Bacterial expansins contribute to the virulence of diverse plant pathogens, yet their biological activity and molecular roles during host interactions remain to be elucidated. Expansin-like protein, Exl1, from phytopathogens from the genus Pectobacterium, activates defense responses in Arabidopsis thaliana involving production of reactive oxygen species (ROS), and the jasmonic acid (JA), ethylene (ET), and salicylic acid (SA) pathways, ultimately reducing disease symptoms upon subsequent infections with P. brasiliense and the fungus Botrytis cinerea. However, the target of Exl1 within the plant cell wall and the downstream pathways associated with these responses are yet to be identified. Here, we analyzed the transcriptomic profile of A. thaliana leaves treated with Exl1 protein to provide a genome-wide transcriptional framework associated with Exl1-triggered immunity. Comparative transcriptomic analysis of Arabidopsis thaliana Col-0 and JA-impaired mutant jar1-1 revealed distinct transcriptional patterns associated with JA-dependent responses at early time points. Abscisic acid (ABA)-related signaling was associated with later stages of the response, supported by the increased expression of the ABA-responsive gene CRK45 six hours after Exl1 treatment, and increased susceptibility of an ABA-impaired mutant. These findings suggest the involvement of multiple phytohormone-related pathways following Exl1 treatment. In parallel, extensive transcriptional reprogramming was observed, across diverse functional categories, reflecting a broad host response associated to the presence of Exl1. Together, these findings suggest that Exl1 induces an integrated signaling network that coordinates immune responses to strengthen plant defense, providing new insight for future functional studies on how bacterial expansins modulate plant-microbe interactions.

Among microbials, Trichoderma spp. have been the focus of significant research due to their capacity to promote plant growth and suppress a wide range of phytopathogens. A total of 27 native isolates of Trichoderma spp. were obtained from diverse agroecological regions of the province of Tucumán, Argentina, and were characterized by their antagonistic activity and phytostimulant potential. In vitro assays revealed the ability of the isolates to combat fungal phytopathogens that affect various economically important crops, such as Penicillium digitatum, Alternaria alternata, Botrytis cinerea, Phytophthora capsici, and Fusarium oxysporum. Furthermore, it was determined that diffusible compounds secreted by Trichoderma isolates did not induce the elongation of the primary root of Arabidopsis thaliana in vitro; however, volatile compounds released by certain isolates not only induced this process but also increased the area occupied by the lateral roots of the plant. Based on this screening, five isolates were selected for further analyses: T. longibrachiatum (CP-1), T. breve (HM-1), T. scalesiae (L1-03), T. yunnanense (M4Ar-05), and T. atrobrunneum (M5Ar-03). The strains were evaluated for their ability to promote the growth of A. thaliana under greenhouse conditions and modulate the expression of growth and defense-related genes. All treated plants exhibited increased biomass and leaf area, accompanied by isolate-dependent changes in the expression of genes involved in plant development and immune responses. These results suggest that the selected Trichoderma spp. possess multiple beneficial traits, with valuable agricultural properties, and provide a basis for the development of bioformulations adapted to local production systems.

Emerging diseases caused by fungi are a serious threat to wildlife biodiversity. The widespread fungal pathogen Batrachochytrium dendrobatidis (Bd) has caused dramatic amphibian population declines and species extinctions worldwide. While many amphibians have been negatively affected by Bd, some populations/species have persisted despite its presence. One factor contributing to amphibian protection against this fungus is the host-associated skin microbiome. In this study, we aimed to identify gene clusters associated with the antifungal activity of amphibian skin bacteria. Specifically, we explored skin bacteria isolated from species that have persisted in the wild despite the presence of Bd: the frogs Agalychnis callidryas, Craugastor fitzingeri, Dendropsophus ebraccatus, and the axolotl Ambystoma altamirani. Bacterial isolates were tested in vitro for their capacity to inhibit the growth of two fungal pathogens: Bd and the phytopathogen Botrytis cinerea (Bc). Genome mining of these bacterial isolates revealed a diverse repertoire of Biosynthetic Gene Clusters (BGCs) and chitin-degrading gene families (ChDGFs) whose composition and abundance differed among bacterial families. We found specific BGCs and ChDGFs that were associated with the capacity of bacteria to inhibit the growth of either Bd or Bc, suggesting that distinct fungi could be inhibited by different molecular mechanisms. By using similarity networks and machine learning, we identified BGCs encoding known antifungal compounds such as viscosin, fengycin, zwittermicin, as well as siderophores and a novel family of beta-lactones. Finally, we propose that the diversity of BGCs found in amphibian skin bacteria comprise a substantial genetic reservoir that could collectively explain the antifungal properties of the amphibian skin microbiome.

