Correlation between diverse cyclic lipopeptides production and regulation of growth and substrate utilization by Bacillus subtilis strains in a particular habitat

Comparative genomics analysis and transposon mutagenesis provides new insights into high menaquinone-7 biosynthetic potential of Bacillus subtilis natto

This research combined Whole-Genome sequencing, intraspecific comparative genomics and transposon mutagenesis to investigate the menaquinone-7 (MK-7) synthesis potential in Bacillus subtilis natto. First, Whole-Genome sequencing showed that Bacillus subtilis natto BN-P15-11-1 contains one single circular chromosome in size of 3,982,436 bp with a GC content of 43.85 %, harboring 4,053 predicted coding genes. Next, the comparative genomics analysis among strain BN-P15-11-1 with model Bacillus subtilis 168 and four typical Bacillus subtilis natto strains proves that the closer evolutionary relationship Bacillus subtilis natto BN-P15-11-1 and Bacillus subtilis 168 both exhibit strong biosynthetic potential. To further dig for MK-7 biosynthesis latent capacity of BN-P15-11-1, we constructed a mutant library using transposons and a high throughput screening method using microplates. We obtained a YqgQ deficient high MK-7 yield strain F4 with a yield 3.02 times that of the parent strain. Experiments also showed that the high yield mutants had defects in different transcription and translation regulatory factor genes, indicating that regulatory factor defects may affect the biosynthesis and accumulation of MK-7 by altering the overall metabolic level. The findings of this study will provide more novel insights on the precise identification and rational utilization of the Bacillus subtilis subspecies for biosynthesis latent capacity.

The volatile organic compound acetoin enhances the colonization of Azorhizobium caulinodans ORS571 on Sesbania rostrata

Chemoreceptors play a crucial role in assisting bacterial sensing and response to environmental stimuli. Genome analysis of Azorhizobium caulinodans ORS571 revealed the presence of 43 putative chemoreceptors, but their biological functions remain largely unknown. In this study, we identified the chemoreceptor AmaP (methyl-accepting protein of A. caulinodans), characterized by the presence of the CHASE3 domain and exhibited a notable response to acetoin. Thus, we investigated the effect of acetoin sensing on its symbiotic association with the host. Our findings uncovered a compelling role for acetoin as a key player in enhancing various facets of A. caulinodans ORS571's performance including biofilm formation, colonization, and nodulation abilities. Notably, acetoin bolstered A. caulinodans ORS571's efficacy in promoting the growth of S. rostrata, even under moderate salt stress conditions. This study not only broadens our understanding of the AmaP protein with its distinctive CHASE3 domain but also highlights the promising potential of acetoin in fortifying the symbiotic relationship between A. caulinodans and Sesbania rostrata.

The elucidation of the multimodal action of the investigational anti-Candida lipopeptide (AF4) lead from Bacillus subtilis

Background: Candida species are the main etiological agents for candidiasis, and Candida albicans are the most common infectious species. Candida species' growing resistance to conventional therapies necessitates more research into novel antifungal agents. Antifungal peptides isolated from microorganisms have potential applications as novel therapeutics. AF4 a Bacillus-derived lipopeptide demonstrating broad-spectrum antifungal activity has been investigated for its ability to cause cell death in Candida species via membrane damage and oxidative stress. Methods: Using biophysical techniques, the secondary structure of the AF4 lipopeptide was identified. Scanning electron microscopy and confocal microscopy with fluorescent dyes were performed to visualise the effect of the lipopeptide. The membrane disruption and permeabilization were assessed using the 1,6-diphenyl hexatriene (DPH) fluorescence assay and flow cytometric (FC) assessment of propidium iodide (PI) uptake, respectively. The reactive oxygen species levels were estimated using the FC assessment. The induction of apoptosis and DNA damage were studied using Annexin V-FITC/PI and DAPI. Results: Bacillus-derived antifungal variant AF4 was found to have structural features typical of lipopeptides. Microscopy imaging revealed that AF4 damages the surface of treated cells and results in membrane permeabilization, facilitating the uptake of the fluorescent dyes. A loss of membrane integrity was observed in cells treated with AF4 due to a decrease in DPH fluorescence and a dose-dependent increase in PI uptake. Cell damage was also determined from the log reduction of viable cells treated with AF4. AF4 treatment also caused elevated ROS levels, induced phosphatidylserine externalisation, late-stage apoptosis, and alterations to nuclear morphology revealed by DAPI fluorescence. Conclusion: Collectively, the mode of action studies revealed that AF4 acts primarily on the cell membrane of C. albicans and has the potential to act as an antifungal drug candidate.

Dual Inoculation of Plant Growth-Promoting Bacillus endophyticus and Funneliformis mosseae Improves Plant Growth and Soil Properties in Ginger

Co-inoculation with beneficial microbes has been suggested as a useful practice for the enhancement of plant growth, nutrient uptake, and soil nutrients. For the first time in Uzbekistan the role of plant-growth-promoting Bacillus endophyticus IGPEB 33 and arbuscular mycorrhizal fungi (AMF) on plant growth, the physiological properties of ginger (Zingiber officinale), and soil enzymatic activities was studied. Moreover, the coinoculation of B. endophyticus IGPEB 33 and AMF treatment significantly increased the plant height by 81%, leaf number by 70%, leaf length by 82%, and leaf width by 40% compared to the control. B. endophyticus IGPEB 33 individually increased plant height significantly by 51%, leaf number by 56%, leaf length by 67%, and leaf width by 27% as compared to the control treatment. Compared to the control, B. endophyticus IGPEB 33 and AMF individually significantly increased chlorophyll a by 81-58%, chlorophyll b by 68-37%, total chlorophyll by 74-53%, and carotenoid content by 67-55%. However, combination of B. endophyticus IGPEB 33 and AMF significantly increased chlorophyll a by 86%, chlorophyll b by 72%, total chlorophyll by 82%, and carotenoid content by 83% compared to the control. Additionally, plant-growth-promoting B. endophyticus IGPEB 33 and AMF inoculation improved soil nutrients and soil enzyme activities compared to the all treatments. Co-inoculation with plant-growth-promoting B. endophyticus and AMF could be an alternative for the production of ginger that is more beneficial to soil nutrient deficiencies. We suggest that a combination of plant-growth-promoting B. endophyticus and AMF inoculation could be a more sustainable and eco-friendly approach in a nutrient-deficient soil.

Control strategies for biofilm control in reclaimed water distribution systems from the perspective of microbial antagonism and electrochemistry

Biofilm formation in reclaimed water (RW) distribution systems presents significant technical challenges to RW utilization. Two main technologies to control biofilm formation, microbial antagonism (MA) and electrochemical oxidation (EO), are not yet widely used in drip irrigation systems (DIS) and their mechanisms of action need further clarification. In this study, we first showed that the MA and EO treatments reduced biofilm formation by about 62% and 68%, respectively, and extracellular polymeric substance (EPS) content by 14% and 49%, respectively, in biofilms compared with raw RW type 1 (R-RW1) in unused pipes, thus effectively improving the performance of DIS. When MA-RW and EO-RW were applied to already clogged systems, the degree of clogging alleviation varied depending on the severity of the original clogging. We recommend adding the antagonist, Bacillus subtilis, to RW at 25% clogging for the maximum effect and to slow the microbial adaptation process. Compared to MA, the recovery effect of EO was slower initially but lasted longer and had a significantly better alleviating effect on severely clogged pipelines. Illumina Mi-SEQ high-throughput sequencing data showed that both MA and EO resulted in a significant decrease in microbial diversity, dynamic changes in bacterial community structure, and disruption of network interaction and network modularity. Meanwhile, both treatments promoted the growth of specific microorganisms, enhanced the interaction between certain microbial components, and improved the efficiency of information, matter, and energy exchange within the modules. In summary, we verified the dredging effect of two strategies on DIS under different water conditions, revealed the differences in their mechanisms of action, and proposed their application scenarios. Our results will help improve the efficiency of RW in agricultural drip irrigation systems and effectively reduce maintenance costs.

