Aktar W, Sengupta D, Chowdhury A. Impact of pesticides use in agriculture: their benefits and hazards. Interdiscip Toxicol. 2009;2:1–12.
Article
Google Scholar
Vessey JK. Plant growth promoting rhizobacteria as biofertilizers. Plant Soil. 2003;255:571–86.
Article
CAS
Google Scholar
Verschuere L, Rombaut G, Sorgeloos P, Verstraete W. Probiotic bacteria as biological control agents in aquaculture. Microbiol Mol Biol Rev. 2000;64:655–71.
Article
CAS
Google Scholar
Gong AD, Li HP, Yuan QS, Song XS, Yao W, He WJ, et al. Antagonistic mechanism of iturin a and plipastatin a from Bacillus amyloliquefaciens S76-3 from wheat spikes against Fusarium graminearum. PLoS One. 2015;10:e0116871.
Article
Google Scholar
Compant S, Duffy B, Nowak J, Clément C, Barka EA. Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl Environ Microbiol. 2005;71(9):4951–9.
Article
CAS
Google Scholar
Ruiz-García C, Béjar V, Martínez-Checa F, Llamas I, Quesada E. Bacillus velezensis sp. nov., a surfactant-producing bacterium isolated from the river Vélez in Málaga, southern Spain. Int J Syst Evol Micr. 2005;55:191–5.
Article
Google Scholar
Palazzini JM, Dunlap CA, Bowman MJ, Chulze SN. Bacillus velezensis RC 218 as a biocontrol agent to reduce Fusarium head blight and deoxynivalenol accumulation: genome sequencing and secondary metabolite cluster profiles. Microbiol Res. 2016;192:30–6.
Article
CAS
Google Scholar
Gao Z, Zhang B, Liu H, Han J, Zhang Y. Identification of endophytic Bacillus velezensis ZSY-1 strain and antifungal activity of its volatile compounds against Alternaria solani and Botrytis cinerea. Biol Control. 2017;105:27–39.
Article
Google Scholar
Case RJ, Boucher Y, Dahllöf I, Holmström C, Doolittle WF, Kjelleberg S. Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol. 2007;73:278–88.
Article
CAS
Google Scholar
Daferera DJ, Ziogas BN, Polissiou MG. The effectiveness of plant essential oils on the growth of Botrytis cinerea, Fusarium sp. and Clavibacter michiganensis subsp. michiganensis. Crop Prot 2003; 22:39–44.
Nandi M, MacDonald J, Liu P, Weselowski B, Yuan ZC. Clavibacter michiganensis ssp. michiganensis: bacterial canker of tomato, molecular interactions and disease management. Mol Plant Pathol. 2018;19:2036–50.
Article
CAS
Google Scholar
Jasim B, Sreelakshmi S, Mathew J, Radhakrishnan EK. Identification of endophytic Bacillus mojavensis with highly specialized broad spectrum antibacterial activity. 3 Biotech. 2016;6:187.
Cai XC, Liu CH, Wang BT, Xue YR. Genomic and metabolic traits endow Bacillus velezensis CC09 with a potential biocontrol agent in control of wheat powdery mildew disease. Microbiol Res. 2017;196:89–94.
Article
CAS
Google Scholar
Fan B, Blom J, Klenk HP, Borriss R. Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis Form an "Operational Group B. amyloliquefaciens" within the B. subtilis Species Complex. Front Microbiol. 2017;8:22.
PubMed
PubMed Central
Google Scholar
van Zyl LJ, Matobole R, Nsole Biteghe FA, Klein T, Kirby B, Trindade M. Draft genome sequences of three Bacillus species from south African marine sponges. Genome Announc. 2016;4:e00143–16.
PubMed
PubMed Central
Google Scholar
Lee H, Kim HY. Lantibiotics, class I bacteriocins from the genus Bacillus. J Microbiol Biotechnol. 2011;21:229–35.
