Genomic and functional features of the biosurfactant producing Bacillus sp. AM13

Lichenysin-like Polypeptide Production by Bacillus licheniformis B3-15 and Its Antiadhesive and Antibiofilm Properties

We report the ability of the crude biosurfactant (BS B3-15), produced by the marine, thermotolerant Bacillus licheniformis B3-15, to hinder the adhesion and biofilm formation of Pseudomonas aeruginosa ATCC 27853 and Staphylococcus aureus ATCC 29213 to polystyrene and human cells. First, we attempted to increase the BS yield, optimizing the culture conditions, and evaluated the surface-active properties of cell-free supernatants. Under phosphate deprivation (0.06 mM) and 5% saccharose, the yield of BS (1.5 g/L) increased by 37%, which could be explained by the earlier (12 h) increase in lchAA expression compared to the non-optimized condition (48 h). Without exerting any anti-bacterial activity, BS (300 µg/mL) prevented the adhesion of P. aeruginosa and S. aureus to polystyrene (47% and 36%, respectively) and disrupted the preformed biofilms, being more efficient against S. aureus (47%) than P. aeruginosa (26%). When added to human cells, the BS reduced the adhesion of P. aeruginosa and S. aureus (10× and 100,000× CFU/mL, respectively) without altering the epithelial cells' viability. As it is not cytotoxic, BS B3-15 could be useful to prevent or remove bacterial biofilms in several medical and non-medical applications.

Identification and characterization of Brevibacillus halotolerans B-4359: a potential antagonistic bacterium against red pepper anthracnose in Korea

Our study aimed to identify potential biocontrol agents (BCAs) against major phytopathogens under in vitro conditions by screening the Freshwater Bioresources Culture Collection (FBCC), Korea. Of the identified 856 strains, only 65 exhibited antagonistic activity, among which only one representative isolation, Brevibacillus halotolerans B-4359 was selected based on its in vitro antagonistic activity and enzyme production. Cell-free culture filtrate (CF) and volatile organic compounds (VOCs) of B-4359 were shown to be effective against the mycelial growth of Colletotrichum acutatum. Notably, B-4359 was found to promote spore germination in C. acutatum instead of exhibiting a suppressive effect when the bacterial suspension was mixed with the spore suspension of C. acutatum. However, B-4359 showed an excellent biological control effect on the anthracnose of red pepper fruits. Compared to other treatments and untreated control, B-4359 played a more effective role in controlling anthracnose disease under field conditions. The strain was identified as B. halotolerans using BIOLOG and 16S rDNA sequencing analyses. The genetic mechanism underlying the biocontrol traits of B-4359 was characterized using the whole-genome sequence of B-4359, which was closely compared with related strains. The whole-genome sequence of B-4359 consisted of 5,761,776 bp with a GC content of 41.0%, including 5,118 coding sequences, 117 tRNA, and 36 rRNA genes. The genomic analysis identified 23 putative secondary metabolite biosynthetic gene clusters. Our results provide a deep understanding of B-4359 as an effective biocontrol agent against red pepper anthracnose for sustainable agriculture.

Molecular characterization of a novel strain of Bacillus halotolerans protecting wheat from sheath blight disease caused by Rhizoctonia solani Kühn

Rhizoctonia solani Kühn naturally infects and causes Sheath blight disease in cereal crops such as wheat, rice and maize, leading to severe reduction in grain yield and quality. In this work, a new bacterial strain Bacillus halotolerans LDFZ001 showing efficient antagonistic activity against the pathogenic strain Rhizoctonia solani Kühn sh-1 was isolated. Antagonistic, phylogenetic and whole genome sequencing analyses demonstrate that Bacillus halotolerans LDFZ001 strongly suppressed the growth of Rhizoctonia solani Kühn sh-1, showed a close evolutionary relationship with B. halotolerans F41-3, and possessed a 3,965,118 bp circular chromosome. Bioinformatic analysis demonstrated that the genome of Bacillus halotolerans LDFZ001 contained ten secondary metabolite biosynthetic gene clusters (BGCs) encoding five non-ribosomal peptide synthases, two polyketide synthase, two terpene synthases and one bacteriocin synthase, and a new kijanimicin biosynthetic gene cluster which might be responsible for the biosynthesis of novel compounds. Gene-editing experiments revealed that functional expression of phosphopantetheinyl transferase (SFP) and major facilitator superfamily (MFS) transporter genes in Bacillus halotolerans LDFZ001 was essential for its antifungal activity against R. solani Kühn sh-1. Moreover, the existence of two identical chitosanases may also make contribution to the antipathogen activity of Bacillus halotolerans LDFZ001. Our findings will provide fundamental information for the identification and isolation of new sheath blight resistant genes and bacterial strains which have a great potential to be used for the production of bacterial control agents.

