Jorge Luis Folch-Mallol

Microorganisms present in the rhizosphere of plants from extreme environments have become a subject of great interest as an alternative to chemical fertilizers for sustainable agriculture. This study focused on the isolation, identification and characterization of extremophilic rhizospheric fungi strains present in a habitat with challenging environmental conditions in terms of temperature, pH, and heavy metal concentrations. Studies were conducted with the aim of finding new microorganisms for the development of novel, robust inoculants that meet the agricultural needs of Solanum lycopersicum, a crop consumed worldwide that, at least in Mexico can be exposed to heat shock in certain seasons. All the strains showed at least five plant growth promoting traits. Noticeably two of the isolated strains (R_34 and R_40) produced indole related compounds (probably indoleacetic acid (IAA)); others hydrolytic enzymes (cellulases, xylanases, and chitinases), as well as siderophores and showed the ability to solubilize inorganic phosphate. All strains reduced the progression of infection caused by Botrytis cinerea on S. lycopersicum leaves and fruits compared to the control, and they also inhibited the growth of various phytopathogenic fungi under in vitro conditions, suggesting an important role in biological control. The microorganisms were identified at the species level through phylogenetic analysis. The fungal strains belonged to the genus Trichoderma sp., Penicillium sp., and Aspergillus sp. In addition, these fungi demonstrated the ability to enhance germination rates, and overall plant growth in S. lycopersicum compared to controls. This research demonstrates that extremophilic fungi can serve as effective probiotics for crops in regions affected by climate variability and heatwaves.

Phosphorus (P) is an essential nutrient in plant development, but its availability in the soil is often limited due to chemical fixation and poor solubility. This study presents the development, characterization and evaluation of a novel granular bioinoculant formulated with Aspergillus tubingensis (P-solubilizing) and Trichoderma virens (P-mineralizing) using clinoptilolite (CZ) as a carrier to improve P bioavailability. The formulation process included the evaluation of the proposed components, the standardization of conidia production in different media cultures and conditions, the elaboration and characterization of the bioinoculant and its evaluation in plants. In this study, in vitro analysis demonstrated the synergistic effect of the components, showing that in all treatments with dual inoculation and CZ, the amount of soluble phosphorus (SP) was higher than in their counterparts (from 27.8 to 36.8 mg·L⁻¹). A concentration greater than 1 × 10⁹ CFU·mL⁻¹ was obtained by standardizing the production of conidia in different media (PDA, V8-Agar and Molasses Agar), which were then used to produce granular batches containing at least 2 × 10⁷ CFU·g⁻¹. Furthermore, the size (88% of the granules measured −1 in 10⁻⁴ dilution), and moisture content of the prototype granules (3.3–3.8%) were confirmed to be within established international quality parameters. Plant evaluations in chili and tomato demonstrated the formulation efficacy, showing an increase in both soluble and foliar P content (with at least 30% more than controls), alongside improvements in all parameters evaluated that are related to plant growth promotion (with at least 15% more growth than controls). The development of this formulation prototype represents a focused effort toward process standardization and optimization required to validate developed formulations, thus promoting the advancement of applied biotechnology.

Introduction: The genus Trichoderma encompasses cosmopolitan fungi that play key ecological and biotechnological roles, including mycoparasitism, plant growth promotion, and tolerance to abiotic stress. As the catalog of undescribed species continues to expand, the need for precise species delimitation is increasingly evident. Methods: In this work, we isolated strain BMH-0061 as a root endophyte of chili ( Capsicum annuum ) and assessed its phenotypic and antagonistic potential. This strain originated from Mexico’s milpa agroecosystem, an underexplored reservoir of microbial diversity. To robustly evaluate its taxonomic status, we generated a near-complete, telomere-to-telomere genome assembly and assessed its completeness with BUSCO. Subsequently, we evaluated a comprehensive set of genomic coherence metrics, including Average Nucleotide Identity (ANI), Average Amino Acid Identity (AAI), Percentage of Conserved Proteins (POCP), and k-mer composition. Results: Integrative phylogenomic analyses, supported by Bayesian speciation models and clustering-based comparisons, consistently recovered BMH-0061 as an independent lineage. The strain exhibited broad-spectrum mycoparasitism against phytopathogens and tolerance to moderate abiotic stress. Morphological characterization, growth profiles, and multi-gene phylogenies suggested its placement within the Trichoderma genus, but it is distinct from known species. A near-complete telomere-to-telomere genome assembly was obtained, showing a BUSCO completeness of 99.08%. Genomic coherence analyses revealed that strain BMH-0061 shared ANI values ranging from 83.93% to 94.43% with its closest Trichoderma relatives, supporting its distinction as a separate lineage. Discussion: We formally describe this new taxon as Trichoderma tlahuicanensis sp. nov., in honor of the indigenous pre-Hispanic Tlahuica people of Morelos, Mexico. Our work demonstrates how a phylophenetic framework, combining genomic, phylogenetic, genetic diversity, and evolutionary analyses, provides a powerful approach to species delimitation. This integrative strategy confirms the recognition of T. tlahuicanensis as a distinct species while offering a methodological pathway for peers engaged in fungal systematics