A Review on Biotechnological Approaches Applied for Marine Hydrocarbon Spills Remediation

The increasing demand for petroleum products generates needs for innovative and reliable methods for cleaning up crude oil spills. Annually, several oil spills occur around the world, which brings numerous ecological and environmental disasters on the surface of deep seawaters like oceans. Biological and physico-chemical remediation technologies can be efficient in terms of spill cleanup and microorganisms—mainly bacteria—are the main ones responsible for petroleum hydrocarbons (PHCs) degradation such as crude oil. Currently, biodegradation is considered as one of the most sustainable and efficient techniques for the removal of PHCs. However, environmental factors associated with the functioning and performance of microorganisms involved in hydrocarbon-degradation have remained relatively unclear. This has limited our understanding on how to select and inoculate microorganisms within technologies of cleaning and to optimize physico-chemical remediation and degradation methods. This review article presents the latest discoveries in bioremediation techniques such as biostimulation, bioaugmentation, and biosurfactants as well as immobilization strategies for increasing the efficiency. Besides, environmental affecting factors and microbial strains engaged in bioremediation and biodegradation of PHCs in marines are discussed.

Iturin: cyclic lipopeptide with multifunction biological potential

Iturin, a metabolite produced by Bacillus subtilis, has a broad-spectrum antibacterial effect, and because they are secreted in the rhizosphere of plants, iturins are often mixed with many organic molecules. In recent years, people have improved their separation and purification methods but still cannot achieve simple and effective procedures, making Iturins an ideal biological control agent for insects and bacteria; commercial value still cannot be realized. With the in-depth studies of Iturins, its anti-cancer, hemolysis and other biological activities have gradually been discovered. This article reviews the branches of the Iturin family, structural features of these metabolite, separation and purification methods used for producing it, culture optimization, and various biological activities of the Iturin family, such as insecticidal, antibacterial, hemolytic and anticarcinogenic properties, among others have been summarized. Furthermore, this review revealed some commercial applications of Iturins and their relevance in research works. For example, in food packaging, clean water has good development potential.This can promote the commercial application of Iturins instead of other chemical and biological control agents that are environmentally friendly, pollution-free and have no side effects on humans. Furthermore, work documented anticancer, hemolytic and other biological activities of Iturin.

Bacterial strains integrated with surfactin molecules of Bacillus subtilis MTCC441 enrich nematocidal activity against Meloidogyne incognita

Bacteria secrete lipopeptide (surfactin) molecules, which are known to act as natural antibiotics. Recently, research on lipopeptide molecules has grown because of their role in increasing resistance to plant pathogens. Isolated surfactin molecules at several concentrations, viz. 35, 25, 15 and 5 ppm, were used in an in vitro study for analysis of egg hatching inhibition and second-stage juvenile (J2) mortality of the nematode Meloidogyne incognita. Cell suspensions (1.2 × 10⁸  cfu·ml^-1 ) of both Bacillus subtilis (MTCC-441) and Pseudomonas putida (MTCC-102) were used in J2 inoculated tomato plants. Root-dip treatment of tomato seedlings with the crude lipopeptide (35 ppm) was also performed to analyse biocontrol potential. MALDI-TOF MS analysis was conducted to determine specific lipopeptide molecules. Data showed nematode egg mortality of 85% in the 35 ppm surfactin concentration 96 h after exposure. The maximum ovicidal activity was 83.97% after incubation with 35 ppm surfactin for the same exposure period. Plant growth attributes and biochemical parameters were significantly improved when bacterial cultures were applied before J2 inoculation of tomato seedlings. We also recorded a reduction in egg masses, nematode population and root galling. The J2 penetration into tomato roots was effective in the root-dip experiments. Surfactin mass peak was determined at m/z 1058 [M+Na]⁺ using MALDI-TOF MS. These results indicate that bacterial cell suspensions can be used as a potent and versatile source to deal with nematode infection and provide a rich source of bioactive compounds with antinematode activity.

Characterization of lipopeptide biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis: The role of biosurfactant in carbazole solubilisation

AIM

Characterization of biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis and proteomic analysis of intracellular proteins of bacterium while growing on glucose and carbazole medium.

METHODS AND RESULTS

The bacterium R. cervicalis was isolated from a soil sample contaminated with crude petroleum oil. PCR amplification ascertained the existence of some hydrocarbon-degrading catabolic genes (alkB and PAH-RHDα, C12O, and C23O) in the bacterial genome. GC-MS and RP-HPLC analyses demonstrated 62% and 60% carbazole degradation, respectively, by R. cervicalis 144 h post-incubation at 37℃ and pH 6.5. Due to the paucity of protein databases, expressions of only 29 and 14 intracellular proteins were explicitly recognized and quantitated by mass spectrometry analysis when R. cervicalis was grown in carbazole and glucose medium, respectively. FTIR, NMR and HR-MS/MS analyses demonstrated the lipopeptide nature of the purified biosurfactant produced by R. cervicalis. The biosurfactant is also presumed to assist in the solubilization of carbazole.

CONCLUSION

The isolated R. cervicalis strain is a potential candidate for the bioremediation of carbazole in petroleum-oil-contaminated sites.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report of the promising R. cervicalis strain proficient in carbazole biodegradation.

Two Novel Bacillus Strains (subtilis and simplex Species) with Promising Potential for the Biocontrol of Zymoseptoria tritici, the Causal Agent of Septoria Tritici Blotch of Wheat

Two novel Algerian field-collected isolates were selected for their antifungal activity against Zymoseptoria tritici (teleomorph Mycosphaerella graminicola). The novel strains, termed Alg.24B1 and Alg.24B2, were identified as Bacillus subtilis and Bacillus simplex since their respective nucleotide sequences of the 16S rRNA gene were 100% and 99.93% identical to those of B. subtilis and B. simplex, respectively. The antifungal activities of Alg.24B1 and Alg.24B2 were evaluated by the well diffusion method and compared to those of other Bacillus species. The maximum activity was obtained after two days of confrontation of the bacterial strain supernatants with the fungus for Alg.24B1 and three days for Alg.24B2. Furthermore, the metabolites responsible for the antifungal activity of both strains were detected by the investigation of either gene presence (PCR) or molecule production (activity detection of lytic enzymes and HPLC detection of lipopeptides). Overall, this study showed that in addition to their ability to produce lytic enzymes (protease and β-glucanase), both strains coproduce three types of lipopeptides viz. surfactin, iturin, and fengycin. Thus, the biofungicide activity of both strains may be a result of a combination of different mechanisms. Therefore, they had a great potential to be used as biocontrol agents to effectively manage septoria tritici blotch of wheat (STB).

