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Editorial: Global excellence in plant science: Southeast Asia

Doni F, Mispan MS

Front Plant Sci, 2023;14:1285250.
PMID: 37746022 DOI: 10.3389/fpls.2023.1285250
Endophytic strains of Trichoderma increase plants' photosynthetic capability

Harman GE, Doni F, Khadka RB, Uphoff N

J Appl Microbiol, 2021 Feb;130(2):529-546.
PMID: 31271695 DOI: 10.1111/jam.14368

The world faces two enormous challenges that can be met, at least in part and at low cost, by making certain changes in agricultural practices. There is need to produce enough food and fibre for a growing population in the face of adverse climatic trends, and to remove greenhouse gases to avert the worst consequences of global climate change. Improving photosynthetic efficiency of crop plants can help meet both challenges. Fortuitously, when crop plants' roots are colonized by certain root endophytic fungi in the genus Trichoderma, this induces up-regulation of genes and pigments that improve the plants' photosynthesis. Plants under physiological or environmental stress suffer losses in their photosynthetic capability through damage to photosystems and other cellular processes caused by reactive oxygen species (ROS). But certain Trichoderma strains activate biochemical pathways that reduce ROS to less harmful molecules. This and other mechanisms described here make plants more resistant to biotic and abiotic stresses. The net effect of these fungi's residence in plants is to induce greater shoot and root growth, increasing crop yields, which will raise future food production. Furthermore, if photosynthesis rates are increased, more CO2 will be extracted from the atmosphere, and enhanced plant root growth means that more sequestered C will be transferred to roots and stored in the soil. Reductions in global greenhouse gas levels can be accelerated by giving incentives for climate-friendly carbon farming and carbon cap-and-trade programmes that reward practices transferring carbon from the atmosphere into the soil, also enhancing soil fertility and agricultural production.
Editorial: Soil biota and climate smart crops

Cheng A, Gajic G, Doni F

Front Plant Sci, 2023;14:1250831.
PMID: 37538065 DOI: 10.3389/fpls.2023.1250831
Fulltext Benefits to Plant Health and Productivity From Enhancing Plant Microbial Symbionts

Harman G, Khadka R, Doni F, Uphoff N

Front Plant Sci, 2020;11:610065.
PMID: 33912198 DOI: 10.3389/fpls.2020.610065

Plants exist in close association with uncountable numbers of microorganisms around, on, and within them. Some of these endophytically colonize plant roots. The colonization of roots by certain symbiotic strains of plant-associated bacteria and fungi results in these plants performing better than plants whose roots are colonized by only the wild populations of microbes. We consider here crop plants whose roots are inhabited by introduced organisms, referring to them as Enhanced Plant Holobionts (EPHs). EPHs frequently exhibit resistance to specific plant diseases and pests (biotic stresses); resistance to abiotic stresses such as drought, cold, salinity, and flooding; enhanced nutrient acquisition and nutrient use efficiency; increased photosynthetic capability; and enhanced ability to maintain efficient internal cellular functioning. The microbes described here generate effects in part through their production of Symbiont-Associated Molecular Patterns (SAMPs) that interact with receptors in plant cell membranes. Such interaction results in the transduction of systemic signals that cause plant-wide changes in the plants' gene expression and physiology. EPH effects arise not only from plant-microbe interactions, but also from microbe-microbe interactions like competition, mycoparasitism, and antibiotic production. When root and shoot growth are enhanced as a consequence of these root endophytes, this increases the yield from EPH plants. An additional benefit from growing larger root systems and having greater photosynthetic capability is greater sequestration of atmospheric CO2. This is transferred to roots where sequestered C, through exudation or root decomposition, becomes part of the total soil carbon, which reduces global warming potential in the atmosphere. Forming EPHs requires selection and introduction of appropriate strains of microorganisms, with EPH performance affected also by the delivery and management practices.
Roles of microbes in supporting sustainable rice production using the system of rice intensification

Doni F, Mispan MS, Suhaimi NSM, Ishak N, Uphoff N

Appl Microbiol Biotechnol, 2019 Jul;103(13):5131-5142.
PMID: 31101941 DOI: 10.1007/s00253-019-09879-9