CAS
PubMed
Google Scholar
Van der Donk WA, Nair SK. Structure and mechanism of lanthipeptide biosynthetic enzymes. Curr Opin Struc Biol. 2014;29:58–66.
Article
Google Scholar
López-Lara IM, Geiger O. Bacterial lipid diversity. Biochim Biophys Acta. 1862;2017:1287–99.
Google Scholar
Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, et al. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell. 2014;158:412–21.
Article
CAS
Google Scholar
Schöner TA, Gassel S, Osawa A, Tobias NJ, Okuno Y, Sakakibara Y, et al. Aryl polyenes, a highly abundant class of bacterial natural products, are functionally related to antioxidative carotenoids. Chembiochem. 2016;17:247–53.
Article
Google Scholar
Ryu CM1, Farag MA, Hu CH, Reddy MS, Kloepper JW, Paré PW. Bacterial volatiles induce systemic resistance in Arabidopsis. Plant Physiol. 2004;134:1017–26.
Article
CAS
Google Scholar
Palmer T, Berks BC. The twin-arginine translocation (tat) protein export pathway. Nat Rev Microbiol. 2012;10:483–96.
Article
CAS
Google Scholar
Denks K, Vogt A, Sachelaru I, Petriman NA, Kudva R, Koch HG. The sec translocon mediated protein transport in prokaryotes and eukaryotes. Mol Membr Biol. 2014;31:58–84.
Article
CAS
Google Scholar
Peypoux F, Michel G. Controlled biosynthesis of Val7- and Leu7-surfactins. Appl Microbiol Biot. 1992;36:515–7.
Article
CAS
Google Scholar
Li YM, Haddad NIA, Yang SZ, Mu BZ. Variants of lipopeptides produced by Bacillus licheniformis HSN221 in different medium components evaluated by a rapid method ESI-MS. Int J Pept Res Ther. 2008;14:229–35.
Article
CAS
Google Scholar
Baumgart R, Kluge B, Ullrich C, Vater J, Ziessow D. Identification of amino acid substitutions in the lipopeptide surfactin using 2D NMR spectroscopy. Biochem Biophys Res Commun. 1991;177:998–1005.
Article
CAS
Google Scholar
Sarwar A, Hassan MN, Imran M, Iqbal M, Majeed S, Brader G, Sessitsch A, Hafeez FY. Biocontrol activity of surfactin a purified from Bacillus NH-100 and NH-217 against rice bakanae disease. Microbiol Res. 2018;209:1–13.
Article
CAS
Google Scholar
Goussous SA, Casford MTL, Murphy AC, Salmond GPC, Leeper FJ, Davies PB. Structure of the fundamental lipopeptide surfactin at the air/water interface investigated by sum frequency generation spectroscopy. J Phys Chem B. 2017;121:5072–7.
Article
CAS
Google Scholar
Hamley IW. Lipopeptides: from self-assembly to bioactivity. Chem Commun. 2015;51:8574–83.
Article
CAS
Google Scholar
Zhao H, Shao D, Jiang C, Shi J, Li Q, Huang Q, Rajoka MSR, Yang H, Jin. Biological activity of lipopeptides from Bacillus. Appl Microbiol Biotechnol 2017;101:5951–5960.
Stubbendieck RM, Straight PD. Multifaceted interfaces of bacterial competition. J Bacteriol. 2016;198:2145–55.
Article
CAS
Google Scholar
Cawoy H, Mariutto M, Henry G, Fisher C, Vasilyeva N, Thonart P, Dommes J, Ongena M. Plant defense stimulation by natural isolates of Bacillus depends on efficient surfactin production. Mol Plant Microbe In. 2014;27:87–100.
Article
CAS
Google Scholar
Paraszkiewicz K, Bernat P, Siewiera P, Moryl M, Sas-Paszt L, Trzciński P, Jałowiecki L, Płaza G. Agricultural potential of rhizospheric Bacillus subtilis strains exhibiting varied efficiency of surfactin production. Sci Hortic-Amsterdam. 2017;225:802–9.
