Non-peptide metabolites from the genus Bacillus

Mechanism of a novel Bacillus subtilis JNF2 in suppressing Fusarium oxysporum f. sp. cucumerium and enhancing cucumber growth

Cucumber Fusarium wilt caused by Fusarium oxysporum f. sp. cucumerium (FOC), is a prevalent soil-borne disease. In this study, Bacillus subtilis JNF2, isolated from the high incidence area of cucumber Fusarium wilt in Luoyang, demonstrated significant inhibitory effects on FOC and promoted cucumber seedling growth. The biocontrol mechanism of strain JNF2 were elucidated through morphological observation, physiological and biochemical experiments, and whole genome sequence analysis. Pot experiments revealed an 81.33 ± 0.21% control efficacy against Fusarium wilt, surpassing the 64.10 ± 0.06% efficacy of hymexazol. Seedlings inoculated with JNF2 exhibited enhanced stem thickness and leaf area compared to control and hymexazol-treated plants. Physiological tests confirmed JNF2's production of indole-3-acetic acid (IAA), siderophores, and hydrolytic enzymes, such as β-1,3-glucanase, amylase, and protease, which inhibited FOC growth and promoted plant development. Genome analysis identified genes encoding antimicrobial peptides and hydrolases, as well as a novel glycocin synthetic gene cluster. These findings underscore B. subtilis JNF2's potential as a biocontrol agent for sustainable cucumber cultivation.

Secondary Metabolites of Halobacillus sp.: Antimicrobial and Antioxidant Activity, Biological Compatibility, and Gas Chromatography-Mass Spectrometry (GC-MS) Analysis

Background The rise of infectious diseases and the emergence of resistant pathogens pose significant challenges to human health. In response to this global threat, researchers are exploring novel sources of bioactive compounds for effective antimicrobial therapies. One avenue of investigation is the study of halophilic bacteria and their secondary metabolites. These bacteria thrive under extreme conditions and produce valuable bioactive metabolites, which have the potential for therapeutic applications. Methods In this study, the potent bacterial cultures obtained from the Payanur salt pan, Tamil Nadu, were analyzed for the antimicrobial activity of their metabolites. The secondary metabolites were obtained from the halophilic bacteria by culturing the bacteria in 8% NaCl. The resultant secondary metabolites produced were extracted using ethyl acetate and their antimicrobial property was studied using the well diffusion method. The minimum inhibitory concentration (MIC) of these metabolites against five clinical pathogens, namely, Staphylococcus aureus, Escherichia coli, Enterococcus faecalis, Pseudomonas aeruginosa, and Candida albicans was determined. Their antioxidant property was studied using the DPPH (2,2-diphenyl-1-picrylhydrazyl) method and biological compatibility was determined by hemolytic assay of the secondary metabolites. Results The potent halophilic bacteria isolated from salt pan bacteria were phenotypically and genotypically identified as Halobacillus sp. The secondary metabolites extracted from these bacteria yielded 110 mg of crude metabolites. The antimicrobial activity of crude metabolites shows a moderate zone of inhibition of 14 mm for P. aeruginosa, 13 mm for E. coli and C. albicans, and 11 mm for S. aureus. The minimum inhibitory concentration was 128 µg/mL for E. coli, P. aeruginosa, and C. albicans, which was found to be the best growth inhibition concentration. The DPPH scavenging activity shows a higher activity till the concentration of 64 µg/mL. The hemolytic activity of 25% is obtained at 128 µg/mL and below 64 µg/mL, there is no hemolytic activity. The gas chromatography-mass spectrometry (GC-MS) analysis of the secondary metabolites shows the presence of 17 compounds. Among them, there were four major compounds: (i) cyclo(L-prolyl-L-valine) (probability of 95.63%), (ii) pyrrolo[1,2-a]pyrazine- 1,4-dione,hexahydro-3-(2-methylpropl) (probability of 94.45%), (iii) 2,5-piperazinedione,3,6-bis(2-methylpropyl) (probability of 71.94%) and (iv) pyrrolo[1,2-a]pyrazine-1,4-dione,hexahydro-3-(phenylmethyl) (probability of 88.01%). Conclusion In conclusion, the isolated bacterium is confirmed to be Halobacillus sp. and the secondary metabolites produced by this bacterium could be the potential source for the development of novel antimicrobial and antioxidant compounds that are highly biologically compatible. Further research may help to develop novel compounds in the pharmaceutical industry.

Molecular docking, molecular dynamics simulations and binding free energy studies of interactions between Mycobacterium tuberculosis Pks13, PknG and bioactive constituents of extremophilic bacteria

Mycobacterial pathogens present a significant challenge to disease control efforts globally due to their inherent resistance to multiple antibiotics. The rise of drug-resistant strains of Mycobacterium tuberculosis has prompted an urgent need for innovative therapeutic solutions. One promising way to discover new tuberculosis drugs is by utilizing natural products from the vast biochemical space. Multidisciplinary methods can used to harness the bioactivity of these natural products. This study aimed to evaluate the antimycobacterial efficacy of functional crude extracts from bacteria isolated from gold mine tailings in South Africa. Bacterial strains were identified using 16S rRNA sequencing. The crude extracts obtained from the bacteria were tested against Mycobacterium tuberculosis H37Rv, Mycobacterium smegmatis mc2155, and Mycobacterium aurum A+. Untargeted HPLC-qTOF and molecular networking were used to identify the functional constituents present in extracts that exhibited inhibitory activity. A virtual screening workflow (VSW) was used to filter compounds that were strong binders to Mycobacterium tuberculosis Pks13 and PknG. The ligands returned from the VSW were subjected to optimization using density functional theory (DFT) at M06-2X/6-311++ (d,p) level of theory and basis set implemented in Gaussian16 Rev.C01. The optimized ligands were re-docked against Mycobacterium tuberculosis Pks13 and PknG. Molecular dynamics simulation and molecular mechanics generalized born surface area were used to evaluate the stability of the protein-ligand complexes formed by the identified hits. The hit that showed promising binding characteristics was virtually modified through multiple synthetic routes using reaction-driven enumeration. Three bacterial isolates showed significant activity against the two strains of Mycobacterium, while only two, Bacillus subtilis and Bacillus licheniformis, exhibited activity against both Mycobacterium tuberculosis H37Rv, Mycobacterium smegmatis mc2155, and Mycobacterium aurum A+. The tentatively identified compounds from the bacterial crude extracts belonged to various classes of natural compounds associated with antimicrobial activity. Two compounds, cyclo-(L-Pro-4-OH-L-Leu) and vazabitide A, showed strong binding against PknG and Pks13, with pre-MD MM-GBSA values of - 42.8 kcal/mol and - 47.6 kcal/mol, respectively. The DFT-optimized compounds exhibited the same docking scores as the ligands optimized using the OPSL-4 force field. After modifying vazabitide A, its affinity to the Pks13 binding site increased to - 85.8 kcal/mol, as revealed by the post-MD MM-GBSA analysis. This study highlights the potential of bacteria isolates from gold mine tailings as a source of new scaffolds for designing and optimizing anti-Mycobacterium agents. These agents synthesized in-silico can be further tested in-vitro to evaluate their efficacy.

