Cyclic lipopeptide signature as fingerprinting for the screening of halotolerant Bacillus strains towards microbial enhanced oil recovery

Genome mining conformance to metabolite profile of Bacillus strains to control potato pathogens

Biocontrol agents are safe and effective methods for controlling plant disease pathogens, such as Fusarium solani, which causes dry wilt, and Pectobacterium spp., responsible for potato soft rot disease. Discovering agents that can effectively control both fungal and bacterial pathogens in potatoes has always presented a challenge. Biological controls were investigated using 500 bacterial strains isolated from rhizospheric microbial communities, along with two promising biocontrol strains: Pseudomonas (T17-4 and VUPf5). Bacillus velezensis (Q12 and US1) and Pseudomonas chlororaphis VUPf5 exhibited the highest inhibition of fungal growth and pathogenicity in both laboratory (48%, 48%, 38%) and greenhouse (100%, 85%, 90%) settings. Q12 demonstrated better control against bacterial pathogens in vivo (approximately 50%). Whole-genome sequencing of Q12 and US1 revealed a genome size of approximately 4.1 Mb. Q12 had 4413 gene IDs and 4300 coding sequences, while US1 had 4369 gene IDs and 4255 coding sequences. Q12 exhibited a higher number of genes classified under functional subcategories related to stress response, cell wall, capsule, levansucrase synthesis, and polysaccharide metabolism. Both Q12 and US1 contained eleven secondary metabolite gene clusters as identified by the antiSMASH and RAST servers. Notably, Q12 possessed the antibacterial locillomycin and iturin A gene clusters, which were absent in US1. This genetic information suggests that Q12 may have a more pronounced control over bacterial pathogens compared to US1. Metabolic profiling of the superior strains, as determined by LC/MS/MS, validated our genetic findings. The investigated strains produced compounds such as iturin A, bacillomycin D, surfactin, fengycin, phenazine derivatives, etc. These compounds reduced spore production and caused deformation of the hyphae in F. solani. In contrast, B. velezensis UR1, which lacked the production of surfactin, fengycin, and iturin, did not affect these structures and failed to inhibit the growth of any pathogens. Our findings suggest that locillomycin and iturin A may contribute to the enhanced control of bacterial pectolytic rot by Q12.

Classification, application, multifarious activities and production improvement of lipopeptides produced by Bacillus

Lipopeptides, a class of compounds consisting of a peptide ring and a fatty acid chain, are secondary metabolites produced by Bacillus spp. As their hydrophilic and oleophilic properties, lipopeptides are widely used in food, medicine, environment and other industrial or agricultural fields. Compared with artificial synthetic surfactants, microbial lipopeptides have the advantages of low toxicity, high efficiency and versatility, resulting in urgent market demand and broad development prospect of lipopeptides. However, due to the complex metabolic network and precursor requirements of synthesis, the specific and strict synthesis pathway, and the coexistence of multiple homologous substances, the production of lipopeptides by microorganisms has the problems of high cost and low production efficiency, limiting the mass production of lipopeptides and large-scale application in industry. This review summarizes the types of Bacillus-produced lipopeptides and their biosynthetic pathways, introduces the versatility of lipopeptides, and describes the methods to improve the production of lipopeptides, including genetic engineering and optimization of fermentation conditions.

Genomic Analysis of Surfactant-Producing Bacillus vallismortis TIM68: First Glimpse at Species Pangenome and Prediction of New Plipastatin-Like Lipopeptide

Surfactants are applied in several industrial processes when the modification of interface activity and the stability of colloidal systems are required. Lipopeptides are a class of microbial biosurfactants produced by species of the Bacillus genus. The present study aimed at assembling and analyzing the genome of a new Bacillus vallismortis strain, TIM68, that was shown to produce surfactant lipopeptides. The draft genome was also screened for common virulence factors and antibiotics resistance genes to investigate the strain biosafety. Comparative genomics analyses, i.e., synteny, average nucleotide identity (ANI), and pangenome, were also carried out using strain TIM68 and publicly available B. vallismortis complete and partial genomes. Three peptide synthetase operons were found in TIM68 genome, and they were surfactin A, mojavensin, and a novel plipastatin-like lipopeptide named vallisin. No virulence factors that render pathogenicity to the strain have been identified, but a region of prophage, that may contain unknown pathogenic factors, has been predicted. The pangenome of the species was characterized as closed, with 57% of genes integrating the core genome. The results obtained here on the genetic potential of TIM68 strain should contribute to its exploration in biotechnological applications.