Article
CAS
Google Scholar
Kearns DB. A field guide to bacterial swarming motility. Nat Rev Microbiol. 2010;8:634–44.
Article
CAS
Google Scholar
Turner S, Pryer KM, Miao VP, Palmer JD. Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol. 1999;46:327–38.
Article
CAS
Google Scholar
Löytynoja A, Goldman N. WebPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics. 2010;11:579.
Article
Google Scholar
Dunlap CA, Kim SJ, Kwon SW, Rooney AP. Bacillus velezensis is not a later heterotypic synonym of Bacillus amyloliquefaciens; Bacillus methylotrophicus, Bacillus amyloliquefaciens subsp plantarum and 'Bacillus oryzicola' are later heterotypic synonyms of Bacillus velezensis based on phylogenomics. Int J Syst Evol Microbiol. 2016;66:1212–7.
Article
CAS
Google Scholar
Ronquist F, Teslenko M, van der Mark P, Ayres D, Darling A, Höhna S, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61:539–42.
Article
Google Scholar
Stöver BC, Müller KF. TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics. 2010;11:7.
Article
Google Scholar
Laatsch H. Antibase version 4.0: the natural compound identifier. Wiley-VCH Verlag GmbH & Co. KGaA, 2012.
Heeb S, Itoh Y, Nishijyo T, Schnider U, Keel C, Wade J, Walsh U, O’Gara F, Haas D. Small, stable shuttle vectors based on the minimal pVS1 replicon for use in gram-negative, plant associated bacteria. Mol Plant-Microbe Interact. 2000;13:232–7.
Article
CAS
Google Scholar
Bloemberg GV, Wijfjes AH, Lamers GE, Stuurman N, Lugtenberg BJ. Simultaneous imaging of Pseudomonas fluorescens WCS365 populations expressing three different autofluorescent proteins in the rhizosphere: new perspectives for studying microbial communities. Mol Plant-Microbe Interact. 2000;13:1170–6.
Article
CAS
Google Scholar
Nathoo N, Bernards MA, MacDonald J, Yuan ZC. A hydroponic co-cultivation system for simultaneous and systematic analysis of plant-microbe molecular interactions and signaling. JOVE-J Vis Exp. 2017;125:e55955.
Google Scholar
Joshi NA, Fass JN. Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files. GitHub. 2011. https://github.com/najoshi/sickle. Accessed 1 June 2017.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.
Article
CAS
Google Scholar
Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14:1394–403.
Article
CAS
Google Scholar
Burland TG. DNASTAR’s Lasergene sequence analysis software. In: Misener S, Krawetz SA, editors. Bioinformatics methods and protocols. Totowa, NJ, USA: Humana press Inc; 1999. p. 71–91.
Chapter
Google Scholar
Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, Grechkin Y, et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 2012;40:D115–22.
Article
CAS
Google Scholar
Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci. 2010;2:142–8.
Article
Google Scholar
Weber T, Blin K, Duddela S, Krug D, Kim H, Bruccoleri R, et al. AntiSMASH 3.0 - a comprehensive resource for the genome mining ofbiosynthetic gene clusters. Nucleic Acids Res. 2015;43:W237–43.
Article
CAS
Google Scholar
Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A. UniProtKB/Swiss-Prot: the manually annotated section of the UniProt KnowledgeBase. In: Edwards D, editor. Plant bioinformatics: methods and protocols. Totowa, NJ, USA: Humana press Inc; 2007. p. 89–112.
Chapter
Google Scholar
Lund T, De Buyser ML, Granum PE. A new cytotoxin from Bacillus cereus that may cause necrotic enteritis. Molecular Microbial. 2000;8:254–61.
Article
Google Scholar
Vanneste JL. Fire blight: the disease and its causative agent, Erwinia amylovora. 2000: CABI.
