Effect of co-application of Trichoderma spp. with organic composts on plant growth enhancement, soil enzymes and fungal community in soil

Trichoderma afroharzianum T22 Induces Rhizobia and Flavonoid-Driven Symbiosis to Promote Tolerance to Alkaline Stress in Garden Pea

Soil alkalinity is a limiting factor for crops, yet the role of beneficial fungi in mitigating this abiotic stress in garden pea is understudied. In this study, Trichoderma afroharzianum T22 colonised the roots of garden pea cultivars exposed to soil alkalinity in a host-specific manner. In alkaline-exposed Sugar Snap, T22 improved growth parameters, consistent with increased tissue mineral content, particularly Fe and Mn, as well as enhanced rhizosphere siderophore levels. The split-root assay demonstrated that the beneficial effects of T22 on alkaline stress mitigation are the result of a whole-plant association rather than localised root-specific effects. RNA-seq analysis showed 575 and 818 differentially expressed genes upregulated and downregulated in the roots inoculated with T22 under alkaline conditions. The upregulated genes were mostly involved in the flavonoid biosynthetic pathway (monooxygenase activity, ammonia-lyase activity, 4-coumarate-CoA ligase), along with genes related to mineral transport and redox homoeostasis. Further, a flavonoid precursor restored plant health even in the absence of T22, confirming the role of microbial symbiosis in mitigating alkaline stress. Interestingly, T22 restored the abundance of rhizobia, particularly Rhizobium leguminosarum and Rhizobium indicum, along with the induction of NifA, NifD, and NifH in nodules, suggesting a connection between T22 and rhizobia under soil alkalinity. Further, the elevated rhizosphere siderophore, root flavonoid, expression of PsCoA (4-coumarate-CoA ligase) as well as the relative abundance of TaAOX1 and R. leguminosarum diminished when T22 was substituted with exogenous Fe. This suggests that exogenous Fe eliminates the need for microbiome-driven mineral mobilisation, while T22-mediated alkaline stress mitigation depends on flavonoid-driven symbiosis and R. leguminosarum abundance. It was further supported by the positive interaction of T22 on R. leguminosarum growth in alkaline media. Thus, the beneficial effect of T22 on rhizobia likely stems from their interactions, not solely from the improved mineral status, particularly Fe, in plants. This study provides the first mechanistic insights into T22 interactions with host and rhizobia, advancing microbiome strategies to alleviate soil alkalinity in peas and other legumes.

Bioherbicides: revolutionizing weed management for sustainable agriculture in the era of One-health

The main objective of agricultural weed management is to increase crop productivity to maintain a delicate balance between food demand and supply for an increasing population and ensure food security globally. Agriculture plays a significant role in the social life and economy of many developed or developing countries. Blind use of chemical herbicides to maximize crop production exerts many negative environmental impacts and develops resistance among the weed biotypes against herbicides, even representing a high risk to the environment and human health. Thus, in the last few years, the research activities of scientists have increased to find alternative weed control methods. Bioherbicides or biological management of weeds is an emerging topic with decent potential for sustainable crop production. Biological management of weeds has numerous positive aspects and advantages over chemical control, such as being highly selective, specific toward targeted weeds, sustainable, and having minimize harmful effect on the main crop, environment, and humans. Several biological agents, such as bacteria, fungi and viruses, also plant extracts and essential oils, have been introduced, and their bioherbicidal potential has been explored in weed management. To develop an effective bioherbicide, specific and complex types of interaction have been developed between targeted weeds and biological agents. Whereas a limited number of bioherbicides have performed successfully under field conditions to control specific weeds, nonetheless, the efficiency of many other bioherbicidal agents is still inadequate due to many reasons, such as formulation, less persistence in the field as well as lack of host-agent interaction. This critical review paper discusses several different biological methods of weed management, their advantages and disadvantages, and the importance of bioherbicides as weed-controlling agents to achieve global sustainable crop production, in the era of One-health.

Enhancing the Resilience of Agroecosystems Through Improved Rhizosphere Processes: A Strategic Review

As farming practices evolve and climate conditions shift, achieving sustainable food production for a growing global population requires innovative strategies to optimize environmentally friendly practices and minimize ecological impacts. Agroecosystems, which integrate agricultural practices with the surrounding environment, play a vital role in maintaining ecological balance and ensuring food security. Rhizosphere management has emerged as a pivotal approach to enhancing crop yields, reducing reliance on synthetic fertilizers, and supporting sustainable agriculture. The rhizosphere, a dynamic zone surrounding plant roots, hosts intense microbial activity fueled by root exudates. These exudates, along with practices such as green manure application and intercropping, significantly influence the soil's microbial community structure. Beneficial plant-associated microbes, including Trichoderma spp., Penicillium spp., Aspergillus spp., and Bacillus spp., play a crucial role in improving nutrient cycling and promoting plant health, yet their interactions within the rhizosphere remain inadequately understood. This review explores how integrating beneficial microbes, green manures, and intercropping enhances rhizosphere processes to rebuild microbial communities, sequester carbon, and reduce greenhouse gas emissions. These practices not only contribute to maintaining soil health but also foster positive plant-microbe-rhizosphere interactions that benefit entire ecosystems. By implementing such strategies alongside sound policy measures, sustainable cropping systems can be developed to address predicted climate challenges. Strengthening agroecosystem resilience through improved rhizosphere processes is essential for ensuring food security and environmental sustainability in the future. In conclusion, using these rhizosphere-driven processes, we could develop more sustainable and resilient agricultural systems that ensure food security and environmental preservation amidst changing climate situations.

