Complete Genome Sequence Analysis of Bacillus subtilis Bbv57, a Promising Biocontrol Agent against Phytopathogens

Metagenomics approaches in unveiling the dynamics of Plant Growth-Promoting Microorganisms (PGPM) vis-à-vis Phytophthora sp. suppression in various crop ecological systems

Phytophthora species are destructive pathogens causing yield losses in different ecological systems, such as potato, black pepper, pepper, avocado, citrus, and tobacco. The diversity of plant growth-promoting microorganisms (PGPM) plays a crucial role in disease suppression. Knowledge of metagenomics approaches is essential for assessing the dynamics of PGPM and Phytophthora species across various ecosystems, facilitating effective management strategies for better crop protection. This review discusses the dynamic interplay between PGPM and Phytophthora sp. using metagenomics approaches that sheds light on the potential of PGPM strains tailored to specific crop ecosystems to bolster pathogen suppressiveness.

Unleashing Bacillus species as versatile antagonists: Harnessing the biocontrol potentials of the plant growth-promoting rhizobacteria to combat Macrophomina phaseolina infection in Gloriosa superba

Charcoal rot caused by Macrophomina phaseolina is one of the most devastating diseases that cause severe yield loss in Gloriosa superba cultivation. Plant growth-promoting rhizobacteria (PGPR) are extensively harnessed as biocontrol agents due to their effectiveness in combating a wide array of plant pathogens through a multifaceted approach. The present study delved into the mechanisms underlying its ability to inhibit root rot pathogen and its capacity to promote plant growth in G. superba, commonly known as glory lily. PGPR isolated from the rhizosphere of glory lily were subjected to in vitro assessments using the dual plate technique. The isolated Bacillus subtilis BGS-10 and B. velezensis BGS-21 showed higher mycelial inhibition (61%) against M. phaseolina. These strains also promote plant growth by producing indole-3-acetic acid, siderophore, ammonia, amylase, cellulase, pectinase, xylanase, and lipase chemicals. Genome screening of BGS-10 and BGS-21 revealed the presence of antimicrobial peptide genes such as Iturin (ituD gene), surfactin (srfA and sfp genes) along with the mycolytic enzyme β-1,3-glucanase. Further, the presence of secondary metabolites in the bacterial secretome was identified through gas chromatography-mass spectrometry (GC/MS) analysis. Notably, pyrrolo[1,2-a] pyrazine-1,4-dione, hexahydro-3-(2-methylpropyl), 9 H-pyrido[3,4-b] indole and L-leucyl-D-leucine exhibited the highest docking score against enzymes responsible for pathogen growth and plant cell wall degradation. Under glasshouse conditions, tuber treatment and soil application of talc-based formulation of B. subtilis BGS-10 and B. velezensis BGS-21 suppress the root rot incidence with a minimal disease incidence of 27.78% over untreated control. Concurrently, there was a notable induction of defense-related enzymes, including peroxidase (PO), polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL), in glory lily. Therefore, it can be concluded that plant growth-promoting Bacillus strains play a significant role in fortifying the plant's defense mechanisms against the root rot pathogen.

A polylactic acid degrading lipase from Bacillus safensis: Characterization and structural analysis

A polylactic acid degrading triacylglycerol lipase (TGL) was identified from Bacillus safensis based on genome annotation and validated by real-time quantitative PCR. TGL displayed optimal activity at pH 9.0 and 55 °C. It maintained stability at pH 9.0 and temperatures 45 °C. The activity of TGL was found to benefit from the presence of potassium sodium ions, and low concentrations of Triton X-100. The TGL could erode the surface of polylactic acid films and increase its hydrophilicity. The hydrolysis products of polylactic acid by TGL were lactate monomer and dimer. TGL contains a classical catalytic triad structure of lipase (Ser77, Asp133, and His156) and an Ala-X-Ser-X-Gly sequence. Compared with some lipases produced by the same genus Bacillus, TGL is highly conserved in its amino acid sequence, mainly reflected in the amino acid residues that exercise the enzyme activity, including the catalytic activity center and the substrate binding sites.

