The present invention refers to a process for increasing the production of biomass and metabolites of microorganisms of Bacillus sp. species. Obtained metabolites are lipopeptide compounds of the fengycin, surfactin, and iturin families, which exhibit antimicrobial activity.The invention further includes biocidal compositions comprising Bacillus subtilis EA-CB 0015, Bacillus amyloliquefaciens EA-CB0959, and/or metabolites thereof, either alone or together with other biocidal agents, and the use of these compositions for the treatment of diseases caused by various phytopathogenic agents, including Mycosphaerella fijiensis, in a variety of crops.