What first inspired you to study Trichoderma, and how did this research begin?
Initially, we started working on tea microbiome research proposal (funded by Anusandhan National Research Foundation, Project File No. SRG/2020/000586) to understand the role of tea roots associated beneficial microbiota for sustained leaf phytochemical production1. The tea gardens of West Bengal, India are extraordinary places, both culturally and ecologically, but beneath that beauty lies a quiet crisis. Decades of continuous cultivation in the same acidic soil strip these plantations of their microbial vitality, and with it, the flavour, health, and resilience of the tea plant itself. Yet when we began examining the soil and root environments of healthy tea plants using shotgun metagenomics, a culture- independent technique that reads the genetic signatures of every organism present in a sample, we kept encountering the same fungus: Trichoderma. It appeared consistently, almost loyally, in association with the roots of plants that were doing well. That pattern was too compelling to ignore as we were trying to prepare a plant specific “synthetic personalized microbiome”. We began asking whether this organism was merely a bystander or whether it was actively contributing to plant health by establishing protocooperation with other microbiota of the same niche, in ways that had been underestimated. That single question set off what has now become a multi-year programme of research spanning whole- genome sequencing, metabolomics, transcriptomics, and its attribute to plant physiology.
Can you explain in simple terms what Trichoderma is and why it is helpful for plants?
Trichoderma is a soil-dwelling beneficial fungus, and an unusually versatile one. Unlike pathogenic fungi that harm plants, Trichoderma establishes a mutualistic relationship with plant roots, offering protection and nourishment in exchange for a foothold in the rhizosphere. Its roles are genuinely multiple. It acts as a biological sentinel, capable of hunting down and destroying disease-causing fungi through a process called mycoparasitism, physically coiling around and dismantling pathogens before they can do damage. At the same time, it works like a biochemist for the plant, producing growth-promoting hormones such as indole-3-acetic acid, solubilizing locked forms of phosphorus and trace minerals in the soil, and releasing these nutrients into a form the plant can actually absorb. During certain biotic and abiotic stress the host plant’s alters its metabolic foot prints. Most interesting, Trichoderma can “cross-talk” with the plant in its own chemical language and support them to allocate nutrients when the plant needs it most. Additionally these molecular signals effectively primes the plant’s immune system to cope up with similar challenges against similar future threats. While inoculating tea seedlings with the indigenous Trichoderma strain, it was evident that the fungal strain was able to establish itself in the root which produced measurable improvements in plant health and, a significant boost in flavonoid accumulation, responsible for much of tea’s medicinal and commercial value2.
Your study shows that different strains of Trichoderma can do different jobs, why is that important for agriculture and industry?
While most microbial interactions are host-specific, our pan-genome approach directly decodes the fundamental question of how Trichoderma’s conserved and variable genetic elements shape these interactions among hosts. Pan- genome analysis involves likening the complete genetic repertoires of multiple strains of the same organism concurrently. In our study, twenty-five industrially and agriculturally important Trichoderma strains were selected based on overall genome completeness. The analysis showed remarkable genetic diversity among the selected strains which a shared similar core. All strains carry approximately 4,960 genes encoding essential biological functions. But beyond that shared foundation, each strain maintains its own patterns of accessory and unique genes that confer highly specialized competencies. For example, T. reesei QM6a, carries 322 strain-specific genes strongly originated for secretion of cellulolytic enzymes, self-explaining why this strain governs industrial applications such as biofuel production and textile processing3. Notably, bio-control strains like T. harzianum CBS226.95 carry extended gene sets tied of secondary metabolism and pathogen defence. The exacting part of this work was to identify a strain which can be utilized in dual purpose, i.e. crop protectors and as industrial enzyme producers. This has actual real-world implications. Rather than isolating and experimenting a Trichoderma strain based on trial and error, we can now use genomic resources to make coherent, informed choices, matching the appropriate strain to the appropriate application. It is, in essence, precision microbiology.
What surprised you the most about how this fungus helps plants grow and fight diseases?