Dutkiewicz J, Mackiewicz B, Kinga-Lemieszek M, Golec M, Milanowski J. Pantoea agglomerans: a mysterious bacterium of evil and good. Part III. Deleterious effects: infections of humans, animals and plants. Ann Agric Environ Med. 2016;23:197–205.
Article
CAS
Google Scholar
Wei CF, Kvitko BH, Shimizu R, Crabill E, Alfano JR, Lin NC, Martin GB, Huang HC, Collmer A. A Pseudomonas syringae pv. Tomato DC3000 mutant lacking the type III effector HopQ1-1 is able to cause disease in the model plant Nicotiana benthamiana. Plant J. 2007;51:32–46.
Article
CAS
Google Scholar
Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, Arlat M, Billault A, Brottier P, Camus JC, Cattolico L, Chandler M, Choisne N, Claudel-Renard C, Cunnac S, Demange N, Gaspin C, Lavie M, Moisan A, Robert C, Saurin W, Schiex T, Siguier P, Thébault P, Whalen M, Wincker P, Levy M, Weissenbach J, Boucher CA. Genome sequence of the plant pathogen Ralstonia solanacearum. Nature. 2002;415:497–502.
Article
CAS
Google Scholar
Vicente JG, Holub EB. Xanthomonas campestris pv. campestris (cause of black rot of crucifers) in the genomic era is still a worldwide threat to brassica crops. Mol Plant Pathol. 2013;14:2–18.
Article
CAS
Google Scholar
Fontenelle ADB, Guzzo SD, Lucon CMM, Harakava R. Growth promotion and induction of resistance in tomato plant against Xanthomonas euvesicatoria and Alternaria solani by Trichoderma spp. Crop Prot. 2011;30:1492–500.
Article
Google Scholar
Manamgoda DS, Cai L, Bahkali AH, Chukeatirote E, Hyde KD. Cochliobolus: an overview and current status of species. Fungal Divers. 2011;51:3–42.
Article
Google Scholar
Fravel D, Olivain C, Alabouvette C. Fusarium oxysporum and its biocontrol. New Phytol. 2003;157:493–502.
Article
Google Scholar
Zhang N, O'Donnell K, Sutton DA, Nalim FA, Summerbell RC, Padhye AA, Geiser DM. Members of the Fusarium solani species complex that cause infections in both humans and plants are common in the environment. J Clin Microbiol. 2006;44:2186–90.
Article
CAS
Google Scholar
Mecteau MR, Arul J, Tweddell RJ. Effect of organic and inorganic salts on the growth and development of Fusarium sambucinum, a causal agent of potato dry rot. Mycol Res. 2002;106:688–96.
Article
CAS
Google Scholar
Sutton J. Epidemiology of wheat head blight and maize ear rot caused by Fusarium graminearum. Can J Plant Pathol. 1982;4:195–209.
Article
Google Scholar
Munda A, Viršček-Marn M. First report of brown rot caused by Monilinia fructicola affecting peach orchards in Slovenia. Plant Dis. 2010;94:1166.
Article
Google Scholar
Porter I, Merriman P, Keane P. Integrated control of pink root (Pyrenochaeta terrestris) of onions by dazomet and soil solarization. Crop and Pasture Sci. 1989;40:861–9.
Article
Google Scholar
Parmeter JR. Rhizoctonia solani, biology and pathology. 1970: Univ of California Press.
Madden L, Pennypacker S, MacNab A. FAST, a forecast system for Alternaria solani on tomato. Phytopathology. 1978;68:1354–8.
Article
Google Scholar
Botha WJ, Coetzer RLJ. Species of Pythium associated with root-rot of vegetables in South Africa. S Afr J Bot. 1996;62:196–203.
Article
Google Scholar
Matoba Y, Kondo N, Akino S, Kodama F, Naito S, Ebe S. Identification and pathogenicity of Pythium species causing damping-off of kidney bean. J Gen Plant Pathol. 2008;74:81–5.
Article
Google Scholar