Fierer N. 2017. Embracing the unknown: Disentangling the complexities of the soil microbiome. Nat Rev Microbiol 15:579-590. https://doi.org/10 .1038/nrmicro.2017.87.
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. https://doi.org/10 .1111/1574-6976.12028.
Müller DB, Vogel C, Bai Y, Vorholt JA. 2016. The plant microbiota: Systemslevel insights and perspectives. Annu Rev Genet 50:211-234. https://doi .org/10.1146/annurev-genet-120215-034952.
Penha RO, Vandenberghe LPS, Faulds C, Soccol VT, Soccol CR. 2020. Bacillus lipopeptides as powerful pest control agents for a more sustainable and healthy agriculture: Recent studies and innovations. Planta 251:70. https://doi.org/10.1007/s00425-020-03357-7.
Grubbs KJ, Bleich RM, SantaMaria KC, Allen SE, Farag S, AgBiome Team, Shank EA, Bowers AA. 2017. Large-scale bioinformatics analysis of Bacillus genomes uncovers conserved roles of natural products in bacterial physiology.mSystems 2:e00040-17. https://doi.org/10.1128/mSystems.00040-17.
Harwood CR, Mouillon J-M, Pohl S, Arnau J. 2018. Secondarymetabolite production and the safety of industrially important members of the Bacillus subtilis group. FEMSMicrobiol Rev 42:721-738. https://doi.org/10.1093/femsre/fuy028.
Ye M, Tang X, Yang R, Zhang H, Li F, Tao F, Li F, Wang Z. 2018. Characteristics and application of a novel species of Bacillus: Bacillus velezensis. ACS Chem Biol 13:500-505. https://doi.org/10.1021/acschembio.7b00874.
Rabbee MF, Ali MS, Choi J, Hwang BS, Jeong SC, Baek KH. 2019. Bacillus velezensis: A valuable member of bioactive molecules within plant microbiomes. Molecules 24:1046. https://doi.org/10.3390/molecules24061046.
Pieterse CM, Zamioudis C, Berendsen RL, Weller DM, Van Wees SCM, Bakker PAHM. 2014. Induced systemic resistance by beneficial microbes. Annu Rev Phytopathol 52:347-375. https://doi.org/10.1146/annurev-phyto -082712-102340.
Köhl J, Kolnaar R, Ravensberg WJ. 2019. Mode of action of microbial biological control agents against plant diseases: Relevance beyond efficacy. Front Plant Sci 10:845. https://doi.org/10.3389/fpls.2019.00845.
TraxlerMF, Kolter R. 2015. Natural products in soilmicrobe interactions and evolution. Nat Prod Rep 32:956-970. https://doi.org/10.1039/c5np00013k.
Raaijmakers JM, Mazzola M. 2012. Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria. Annu Rev Phytopathol 50:403-424. https://doi.org/10.1146/annurev-phyto-081211 -172908.
Li Y, Rebuffat S. 2020. The manifold roles of microbial ribosomal peptidebased natural products in physiology and ecology. J Biol Chem 295: 34-54. https://doi.org/10.1074/jbc.REV119.006545.
Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, IMG/M Data Consortium, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA. 2021. A genomic catalog of Earth's microbiomes. Nat Biotechnol 39:499-509. https://doi.org/10.1038/s41587-020-0718-6.
Schmidt R, Ulanova D, Wick LY, Bode HB, Garbeva P. 2019. Microbe-driven chemical ecology: Past, present and future. ISME J 13:2656-2663. https://doi.org/10.1038/s41396-019-0469-x.
Hibbing ME, Fuqua C, Parsek MR, Peterson SB. 2010. Bacterial competition: Surviving and thriving in the microbial jungle. Nat Rev Microbiol 8: 15-25. https://doi.org/10.1038/nrmicro2259.
Andri_c S, Meyer T, Ongena M. 2020. Bacillus responses to plant-associated fungal and bacterial communities. Front Microbiol 11:1350. https://doi .org/10.3389/fmicb.2020.01350.
Eckshtain-Levi N, Harris SL, Roscios RQ, Shank EA. 2020. Bacterial community members increase Bacillus subtilismaintenance on the roots of Arabidopsis thaliana. Phytobiomes J 4:303-313. https://doi.org/10.1094/pbiomes-02-20-0019-r.
Yannarell SM, Grandchamp GM, Chen SY, Daniels KE, Shank EA. 2019. A dual-species biofilm with emergent mechanical and protective properties. J Bacteriol 201:e00670-18. https://doi.org/10.1128/JB.00670-18.