Thermophilic fungi have been seldom studied despite the fact that they can contribute to understanding ecological mechanisms of adaptation in diverse environments and have attractive toolboxes with a wide range of biotechnological applications. This work describes for the first time an endophytic and thermophilic strain of Aspergillus brasiliensis that was isolated in the crater of the active volcano “El Chichonal” in Mexico. This strain was capable of surviving in soil with a temperature of 60 °C and a pH of neutral acidity, which preluded a high thermostability and a potential in industrial application. The complete genome of A. brasiliensis E_15.1 was sequenced and assembled in 37 Mb of genomic DNA. We performed a comprehensive phylogenomic analysis for the precise taxonomic identification of this species as a novel strain of Aspergillus brasiliensis. Likewise, the predicted coding sequences were classified according to various functions including Carbohydrate-Active Enzymes (CAZymes), biosynthetic gene clusters of secondary metabolites (BGCs), and metabolic pathways associated with plant growth promotion. A. brasiliensis E_15.1 was found to degrade chitin, chitooligosaccharides, xylan, and cellulose. The genes to biosynthesize clavaric acid (a triterpene with antitumor activity) were found, thus probably having antitumor activity. In addition to the genomic analysis, a set of enzymatic assays confirmed the thermostability of extracellular xylanases and cellulases of A. brasiliensis E_15.1. The enzymatic repertoire of A. brasiliensis E_15.1 suggests that A. brasiliensis E_15.1 has a high potential for industrial application due to its thermostability and can promote plant growth at high temperatures. Finally, this strain constitutes an interesting source of terpenoids with pharmacological activity.

Thermophilic fungi constitute an interesting study model for understanding ecologi-cal mechanisms of adaptation in diverse environments and have attractive toolboxes with a wide range of biotechnological applications. This work describes for the first time an endophytic and thermophilic strain of Aspergillus brasiliensis that was isolated in the crater of the active volcano "El Chichonal" in Mexico. The average temperature of the collection site was around 60 °C and the soil pH was moderately acidic. The complete genome of A. brasiliensis E_15.1 was sequenced and assembled in about 37 Mb of genomic DNA. We performed a comprehensive phylogenomic anal-ysis for the precise taxonomic identification of this species as a novel strain of Aspergillus brasil-iensis. Likewise, the predicted coding sequences were classified according to various functions including Carbohydrate-Active Enzymes (CAZymes), biosynthetic gene clusters of secondary metabolites (BGCs), and metabolic pathways associated with plant growth promotion. Among the functional traits identified was the degradation of chitin, chitooligosaccharides, xylan, and cellulose, as well as the biosynthesis of clavaric acid, a triterpene with antitumor activity due to its ability to inhibit Farnesyl-protein transferase. In addition to the genomic analysis, a set of en-zymatic assays confirmed the thermostability of extracellular xylanases, cellulases of A. brasili-ensis E_15.1. Our findings suggest that the enzymatic repertoire of A. brasiliensis E_15.1 has a high potential for industrial application due to its thermostability and can promote plant growth at high temperatures. Finally, this strain constitutes an interesting source of terpenoids with pharmacological activity.

