Complete genome sequence of Bacillus velezensis LM2303, a biocontrol strain isolated from the dung of wild yak inhabited Qinghai-Tibet plateau

Biocontrol manufacturing and agricultural applications of Bacillus velezensis

Many microorganisms have been reported as bioagents for producing ecofriendly, cost-effective, and safe products. Some Bacillus species of bacteria can be used in agricultural applications. Bacillus velezensis in particular has shown promising results for controlling destructive phytopathogens and in biofungicide manufacturing. Some B. velezensis strains can promote plant growth and display antibiotic activities against plant pathogen agents. In this review, we focus on the often-overlooked potential properties of B. velezensis as a bioagent for applications that will extend beyond the traditional agricultural uses. We delve into its versatility and future prospects, the challenges such uses may encounter, and some drawbacks associated with B. velezensis-based products.

Genomic analysis reveals genes that encode the synthesis of volatile compounds by a Bacillus velezensis-based biofungicide used in the treatment of grapes to control Aspergillus carbonarius

Fungal control strategies based on the use of Bacillus have emerged in agriculture as eco-friendly alternatives to replace/reduce the use of synthetic pesticides. Bacillus sp. P1 was reported as a new promising strain for control of Aspergillus carbonarius, a known producer of ochratoxin A, categorized as possible human carcinogen with high nephrotoxic potential. Grape quality can be influenced by vineyard management practices, including the use of fungal control agents. The aim of this study was to evaluate, for the first time, the quality parameters of Chardonnay grapes exposed to an antifungal Bacillus-based strategy for control of A. carbonarius, supporting findings by genomic investigations. Furthermore, genomic tools were used to confirm that the strain P1 belongs to the non-pathogenic species Bacillus velezensis and also to certify its biosafety. The genome of B. velezensis P1 harbors genes that are putatively involved in the production of volatiles and hydrolytic enzymes, which are responsible for releasing the free form of aroma compounds. In addition to promote biocontrol of phytopathogenic fungi and ochratoxins, the treatment with B. velezensis P1 did not change the texture (hardness and firmness), color and pH of the grapes. Heat map and hierarchical clustering analysis (HCA) of volatiles evaluated by GC/MS revealed that Bacillus-treated grapes showed higher levels of compounds with a pleasant odor descriptions such as 3-hydroxy-2-butanone, 2,3-butanediol, 3-methyl-1-butanol, 3,4-dihydro-β-ionone, β-ionone, dihydroactinidiolide, linalool oxide, and β-terpineol. The results of this study indicate that B. velezensis P1 presents desirable properties to be used as a biocontrol agent.

Complete genome sequence analysis of Bacillus velezensis A5, a promising biocontrol agent from the Pacific Ocean

Tobacco bacterial wilt (TBW) caused by Ralstonia solanacearum is a serious soil-borne disease, which seriously damages the growth of tobacco crops. Bacillus velezensis A5 was isolated from 3000 m deep-sea sediments of the Pacific Ocean, and was found to be antagonistic to TBW. Here, we report the complete genome sequence of strain A5, which has a 4,000,699-bp single circular chromosome with 3827 genes and a G + C content of 46.44%, 87 tRNAs, and 27 rRNAs. A total of 12 gene clusters were identified in the genome of strain A5, which were responsible for the biosynthesis of antibacterial compounds, including surfactin, bacillaene, fengycin, difficidin, bacillibactin, and bacilysin. Additionally, strain A5 was found to contain a series of genes related to the biosynthesis of carbohydrate-active enzymes and secreted proteins. Our results indicate that strain A5 can be considered a promising biocontrol agent against TBW in agricultural fields.

The antifungal substance from Bacillus velezensis B-3 improved the malt quality against premature yeast flocculation induced by Fusarium graminearum infection

Malt produced from barley contaminated with Fusarium graminearum can cause premature yeast flocculation (PYF) in beer fermentation, which ultimately affects the production efficiency and flavor quality of beer. In this study, a strain of Bacillus velezensis B-3 that was isolated from soil displayed strong antifungal activity against F. graminearum. The antifungal substances were extracted and separated by ammonium sulfate fractional precipitation and semipreparative high-performance liquid chromatography to obtain fraction VI with the strongest antifungal activity. Ultra-performance liquid chromatography-quadrupole-time-of-flight-mass spectrometry was used to identify that the fraction contained lipopeptides such as iturin A, surfactant B, and surfactant C. The minimum inhibitory concentration of the fraction was 0.2 mg/mL, and confocal laser scanning microscopy showed that the morphology of F. graminearum hyphae was obviously abnormal, with most of them were dead. Antifungal fraction VI could inhibit the growth of F. graminearum and avoid the production of PYF factor during malting but did not affect other qualities of malt. Therefore, the development of antimicrobial agents against Fusarium provides an effective potential strategy to control the production of PYF factors for malt-manufacturing enterprises. PRACTICAL APPLICATION: Antifungal fraction VI could inhibit the growth of F. graminearum and the formation of DON during malting but did not affect other qualities of malt. The levels of soluble nitrogen, free amino nitrogen, and color experienced a substantial reduction compared to the malt infected by F. graminearum. The PYF phenomenon was significantly improved, the number of suspended yeast cells and the degree of fermentation were increased, and the level of residual extract in the wort was low, close to that of control malt.