Optimization and characterization of biosurfactant produced by indigenous Brevibacillus borstelensis isolated from a low permeability reservoir for application in MEOR

Biosurfactants are expected to be a key factor for microbial enhanced oil recovery (MEOR). In this study, we described the novel biosurfactant-producing strain Brevibacillus borstelensis YZ-2 isolated from a low permeability oil reservoir. We purified and characterized the biosurfactants produced by this YZ-2 strain via thin-layer chromatography and MALDI-TOF-MS, revealing them to be fengycins. We additionally used a Box–Behnken design approach to optimize fermentation conditions in order to maximize the biosurfactants production. Core flooding experiments showed that biosurfactants produced by YZ-2 can significantly enhance crude oil recovery. Micro-model tests showed that emulsification and IFT reduction was the main EOR mechanism of the YZ biosurfactant in the oil wet model. In summary, these findings highlight the potential of Brevibacillus borstelensis YZ-2 and its metabolites for MEOR.

Biosurfactants are expected to be a key factor for microbial enhanced oil recovery (MEOR).

Effects of lipopeptide biosurfactants on clinical strains of Malassezia furfur growth and biofilm formation

Lipopeptide biosurfactants (LBs) are biological molecules with low toxicity that have aroused growing interest in the pharmaceutical industry. Their chemical structure confers antimicrobial and antibiofilm properties against different species. Despite their potential, few studies have demonstrated their capability against Malassezia spp., commensal yeasts which can cause dermatitis and serious infections. Thus, the aim of this study was to evaluate the antifungal activity of biosurfactants produced by new strains of Bacillus subtilis TIM10 and B. vallismortis TIM68 against M. furfur and their potential for removal and inhibition of yeast biofilms. Biosurfactants were classified as lipopeptides by FTIR, and their composition was characterized by ESI-Q-TOF/MS, showing ions for iturin, fengycin, and surfactin, with a greater abundance of surfactin. Through the broth microdilution method, both biosurfactants inhibited the growth of clinical M. furfur strains. Biosurfactant TIM10 showed greater capacity for growth inhibition, with no statistical difference compared to those obtained by the commercial antifungal fluconazole for M. furfur 153DR5 and 154DR8 strains. At minimal inhibitory concentrations (MIC-2), TIM10 and TIM68 were able to inhibit biofilm formation, especially TIM10, with an inhibition rate of approximately 90%. In addition, both biosurfactants were able to remove pre-formed biofilm. Both biosurfactants showed no toxicity against murine fibroblasts, even at concentrations above MIC-2. Our results show the effectiveness of LBs in controlling the growth and biofilm formation of M. furfur clinical strains and highlight the potential of these agents to compose new formulations for the treatment of these fungi.

Bacillus spp. metabolites are effective in eradicating Aedes aegypti (Diptera: Culicidae) larvae with low toxicity to non-target species

The growing spread of dengue, chikungunya and Zika viruses demand the development of new and environmentally safe control methods for their vector, the mosquito Aedes aegypti. This study aims to find novel larvicidal agents from mutualistic (endophytic and rhizospheric) or edaphic bacteria that have no action against non-target organisms. Eleven out of the 254 bacterial strains tested were able to kill Ae. aegypti larvae. Larvicidal activity did not depend on presence of cells, since culture supernatants or crude lipopeptide extracts (CLEs) killed the larvae. Bacillus safensis BacI67 and Bacillus paranthracis C21 supernatants were the best performing supernatants, displaying the lowest lethal concentrations (LC50 = 31.11 µL/mL and 45.84 µL/mL, respectively). Bacillus velezensis B64a and Bacillus velezensis B15 produced the best performing CLEs (LC50 = 0.11 mg/mL and 0.12 mg/mL, respectively). Mass spectrometry analysis of CLEs detected a mixture of surfactins, iturins, and fengycins. The samples tested were weakly- or non-toxic to mammalian cells (RAW 264.7 macrophages and VERO cells) and non-target organisms (Caenorhabditis elegans, Galleria mellonella, Scenedesmus obliquus, and Tetrahymena pyriformis) - especially B. velezensis B15 CLE. The biosynthetic gene clusters related to secondary metabolism identified by whole genome sequencing of the four best performing bacteria strains revealed clusters for bacteriocin, beta-lactone, lanthipeptide, non-ribosomal peptide synthetases, polyketide synthases (PKS), siderophores, T3PKS, type 1 PKS-like, terpenes, thiopeptides, and trans-AT-PKS. Purification of lipopeptides may clarify the mechanisms by which these extracts kill Ae. aegypti larvae.