IMPORTANCE

A new Bacillus halotolerans strain Bacillus halotolerans LDFZ001 resistant to sheath blight in wheat is isolated. Bacillus halotolerans LDFZ001 harbors a new kijanimicin biosynthetic gene cluster, and the functional expression of SFP and MFS contribute to its antipathogen ability.

Bacteria Halotolerant from Karst Sinkholes as a Source of Biosurfactants and Bioemulsifiers

Halotolerant bacteria with biosurfactant (BS) and bioemulsifiers (BE) activity can coexist in Karstic sinkholes with marine influence. Two sinkholes in the Yucatan peninsula were selected to isolate bacteria with BE and BS activity stable in NaCl. The optimal time, the effect of nitrogen and carbon source in the medium, and the conditions (agitation, pH and salinity) for the production of BS and BE compounds in planktonic and sessile (stimulate the formation of biofilms in cell roller) culture were determined. Eighty strains showed the highest emulsification activity (EI24 ≥ 50%) and drop-collapse ≥ 4 mm. 87% of the strains are moderately halotolerant, and 21% bordered the limit of extreme halotolerance. Twenty-four strains maintained or improved their BS and BE activity under salinity conditions at 5% and 10%, being the most active genera Bacillus, Paenibacillus and Lysinibacillus, identified by sequencing of the 16S rRNA gene. The results show that the nitrogen source positively affects the BS and BE activity, regardless of the type of culture. The sessile culture markedly stimulated BS activity with significant differences. However, we did not find a greater influence on the culture conditions. The results suggest that halotolerant bacteria from sinkholes could be implemented in bioremediation and other biotechnological applications.

Draft genome sequence and potential identification of a biosurfactant from Brevibacterium casei strain LS14 an isolate from fresh water Loktak Lake

This study reports the whole-genome sequencing and sequence analysis of a bacterial isolate Brevibacterium casei strain LS14, isolated from Loktak Lake, Imphal, India. The de novo assembled genome reported in this paper featured a size of 3,809,532 bp, has GC content of 68% and contains 3602 genomic features, including 3551 protein-coding genes, 46 tRNA and 5rRNA. A biosurfactant biosynthesis gene cluster in the genome of the isolated strain was identified using AntiSMASH online tool V3.0.5 and KAAS (KEGG Automatic Annotation Server). The presence of biosurfactant was demonstrated by drop collapse, oil displacement and emulsification index. Subsequent chemical characterization using FTIR and LC-MS analyses revealed surfactin and terpene containing biosurfactant moieties. Also, the presence of genes involved in terpenoid synthesis pathway in the genome sequence may account for biosurfactant terpenoid backbone, but genes for later-stage conversion of terpenoid to biosurfactant were not ascertained.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02867-9.

A review on biosurfactants: properties, applications and current developments

Microbial surfactants are a large number of amphipathic biomolecules with a myriad of biomolecule constituents from various microbial sources that have been studied for their surface tension reduction activities. With unique properties, their applications have been increased in different areas including environment, medicine, healthcare, agriculture and industries. The present review aims to study the biochemistry and biosynthesis of biosurfactants exhibiting varying biomolecular structures which are produced by different microbial sources. It also provides details on roles played by biosurfactants in nature as well as their potential applications in various sectors. Basic biomolecule content of all the biosurfactants studied showed presence of carbohydrates, aminoacids, lipids and fattyacids. The data presented here would help in designing, synthesis and application of tailor-made novel biosurfactants. This would pave a way for perspectives of research on biosurfactants to overcome the existing bottlenecks in this field.

Integrated Genomic and Functional Characterization of the Anti-diabetic Potential of Arthrobacter sp. SW1

For decades, bacterial natural products have served as valuable resources for developing novel drugs to treat several human diseases. Recent advancements in the integrative approach of using genomic and functional tools have proved beneficial in obtaining a comprehensive understanding of these biomolecules. This study presents an in-depth characterization of the anti-diabetic activity exhibited by a bacterial isolate SW1, isolated from an effluent treatment plant. As a primary screening, we assessed the isolate for its potential to inhibit alpha-amylase and alpha-glucosidase enzymes. Upon confirmation, we further utilized LC-MS, ESI-MS/MS, and NMR spectroscopy to identify and characterize the biomolecule. These efforts were coupled with the genomic assessment of the biosynthetic gene cluster involved in the anti-diabetic compound production. Our investigation discovered that the isolate SW1 inhibited both α-amylase and α-glucosidase activity. The chemical analysis suggested the production of acarbose, an anti-diabetic biomolecule, which was further confirmed by the presence of biosynthetic gene cluster "acb" in the genome. Our in-depth chemical characterization and genome mining approach revealed the potential of bacteria from an unconventional niche, an effluent treatment plant. To the best of our knowledge, it is one of the first few reports of acarbose production from the genus Arthrobacter.

