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Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture-insights from genomics.

ABSTRACT: Trichoderma hamatum strain GD12 is unique in that it can promote plant growth, activate biocontrol against pre- and post-emergence soil pathogens and can induce systemic resistance to foliar pathogens. This study extends previous work in lettuce to demonstrate that GD12 can confer beneficial agronomic traits to other plants, providing examples of plant growth promotion in the model dicot, Arabidopsis thaliana and induced foliar resistance to Magnaporthe oryzae in the model monocot rice. We further characterize the lettuce-T. hamatum interaction to show that bran extracts from GD12 and an N-acetyl-?-D-glucosamindase-deficient mutant differentially promote growth in a concentration dependent manner, and these differences correlate with differences in the small molecule secretome. We show that GD12 mycoparasitises a range of isolates of the pre-emergence soil pathogen Sclerotinia sclerotiorum and that this interaction induces a further increase in plant growth promotion above that conferred by GD12. To understand the genetic potential encoded by T. hamatum GD12 and to facilitate its use as a model beneficial organism to study plant growth promotion, induced systemic resistance and mycoparasitism we present de novo genome sequence data. We compare GD12 with other published Trichoderma genomes and show that T. hamatum GD12 contains unique genomic regions with the potential to encode novel bioactive metabolites that may contribute to GD12's agrochemically important traits.

SUBMITTER: Studholme DJ

PROVIDER: S-EPMC3726867 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture-insights from genomics.

Studholme David J DJ Harris Beverley B Le Cocq Kate K Winsbury Rebecca R Perera Venura V Ryder Lauren L Ward Jane L JL Beale Michael H MH Thornton Chris R CR Grant Murray M

Frontiers in plant science 20130730

Trichoderma hamatum strain GD12 is unique in that it can promote plant growth, activate biocontrol against pre- and post-emergence soil pathogens and can induce systemic resistance to foliar pathogens. This study extends previous work in lettuce to demonstrate that GD12 can confer beneficial agronomic traits to other plants, providing examples of plant growth promotion in the model dicot, Arabidopsis thaliana and induced foliar resistance to Magnaporthe oryzae in the model monocot rice. We furth ...[more]

PMID: 23908658

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Project description:BackgroundEfficient biomass bioconversion is a promising solution to alternative energy resources and environmental issues associated with lignocellulosic wastes. The Trichoderma species of cellulolytic fungi have strong cellulose-degrading capability, and their cellulase systems have been extensively studied. Currently, a major limitation of Trichoderma strains is their low production of β-glucosidases.ResultsWe isolated two Trichoderma hamatum strains YYH13 and YYH16 with drastically different cellulose degrading efficiencies. YYH13 has higher cellobiose-hydrolyzing efficiency. To understand mechanisms underlying such differences, we sequenced the genomes of YYH13 and YYH16, which are essentially identical (38.93 and 38.92 Mb, respectively) and are similar to that of the T. hamatum strain GD12. Using GeneMark-ES, we annotated 11,316 and 11,755 protein-coding genes in YYH13 and YYH16, respectively. Comparative analysis identified 13 functionally important genes in YYH13 under positive selection. Through examining orthologous relationships, we identified 172,655, and 320 genome-specific genes in YYH13, YYH16, and GD12, respectively. We found 15 protease families that show differences between YYH13 and YYH16. Enzymatic tests showed that exoglucanase, endoglucanase, and β-glucosidase activities were higher in YYH13 than YYH16. Additionally, YYH13 contains 10 families of carbohydrate-active enzymes, including GH1, GH3, GH18, GH35, and GH55 families of chitinases, glucosidases, galactosidases, and glucanases, which are subject to stronger positive selection pressure. Furthermore, we found that the β-glucosidase gene (YYH1311079) and pGEX-KG/YYH1311079 bacterial expression vector may provide valuable insight for designing β-glucosidase with higher cellobiose-hydrolyzing efficiencies.ConclusionsThis study suggests that the YYH13 strain of T. hamatum has the potential to serve as a model organism for producing cellulase because of its strong ability to efficiently degrade cellulosic biomass. The genome sequences of YYH13 and YYH16 represents a valuable resource for studying efficient production of biofuels.