Colletotrichum tropicale is an endophyte that has been reported as a pathogen in ripe mango fruits (Mangifera indica L. cv. Azúcar) in Magdalena, Colombia, causing anthracnose. However, gene expression in the host that promotes its lifestyle transition remains unknown. This study aimed to analyze gene expression during the interaction between ripe mango fruit cv. Azúcar and C. tropicale to identify differentially expressed host genes that facilitate the pathogen’s infection process. RNA sequencing (RNA-seq) analysis was conducted at 0 and 12 h post inoculation (hpi), including de novo assembly and bioinformatic functional annotation using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). A total of 5,435 differentially expressed genes (DEGs) were identified in the interaction, of which only 421 DEGs were detected in ripe mango fruits. Among these, 379 were upregulated and 42 were downregulated (T0 vs. T12 hpi). GO functional annotation of downregulated fruit genes revealed that the molecular functions affected at 12 hpi were related to the plant’s defensive oxidative burst mediated by reactive oxygen species (ROS)—including NADPH oxidase activity, hydrogen peroxide formation, and the action of peroxidases and oxidoreductase enzymes—whereas upregulated genes were associated with stress response, defense, transferase activity, and kinase activity. KEGG analysis identified pathways related to mitogen-activated protein kinase (MAPK) signaling, pathogen-associated molecular pattern (PAMP)-triggered immunity, and phenylalanine metabolism. In conclusion, ripe mango fruit cv. Azúcar activates a defense response against C. tropicale at 12 hpi that does not overcome the pathogen’s initial quiescent phase but instead facilitates conditions for its establishment by suppressing oxidative burst pathways, which may later contribute to oxidative stress during the necrotrophic phase.

BACKGROUND:Modern agriculture is based on the application of synthetic agrochemicals to control multiple abiotic and biotic stresses. Nevertheless, owing to their negative effect on ecosystems and human health, their application is increasingly restricted. The use of plant growth-promoting bacteria (PGPB) as well as biological control agents (BCAs) represents a sustainable alternative to chemical pesticides and fertilizers. Bacillus velezensis 83 (Bv83) has been described as a BCA against several fungal phytopathogens. RESULTS:In this work, we further study the molecular mechanisms behind the biological control capabilities of Bv83 using the pathosystem Arabidopsis thaliana-Botrytis cinerea. We used an in vitro system that can determine whether Bv83 can protect the plant triggering induced systemic resistance to B. cinerea. This protection was mediated by the accumulation of acetoin and the activation of phytohormone-induced mechanisms, in particular, jasmonic acid- and salicylic acid (SA)-mediated defense responses. Remarkably, we determined that in SA-impaired mutants, acetoin biosynthesis was severely reduced. CONCLUSION:Our work provides valuable information that advances our understanding of the biostimulant effect induced by the BCA Bv83. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Postharvest diseases caused by phytopathogenic fungi represent one of the main challenges in the agricultural industry, leading to significant losses in fruit production. Although chemical treatments have been widely used for the control of these pathogens, the emergence of resistant strains and concerns regarding food safety and environmental impact have driven the search for novel effective and eco-friendly alternatives, such as the use of biological control agents (BCAs). Previously, we demonstrated that bacteria isolated from frog skin inhibit the growth of the phytopathogenic fungus Botrytis cinerea. Based on these findings, in this study we aimed to investigate the biocontrol potential of three bacterial isolates obtained from the skin of the frog Craugastor fitzingeri. Dual culture assays showed that these bacteria strongly inhibited the mycelial growth of several postharvest fungal phytopathogens, including Penicillium digitatum, P. italicum, Alternaria alternata, Aspergillus niger, and Alternaria solani. This antagonistic activity was further confirmed through assays using bacterial filtrates (BFs) and volatile organic compounds (VOCs), effectively delaying or suppressing fungal development under in vitro conditions. Additionally, in vivo experiments on citrus fruits, tomato, and blueberry demonstrated that treatments with bacterial cell suspensions or BFs significantly reduced disease incidence caused by P. digitatum, A. alternata, and B. cinerea. However, no inhibitory effects were observed against Geotrichum citri-aurantii, Fusarium sp., Fusarium oxysporum, and Phytophthora capsici, suggesting a degree of specificity. Our findings highlight the potential of frog skin-associated bacteria as a novel source of BCAs for the sustainable management of postharvest diseases in fruits.