Whole Genome Sequencing and Root Colonization Studies Reveal Novel Insights in the Biocontrol Potential and Growth Promotion by Bacillus subtilis MBI 600 on Cucumber

Bacillus spp. MBI 600 is a gram-positive bacterium and is characterized as a PGPR strain involved in plant growth promotion and control of various plant pathogens which has recently been introduced into the agricultural practice. In this study we performed a Next Generation Sequencing analysis, to analyze the full genome of this microorganism and to characterize it taxonomically. Results showed that MBI 600 strain was phylogenetically close to other Bacillus spp. strains used as biocontrol agents and identified as B. subtilis. GOG analysis showed clusters contributed to secondary metabolites production such as fengycin and surfactin. In addition, various genes which annotated according to other plant-associated strains, showed that play a main role in nutrient availability from soil. The root colonization ability of MBI 600 strain was analyzed in vivo with a yellow fluorescence protein (yfp) tag. Confocal laser scanning microscopy of cucumber roots treated with yfp-tagged MBI 600 cells, revealed that the strain exhibits a strong colonization ability of cucumber roots, although it is affected significantly by the growth substrate of the roots. In vitro and in planta experiments with MBI 600 strain and F. oxysporum f.sp. radicis cucumerinum and P. aphanidernatum, showed a high control ability against these soilborne pathogens. Overall, our study demonstrates the effectiveness of MBI 600 in plant growth promotion and antagonism against different pathogens, highlighting the use of this microorganism as a biocontrol agent.

Planococcus Species - An Imminent Resource to Explore Biosurfactant and Bioactive Metabolites for Industrial Applications

The marine environment represents a well-off and diverse group of microbes, which offers an enormous natural bioactive compounds of commercial importance. These natural products have expanded rigorous awareness due to their widespread stability and functionality under harsh environmental conditions. The genus Planococcus is a halophilic bacterium known for the production of diverse secondary metabolites such as 2-acetamido-2-deoxy-α-d-glucopyranosyl-(1, 2)-β-d-fructofuranose exhibiting stabilizing effect and methyl glucosyl-3,4-dehydro-apo-8-lycopenoate displaying antioxidant activity. The genus Planococcus is reported generally for hydrocarbon degradation in comparison with biosurfactant/bioemulsifier secretion. Although Planococcus was proposed in 1894, it seized long stretch (till 1970) to get accommodated under the genus Planococcus authentically. Large-scale biosurfactant production from Planococcus was reported in 2014 with partial characterization. For the first time in 2019, we documented genomic and functional analysis of Planococcus sp. along with the physico-chemical properties of its biosurfactant. In 2020, again we screened biosurfactant for pharmacological applications. The present review discusses the comprehensive genomic insights and physical properties of Planococcus-derived biosurfactant. Moreover, we also highlight the prospects and challenges in biosurfactant production from Planococcus sp. Among ∼102 reports on biosurfactant produced by marine bacteria, 43 were of glycolipid and 59 were non-glycolipid type. Under other biosurfactant type, they were identified as lipopeptide (20) like surfactin (5), glycolipoprotein/lipoprotein (12), and other non-glycolipid (22). Planococcus sp. generally produces glycolipid-type biosurfactant (4) and exopolysaccharides (2). The single report documented in the literature is on biosurfactant production (glycolipid +non glycolipid) by diverse marine microbes (39) suggesting their novelty and diversity for biosurfactant secretion.

