Antibiotic Biosynthesis Genes Research Articles

Co-Culture of White Rot Fungi Pleurotus ostreatus P5 and Bacillus amyloliquefaciens B2: A Strategy to Enhance Lipopeptide Production and Suppress of Fusarium Wilt of Cucumber.

Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum (FOC), poses a serious threat to cucumber productivity. Compared to traditional chemical pesticides, biological control strategies have attracted more attention recently owing to their effectiveness against pathogens and their environmental safety. This study investigated the effect of white rot fungi Pleurotus ostreatus P5 on the production of cyclic lipopeptides (CLPs) of Bacillus amyloliquefaciens B2 and the potential co-culture filtrate of strains B2 and P5 to control cucumber Fusarium wilt. A PCR amplification of CLP genes revealed that B. amyloliquefaciens B2 had two antibiotic biosynthesis genes, namely, ituA and srf, which are involved in iturin A and surfactin synthesis. Liquid chromatography with tandem mass spectrometry (LC-MS/MS) revealed that CLPs derived from strain B2 contained two families, iturin A (C14, C15) and surfactin (C12-C17). The co-culture exhibited an enhanced accumulation of iturin A and surfactin compared to the monoculture of strain B2. Furthermore, the gene expressions of ituA and srf were both significantly upregulated when co-cultured with the fungus compared to monocultures. In an in vitro experiment, the co-culture filtrate and monoculture filtrate of B. amyloliquefaciens B2 inhibited mycelial growth by 48.2% and 33.2%, respectively. In a greenhouse experiment, the co-culture filtrate was superior to the monoculture filtrate in controlling cucumber Fusarium wilt disease and in the promotion of plant growth. Co-culture filtrate treatment significantly enhanced the microbial metabolic activity and decreased the abundance of FOC in the rhizosphere soil. These results show that the co-culture of P. ostreatus P5 and B. amyloliquefaciens B2 has great potential in cucumber Fusarium wilt disease prevention by enhancing the production of bacterial CLPs.

Study of new biocontrol bacterial agent Bacillus velezensis S41L against Rosellinia necatrix

White root rot in woody plants is mainly caused by the necrotrophic phytopathogenic fungus Rosellinia necatrix. In this study, we isolate antagonistic bacteria from rhizospheric soil from asymptomatic pear trees infested with white root rot. Furthermore, we isolated 40 bacterial strains and screened them for antagonistic activity against R. necatrix. Then, we selected antagonists that retarded pathogen growth for >30 days. Finally, the strain that exhibited >80 % inhibitory activity against all R. necatrix strains (Korean Agricultural Culture Collection 40446, 40445, 40447, and 40168), demonstrating its effectiveness in controlling this pathogen prevalent in Korean pear and apple orchards, was selected for further experiments. Strain S41L (OP349111) showed the most potent growth-inhibitory activity against the tested phytopathogens. Microbiological and 16S rRNA gene sequencing analyses revealed that the bacterial isolate belonged to the Bacillus genus and had 100 % nucleotide sequence similarity with Bacillus velezensis in GenBank. This strain also harbored antibiotic biosynthesis genes and possessed plant growth-promoting traits such as phosphate solubilization, indole-3-acetic acid, and siderophore production.

Multifaceted Bacillus spp. for the management of cotton bacterial blight caused by Xanthomonas citri pv. malvacearum

Bacterial antagonists against plant pathogens are widely exploited for the biological management of plant diseases. In the present study, antagonists were isolated from cotton plant associated bacteria such as endophytes (74 isolates), phylloplane (32 isolates) and cotton rhizosphere soils (48 isolates). Their efficacy against X. citri pv. malvacearum (Xcm) were evaluated in vitro by agar well diffusion technique. Among the isolates, the endophyte Bacillus amyloliquefaciens strain ETL2 was very effective in inhibiting the Xcm growth with an area of 983.76 mm2 followed by Bacillus velezensis strain ELS2 with an area of 944.41 mm2. PCR amplification of antimicrobial peptide (AMP) genes revealed that B. amyloliquefaciens strain ETL2 had maximum of 8 antibiotic biosynthesis genes namely, ItuC, bacA, bacD, bamC, fenCEA, sfrA, spaCS and mycC that produced antibiotics Iturin, bacilysin, bacillomycin, fengycin, surfactin, subtilin and mycosubtilin. Further, B. amyloliquefaciens strain ETL2 associated with Xcm inhibition was identified as aromatic hydrocarbons, phenols and fatty acids by Gas chromatography and mass-spectrometry (GC–MS) analysis of culture extracts. Delivery of B. amyloliquefaciens strain ETL2 and B. velezensis strain ELS2 as seed treatment and foliar spray was found promising for the management of bacterial blight of cotton in pot and field experiments. In pot and field experiments, the maximum plant growth promotion and seed cotton yield were observed in the plants treated with B. amyloliquefaciens strain ETL2 followed by B. velezensis strain ELS2 with better disease control efficiency compared to chemical control agents and chemical plant defense inducers.