Draft genome sequence of Bacillus sp. strain X and Salarachaeum sp. strain III isolated from Lake Karum, Danakil Depression, Ethiopia

Here, we report the draft genome sequences of strains of Bacillus and Salarachaeum that were isolated from hypersaline water samples collected from Lake Karum, Danakil Depression, Ethiopia. The sequences pave the way for more targeted studies into the potential biological activities and secondary metabolite synthesis of these organisms.

Isotropic Silver Nanoparticles from Cytobacillus kochii Strain SW6 Isolated from Bay of Bengal Sea Sediment Water and Their Antimicrobial, Antioxidant, and Catalytic Potential

Green synthesis of nanoparticles provides numerous advantages over physical and chemical methods because of low toxicity, high yields, cost-effectiveness, environmentally benign, and energy efficiency. Therefore, we focused on the facile and green synthesis of isotropic silver nanoparticles using the metabolic extract of Cytobacillus kochii. During synthesis, the physicochemical parameters were optimized and validated using the response surface methodology statistical tool. The presence of potent bioactive compounds that aid in the biofabrication of nanoparticles was identified in the gas chromatography-mass spectroscopy analysis and the synthesis was confirmed by surface plasmon resonance peak at 420 nm. Characterization of nanoparticles was performed by high-resolution transmission electron microscopy, Fourier transform infrared spectroscopy, dynamic light scattering, and X-ray diffraction. The synthesized nanoparticles showed potent antioxidant properties and displayed an excellent catalytic reduction potential in the degradation of hazardous dyes, such as methylene blue, phenol red, and 4-nitrophenol. Furthermore, compared to the chemically synthesized silver nanoparticles and crude extract, the biogenic silver nanoparticles exhibited a broad-spectrum antimicrobial potential. Our results demonstrate that the reported silver nanoparticles with unique characteristics might be of great promise as biomedical and catalytic agents for industrial applications.

Biological potential of Bacillus subtilis BS45 to inhibit the growth of Fusarium graminearum through oxidative damage and perturbing related protein synthesis

Fusarium root rot (FRR) caused by Fusarium graminearum poses a threat to global food security. Biological control is a promising control strategy for FRR. In this study, antagonistic bacteria were obtained using an in-vitro dual culture bioassay with F. graminearum. Molecular identification of the bacteria based on the 16S rDNA gene and whole genome revealed that the species belonged to the genus Bacillus. We evaluated the strain BS45 for its mechanism against phytopathogenic fungi and its biocontrol potential against FRR caused by F. graminearum. A methanol extract of BS45 caused swelling of the hyphal cells and the inhibition of conidial germination. The cell membrane was damaged and the macromolecular material leaked out of cells. In addition, the mycelial reactive oxygen species level increased, mitochondrial membrane potential decreased, oxidative stress-related gene expression level increased and oxygen-scavenging enzyme activity changed. In conclusion, the methanol extract of BS45 induced hyphal cell death through oxidative damage. A transcriptome analysis showed that differentially expressed genes were significantly enriched in ribosome function and various amino acid transport pathways, and the protein contents in cells were affected by the methanol extract of BS45, indicating that it interfered with mycelial protein synthesis. In terms of biocontrol capacity, the biomass of wheat seedlings treated with the bacteria increased, and the BS45 strain significantly inhibited the incidence of FRR disease in greenhouse tests. Therefore, strain BS45 and its metabolites are promising candidates for the biological control of F. graminearum and its related root rot diseases.

Unveiling the complete genome sequence of Alicyclobacillus acidoterrestris DSM 3922T, a taint-producing strain

Several species from the Alicyclobacillus genus have received much attention from the food and beverages industries. Their presence has been co-related with spoilage events of acidic food matrices, namely fruit juices and other fruit-based products, the majority attributed to Alicyclobacillus acidoterrestris. In this work, a combination of short and long reads enabled the assembly of the complete genome of A. acidoterrestris DSM 3922T, perfecting the draft genome already available (AURB00000000), and revealing the presence of one chromosome (4,222,202 bp; GC content 52.3%) as well as one plasmid (124,737 bp; GC content 46.6%). From the 4,288 genes identified, 4,004 sequences were attributed to coding sequences with proteins, with more than 80% being functionally annotated. This allowed the identification of metabolic pathways and networks and the interpretation of high-level functions with significant reliability. Furthermore, the additional genes of interest related to spore germination, off-flavor production, namely the vdc cluster, and CRISPR arrays, were identified. More importantly, this is the first complete and closed genome sequence for a taint-producing Alicyclobacillus species and thus represents a valuable reference for further comparative and functional genomic studies.

New Polyfunctional Biorationals Use to Achieve Competitive Yield of Organic Potatoes in the North-West Russian Ecosystem

To increase the organic potato yield, it is necessary to provide the crop with sufficient nutrients and effective means of biocontrol the diseases. The research goal was to characterize the biorationals’ efficacy to achieve competitive organic potatoes’ yield under various weather conditions. A 4-year trial was carried out in the Leningrad region using Udacha variety potatoes. The tests used liquid forms of new polyfunctional biologicals Kartofin based on highly active Bacillus subtilis I-5-12/23 and organic fertilizer BIAGUM obtained from poultry manure by aerobic fermentation in a closed biofermenter. Significant stimulation in plant growth and development to the flowering phase regardless of the hydrothermal conditions of the growing season was noted. The stimulating effect was determined by the combined use of biorationals pro rata to BIAGUM dose. Kartofin biologicals and BIAGUM almost doubled the potato tubers’ yield compared to the control, regardless of the growing season conditions. At the flowering phase, the biological efficacy in potato fungal diseases incidence and development was near 90% under optimal and 50–75% under drought hydrothermal conditions. At the end of vegetation, the efficiency in fungal diseases incidence and development made up 45–65% under optimal and 45–70% under dry conditions. BIAGUM effectiveness in reducing disease development reached 45–50% regardless of growing season conditions.