The system of rice intensification (SRI) is an agroecological approach to rice cultivation that seeks to create optimal conditions for healthy plant growth by minimizing inter-plant competition, transplanting widely spaced young single seedlings, and optimizing favorable soil conditions with organic amendments, increased soil aeration by weeding, and controlled water management. These practices improve rice plant growth with yields up to three times more than with conventional cultivation methods, and increase crop resilience under biotic and abiotic stresses. This review discusses the roles of beneficial microbes in improving rice plant growth, yield, and resilience when SRI practices are used, and how these modifications in plant, soil, water, and nutrient management affect the populations and diversity of soil microorganisms. Mechanisms whereby symbiotic microbes support rice plants' growth and performance are also discussed.
Fulltext Formulation of Trichoderma sp. SL2 inoculants using different carriers for soil treatment in rice seedling growth

Doni F, Isahak A, Che Mohd Zain CR, Mohd Ariffin S, Wan Mohamad WN, Wan Yusoff WM

Springerplus, 2014;3:532.
PMID: 25279323 DOI: 10.1186/2193-1801-3-532

BACKGROUND: Trichoderma sp. SL2 has been previously reported to enhance rice germination, vigour, growth and physiological characteristics. The use of Potato Dextrose Agar as carrier of Trichoderma sp. SL2 inoculant is not practical for field application due to its short shelf life and high cost. This study focuses on the use of corn and sugarcane bagasse as potential carriers for Trichoderma sp. SL2 inoculants.
FINDINGS: A completely randomized design was applied for this study. Trichoderma sp. SL2 suspension mixed with corn and sugarcane bagasse were used as treatment mixture in soil. Growth parameters including rice seedling height, root length, wet weight, leaf number and biomass were measured and compared to control. The results showed that Trichoderma sp. SL2 mixed with corn significantly enhanced rice seedlings root length, wet weight and biomass compared to Trichoderma sp. SL2 mixed with sugarcane bagasse and control.
CONCLUSION: Corn can be a potential carrier for Trichoderma spp. inoculants for field application.
Fulltext Physiological and growth response of rice plants (Oryza sativa L.) to Trichoderma spp. inoculants

Doni F, Isahak A, Che Mohd Zain CR, Wan Yusoff WM

AMB Express, 2014;4:45.
PMID: 24949276 DOI: 10.1186/s13568-014-0045-8

Trichoderma spp., a known beneficial fungus is reported to have several mechanisms to enhance plant growth. In this study, the effectiveness of seven isolates of Trichoderma spp. to promote growth and increase physiological performance in rice was evaluated experimentally using completely randomized design under greenhouse condition. This study indicated that all the Trichoderma spp. isolates tested were able to increase several rice physiological processes which include net photosynthetic rate, stomatal conductance, transpiration, internal CO2 concentration and water use efficiency. These Trichoderma spp. isolates were also able to enhance rice growth components including plant height, leaf number, tiller number, root length and root fresh weight. Among the Trichoderma spp. isolates, Trichoderma sp. SL2 inoculated rice plants exhibited greater net photosynthetic rate (8.66 μmolCO2 m(-2) s(-1)), internal CO2 concentration (336.97 ppm), water use efficiency (1.15 μmoCO2/mmoH2O), plant height (70.47 cm), tiller number (12), root length (22.5 cm) and root fresh weight (15.21 g) compared to the plants treated with other Trichoderma isolates tested. We conclude that beneficial fungi can be used as a potential growth promoting agent in rice cultivation.
The diversity of rhizospheric bacterial communities associated with Trichoderma-treated rice fields

Abdullah NS, Doni F, Chua KO, Mispan MS, Saiman MZ, Mohd Yusuf Y, et al.

Lett Appl Microbiol, 2022 Dec;75(6):1645-1650.
PMID: 36073093 DOI: 10.1111/lam.13832

Microbial-based fertilizer has been widely used as a healthier and better alternative to agrochemical products. However, the effects of biofertilizers on the rhizospheric microbiota has rarely been investigated. Thus, the aim of this study was to investigate the effects of symbiotic fungus Trichoderma asperellum SL2-based inoculant on the soil bacterial population through next generation sequencing using a metabarcoding approach. The treatment plots were treated with T. asperellum SL2 spore suspension, while the control plots were treated with sterilized distilled water. The results showed similar bacterial microbiome profiles in the soil of control and T. asperellum SL2-treated plots. In conclusion, the application of the T. asperellum SL2 inoculant had not exerted a negative impact towards the bacterial population as similar observation was reflected in control plots. Nonetheless, future research should be conducted to investigate the effects of repeated application of T. asperellum SL2 over a longer period on the rice microbiota communities.
Fulltext Microbial Contributions for Rice Production: From Conventional Crop Management to the Use of 'Omics' Technologies

Doni F, Suhaimi NSM, Mispan MS, Fathurrahman F, Marzuki BM, Kusmoro J, et al.

