. Cell Host Microbe. 2017;22:142–55.
Google Scholar
Douglas AE. The microbial exometabolome: ecological resource and architect of microbial communities. PTRBAE. 2020;375:20190250.
Google Scholar
Turroni F, Milani C, Duranti S, Mahony J, van Sinderen D, Ventura M. Glycan utilization and cross-feeding activities by Bifidobacteria. Trends Microbiol. 2018;26:339–50.
Google Scholar
Evans CR, Kempes CP, Price-Whelan A, Dietrich LEP. Metabolic heterogeneity and cross-feeding in bacterial multicellular systems. Trends Microbiol. 2020;28:732–43.
Google Scholar
Smith NW, Shorten PR, Altermann E, Roy NC, McNabb WC. The classification and evolution of bacterial cross-feeding. Front Ecol Evol. 2019;7:153.
Google Scholar
Santoyo G, del Orozco-Mosqueda MC, Govindappa M. Mechanisms of biocontrol and plant growth-promoting activity in soil bacterial species of Bacillus and Pseudomonas: a review. Biocontrol Sci Technol. 2012;22:855–72.
Google Scholar
Borriss R. Use of plant-associated Bacillus strains as biofertilizers and biocontrol agents in agriculture. Bacteria in agrobiology: plant growth responses. Springer: Berlin; 2011. 41–76.
Xiong W, Guo S, Jousset A, Zhao Q, Wu H, Li R, et al. Bio-fertilizer application induces soil suppressiveness against Fusarium wilt disease by reshaping the soil microbiome. Soil Biol Biochem. 2017;114:238–47.
Google Scholar
Qin Y, Shang Q, Zhang Y, Li P, Chai Y. Bacillus amyloliquefaciens L-S60 reforms the rhizosphere bacterial community and improves growth conditions in cucumber plug seedling. Front Microbiol. 2017;8:2620.
Google Scholar
Compant S, Samad A, Faist H, Sessitsch A. A review on the plant microbiome: ecology, functions, and emerging trends in microbial application. J Adv Res. 2019;19:29–37.
Google Scholar
Cao Y, Zhang Z, Ling N, Yuan Y, Zheng X, Shen B, et al. Bacillus subtilis SQR9 can control Fusarium wilt in cucumber by colonizing plant roots. Biol Fertil Soils. 2011;47:495–506.
Google Scholar
Xu Z, Shao J, Li B, Yan X, Shen Q, Zhang R. Contribution of bacillomycin D in Bacillus amyloliquefaciens SQR9 to antifungal activity and biofilm formation. Appl Environ Microbiol. 2013;79:808–15.
Google Scholar
Chen L, Liu Y, Wu G, Veronican Njeri K, Shen Q, Zhang N, et al. Induced maize salt tolerance by rhizosphere inoculation of Bacillus amyloliquefaciens SQR9. Physiol plant. 2016;158:34–44.
Google Scholar
Blake C, Nordgaard Christensen M, Kovács ÁT. Molecular aspects of plant growth promotion and protection by Bacillus subtilis. Mol Plant Microbe Interact. 2020;34:15–25.
Google Scholar
Al-Ali A, Deravel J, Krier F, Béchet M, Ongena M, Jacques P. Biofilm formation is determinant in tomato rhizosphere colonization by Bacillus velezensis FZB42. Environ Sci Pollut Res. 2018;25:29910–20.
Google Scholar
Xu Z, Mandic-Mulec I, Zhang H, Liu Y, Sun X, Feng H, et al. Antibiotic bacillomycin D affects iron acquisition and biofilm formation in Bacillus velezensis through a Btr-mediated FeuABC-dependent pathway. Cel Rep. 2019;29:1192–202.
Google Scholar
Murashige T, Skoog F. A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant. 1962;15:473–97.
Google Scholar
Bai Y, Müller DB, Srinivas G, Garrido-Oter R, Potthoff E, Rott M, et al. Functional overlap of the Arabidopsis leaf and root microbiota. Nature. 2015;528:364–9.
Google Scholar
Zhou C, Shi L, Ye B, Feng H, Zhang J, Zhang R, et al. pheS *, an effective host-genotype-independent counter-selectable marker for marker-free chromosome deletion in Bacillus amyloliquefaciens. Appl Microbiol Biotechnol. 2017;101:217–27.
Google Scholar
Feng H, Zhang N, Fu R, Liu Y, Krell T, Du W, et al. Recognition of dominant attractants by key chemoreceptors mediates recruitment of plant growth-promoting rhizobacteria. Environ Microbiol. 2019;21:402–15.
Google Scholar
Lambertsen L, Sternberg C, Molin S. Mini-Tn7 transposons for site-specific tagging of bacteria with fluorescent proteins. Environ Microbiol. 2004;6:726–32.
Google Scholar
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.
Google Scholar
Machado D, Andrejev S, Tramontano M, Patil KR. Fast automated reconstruction of genome-scale metabolic models for microbial species and communities. Nucleic Acids Res. 2018;46:7542–53.
Google Scholar
Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, et al. MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020;38:272–6.