Whole genome analysis of Bacillus velezensis 160, biological control agent of corn head smut

Corn head smut is a disease caused by the fungus Sporisorium reilianum. This phytosanitary problem has existed for several decades in the Mezquital Valley, an important corn-producing area in central Mexico. To combat the problem, a strain identified as Bacillus subtilis 160 was applied in the field, where it decreased disease incidence and increased crop productivity. In this study, the sequencing and analysis of the whole genome sequence of this strain were carried out to identify its genetic determinants for the production of antimicrobials. The B. subtilis 160 strain was found to be Bacillus velezensis. Its genome has a size of 4,297,348 bp, a GC content of 45.8%, and 4,174 coding sequences. Comparative analysis with the genomes of four other B. velezensis strains showed that they share 2,804 genes and clusters for the production of difficidin, bacillibactin, bacilysin, macrolantin, bacillaene, fengycin, butirosin A, locillomycin, and surfactin. For the latter metabolite, unlike the other strains that have only one cluster, B. velezensis 160 has three. A cluster for synthesizing laterocidine, an antimicrobial reported only in Brevibacillus laterosporus, was also identified.

IMPORTANCE

In this study, we performed sequencing and analysis of the complete genome of the strain initially identified as Bacillus subtilis 160 as part of its characterization. This bacterium has shown its ability to control corn head smut in the field, a disease caused by the basidiomycete fungus Sporisorium reilianum. Analyzing the complete genome sequence not only provides a more precise taxonomic identification but also sheds light on the genetic potential of this bacterium, especially regarding mechanisms that allow it to exert biological control. Employing molecular and bioinformatics tools in studying the genomes of agriculturally significant microorganisms offers insights into the development of biofungicides and bioinoculants. These innovations aim to enhance plant growth and pave the way for strategies that boost crop productivity.

Characterization and evaluation of Bacillus subtilis GYUN-2311 as a biocontrol agent against Colletotrichum spp. on apple and hot pepper in Korea

Crop plants are vulnerable to a variety of diseases, including anthracnose, caused by various species of Colletotrichum fungi that damages major crops, including apples and hot peppers. The use of chemical fungicides for pathogen control may lead to environmental pollution and disease resistance. Therefore, we conducted this research to develop a Bacillus subtilis-based biological control agent (BCA). B. subtilis GYUN-2311 (GYUN-2311), isolated from the rhizosphere soil of an apple orchard, exhibited antagonistic activity against a total of 12 fungal pathogens, including eight Colletotrichum species. The volatile organic compounds (VOCs) and culture filtrate (CF) from GYUN-2311 displayed antifungal activity against all 12 pathogens, with 81% control efficiency against Fusarium oxysporum for VOCs and 81.4% control efficacy against Botryosphaeria dothidea for CF. CF also inhibited germination and appressorium formation in Colletotrichum siamense and C. acutatum. The CF from GYUN-2311 showed antifungal activity against all 12 pathogens in different media, particularly in LB medium. It also exhibited plant growth-promoting (PGP) activity, lytic enzyme activity, siderophore production, and the ability to solubilize insoluble phosphate. In trials on apples and hot peppers, GYUN-2311 effectively controlled disease, with 75 and 70% control efficacies against C. siamense in wounded and unwounded apples, respectively. Similarly, the control efficacy of hot pepper against C. acutatum in wounded inoculation was 72%. Combined application of GYUN-2311 and chemical suppressed hot pepper anthracnose to a larger extent than other treatments, such as chemical control, pyraclostrobin, TK®, GYUN-2311 and cross-spraying of chemical and GYUN-2311 under field conditions. The genome analysis of GYUN-2311 identified a circular chromosome comprising 4,043 predicted protein-coding sequences (CDSs) and 4,096,969 bp. B. subtilis SRCM104005 was the strain with the highest average nucleotide identity (ANI) to GYUN-2311. AntiSMASH analysis identified secondary metabolite biosynthetic genes, such as subtilomycin, bacillaene, fengycin, bacillibactin, pulcherriminic acid, subtilosin A, and bacilysin, whereas BAGEL analysis confirmed the presence of competence (ComX). Six secondary metabolite biosynthetic genes were induced during dual culture in the presence of C. siamense. These findings demonstrate the biological control potential of GYUN-2311 against apple and hot pepper anthracnose.