Project description:As global health care demand continues to increase, medicinal plant productivity must progress without exhausting critical environmental resources. Hence, it is important to explore practices that can improve the quality, safety, and sustainability of medicinal plants, as well as ecological stability. Organic farming has recently gained significance as a sustainable cultivation alternative owing to increased awareness of the adverse effects of conventional cultivation method. Here, this study aimed to investigate the feasibility of organic farming as a solution for sustainable cultivation of medicinal plants from multiple perspectives and long-term benefits to the environment. Organic agricultural practices of medicinal plants were evaluated from a multi-dimensional perspective (environment, economy, and society) using extensive research data and literature and field surveys. Data from medicinal plant cultivation in Inner Mongolia were acquired for 76 sites from four data stations between 2014 and 2021. Data analysis revealed that organic medicinal plants can improve safety by reducing pesticide exposure risks. Simultaneously, organic agriculture of medicinal plants can improve biodiversity by effectively reducing pesticide and fertilizer use, which also provides natural safe products for health care. With the improvement of quality, the retail price will have a certain advantage, which will improve the income of farmers. Moreover, organic agriculture enhanced profitability because of the higher organic premium on medicinal plant products and improved ecosystem stability by increasing plant diversity. The findings of this study suggest that organic cultivation strategies can improve the quality and safety of medicinal plants and further provide a basis for promoting the sustainable development and ecological stability of medicinal plants. However, not all medicinal plant cultivators are guaranteed to adopt organic farming practices, but if all technological elements are correctly applied, the system can be maintained sustainably to expand the area of organically cultivated plants in the future.

Project description:Theobroma cacao (cacao) is cultivated in tropical climates and is exposed to drought stress. The impact of the endophytic fungus Trichoderma hamatum isolate DIS 219b on cacao's response to drought was studied. Colonization by DIS 219b delayed drought-induced changes in stomatal conductance, net photosynthesis, and green fluorescence emissions. The altered expression of 19 expressed sequence tags (ESTs) (seven in leaves and 17 in roots with some overlap) by drought was detected using quantitative real-time reverse transcription PCR. Roots tended to respond earlier to drought than leaves, with the drought-induced changes in expression of seven ESTs being observed after 7 d of withholding water. Changes in gene expression in leaves were not observed until after 10 d of withholding water. DIS 219b colonization delayed the drought-altered expression of all seven ESTs responsive to drought in leaves by > or = 3 d, but had less influence on the expression pattern of the drought-responsive ESTs in roots. DIS 219b colonization had minimal direct influence on the expression of drought-responsive ESTs in 32-d-old seedlings. By contrast, DIS 219b colonization of 9-d-old seedlings altered expression of drought-responsive ESTs, sometimes in patterns opposite of that observed in response to drought. Drought induced an increase in the concentration of many amino acids in cacao leaves, while DIS 219b colonization caused a decrease in aspartic acid and glutamic acid concentrations and an increase in alanine and gamma-aminobutyric acid concentrations. With or without exposure to drought conditions, colonization by DIS 219b promoted seedling growth, the most consistent effects being an increase in root fresh weight, root dry weight, and root water content. Colonized seedlings were slower to wilt in response to drought as measured by a decrease in the leaf angle drop. The primary direct effect of DIS 219b colonization was promotion of root growth, regardless of water status, and an increase in water content which it is proposed caused a delay in many aspects of the drought response of cacao.

Project description:Aquatic weeds such as muskgrass (Chara spp.), water hyacinth (Eichhornia crassipes), water lettuce (Pistia stratiotes), hydrilla (Hydrilla verticillate), filamentous algae (Lyngbya wollei), and duckweed (Lemna minor) thrive in farm canals within the Everglades Agricultural Area of South Florida. Their presence, particularly during the summer months is an environmental concern with regards to water quality, in addition to being a nuisance because of their ability to multiply and spread rapidly in open waters causing restricted drainage/irrigation flow and low dissolved oxygen levels. Chemical control is effective but can have undesirable off-target effects, so reduced herbicide use is desirable. Hence, need exists to discover ways in which these weeds could be best managed or utilized. The objective of this research was to evaluate the allelopathic effect of these weeds to determine their use as potential biopesticides. Six aqueous extracts were tested against 100 bacterial strains isolated from plants and soil to evaluate their antimicrobial activity. These extracts were also used to determine their insecticidal and antifeedant effects on fall armyworm (FAW, Spodoptera frugiperda). Both extracts and powder form of the aquatic weeds were tested for their herbicidal activity towards seed germination and growth of three common terrestrial weed species. At a dilution of 1:100 and 1:1,000, none of the aquatic weeds inhibited in-vitro growth of the bacterial strains, with one exception (filamentous algae extract at 1:100 reduced growth of one bacterial isolate by 54%). Water lettuce reduced the survival rate of FAW by 14% while hydrilla and duckweed caused 11% and 9% reduction of FAW growth, respectively. Powdered duckweed inhibited the growth of nutsedge by 41%, whereas filamentous algae powder and extract reduced germination of amaranth by 20% and 28%, respectively. Harvesting these weeds and converting them into useable compounds could not only eliminate the in situ farm canal and water quality problems but also result in development of new soil amendments or biopesticides.

Dataset Information

Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture-insights from genomics.

Publications

Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture-insights from genomics.

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