Using Plate-Wash PCR and High-Throughput Sequencing to Measure Cultivated Diversity for Natural Product Discovery Efforts

Molecular techniques continue to reveal a growing disparity between the immense diversity of microbial life and the small proportion that is in pure culture. The disparity, originally dubbed “the great plate count anomaly” by Staley and Konopka, has become even more vexing given our increased understanding of the importance of microbiomes to a host and the role of microorganisms in the vital biogeochemical functions of our biosphere. Searching for novel antimicrobial drug targets often focuses on screening a broad diversity of microorganisms. If diverse microorganisms are to be screened, they need to be cultivated. Recent innovative research has used molecular techniques to assess the efficacy of cultivation efforts, providing invaluable feedback to cultivation strategies for isolating targeted and/or novel microorganisms. Here, we aimed to determine the efficiency of cultivating representative microorganisms from a non-human, mammalian microbiome, identify those microorganisms, and determine the bioactivity of isolates. Sequence-based data indicated that around 57% of the ASVs detected in the original inoculum were cultivated in our experiments, but nearly 53% of the total ASVs that were present in our cultivation experiments were not detected in the original inoculum. In light of our controls, our data suggests that when molecular tools were used to characterize our cultivation efforts, they provided a more complete and more complex, understanding of which organisms were present compared to what was eventually detected during cultivation. Lastly, about 3% of the isolates collected from our cultivation experiments showed inhibitory bioactivity against an already multidrug-resistant pathogen panel, further highlighting the importance of informing and directing future cultivation efforts with molecular tools.

Biological and chemical characterization of antimicrobial activity in Arthrobacter spp. isolated from disease-suppressive compost

Antagonistic bacteria can act as biocontrol agents against various phytopathogens. Recently, Arthrobacter spp. demonstrated antifungal activity, but were not further characterized. In this study, the antimicrobial activity of Arthrobacter humicola strains M9-1A, M9-2, and M9-8, and Arthrobacter psychrophenolicus strain M9-17 were evaluated against nine plant pathogens in vitro, and their cell-free filtrates were additionally assessed for inhibition of Alternaria alternata and suppression of black mold disease on tomato fruit. Results indicated that A. humicola M9-1A and A. psychrophenolicus M9-17 were the most inhibitory, reducing growth of seven of the pathogens studied. Cell-free filtrates of A. psychrophenolicus M9-17 reduced the growth of most pathogens. All cell-free bacterial filtrates, except those from A. humicola M9-2, suppressed black mold on tomato fruit. Disk diffusion assays with ethyl acetate soluble culture filtrate extracts of all bacteria reduced the mycelial growth of A. alternata. Clear inhibition zones were observed for A. psychrophenolicus M9-17 extracts using drop bioassays. The antifungal compound N-acetyltryptamine was purified and characterized from the A. psychrophenolicus M9-17 cell-free ethyl acetate soluble extract. This study suggests that antibiosis may play a key role in the antimicrobial activity of Arthrobacter spp.

Technologically relevant Bacillus species and microbial safety of West African traditional alkaline fermented seed condiments

Fermented food condiments serve as a major source of nutrients to many homes in West Africa, especially among the rural poor who use these condiments as a cheap source of protein substitute for milk and other animal protein sources. Traditional fermented West African condiments are produced by spontaneous fermentation of legumes and protein-rich seeds of both cultivated and wild plant species. These fermented condiments are culturally accepted and widely produced in the West African sub-region, and rely on indigenous microbiota responsible for taste, texture, aroma development and the overall unique product characteristics. Detailed understanding of fermentation microbiota and their unique technological and functional properties are fundamental in developing products with enhanced quality and safety, as well as development of specific locally adapted starter cultures. Technologically relevant Bacillus spp., mainly Bacillus subtilis, are the predominant fermentative bacteria responsible for the natural fermentation of condiments across West Africa. Other species of Bacillus including B. amyloliquefaciens, B. licheniformis, B. pumilus, B. megaterium, B. sphaericus, B. cereus, B. badius and B. fusiformis are also frequently involved in the fermentation process. These bacterial species are responsible for flavor development, bio-conversion of complex food molecules, and production of antimicrobial compounds that impact shelf-life and safety, and in some instances, may confer host-beneficial health effects beyond basic nutrition. First, this review provides currently available information on the technologically relevant Bacillus species isolated from fermented food condiments in nine (9) West African countries. In addition, perspectives on harnessing the potentials of the technologically beneficial bacterial strains in fermented condiments in West Africa for enhanced food safety, quality and overall food security is presented.

Inducible Antibacterial Activity in the Bacillales by Triphenyl Tetrazolium Chloride

The world is in the midst of an antimicrobial resistance crisis, driving a need to discover novel antibiotic substances. Using chemical cues as inducers to unveil a microorganism's full metabolic potential is considered a successful strategy. To this end, we investigated an inducible antagonistic behavior in multiple isolates of the order Bacillales, where large inhibition zones were produced against Ralstonia solanacearum only when grown in the presence of the indicator triphenyl tetrazolium chloride (TTC). This bioactivity was produced in a TTC-dose dependent manner. Escherichia coli and Staphylococcus sp. isolates were also inhibited by Bacillus sp. strains in TTC presence, to a lesser extent. Knockout mutants and transcriptomic analysis of B. subtilis NCIB 3610 cells revealed that genes from the L-histidine biosynthetic pathway, the purine, pyrimidine de novo synthesis and salvage and interconversion routes, were significantly upregulated. Chemical space studied through metabolomic analysis, showed increased presence of nitrogenous compounds in extracts from induced bacteria. The metabolites orotic acid and L-phenylalaninamide were tested against R. solanacearum, E. coli, Staphylococcus sp. and B. subtilis, and exhibited activity against pathogens only in the presence of TTC, suggesting a biotransformation of nitrogenous compounds in Bacillus sp. cells as the plausible cause of the inducible antagonistic behavior.

Antibiofilm activity of symbiotic Bacillus species associated with marine gastropods

Purpose

Generally, symbiotic marine bacteria are renowned for the synthesis of compounds with bioactive properties, and this has been documented in many previous studies. Therefore, the present study was aimed to isolate novel bacterial symbionts of gastropods that have the ability to synthesize bioactive compounds. These bioactive compounds could be used effectively as antibiofilm agents in order to overcome the problems associated with biofilm.

Methods

The bacteria associated with the surface of marine gastropods were isolated and characterized. Following this, the bacterial metabolites were extracted and their antibiofilm effect was evaluated on biofilm-forming bacteria on artificial substrates. Moreover, the biofilm-forming bacterium Alteromonas sp. was treated with the extracts of symbiotic bacteria in order to evaluate the influence of extracts over the synthesis of extracellular polymeric substance (EPS). Besides, the biologically active chemical constituents of the extracts were separated using thin-layer chromatography and subjected to gas chromatography and mass spectrometry (GC-MS) analysis for characterization.

Results

Three bacterial strains belonging to the species Bacillus firmus, Bacillus cereus and Bacillus subtilis were identified from the bacterial community associated with the gastropods. The antibiofilm assays revealed that the extract of three symbiotic bacteria significantly (p < 0.05) reduced the biofilm formation by the marine bacterium Alteromonas sp. on artificial materials. Also, the EPS synthesis by Alteromonas sp. was significantly inhibited due to symbiotic bacterial extract treatment. The chemical composition of the bioactive fraction isolated from the symbiotic bacteria extract revealed that most of the detected compounds were belonging to aromatic acid, fatty acid and carboxylic acid.