Flemming HC, Wingender J, Szewzyk U, Steinberg P, Rice SA, Kjelleberg S. 2016. Biofilms: An emergent form of bacterial life. Nat Rev Microbiol 14: 563-575. https://doi.org/10.1038/nrmicro.2016.94.
Shank EA, Klepac-Ceraj V, Collado-Torres L, Powers GE, Losick R, Kolter R. 2011. Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. Proc Natl Acad Sci U S A 108:E1236-E1243. https://doi.org/10.1073/pnas.1103630108.
Lopez D, Fischbach MA, Chu F, Losick R, Kolter R. 2009. Structurally diverse natural products that cause potassium leakage trigger multicellularity in Bacillus subtilis. Proc Natl Acad Sci U S A 106:280-285. https://doi .org/10.1073/pnas.0810940106.
Bleich R, Watrous JD, Dorrestein PC, Bowers AA, Shank EA. 2015. Thiopeptide antibiotics stimulate biofilm formation in Bacillus subtilis. Proc Natl Acad Sci U S A 112:3086-3091. https://doi.org/10.1073/pnas.1414272112.
Arnaouteli S, Bamford NC, Stanley-Wall NR, Kovács ÁT. 2021. Bacillus subtilis biofilm formation and social interactions. Nat Rev Microbiol 19: 600-614. https://doi.org/10.1038/s41579-021-00540-9.
Liu Y, Kyle S, Straight PD. 2018. Antibiotic stimulation of a Bacillus subtilis migratory response. mSphere 3:e00586-17. https://doi.org/10.1128/mSphere .00586-17.
Stubbendieck RM, Straight PD. 2015. Escape from lethal bacterial competition through coupled activation of antibiotic resistance and a mobilized subpopulation. PLoS Genet 11:e1005722. https://doi.org/10.1371/journal .pgen.1005722.
Grandchamp GM, Caro L, Shank EA. 2017. Pirated siderophores promote sporulation in Bacillus subtilis. Appl Environ Microbiol 83:e03293-16. https://doi.org/10.1128/AEM.03293-16.
Müller S, Strack SN, Ryan SE, Kearns DB, Kirby JR. 2015. Predation by Myxococcus xanthus induces Bacillus subtilis to form spore-filled megastructures. Appl Environ Microbiol 81:203-210. https://doi.org/10.1128/AEM .02448-14.
Raaijmakers JM, de Bruijn I, Nybroe O, Ongena M. 2010. Natural functions of lipopeptides from Bacillus and Pseudomonas: More than surfactants and antibiotics. FEMS Microbiol Rev 34:1037-1062. https://doi.org/10 .1111/j.1574-6976.2010.00221.x.
Zboralski A, Filion M. 2020. Genetic factors involved in rhizosphere colonization by phytobeneficial Pseudomonas spp. Comput Struct Biotechnol J 18:3539-3554. https://doi.org/10.1016/j.csbj.2020.11.025.
Rieusset L, Rey M, Muller D, Vacheron J, Gerin F, Dubost A, Comte G, Prigent-Combaret C. 2020. Secondary metabolites from plant-associated Pseudomonas are overproduced in biofilm. Microb Biotechnol 13: 1562-1580. https://doi.org/10.1111/1751-7915.13598.
Nguyen DD, Melnik AV, Koyama N, Lu X, Schorn M, Fang J, Aguinaldo K, Lincecum TL, Ghequire MGK, Carrion VJ, Cheng TL, Duggan BM, Malone JG, Mauchline TH, Sanchez LM, Kilpatrick AM, Raaijmakers JM, De Mot R, Moore BS, Medema MH, Dorrestein PC. 2016. Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides. Nat Microbiol 2:16197. https://doi.org/10.1038/nmicrobiol.2016.197.
Götze S, Stallforth P. 2020. Structure, properties, and biological functions of nonribosomal lipopeptides from pseudomonads. Nat Prod Rep 37: 29-54. https://doi.org/10.1039/c9np00022d.
Geudens N, Martins JC. 2018. Cyclic lipodepsipeptides from Pseudomonas spp.-biological Swiss-army knives. Front Microbiol 9:1867. https://doi .org/10.3389/fmicb.2018.01867.