Complete genome analysis of Bacillus subtilis TY-1 reveals its biocontrol potential against tobacco bacterial wilt

Bacillus subtilis TY-1 was isolated from 2000 m-deep sea sediments of the Western Pacific Ocean, which was found to exhibit strong antagonistic activity against tobacco bacterial wilt caused by Ralstonia solanacearum. Here, we present the annotated complete genomic sequence of the strain Bacillus subtilis TY-1. The genome consists of a 4,030,869-bp circular chromosome with a G + C content of 43.88%, 86 tRNAs, and 30 rRNAs. Genomic analysis identified a large number of gene clusters involved in the biosynthesis of antibacterial metabolites, including lipopeptides(surfactin, bacillibactin, and fengycin) and polyketides(bacillaene). Meanwhile, numerous genes encoding carbohydrate-active enzymes and secreted proteins were found in TY-1. These findings suggest that Bacillus subtilis TY-1 appears to be a potential biocontrol agent against tobacco bacterial wilt in agricultural fields.

A Bacillus-based biofungicide agent prevents ochratoxins occurrence in grapes and impacts the volatile profile throughout the Chardonnay winemaking stages

Bacillus-based biocontrol agents have emerged as a strategy to eliminate or reduce the use of synthetic fungicides that are detrimental to health and the environment. In vineyards, a special concern arises from the control of Aspergillus carbonarius, a fungus known for its potential to produce ochratoxins. Ochratoxin A (OTA) is the most toxic form among ochratoxins and its maximum limit in wine has been established in Europe and Brazil as 2 μg/kg. Wine quality, especially the volatile profile, may be influenced by the antifungal strategies, since fungicide residues are transferred from grapes to must during winemaking. The objective of this study was to evaluate, for the first time, the impact of a biocontrol strategy containing Bacillus velezensis P1 on the volatile profile and occurrence of ochratoxins when grapes infected with A. carbonarius were used in winemaking. The evaluation of ochratoxins was carried out by liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-QToF-MS), and volatile compounds were analyzed using comprehensive two-dimensional gas chromatography coupled to quadrupole mass spectrometry (GC × GC/qMS). Six ochratoxins were identified in must prepared with Chardonnay grapes inoculated with A. carbonarius (ochratoxin α, ochratoxin β, ochratoxin α methyl-ester, ochratoxin α amide, N-formyl-ochratoxin α amide and OTA). Although winemaking causes a decrease in the levels of all forms of ochratoxins, the co-occurrence of these mycotoxins was verified in wine made with grapes containing A. carbonarius. B. velezensis P1 prevented the occurrence of ochratoxins in must, ensuring the safety of wines. Regarding the volatile profile, a predominant presence of terpenic compounds was verified in samples treated with B. velezensis when compared with those not treated with the biocontrol strategy, whereas the presence of A. carbonarius resulted in a higher concentration of volatile compounds with an odor described as fatty/waxy, possibly compromising wine quality. Therefore, B. velezensis P1 is a new biofungicide possibility to produce ochratoxin-free grapes and high-quality wines.

Complete genome sequence of Bacillus Licheniformis NWMCC0046, a candidate for the laundry industry

In this study, selected properties of protease and the complete genome sequence of Bacillus licheniformis NWMCC0046 were investigated, to discover laundry applications and other potential probiotic properties of this strain. Partial characterization of B. licheniformis NWMCC0046 showed that its protease has good activity both in alkaline environments and at low temperatures. Also, the protease is compatible with commercial detergents and can be used as a detergent additive for effective stain removal at low temperatures. The complete genome sequence of B. licheniformis NWMCC0046 is comprised of a 4,321,565 bp linear chromosome with a G + C content of 46.78% and no plasmids. It had 4504 protein-encoding genes, 81 transfer RNA (tRNA) genes, and 24 ribosomal RNA (rRNA) genes. Genomic analysis revealed genes involved in exocellular enzyme production and probiotic properties. In addition, genomic sequence analysis revealed specific genes encoding carbohydrate metabolism pathways, resistance, and cold adaptation capacity. Overall, protease properties show its potential as a detergent additive enzyme. The complete genome sequence information of B. licheniformis NWMCC0046 was obtained, and functional prediction revealed its numerous probiotic properties.