Conclusion

The results of this study clearly revealed that the bacteria belonging to the above listed Bacillus species can be considered as a promising source of natural antibiofilm agents.

Diversity of sugarcane root-associated endophytic Bacillus and their activities in enhancing plant growth

AIMS

Plant tissues are the reservoirs of beneficial and harmful microbes that regulates plant growth. In the present study, we investigated the diversity, function and colonization of sugarcane roots associated with Bacillus spp.

METHODS AND RESULTS

A total of 20 Bacillus strains were isolated and identified by 16S rRNA gene sequencing, and their genetic diversity was examined by BOX, ERIC, REP, (GTG)₅ PCR techniques. Among all Bacillus isolates, 65% showed indole acetic acid-like compounds production, 50% solubilized phosphorus and 25% of the isolates were able to secrete siderophore. Moreover, all 20 Bacillus isolates showed antifungal activity against eight fungal pathogens and 11 of them (55%) antagonized tomato grey mold. Based on the plant growth-promoting traits and antifungal potential, isolate Y8 was selected for root and plant tissue colonization assays and a greenhouse-level sugarcane growth promotion study. Fluorescence microscopy results confirmed that isolate Y8 has a strong ability to colonize in the sugarcane root and leaves, and the root surface association of Y8 was confirmed by scanning electron microscopy. Furthermore, greenhouse experimental results demonstrated that Y8 has a significant effect on enhancing sugarcane biomass and root length.

CONCLUSIONS

Endophytic Bacillus strains have growth-promoting properties and anti-fungal ability that can enhance plant fitness in an eco-friendly manner.

SIGNIFICANCE AND IMPACT OF THE STUDY

Endophytic Bacillus strains would be a potential alternative to chemical fertilizer as well as a biocontrol agent in the future.

A genomic island in a plant beneficial rhizobacterium encodes novel antimicrobial fatty acids and a self-protection shield to enhance its competition

Rhizobacteria devote a relatively large percentage of their genomes to encode bioactive natural products that are important for competition in the rhizosphere. In this study, a plant beneficial rhizobacterium Bacillus velezensis SQR9 was discovered to produce novel antibacterial fatty acids, Bacillunoic acids, which are encoded on a genomic island (GI). This GI contains a hybrid type I fatty acid synthase (FAS)-polyketide synthase (PKS) system and an ABC transporter. The FAS was predicted to synthesize a primer that was transferred to the PKS to synthesize Bacillunoic acids. The synthesized Bacillunoic acids inhibit the growth of diverse bacteria, with the strongest activity against closely related Bacillus strains, the ABC transporter exported the toxic Bacillunoic acids upon their induction for protecting the producing strain. The inhibition of other Bacillus strains by Bacillunoic acids extended the antimicrobial spectrum of SQR9 and enhanced its competition with closely related root-associated bacteria. So, through the obtaining of this GI by horizontal gene transfer, strain SQR9 not only acquired a competitive weapon but also acquired a self-protecting shield, which increased its competition with other rhizobacteria.

Phylogenetic Analysis and Screening of Antimicrobial and Antiproliferative Activities of Culturable Bacteria Associated with the Ascidian Styela clava from the Yellow Sea, China

Over 1,000 compounds, including ecteinascidin-743 and didemnin B, have been isolated from ascidians, with most having bioactive properties such as antimicrobial, antitumor, and enzyme-inhibiting activities. In recent years, direct and indirect evidence has shown that some bioactive compounds isolated from ascidians are not produced by ascidians themselves but by their symbiotic microorganisms. Isolated culturable bacteria associated with ascidians and investigating their potential bioactivity are an important approach for discovering novel compounds. In this study, a total of 269 bacteria were isolated from the ascidian Styela clava collected from the coast of Weihai in the north of the Yellow Sea, China. Phylogenetic relationships among 183 isolates were determined using their 16S rRNA gene sequences. Isolates were tested for antimicrobial activity against seven indicator strains, and an antiproliferative activity assay was performed to test for inhibition of human hepatocellular carcinoma Bel 7402 and human cervical carcinoma HeLa cell proliferation. Our results showed that the isolates belonged to 26 genera from 18 families in four phyla (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes). Bacillus and Streptomyces were the most dominant genera; 146 strains had potent antimicrobial activities and inhibited at least one of the indicator strains. Crude extracts from 29 strains showed antiproliferative activity against Bel 7402 cells with IC₅₀ values below 500 μg·mL^-1, and 53 strains showed antiproliferative activity against HeLa cells, with IC₅₀ values less than 500 μg·mL^-1. Our results suggest that culturable bacteria associated with the ascidian Styela clava may be a promising source of novel bioactive compounds.

Oncolytic Bacteria and their potential role in bacterium-mediated tumour therapy: a conceptual analysis

As the human microbiota has been confirmed to be of great significance in maintaining health, the dominant bacteria in them have been applied as probiotics to treat various diseases. After the detection of bacteria in tumours, which had previously been considered a sterile region, these bacteria have been isolated and genetically modified for use in tumour therapy. In this review, we sum up the main types of bacteria used in tumour therapy and reveal the mechanisms of both wild type and engineered bacteria in eliminating tumour cells, providing potential possibilities for newly detected, genetically modified, tumour-associated bacteria in anti-tumour therapy.

Bacilohydrin A, a New Cytotoxic Cyclic Lipopeptide of Surfactins Class Produced by Bacillus sp. SY27F from the Indian Ocean Hydrothermal Vent

Bacilohydrin A, a new cyclic lipopeptide composed of seven mixed D/L-amino acids (L-Ile1—L-Leu2—D-Asp3—L-Val4—L-Leu5—L-Leu6—L-Gln7) and a ( R)-3-hydroxy-12-methyltetradecanoic acid (HMT) residue, was isolated from the crude culture extract of Bacillus sp. SY27F, which was obtained from the Indian Ocean hydrothermal vent. Its planar structure was elucidated by spectroscopic analyses, including 1D and 2D NMR spectroscopy, mass spectrometry (MS), and secondary ion mass spectrometry (MS/MS), whereas its absolute configuration was determined by modified Marfey's analysis. Bacilohydrin A displayed significant cytotoxicities against DU-145, MCF-7 and HepG2 cancer cell lines with IC50 values of 50.3-175.1 nM. Additionally, this is the first time to determine the absolute configuration of a D-aspartic acid residue in surfactin class.