Loper JE, Hassan KA, Mavrodi DV, Davis EW, Lim CK, Shaffer BT, Elbourne LDH, Stockwell VO, Hartney SL, Breakwell K, Henkels MD, Tetu SG, Rangel LI, Kidarsa TA, Wilson NL, van de Mortel JE, Song C, Blumhagen R, Radune D, Hostetler JB, Brinkac LM, Durkin AS, Kluepfel DA, Wechter WP, Anderson AJ, Kim YC, Pierson LS, Pierson EA, Lindow SE, Kobayashi DY, Raaijmakers JM, Weller DM, Thomashow LS, Allen AE, Paulsen IT. 2012. Comparative genomics of plantassociated Pseudomonas spp.: Insights into diversity and inheritance of traits involved inmultitrophic interactions. PLoS Genet 8:e1002784. https://doi.org/10 .1371/journal.pgen.1002784.
Powers MJ, Sanabria-Valentín E, Bowers AA, Shank EA. 2015. Inhibition of cell differentiation in Bacillus subtilis by Pseudomonas protegens. J Bacteriol 197:2129-2138. https://doi.org/10.1128/JB.02535-14.
Sun X, Xu Z, Xie J, Hesselberg-Thomsen V, Tan T, Zheng D, Strube ML, Dragoš A, Shen Q, Zhang R, Kovács ÁT. 2021. Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions. ISME J. https://doi.org/10.1038/s41396-021-01125-3.
Ansari FA, Ahmad I. 2019. Fluorescent Pseudomonas-FAP2 and Bacillus licheniformis interact positively in biofilm mode enhancing plant growth and photosynthetic attributes. Sci Rep 9:4547. https://doi.org/10.1038/s41598-019-40864-4.
Molina-Santiago C, Pearson JR, Navarro Y, Berlanga-Clavero MV, Caraballo-Rodriguez AM, Petras D, García-Martín ML, Lamon G, Haberstein B, Cazorla FM, de Vicente A, Loquet A, Dorrestein PC, Romero D. 2019. The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization. Nat Commun 10:1919. https://doi.org/10 .1038/s41467-019-09944-x.
Molina-Santiago C, Vela-Corcía D, Petras D, Díaz-Martínez L, Pérez-Lorente AI, Sopeña-Torres S, Pearson J, Caraballo-Rodríguez AM, Dorrestein PC, de Vicente A, Romero D. 2021. Chemical interplay and complementary adaptative strategies toggle bacterial antagonism and co-existence. Cell Rep 36:109449. https://doi.org/10.1016/j.celrep.2021.109449.
Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, Van Wezel GP, Medema MH, Weber TH. 2021. General rights antiSMASH 6.0: Improving cluster detection and comparison capabilities. Nucleic Acids Res 49: W29-W35. https://doi.org/10.1093/nar/gkab335.
Nihorimbere V, Cawoy H, Seyer A, Brunelle A, Thonart P, Ongena M. 2012. Impact of rhizosphere factors on cyclic lipopeptide signature from the plant beneficial strain Bacillus amyloliquefaciens S499. FEMS Microbiol Ecol 79:176-191. https://doi.org/10.1111/j.1574-6941.2011.01208.x.
Youard ZA, Wenner N, Reimmann C. 2011. Iron acquisition with the natural siderophore enantiomers pyochelin and enantio-pyochelin in Pseudomonas species. Biometals 24:513-522. https://doi.org/10.1007/s10534 -010-9399-9.
Mavrodi DV, Parejko JA, Mavrodi OV, Kwak YS, Weller DM, Blankenfeldt W, Thomashow LS. 2013. Recent insights into the diversity, frequency and ecological roles of phenazines in fluorescent Pseudomonas spp. Environ Microbiol 15:675-686. https://doi.org/10.1111/j.1462-2920.2012.02846.x.
D'aes J, Hua GKH, De Maeyer K, Pannecoucque J, Forrez I, Ongena M, Dietrich LEP, Thomashow LS, Mavrodi DV, Höfte M. 2011. Biological control of Rhizoctonia root rot on bean by phenazineand cyclic lipopeptide-producing Pseudomonas CMR12a. Phytopathology 101:996-1004. https://doi.org/10.1094/PHYTO-11-10-0315.
Hoff G, Arias AA, Boubsi F, Prši_c J, Meyer T, IbrahimHMM, Steels S, Luzuriaga P, Legras A, Franzil L, Lequart-Pillon M, Rayon C, Osorio V, de Pauw E, Lara Y, Deboever E, de Coninck B, Jacques P, Deleu M, Petit E, Van Wuytswinkel O, Ongena M. 2021. Surfactin stimulated by pectin molecular patterns and root exudates acts as a key driver of the Bacillus-plant mutualistic interaction. mBio 12:e01774-21. https://doi.org/10.1128/mBio.01774-21.
Salari F, Zare-Mirakabad F, Alavi MH, Girard L, Ghafari M, De Mot R, Rokni-Zadeh H. 2020. Draft genome sequence of Pseudomonas aeruginosa strain LMG 1272, an atypical white line reaction producer. Microbiol Resour Announc 9:e01363-19. https://doi.org/10.1128/MRA.01363-19.