Plants and microorganisms establish beneficial associations that can improve their development and growth. Recently, it has been demonstrated that bacteria isolated from the skin of amphibians can contribute to plant growth and defense. However, the molecular mechanisms involved in the beneficial effect for the host are still unclear. In this work, we explored whether bacteria isolated from three tropical frogs species can contribute to plant growth. After a wide screening, we identified three bacterial strains with high biostimulant potential, capable of modifying the root structure of Arabidopsis thaliana plants. In addition, applying individual bacterial cultures to Solanum lycopersicum plants induced an increase in their growth. To understand the effect that these microorganisms have over the host plant, we analysed the transcriptomic profile of A. thaliana during the interaction with the C32I bacterium, demonstrating that the presence of the bacteria elicits a transcriptional response associated to plant hormone biosynthesis. Our results show that amphibian skin bacteria can function as biostimulants to improve agricultural crops growth and development by modifying the plant transcriptomic responses.

Main conclusion The biostimulant Hanseniaspora opuntiae regulates Arabidopsis thaliana root development and resistance to Botrytis cinerea . Abstract Beneficial microbes can increase plant nutrient accessibility and uptake, promote abiotic stress tolerance, and enhance disease resistance, while pathogenic microorganisms cause plant disease, affecting cellular homeostasis and leading to cell death in the most critical cases. Commonly, plants use specialized pattern recognition receptors to perceive beneficial or pathogen microorganisms. Although bacteria have been the most studied plant-associated beneficial microbes, the analysis of yeasts is receiving less attention. This study assessed the role of Hanseniaspora opuntiae, a fermentative yeast isolated from cacao musts, during Arabidopsis thaliana growth, development, and defense response to fungal pathogens. We evaluated the A. thaliana–H. opuntiae interaction using direct and indirect in vitro systems. Arabidopsis growth was significantly increased seven days post-inoculation with H. opuntiae during indirect interaction. Moreover, we observed that H. opuntiae cells had a strong auxin-like effect in A. thaliana root development during in vitro interaction. We show that 3-methyl-1-butanol and ethanol are the main volatile compounds produced by H. opuntiae. Subsequently, it was determined that A. thaliana plants inoculated with H. opuntiae have a long-lasting and systemic effect against Botrytis cinerea infection, but independently of auxin, ethylene, salicylic acid, or jasmonic acid pathways. Our results demonstrate that H. opuntiae is an important biostimulant that acts by regulating plant development and pathogen resistance through different hormone-related responses.

In plants, small RNAs (sRNAs), mainly microRNAs (miRNAs) and small interfering RNAs (siRNAs), have been described as key regulators of plant development, growth, and abiotic and biotic responses. Despite reports indicating the involvement of certain sRNAs in regulating the interaction between Botrytis cinerea (a major necrotrophic fungal phytopathogen) and host plants, there remains a lack of analysis regarding the potential regulatory roles of plant sRNAs during early stages of the interaction despite early immune responses observed then during infection. We present the first transcriptome-wide analysis of small RNA expression on the early interaction between the necrotrophic fungus Botrytis cinerea and the model plant Arabidopsis thaliana. We found that evolutionary conserved A. thaliana miRNAs were the sRNAs that accumulated the most in the presence of B. cinerea. The upregulation of miR167, miR159 and miR319 was of particular interest because these, together with their target transcripts, are involved in the fine regulation of the plant hormone signaling pathways. We also describe that miR173, which triggers the production of secondary siRNAs from TAS1 and TAS2 loci, as well as secondary siRNAs derived from these loci, is upregulated in response to B. cinerea. Thus, at an early stage of the interaction there are transcriptional changes of sRNA-guided silencing pathway genes and of a subset of sRNAs that targeted genes from the PPR gene superfamily, and these may be important mechanisms regulating the interaction between A. thaliana and B. cinerea. This work provides the basis for a better understanding of the regulation mediated by sRNAs during early B. cinerea-plant interaction and may help in the development of more effective strategies for its control.