Effects of exogenous microbial inoculum on the structure and dynamics of bacterial communities in swine carcass composting

Composting is a widely accepted method for the disposal of deceased livestock. It is a biological self-heating process during which animal carcasses are converted to fertilizer products. Additional inoculants can facilitate the composting progress. This study investigated how the addition of microbial inoculants could improve the composting effectiveness and could change the structure and dynamics of bacterial communities in the carcass composting process. Four strains of Bacillus were inoculated into the swine carcass composting piles. The groups with the additional inoculants showed a higher temperature in the thermophilic phase and higher germination indices in the composted products. The sequencing results showed that the dominant phyla were Proteobacteria, Firmicutes, and Actinobacteria, and the dominant classified genera were Brevibacterium and Bacillus. Canonical correlation analysis showed that temperature and moisture exerted a stronger influence on the bacterial community diversity. The interaction network of dominant genera and the abundance variation of the bacterial community demonstrated that the inoculated bacterial agent changed the structure of bacterial communities and enriched the diversity of the species due to antagonism and symbiosis among the dominant bacterial communities.

Rice Phyllosphere Bacillus Species and Their Secreted Metabolites Suppress Aspergillus flavus Growth and Aflatoxin Production In Vitro and In Maize Seeds

The emergence of super-toxigenic strains by recombination is a risk from an intensive use of intraspecific aflatoxin (AF) biocontrol agents (BCAs). Periodical alternation with interspecific-BCAs will be safer since they preclude recombination. We are developing an AF-biocontrol system using rice-associated Bacilli reported previously (RABs). More than 50% of RABs inhibited the growth of multiple A. flavus strains, with RAB4R being the most inhibitory and RAB1 among the least. The fungistatic activity of RAB4R is associated with the lysis of A. flavus hyphal tips. In field trails with the top five fungistatic RABs, RAB4R consistently inhibited AF contamination of maize by Tox4, a highly toxigenic A. flavus strain from Louisiana corn fields. RAB1 did not suppress A. flavus growth, but strongly inhibited AF production. Total and HPLC-fractionated lipopeptides (LPs) isolated from culture filtrates of RAB1 and RAB4R also inhibited AF accumulation. LPs were stable in vitro with little loss of activity even after autoclaving, indicating their potential field efficacy as a tank-mix application. A. flavus colonization and AF were suppressed in RAB1- or RAB4R-coated maize seeds. Since RAB4R provided both fungistatic and strong anti-mycotoxigenic activities in the laboratory and field, it can be a potent alternative to atoxigenic A. flavus strains. On the other hand, RAB1 may serve as an environmentally safe helper BCA with atoxigenic A. flavus strains, due its lack of strong fungistatic and hemolytic activities.

Fungal Competitors Affect Production of Antimicrobial Lipopeptides in Bacillus subtilis Strain B9-5

Bacillus subtilis has shown success in antagonizing plant pathogens where strains of the bacterium produce antimicrobial cyclic lipopeptides (CLPs) in response to microbial competitors in their ecological niche. To gain insight into the inhibitory role of these CLPs, B. subtilis strain B9-5 was co-cultured with three pathogenic fungi. Inhibition of mycelial growth and spore germination was assessed and CLPs produced by B. subtilis B9-5 were quantified over the entire period of microbial interaction. B. subtilis B9-5 significantly inhibited mycelial growth and spore germination of Fusarium sambucinum and Verticillium dahliae, but not Rhizopus stolonifer. LC-MS analysis revealed that B. subtilis differentially produced fengycin and surfactin homologs depending on the competitor. CLP quantification suggested that the presence of Verticillium dahliae, a fungus highly sensitive to the compounds, caused an increase followed by a decrease in CLP production by the bacterium. In co-cultures with Fusarium sambucinum, a moderately sensitive fungus, CLP production increased more gradually, possibly because of its slower rate of spore germination. With co-cultures of the tolerant fungus Rhizopus stolonifer, B. subtilis produced high amounts of CLPs (per bacterial cell) for the duration of the interaction. Variations in CLP production could be explained, in part, by the pathogens' overall sensitivities to the bacterial lipopeptides and/or the relative growth rates between the plant pathogen and B. subtilis. CLP production varied substantially temporally depending on the targeted fungus, which provides valuable insight concerning the effectiveness of B. subtilis B9-5 protecting its ecological niche against the ingress of these pathogens.

Bacilotetrins A and B, Anti-Staphylococcal Cyclic-Lipotetrapeptides from a Marine-Derived Bacillus subtilis

LC-MS and NMR spectroscopy guided metabolic profiling and dereplication of a crude extract obtained from the fermentation of a marine-derived bacterium, Bacillus subtilis, followed by chromatographic isolation yielded two new cyclic-lipotetrapeptides, bacilotetrins A (1) and B (2). Based on extensive 1D and 2D NMR and high-resolution ESIMS data analysis, the structures of 1 and 2 were elucidated, revealing the unique structures of these lipopeptides consisting of three leucines and a glutamic acid residue cyclized with a lipophilic 3-hydroxy fatty acid. The absolute stereochemistries at selected stereocenters in 1 and 2 were assigned by chemical derivatization and comparison to literature data. Compounds 1 and 2 exhibited anti-MRSA activity with MIC values of 8 to 32 μg/mL. However, these compounds showed no cytotoxicity when tested against prostate and liver cancer cell lines using the standard SRB assay.

The Diversity, Growth Promoting Abilities and Anti-microbial Activities of Bacteria Isolated from the Fruiting Body of Agaricus bisporus

Agaricus bisporus plays an important role in ecological processes and is one of the most widely cultivated mushrooms worldwide. Mushroom growth-promoting bacteria have been isolated from casing soil and compost, but microorganisms in the fruiting body have received only a little attention. To get an overview of phylogenetic diversity of microorganisms in the fruiting body of A. bisporus, as well as to screen antimicrobial and mushroom growth-promoting strains, and eventually intensify mushroom production, we isolated and characterized microorganisms from the fruiting body of A. bisporus. In total, 55 bacterial strains were isolated, among which nine isolates represented Actinomycetes. All the isolates were analyzed by 16S rRNA gene RFLP and sixteen representative strains by 16S rRNA gene sequencing. According to the phylogenetic analysis, eleven isolates represented the Gram positive Bacillus, Lysinibacillus, Paenibacillus, Pandorea and Streptomyces genera, and five isolates belonged to the Gram negative Alcaligenes and Pseudomonas genera. The bacteria isolated from the fruiting body of A. bisporus had broad-spectrum antimicrobial activities and potential mushroom growth-promoting abilities.

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.

