Trichoderma - genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture

Trichoderma and Mycosynthesis of Metal Nanoparticles: Role of Their Secondary Metabolites

Nanocompounds are widely used in many fields such as environmental, medicine, or agriculture. Nowadays, these nanocompounds are mainly synthesized by chemical methods, causing environmental pollution and potential health problems. Thus, microorganisms have been investigated as potential nanoparticle green biosynthesizers. The main research is focused on the synthesis of nanoparticles (NPs) using algae, yeast, bacteria, and fungi. Among them, fungi have been the most used, due to their simple and effective mycosynthesis. Fungi as well as other organisms involved in green synthesis of NPs use their secondary metabolites (SMs) to mediate and catalyze the reactions to produce metal nanoparticles (MNPs) as well as being able to act as capping agents producing different physicochemical characteristics and biological activities in the MNPs. Among the various fungi used for mycosynthesis are Trichoderma species, which mediate the production of Ag, Cu, CuO, Zn, ZnO, and other MNPs. Here, we review the main SMs from Trichoderma that have been reported or suggested to contribute to synthesize or act as capping agents and their applications, as well as present the main challenges faced by this type of synthesis.

Mycorrhizosphere bacteria inhibit greenhouse gas emissions from microplastics contaminated soil by regulating soil enzyme activities and microbial community structure

Microplastics (MPs) accumulation in terrestrial ecosystems can affect greenhouse gases (GHGs) production by altering microbial and soil structure. Presently, research on the MPs effect on plants is not consistent, and underlying molecular mechanisms associated with GHGs are yet unknown. For the first time, we conducted a microcosm study to explore the impact of MPs addition (Raw vs. aged) and Trichoderma longibrachiatum and Bacillus subtilis inoculation (Sole vs. combination) on GHGs emission, soil community structure, physiochemical properties, and enzyme activities. Our results indicated that the addition of aged MPs considerably enhanced the GHGs emissions (N2O (+16%) and CO2 (+21%), respectively), C and N cycling gene expression, microbial biomass carbon, and soil physiochemical properties than raw MPs. However, the soil microbial community structure and enzyme activities were enhanced in raw MPs added treatments, irrespective of the MPs type added to soil. However, microbial inoculation significantly reduced GHGs emission by altering the expression of C and N cycling genes in both types of MPs added treatments. The soil microbial community structure, enzymes activities, physiochemical properties and microbial biomass carbon were enhanced in the presence of microbial inoculation in both type of MPs. Among sole and combined inoculation of Trichoderma and Bacillus subtilis, the co-applied Trichoderma and Bacillus subtilis considerably reduced the GHGs emission (N2O (-64%) and CO2 (-61%), respectively) by altering the expression of C and N cycling genes regardless of MPs type used. The combined inoculation also enhanced soil enzyme activities, microbial community structure, physiochemical properties and microbial biomass carbon in both types of MPs treatment. Our findings provide evidence that polyethylene MPs likely pose a high risk of GHGs emission while combined application of Trichoderma and Bacillus subtilis significantly reduced GHGs emission by altering C and N cycling gene expression, soil microbial community structure, and enzyme activities under MPs pollution in a terrestrial ecosystem.

Mechanisms for plant growth promotion activated by Trichoderma in natural and managed terrestrial ecosystems

Trichoderma spp. are free-living fungi present in virtually all terrestrial ecosystems. These soil fungi can stimulate plant growth and increase plant nutrient acquisition of macro- and micronutrients and water uptake. Generally, plant growth promotion by Trichoderma is a consequence of the activity of potent fungal signaling metabolites diffused in soil with hormone-like activity, including indolic compounds as indole-3-acetic acid (IAA) produced at concentrations ranging from 14 to 234 μg l-1, and volatile organic compounds such as sesquiterpene isoprenoids (C15), 6-pentyl-2H-pyran-2-one (6-PP) and ethylene (ET) produced at levels from 10 to 120 ng over a period of six days, which in turn, might impact plant endogenous signaling mechanisms orchestrated by plant hormones. Plant growth stimulation occurs without the need of physical contact between both organisms and/or during root colonization. When associated with plants Trichoderma may cause significant biochemical changes in plant content of carbohydrates, amino acids, organic acids and lipids, as detected in Arabidopsis thaliana, maize (Zea mays), tomato (Lycopersicon esculentum) and barley (Hordeum vulgare), which may improve the plant health status during the complete life cycle. Trichoderma-induced plant beneficial effects such as mechanisms of defense and growth are likely to be inherited to the next generations. Depending on the environmental conditions perceived by the fungus during its interaction with plants, Trichoderma can reprogram and/or activate molecular mechanisms commonly modulated by IAA, ET and abscisic acid (ABA) to induce an adaptative physiological response to abiotic stress, including drought, salinity, or environmental pollution. This review, provides a state of the art overview focused on the canonical mechanisms of these beneficial fungi involved in plant growth promotion traits under different environmental scenarios and shows new insights on Trichoderma metabolites from different chemical classes that can modulate specific plant growth aspects. Also, we suggest new research directions on Trichoderma spp. and their secondary metabolites with biological activity on plant growth.