Exploring the impact of paracetamol on the transcriptome of Streptococcus pneumoniae D39

IntroductionParacetamol (acetaminophen) is a medicine used for the treatment of fever, pain, and inflammation during pneumococcal infection. ObjectivesTo see how paracetamol affects the transcriptional profile of Streptococcus pneumonia across the genome. MethodsIn this study, microarray analysis was performed for transcriptional profiling. ResultsTranscriptome data showed differential expression of several genes in S. pneumoniae D39 wild-type incorporated with paracetamol in the growth medium. Furthermore, these genes were categorized using Clusters of Orthologous Groups (COG) functional categorization on the basis of the suspected functions of the respective proteins. The majority of differentially expressed genes are in COG categories E (Amino acid transport and metabolism) and I (Lipid transport and metabolism). Analysis of protein–protein interaction networks exhibited compactly connected networks between fatty acid transport/biosynthesis and antibiotic biosynthesis genes. Moreover, pathways enrichment analysis revealed that fatty acid metabolism and biosynthesis genes were significantly affected under the criteria we've established. ConclusionThese results suggest the fatty acid biosynthesis and metabolism genes to be potential target of paracetamol in S. pneumoniae D39 wild-type.

Characterization of subtilosin gene in wild type Bacillus spp. and possible physiological role

In a designed study to screen for antimicrobial exhibiting bacteria using molecular aspects, Bacillus species were considered to investigate antibiotic biosynthesis genes. 28 bacterial strains and 3 induced mutants were screened for the presence of subtilosin gene (sbo) and subtilosin through PCR and Mass spectrometry respectively. Sbo gene was detected in 16 out of 28 Bacillus strains. The results from gene sequences deliberated by multiple sequence alignments revealed high-level homology to the sequences of the sbo-alb gene locus of B. subtilis 168 and the other limited reported strains. Hence, this report provided additional strains to support the idea of subtilosin gene predominance amongst Bacillus strains isolated from environment and to find different species containing homologous genes, furthermore the utilization of its conserved region as a means of identifying Bacillus spp. that produce subtilosin. This is the first report to confirm the detection of subtilosin production from B. amyloliquefaciens.

Penicillin-Binding Proteins, β-Lactamases, and β-Lactamase Inhibitors in β-Lactam-Producing Actinobacteria: Self-Resistance Mechanisms.

The human society faces a serious problem due to the widespread resistance to antibiotics in clinical practice. Most antibiotic biosynthesis gene clusters in actinobacteria contain genes for intrinsic self-resistance to the produced antibiotics, and it has been proposed that the antibiotic resistance genes in pathogenic bacteria originated in antibiotic-producing microorganisms. The model actinobacteria Streptomyces clavuligerus produces the β-lactam antibiotic cephamycin C, a class A β-lactamase, and the β lactamases inhibitor clavulanic acid, all of which are encoded in a gene supercluster; in addition, it synthesizes the β-lactamase inhibitory protein BLIP. The secreted clavulanic acid has a synergistic effect with the cephamycin produced by the same strain in the fight against competing microorganisms in its natural habitat. High levels of resistance to cephamycin/cephalosporin in actinobacteria are due to the presence (in their β-lactam clusters) of genes encoding PBPs which bind penicillins but not cephalosporins. We have revised the previously reported cephamycin C and clavulanic acid gene clusters and, in addition, we have searched for novel β-lactam gene clusters in protein databases. Notably, in S. clavuligerus and Nocardia lactamdurans, the β-lactamases are retained in the cell wall and do not affect the intracellular formation of isopenicillin N/penicillin N. The activity of the β-lactamase in S. clavuligerus may be modulated by the β-lactamase inhibitory protein BLIP at the cell-wall level. Analysis of the β-lactam cluster in actinobacteria suggests that these clusters have been moved by horizontal gene transfer between different actinobacteria and have culminated in S. clavuligerus with the organization of an elaborated set of genes designed for fine tuning of antibiotic resistance and cell wall remodeling for the survival of this Streptomyces species. This article is focused specifically on the enigmatic connection between β-lactam biosynthesis and β-lactam resistance mechanisms in the producer actinobacteria.