Diversity Analysis and Bioresource Characterization of Halophilic Bacteria Isolated from a South African Saltpan

Though intensive research has been channeled towards the biotechnological applications of halophiles and other extremophilic microbes, these studies have not been, by any means, exhaustive. Saline environments still offer a vast diversity of microbes with potential to produce an array of natural products which can only be unlocked by concerted research efforts. In this study, a combination of culture and molecular approaches were employed to characterize halophilic bacteria from saltpan water samples and profile their potential biotechnological applications. Physicochemical analysis of the water samples showed that pH was alkaline (pH 8.8), with a salinity of 12.8%. 16S rRNA gene targeted amplicon analysis produced 10 bacterial phyla constituting of Bacteroidetes (30.57%), Proteobacteria (15.27%), Actinobacteria (9.05%), Planctomycetes (5.52%) and Cyanobacteria (3.18%). Eighteen strains were identified using sequencing analysis of the culturable bacterial strains. From these, the strains SP7 and SP9 were positive for cellulase production while the strains SP4, SP8 and SP22 were positive for lipase production. Quantitative enzyme assays showed moderate extracellular cellulase activity (1.95 U/mL) and lipase activity (3.71 U/mL) by the isolate SP9 and SP4 respectively. Further, of the six isolates, the isolate SP9 exhibited exploitable potential in the bioremediation of hydrocarbon pollution as demonstrated by its fairly high activity against benzanthracene (70% DCPIP reduction). Elucidation of the isolates secondary metabolites showed the production of the molecules 2,3-butanediol, hexahydro-3-(2-methylpropyl)pyrrole[1,2a]pyrazine-1,4-dione, aziridine, dimethylamine and ethyl acetate (GC-MS) and oxypurinol and 5-hydroxydecanoic acid (LC-MS), particularly by the isolate Salinivibrio sp. SP9. Overall, the study showed that the isolated halophiles can produce secondary metabolites with potential industrial and pharmaceutical application.

Physiological and molecular characterization of compost bacteria antagonistic to soil-borne plant pathogens

Disease suppressive composts have the potential to mitigate the risks associated with chemical pesticides. One of the main characteristics responsible for the suppressive nature of composts is their microbiological populations. To gain insight into the determinants responsible for their suppressive effects, we assayed composts to (i) isolate and identify beneficial antagonistic bacteria, (ii) quantify their antifungal and anti-oomycetal activities, (iii) extract inhibitory compounds produced by the bacteria, and (iv) identify antimicrobial lipopeptides produced by these bacteria. The antagonistic bacteria belonged to the genera Arthrobacter, Pseudomonas, Bacillus, Brevibacillus, Paenibacillus, and Rummeliibacillus and had the ability to antagonise the growth of Fusarium sambucinum, Verticillium dahliae, and (or) Pythium sulcatum. These bacteria produced antimicrobial compounds that affected the mycelial growth and (or) conidial germination of the pathogens. Mass spectrometry analyses showed the presence of various antimicrobial lipopeptides in Bacillus and Bacillus-related spp. extracts, demonstrating that they are responsible, at least in part, for the antagonistic activity of the bacteria. Results from this work provide greater insight into some of the biological, biochemical, and physiological determinants of suppressiveness in composts involved in the control of plant pathogens.

Characterization and mechanism of anti-Aeromonas salmonicida activity of a marine probiotic strain, Bacillus velezensis V4

The bacterium Aeromonas salmonicida is the causative agent of furunculosis, a systemic, ubiquitous disease of fish in the salmon family, characterized by high mortality and morbidity. Probiotics are a promising approach for prevention of furunculosis in aquaculture. A bacterial strain with anti-A. salmonicida properties, Bacillus velezensis V4, was isolated and the mechanisms underlying these properties were investigated. Anti-A. salmonicida compounds present in cell-free supernatant of V4 were purified and structurally identified as members of the iturin, macrolactin, and difficidin groups. The compounds contributed jointly to inhibition of A. salmonicida, and the diversity of the compounds was related to the versatility of their mode of action. Addition of the compounds to A. salmonicida cell suspensions reduced cell density. Analyses by confocal microscopy and scanning electron microscopy revealed cell membrane disruption, deletion of cellular content, and cell lysis of A. salmonicida. The V4 genome was sequenced, and gene clusters involved in synthesis of anti-Aeromonas compounds were detected and identified. A possible probiotic effect on growth performance of Oncorhynchus mykiss (rainbow trout) was investigated by addition of 0, 1, and 3 % (v/w) V4. Relative to control, mortality was reduced 27.25 % in the 1 % addition group and 81.86 % in the 3 % addition group. Feed coefficient ratio was reduced 19.49 % and weight gain ratio was increased 71.22 % in the 1 % addition group. Our findings demonstrate that V4 is an effective probiotic strain in O. mykiss and has clear potential for both control of furunculosis and growth promotion of aquaculture animals.

Marine Enzymes: Production and Applications for Human Health

Marine microbial enzymes have wide applications in bioindustries. Selection of microorganisms for enzyme production at the industrial level requires good yield and high production rate. A number of enzymes such as amylase, caseinase, lipase, gelatinase, and DNases have been discovered from microbes isolated from extreme marine environments. Such enzymes are thermostable, tolerant to a varied range of pH and other harsh conditions required in industrial applications. Novelty in their structure and characteristics has shown promising scope to the researchers in academia and industry. In this chapter, we present a bird's eye view on recent research works in the field of enzyme production from marine origin as well as their potential biological applications relevant to human health.

Engineering microbial hosts for production of bacterial natural products

Covering up to end 2015Microbial fermentation provides an attractive alternative to chemical synthesis for the production of structurally complex natural products. In most cases, however, production titers are low and need to be improved for compound characterization and/or commercial production. Owing to advances in functional genomics and genetic engineering technologies, microbial hosts can be engineered to overproduce a desired natural product, greatly accelerating the traditionally time-consuming strain improvement process. This review covers recent developments and challenges in the engineering of native and heterologous microbial hosts for the production of bacterial natural products, focusing on the genetic tools and strategies for strain improvement. Special emphasis is placed on bioactive secondary metabolites from actinomycetes. The considerations for the choice of host systems will also be discussed in this review.

Bioactive natural products from novel microbial sources

Despite the importance of microbial natural products for human health, only a few bacterial genera have been mined for the new natural products needed to overcome the urgent threat of antibiotic resistance. This is surprising, given that genome sequencing projects have revealed that the capability to produce natural products is not a rare feature among bacteria. Even the bacteria occurring in the human microbiome produce potent antibiotics, and thus potentially are an untapped resource for novel compounds, potentially with new activities. This review highlights examples of bacteria that should be considered new sources of natural products, including anaerobes, pathogens, and symbionts of humans, insects, and nematodes. Exploitation of these producer strains, combined with advances in modern natural product research methodology, has the potential to open the way for a new golden age of microbial therapeutics.

