Corrigendum: Bacillus velezensis FZB42 in 2018: The Gram-Positive Model Strain for Plant Growth Promotion and Biocontrol

Bacillus velezensis S141, a soybean growth-promoting bacterium, hydrolyzes isoflavone glycosides into aglycones

Bacillus velezensis S141, a plant growth-promoting rhizobacteria (PGPR), was isolated from a soybean field in Thailand. Previous studies demonstrated that S141 enhanced soybean growth, stimulating nodulation for symbiotic nitrogen fixation with soybean root nodule bacteria, including Bradyrhizobium diazoefficience USDA110. Isoflavone glycosides are produced in soybean roots and hydrolyzed into their aglycones, triggering nodulation. This study revealed that S141 efficiently hydrolyzed two isoflavone glycosides in soybean roots (daidzin and genistin) to their aglycones (daidzein and genistein, respectively). However, S141, Bacillus subtilis 168, NCIB3610, and B. velezensis FZB42 hydrolyzed isoflavone glucosides into aglycones. A BLASTp search suggested that S141 and the other three strains shared four genes encoding β-glucosidases corresponding to bglA, bglC, bglH, and gmuD in B. subtilis 168. The gene inactivation analysis of B. subtilis 168 revealed that bglC encoded the major β-glucosidase, contributing about half of the total activity to hydrolyze isoflavone glycosides and that bglA, bglH, and gmuD, all barely committed to the hydrolysis of isoflavone glycosides. Thus, an unknown β-glucosidase exists, and our genetic knowledge of β-glucosidases was insufficient to evaluate the ability to hydrolyze isoflavone glycosides. Nevertheless, S141 could predominate in the soybean rhizosphere, releasing isoflavone aglycones to enhance soybean nodulation.

Genome sequencing and analysis of Bacillus velezensis VJH504 reveal biocontrol mechanism against cucumber Fusarium wilt

One major issue in reducing cucumber yield is the destructive disease Cucumber (Cucumis sativus L.) wilt disease caused by Fusarium oxysporum f. sp. cucumerinum (Foc). When using the isolate VJH504 isolated from cucumber rhizosphere soil and identified as Bacillus velezensis, the growth of Foc in the double culture experiment was effectively inhibited. Phenotypic, phylogenetic, and genomic analyses were conducted to enhance understanding of its biocontrol mechanism. According to the result of the phenotype analysis, B. velezensis VJH504 could inhibit cucumber fusarium wilt disease both in vitro and in vivo, and significantly promote cucumber seed germination and seedling growth. Additionally, the tests of growth-promoting and biocontrol characteristics revealed the secretion of proteases, amylases, β-1,3-glucanases, cellulases, as well as siderophores and indole-3-acetic acid by B. velezensis VJH504. Using the PacBio Sequel II system, we applied the complete genome sequencing for B. velezensis VJH504 and obtained a single circular chromosome with a size of 3.79 Mb. A phylogenetic tree was constructed based on the 16S rRNA gene sequences of B. velezensis VJH504 and 13 other Bacillus species, and Average Nucleotide Identity (ANI) analysis was performed using their whole-genome sequences, confirming isolateVJH504 as B. velezensis. Following this, based on the complete genome sequence od B. velezensis VJH504, specific functional analysis, Carbohydrate-Active Enzymes (CAZymes) analysis, and secondary metabolite analysis were carried out, predicting organism's abilities for biofilm formation, production of antifungal CAZymes, and synthesis of antagonistic secondary metabolites against pathogens. Afterwards, a comparative genomic analysis was performed between B. velezensis VJH504 and three other B. velezensis strains, revealing subtle differences in their genomic sequences and suggesting the potential for the discovery of novel antimicrobial substances in B. velezensis VJH504. In conclusion, the mechanism of B. velezensis VJH504 in controlling cucumber fusarium wilt was predicted to appear that B. velezensis VJH504is a promising biocontrol agent, showcasing excellent application potential in agricultural production.