Characterization and Cytotoxic Effect of Biosurfactants Obtained from Different Sources

In this work, five biosurfactant extracts, obtained from different sources, all of them with demonstrated antimicrobial properties, were characterized and subjected to a cytotoxic study using mouse fibroblast cells (NCTC clone 929). Biosurfactant extracts obtained directly from corn steep water (CSW) showed similar surfactant characteristics to those of the extracellular biosurfactant extract produced by Bacillus isolated from CSW and grown in tryptic soy broth, observing that they are amphoteric, consisting of viscous and yellowish liquid with no foaming capacity. Contrarily, cell-bound biosurfactant extracts produced from Lactobacillus pentosus or produced by Bacillus sp isolated from CSW are nonionic, consisting of a white powder with foaming capacity. All the biosurfactants possess a similar fatty acid composition. The cytotoxic test revealed that the extracts under evaluation, at a concentration of 1 g/L, were not cytotoxic for fibroblasts (fibroblast growth > 90%). The biosurfactant extract obtained from CSW with ethyl acetate, at 1 g/L, showed the highest cytotoxic effect but above the cytotoxicity limit established by the UNE-EN-ISO10993-5. It is remarkable that the cell-bound biosurfactant produced by L. pentosus, at a concentration of 1 g/L, promoted the growth of the fibroblast up to 113%.

Mechanism of Antibacterial Activity of Bacillus amyloliquefaciens C-1 Lipopeptide toward Anaerobic Clostridium difficile

Probiotics may offer an attractive alternative for standard antibiotic therapy to treat Clostridium difficile infections (CDI). In this study, the antibacterial mechanism in vitro of newly isolated B. amyloliquefaciens C-1 against C. difficile was investigated. The lipopeptides surfactin, iturin, and fengycin produced by C-1 strongly inhibited C. difficile growth and viability. Systematic research of the bacteriostatic mechanism showed that the C-1 lipopeptides damage the integrity of the C. difficile cell wall and cell membrane. In addition, the lipopeptide binds to C. difficile genomic DNA, leading to cell death. Genome resequencing revealed many important antimicrobial compound-encoding clusters, including six nonribosomal peptides (surfactins (srfABCD), iturins (ituABCD), fengycins (fenABCDE), bacillibactin (bmyABC), teichuronic, and bacilysin) and three polyketides (bacillaene (baeEDLMNJRS), difficidin (difABCDEFGHIJ), and macrolactin (mlnABCDEFGHI)). In addition, there were other beneficial genes, such as phospholipase and seven siderophore biosynthesis gene clusters, which may contribute synergistically to the antibacterial activity of B. amyloliquefaciens C-1. We suggest that proper application of antimicrobial peptides may be effective in C. difficile control.

Novel Bacillus cereus strain from electrokinetically remediated saline soil towards the remediation of crude oil

A new strain SWH-15 was successfully isolated after initial electrokinetic remediation experiment using the same saline soil sampled from Shengli Oilfield, China. Four methods (morphological and biochemical characteristics, whole-cell fatty acid methyl esters (FAMEs) analysis, 16S rRNA sequence analysis and DNA G + C content and DNA-DNA hybridization analysis) were used to identify the taxonomic status of SWH-15 and confirmed that SWH-15 was a novel species of the Bacillus (B.) cereus group. Then, we assessed the degrading ability of the novel strain SWH-15 to crude oil through a microcosm experiment with four treatments, including control (CK), bioremediation using SWH-15 (Bio), electrokinetic remediation (EK), and combined bioremediation and electrokinetic remediation (Bio + EK). The results showed that the Bio + EK combined remediation treatment was more effective than the CK, Bio, and EK treatments in degrading crude oil contaminants. Bioaugmentation, by addition of the strain SWH-15 had synergistic effect with EK in Bio + EK treatment. Bacterial community analysis showed that electrokinetic remediation alone significantly altered the bacterial community of the saline soil. The addition of the strain SWH-15 alone had a weak effect on the bacterial community. However, the strain SWH-15 boosted the growth of other bacterial species in the metabolic network and weakened the impact of electrical field on the whole bacterial community structure in the Bio + EK treatment.