Comparative Genomic Analysis of Streptococcus pneumoniae Strains: Penicillin Non-susceptible Multi-drug-Resistant Serotype 19A Isolates.

Streptococcus pneumoniae can cause several diseases including otitis media, sinusitis, pneumonia, sepsis and meningitis. The introduction of pneumococcal vaccines has changed the molecular epidemiological and antibiotic resistance profiles of related diseases. Analysis of molecular patterns and genome sequences of clinical strains may facilitate the identification of novel drug resistance mechanism. Three multidrug resistance 19A isolates were verified, serotyped and the complete genomes were sequenced combining the Pacific Biosciences and the Illumina Miseq platform. Genomic annotation revealed that similar central networks were found in the clinical isolates, and Mauve alignments indicated high similarity between different strains. The pan-genome analysis showed the shared and unique cluster in the strains. Mobile elements were predicted in the isolates including prophages and CRISPER systems, which may participate in the virulence and antibiotic resistance of the strains. The presence of 31 virulence factor genes was predicted from other pathogens for PRSP 19339 and 19343, while 30 for PRSP 19087. Meanwhile, 33 genes antibiotic resistance genes were predicted including antibiotic resistance genes, antibiotic-target genes and antibiotic biosynthesis genes. Further analysis of the antibiotic resistance genes revealed new mutations in the isolates. By comparative genomic analysis, we contributed to the understanding of resistance mechanism of the clinical isolates with other serotype strains, which could facilitate the concrete drug resistance mechanism study.

The occurrence and diversity of antibiotic resistance and virulence factor genes in wastewater from four North American treatment plants

The total ARGs and VFGs declined after treatments. Antibiotic biosynthesis genes were amplified during activated sludge processes. Multidrug ARGs dominate in wastewater.

Two Pathway-Specific Transcriptional Regulators, PltR and PltZ, Coordinate Autoinduction of Pyoluteorin in Pseudomonas protegens Pf-5.

Antibiotic biosynthesis by microorganisms is commonly regulated through autoinduction, which allows producers to quickly amplify the production of antibiotics in response to environmental cues. Antibiotic autoinduction generally involves one pathway-specific transcriptional regulator that perceives an antibiotic as a signal and then directly stimulates transcription of the antibiotic biosynthesis genes. Pyoluteorin is an autoregulated antibiotic produced by some Pseudomonas spp. including the soil bacterium Pseudomonas protegens Pf-5. In this study, we show that PltR, a known pathway-specific transcriptional activator of pyoluteorin biosynthesis genes, is necessary but not sufficient for pyoluteorin autoinduction in Pf-5. We found that pyoluteorin is perceived as an inducer by PltZ, a second pathway-specific transcriptional regulator that directly represses the expression of genes encoding a transporter in the pyoluteorin gene cluster. Mutation of pltZ abolished the autoinducing effect of pyoluteorin on the transcription of pyoluteorin biosynthesis genes. Overall, our results support an alternative mechanism of antibiotic autoinduction by which the two pathway-specific transcriptional regulators PltR and PltZ coordinate the autoinduction of pyoluteorin in Pf-5. Possible mechanisms by which PltR and PltZ mediate the autoinduction of pyoluteorin are discussed.

Incipient genome erosion and metabolic streamlining for antibiotic production in a defensive symbiont

Genome erosion is a frequently observed result of relaxed selection in insect nutritional symbionts, but it has rarely been studied in defensive mutualisms. Solitary beewolf wasps harbor an actinobacterial symbiont of the genus Streptomyces that provides protection to the developing offspring against pathogenic microorganisms. Here, we characterized the genomic architecture and functional gene content of this culturable symbiont using genomics, transcriptomics, and proteomics in combination with in vitro assays. Despite retaining a large linear chromosome (7.3 Mb), the wasp symbiont accumulated frameshift mutations in more than a third of its protein-coding genes, indicative of incipient genome erosion. Although many of the frameshifted genes were still expressed, the encoded proteins were not detected, indicating post-transcriptional regulation. Most pseudogenization events affected accessory genes, regulators, and transporters, but "Streptomyces philanthi" also experienced mutations in central metabolic pathways, resulting in auxotrophies for biotin, proline, and arginine that were confirmed experimentally in axenic culture. In contrast to the strong A+T bias in the genomes of most obligate symbionts, we observed a significant G+C enrichment in regions likely experiencing reduced selection. Differential expression analyses revealed that-compared to in vitro symbiont cultures-"S. philanthi" in beewolf antennae showed overexpression of genes for antibiotic biosynthesis, the uptake of host-provided nutrients and the metabolism of building blocks required for antibiotic production. Our results show unusual traits in the early stage of genome erosion in a defensive symbiont and suggest tight integration of host-symbiont metabolic pathways that effectively grants the host control over the antimicrobial activity of its bacterial partner.