Bacillus velezensis: A Treasure House of Bioactive Compounds of Medicinal, Biocontrol and Environmental Importance

Bacillus velezensis gram-positive bacterium, is frequently isolated from diverse niches mainly soil, water, plant roots, and fermented foods. B. velezensis is ubiquitous, non-pathogenic and endospore forming. Being frequently isolated from diverse plant holobionts it is considered host adapted microorganism and recognized of high economic importance given its ability to promote plant growth under diverse biotic and abiotic stress conditions. Additionally, the species suppress many plant diseases, including bacterial, oomycete, and fungal diseases. It is also able after plant host root colonization to induce unique physiological situation of host plant called primed state. Primed host plants are able to respond more rapidly and/or effectively to biotic or abiotic stress. Moreover, B. velezenis have the ability to resist diverse environmental stresses and help host plants to cope with, including metal and xenobiotic stresses. Within species B. velezensis strains have unique abilities allowing them to adopt different life styles. Strain level abilities knowledge is warranted and could be inferred using the ever-expanding new genomes list available in genomes databases. Pangenome analysis and subsequent identification of core, accessory and unique genomes is actually of paramount importance to decipher species full metabolic capacities and fitness across diverse environmental conditions shaping its life style. Despite the crucial importance of the pan genome, its assessment among large number of strains remains sparse and systematic studies still needed. Extensive knowledge of the pan genome is needed to translate genome sequencing efforts into developing more efficient biocontrol agents and bio-fertilizers. In this study, a genome survey of B. velezensis allowed us to (a) highlight B. velezensis species boundaries and show that Bacillus suffers taxonomic imprecision that blurs the debate over species pangenome; (b) identify drivers of their successful acquisition of specific life styles and colonization of new niches; (c) describe strategies they use to promote plant growth and development; (d) reveal the unlocked strain specific orphan secondary metabolite gene clusters (biosynthetic clusters with corresponding metabolites unknown) that product identification is still awaiting to amend our knowledge of their putative role in suppression of pathogens and plant growth promotion, and (e) to describe a dynamic pangenome with a secondary metabolite rich accessory genome.

Isolation and Characterization of Strain Exiguobacterium sp. KRL4, a Producer of Bioactive Secondary Metabolites from a Tibetan Glacier

Extremophilic microorganisms represent a unique source of novel natural products. Among them, cold adapted bacteria and particularly alpine microorganisms are still underexplored. Here, we describe the isolation and characterization of a novel Gram-positive, aerobic rod-shaped alpine bacterium (KRL4), isolated from sediments from the Karuola glacier in Tibet, China. Complete phenotypic analysis was performed revealing the great adaptability of the strain to a wide range of temperatures (5-40 °C), pHs (5.5-8.5), and salinities (0-15% w/v NaCl). Genome sequencing identified KRL4 as a member of the placeholder genus Exiguobacterium_A and annotation revealed that only half of the protein-encoding genes (1522 of 3079) could be assigned a putative function. An analysis of the secondary metabolite clusters revealed the presence of two uncharacterized phytoene synthase containing pathways and a novel siderophore pathway. Biological assays confirmed that the strain produces molecules with antioxidant and siderophore activities. Furthermore, intracellular extracts showed nematocidal activity towards C. elegans, suggesting that strain KRL4 is a source of anthelmintic compounds.

Comparative genomic and secretomic characterisation of endophytic Bacillus velezensis LC1 producing bioethanol from bamboo lignocellulose

Bacillus is an excellent organic matter degrader, and it has exhibited various abilities required for lignocellulose degradation. Several B. velezensis strains encode lignocellulosases, however their ability to efficiently transform biomass has not been appreciated. In the present study, through the comparative genomic analysis of the whole genome sequences of 21 B. velezensis strains, CAZyome related to lignocellulose degradation was identified and their similarities and differences were compared. Subsequently, the secretome of B. velezensis LC1 by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were identified and confirmed that a considerable number of proteins were involved in lignocellulose degradation. Moreover, after 6-day treatment, the degradation efficiency of the B. velezensis LC1 toward cellulose, hemicellulose and lignin were 59.90%, 75.44% and 23.41%, respectively, the hydrolysate was subjected to ethanol fermentation with Saccharomyces cerevisiae and Escherichia coli KO11, yielded 10.44 g/L ethanol after 96 h. These results indicate that B. velezensis LC1 has the ability to effectively degrade bamboo lignocellulose and has the potential to be used in bioethanol production.

