Nowadays, population growth, the global temperature increase, and the appearance of emerging diseases in important crops generate uncertainty regarding world food security. The use of agrochemicals has been the “go-to” solution for the control of phytopathogenic microorganisms, such as Magnaporte oryzae, causing blast disease in rice and other cereals; Botrytis cinerea, causing gray mold in over 500 plant species; and Puccinia spp., causing rust in cereals. However, their excessive use has harmed human health, as well as ecosystems (contaminating water, and contributing to soil degradation); besides, phytopathogens can develop resistance to them. The inoculation of plant growth-promoting microorganisms (PGPMs) to crops is a sustainable strategy for increasing the yield and quality of crops and mitigating biotic stresses. Likewise, PGPMs, such as Pseudomonas, Bacillus, and Trichoderma, can trigger a series of signals and reactions in the plant that lead to the induction of systemic resistance, a mechanism by which plants react to microorganism stimulation by activating their defense system, resulting in protection against future pathogen attack. These plant defense mechanisms help to mitigate biotic stresses that threaten global food security. Thus, the study of these mechanisms at molecular, transcriptomic, and metabolomic levels is indispensable to elucidate how stresses affect globally important crops.

Strain 53B2 was isolated from a commercial maize (Zea mays L.) field located in the Yaqui Valley, Mexico. Its draft genome comprises 5,844,085 bp, with a G + C content of 37.5%, an N50 of 602,122 bp, an L50 of 4, and a total of 129 contigs. Genome-based taxonomic affiliation showed this strain belonged to Priestia megaterium. Genome annotation revealed 6394 coding DNA sequences (CDSs), organized into 332 subsystems. Among these, several CDSs were associated with traits relevant to plant growth promotion, including categories such as iron acquisition and metabolism (40 CDSs) and secondary metabolism (6 CDSs), among others. In vitro metabolic assays supported genomic predictions, confirming the strain’s ability to produce IAA, solubilize phosphate, and tolerate abiotic stress. Additionally, greenhouse trials demonstrated that inoculation with Priestia megaterium 53B2 significantly enhanced plant growth parameters (p ≤ 0.05) versus uninoculated control: stem height increased by 22.8%, root length by 35.7%, stem and root fresh weights by 39.6% and 66.1%, and stem and root dry weights by 33.7% and 44.7%, respectively. This first report on the beneficial potential of Priestia megaterium 53B2 highlights its potential as a sustainable bioinoculant for maize cultivation.

It is essential to hunt for new technologies that promote sustainable practices for agroecosystems; thus, the bioprospecting of beneficial microorganisms complementing with mutation induction techniques to improve their genomic, metabolic, and functional traits is a promising strategy for the development of sustainable microbial inoculants. Bacillus cabrialesii subsp. cabrialesii strain TE3^T, a previously recognized plant growth-promoting and biological control agent, was subjected to UV mutation induction to improve these agro-biotechnological traits. Dilutions were made which were spread on Petri dishes and placed under a 20 W UV lamp at 10-min intervals for 60 min. After the UV-induced mutation of this strain, 27 bacterial colonies showed morphological differences compared to the wild-type strain; however, only a strain named TE3^T-UV25 showed an improvement in 53.6% of the biocontrol against Bipolaris sorokiniana vs. the wild-type strain, by competition of nutrient and space (only detected in the mutant strain), as well as diffusible metabolites. Furthermore, the ability to promote wheat growth was evaluated by carrying out experiments under specific greenhouse conditions, considering un-inoculated, strain TE3^T, and strain TE3^T-UV25 treatments. Thus, after 120 days, biometric traits in seedlings were quantified and statistical analyses were performed, which showed that strain TE3^T-UV25 maintained its ability to promote wheat growth in comparison with the wild-type strain. On the other hand, using bioinformatics tools such as ANI, GGDC, and TYGS, the Overall Genome Relatedness Index (OGRI) and phylogenomic relationship of mutant strain TE3^T-UV25 were performed, confirming that it changed its taxonomic affiliation from B. cabrialesii subsp. cabrialesii to Bacillus subtilis. In addition, genome analysis showed that the mutant, wild-type, and B. subtilis strains shared 3654 orthologous genes; however, a higher number of shared genes (3954) was found between the TE3^T-UV25 mutant strain and B. subtilis 168, while the mutant strain shared 3703 genes with the wild-type strain. Genome mining was carried out using the AntiSMASH v7.0 web server and showed that mutant and wild-type strains shared six biosynthetic gene clusters associated with biocontrol but additionally, pulcherriminic acid cluster only was detected in the genome of the mutant strain and Rhizocticin A was exclusively detected in the genome of the wild-type strain. Finally, using the PlaBase tool, differences in the number of genes (17) associated with beneficial functions in agroecosystems were detected in the genome of the mutant vs. wild-type strain, such as biofertilization, bioremediation, colonizing plant system, competitive exclusion, phytohormone, plant immune response stimulation, putative functions, stress control, and biocontrol. Thus, the UV-induced mutation was a successful strategy to improve the bioactivity of B. cabrialesii subsp. cabrialesii TE3^T related to the agro-biotecnology applications. The obtained mutant strain, B. subtilis TE3^T-UV25, is a promising strain to be further studied as an active ingredient for the bioformulation of bacterial inoculants to migrate sustainable agriculture.