Int J Mol Sci, 2022 Jan 10;23(2).
PMID: 35054923 DOI: 10.3390/ijms23020737

Rice, the main staple food for about half of the world's population, has had the growth of its production stagnate in the last two decades. One of the ways to further improve rice production is to enhance the associations between rice plants and the microbiome that exists around, on, and inside the plant. This article reviews recent developments in understanding how microorganisms exert positive influences on plant growth, production, and health, focusing particularly on rice. A variety of microbial species and taxa reside in the rhizosphere and the phyllosphere of plants and also have multiple roles as symbiotic endophytes while living within plant tissues and even cells. They alter the morphology of host plants, enhance their growth, health, and yield, and reduce their vulnerability to biotic and abiotic stresses. The findings of both agronomic and molecular analysis show ways in which microorganisms regulate the growth, physiological traits, and molecular signaling within rice plants. However, many significant scientific questions remain to be resolved. Advancements in high-throughput multi-omics technologies can be used to elucidate mechanisms involved in microbial-rice plant associations. Prospectively, the use of microbial inoculants and associated approaches offers some new, cost-effective, and more eco-friendly practices for increasing rice production.
Evaluating the underlying physiological and molecular mechanisms in the system of rice intensification performance with Trichoderma-rice plant symbiosis as a model system

Doni F, Safitri R, Suhaimi NSM, Miranti M, Rossiana N, Mispan MS, et al.

Front Plant Sci, 2023;14:1214213.
PMID: 37692429 DOI: 10.3389/fpls.2023.1214213

The system of rice intensification (SRI) is an extensively-researched and increasingly widely-utilized methodology for alleviating current constraints on rice production. Many studies have shown physiological and morphological improvements in rice plants induced by SRI management practices to be very similar to those that are associated with the presence of beneficial microbial endophytes in or around rice plants, especially their roots. With SRI methods, grain yields are increased by 25-100% compared to conventional methods, and the resulting plant phenotypes are better able to cope with biotic and abiotic stresses. SRI management practices have been shown to be associated with significant increases in the populations of certain microorganisms known to enhance soil health and plant growth, e.g., Azospirillum, Trichoderma, Glomus, and Pseudomonas. This article evaluates the effects of applying Trichoderma as a model microbe for assessing microbial growth-promotion, biological control activity, and modulation of gene expression under the conditions created by SRI practices. Information about the molecular changes and interactions associated with certain effects of SRI management suggests that these practices are enhancing rice plants' expression of their genetic potentials. More systematic studies that assess the effects of SRI methods respectively and collectively, compared with standard rice production methods, are needed to develop a more encompassing understanding of how SRI modifications of crops' growing environment elicit and contribute to more robust and more productive phenotypes of rice.
Bioprospecting the roles of Trichoderma in alleviating plants' drought tolerance: Principles, mechanisms of action, and prospects

Akbari SI, Prismantoro D, Permadi N, Rossiana N, Miranti M, Mispan MS, et al.

Microbiol Res, 2024 Jun;283:127665.
PMID: 38452552 DOI: 10.1016/j.micres.2024.127665

Drought-induced stress represents a significant challenge to agricultural production, exerting adverse effects on both plant growth and overall productivity. Therefore, the exploration of innovative long-term approaches for addressing drought stress within agriculture constitutes a crucial objective, given its vital role in enhancing food security. This article explores the potential use of Trichoderma, a well-known genus of plant growth-promoting fungi, to enhance plant tolerance to drought stress. Trichoderma species have shown remarkable potential for enhancing plant growth, inducing systemic resistance, and ameliorating the adverse impacts of drought stress on plants through the modulation of morphological, physiological, biochemical, and molecular characteristics. In conclusion, the exploitation of Trichoderma's potential as a sustainable solution to enhance plant drought tolerance is a promising avenue for addressing the challenges posed by the changing climate. The manifold advantages of Trichoderma in promoting plant growth and alleviating the effects of drought stress underscore their pivotal role in fostering sustainable agricultural practices and enhancing food security.