Isolation of hydroquinone (benzene-1,4-diol) metabolite from halotolerant Bacillus methylotrophicus MHC10 and its inhibitory activity towards bacterial pathogens

A halotolerant bacterial isolate-MHC10 with broad spectrum antibacterial activity against clinical pathogens was isolated from saltpans located in Tuticorin and Chennai (India). 16S rRNA gene analysis of MHC10 revealed close similarity to that of Bacillus methylotrophicus. The culture conditions of B. methylotrophicus MHC10 strain were optimized for antibacterial production using different carbon and nitrogen sources, as well as varying temperature, pH, sodium chloride (NaCl) concentrations and incubation periods. The maximum antibacterial activity of B. methylotrophicus MHC10 was attained when ZMB was optimized with 1 % (w/v) glucose, 0.1 % (w/v) soybean meal which corresponded to a C/N ratio of 38.83, temperature at 37 °C, pH 7.0 and 8 % NaCl. The activity remained stable between 72 and 96 h and then drastically decreased after 96 h. Solvent extraction followed by chromatographic purification steps led to the isolation of hydroquinone (benzene-1,4-diol). The structure of the purified compound was elucidated based on FTIR, (1)H NMR, and (13)C NMR spectroscopy. The compound exhibited efficient antibacterial activity against both Gram-positive and Gram-negative bacterial pathogens. The minimum inhibitory concentration (MIC) for Gram-positive pathogens ranged from 15.625 to 62.5 µg/mL(-1), while it was between 7.81 and 250 µg/mL(-1) for Gram-negative bacterial pathogens. This is the first report of hydroquinone produced by halotolerant B. methylotrophicus exhibiting promising antibacterial activity.

Bacillusin A, an Antibacterial Macrodiolide from Bacillus amyloliquefaciens AP183

Bioassay-guided fractionation of the organic extracts of a Bacillus amyloliquefaciens strain (AP183) led to the discovery of a new macrocyclic polyene antibiotic, bacillusin A (1). Its structure was assigned by interpretation of NMR and MS spectroscopic data as a novel macrodiolide composed of dimeric 4-hydroxy-2-methoxy-6-alkenylbenzoic acid lactones with conjugated pentaene-hexahydroxy polyketide chains. Compound 1 showed potent antibacterial activities against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium with minimum inhibitory concentrations in a range of 0.6 to 1.2 μg/mL. The biosynthetic significance of this unique class of antibiotic compounds is briefly discussed.

Directed natural product biosynthesis gene cluster capture and expression in the model bacterium Bacillus subtilis

Bacilli are ubiquitous low G+C environmental Gram-positive bacteria that produce a wide assortment of specialized small molecules. Although their natural product biosynthetic potential is high, robust molecular tools to support the heterologous expression of large biosynthetic gene clusters in Bacillus hosts are rare. Herein we adapt transformation-associated recombination (TAR) in yeast to design a single genomic capture and expression vector for antibiotic production in Bacillus subtilis. After validating this direct cloning “plug-and-play” approach with surfactin, we genetically interrogated amicoumacin biosynthetic gene cluster from the marine isolate Bacillus subtilis 1779. Its heterologous expression allowed us to explore an unusual maturation process involving the N-acyl-asparagine pro-drug intermediates preamicoumacins, which are hydrolyzed by the asparagine-specific peptidase into the active component amicoumacin A. This work represents the first direct cloning based heterologous expression of natural products in the model organism B. subtilis and paves the way to the development of future genome mining efforts in this genus.

Lipopeptides as main ingredients for inhibition of fungal phytopathogens by Bacillus subtilis/amyloliquefaciens

Some isolates of the Bacillus subtilis/amyloliquefaciens species are known for their plant protective activity against fungal phytopathogens. It is notably due to their genetic potential to form an impressive array of antibiotics including non-ribosomal lipopeptides (LPs). In the work presented here, we wanted to gain further insights into the relative role of these LPs in the global antifungal activity of B. subtilis/amyloliquefaciens. To that end, a comparative study was conducted involving multiple strains that were tested against four different phytopathogens. We combined various approaches to further exemplify that secretion of those LPs is a crucial trait in direct pathogen ward off and this can actually be generalized to all members of these species. Our data illustrate that for each LP family, the fungitoxic activity varies in function of the target species and that the production of iturins and fengycins is modulated by the presence of pathogens. Our data on the relative involvement of these LPs in the biocontrol activity and modulation of their production are discussed in the context of natural conditions in the rhizosphere.

Cellular Lipid Composition Affects Sensitivity of Plant Pathogens to Fengycin, an Antifungal Compound Produced by Bacillus subtilis Strain CU12

Fengycin is an antimicrobial cyclic lipopeptide produced by various Bacillus subtilis strains, including strain CU12. Direct effects of fengycin include membrane pore formation and efflux of cellular contents leading to cell death in sensitive microorganisms. In this study, four plant pathogens were studied in order to elucidate the role of membrane lipids in their relative sensitivity to fengycin. Inhibition of mycelial growth in these pathogens varied considerably. Analysis of membrane lipids in these microorganisms indicated that sensitivity correlated with low ergosterol content and shorter phospholipid fatty acyl chains. Sensitivity to fengycin also correlated with a lower anionic/zwitterionic phospholipid ratio. Our data suggest that decreased fluidity buffering capacity, as a result of low ergosterol content, and higher intrinsic fluidity afforded by short fatty acyl chain length may increase the sensitivity of microbial membranes to fengycin. Our results also suggest that lower content in anionic phospholipids may increase fengycin insertion into the membrane through reduced electrostatic repulsion with the negatively charged fengycin. The intrinsic membrane lipid composition may contribute, in part, to the observed level of antimicrobial activity of fengycin in various plant pathogens.

Biocontrol of Aspergillus species on peanut kernels by antifungal diketopiperazine producing Bacillus cereus associated with entomopathogenic nematode

The rhabditid entomopathogenic nematode associated Bacillus cereus and the antifungal compounds produced by this bacterium were evaluated for their activity in reducing postharvest decay of peanut kernels caused by Aspergillus species in in vitro and in vivo tests. The results showed that B. cereus had a significant effect on biocontrol effectiveness in in vitro and in vivo conditions. The antifungal compounds produced by the B. cereus were purified using silica gel column chromatography and their structure was elucidated using extensive spectral analyses. The compounds were identified as diketopiperazines (DKPs) [cyclo-(L-Pro-Gly), cyclo(L-Tyr-L-Tyr), cyclo-(L-Phe-Gly) and cyclo(4-hydroxy-L-Pro-L-Trp)]. The antifungal activities of diketopiperazines were studied against five Aspergillus species and best MIC of 2 µg/ml was recorded against A. flavus by cyclo(4-hydroxy-L-Pro-L-Trp). To investigate the potential application of cyclo(4-hydroxy-L-Pro-L-Trp) to eliminate fungal spoilage in food and feed, peanut kernels was used as a food model system. White mycelia and dark/pale green spores of Aspergillus species were observed in the control peanut kernels after 2 days incubation. However the fungal growth was not observed in peanut kernels treated with cyclo(4-hydroxy-L-Pro-L-Trp). The cyclo(4-hydroxy-L-Pro-L-Trp) was nontoxic to two normal cell lines [fore skin (FS) normal fibroblast and African green monkey kidney (VERO)] up to 200 µg/ml in MTT assay. Thus the cyclo(4-hydroxy-L-Pro-L-Trp) identified in this study may be a promising alternative to chemical preservatives as a potential biopreservative agent which prevent fungal growth in food and feed. To the best of our knowledge, this is the first report demonstrating that the entomopathogenic nematode associated B. cereus and cyclo(4-hydroxy-L-Pro-L-Trp) could be used as a biocontrol agents against postharvest fungal disease caused by Aspergillus species.