Acquisition of antibiotic resistance genes on human skin after swimming in the ocean

The skin is a complex organ responsible for protecting the body from physical, chemical and biological insults. The skin microbiome is known to play an important role in protecting the host from skin infections. This study examined the skin microbiome and the changes in antibiotic resistance genes (ARGs), antibiotic biosynthesis genes (ABSGs) and virulence factor genes (VFGs) on human skin before and after swimming in the ocean. Skin microbiome samples were collected from human participants before and after they swam in the ocean, and at 6 h and 24 h post-swim. The samples were analyzed using 16S rRNA gene and shotgun metagenomic sequencing. The results showed that not only is the skin microbiome composition altered after swimming, but the abundance and diversity of ARGs, ABSGs and VFGs on the skin increased post-swim. Overall, there was an increase in total ARGs by 70.6% from before to after swimming. The elevated number of ARGs persisted and continued to increase for at least 6 h post-swim with greater than a 300% increase in comparison with samples collected before ocean swimming. The outcomes of the study support the epidemiological observations of increased risk of skin infections after swimming in the ocean. Cleaning the skin immediately after recreational ocean activities is recommended to reduce the opportunity for infection.

Draft genome sequence data of Paenibacillus Polymyxa strain TH2H2, isolated from a tomato flower in Korea.

Members of the genus Paenibacillus are known for their production of useful substances, and some species of the genus are recognized to be plant growth-promoting rhizobacteria. Paenibacillus polymyxa TH2H2, isolated from a tomato flower, had antifungal activity. Here, the draft genome sequence of Paenibacillus polymyxa TH2H2 is reported. The 5,983,104-bp genome, with a G+C content of 45.31%, comprised 5,221 protein-coding genes, 64 ribosomal RNA and 100 transfer RNA. Three intact antibiotic biosynthesis gene clusters were identified using antiSMASH. These encoded the antifungal agent fusaricidin and two antibacterial agents, tridecaptin and polymyxin. Sequence data have been deposited in the DDBJ/ENA/GenBank database under the accession number RPDG01000000. The version described in this paper is RPDG00000000.1. The BioProject ID in the GenBank database is PRJNA505713.

Identification and characterization of the Bacillus atrophaeus strain J-1 as biological agent of apple ring rot disease

Bacillus species are promising agents for the biological control of postharvest diseases. Based on the morphological, physiological and biochemical characteristics and 16S rRNA gene sequence analysis, the bacterial strain J-1 was identified as Bacillus atrophaeus. The B. atrophaeus strain J-1 showed broad spectrum antifungal activity against various plant pathogenic fungi. In assays in vitro the metabolites contained in the B. atrophaeus strain J-1 cell-free filtrate had a strong inhibitory effect on Botryosphaeria dothidea. The cell-free filtrate inhibited the growth of B. dothidea in vivo and reduced the disease incidence. Furthermore, PCR detection showed that the strain J-1 had lipopeptide antibiotic biosynthesis genes: fengycin, iturin A and surfactin. The lipopeptide crude extractions from the strain J-1 cell-free filtrate significantly suppressed the growth of B. dothidea. C14 iturin A was isolated by bioactivity-guided fractionation and identified by liquid chromatography–electronic spray ionization–tandem mass spectrometry analysis. This paper is the first to report that B. atrophaeus J-1 efficiently controls apple ring rot disease caused by B. dothidea. Using the B. atrophaeus strain J-1 may provide an alternative control method for the prevention apple ring rot disease.

Two New Biocontrol Agents Against Clubroot Caused by Plasmodiophora brassicae.