Complete genome sequence and antimicrobial activity of Bacillus velezensis JT3-1, a microbial germicide isolated from yak feces

Bacillus velezensis JT3-1 was isolated from feces of the domestic yak (Bos grunniens) in Gansu province of China. Aim to know whether B. velezensis JT3-1 has the potency to be developed as a probiotic bacterium, works on the complete genome sequence, antimicrobial activity, growth performance in calves, and treatment effect on calf diarrhea of B. velezensis JT3-1 were carried out. The results showed that the complete genome of B. velezensis JT3-1 contains one gapless circular chromosome which is 3,929,799 bp, and has 3761 protein-encoding genes with an average GC content of 46.50%. From the antimicrobial activity results, B. velezensis JT3-1 has shown strong antagonistic activities against Listeria monocytogenes, Staphylococcus aureus, Escherichia coli, Salmonella Typhimurium, Mannheimia haemolytica, Staphylococcus hominis, Clostridium perfringens, and Mycoplasma bovis. Compared with the control group, the average weight of the experiment animals from Bv1 group and Bv2 group which were supplemented with B. velezensis JT3-1 was significantly increased (P < 0.05). Meanwhile, the Bv1 and Bv2 supplement significantly improved the level of IgA, IgG, IgM, and IFN-γ in calves as compared with the controls (P < 0.05), but the IL-2 level was not obviously changed between the three groups. In addition, B. velezensis JT3-1 showed a good effect against diarrhea, as the cure rate reached 95.0% (171/180) in newborn calves (Angus cattle) in Xinjiang, and 100.0% (149/149) in yak calves in Qinghai, respectively. Our study will lay a good foundation for the elucidation of the molecular mechanisms of its antimicrobial activity, and supports the hypothesis that JT3-1 has the potential to be developed as a probiotic bacterium in cattle.

Bacillus velezensis: phylogeny, useful applications, and avenues for exploitation

Some members of the Bacillus velezensis (Bv) group (e.g., Bv FZB42T and AS3.43) were previously assigned grouping with B. subtilis and B. amyloliquefaciens, based on the fact that they shared a 99% DNA-DNA percentage phylogenetic similarity. However, hinging on current assessments of the pan-genomic reassignments, the differing phylogenomic characteristics of Bv from B. subtilis and B. amyloliquefaciens are now better understood. Within this re-grouping/reassignment, the various strains within the Bv share a close phylogenomic resemblance, and a number of these strains have received a lot of attention in recent years, due to their genomic robustness, and the growing evidence for their possible utilization in the agricultural industry for managing plant diseases. Only a few applications for their use medicinally/pharmaceutically, environmentally, and in the food industry have been reported, and this may be due to the fact that the majority of those strains investigated are those typically occurring in soil. Although the intracellular unique biomolecules of Bv strains have been revealed via in silico genome modeling and investigated using transcriptomics and proteomics, a further inquisition into the Bv metabolome using newer technologies such as metabolomics could elucidate additional applications of this economically relevant Bacillus species, beyond that of primarily the agricultural sector.

Draft Genome Sequence of Bacillus velezensis CE2, Which Genetically Encodes a Novel Multicomponent Lantibiotic

Bacillus velezensis CE2 produces potent antimicrobial compound(s). The draft genome sequence of the strain reported here is 4.1 Mb with a G+C content of 46.1%.

Bacillus velezensis CE2 produces potent antimicrobial compound(s). The draft genome sequence of the strain reported here is 4.1 Mb with a G+C content of 46.1%. Whole-genome sequencing revealed that the strain genetically encodes a novel multicomponent lantibiotic, velezensicidin.

