The genetic and regulatory mechanisms underlying IAA production and phosphate solubilization in Trichoderma remain poorly characterized, with limited genomic information available on genes encoding auxin-related enzymes, phytases, acid phosphatases, and those involved in organic acid biosynthesis.
Abstract
The growing global population and rising food demand have intensified reliance on chemical fertilizers, leading to soil degradation, environmental pollution, and heavy metal accumulation. As a sustainable alternative, Trichoderma spp. have gained prominence as bioinoculants due to their diverse plant growth-promoting abilities. However, emerging evidence highlights strain-specific variability and regulatory complexity in their beneficial traits, aspects that remain insufficiently addressed in current literature. This review explores the molecular basis of three key mechanisms: (i) indole-3-acetic acid (IAA) biosynthesis through indole-3-pyruvic acid (IPA), indole-3-acetamide (IAM), and tryptophan-independent pathways; (ii) phosphate solubilization mediated by phytase, phosphatase, and organic acid production; and (iii) iron (Fe) acquisition through siderophore production, primarily synthesized by nonribosomal peptide synthetases (NRPSs). Not all Trichoderma species exhibit the full spectrum of plant growth-promoting traits; while some are efficient in phosphate solubilization, others may primarily contribute through IAA production or siderophore production. Genomic and bioinformatic studies have revealed that T. atroviride, T. asperellum, T. virens, T. harzianum, T. citrinoviride, T. reesei, T. longibrachiatum, and T. koningiopsis harbor putative genes encoding proteins homologous to enzymes associated with IAA production, such as flavin monooxygenase and indoleamine-2,3-dioxygenase, as well as genes involved in siderophore production, including sidA, sidF, sidL, sidC, sidD, and sidG. However, the genetic and regulatory mechanisms underlying IAA production and phosphate solubilization in Trichoderma remain poorly characterized, with limited genomic information available on genes encoding auxin-related enzymes, phytases, acid phosphatases, and those involved in organic acid biosynthesis. These findings highlight the importance of targeted molecular research to support the development of strain-specific bioformulations that enhance nutrient use efficiency, reduce chemical inputs, and advance sustainable agricultural practices.
Findings indicate that Cupriavidus metallidurans YX16 is a salt-tolerant plant growth-promoting rhizobacterium (PGPR) that effectively alleviates salt-induced damage and promotes maize growth, providing a basis for the development of microbial agents for the amelioration of saline-alkali soils.
Bacillus velezensis TRQ67 is highlighted 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.
Kevin Montañez-Acosta, A. C. Montoya-Martínez, Ixchel Campos-Avelar et al.· Microorganisms· 0 citations
Juniperus species are a rich source of pharmacologically important secondary metabolites, including terpenoids, lignans, flavonoids, and phenolic compounds. However, the commercial utilization of these metabolites is limited by the plant’s slow growth, poor natural regeneration, and environmental variability affecting metabolite accumulation. Integrating plant tissue culture with elicitation strategies is a promising approach for sustainably producing these valuable compounds. This review summarizes the diversity, biological activities, and biotechnological significance of secondary metabolites in Juniperus, focusing on tissue culture systems and enhancement of metabolite biosynthesis through elicitors. It critically evaluates the current knowledge of the effects of signaling compounds such as methyl jasmonate (MeJA), jasmonic acid (JA), and salicylic acid (SA), as well as other abiotic and biotic elicitors including silver nanoparticles (AgNPs), chitosan, and chito-oligosaccharides. Particular attention is given to their effects on podophyllotoxin, phenolic, flavonoid, and other bioactive metabolite accumulation. Elicitation responses appear to depend strongly on species, culture system, elicitor type, and treatment conditions. This review also highlights major knowledge gaps, particularly the limited understanding of the regulatory mechanisms controlling secondary-metabolite biosynthesis in Juniperus species. Overall, the available evidence suggests that integrating optimized elicitation strategies with transcriptomics, metabolomics, and metabolic engineering could improve our understanding of secondary metabolite regulation and facilitate the development of sustainable Juniperus tissue culture platforms for producing high-value natural products.