Munsch P, Alatossava T. 2002. The white-line-in-agar test is not specific for the two cultivated mushroom associated pseudomonads, Pseudomonas tolaasii and Pseudomonas "reactans". Microbiol Res 157:7-11. https://doi.org/10.1078/0944-5013-00125.
van Gestel J, Vlamakis H, Kolter R. 2015. From cell differentiation to cell collectives: Bacillus subtilis uses division of labor to migrate. PLoS Biol 13: E1002141. https://doi.org/10.1371/journal.pbio.1002141.
Kinsinger RF, Shirk MC, Fall R. 2003. Rapid surface motility in Bacillus subtilis is dependent on extracellular surfactin and potassium ion. J Bacteriol 185:5627-5631. https://doi.org/10.1128/JB.185.18.5627-5631.2003.
Angelini TE, Roper M, Kolter R, Weitz DA, Brenner MP. 2009. Bacillus subtilis spreads by surfing on waves of surfactant. Proc Natl Acad Sci U S A 106: 18109-18113. https://doi.org/10.1073/pnas.0905890106.
Olorunleke FE, Hua GKH, Kieu NP, Ma Z, Höfte M. 2015. Interplay between orfamides, sessilins and phenazines in the control of Rhizoctonia diseases by Pseudomonas sp. CMR12a. Environ Microbiol Rep 7:774-781. https://doi.org/10.1111/1758-2229.12310.
Oni FE, Geudens N, Omoboye OO, Bertier L, Hua HGK, Adiobo A, Sinnaeve D, Martins JC, Höfte M. 2019. Fluorescent Pseudomonas and cyclic lipopeptide diversity in the rhizosphere of cocoyam(Xanthosoma sagittifolium). EnvironMicrobiol 21:1019-1034. https://doi.org/10.1111/1462-2920.14520.
Girard L, Lood C, Höfte M, Vandamme P, Rokni-Zadeh H, Van Noort V, Lavigne R, De Mot R. 2021. The ever-expanding Pseudomonas genus: Description of 43 new species and partition of the Pseudomonas putida group. Microorganisms 9: 1766. https://doi.org/10.3390/microorganisms9081766.
Biessy A, Novinscak A, Blom J, Léger G, Thomashow LS, Cazorla FM, Josic D, Filion M. 2019. Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp. Environ Microbiol 21:437-455. https://doi.org/10.1111/1462-2920.14476.
Flury P, Aellen N, Ruffner B, Péchy-Tarr M, Fataar S, Metla Z, Dominguez-Ferreras A, Bloemberg G, Frey J, Goesmann A, Raaijmakers JM, Duffy B, Höfte M, Blom J, Smits THMM, Keel C, Maurhofer M. 2016. Insect pathogenicity in plant-beneficial pseudomonads: Phylogenetic distribution and comparative genomics. ISME J 10:2527-2542. https://doi.org/10.1038/ismej.2016.5.
Hesse C, Schulz F, Bull CT, Shaffer BT, Yan Q, Shapiro N, Hassan KA, Varghese N, Elbourne LDH, Paulsen IT, Kyrpides N, Woyke T, Loper JE. 2018. Genome-based evolutionary history of Pseudomonas spp. Environ Microbiol 20:2142-2159. https://doi.org/10.1111/1462-2920.14130.
Lalucat J, Mulet M, Gomila M, García-Valdés E. 2020. Genomics in bacterial taxonomy: Impact on the genus Pseudomonas. Genes 11:139. https://doi .org/10.3390/genes11020139.
Girard L, HöfteM, DeMot R. 2020. Lipopeptide families at the interface between pathogenic and beneficial Pseudomonas-plant interactions. Crit Rev Microbiol 46:397-419. https://doi.org/10.1080/1040841X.2020.1794790.
Michelsen CF, Watrous J, Glaring MA, Kersten R, Koyama N, Dorrestein PC, Stougaard P. 2015. Nonribosomal peptides, key biocontrol components for Pseudomonas fluorescens In5, isolated from a Greenlandic suppressive soil. mBio 6:e00079-15. https://doi.org/10.1128/mBio.00079-15.
Emanuele MC, Scaloni A, Lavermicocca P, Jacobellis NS, Camoni L, Di Giorgio D, Pucci P, Paci M, Segre A, Ballio A. 1998. Corceptins, new bioactive lipodepsipeptides from cultures of Pseudomonas corrugata. FEBS Lett 433:317-320. https://doi.org/10.1016/s0014-5793(98)00933-8.