Strain TE5 was isolated from a wheat (Triticum turgidum L. subsp. durum) rhizosphere grown in a commercial field of wheat in the Yaqui Valley in Mexico. In this work, we present strain TE5 as a promising biological control agent against Bipolaris sorokiniana. First, after its genome sequencing through Illumina NovaSeq, this strain showed a genome size of 4,262,927 bp, with a 43.74% G + C content, an N50 value of 397,059 bp, an L50 value of 4 bp, and 41 contigs (>500 bp). Taxonomical affiliation was carried out by using overall genome relatedness indexes (OGRIs) and the construction of a phylogenomic tree based on the whole genome. The results indicated that strain TE5 identifies with Bacillus cabrialesii subsp. cabrialesii. Genomic annotation using Rapid Annotation Using Subsystems Technology (RAST) and Rapid Prokaryotic Genome Annotation (Prokka) indicated the presence of 4615 coding DNA sequences (CDSs) distributed across 330 subsystems, which included gene families associated with biocontrol, stress response, and iron competition. Furthermore, when the antiSMASH 7.1 platform was used for genome mining, the results indicated the presence of seven putative biosynthetic gene clusters related to the production of biocontrol metabolites, namely subtilosin A, bacillibactin, fengycin, bacillaene, bacilysin, surfactin, and rhizocticin A. Moreover, the antifungal activity of strain TE5 and its cell-free extract (CFE) was evaluated against Bipolaris sorokiniana, an emergent wheat pathogen. The results of in vitro dual confrontation showed fungal growth inhibition of 67% by strain TE5. Additionally, its CFE almost completely inhibited (93%) the growth of the studied phytopathogenic fungus on liquid media. Further observations of the impact of these bacterial metabolites on fungal spore germination exhibited inhibition of fungal spores through degrading the germinative hypha, avoiding mycelium development. Finally, the protective effect of strain TE5 against Bipolaris sorokiniana was evaluated for wheat seedlings. The results showed a significant decrease (83%) in disease severity in comparison with the plant infection without inoculation of the biological control agent. Thus, this work proposes Bacillus cabrialesii subsp. cabrialesii strain TE5 as a promising biological control agent against the wheat pathogen Bipolaris sorokiniana while suggesting lipopeptides as the potential mode of action, together with plant growth and defense stimulation.

Strain 11B20 was isolated from a commercial field of maize (Zea mays L.) located in the Yaqui Valley, Mexico. The draft genome sequence revealed a genomic size of 3,759,824 bp, 41.6% G + C content, 973,288 bp N50, 2 L50, and 29 contigs. According to the 16S rRNA gene, strain 11B20 belongs to the genus Bacillus. Genome annotation revealed 3952 coding DNA sequences (CDSs) grouped into 319 subsystems. Among these, several CDSs were associated with traits related to plant growth promotion, including (i) virulence, disease, and defense (33 CDSs); (ii) iron acquisition and metabolism (28 CDSs); and (iii) secondary metabolism (6 CDSs), among others. In vitro, metabolic analysis (IAA, siderophore biosynthesis; phosphorus solubilization; and tolerance to thermal, hydric, and saline stress) confirmed the genomic background of this strain. Finally, in planta assays showed that the inoculation of Bacillus sp. 11B20 significantly (p ≤ 0.05) increased the root length (48.2%) and root dry weight (35.4%) versus non-inoculated maize plants. Thus, this is the first report of Bacillus sp. 11B20 as a promising beneficial strain for sustainable corn production, and further research is needed to ensure the success of the application of this strain in agriculture.

The rising global food demand requires boosting agricultural productivity without compromising environmental sustainability, especially in the face of intensive agrochemical use and soil degradation. Based on this, strain TRQ67 was isolated from wheat rhizosphere soil in the Yaqui Valley, Mexico, and characterized morphologically, biochemically, and genomically. Strain TRQ67 possesses a genome of 4.04 Mbp across 37 contigs with a G + C content of 46.3%, comprising 4127 coding DNA sequences (CDSs), and was identified as Bacillus velezensis through Overall Genome Relatedness Indices (OGRIs), including Average Nucleotide Identity (OrthoANI = 99.12%) and Genome-to-Genome Distance Calculator (Formula 2: 92.6%). The genome revealed key functional genes associated with auxin biosynthesis (trpABCDEF and yhcX), iron acquisition (dhbABF), nutrient solubilization (gabD, acnAB and pyc), stress response (clpCEPX and pspA), antifungal metabolite synthesis (srfAABCD, fenABCD and bmyABC), chemotaxis and motility (cheABCD, motAB, flgBCDEF, swrC), bacterial fitness (acoABR, acuABC and budABC), exopolysaccharide production (epsDEFHI), sporulation (spo0ABEF) and bioremediation. Predicted gene functions were supported by in vitro phenotypic assays; strain TRQ67 was able to solubilize phosphate (Solubilization Index of 4.1 ± 0.46), biosynthesize siderophores (Production Index of 1.70 ± 0.16), and produce indoles (6.52 ± 0.63 µg mL⁻¹). Furthermore, this strain demonstrated antagonistic activity against phytopathogenic fungi Fusarium languescens and Bipolaris sorokiniana, resulting in reductions in fungal growth area of 87.33% and 89.28%, respectively. These antagonistic effects are consistent with the presence of Biosynthetic Gene Clusters (BGCs) encoding lipopeptides (surfactin and fengycin), polyketides (difficidin, bacillaene and macrolactin H), dipeptides (bacilysin) and siderophores (bacillibactin), as identified through antiSMASH analysis. Finally, the strain significantly improved root (27.63%) and shoot (5.82%) biomass in wheat plants under controlled conditions. These results highlight Bacillus velezensis TRQ67 as a promising microbial inoculant with plant growth promotion capabilities and potential antifungal activity against phytopathogenic fungi, as evidenced by strong in vitro antagonistic activity, supporting its further evaluation for sustainable agricultural practices.