Botrytis cinerea is the causal agent of gray mold, which affects a wide variety of plant species. Chemical agents have been used to prevent the disease caused by this pathogenic fungus. However, their toxicity and reduced efficacy have encouraged the development of new biological control alternatives. Recent studies have shown that bacteria isolated from amphibian skin display antifungal activity against plant pathogens. However, the mechanisms by which these bacteria act to reduce the effects of B. cinerea are still unclear. From a diverse collection of amphibian skin bacteria, three proved effective in inhibiting the development of B. cinerea under in vitro conditions. Additionally, the individual application of each bacterium on the model plant Arabidopsis thaliana, Solanum lycopersicum and post-harvest blueberries significantly reduced the disease caused by B. cinerea. To understand the effect of bacteria on the host plant, we analyzed the transcriptomic profile of A. thaliana in the presence of the bacterium C32I and the fungus B. cinerea, revealing transcriptional regulation of defense-related hormonal pathways. Our study shows that bacteria from the amphibian skin can counteract the activity of B. cinerea by regulating the plant transcriptional responses.

Botrytis cinerea is a necrotrophic fungus that can cause gray mold in over 1400 plant species. Once it is detected by Arabidopsis thaliana, several defense responses are activated against this fungus. The proper activation of these defenses determines plant susceptibility or resistance. It has been proposed that the RAC/ROP small GTPases might serve as a molecular link in this process. In this study, we investigate the potential role of the Arabidopsis RAC7 gene during infection with B. cinerea. For that, we evaluated A. thaliana RAC7-OX lines, characterized by the overexpression of the RAC7 gene. Our results reveal that these RAC7-OX lines displayed increased susceptibility to B. cinerea infection, with enhanced fungal colonization and earlier lesion development. Additionally, they exhibited heightened sensitivity to bacterial infections caused by Pseudomonas syringae and Pectobacterium brasiliense. By characterizing plant canonical defense mechanisms and performing transcriptomic profiling, we determined that RAC7-OX lines impaired the plant transcriptomic response before and during B. cinerea infection. Global pathway analysis of differentially expressed genes suggested that RAC7 influences pathogen perception, cell wall homeostasis, signal transduction, and biosynthesis and response to hormones and antimicrobial compounds through actin filament modulation. Herein, we pointed out, for first time, the negative role of RAC7 small GTPase during A. thaliana–B. cinerea interaction.

The Lotus japonicus population carrying new Lotus retrotransposon 1 (LORE1) insertions represents a valuable biological resource for genetic research. New insertions were generated by activation of the endogenous retroelement LORE1a in the germline of the G329-3 plant line and arranged in a 2-D system for reverse genetics. LORE1 mutants identified in this collection contributes substantially to characterize candidate genes involved in symbiotic association of L. japonicus with its cognate symbiont, the nitrogen-fixing bacteria Mesorhizobium loti that infects root nodules intracellularly. In this study we aimed to identify novel players in the poorly explored intercellular infection induced by Agrobacterium pusense IRBG74 sp. For this purpose, a forward screen of > 200,000 LORE1 seedlings, obtained from bulk propagation of G329-3 plants, inoculated with IRBG74 was performed. Plants with perturbed nodulation were scored and the offspring were further tested on plates to confirm the symbiotic phenotype. A total of 110 Lotus mutants with impaired nodulation after inoculation with IRBG74 were obtained. A comparative analysis of nodulation kinetics in a subset of 20 mutants showed that most of the lines were predominantly affected in nodulation by IRBG74. Interestingly, additional defects in the main root growth were observed in some mutant lines. Sequencing of LORE1 flanking regions in 47 mutants revealed that 92 Lotus genes were disrupted by novel LORE1 insertions in these lines. In the IM-S34 mutant, one of the insertions was located in the 5´UTR of the LotjaGi5g1v0179800 gene, which encodes the AUTOPHAGY9 protein. Additional mutant alleles, named atg9-2 and atg9-3, were obtained in the reverse genetic collection. Nodule formation was significantly reduced in these mutant alleles after M. loti and IRBG74 inoculation, confirming the effectiveness of the mutant screening. This study describes an effective forward genetic approach to obtain novel mutants in Lotus with a phenotype of interest and to identify the causative gene(s).