Mitigating water deficit stress in lemon balm (Melissa officinalis L.) through integrated soil amendments: A pathway to sustainable agriculture

Lemon balm (Melissa officinalis L.) is a valuable medicinal plant, but its growth can be significantly impacted by drought stress. This study aimed to mitigate the adverse effects of water deficit stress on lemon balm biomass by integrating poultry manure compost, poultry manure biochar, NPK fertilizer, Trichoderma harzianum, Thiobacillus thioparus, and elemental sulfur as soil amendments. The experiment was conducted in a greenhouse using a completely randomized design with a factorial arrangement, consisting of three replicates. It included a water deficit stress factor at three levels (95-100%, 75-80%, and 55-60% of field capacity) and a soil amendment treatment factor with eleven different fertilizer levels. Treatments included control (no amendment), NPK fertilizer, poultry manure compost, poultry manure biochar, and combinations of these with T. harzianum, T. thioparus, and elemental sulfur under various water deficit levels. Water deficit stress significantly reduced photosynthetic pigments, gas exchange parameters, chlorophyll fluorescence, relative water content, and antioxidant enzyme activity, while increasing membrane permeability and lipid peroxidation in lemon balm plants. However, the integrated application of organic, biological, and chemical amendments mitigated these negative impacts. The combined treatment of poultry manure compost, poultry manure biochar, NPK fertilizer, T. harzianum, T. thioparus, and elemental sulfur was the most effective in improving the morpho-physiological properties (1.97-60%) and biomass (2.31-2.76 times) of lemon balm under water deficit stress. The results demonstrate the potential of this holistic approach to enhance the resilience of lemon balm cultivation in water-scarce environments. The integration of organic, biological, and chemical amendments can contribute to sustainable agricultural practices by improving plant morphological and physiological properties and plant performance under drought conditions.

Holistic Approaches to Plant Stress Alleviation: A Comprehensive Review of the Role of Organic Compounds and Beneficial Bacteria in Promoting Growth and Health

Plants select microorganisms from the surrounding bulk soil, which act as a reservoir of microbial diversity and enrich a rhizosphere microbiome that helps in growth and stress alleviation. Plants use organic compounds that are released through root exudates to shape the rhizosphere microbiome. These organic compounds are of various spectrums and technically gear the interplay between plants and the microbial world. Although plants naturally produce organic compounds that influence the microbial world, numerous efforts have been made to boost the efficiency of the microbiome through the addition of organic compounds. Despite further crucial investigations, synergistic effects from organic compounds and beneficial bacteria combinations have been reported. In this review, we examine the relationship between organic compounds and beneficial bacteria in determining plant growth and biotic and abiotic stress alleviation. We investigate the molecular mechanism and biochemical responses of bacteria to organic compounds, and we discuss the plant growth modifications and stress alleviation done with the help of beneficial bacteria. We then exhibit the synergistic effects of both components to highlight future research directions to dwell on how microbial engineering and metagenomic approaches could be utilized to enhance the use of beneficial microbes and organic compounds.

Construction, Characterization, and Application of an Ammonium Transporter (AmtB) Deletion Mutant of the Nitrogen-Fixing Bacterium Kosakonia radicincitans GXGL-4A in Cucumis sativus L. Seedlings

Nitrogen is an important factor affecting crop yield, but excessive use of chemical nitrogen fertilizer has caused decline in nitrogen utilization and soil and water pollution. Reducing the utilization of chemical nitrogen fertilizers by biological nitrogen fixation (BNF) is feasible for green production of crops. However, there are few reports on how to have more ammonium produced by nitrogen-fixing bacteria (NFB) flow outside the cell. In the present study, the amtB gene encoding an ammonium transporter (AmtB) in the genome of NFB strain Kosakonia radicincitans GXGL-4A was deleted and the △amtB mutant was characterized. The results showed that deletion of the amtB gene had no influence on the growth of bacterial cells. The extracellular ammonium nitrogen (NH₄⁺) content of the △amtB mutant under nitrogen-free culture conditions was significantly higher than that of the wild-type strain GXGL-4A (WT-GXGL-4A), suggesting disruption of NH₄⁺ transport. Meanwhile, the plant growth-promoting effect in cucumber seedlings was visualized after fertilization using cells of the △amtB mutant. NFB fertilization continuously increased the cucumber rhizosphere soil pH. The nitrate nitrogen (NO₃^-) content in soil in the △amtB treatment group was significantly higher than that in the WT-GXGL-4A treatment group in the short term but there was no difference in soil NH₄⁺ contents between groups. Soil enzymatic activities varied during a 45-day assessment period, indicating that △amtB fertilization influenced soil nitrogen cycling in the cucumber rhizosphere. The results will provide a solid foundation for developing the NFB GXGL-4A into an efficient biofertilizer agent.