Bacillus subtilis EA-CB0575 genome reveals clues for plant growth promotion and potential for sustainable agriculture

Bacillus subtilis is a remarkably diverse bacterial species that displays many ecological functions. Given its genomic diversity, the strain Bacillus subtilis EA-CB0575, isolated from the rhizosphere of a banana plant, was sequenced and assembled to determine the genomic potential associated with its plant growth promotion potential. The genome was sequenced by Illumina technology and assembled using Velvet 1.2.10, resulting in a whole genome of 4.09 Mb with 4332 genes. Genes involved in the production of indoles, siderophores, lipopeptides, volatile compounds, phytase, bacilibactin, and nitrogenase were predicted by gene annotation or by metabolic pathway prediction by RAST. These potential traits were determined using in vitro biochemical tests, finding that B. subtilis EA-CB0575 produces two families of lipopeptides (surfactin and fengycin), solubilizes phosphate, fixes nitrogen, and produces indole and siderophores compounds. Finally, strain EA-CB0575 increased 34.60% the total dry weight (TDW) of tomato plants with respect to non-inoculated plants at greenhouse level. These results suggest that the identification of strain-specific genes and predicted metabolic pathways might explain the strain potential to promote plant growth by several mechanisms of action, accelerating the development of plant biostimulants for sustainable agricultural.

Genomic Insights of Halophilic Planococcus maritimus SAMP MCC 3013 and Detail Investigation of Its Biosurfactant Production

Moderate halophilic bacteria thrive in saline conditions and produce biosurfactant (BS) which facilitates the oil scavenging activity in the oil polluted surroundings. Production of such unusual bioactive molecules plays a vital role for their survival in an extreme and adverse environment. Current research deals with isolation of Planococcus maritimus strain SAMP MCC 3013 from Indian Arabian coastline sea water for BS production. The bacterium tolerated up to 2.7 M NaCl demonstrating osmotic stress bearable physiological systems. We used integrated approach to explore the genomic insight of the strain SAMP and displayed the presence of gene for BS biosynthesis. The genome analysis revealed this potential to be intrinsic to the strain. Preliminary screening techniques viz., surface tension (SFT), drop collapse (DC) and oil displacement (OD) showed SAMP MCC 3013 as a potent BS producer. BS reduced SFT of phosphate buffer saline (PBS) pH: 7.0 from 72 to 30 mN/m with a critical micelle concentration (CMC) value of 1.3 mg/mL. Subsequent investigation on chemical characterization, using thin layer chromatography (TLC), Fourier transform infrared spectroscopy (FT-IR), nuclear magnetic resonance (1H NMR and 13C NMR) and liquid chromatography mass spectrometry (LC-MS) revealed terpene containing BS having sugar, lipid moieties. The genomic sequence analysis of P. maritimus SAMP showed complete genes in the pathway for the synthesis of terpenoid. Probably terpenoid is the accountable backbone molecule for the BS production, but the later stages of terpenoid conversion to the BS could not be found. Moreover, it is important to highlight that till today; no single report documents the in-detailed physico-chemical characterization of BS from Planococcus sp. Based on genomic and functional properties, the term terpene containing BS is denoted for the surfactant produced by P. maritimus.

Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil

One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydrocarbons in contaminated soils. The genome of B. subtilis MJ01 was sequenced and assembled by PacBio RS sequencing technology. One big contig with a length of 4,108,293 bp without any gap was assembled. Genome annotation and prediction of gene showed that MJ01 genome is very similar to B. subtilis spizizenii TU-B-10 (95% similarity). The comparison and analysis of orthologous genes carried out between B. subtilis MJ01, reference strain B. subtilis subsp. subtilis str. 168, and close relative spizizenii TU-B-10 by microscope platform and various bioinformatics tools. More than 88% of 4269 predicted coding sequences in MJ01 had at least one similar sequence in genome of reference strain and spizizenii TU-B-10. Despite this high similarity, some differences were detected among encoding sequences of non-ribosome protein and bacteriocins in MJ01 and spizizenii TU-B-10. MJ01 has unique nucleotide sequences and a novel predicted lasso-peptide bacteriocin; it also has not any similar nucleotide sequence in non-redundant nucleotide data base.

Genome sequence and comparative analysis of Bacillus cereus BC04, reveals genetic diversity and alterations for antimicrobial resistance

In this study, we delineated the genome sequence of a Bacillus cereus strain BC04 isolated from a stool sample in India. The draft genome is 5.1 Mb in size and consists of total 109 scaffolds, GC content is 35.2% with 5182 coding genes. The comparative analysis with other completely sequenced genomes highlights the unique presence of genomic islands, hemolysin, capsular synthetic protein, modifying enzymes accC7 and catA15, regulators of antibiotic resistance MarR and LysR with annotated functions related to virulence, stress response, and antimicrobial resistance. Overall, this study not only signifies the genetic diversity in gut isolate BC04 in particular, but also pinpoints the presence of unique genes possessed by B. cereus which can be pertinently exploited to design novel drugs and intervention strategies for the treatment of food borne diseases.