Molecular Aspects of Plant Growth Promotion and Protection by Bacillus subtilis

Bacillus subtilis is one of the most widely studied plant growth-promoting rhizobacteria. It is able to promote plant growth as well as control plant pathogens through diverse mechanisms, including the improvement of nutrient availability and alteration of phytohormone homeostasis as well as the production of antimicrobials and triggering induced systemic resistance, respectively. Even though its benefits for crop production have been recognized and studied extensively under laboratory conditions, the success of its application in fields varies immensely. It is widely accepted that agricultural application of B. subtilis often fails because the bacteria are not able to persist in the rhizosphere. Bacterial colonization of plant roots is a crucial step in the interaction between microbe and plant and seems, therefore, to be of great importance for its growth promotion and biocontrol effects. A successful root colonization depends thereby on both bacterial traits, motility and biofilm formation, as well as on a signal interplay with the plant. This review addresses current knowledge about plant-microbial interactions of the B. subtilis species, including the various mechanisms for supporting plant growth as well as the necessity for the establishment of the relationship.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.

Kinetic study and characterization of surfactin production by Bacillus subtilis UFPEDA 438 using sugarcane molasses as carbon source

The present study evaluated the surfactin production by Bacillus subtilis UFPEDA 438 using sugarcane molasses as a substrate. The effects of the cultivation conditions (temperature, agitation and aeration ratio) on the biosurfactant production and kinetic parameters were investigated. Characteristics of the biosurfactant were obtained after analyses of the emulsification index (EI) and critical micellar concentration (CMC) of the fermentation broth. The results showed that in relation to the product its formation kinetics is strongly affected by operational conditions. It was also observed that surfactin production can be partially dependent or fully independent on microbial growth. The maximum values of surfactin concentration (199.45 ± 0.13 mg/L) and productivity (8,187 mg/L.h) were obtained in the culture under cultivation time of 24 h, temperature of 36 °C, agitation of 100 rpm and aeration ratio of 0.4. Under optimal conditions, the fermentation broth achieved good emulsification capacity (EI >40%) and CMC value of 20.73 mg/L. The results revealed that Bacillus subtilis UFPEDA 438 is a good producer of biosurfactant and that sugarcane molasses is a viable substrate for the production of surfactin.

Microbial Culture in Minimal Medium With Oil Favors Enrichment of Biosurfactant Producing Genes

The waste produced by petrochemical industries has a significant environmental impact. Biotechnological approaches offer promising alternatives for waste treatment in a sustainable and environment-friendly manner. Microbial consortia potentially clean up the wastes through degradation of hydrocarbons using biosurfactants as adjuvants. In this work, microbial consortia were obtained from a production water (PW) sample from a Brazilian oil reservoir using enrichment and selection approaches in the presence of oil as carbon source. A consortium was obtained using Bushnell-Haas (BH) mineral medium with petroleum. In parallel, another consortium was obtained in yeast extract peptone dextrose (YPD)-rich medium and was subsequently compared to the BH mineral medium with petroleum. Metagenomic sequencing of these microbial communities showed that the BH consortium was less diverse and predominantly composed of Brevibacillus genus members, while the YPD consortium was taxonomically more diverse. Functional annotation revealed that the BH consortium was enriched with genes involved in biosurfactant synthesis, while the YPD consortium presented higher abundance of hydrocarbon degradation genes. The comparison of these two consortia against consortia available in public databases confirmed the enrichment of biosurfactant genes in the BH consortium. Functional assays showed that the BH consortium exhibits high cellular hydrophobicity and formation of stable emulsions, suggesting that oil uptake by microorganisms might be favored by biosurfactants. In contrast, the YPD consortium was more efficient than the BH consortium in reducing interfacial tension. Despite the genetic differences between the consortia, analysis by a gas chromatography-flame ionization detector showed few significant differences regarding the hydrocarbon degradation rates. Specifically, the YPD consortium presented higher degradation rates of C12 to C14 alkanes, while the BH consortium showed a significant increase in the degradation of some polycyclic aromatic hydrocarbons (PAHs). These data suggest that the enrichment of biosurfactant genes in the BH consortium could promote efficient hydrocarbon degradation, despite its lower taxonomical diversity compared to the consortium enriched in YPD medium. Together, these results showed that cultivation in a minimal medium supplemented with oil was an efficient strategy in selecting biosurfactant-producing microorganisms and highlighted the biotechnological potential of these bacterial consortia in waste treatment and bioremediation of impacted areas.

Complete Genome Sequence of the Biocontrol Agent Bacillus velezensis UFLA258 and Its Comparison with Related Species: Diversity within the Commons

In this study, the full genome sequence of Bacillus velezensis strain UFLA258, a biological control agent of plant pathogens was obtained, assembled, and annotated. With a comparative genomics approach, in silico analyses of all complete genomes of B. velezensis and closely related species available in the database were performed. The genome of B. velezensis UFLA258 consisted of a single circular chromosome of 3.95 Mb in length, with a mean GC content of 46.69%. It contained 3,949 genes encoding proteins and 27 RNA genes. Analyses based on Average Nucleotide Identity and Digital DNA–DNA Hybridization and a phylogeny with complete sequences of the rpoB gene confirmed that 19 strains deposited in the database as Bacillus amyloliquefaciens were in fact B. velezensis. In total, 115 genomes were analyzed and taxonomically classified as follows: 105 were B. velezensis, 9 were B. amyloliquefaciens, and 1 was Bacillus siamensis. Although these species are phylogenetically close, the combined analyses of several genomic characteristics, such as the presence of biosynthetic genes encoding secondary metabolites, CRISPr/Cas arrays, Average Nucleotide Identity and Digital DNA–DNA Hybridization, and other information on the strains, including isolation source, allowed their unequivocal classification. This genomic analysis expands our knowledge about the closely related species, B. velezensis, B. amyloliquefaciens, and B. siamensis, with emphasis on their taxonomical status.

Antimicrobial, anti-biofilm, and anti-proliferative activities of lipopeptide biosurfactant produced by Acinetobacter junii B6

Lipopeptide biosurfactants (LPBs) are amphiphilic compounds produced by microorganisms exhibiting various biological activities. The main aim of the present study was to assess the in vitro antimicrobial, anti-biofilm, and cytotoxic effects of LPB produced by Acinetobacter junii (AjL). We determined AjL minimum inhibitory concentration (MIC) against both Gram-positive and Gram-negative bacteria as well as two fungal strains. Also, the anti-biofilm activity of AjL against the biofilm produced by clinically isolated bacterial strains was investigated. The AjL non-selectively showed activity against both Gram-positive and Gram-negative bacterial strains. The obtained results of the present study exhibited that the AjL in concentrations nearly below critical micelle concentration (CMC) has an effective antibacterial activity. It was found that the MIC values of AjL were lower than standard antifungal and it exhibited nearly 100% inhibition against Candida utilis. The attained results of the biofilm formation revealed that AjL disrupted the biofilm of Proteus mirabilis, Staphylococcus aureus, and Pseudomonas aeruginosa at 1250 μg/ml and 2500 μg/ml concentrations. The attained results of cytotoxic effect (determined by WST-1 assay) of the AjL revealed IC₅₀ of 7.8 ± 0.4 mg/ml, 2.4 ± 0.5 mg/ml, and 5.7 ± 0.1 mg/ml, against U87, KB, and HUVEC cell lines, respectively. The results indicated that AjL has a potential application in the relatively new field of biomedicine.