Trichoderma hamatum and Its Benefits

Trichoderma hamatum (Bonord.) Bainier (T. hamatum) belongs to Hypocreaceae family, Trichoderma genus. Trichoderma spp. are prominently known for their biocontrol activities and plant growth promotion. Hence, T. hamatum also possess several beneficial activities, such as antimicrobial activity, antioxidant activity, insecticidal activity, herbicidal activity, and plant growth promotion; in addition, it holds several other beneficial properties, such as resistance to dichlorodiphenyltrichloroethane (DDT) and degradation of DDT by certain enzymes and production of certain polysaccharide-degrading enzymes. Hence, the current review discusses the beneficial properties of T. hamatum and describes the gaps that need to be further considered in future studies, such as T. hamatum's potentiality against human pathogens and, in contrast, its role as an opportunistic human pathogen. Moreover, there is a need for substantial study on its antiviral and antioxidant activities.

RGS4 impacts carbohydrate and siderophore metabolism in Trichoderma reesei

BACKGROUND

Adaptation to complex, rapidly changing environments is crucial for evolutionary success of fungi. The heterotrimeric G-protein pathway belongs to the most important signaling cascades applied for this task. In Trichoderma reesei, enzyme production, growth and secondary metabolism are among the physiological traits influenced by the G-protein pathway in a light dependent manner.

RESULTS

Here, we investigated the function of the SNX/H-type regulator of G-protein signaling (RGS) protein RGS4 of T. reesei. We show that RGS4 is involved in regulation of cellulase production, growth, asexual development and oxidative stress response in darkness as well as in osmotic stress response in the presence of sodium chloride, particularly in light. Transcriptome analysis revealed regulation of several ribosomal genes, six genes mutated in RutC30 as well as several genes encoding transcription factors and transporters. Importantly, RGS4 positively regulates the siderophore cluster responsible for fusarinine C biosynthesis in light. The respective deletion mutant shows altered growth on nutrient sources related to siderophore production such as ornithine or proline in a BIOLOG phenotype microarray assay. Additionally, growth on storage carbohydrates as well as several intermediates of the D-galactose and D-arabinose catabolic pathway is decreased, predominantly in light.

CONCLUSIONS

We conclude that RGS4 mainly operates in light and targets plant cell wall degradation, siderophore production and storage compound metabolism in T. reesei.

The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics

Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.

MAPkinases regulate secondary metabolism, sexual development and light dependent cellulase regulation in Trichoderma reesei

The filamentous fungus Trichoderma reesei is a prolific producer of plant cell wall degrading enzymes, which are regulated in response to diverse environmental signals for optimal adaptation, but also produces a wide array of secondary metabolites. Available carbon source and light are the strongest cues currently known to impact secreted enzyme levels and an interplay with regulation of secondary metabolism became increasingly obvious in recent years. While cellulase regulation is already known to be modulated by different mitogen activated protein kinase (MAPK) pathways, the relevance of the light signal, which is transmitted by this pathway in other fungi as well, is still unknown in T. reesei as are interconnections to secondary metabolism and chemical communication under mating conditions. Here we show that MAPkinases differentially influence cellulase regulation in light and darkness and that the Hog1 homologue TMK3, but not TMK1 or TMK2 are required for the chemotropic response to glucose in T. reesei. Additionally, MAPkinases regulate production of specific secondary metabolites including trichodimerol and bisorbibutenolid, a bioactive compound with cytostatic effect on cancer cells and deterrent effect on larvae, under conditions facilitating mating, which reflects a defect in chemical communication. Strains lacking either of the MAPkinases become female sterile, indicating the conservation of the role of MAPkinases in sexual fertility also in T. reesei. In summary, our findings substantiate the previously detected interconnection of cellulase regulation with regulation of secondary metabolism as well as the involvement of MAPkinases in light dependent gene regulation of cellulase and secondary metabolite genes in fungi.