A. Orken, D. Tussipkan, S. Manabayeva· Plants· 0 citations
This study introduces L. aquatilis strain MC3 as an emerging candidate for bioinoculant development and one of the first reports for identification of L. aquatilis as multifunctional PGPR from Himalayan ecosystems.
S. Devi, Riya Chandel, D. Thakur et al.· Frontiers in Systems Biology· 0 citations
With the growing importance of sustainable fruit production and the increasing demand for reduced reliance on chemical fertilizers and pesticides, plant growth-promoting rhizobacteria (PGPR) have attracted considerable attention as promising biological resources in orchard systems. However, current research is mainly constrained by an overreliance on single-trait interpretations of PGPR function, which cannot fully explain their performance under the complex, heterogeneous, and long-term conditions of perennial fruit production. This review provides a systematic overview of the emerging roles of PGPR in fruit production systems from a system-level perspective. Drawing on representative recent studies, this review first summarizes the shift from classical growth-promotion functions to integrated system-level regulation. It then discusses current research progress from three interrelated dimensions: rhizosphere engineering and synthetic microbiome assembly, physiological regulation of plant stress tolerance, and molecular signaling associated with induced systemic resistance. Particular emphasis is placed on key mechanisms including extracellular polymeric substance secretion, ACC deaminase activity, antioxidant regulation, hormone crosstalk, and defense priming, as well as on the role of multi-strain consortia and multi-omics approaches in linking microbial traits with host responses and rhizosphere ecological processes. This review shows that PGPR in fruit production systems function not only as direct growth promoters but also as regulators of interconnected plant–soil-microbiome processes involved in nutrient acquisition, stress adaptation, disease resistance, and fruit quality formation. Nevertheless, important limitations remain, including inconsistent field performance, weak colonization persistence, insufficient fruit tree-specific evidence, formulation difficulties, and biosafety concerns. Future research should focus on host- and environment-specific inoculant design, mechanistic validation under orchard conditions, integration of multi-omics with long-term field evaluation, and the development of persistence-oriented and safety-assessed application strategies, thereby providing a stronger theoretical and practical foundation for sustainable orchard management.
Mengqi Zhao, Ming Li, Biao Zhang· Frontiers in Microbiology· 0 citations
Plant growth-promoting bacteria (PGPB) enhance plant growth through multiple mechanisms; however, the underlying plant molecular response pathways remain insufficiently understood, particularly those mediated by bacterial volatile organic compounds (VOCs). In this study, a Bacillus strain, designated PAR690, capable of producing growth-promoting VOCs, was isolated from the rhizosphere soil of Achnatherum inebrians. Split-plate assays demonstrated that PAR690 significantly increased chlorophyll a/b, carotenoids, and total chlorophyll contents in Arabidopsis, while simultaneously promoting the accumulation of reducing sugars, soluble sugars, and starch. GC/MS analysis revealed that growth-promoting VOCs produced by Bacillus sp. PAR690 include acetoin, 2,3-butanediol, and indole. Transcriptomic analyses revealed that PAR690 significantly upregulated multiple key genes involved in the "Photosynthesis-antenna proteins", "Photosynthesis, light harvesting", and "Chlorophyll catabolic process" pathways. In addition, PAR690 downregulated the expression of methyl esterase 16 while upregulating chlorophyllase 1, thereby maintaining chlorophyll homeostasis under conditions of elevated chlorophyll content. PAR690 also enhanced nitrogen uptake and accumulation by inducing the expression of nitrate transporter 2.1 and nitrate transporter 2.5. Moreover, PAR690 significantly increased anthocyanin accumulation in Arabidopsis, an effect closely associated with the upregulation of genes related to UDP-glucose: flavonoid 3-O-glucosyltransferase and production of anthocyanin pigment 1. Collectively, these findings elucidate the potential mechanisms by which Bacillus sp. PAR690 promotes plant growth via VOC-mediated regulation at both physiological and transcriptional levels, providing new insights into PGPB-plant interactions.
Yang Yang, Jie Jin, Ronggui Liu et al.· BMC Plant Biology· 0 citations