Clubroot disease caused by Plasmodiophora brassicae can lead to serious yield losses in crucifers such as Brassica napus. In this study, 323 bacterial strains were isolated from the rhizosphere of severely diseased B. napus in Dangyang county, Hubei province, China. Antagonistic strains were first identified based on dual culture inhibition zones with Fusarium oxysporum and Magnaporthe oryzae. These were then further screened in germination inhibition and viability assays of resting spores of P. brassicae. Finally, eight of the antagonistic strains were found to significantly reduce the disease severity of clubroot by more than 40% under greenhouse conditions, and two strains, F85 and T113, were found to have efficacy of more than 80%. Root hair infection experiments showed that F85 and T113 can inhibit early infection of root hairs, reduce the differentiation of primary plasmodia of P. brassicae, and inhibit formation of secondary zoosporangia. Based on sequence analysis of 16S rDNA gene, gyrA gene and 22 housekeeping genes as well as carbon source utilization analysis, the F85 was identified as Bacillus velezensis and T113 as Bacillus amyloliquefaciens. Genome analysis, PCR and RT-PCR detection revealed that both F85 and T113 harbor various antibiotic biosynthesis gene clusters required to form peptides with antimicrobial activity. To our knowledge, this is the first report of B. velezensis as a biocontrol agent against clubroot disease.

The endophytic strain Bacillus velezensis OEE1: An efficient biocontrol agent against Verticillium wilt of olive and a potential plant growth promoting bacteria

The use of antagonists in the biocontrol of soilborne pathogens is a promising approach to manage many diseases. In this context, Bacillus velezensis strain OEE1, isolated from endogenous root tissue of olive trees, showed the most effective antifungal activity under in vitro conditions against V. dahliae with inhibition rate exceeding 92% using the dual culture method to investigate effects of diffusible compounds. This antagonism was also demonstrated with volatile and extracellular compounds where fungus growth was reduced by about 40% and 60% respectively. Gnotobiotic study of axenic in vitro olive plants, artificially inoculated with V. dahliae, using B. velezensis OEE1 cells led to a considerable reduction in Verticillium wilt severity and the disease index effectively decreased for preventive and curative treatments. Vegetative growth showed equally an interesting improvement. These potentialities are provided due to the production of numerous secondary metabolites detected by antibiotic biosynthesis genes amplification. The efficacy of B. velezensis OEE1 to suppress Verticillium wilt of olive tree was evaluated also under field conditions. This experiment revealed that B. velezensis OEE1 significantly decreased final mean disease severity index (FMS), percentage of dead plants (PDP) and area under disease progress curve (AUDPC) and reduced similarly microsclerotia density in the naturally infested soil.

Use of Phyllosphere-associated Lactic Acid Bacteria as Biocontrol Agents to Reduce Salmonella enterica Serovar Poona Growth on Cantaloupe Melons

Foodborne illness associated with fresh, ready-to-eat produce continues to be a significant challenge to public health. In this study, we created a phyllosphere-associated lactic acid bacteria (PLAB) library and screened it via a high-throughput in vitro fluorescent assay to identify bacteria capable of inhibiting the growth of the pathogenic bacterium Salmonella enterica. One isolate, 14B4, inhibited the growth of S. enterica by >45-fold in vitro; it was able to grow and persist on the surfaces of cantaloupe melons at both ambient (25°C) and refrigerator (5°C) temperatures. Isolate 14B4 inhibited the growth of S. enterica on the surfaces of cantaloupes by >3 log when incubated at 25°C for 24 h and by >4 log when the cantaloupes were stored at 5°C for 3 days and the temperature was shifted to 25°C for 2 days. Genomic DNA sequence analysis of isolate 14B4 revealed that it was Lactococcus lactis and that it did not contain any known antibiotic biosynthesis gene clusters, antibiotic resistance genes, or genes encoding any known virulence factors. Organic acid analysis revealed that L. lactis produces substantial amounts of lactic acid, which is likely the inhibitory substance that reduced the growth of Salmonella on the cantaloupes.

Fusaricidin Produced by Paenibacillus polymyxa WLY78 Induces Systemic Resistance against Fusarium Wilt of Cucumber.

Cucumber is an important vegetable crop in China. Fusarium wilt is a soil-borne disease that can significantly reduce cucumber yields. Paenibacillus polymyxa WLY78 can strongly inhibit Fusarium oxysporum f. sp. Cucumerium, which causes Fusarium wilt disease. In this study, we screened the genome of WLY78 and found eight potential antibiotic biosynthesis gene clusters. Mutation analysis showed that among the eight clusters, the fusaricidin synthesis (fus) gene cluster is involved in inhibiting the Fusarium genus, Verticillium albo-atrum, Monilia persoon, Alternaria mali, Botrytis cinereal, and Aspergillus niger. Further mutation analysis revealed that with the exception of fusTE, the seven genes fusG, fusF, fusE, fusD, fusC, fusB, and fusA within the fus cluster were all involved in inhibiting fungi. This is the first time that demonstrated that fusTE was not essential. We first report the inhibitory mode of fusaricidin to inhibit spore germination and disrupt hyphal membranes. A biocontrol assay demonstrated that fusaricidin played a major role in controlling Fusarium wilt disease. Additionally, qRT-PCR demonstrated that fusaricidin could induce systemic resistance via salicylic acid (SA) signal against Fusarium wilt of cucumber. WLY78 is the first reported strain to both produce fusaricidin and fix nitrogen. Therefore, our results demonstrate that WLY78 will have great potential as a biocontrol agent in agriculture.