Survival strategies of Bacillus spp. in saline soils: Key factors to promote plant growth and health

Soil salinity is one of the most important abiotic factors that affects agricultural production worldwide. Because of saline stress, plants face physiological changes that have negative impacts on the various stages of their development, so the employment of plant growth-promoting bacteria (PGPB) is one effective means to reduce such toxic effects. Bacteria of the Bacillus genus are excellent PGPB and have been extensively studied, but what traits makes them so extraordinary to adapt and survive under harsh situations? In this work we review the Bacillus' innate abilities to survive in saline stressful soils, such as the production osmoprotectant compounds, antioxidant enzymes, exopolysaccharides, and the modification of their membrane lipids. Other survival abilities are also discussed, such as sporulation or a reduced growth state under the scope of a functional interaction in the rhizosphere. Thus, the most recent evidence shows that these saline adaptive activities are important in plant-associated bacteria to potentially protect, direct and indirect plant growth-stimulating activities. Additionally, recent advances on the mechanisms used by Bacillus spp. to improve the growth of plants under saline stress are addressed, including genomic and transcriptomic explorations. Finally, characterization and selection of Bacillus strains with efficient survival strategies are key factors in ameliorating saline problems in agricultural production.

Whole-genome sequencing and antimicrobial potential of bacteria isolated from Polish honey

The aim of this study was the whole-genome analysis and assessment of the antimicrobial potential of bacterial isolates from honey harvested in one geographical location-the north of Poland. In total, 132 strains were derived from three honey samples, and the antimicrobial activity of CFAM (cell-free after-culture medium) was used as a criterion for strain selection and detailed genomic investigation. Two of the tested isolates (SZA14 and SZA16) were classified as Bacillus paralicheniformis, and one isolate (SZB3) as Bacillus subtilis based on their ANI and phylogenetic analysis relatedness. The isolates SZA14 and SZA16 were harvested from the same honey sample with a nucleotide identity of 98.96%. All three isolates have been found to be potential producers of different antimicrobial compounds. The secondary metabolite genome mining pipeline (antiSMASH) identified 14 gene cluster coding for non-ribosomal peptide synthetases (NRPs), polyketide synthases (PKSs), and ribosomally synthesized and post-translationally modified peptides (RiPPs) that are potential sources of novel antibacterials. The BAGEL4 analysis revealed the presence of nine putative gene clusters of interest in the isolates SZA14 and SZA16 (including the presence of six similar clusters present in both isolates, coding for the production of enterocin Nkr-5-3B, haloduracin-alpha, sonorensin, bottromycin, comX2, and lasso peptide), and four in B. subtilis isolate SZB3 (competence factor, sporulation-killing factor, subtilosin A, and sactipeptides). The outcomes of this study confirm that honey-derived Bacillus spp. strains can be considered potential producers of a broad spectrum of antimicrobial agents. KEY POINTS: • Bacteria of the genus Bacillus are an important component of honey microbiota. • Honey-derived Bacillus spp. strains are potential producers of new antimicrobials.

Isolation and Identification of Biocontrol Bacteria against Atractylodes Chinensis Root Rot and Their Effects