Aphicidal Activity of Surfactants Produced by Bacillus atrophaeus L193

The biosurfactants produced by Bacillus atrophaeus L193 was examined by their use in the control of the aphid Rhopalosiphum padi in order to suggest a friendly alternative to chemical pesticides. A screening of different culture media demonstrated the highest biosurfactant production by L193 in TSB supplemented with colloidal chitin. Surfactants, which are produced in large quantities (2.04 g/L), reduce surface tension to 33 mN/m. Electrospray Q-TOFS MS analysis demonstrated that lipopeptides, such as surfactins, fengycins, bacillomycins and iturins, are the predominant metabolites present in biosurfactants produced by strain L193. Treatment with L193 surfactants led to an aphid mortality rate of 59.8% within 24 h. Microscopy analysis showed that these compounds caused insect death by affecting cuticle membranes. An evaluation of aphid feeding activity also demonstrated that aphid feeding capacity is affected by treatment with surfactants. Moreover, microbial cultures of strain L193 and their supernatants also showed high levels of activity against R. padi, which is probably due to the presence of surfactants and hydrolytic enzymes such as proteases and glucanases. This study demonstrates that B. atrophaeus L193 is an effective treatment for plants affected by aphids.

A new cyclic lipopeptide isolated from Bacillus amyloliquefaciens HAB-2 and safety evaluation

Bacillus is the most widely studied biocontrol agent and has been extensively used in the development of biopesticides and fungicides. In this study, a new cyclic lipopeptide was isolated from Bacillus amyloliquefaciens HAB-2 by column chromatography on silica gel and Sephadex LH-20, and its structures was elucidated on the basis of spectroscopic analysis. This compound is a bacillomycin d-like compound, named as bacillomycin DC. The activity of bacillomycin DC was evaluated against C. gloeosporioides Penz. The median inhibitory concentration of bacillomycin DC was 1.21μg/mL. In addition, bacillomycin DC may have low toxicity to aquatic species as indicated by its 96h half maximum lethal concentration of 22.20μg/mL to zebrafish (Danio rerio). Our current study further provides evidence that bacillomycin DC is a potent fungicide against C. gloeosporioides Penz.

Biocontrol activity of surfactin A purified from Bacillus NH-100 and NH-217 against rice bakanae disease

The potential of the Bacillus genus to antagonize phytopathogens is associated with the production of cyclic lipopeptides. Depending upon the type of lipopeptide, they may serve as biocontrol agents that are eco-friendly alternatives to chemical fertilizers. This study evaluates the biocontrol activity of surfactin-producing Bacillus (SPB) strains NH-100 and NH-217 and purified surfactin A from these strains against rice bakanae disease. Biologically active surfactin fractions were purified by HPLC, and surfactin A variants with chain lengths from C12 to C16 were confirmed by LCMS-ESI. In hemolytic assays, a positive correlation between surfactin A production and halo zone formation was observed. The purified surfactin A had strong antifungal activity against Fusarium oxysporum, F. moniliforme, F. solani, Trichoderma atroviride and T. reesei. Maximum fungal growth suppression (84%) was recorded at 2000 ppm against F. moniliforme. Surfactin A retained antifungal activity at different pH levels (5-9) and temperatures (20, 50 and 121 °C). Hydroponic and pot experiments were conducted to determine the biocontrol activity of SPB strains and the purified surfactin A from these strains on Super Basmati rice. Surfactin production in the rice rhizosphere was detected by LCMS-ESI at early growth stages in hydroponics experiments inoculated with SPB strains. However, the maximum yield was observed with a consortium of SPB strains (T4) and purified surfactin A (T5) treatments in the pot experiment. The outcomes of the present study revealed that surfactin A significantly reduced rice bakanae disease by up to 80%. These findings suggest that purified surfactin A could be an effective biocontrol agent against bakanae disease in rice and should be incorporated into strategies for disease management.

Characterization of lpaH2 gene corresponding to lipopeptide synthesis in Bacillus amyloliquefaciens HAB-2

Background

Bacillus spp. have prominent ability to suppress plant pathogens and corresponding diseases. Previous analyses of Bacillus spp. revealed numerous gene clusters involved in nonribosomal synthesis of cyclic lipopeptides with distinct antimicrobial action. The 4′-phosphopantetheinyl transferase (PPTase) encoded by sfp gene is a key factor in lipopeptide synthesis in Bacillus spp. In previous study, B. amyloliquefaciens strain HAB-2 was found to inhibit a broad range of plant pathogens, which was attributed to its secondary metabolite lipopeptide.

Results

A sfp homologue lpaH2 which encoded phosphopantetheinyl transferase but shared 71% sequence similarity was detected in strain HAB-2. Disruption of lpaH2 gene resulted in losing the ability of strain HAB-2 to produce lipopeptide, as well as antifungal and hemolytic activities. When lpaH2 replaced sfp gene of B. subtilis strain 168, a non-lipopeptide producer, the genetically engineered strain 168 could produced lipopeptides and recovered antifungal activity. Quantitative PCR assays indicated that, the expression level of lpaH2 in B. subtilis 168 strain decrease to 0.27-fold compared that of the wild type B. amyloliquefaciens strain HAB-2.

Conclusion

Few studies have reported about lpa gene which can replace sfp gene in the different species. Taken together, our study showed for the first time that lpaH2 from B. amyloliquefaciens could replace sfp gene.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-1134-z) contains supplementary material, which is available to authorized users.

Antibiosis and bmyB Gene Presence As Prevalent Traits for the Selection of Efficient Bacillus Biocontrol Agents against Crown Gall Disease

This study aimed to improve the screening method for the selection of Bacillus biocontrol agents against crown gall disease. The relationship between the strain biocontrol ability and their in vitro studied traits was investigated to identify the most important factors to be considered for the selection of effective biocontrol agents. In fact, previous selection procedure relying only on in vitro antibacterial activity was shown to be not suitable in some cases. A direct plant-protection strategy was performed to screen the 32 Bacillus biocontrol agent candidates. Moreover, potential in vitro biocontrol traits were investigated including biofilm formation, motility, hemolytic activity, detection of lipopeptide biosynthetic genes (sfp, ituC and bmyB) and production of antibacterial compounds. The obtained results indicated high correlations of the efficiency of the biocontrol with the reduction of gall weight (p = 0.000) and the antibacterial activity in vitro (p = 0.000). Moreover, there was strong correlations of the efficiency of the biocontrol (p = 0.004) and the reduction in gall weight (p = 0.000) with the presence of the bmyB gene. This gene directs the synthesis of the lipopeptide bacillomycin belonging to the iturinic family of lipopeptides. These results were also confirmed by the two-way hierarchical cluster analysis and the correspondence analysis showing the relatedness of these four variables. According to the obtained results a new screening procedure of Bacillus biocontrol agents against crown gall disease could be advanced consisting on two step selection procedure. The first consists on selecting strains with high antibacterial activity in vitro or those harbouring the bmyB gene. Further selection has to be performed on tomato plants in vivo. Moreover, based on the results of the biocontrol assay, five potent strains exhibiting high biocontrol abilities were selected. They were identified as Bacillus subtilis or Bacillus amyloliquefaciens. These strains were found to produce either surfactin or surfactin and iturin lipopeptides. In conclusion, our study presented a new and effective method to evaluate the biocontrol ability of antagonistic Bacillus strains against crown gall disease that could increase the efficiency of screening method of biocontrol agents. Besides, the selected strains could be used as novel biocontrol agents against pathogenic Agrobacterium tumefaciens strains.