Synergistic Effects of Trichoderma harzianum, 1,3 Dichloropropene and Organic Matter in Controlling the Root-Knot Nematode Meloidogyne incognita on Tomato

Environmental concerns raised by synthetic nematicides are encouraging integrated management strategies based on their combination with non-chemical control tools, such as biocontrol agents and/or organic amendments. In this study, the combination of the fumigant 1,3-dichloropropene (1,3-D) with a commercial formulation of the biocontrol agent Trichoderma harzianum (TH) and an organic fertilizer (OF) was investigated in two consecutive tomato crops for its effect on the root-knot nematode Meloidogyne incognita and plant growth and yield. The application of 1,3-D was only performed on the first crop, while TH and OF were provided to both crops. Almost all treatments significantly reduced nematode infestation in both crops, though the greatest nematicidal effect was caused by a combination of the three products. The treatment with 1,3-D limited its nematicidal efficacy to the first crop only. Fumigant integration with TH and OF also resulted in the greatest increases of plant growth and yield. Therefore, the integrated management of root-knot nematodes with a soil fumigant, a bionematicide as T. harzianum and a source of organic matter demonstrated effective nematode suppression though limiting the number of chemical applications.

Trichoderma atroviride seed dressing influenced the fungal community and pathogenic fungi in the wheat rhizosphere

Fusarium crown rot and wheat sharp eyespot are major soil-borne diseases of wheat, causing serious losses to wheat yield in China. We applied high-throughput sequencing combined with qPCR to determine the effect of winter wheat seed dressing, with either Trichoderma atroviride HB20111 spore suspension or a chemical fungicide consisting of 6% tebuconazole, on the fungal community composition and absolute content of pathogens Fusarium pseudograminearum and Rhizoctonia cerealis in the rhizosphere at 180 days after planting. The results showed that the Trichoderma and chemical fungicide significantly reduced the amount of F. pseudograminearum in the rhizosphere soil (p < 0.05), and also changed the composition and structure of the fungal community. In addition, field disease investigation and yield measurement showed that T. atroviride HB20111 treatment reduced the whiteheads with an average control effect of 60.1%, 14.9% higher than the chemical treatment; T. atroviride HB20111 increased yield by 7.7%, which was slightly more than the chemical treatment. Therefore, T. atroviride HB20111 was found to have the potential to replace chemical fungicides to control an extended range of soil-borne diseases of wheat and to improve wheat yield.

Green manure incorporation accelerates enzyme activity, plant growth, and changes in the fungal community of soil

Green manure can sustain agricultural production, preserve biodiversity, and mitigate soil degradation caused by long-term application of chemical fertilizers. Moreover, the application of green manure can improve soil health through increased soil biological activities. Nevertheless, little attention has been paid to the effects of leguminous and non-leguminous plants on phosphorus- and carbon-related enzyme activities and fungal community composition in soil. In this study, a pot experiment was carried out to elucidate the effects of two green manures on plant growth promoting potential, phosphorus- and carbon-related enzyme activities, and soil fungal community composition. Two green manure treatments (Brassica juncea and hairy vetch), poultry compost and control (no amendment) were applied and soil samples were collected after incorporation of green manure and after plant harvest. The results revealed that plant growth with hairy vetch was significantly higher than that with B. juncea and poultry compost, and soil enzyme activities were markedly higher with hairy vetch than with B. juncea. Both green manure amendments altered the soil fungal community composition. It is possible that the incorporation of green manure into soil and their mineralization and decomposition were controlled by the carbon: nitrogen ratio of the manures and that these manures were easily degradable by soil fungi. In particular, the incorporation of leguminous (hairy vetch) green manure with a low carbon: nitrogen ratio resulted in better plant growth through fast mineralization. Our findings suggest that green manure incorporation is an effective practice and provides substantial benefits to the soil-plant system.

Effect of a Wood-Based Carrier of Trichoderma atroviride SC1 on the Microorganisms of the Soil

Wood pellets can sustain the growth of Trichoderma spp. in soil; however, little is known about their side effects on the microbiota. The aims of this study were to evaluate the effect of wood pellets on the growth of Trichoderma spp. in bulk soil and on the soil microbial population's composition and diversity. Trichoderma atroviride SC1 coated wood pellets and non-coated pellets were applied at the level of 10 g∙kg-1 of soil and at the final concentration of 5 × 103 conidia∙g-1 of soil and compared to a conidial suspension applied at the same concentration without the wood carrier. Untreated bulk soil served as a control. The non-coated wood pellets increased the total Trichoderma spp. population throughout the experiment (estimated as colony-forming unit g-1 of soil), while wood pellets coated with T. atroviride SC1 did not. The wood carrier increased the richness, and temporarily decreased the diversity, of the bacterial population, with Massilia being the most abundant bacterial genus, while it decreased both the richness and diversity of the fungal community. Wood pellets selectively increased fungal species having biocontrol potential, such as Mortierella, Cladorrhinum, and Stachybotrys, which confirms the suitability of such carriers of Trichoderma spp. for soil application.