Bacillus licheniformis JF-22 to Control Meloidogyne incognita and Its Effect on Tomato Rhizosphere Microbial Community

Meloidogyne incognita is one of the most destructive soil pests, causing serious economic losses in tomato production. Here, in vitro experiments demonstrated that the Bacillus licheniformis strain JF-22 has the potential to prevent M. incognita infection. A pot experiment confirmed that B. licheniformis strain JF-22 isolated from the tomato rhizosphere soil and planted in the tomato root-knot nematode disease area effectively prevented and controlled M. incognita, reducing its negative effect on tomato growth. Additionally, the composition of volatile substances secreted by B. licheniformis strain JF-22 was analyzed using solid-phase microextraction and gas chromatography–mass spectrometry. We detected acetoin, 2,3-Butanediol, [R-(R*,R*) ]-, and hexamethyl cyclotrisiloxane as the main components among these volatiles. Using MiSeq sequencing technology and bioinformatics, we analyzed the influence of B. licheniformis strain JF-22 on the microbial community of the tomato rhizosphere. B. licheniformis strain JF-22 changed the composition of the microbial community; particularly, it significantly reduced the diversity of the fungal community. Furthermore, using the FUNGuild and PICRUSt databases, we predicted the effect of JF-22 on microbial community function. In conclusion, B. licheniformis strain JF-22 may be considered as a potential biocontrol agent against M. incognita.

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.

Diversity, enzyme production and antibacterial activity of Bacillus strains isolated from sesame-flavored liquor Daqu

Daqu provides enzymes and precursors for liquor fermentation, and is the core of liquor fermentation. In this study, 11 Bacillus strains were isolated from sesame-flavored liquor Daqu, which can not only produce protease and amylase, but also have antagonistic effects on common pathogens Escherichia coli and Staphylococcus aureus. According to the gyrA gene phylogeny analysis, these 11 Bacillus strains belong to three species, B1, Y14, Y15, and YPDW9 belong to Bacillus mojavensis, W7, W13, YPDW6, and YPDW12 belong to Bacillus subtilis, and W14, Y5, and YPDW1 belong to Bacillus velezensis. According to the results of random amplified polymorphic DNA (RAPD) typing, there are three strains in Bacillus mojavensis, among which Y14 and Y15 are the same ones. All four Bacillus subtilis strains and three Bacillus velezensis strains are different. The specific primers were used to randomly amplify the biological control genes expressing lipopeptide antibiotics (bioA, bmyB, ituC, fenD, srfAA, srfAB, yngG,and yndJ), and the results showed that antagonistic genes other than fenD gene were amplified in four Bacillus mojavensis strains; Bacillus subtilis amplification was significantly different, but srfAA, bmyB and yndJ genes were all present; All genes were amplified in Bacillus velezensis except YPDW1 without ituC. This research provides new ideas for strengthening Daqu and lays a foundation for improving the quality of liquor.

Phage-Resistant Bacteria Reveal a Role for Potassium in Root Colonization

Bacteriophage predation is an important factor in bacterial community dynamics and evolution. Phage-bacterium interaction has mainly been studied in lab cultures, while dynamics in natural habitats, and especially in the plant root niche, are underexplored. To better understand this process, we characterized infection of the soil bacterium Bacillus subtilis NCBI 3610 by the lytic phage SPO1 during growth in LB medium and compared it to root colonization. Resistance in vitro was primarily through modification of the phage receptor. However, this type of resistance reduced the ability to colonize the root. From a line that survived phage infection while retaining the ability to colonize the root, we identified a new phage resistance mechanism involving potassium (K⁺) ion influx modulation and enhanced biofilm formation. Furthermore, we show that potassium serves as a stimulator of root colonization among diverse growth-promoting bacilli species, with implications for plant health.

Genetic Screening and Expression Analysis of Psychrophilic Bacillus spp. Reveal Their Potential to Alleviate Cold Stress and Modulate Phytohormones in Wheat

Abiotic stress in plants pose a major threat to cereal crop production worldwide and cold stress is also notorious for causing a decrease in plant growth and yield in wheat. The present study was designed to alleviate cold stress on plants by inoculating psychrophilic PGPR bacteria belonging to Bacillus genera isolated from extreme rhizospheric environments of Qinghai-Tibetan plateau. The genetic screening of psychrophilic Bacillus spp. CJCL2, RJGP41 and temperate B. velezensis FZB42 revealed presence of genetic features corresponding to cold stress response, membrane transport, signal transduction and osmotic regulation. Subsequently, the time frame study for the expression of genes involved in these pathways was also significantly higher in psychrophilic strains as analyzed through qPCR analysis at 4 ℃. The inoculated cold tolerant Bacillus strains also aided in inducing stress response in wheat by regulating abscisic acid, lipid peroxidation and proline accumulation pathways in a beneficial manner. Moreover, during comparative analysis of growth promotion in wheat all three Bacillus strains showed significant results at 25 ℃. Whereas, psychrophilic Bacillus strains CJCL2 and RJGP41 were able to positively regulate the expression of phytohormones leading to significant improvement in plant growth under cold stress.