Study of the correlation between fengycin promoter expression and its production by Bacillus subtilis under different culture conditions and the impact on surfactin production

This work aimed to rely expression of the fengycin promoter to fengycin production under different culture conditions. To this end, Bacillus subtilis BBG208, derived from BBG21, which is a fengycin overproducing strain carrying the green fluorescent protein (GFP) under the control of fengycin promoter, was used to assess the effects of different carbon and nitrogen sources on surfactin and fengycin production and the fengycin promoter expression. The data showed that some carbon sources oriented synthesis of one family of lipopeptides, while most of the nitrogen sources allowed high co-production of fengycin and surfactin. High expressions of promoter P_fen and fengycin synthesis were obtained with urea or urea + ammonium mixture as nitrogen source and mannitol as carbon source. Moreover, temperature, pH and oxygenation influenced their biosynthesis based on the nutrition conditions. Optimization of the production medium increased the fengycin production to 768 mg L^-1, which is the highest level reported for this strain. This study defines the suitable nutrient conditions allowing as well the highest expression of the fengycin promoter and portrays the conditions relying on the fengycin and surfactin production.

The Profile and Antimicrobial Activity of Bacillus Lipopeptide Extracts of Five Potential Biocontrol Strains

In this study the efficacy of two different methods for extracting lipopeptides produced by five Bacillus strains-ethyl acetate extraction, and acid precipitation followed by methanol extraction—was investigated using mass spectrometry. High performance thin layer chromatography (HPTLC) was also used for the simultaneous separation of complex mixtures of lipopeptide extracts and for the determination of antimicrobial activity of their components. The mass spectra clearly showed well-resolved groups of peaks corresponding to different lipopeptide families (kurstakins, iturins, surfactins, and fengycins). The ethyl acetate extracts produced the most favorable results. The extracts of SS-12.6, SS-13.1, and SS-38.4 showed the highest inhibition zones. An iturin analog is responsible for the inhibition of Xanthomonas arboricola and Pseudomonas syringae phytopathogenic strains. HPTLC bioautography effectively identified the active compounds from a mixture of lipopeptide extracts, proving in situ its potential for use in direct detection and determination of antimicrobials. In the test of potential synergism among individual extracts used in different mixtures, stronger antimicrobial effects were not observed. Biochemical and phylogenetic analysis clustered isolates SS-12.6, SS-13.1, SS-27.2, and SS-38.4 together with Bacillus amyloliquefaciens, while SS-10.7 was more closely related to Bacillus pumilus.

Role of Bacillus licheniformis VS16-Derived Biosurfactant in Mediating Immune Responses in Carp Rohu and its Application to the Food Industry

Multifarious applications of Bacillus licheniformis VS16-derived biosurfactant were explored. Labeo rohita fingerlings were injected intraperitoneally with 0.1 mL of phosphate-buffered saline (PBS) containing purified biosurfactant at 0 (control), 55 (S55), 110 (S110), 220 (S220), or 330 (S330) μg mL^-1 concentrations. Various immunological parameters and the expression of immune-related genes were measured at 7, 14, and 21 days post-administration (dpa). At 21 dpa, fish were challenged with Aeromonas hydrophila and mortality was recorded for 14 days. Immune parameters such as lysozyme levels (39.29 ± 2.14 U mL^-1), alternative complement pathway (61.21 ± 2.38 U mL^-1), and phagocytic activities (33.37 ± 1.2%) were maximum (P < 0.05) in the S220 group at 14 dpa; but immunoglobulin levels (11.07 ± 0.83 mg mL^-1) were highest in the S220 group at 7 dpa, compared to that in controls. Activities of digestive enzymes (amylase, protease, and lipase) were higher (P < 0.05) in the S220 and S330 groups than in the control group. Regarding cytokine gene expression, pro-inflammatory cytokines (TNF-α and IL-1β) were down-regulated (P < 0.05) in the S220 and S330 groups. Expression of IL-10, TGF-β, and IKB-α were up-regulated in the S220 and S330 groups at 14 dpa, with the highest levels in the S220 group. The expression of NF-κB p65 and IKK-β were down-regulated in treatment groups, and were lowest (P < 0.05) in the S220 group. The highest post-challenge survival rate (72.7%) was recorded in S220 group. Further, the potential of this substance to inhibit biofilm formation, and heavy metal removal from vegetables were also evaluated. Biosurfactant was effective in inhibiting biofilm formation up to 54.71 ± 1.27%. Moreover, it efficiently removed cadmium (Cd) from tested vegetables such as carrot, radish, ginger, and potato, with the highest removal efficiency (60.98 ± 1.29%) recorded in ginger contaminated with Cd. Collectively, these results suggest that isolated biosurfactant could be used in the aquaculture industry, in addition to its potential application to the food industry.

An improvement of surfactin production by B. subtilis BBG131 using design of experiments in microbioreactors and continuous process in bubbleless membrane bioreactor

Culture medium elements were analysed by a screening DoE to identify their influence in surfactin specific production by a surfactin constitutive overproducing Bacillus subtilis strain. Statistics pointed the major enhancement caused by high glutamic acid concentrations, as well as a minor positive influence of tryptophan and glucose. Successively, a central composite design was performed in microplate bioreactors using a BioLector®, in which variations of these impressive parameters, glucose, glutamic acid and tryptophan concentrations were selected for optimization of product-biomass yield (YP/X). Results were exploited in combination with a RSM. In absolute terms, experiments attained an YP/X 3.28-fold higher than those obtained in Landy medium, a usual culture medium used for lipopeptide production by B. subtilis. Therefore, two medium compositions for enhancing biomass and surfactin specific production were proposed and tested in continuous regime in a bubbleless membrane bioreactor. An YP/X increase of 2.26-fold was observed in bioreactor scale.

Termitarium-inhabiting Bacillus endophyticus TSH42 and Bacillus cereus TSH77 colonizing Curcuma longa L.: isolation, characterization, and evaluation of their biocontrol and plant-growth-promoting activities

Bacillus strains were isolated from termitarium soil and screened for their antifungal activity through the production of diffusible and volatile metabolites. Further, the bacterial strains that showed antifungal activity were evaluated for their biocontrol potential on the basis of their plant-growth-promoting attributes. Termitarium-inhabiting Bacillus strains TSH42 and TSH77 significantly reduced the growth of pathogenic fungus Fusarium solani, controlled the symptoms of rhizome rot in turmeric (Curcuma longa L.), and demonstrated various plant-growth-promoting traits in different in vitro assays. On the basis of morphological, physiological, biochemical, and 16S rDNA characteristics, isolates TSH42 and TSH77 were identified as Bacillus endophyticus (KT379993) and Bacillus cereus (KT379994), respectively. Through liquid chromatography - mass spectrometry analysis, acidified cell-free culture filtrate (CFCF) of B. cereus TSH77 was shown to contain surfactin and fengycin, while CFCF of B. endophyticus TSH42 contained iturin in addition to surfactin and fengycin. Treatment of the turmeric (C. longa L.) plants with TSH42 and TSH77 significantly reduced the percentage incidence of rhizome rot disease caused by F. solani. The same treatment also increased the fresh rhizome biomass and plant growth in greenhouse conditions.