Google Scholar
Zelezniak A, Andrejev S, Ponomarova O, Mende DR, Bork P, Patil KR. Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proc Natl Acad Sci USA. 2015;112:6449–54.
Google Scholar
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.
Google Scholar
Parks DH, Tyson GW, Hugenholtz P, Beiko RG. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics. 2014;30:3123–4.
Google Scholar
Branda SS, González-Pastor JE, Ben-Yehuda S, Losick R, Kolter R. Fruiting body formation by Bacillus subtilis. Proc Natl Acad Sci USA. 2001;98:11621–6.
Google Scholar
Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31:3691–3.
Google Scholar
Langdon WB. Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks. BioData Min. 2015;8:1–7.
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:1–21.
Google Scholar
Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol. 2017;34:2115–22.
Google Scholar
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔ C(T) method. Methods. 2001;25:402–8.
Google Scholar
Ling N, Raza W, Ma J, Huang Q, Shen Q. Identification and role of organic acids in watermelon root exudates for recruiting Paenibacillus polymyxa SQR-21 in the rhizosphere. Eur J Soil Biol. 2011;47:374–9.
Google Scholar
Gordillo F, Chávez FP, Jerez CA. Motility and chemotaxis of Pseudomonas sp. B4 towards polychlorobiphenyls and chlorobenzoates. FEMS Microbiol Ecol. 2007;60:322–8.
Google Scholar
Dragoš A, Kiesewalter H, Martin M, Hsu CY, Hartmann R, Wechsler T, et al. Division of labor during biofilm matrix production. Curr Biol. 2018;28:1903–.e5.
Google Scholar
Ahmad F, Ahmad I, Khan MS. Screening of free-living rhizospheric bacteria for their multiple plant growth promoting activities. Microbiol Res. 2008;163:173–81.
Google Scholar
Lynne AM, Haarmann D, Louden BC. Use of blue agar CAS assay for siderophore detection. J Microbiol Biol Educ. 2011;12:51–53.
Google Scholar
Nautiyal CS. An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS Microbiol Lett. 1999;170:265–70.
Google Scholar
Ansari FA, Ahmad I. Fluorescent Pseudomonas -FAP2 and Bacillus licheniformis interact positively in biofilm mode enhancing plant growth and photosynthetic attributes. Sci Rep. 2019;9:1–12.
Santhanam R, Menezes RC, Grabe V, Li D, Baldwin IT, Groten K. A suite of complementary biocontrol traits allows a native consortium of root‐associated bacteria to protect their host plant from a fungal sudden‐wilt disease. Mol Ecol. 2019;28:1154–69.
Google Scholar
Santhanam R, Luu VT, Weinhold A, Goldberg J, Oh Y, Baldwin IT. Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping. Proc Natl Acad Sci USA. 2015;112:E5013–E5120.
Google Scholar
Berendsen RL, Vismans G, Yu K, Song Y, de Jonge R, Burgman WP, et al. Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME J. 2018;12:1496–507.
Google Scholar
Ren D, Madsen JS, Sørensen SJ, Burmølle M. High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation. ISME J. 2015;9:81–89.
Google Scholar
Oliveira NM, Martinez-Garcia E, Xavier J, Durham WM, Kolter R, Kim W, et al. Biofilm formation as a response to ecological competition. PLoS Biol. 2015;13:1–23.
Gallegos-Monterrosa R, Mhatre E, Kovács ÁT. Specific Bacillus subtilis 168 variants form biofilms on nutrient-rich medium. Microbiology. 2016;162:1922–32.
Google Scholar
Shao J, Xu Z, Zhang N, Shen Q, Zhang R. Contribution of indole-3-acetic acid in the plant growth promotion by the rhizospheric strain Bacillus amyloliquefaciens SQR9. Biol Fertil Soils. 2015;51:321–30.
Google Scholar
Stopnisek N, Shade A. Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype. ISME J. 2021;15:2708–22.
Google Scholar
Sivasakthi S, Usharani G, Saranraj P. Biocontrol potentiality of plant growth promoting bacteria (PGPR)—Pseudomonas fluorescens and Bacillus subtilis: a review. Afr J Agric Res. 2014;9:1265–77.
Dardanelli MS, Manyani H, González-Barroso S, Rodríguez-Carvajal MA, Gil-Serrano AM, Espuny MR, et al. Effect of the presence of the plant growth promoting rhizobacterium (PGPR) Chryseobacterium balustinum Aur9 and salt stress in the pattern of flavonoids exuded by soybean roots. Plant Soil. 2010;328:483–93.
Google Scholar
Gómez Expósito R, Postma J, Raaijmakers JM, de Bruijn I. Diversity and activity of Lysobacter species from disease suppressive soils. Front Microbiol. 2015;6:1243.
Google Scholar
Han Q, Ma Q, Chen Y, Tian B, Xu L, Bai Y, et al. Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean. ISME J. 2020;14:1915–28.
Google Scholar
Peterson SB, Dunn AK, Klimowicz AK, Handelsman J. Peptidoglycan from Bacillus cereus mediates commensalism with rhizosphere bacteria from the Cytophaga-Flavobacterium group. Appl Environ Microbiol. 2006;72:5421–7.