We started the work expecting to document standard bio-control activity, which was a part of traditional knowledge and previous scientific experiments. What we did not expect was the magnitude to which Trichoderma could influence into a plant’s metabolic architecture and re-modulate it. When we performed whole-genome sequencing of our tea root-isolated strain, Trichoderma sp. AM6, we found that it possesses a fully functional mevalonate pathway, the biochemical equipment responsible for synthesizing terpenoids, a chemically diverse class of compounds that contribute directly to tea’s aroma, flavor, and growth promoting properties. When we inoculated tea seedlings with this strain and examined what happened at the transcriptomic level, we found that the plant itself responded by up-regulating HMGCR, a key regulatory enzyme in the mevalonate pathway, while simultaneously down regulating DXS, which drives a competing biosynthetic route. In consequence, the plant alters its entire terpenoid production strategy in response to the fungal challenge4. That degree of metabolic alteration was not something we had anticipated. Alongside this, our co-inoculation experiments, combining Trichoderma with a synthetic consortium (Syn-com) of beneficial bacteria and mycorrhizal fungi, produced a 55.2% increase in total flavonoid content compared to un-inoculated controls. The impression that a beneficial soil fungus could so unambiguously and significantly reshape the secondary chemistry and alters host specificity of a commercially important crop plant remains, the most striking finding of this entire study.
Do you think Trichoderma could reduce the need for chemical fertilizers and pesticides in the future?
Frankly speaking, yes; but not entirely, as several other factors like environmental stress, host specificity to a particular plant, application strategies, etc. play a very pivotal role to make it successful during field application. As most of the field application are based on carrier (solid/ liquid) based Trichoderma inoculum, proper storage to maintain the self-life of becomes very important, while storage and transportation. Efficient Trichoderma inoculum facilitate plants to access zinc, phosphorus, iron and other soil-bound macro and micro nutrients, which are usually not accessible to plant alone. Additionally it produces several phytohormones like IAA, cytokinins, gibberellins, etc. which stimulate plants physiological growth, and reduced recurring use of several chemical fertilizers. While discussing about their indirect plant growth promoting attributes, Trichoderma produces several secretory and volatile secondary metabolites which suppress soil-borne pathogens such as Fusarium, Rhizoctonia, and Pythium, through mycoparasitism, antibiosis etc. These secondary metabolites induced plant resistance against a plethora of pathogens, reducing the dependency on fungicides and pesticides. In our experimental set up, plants were treated with a Trichoderma-based solid formulation which maintained a NDVI vegetation index values above 0.6, a threshold associated with healthy, productive vegetation, without any synthetic chemical fertilizer and pesticides5. Trichoderma‘s performance varies with soil pH, temperature, existing microbial communities, and crop type. It is a biological system, not a chemical formulation, and biological systems are context- dependent. The strategic path forward is not wholesale replacement of agrochemicals overnight, but the development of genome-informed, crop-specific bio-formulations that gradually reduce chemical dependency in a targeted, sustainable way.
What are the next steps, and what still needs to be discovered before we can use Trichoderma even more effectively?
There is no shortage of open questions, and that is precisely what makes this field so energizing to work in. Our pan-genome analysis showed that Trichoderma harbors what geneticists call an open pan- genome: as more strains are sequenced, new genes keep appearing in the collective pool, suggesting that the functional diversity of this genus has not yet been fully mapped. A large proportion of the genes we identified carry no assigned function. Those gaps represent real opportunity, functions we simply do not yet understand, some of which may have significant applied value. On the metabolomics side, untargeted profiling of a single Trichoderma strain identified over 11,841 secondary metabolites, more than 1,200 of which could not be matched to any compound in existing databases3. That points to a significant reservoir of potentially novel bioactive chemistry waiting to be characterized. Beyond discovery, the translation challenge is equally pressing. Our experiments have so far been conducted under controlled pot conditions. Before Trichoderma-based formulations can be applied at large scale application, multi-locus field validation need to rigorously performed across different crops, soil types, seasonal conditions, and farming systems. Additionally we need to understand how Trichoderma interacts with the flora and fauna of a specific niche, particularly mycorrhizal fungi and other microbial community. Lastly, designing truly effective bio-formulations will need holistic ecosystem, not just optimizing Trichoderma in isolation.