Bacillus velezensis RC 218 as a biocontrol agent to reduce Fusarium head blight and deoxynivalenol accumulation: Genome sequencing and secondary metabolite cluster profiles

Bacillus subtilis RC 218 was originally isolated from wheat anthers as a potential antagonist of Fusarium graminearum, the causal agent of Fusarium head blight (FHB). It was demonstrated to have antagonist activity against the plant pathogen under in vitro and greenhouse assays. The current study extends characterizing B. subtilis RC 218 with a field study and genome sequencing. The field study demonstrated that B. subtilis RC 218 could reduce disease severity and the associated mycotoxin (deoxynivalenol) accumulation, under field conditions. The genome sequencing allowed us to accurately determine the taxonomy of the strain using a phylogenomic approach, which places it in the Bacillus velezensis clade. In addition, the draft genome allowed us to use bioinformatics to mine the genome for potential metabolites. The genome mining allowed us to identify 9 active secondary metabolites conserved by all B. velezensis strains and one additional secondary metabolite, the lantibiotic ericin, which is unique to this strain. This study represents the first confirmed production of ericin by a B. velezensis strain. The genome also allowed us to do a comparative genomics with its closest relatives and compare the secondary metabolite production of the publically available B. velezensis genomes. The results showed that the diversity in secondary metabolites of strains in the B. velezensis clade is driven by strains making different antibacterials.

The synergetic effect of starch and alpha amylase on the biodegradation of n-alkanes

The impact of adding soluble starch on biodegradation of n-alkanes (C10-C14) by Bacillus subtilis TB1 was investigated. Gas chromatography was employed to measure the residual hydrocarbons in the system. It was observed that the efficiency of biodegradation improved with the presence of starch and the obtained residual hydrocarbons in the system were 53% less than the samples without starch. The produced bacterial enzymes were studied through electrophoresis and reverse zymography for explaining the observations. The results indicated that the produced amylase by the bacteria can degrade hydrocarbons and the same was obtained by the application of a commercial alpha amylase sample. In addition, in silico docking of alpha-amylase with n-alkanes with different molecular weights was studied by Molegro virtual docker which showed high negative binding energies and further substantiated the experimental observations. Overall, the findings confirmed the catalytic effect of alpha amylase on n-alkanes degradation.

Production and identification of iturin A lipopeptide from Bacillus methyltrophicus TEB1 for control of Phoma tracheiphila

A lipopeptide-producing endophytic Bacillus methyltrophicus TEB1 strain exhibited potent antifungal activity against Phoma tracheiphila. Lipopeptide production started at the early growth phase plateaued after 36 h of culture where it reduced the mycelium growth by 80%. The crude lipopeptide extract harvested at the stationary phase efficiently inhibited the growth of P. tracheiphila mycelium and MIC values displaying 50 and 90% inhibition of conidia germination were around 47.5 and 100 μg ml(-1) , respectively. Increasing lipopeptide extract till 3 mg ml(-1) induced 10% swelling and 3% crumbling of P. tracheiphila conidia whereas 5 mg ml(-1) induced 40% swelling and 20% crumbling. Mass spectrometry analysis of the lipopeptide extract indicated that surfactin production took place from 12 to 20 h, iturin A from 16 to 72 h, and fengycin from 12 to 72 h and that the main active compound against P. tracheiphila was identified as C15 iturin A lipopeptide. Iturin A appeared as a potential biological control agent able to substitute the currently used chemical pesticides in agriculture.

Proteomics and Metabolomics Analyses to Elucidate the Desulfurization Pathway of Chelatococcus sp

Desulfurization of dibenzothiophene (DBT) and alkylated DBT derivatives present in transport fuel through specific cleavage of carbon-sulfur (C-S) bonds by a newly isolated bacterium Chelatococcus sp. is reported for the first time. Gas chromatography-mass spectrometry (GC-MS) analysis of the products of DBT degradation by Chelatococcus sp. showed the transient formation of 2-hydroxybiphenyl (2-HBP) which was subsequently converted to 2-methoxybiphenyl (2-MBP) by methylation at the hydroxyl group of 2-HBP. The relative ratio of 2-HBP and 2-MBP formed after 96 h of bacterial growth was determined at 4:1 suggesting partial conversion of 2-HBP or rapid degradation of 2-MBP. Nevertheless, the enzyme involved in this conversion process remains to be identified. This production of 2-MBP rather than 2-HBP from DBT desulfurization has a significant metabolic advantage for enhancing the growth and sulfur utilization from DBT by Chelatococcus sp. and it also reduces the environmental pollution by 2-HBP. Furthermore, desulfurization of DBT derivatives such as 4-M-DBT and 4, 6-DM-DBT by Chelatococcus sp. resulted in formation of 2-hydroxy-3-methyl-biphenyl and 2-hydroxy -3, 3/- dimethyl-biphenyl, respectively as end product. The GC and X-ray fluorescence studies revealed that Chelatococcus sp. after 24 h of treatment at 37°C reduced the total sulfur content of diesel fuel by 12% by per gram resting cells, without compromising the quality of fuel. The LC-MS/MS analysis of tryptic digested intracellular proteins of Chelatococcus sp. when grown in DBT demonstrated the biosynthesis of 4S pathway desulfurizing enzymes viz. monoxygenases (DszC, DszA), desulfinase (DszB), and an NADH-dependent flavin reductase (DszD). Besides, several other intracellular proteins of Chelatococcus sp. having diverse biological functions were also identified by LC-MS/MS analysis. Many of these enzymes are directly involved with desulfurization process whereas the other enzymes/proteins support growth of bacteria at an expense of DBT. These combined results suggest that Chelatococcus sp. prefers sulfur-specific extended 4S pathway for deep-desulphurization which may have an advantage for its intended future application as a promising biodesulfurizing agent.

Structural and physico-chemical characterization of a dirhamnolipid biosurfactant purified from Pseudomonas aeruginosa: application of crude biosurfactant in enhanced oil recovery

The present study describes the structural characterization and biotechnological application of a dirhamnolipid biosurfactant produced byPseudomonas aeruginosastrain NBTU-01 isolated from a petroleum oil-contaminated soil sample.

Lipopeptide surfactants: Production, recovery and pore forming capacity

Lipopeptides are microbial surface active compounds produced by a wide variety of bacteria, fungi and yeast. They are characterized by highly structural diversity and have the ability to decrease the surface and interfacial tension at the surface and interface, respectively. Surfactin, iturin and fengycin of Bacillus subtilis are among the most studied lipopeptides. This review will present the main factors encountering lipopeptides production along with the techniques developed for their extraction and purification. Moreover, we will discuss their ability to form pores and destabilize biological membrane permitting their use as antimicrobial, hemolytic and antitumor agents. These open great potential applications in biomediacal, pharmaceutic and agriculture fields.