Interaction of antimicrobial cyclic lipopeptides from Bacillus subtilis influences their effect on spore germination and membrane permeability in fungal plant pathogens

Bacillus subtilis cyclic lipopeptides are known to have various antimicrobial effects including different types of interactions with the cell membranes of plant pathogenic fungi. The various spectra of activities of the three main lipopeptide families (fengycins, iturins, and surfactins) seem to be linked to their respective mechanisms of action on the fungal biomembrane. Few studies have shown the combined effect of more than one family of lipopeptides on fungal plant pathogens. In an effort to understand the effect of producing multiple lipopeptide families, sensitivity and membrane permeability of spores from four fungal plant pathogens (Alternaria solani, Fusarium sambucinum, Rhizopus stolonifer, and Verticillium dahliae) were assayed in response to lipopeptides, both individually and as combined treatments. Results showed that inhibition of spores was highly variable depending on the tested fungus-lipopeptide treatment. Results also showed that inhibition of the spores was closely associated with SYTOX stain absorption suggesting effects of efficient treatments on membrane permeability. Combined lipopeptide treatments revealed additive, synergistic or sometimes mutual inhibition of beneficial effects.

Spatiotemporal monitoring of the antibiome secreted by Bacillus biofilms on plant roots using MALDI mass spectrometry imaging

Some soil Bacilli living in association with plant roots can protect their host from infection by pathogenic microbes and are therefore being developed as biological agents to control plant diseases. The plant-protective activity of these bacteria has been correlated with the potential to secrete a wide array of antibiotic compounds upon growth as planktonic cells in isolated cultures under laboratory conditions. However, in situ expression of these antibiotics in the rhizosphere where bacterial cells naturally colonize root tissues is still poorly understood. In this work, we used matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) to examine spatiotemporal changes in the secreted antibiome of Bacillus amyloliquefaciens developing as biofilms on roots. Nonribosomal lipopeptides such as the plant immunity elicitor surfactin or the highly fungitoxic iturins and fengycins were readily produced albeit in different time frames and quantities in the surrounding medium. Interestingly, tandem mass spectrometry (MS/MS) experiments performed directly from the gelified culture medium also allowed us to identify a new variant of surfactins released at later time points. However, no other bioactive compounds such as polyketides were detected at any time, strongly suggesting that the antibiome expressed in planta by B. amyloliquefaciens does not reflect the vast genetic arsenal devoted to the formation of such compounds. This first dynamic study reveals the power of MALDI MSI as tool to identify and map antibiotics synthesized by root-associated bacteria and, more generally, to investigate plant-microbe interactions at the molecular level.

Gageostatins A-C, antimicrobial linear lipopeptides from a marine Bacillus subtilis

Concerning the requirements of effective drug candidates to combat against high rising multidrug resistant pathogens, we isolated three new linear lipopeptides, gageostatins A–C (1–3), consisting of hepta-peptides and new 3-β-hydroxy fatty acids from the fermentation broth of a marine-derived bacterium Bacillus subtilis. Their structures were elucidated by analyzing a combination of extensive 1D, 2D NMR spectroscopic data and high resolution ESIMS data. Fatty acids, namely 3-β-hydroxy-11-methyltridecanoic and 3-β-hydroxy-9,11-dimethyltridecanoic acids were characterized in lipopeptides 1 and 2, respectively, whereas an unsaturated fatty acid (E)-7,9-dimethylundec-2-enoic acid was assigned in 3. The 3R configuration of the stereocenter of 3-β-hydroxy fatty acids in 1 and 2 was established by Mosher’s MTPA method. The absolute stereochemistry of amino acid residues in 1–3 was ascertained by acid hydrolysis followed by Marfey’s derivatization studies. Gageostatins 1–3 exhibited good antifungal activities with MICs values of 4–32 µg/mL when tested against pathogenic fungi (R. solani, B. cinerea and C. acutatum) and moderate antibacterial activity against bacteria (B. subtilis, S. aeureus, S. typhi and P. aeruginosa) with MICs values of 8–64 µg/mL. Futhermore, gageostatins 1–3 displayed cytotoxicity against six human cancer cell lines with GI₅₀ values of 4.6–19.6 µg/mL. It is also noteworthy that mixed compounds 1+2 displayed better antifungal and cytotoxic activities than individuals.

Diversity of secondary metabolites from marine Bacillus species: chemistry and biological activity

Marine Bacillus species produce versatile secondary metabolites including lipopeptides, polypeptides, macrolactones, fatty acids, polyketides, and isocoumarins. These structurally diverse compounds exhibit a wide range of biological activities, such as antimicrobial, anticancer, and antialgal activities. Some marine Bacillus strains can detoxify heavy metals through reduction processes and have the ability to produce carotenoids. The present article reviews the chemistry and biological activities of secondary metabolites from marine isolates. Side by side, the potential for application of these novel natural products from marine Bacillus strains as drugs, pesticides, carotenoids, and tools for the bioremediation of heavy metal toxicity are also discussed.

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.

Fengycin C produced by Bacillus subtilis EA-CB0015

Bacillus subtilis EA-CB0015 was isolated from the phyllosphere of a banana plant and tested for its potential to produce bioactive compounds against Mycosphaerella fijiensis. Using a dual plate culture technique the cell-free supernatant of B. subtilis EA-CB0015 produced inhibition values of 89 ± 1%. The active compounds were purified by solid-phase extraction and HPLC, and their primary structures determined using mass spectrometry and amino acid analysis. A new fengycin isoform, fengycin C, with the amino acid sequence Glu-Orn-Tyr-Thr-Glu-Val-Pro-Gln-Thr-Ile was isolated. The peptidic moiety differs from fengycin B at position 9 and from fengycin A at positions 6 and 9. The β-hydroxy fatty acyl chain is connected to the N-terminal of the decapeptide and can be saturated or unsaturated, ranging from 14 to 18 carbons. The C-terminal residue of the peptidic moiety is linked to the tyrosine residue at position 3, forming the branching point of the acyl peptide and the eight-membered cyclic lactone.