Aspergillus flavus has been found to be an effective entomopathogenic fungus for various arthropods, including ticks. In particular, natural fungal infections in cattle ticks show promise for biocontrol of the Rhipicephalus (Boophilus) microplus tick, which is a major ectoparasite affecting cattle worldwide. Our study aimed to elucidate the specific entomopathogenic virulence factors encoded in the genome of an A. flavus strain isolated from naturally infected cattle ticks. We performed morphological and biochemical phenotyping alongside complete genome sequencing, which revealed that the isolated fungus was A. flavus related to the L morphotype, capable of producing a range of gene-coded entomopathogenic virulence factors, including ribotoxin, aflatoxin, kojic acid, chitinases, killer toxin, and satratoxin. To evaluate the efficacy of this A. flavus strain against ticks, we conducted experimental bioassays using healthy engorged female ticks. A morbidity rate of 90% was observed, starting at a concentration of 10⁵ conidia/mL. At a concentration of 10⁷ conidia/mL, we observed a 50% mortality rate and a 21.5% inhibition of oviposition. The highest levels of hatch inhibition (30.8%) and estimated reproduction inhibition (34.64%) were achieved at a concentration of 10⁸ conidia/mL. Furthermore, the tick larval progeny that hatched from the infected tick egg masses showed evident symptoms of Aspergillus infection after incubation.

Heavy metal pollution is a worldwide environmental and human health problem. Prosopis laevigata is a hyperaccumulator legume that bioaccumulates Pb, Cu and Zn. With interest in designing phytoremediation strategies for sites contaminated with heavy metals, we isolated and characterized endophytic fungi from the roots of P. laevigata growing on mine tailings located in Morelos, Mexico. Ten endophytic isolates were selected by morphological discrimination and a preliminary minimum inhibitory concentration was determined for zinc, lead and copper. A novel strain of Aspergillus closest to Aspergillus luchuensis was determined to be a metallophile and presented a marked tolerance to high concentrations of Cu, Zn and Pb, so it was further investigated for removal of metals and promotion of plant growth under greenhouse conditions. The control substrate with fungi promoted larger size characters in P. laevigata individuals in comparison with the other treatments, demonstrating that A. luchuensis strain C7 is a growth-promoting agent for P. laevigata individuals. The fungus favors the translocation of metals from roots to leaves in P. laevigata, promoting an increased Cu translocation. This new A. luchuensis strain showed endophytic character and plant growth-promotion activity, high metal tolerance, and an ability to increase copper translocation. We propose it as a novel, effective and sustainable bioremediation strategy for copper-polluted soils.

The Capsicum genus has significant economic importance since it is cultivated and consumed worldwide for its flavor and pungent properties. In 2021, Mexico produced 3.3 billion tons on 45,000 hectares which yielded USD 2 billion in exports to the USA, Canada, Japan, etc. Soil type has a dramatic effect on phosphorus (P) availability for plants due to its ion retention. In a previous study, novel fungal isolates were shown to solubilize and mineralize P in different kinds of soils with different P retention capacities. The aim of this work was to study the effects of the mineralogy of different kinds of “milpa” soils on the germination, biomass production, and P absorption of chili plants (Capsicum annuum). The germination percentage, the germination speed index, and the mean germination time were significantly increased in the plants treated with dual inoculation. Foliar phosphorus, growth variables, and plant biomass of chili plants grown in a greenhouse were enhanced in different soil types and with different inocula. Correlation studies suggested that the most significant performance in the foliar P concentration and in the growth response of plants was achieved in Vertisol with dual inoculation of 7 × 10⁶ mL⁻¹ spores per chili plant, suggesting this would be an appropriate approach to enhance chili cultivation depending on the soil type. This study stresses the importance of careful analysis of the effect of the soil type in the plant–microbe interactions.

Here, we analyzed the effects on Capsicum annuum plants of Trichoderma atroviride P. Karst strains altered in the expression of SWOLLENIN (SWO1), a protein with amorphogenic activity on plant cell wall components. Strains of T. atroviride that overexpressed the Taswo1 gene were constructed as well as deletion mutants. A novel, cheap and accurate method for assessing root colonization was developed. Colonization assays showed that the Taswo1 overexpressing strains invaded the host root better than the WT, resulting in a stronger plant growth-promoting effect. The expression of plant defense marker genes for both the systemic acquired resistance and induced systemic resistance pathways was enhanced in plants inoculated with Taswo1 overexpressing strains, while inoculation with deletion mutant strains resulted in a similar level of expression to that observed upon inoculation with the wild-type strain. Response to pathogen infection was also enhanced in the plants inoculated with the Taswo1 overexpressing strains, and surprisingly, an intermediate level of protection was achieved with the mutant strains. Tolerance to abiotic stresses was also higher in plants inoculated with the Taswo1 overexpressing strains but was similar in plants inoculated with the wild-type or the mutant strains. Compatible osmolyte production in drought conditions was studied. This study may contribute to improving Trichoderma biocontrol and biofertilization abilities.