Google Scholar
Tao C, Li R, Xiong W, Shen Z, Liu S, Wang B, et al. Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression. Microbiome. 2020;8:137.
Google Scholar
Kumar A, Singh J. Biofilms forming microbes: diversity and potential application in plant-microbe interaction and plant growth. Springer: Cham; 2020. 173−97.
Tabassum B, Khan A, Tariq M, Ramzan M, Iqbal Khan MS, Shahid N, et al. Bottlenecks in commercialisation and future prospects of PGPR. Appl Soil Ecol. 2017;121:102–17.
Google Scholar
Madsen JS, Røder HL, Russel J, Sørensen H, Burmølle M, Sørensen SJ. Coexistence facilitates interspecific biofilm formation in complex microbial communities. Environ Microbiol. 2016;18:2565–74.
Google Scholar
Burmølle M, Webb JS, Rao D, Hansen LH, Sørensen SJ, Kjelleberg S. Enhanced biofilm formation and increased resistance to antimicrobial agents and bacterial invasion are caused by synergistic interactions in multispecies biofilms. Appl Environ Microbiol. 2006;72:3916–23.
Google Scholar
Lee KWK, Periasamy S, Mukherjee M, Xie C, Kjelleberg S, Rice SA. Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm. ISME J. 2014;8:894–907.
Google Scholar
Yannarell SM, Grandchamp GM, Chen SY, Daniels KE, Shank EA. A dual-species biofilm with emergent mechanical and protective properties. J Bacteriol. 2019;201:e00670–18.
Google Scholar
Preussger D, Giri S, Muhsal LK, Oña L, Kost C. Reciprocal fitness feedbacks promote the evolution of mutualistic cooperation. Curr Biol. 2020;30:1–11.
Google Scholar
Nadell CD, Drescher K, Foster KR. Spatial structure, cooperation, and competition in biofilms. Nat Rev Microbiol. 2016;14:589–600.
Google Scholar
Estrela S, Sanchez-Gorostiaga A, Vila JCC, Sanchez A. Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments. eLife. 2021;10:e65948.
Google Scholar
Molina-Santiago C, Pearson JR, Navarro Y, Berlanga-Clavero MV, Caraballo-Rodriguez AM, Petras D, et al. The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization. Nat Commun. 2019;10:1919.
Google Scholar
Yan Q, Lopes LD, Shaffer BT, Kidarsa TA, Vining O, Philmus B, et al. Secondary metabolism and interspecific competition affect accumulation of spontaneous mutants in the GacS-GacA regulatory system in Pseudomonas protegens. mBio. 2018;9:e01845–17.
Google Scholar
Mee MT, Collins JJ, Church GM, Wang HH. Syntrophic exchange in synthetic microbial communities. Proc Natl Acad Sci USA. 2014;111:E2149–E2156.
Google Scholar
D’Souza G, Shitut S, Preussger D, Yousif G, Waschina S, Kost C. Ecology and evolution of metabolic cross-feeding interactions in bacteria. Nat Prod Rep. 2018;35:455–88.
Google Scholar
Goldford JE, Lu N, Bajić D, Estrela S, Tikhonov M, Sanchez-Gorostiaga A, et al. Emergent simplicity in microbial community assembly. Science. 2018;361:469–74.
Google Scholar
Lawrence D, Fiegna F, Behrends V, Bundy JG, Phillimore AB, Bell T, et al. Species interactions alter evolutionary responses to a novel environment. PLoS Biol. 2012;10:e1001330.
Google Scholar
Evans R, Beckerman AP, Wright RCT, McQueen-Mason S, Bruce NC, Brockhurst MA. Eco-evolutionary dynamics set the tempo and trajectory of metabolic evolution in multispecies communities. Curr Biol. 2020;30:1–5.
Google Scholar
Gamez RM, Ramirez S, Montes M, Cardinale M. Complementary dynamics of banana root colonization by the plant growth-promoting rhizobacteria Bacillus amyloliquefaciens Bs006 and Pseudomonas palleroniana Ps006 at spatial and temporal scales. Micro Ecol. 2020;80:656–68.
Google Scholar
Feng H, Zhang N, Fu R, Liu Y, Krell T, Du W, et al. Recognition of dominant attractants by key chemoreceptors mediates recruitment of plant growth-promoting rhizobacteria. Environ Microbiol. 2019;21:402–15.
Google Scholar
Feng H, Zhang N, Du W, Zhang H, Liu Y, Fu R, et al. Identification of chemotaxis compounds in root exudates and their sensing chemoreceptors in plant-growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9. Mol Plant Microbe interact. 2018;31:995–1005.
Google Scholar
Xu Z, Xie J, Zhang H, Wang D, Shen Q, Zhang R. Enhanced control of plant wilt disease by a xylose-inducible degQ gene engineered into Bacillus velezensis strain SQR9XYQ. Phytopathology. 2019;109:36–43.
Google Scholar
Source: Ecology - nature.com