Resumen México es el principal productor y exportador de aguacate en el mundo. La principal zona productores es la Región Pacífico Centro de México (Jalisco, Michoacán y Nayarit) donde se cosecha el 96% de la producción nacional. Antracnosis en poscosecha de aguacate, llega a alcanzar entre 20 y 80% de pérdidas por el deterioro de la calidad del fruto de aguacate. El objetivo de la investigación fue diagnosticar el agente causal de antracnosis postcosecha de aguacate en la Región Pacífico Centro de México, el estudio se realizó entre 2019 y 2020. Se muestrearon frutos de aguacate completamente sano y se aislaron hongos patógenos causantes de antracnosis, se realizó una identificaron morfológica, molecular y filogenética, así como su desarrollo bajo estrés de fungicidas. Las características morfológicas indicaron que el hongo causante de antracnosis en postcosecha pertenece a Colletotrichum gloeosporioides sensu lato. Las pruebas moleculares y filogenética identificaron a los hongos como Colletotrichum siamense, hongo endófito, capaz de existir en dos condiciones de vida del fruto (pre y poscosecha). Este hongo bajo un estrés de fungicida permanece en estado inactivo como respuesta hasta que su efecto desaparece.

The rhizobial and the arbuscular mycorrhizal symbioses are present on legume roots and lead to local and systemic transcriptional changes of common and specific plant genes. Among them, some small GTPase proteins called ROPs (Rho of plants) have been shown to be involved in the establishment of the legume-rhizobia interaction. In this study, we aimed to characterise the effects of LjROP3 knockdown in Lotus japonicus on plant physiology and expression of symbiosis-related genes after single and dual inoculation with rhizobia and arbuscular mycorrhizal fungus. In wild-type ( Gifu ) plants, the dual inoculation increased the shoot and root dry weight, nitrogen (derived from symbiosis) and phosphate content, and the number of arbuscules or nodules compared with single inoculation treatments. In addition, we observed a decrease in the expression of genes encoding the mycorrhizal transcription factors LjRAM1 and LjRAM2, and the downstream genes involved in ammonium ( LjAMT2. 2) and phosphate ( LjPT4 and LjPT8 ) uptake by the plant at the arbuscule level when the dual inoculation was compared with fungal inoculation. An alteration in the expression of the Nod factor receptor LjNFR1 , but not of LjNFR5 , was measured in wild-type ( Gifu ) L. japonicus plants compared to rop3 plants under dual inoculation. We have also measured a reduction in the expression of genes encoding rhizobial and mycorrhizal transcription factors ( LjNIN and LjRAM1 ), and of the downstream mycorrhizal genes involved in ammonium ( LjAMT2. 2) and phosphate ( LjPT4 and LjPT8 ) uptake by the plant at the arbuscule level. In addition, the expression of AM fungal genes encoding nutrient transporters (known to be expressed at the arbuscule level) was also altered. In conclusion, despite altered expression of plant genes involved in the functioning of the symbioses, and associated with a reduction in the number of nodules and arbuscules, knockdown of LjROP3 did not alter plant growth and nutrition under dual inoculation, suggesting that the beneficial effects of the dual symbiosis were maintained.

During plant interaction with beneficial microorganisms, fungi secrete a battery of elicitors that trigger plant defenses against pathogenic microorganisms. Among the elicitor molecules secreted by Trichoderma are cerato-platanin proteins, such as EPL1, from Trichoderma atroviride. In this study, Arabidopsis thaliana plants that express the TaEPL1 gene were challenged with phytopathogens to evaluate whether expression of EPL1 confers increased resistance to the bacterial pathogen Pseudomonas syringae and the necrotrophic fungus Botrytis cinerea. Infection assays showed that Arabidopsis EPL1-2, EPL1-3, EPL1-4 expressing lines were more resistant to both pathogens in comparison to WT plants. After Pseudomonas syringae infection, there were reduced disease symptoms (e.g., small chlorotic spots) and low bacterial titers in the three 35S::TaEPL1 expression lines. Similarly; 35S::TaEPL1 expression lines were more resistant to Botrytis cinerea infection, showing smaller lesion size in comparison to WT. Interestingly, an increase in ROS levels was detected in 35S::TaEPL1 expression lines when compared to WT. A higher expression of SA- and JA-response genes occurred in the 35S::TaEPL1 lines, which could explain the resistance of these EPL1 expression lines to both pathogens. We propose that EPL1 is an excellent elicitor, which can be used to generate crops with improved resistance to broad-spectrum diseases.