D'aes J, Kieu NP, Léclère V, Tokarski C, Olorunleke FE, De Maeyer K, Jacques P, Höfte M, Ongena M. 2014. To settle or to move? The interplay between two classes of cyclic lipopeptides in the biocontrol strain Pseudomonas CMR12a. Environ Microbiol 16:2282-2300. https://doi.org/10 .1111/1462-2920.12462.
Rosenberg G, Steinberg N, Oppenheimer-Shaanan Y, Olender T, Doron S, Ben-Ari J, Sirota-Madi A, Bloom-Ackermann Z, Kolodkin-Gal I. 2016. Not so simple, not so subtle: The interspecies competition between Bacillus simplex and Bacillus subtilis and its impact on the evolution of biofilms. NPJ Biofilms Microbiomes 2: 15027. https://doi.org/10.1038/npjbiofilms.2015.27.
Hoefler BC, Gorzelnik KV, Yang JY, Hendricks N, Dorrestein PC, Straight PD. 2012. Enzymatic resistance to the lipopeptide surfactin as identified through imaging mass spectrometry of bacterial competition. Proc Natl Acad Sci U S A 109:13082-13087. https://doi.org/10.1073/pnas.1205586109.
Yang YL, Xu Y, Straight P, Dorrestein PC. 2009. Translating metabolic exchange with imaging mass spectrometry. Nat Chem Biol 5:885-887. https://doi.org/10.1038/nchembio.252.
Straight PD, Willey JM, Kolter R. 2006. Interactions between Streptomyces coelicolor and Bacillus subtilis: Role of surfactants in raising aerial structures. J Bacteriol 188:4918-4925. https://doi.org/10.1128/JB.00162-06.
Watrous J, Hendricks N, Meehan M, Dorrestein PC. 2010. Capturing bacterial metabolic exchange using thin film desorption electrospray ionizationimaging mass spectrometry. Anal Chem 82:1598-1600. https://doi.org/10 .1021/ac9027388.
Luzzatto-Knaan T, Melnik AV, Dorrestein PC. 2019. Mass spectrometry uncovers the role of surfactin as an interspecies recruitment factor. ACS Chem Biol 14:459-467. https://doi.org/10.1021/acschembio.8b01120.
Combes-Meynet E, Pothier JF, Moënne-Loccoz Y, Prigent-Combaret C. 2011. The Pseudomonas secondary metabolite 2, 4-diacetylphloroglucinol is a signal inducing rhizoplane expression of Azospirillum genes involved in plant-growth promotion. Mol Plant Microbe Interact 24:271-284. https://doi.org/10.1094/MPMI-07-10-0148.
Jarmer H, Berka R, Knudsen S, Saxild HH. 2002. Transcriptome analysis documents induced competence of Bacillus subtilis during nitrogen limiting conditions. FEMS Microbiol Lett 206:197-200. https://doi.org/10.1111/j.1574-6968 .2002.tb11009.x.
Bisicchia P, Botella E, Devine KM. 2010. Suite of novel vectors for ectopic insertion of GFP, CFP and IYFP transcriptional fusions in single copy at the amyE and bglS loci in Bacillus subtilis. Plasmid 64:143-149. https://doi.org/10.1016/j.plasmid.2010.06.002.
Martínez-García E, de Lorenzo V. 2011. Engineering multiple genomic deletions in Gram-negative bacteria: Analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440. Environ Microbiol 13: 2702-2716. https://doi.org/10.1111/j.1462-2920.2011.02538.x.
Vacheron J, Péchy-Tarr M, Brochet S, Heiman CM, Stojiljkovic M, Maurhofer M, Keel C. 2019. T6SS contributes to gutmicrobiome invasion and killing of an herbivorous pest insect by plant-beneficial Pseudomonas protegens. ISME J 13: 1318-1329. https://doi.org/10.1038/s41396-019-0353-8.
Pluskal T, Castillo S, Villar-Briones A, Oreši_c M. 2010. MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometrybased molecular profile data. BMC Bioinformatics 11:395. https://doi.org/10.1186/1471-2105-11-395.
Kune C, McCann A, Raphaël LR, Arias AA, Tiquet M, Van Kruining D, Martinez PM, Ongena M, Eppe G, Quinton L, Far J, De Pauw E. 2019. Rapid visualization of chemically related compounds using Kendrick mass defect as a filter in mass spectrometry imaging. Anal Chem 91: 13112-13118. https://doi.org/10.1021/acs.analchem.9b03333.
R Core Team. 2020. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