Fusarium root rot (FRR) seriously affects the growth and productivity of A. chinensis. Therefore, protecting A. chinensis from FRR has become an important task, especially for increasing A. chinensis production. The purpose of this study was to screen FRR control strains from the A. chinensis rhizosphere soil. Eighty-four bacterial strains and seven fungal strains were isolated, and five strains were identified with high inhibitory effects against Fusarium oxysporum (FO): Trichoderma harzianum (MH), Bacillus amyloliquefaciens (CJ5, CJ7, and CJ8), and Bacillus subtilis (CJ9). All five strains had high antagonistic effects in vitro. Results showed that MH and CJ5, as biological control agents, had high control potential, with antagonistic rates of 86.01% and 82.78%, respectively. In the pot experiment, the growth levels of roots and stems of A. chinensis seedlings treated with MH+CJ were significantly higher than those of control plants. The total nitrogen, total phosphorus, total potassium, indoleacetic acid, and chlorophyll contents in A. chinensis leaves were also significantly increased. In the biocontrol test, the combined MH + CJ application significantly decreased the malondialdehyde content in A. chinensis roots and significantly increased the polyphenol oxidase, phenylalanine ammonolyase, and peroxidase ability, indicating a high biocontrol effect. In addition, the application of Bacillus spp. and T. harzianum increased the abundance and diversity of the soil fungal population, improved the soil microbial community structure, and significantly increased the abundance of beneficial strains, such as Holtermanniella and Metarhizium. The abundance of Fusarium, Volutella, and other pathogenic strains was significantly reduced, and the biocontrol potential of A. chinensis root rot was increased. Thus, Bacillus spp. and T. harzianum complex bacteria can be considered potential future biocontrol agents for FRR.

Plant growth-promoting and heavy metal-resistant Priestia and Bacillus strains associated with pioneer plants from mine tailings

Open mine tailings dams are extreme artificial environments containing sizeable potentially toxic elements (PTEs), including heavy metals (HMs), transition metals, and metalloids. Furthermore, these tailings have nutritional deficiencies, including assimilable phosphorus sources, organic carbon, and combined nitrogen, preventing plant colonization. Bacteria, that colonize these environments, have mechanisms to tolerate the selective pressures of PTEs. In this work, several Priestia megaterium (formerly Bacillus megaterium), Bacillus mojavensis, and Bacillus subtilis strains were isolated from bulk tailings, anthills, rhizosphere, and endosphere of pioneer plants from abandoned mine tailings in Zacatecas, Mexico. Bacillus spp. tolerated moderate HMs concentrations, produced siderophores and indole-3-acetic acid (IAA), solubilized phosphates, and reduced acetylene in the presence of HMs. The strains harbored different PIB-type ATPase genes encoding for efflux pumps and Cation Diffusion Facilitator (CDF) genes. Moreover, nifH and nifD nitrogenase genes were detected in P. megaterium and B. mojavensis genomic DNA. They showed similarity with sequences of the beta-Proteobacteria species, which may represent likely horizontal transfer events. These Bacillus species precede the colonization of mine tailings by plants. Their phenotypic and genotypic features could be essential in the natural recovery of the sites by reducing the oxidative stress of HMs, fixing nitrogen, solubilizing phosphate, and accumulating organic carbon. These traits of the strains reflect the adaptations of Bacillus species to the mine tailings environment and could contribute to the success of phytoremediation efforts.

Genome insights into the plant growth-promoting bacterium Saccharibacillus brassicae ATSA2T

Endophytes can facilitate the improvement of plant growth and health in agriculturally important crops, yet their genomes and secondary metabolites remain largely unexplored. We previously isolated Saccharibacillus brassicae strain ATSA2^T from surface-sterilized seeds of kimchi cabbage and represented a novel species of the genus Saccharibacillus. In this study, we evaluated the plant growth-promoting (PGP) effect of strain ATSA2^T in kimchi cabbage, bok choy, and pepper plants grown in soils. We found a significant effect on the shoot and root biomass, and chlorophyll contents following strain ATSA2^T treatment. Strain ATSA2^T displayed PGP traits such as indole acetic acid (IAA, 62.9 μg/mL) and siderophore production, and phosphate solubilization activity. Furthermore, genome analysis of this strain suggested the presence of gene clusters involved in iron acquisition (fhuABD, afuABC, fbpABC, and fepCDG) and phosphate solubilization (pstABCHS, phoABHLU, and phnCDEP) and other phytohormone biosynthesis genes, including indole-3-acetic acid (trpABCDEFG), in the genome. Interestingly, the secondary metabolites cerecidin, carotenoid, siderophore (staphylobactin), and bacillaene underlying plant growth promotion were found in the whole genome via antiSMASH analysis. Overall, physiological testing and genome analysis data provide comprehensive insights into plant growth-promoting mechanisms, suggesting the relevance of strain ATSA2^T in agricultural biotechnology.