Bacillus subtilis subsp. subtilis CBMDC3f with antimicrobial activity against Gram-positive foodborne pathogenic bacteria: UV-MALDI-TOF MS analysis of its bioactive compounds

In this work a new Bacillus sp. strain, isolated from honey, was characterized phylogenetically. Its antibacterial activity against three relevant foodborne pathogenic bacteria was studied; the main bioactive metabolites were analyzed using ultraviolet matrix assisted laser desorption-ionization mass spectrometry (UV-MALDI MS). Bacillus CBMDC3f was phylogenetically characterized as Bacillus subtilis subsp. subtilis after rRNA analysis of the 16S subunit and the gyrA gene (access codes Genbank JX120508 and JX120516, respectively). Its antibacterial potential was evaluated against Listeria monocytogenes (9 strains), B. cereus (3 strains) and Staphylococcus aureus ATCC29213. Its cell suspension and cell-free supernatant (CFS) exerted significant anti-Listeria and anti-S. aureus activities, while the lipopeptides fraction (LF) also showed anti-B. cereus effect. The UV-MALDI-MS analysis revealed surfactin, iturin and fengycin in the CFS, whereas surfactin predominated in the LF. The CFS from CBMDC3f contained surfactin, iturin and fengycin with four, two and four homologues per family, respectively, whereas four surfactin, one iturin and one fengycin homologues were identified in the LF. For some surfactin homologues, their UV-MALDI-TOF/TOF (MS/MS; Laser Induced Decomposition method, LID) spectra were also obtained. Mass spectrometry analysis contributed with relevant information about the type of lipopeptides that Bacillus strains can synthesize. From our results, surfactin would be the main metabolite responsible for the antibacterial effect.

Lipopeptide biosurfactant production bacteria Acinetobacter sp. D3-2 and its biodegradation of crude oil

In this work, a hydrocarbon-degrading bacterium D3-2 isolated from petroleum contaminated soil samples was investigated for its potential effect in biodegradation of crude oil. The strain was identified as Acinetobacter sp. D3-2 based on morphological, biochemical and phylogenetic analysis. The optimum environmental conditions for growth of the bacteria were determined to be pH 8.0, with a NaCl concentration of 3.0% (w/v) at 30 °C. Acinetobacter sp. D3-2 could utilize various hydrocarbon substrates as the sole carbon and energy source. From this study, we also found that the strain had the ability to produce biosurfactant, with the production of 0.52 g L(-1). The surface tension of the culture broth was decreased from 48.02 to 26.30 mN m(-1). The biosurfactant was determined to contain lipopeptide compounds based on laboratory analyses. By carrying out a crude oil degradation assay in an Erlenmeyer flask experiment and analyzing the hydrocarbon removal rate using gas chromatography, we found that Acinetobacter sp. D3-2 could grow at 30 °C in 3% NaCl solution with a preferable ability to degrade 82% hydrocarbons, showing that bioremediation does occur and plays a profound role during the oil reparation process.

Optimization, production and characterization of glycolipid biosurfactant from the marine actinobacterium, Streptomyces sp. MAB36

A potential glycolipid biosurfactant producer Streptomyces sp. MAB36 was isolated from marine sediment samples. Medium composition and culture conditions for the glycolipid biosurfactant production by Streptomyces sp. MAB36 were optimized, using two statistical methods: Plackett-Burman design was applied to find out the key ingredients and conditions for the best yield of glycolipid biosurfactant production and central composite design was used to optimize the concentration of the four significant variables, starch, casein, crude oil and incubation time. Fructose and yeast extract were the best carbon and nitrogen sources for the production of the glycolipid biosurfactant. Biochemical characterizations including FTIR and MS studies suggested the glycolipid nature of the biosurfactant. The isolated glycolipid biosurfactant reduced the surface tension of water from 73.2 to 32.4 mN/m. The purified glycolipid biosurfactant showed critical micelle concentrations of 36 mg/l. The glycolipid biosurfactant was effective at very low concentrations over a wide range of temperature, pH, and NaCl concentration. The purified glycolipid biosurfactant showed strong antimicrobial activity. Thus, the strain Streptomyces sp. MAB36 has proved to be a potential source of glycolipid biosurfactant that could be used for the bioremediation processes in the marine environment.

Ecological and mechanistic insights into the direct and indirect antimicrobial properties of Bacillus subtilis lipopeptides on plant pathogens

Members of the genus Bacillus produce a wide variety of antimicrobial compounds. Cyclic lipopeptides (CLP) produced by Bacillus subtilis strains have been shown to protect host plants from a numbers of pathogens. The representative families of these CLP (surfactins, fengycins, and iturins) share a polypeptide ring linked to a lipid tail of varying length. CLP provide plant protection through a variety of unique mechanisms. Members of the surfactin and fengycin families elicit induced systemic resistance in certain host plants, and they also function by directly affecting the biological membranes of bacterial and fungal pathogens, mainly resulting in membrane pore formation. Specific pore forming mechanisms differ between CLP families, causing differential activities. CLP also may aid in enhanced B. subtilis colonization of the plant environment in addition to potentially preventing the adhesion of competitive microorganisms. Several recent studies have highlighted the control of plant pathogens by CLP-producing B. subtilis strains. Strong ecological advantages through multifaceted activities of CLP provide these strains with immense promise in controlling pathogens in a variety of plant ecosystems.

MALDI TOF MS profiling of bacteria at the strain level: a review

Since the advent of the use of matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOF MS) as a tool for microbial characterization, efforts to increase the taxonomic resolution of the approach have been made. The rapidity and efficacy of the approach have suggested applications in counter-bioterrorism, prevention of food contamination, and monitoring the spread of antibiotic-resistant bacteria. Strain-level resolution has been reported with diverse bacteria, using library-based and bioinformatics-enabled approaches. Three types of characterization at the strain level have been reported: strain categorization, strain differentiation, and strain identification. Efforts to enhance the library-based approach have involved sample pre-treatment and data reduction strategies. Bioinformatics approaches have leveraged the ever-increasing amount of publicly available genomic and proteomic data to attain strain-level characterization. Bioinformatics-enabled strategies have facilitated strain characterization via intact biomarker identification, bottom-up, and top-down approaches. Rigorous quantitative and advanced statistical analyses have fostered success at the strain level with both approaches. Library-based approaches can be limited by effects of sample preparation and culture conditions on reproducibility, whereas bioinformatics-enabled approaches are typically limited to bacteria, for which genetic and/or proteomic data are available. Biological molecules other than proteins produced in strain-specific manners, including lipids and lipopeptides, might represent other avenues by which strain-level resolution might be attained. Immunological and lectin-based chemistries have shown promise to enhance sensitivity and specificity. Whereas the limits of the taxonomic resolution of MALDI TOF MS profiling of bacteria appears bacterium-specific, recent data suggest that these limits might not yet have been reached.

Characterization of the biocontrol activity of pseudomonas fluorescens strain X reveals novel genes regulated by glucose

Pseudomonas fluorescens strain X, a bacterial isolate from the rhizosphere of bean seedlings, has the ability to suppress damping-off caused by the oomycete Pythium ultimum. To determine the genes controlling the biocontrol activity of strain X, transposon mutagenesis, sequencing and complementation was performed. Results indicate that, biocontrol ability of this isolate is attributed to gcd gene encoding glucose dehydrogenase, genes encoding its co-enzyme pyrroloquinoline quinone (PQQ), and two genes (sup5 and sup6) which seem to be organized in a putative operon. This operon (named supX) consists of five genes, one of which encodes a non-ribosomal peptide synthase. A unique binding site for a GntR-type transcriptional factor is localized upstream of the supX putative operon. Synteny comparison of the genes in supX revealed that they are common in the genus Pseudomonas, but with a low degree of similarity. supX shows high similarity only to the mangotoxin operon of Ps. syringae pv. syringae UMAF0158. Quantitative real-time PCR analysis indicated that transcription of supX is strongly reduced in the gcd and PQQ-minus mutants of Ps. fluorescens strain X. On the contrary, transcription of supX in the wild type is enhanced by glucose and transcription levels that appear to be higher during the stationary phase. Gcd, which uses PQQ as a cofactor, catalyses the oxidation of glucose to gluconic acid, which controls the activity of the GntR family of transcriptional factors. The genes in the supX putative operon have not been implicated before in the biocontrol of plant pathogens by pseudomonads. They are involved in the biosynthesis of an antimicrobial compound by Ps. fluorescens strain X and their transcription is controlled by glucose, possibly through the activity of a GntR-type transcriptional factor binding upstream of this putative operon.