Selecting lipopeptide-producing, Fusarium-suppressing Bacillus spp.: Metabolomic and genomic probing of Bacillus velezensis NWUMFkBS10.5

The results of this study indicate that the maize rhizosphere remains a reservoir for microbial strains with unique beneficial properties. The study sought to provide an indigenous Bacillus strain with a bioprotective potential to alleviate maize fusariosis in South Africa. We selected seven Bacillus isolates (MORWBS1.1, MARBS2.7, VERBS5.5, MOREBS6.3, MOLBS8.5, MOLBS8.6, and NWUMFkBS10.5) with biosuppressive effects against two maize fungal pathogens (Fusarium graminearum and Fusarium culmorum) based on 16S rDNA gene characterization and lipopeptide gene analysis. The PCR analysis revealed that lipopeptide genes encoding the synthesis of iturin, surfactin, and fengycin might be responsible for their antifungal activities. Few of the isolates also showed possible biosurfactant capability, and their susceptibility to known antibiotics is indicative of their eco‐friendly attributes. In addition, in silico genomic analysis of our best isolate (Bacillus velezensis NWUMFkBS10.5) and characterization of its active metabolite with FTIR, NMR, and ESI‐Micro‐Tof MS confirmed the presence of valuable genes clusters and metabolic pathways. The versatile genomic potential of our Bacillus isolate emphasizes the continued relevance of Bacillus spp. in biological management of plant diseases.

Analysis of the Complete Genome Sequence of Bacillus atrophaeus GQJK17 Reveals Its Biocontrol Characteristics as a Plant Growth-Promoting Rhizobacterium

Bacillus atrophaeus GQJK17 was isolated from the rhizosphere of Lycium barbarum L. in China, which was shown to be a plant growth-promoting rhizobacterium as a new biological agent against pathogenic fungi and gram-positive bacteria. We present its biological characteristics and complete genome sequence, which contains a 4,325,818 bp circular chromosome with 4,181 coding DNA sequences and a G+C content of 43.3%. A genome analysis revealed a total of 8 candidate gene clusters for producing antimicrobial secondary metabolites, including surfactin, bacillaene, fengycin, and bacillibactin. Some other antimicrobial and plant growth-promoting genes were also discovered. Our results provide insights into the genetic and biological basis of B. atrophaeus strains as a biocontrol agent for application in agriculture.

Comparative genome analysis of Bacillus velezensis reveals a potential for degrading lignocellulosic biomass

Genomes of 24 sequenced Bacillus velezensis strains were characterized to identity shared and unique genes of lignocellulolytic enzymes and predict potential to degrade lignocellulose. All 24 strains had genes that encoded lignocellulolytic enzymes, with potential to degrade cellulose and hemicelluloses. Several lignocellulosic genes related to cellulose degradation were universally present, including one GH5 (endo-1,4-β-glucanase), one GH30 (glucan endo-1,6-β-glucosidase), two GH4 (6-phospho-β-glucosidase, 6-phospho-α-glucosidase), one GH1 (6-phospho-β-galactosidase), one GH16 (β-glucanase) and three GH32 (two sucrose-6-phosphate hydrolase and levanase). However, in the absence of gene(s) for cellobiohydrolase, it was predicted that none of the 24 strains would be able to directly hydrolyse cellulose. Regarding genes for hemicellulose degradation, four GH43 (1,4-β-xylosidase; except strain 9912D), one GH11 (endo-1,4-β-xylanase), three GH43 (two arabinan endo-1,5-α-L-arabinosidase and one arabinoxylan arabinofuranohydrolase), two GH51 (α-N-arabinofuranosidase), one GH30 (glucuronoxylanase), one GH26 (β-mannosidase) and one GH53 (arabinogalactan endo-1,4-β-galactosidase) were present. In addition, two PL1 (pectate lyase) and one PL9 (pectate lyase) with potential for pectin degradation were conserved among all 24 strains. In addition, all 24 Bacillus velezensis had limited representation of the auxiliary activities super-family, consistent with a limited ability to degrade lignin. Therefore, it was predicted that for these bacteria to degrade lignin, pretreatment of lignocellulosic substrates may be required. Finally, based on in silico studies, we inferred that Bacillus velezensis strains may degrade a range of polysaccharides in lignocellulosic biomasses.

Characteristics and Application of a Novel Species of Bacillus: Bacillus velezensis

Bacillus velezensis has been investigated and applied more and more widely recently because it can inhibit fungi and bacteria and become a potential biocontrol agent. In order to provide more clear and comprehensive understanding of B. velezensis for researchers, we collected the recent relevant articles systematically and reviewed the discovery and taxonomy, secondary metabolites, characteristics and application, gene function, and molecular research of B. velezensis. This review will give some direction to the research and application of this strain for the future.

Draft Genome Sequence of Bacillus velezensis GF610, a Producer of Potent Anti-Listeria Agents

Bacillus velezensis GF610 was isolated from soil in Illinois, USA, and found to produce amyloliquecidin GF610, a potent two-component antimicrobial peptide. We report here the GF610 strain draft genome sequence, which contains 4.29 Mb and an overall GC content of 45.91%.