Bacterial Diversity and Population Dynamics During the Fermentation of Palm Wine From Guerrero Mexico.

Palm wine is obtained by fermentation of palm tree sap. In the Pacific coast of Mexico, palm wine is called Tuba and it is consumed as a traditional fermented beverage. Tuba has empirical applications such as an auxiliary in gastrointestinal diseases and a good source of nutrients. In the present study, a next-generation sequencing of the V3–V4 regions of the 16S rRNA gene was employed to analyze bacterial diversity and population dynamics during the fermentation process of Tuba, both in laboratory controlled conditions and in commercial samples from local vendors. Taxonomic identification showed that Fructobacillus was the main genus in all the samples, following by Leuconostoc, Gluconacetobacter, Sphingomonas, and Vibrio. Alpha diversity analysis demonstrated variability between all the samples. Beta diversity clustered the bacterial population according to the collection origin of the sample. Metabolic functional profile inference showed that the members of the bacterial communities may present the vitamin, antibiotic and antioxidant biosynthesis genes. Additionally, we further investigated the correlation between the predominant genera and some composition parameters of this beverage. This study provides the basis of the bacterial community composition and functionality of the fermented beverage.

Genome sequencing of Pediococcus acidilactici (NRCC1), a novel isolate from dromedary camel (Camelus dromedarius) rumen fluid

The lactic acid bacterium Pediococcus acidilactici has recently been reported to help in treating constipation, diarrhea, relieving stress, and enhancing growth rate and immune response in humans, birds, fishes, and small animals. In the present study, we sequenced and analyzed the whole genome of P. acidilactici NRCC1, a novel isolate from rumen fluid of dromedary camel (Camelus dromedarius). The genome of P. acidilactici NRCC1 was assembled into 60 contigs, comprising 1,785,679 bp and 42.5% GC content. The 1705 CDS were predicted and annotated using the RAST server. The genome encodes numerous enzymes for utilization of different carbohydrates. It also harbors genes for antibiotic biosynthesis and many others which might confer probiotic properties. The comparative genome analysis with P. acidilactici DSM 20284 revealed some unique features in P. acidilactici NRCC1. Thus, the genome sequencing of P. acidilactici NRCC1 has opened up new horizons for further research in animal probiotics and feed supplements.

Biocontrol Potentials of Antimicrobial Peptide Producing Bacillus Species: Multifaceted Antagonists for the Management of Stem Rot of Carnation Caused by Sclerotinia sclerotiorum

Bacillus species are widely exploited as biocontrol agents because of their efficiency in impeding various plant pathogens with multifaceted approach. In this study, Bacillus species were isolated from rhizosphere of various plants viz., carnations, cotton, turmeric, and bananas in Tamil Nadu state of India. Their potential to control the mycelial growth of Sclerotinia sclerotiorum was assessed in vitro by dual plate and partition plate techniques. B. amyloliquefaciens strain VB7 was much effective in inhibiting mycelial growth (45% inhibition of over control) and sclerotial production (100%). PCR detection of AMP genes revealed that B. amyloliquefaciens (VB7) had a maximum of 10 diverse antibiotic biosynthesis genes, namely, ituD, ipa14, bacA, bacD, bamC, sfP, spaC, spaS, alba, and albF, that resulted in production of the antibiotics iturin, bacilysin, bacillomycin, surfactin, subtilin, and subtilosin. Further, metabolites from B. amyloliquefaciens strains VB2 and VB7, associated with inhibition of S. sclerotiorum, were identified as phenols and fatty acids by gas chromatography mass spectrometry (GC-MS). Delivery of bacterial suspension of the effective strains of Bacillus spp. as root dip was found promising for the management of stem rot of cultivated carnations. Minimal percent disease incidence (4.6%) and maximum plant growth promotion was observed in the plants treated with B. amyloliquefaciens (VB7).