EDITORIAL article Front. Plant Sci., 07 February 2023Sec. Plant Pathogen Interactions Volume 14 - 2023 | https://doi.org/10.3389/fpls.2023.1129305

Chytridiomycosis, a lethal fungal disease caused by Batrachochytrium dendrobatidis (Bd), is responsible for population declines and extinctions of amphibians worldwide. However, not all amphibian species are equally susceptible to the disease; some species persist in Bd enzootic regions with no population reductions. Recently, it has been shown that the amphibian skin microbiome plays a crucial role in the defense against Bd. Numerous bacterial isolates with the capacity to inhibit the growth of Batrachochytrium fungi have been isolated from the skin of amphibians. Here, we characterized eight Acinetobacter bacteria isolated from the frogs Agalychnis callidryas and Craugastor fitzingeri at the genomic level. A total of five isolates belonged to Acinetobacter pittii,Acinetobacter radioresistens, or Acinetobactermodestus, and three were not identified as any of the known species, suggesting they are members of new species. We showed that seven isolates inhibited the growth of Bd and that all eight isolates inhibited the growth of the phytopathogen fungus Botrytis cinerea. Finally, we identified the biosynthetic gene clusters that could be involved in the antifungal activity of these isolates. Our results suggest that the frog skin microbiome includes Acinetobacter isolates that are new to science and have broad antifungal functions, perhaps driven by distinct genetic mechanisms.

Cell wall integrity is tightly regulated and maintained given that non-physiological modification of cell walls could render plants vulnerable to biotic and/or abiotic stresses. Expansins are plant cell wall-modifying proteins active during many developmental and physiological processes, but they can also be produced by bacteria and fungi during interaction with plant hosts. Cell wall alteration brought about by ectopic expression, overexpression, or exogenous addition of expansins from either eukaryote or prokaryote origin can in some instances provide resistance to pathogens, while in other cases plants become more susceptible to infection. In these circumstances altered cell wall mechanical properties might be directly responsible for pathogen resistance or susceptibility outcomes. Simultaneously, through membrane receptors for enzymatically released cell wall fragments or by sensing modified cell wall barrier properties, plants trigger intracellular signaling cascades inducing defense responses and reinforcement of the cell wall, contributing to various infection phenotypes, in which expansins might also be involved. Here, we review the plant immune response activated by cell wall surveillance mechanisms, cell wall fragments identified as responsible for immune responses, and expansin's roles in resistance and susceptibility of plants to pathogen attack.

Plant food production is affected by multiple abiotic and biotic stresses. To overcome these limiting factors, synthetic agrochemicals are widely used. However, more stringent worldwide regulatory policies and the public demand to reduce their application have led to the search for new ecofriendly alternatives such as biostimulants. Their commercial use is still limited, mostly due to the lack of knowledge of the molecular mechanisms responsible for their effects on plant metabolism. The horseradish Moringa oleifera has been described as a source of metabolites with biostimulant potential in agriculture. In particular, its leaf extracts (MLE) have been used to improve food production by enhancing plant growth and abiotic and biotic stress tolerance. Nevertheless, the molecular basis of changes induced by the application of MLE, in particular to the plant transcriptome, are poorly understood. In this work, using Arabidopsis thaliana as model, we determined that MLEA induced tolerance to salinity and protection against the phytopathogen Botrytis cinerea. Additionally, we characterized the transcriptional changes of phytohormone-induced genes that were caused by MLE. Our work provides novel and valuable information that can help researchers to characterize the biostimulant effects induced by the miracle plant Moringa oleifera. (c) 2021 SAAB. Published by Elsevier B.V. All rights reserved.

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.