Isolation and identification of antifungal peptides from Bacillus BH072, a novel bacterium isolated from honey

A bacterial strain BH072 isolated from a honey sample showed antifungal activity against mold. Based on morphological, biochemical, physiological tests, and analysis of 16S rDNA sequence, the strain was identified to be a new subspecies of Bacillus sp. It had a broad spectrum of antifungal activity against various mold, such as Aspergillus niger, Pythium, and Botrytis cinerea. Six pairs of antifungal genes primers were designed and synthesized, and ituA, hag, tasA genes were detected by PCR analysis. The remarkable antifungal activity could be associated with the co-production of these three peptides. One of them was purified by 30-40% ammonium sulfate precipitation, Sephadex G-75 gel filtration and anion exchange chromatography on D201 resin. The purified peptide was estimated to be 35.615 kDa and identified to be flagellin by micrOTOF-Q II. By using methanol extraction, another substance was isolated from fermentation liquor, and determined to be iturin with liquid chromatography-mass spectrometry (LC-MS) method. The third possible peptide encoded by tasA was not isolated in this study. The culture liquor displayed antifungal activity in a wide pH range (5.0-9.0) and at 40-100°C. The result of the present work suggested that Bacillus BH072 might be a bio-control bacterium of research value.

Effects of critical medium components on the production of antifungal lipopeptides from Bacillus amyloliquefaciens Q-426 exhibiting excellent biosurfactant properties

In this study, influence of three critical parameters nitrogen sources, initial pH and metal ions was discussed in the production of antifungal lipopeptides from Bacillus amyloliquefaciens Q-426. The results revealed that lipopeptide biosynthesis might have relations with the population density of strain Q-426 and some special amino acids. Also, the alkali-resistant strain Q-426 could grow well in the presence of Fe(2+) ions below 0.8 M l(-1) and still maintain the competitive advantage below 0.2 M l(-1). Moreover, lipopeptides exhibited significant inhibitory activities against Curvularia lunata (Walk) Boed even at the extreme conditions of temperature, pH and salinity. Finally, biosurfactant properties of lipopeptides mixture were evaluated by use with totally six different methods including bacterial adhesion to hydrocarbons assay, lipase activity, hemolytic activity, emulsification activity, oil displacement test and surface tension measurement. The research suggested that B. amyloliquefaciens Q-426 may have great potential in agricultural and environmental fields.

Biodegradation of benzene, toluene, and xylene (BTX) in liquid culture and in soil by Bacillus subtilis and Pseudomonas aeruginosa strains and a formulated bacterial consortium

PURPOSE

The major aromatic constituents of petroleum products viz. benzene, toluene, and mixture of xylenes (BTX) are responsible for environmental pollution and inflict serious public concern. Therefore, BTX biodegradation potential of individual as well as formulated bacterial consortium was evaluated. This study highlighted the role of hydrogen peroxide (H(2)O(2)), nitrate, and phosphate in stimulating the biodegradation of BTX compounds under hypoxic condition.

MATERIALS AND METHODS

The individual bacterium viz. Bacillus subtilis DM-04 and Pseudomonas aeruginosa M and NM strains and a consortium comprising of the above bacteria were inoculated to BTX-containing liquid medium and in soil. The bioremediation experiment was carried out for 120 h in BTX-containing liquid culture and for 90 days in BTX-contaminated soil. The kinetics of BTX degradation either in presence or absence of H(2)O(2), nitrate, and phosphate was analyzed using biochemical and gas chromatographic (GC) technique.

RESULTS

Bacterial consortium was found to be superior in degrading BTX either in soil or in liquid medium as compared to degradation of same compounds by individual strains of the consortium. The rate of BTX biodegradation was further enhanced when the liquid medium/soil was exogenously supplemented with 0.01 % (v/v) H(2)O(2), phosphate, and nitrate(.) The GC analysis of BTX biodegradation (90 days post-inoculation) in soil by bacterial consortium confirmed the preferential degradation of benzene compared to m-xylene and toluene.

CONCLUSIONS

It may be concluded that the bacterial consortium in the present study can degrade BTX compounds at a significantly higher rate as compared to the degradation of the same compounds by individual members of the consortium. Further, addition of H(2)O(2) in the culture medium as an additional source of oxygen, and nitrate and phosphate as an alternative electron acceptor and macronutrient, respectively, significantly enhanced the rate of BTX biodegradation under oxygen-limited condition.

The plant-associated Bacillus amyloliquefaciens strains MEP2 18 and ARP2 3 capable of producing the cyclic lipopeptides iturin or surfactin and fengycin are effective in biocontrol of sclerotinia stem rot disease

AIMS

This work was conducted to identify the antifungal compounds produced by two previously isolated Bacillus sp. strains: ARP(2) 3 and MEP(2) 18. Both strains were subjected to further analysis to determine their taxonomic position and to identify the compounds responsible for their antifungal activity as well as to evaluate the efficiency of these strains to control sclerotinia stem rot in soybean.

METHODS AND RESULTS

The antifungal compounds were isolated by acid precipitation of cell-free supernatants, purified by RP-HPLC and then tested for antagonistic activity against Sclerotinia sclerotiorum. Mass spectra from RP-HPLC eluted fractions showed the presence of surfactin C(15) , fengycins A (C(16) -C(17)) and B (C(16)) isoforms in supernatants from strain ARP(2) 3 cultures, whereas the major lipopeptide produced by strain MEP(2) 18 was iturin A C(15) . Alterations in mycelial morphology and sclerotial germination were observed in the presence of lipopeptides-containing supernatants from Bacillus strains cultures. Foliar application of Bacillus amyloliquefaciens strains on soybean plants prior to S. sclerotiorum infection resulted in significant protection against sclerotinia stem rot compared with noninoculated plants or plants inoculated with a nonlipopeptide-producing B. subtilis strain.

CONCLUSIONS

Both strains, renamed as B. amyloliquefaciens ARP(2) 3 and MEP(2) 18, were able to produce antifungal compounds belonging to the cyclic lipopeptide family. Our data suggest that the foliar application of lipopeptide-producing B. amyloliquefaciens strains could be a promising strategy for the management of sclerotinia stem rot in soybean.

SIGNIFICANCE AND IMPACT OF THE STUDY

Sclerotinia stem rot was ranked as one of the most severe soybean disease in Argentina and worldwide. The results of this study showed the potential of B. amyloliquefaciens strains ARP(2) 3 and MEP(2) 18 to control plant diseases caused by S. sclerotiorum.