Hidden Fungi in a Medicinal Weed May Shape Its Tick-Killing Power in Assam

Deep in Assam, along the banks of the Kopili River, an unassuming yellow-flowered weed is quietly hosting a microscopic ecosystem that may hold the key to its medicinal potency. Argemone mexicana, the Mexican prickly poppy, has long been valued in Indian pharmacology for its alkaloids, but a new metagenomic study has revealed for the first time just how rich and structured its fungal microbiome really is. Researchers from Amity University, Assam Agricultural University, and Thiagarajar College sequenced the fungal communities living in the plant’s roots, shoots, and surrounding rhizospheric soil at two locations, Amlighat and Dergaon, uncovering a hidden world dominated by a single phylum and punctuated by a fungus with a remarkable reputation.

The team used Illumina next-generation sequencing to profile the fungal internal transcribed spacer 2 (ITS2) region, a molecular barcode widely employed for fungal identification. By targeting this short stretch of ribosomal DNA, the researchers could detect both culturable and non-culturable fungi, capturing species that would never grow on a laboratory plate. The results were striking: across triplicate samples from all six sample types, the sequencing identified 5 phyla, 32 classes, 39 orders, 68 families, 125 genera, and 273 fungal species, including unknown and unidentified taxa. This level of resolution demonstrates how metagenomic approaches can bypass the limitations of traditional microbiology, which has so far recognized only a small fraction of the estimated 5.1 million fungal species on Earth.

What emerged from the data was a clear pattern of dominance. Ascomycota, the largest phylum of fungi, accounted for between 37.47 and 75.84 percent of all fungal reads across every sample, making it the undisputed ruler of the A. mexicana microbiome. Basidiomycota followed at 3.53 to 6.95 percent, with Zygomycota and unknown taxa rounding out the community. This dominance is not merely a numerical curiosity. Members of Ascomycota are prolific producers of pharmaceutical and commercially important secondary metabolites, including lipases, statins, probiotics, and compounds with antioxidant, antidiabetic, antimicrobial, anticancer, antiviral, and antiprotozoal activities. Their prevalence inside and around A. mexicana suggests they may be intimately involved in the plant’s chemical economy.

The geographic dimension of the study proved equally compelling. Samples from Dergaon consistently showed higher fungal richness than those from Amlighat, as measured by the number of operational taxonomic units (OTUs), the Chao1 index, and phylogenetic diversity. The rhizospheric soil samples were the most diverse of all, with Dergaon soil yielding 2,413.33 OTUs and a Shannon diversity index of 5.84, compared with 2,310 OTUs and 5.65 in Amlighat soil. Roots and shoots harbored far fewer taxa, indicating that the soil environment contains a wide and complex microbial composition that makes it easier for fungi to colonize the roots and then move into the plant’s phyllosphere. These findings align with previous research showing that fungal community structure and function depend heavily on rhizospheric conditions.

Beta diversity analyses, including principal component analysis, hierarchical clustering, UPGMA trees, and network co-occurrence analysis, revealed that the fungal communities of the two locations were mostly similar in composition but differed in relative abundance. Shoots from Amlighat and Dergaon clustered together, as did roots and rhizospheric soils, suggesting that the plant compartment, rather than geography, is the primary driver of community structure. Yet the network analysis showed that the complexity of fungal interactions was highest in the rhizospheric samples, as indicated by the greatest number of nodes and edges, reinforcing the idea that soil is the richest reservoir of fungal diversity feeding into the plant.

Among the genera detected, Meyerozyma was the most abundant across all samples, with relative abundances ranging from 10.46 to 25.06 percent. Ceratocystis, Ganoderma, Cladosporium, Fusarium, and Penicillium were also present in varying amounts. But the most intriguing finding was the consistent presence of Trichoderma species in every single sample, albeit at different relative abundances. This genus is famous in agricultural science as a biocontrol agent and plant growth promoter, and previous work by Verma and colleagues showed that Trichoderma can alter the production of sanguinarine, an acaricidal alkaloid, in Papaver somniferum, the opium poppy. Because P. somniferum and A. mexicana belong to the same family, Papaveraceae, and both produce sanguinarine, the researchers propose that Trichoderma may similarly modulate acaricide production in A. mexicana.

The connection to acaricidal activity is not speculative. An earlier collaborative study by Upadhaya and colleagues tested A. mexicana extracts from the same two locations against ticks and found dramatic differences. Samples from Amlighat killed 80 to 100 percent of ticks, with a mean mortality of 95.0 percent, while samples from Dergaon achieved only 10 to 40 percent mortality, with a mean of 25.0 percent. The current metagenomic data suggest that these differences in tick-killing power may be linked to the distinct fungal communities harbored by plants from each location. Variations in the relative abundance of Trichoderma and other fungi could influence the biosynthesis or accumulation of berberine and sanguinarine, the two acaricidal compounds known from A. mexicana.

The technical rigor of the study deserves attention. The researchers collected roots, shoots, and rhizospheric soil from healthy flowering plants at three sites per location, storing fresh samples in liquid nitrogen. Metagenomic DNA was isolated using the Qiagen DNeasy Power Soil kit for soil and the CTAB method for plant tissues. The ITS2 region was amplified with universal primers ITS3F and ITS4R, producing approximately 250-base-pair amplicons that were used to construct DNA libraries with the NEB Next Ultra kit. Sequencing was performed on an Illumina HiSeq 2500 with 2 × 250-cycle chemistry. Quality control involved removing adapter dimers, eliminating reads with Phred scores below Q30, and deleting reads with more than 5 percent ambiguous bases. Over 80 percent of total reads exhibited Phred scores greater than 30, implying a base call accuracy above 99.9 percent. Taxonomy was assigned using the Ribosomal Database Project classifier against the UNITE fungal reference database, and statistical significance was assessed with ANOVA at p < 0.05.

The broader implications of this work extend beyond a single weed. The northeastern region of India is considered a biodiversity hotspot, yet its microbial diversity remains largely unexplored. By demonstrating that fungal communities associated with a medicinal plant vary between locations and may influence the production of bioactive compounds, the study opens a new frontier in understanding how plant microbiomes shape phytochemistry. If Trichoderma and other fungi can modulate the accumulation of acaricidal alkaloids, then managing the plant microbiome could become a strategy for enhancing the medicinal value of crops and wild plants alike. The findings also underscore the importance of preserving the microbial diversity of biodiversity hotspots, as these hidden communities may hold untapped pharmaceutical potential.

As the researchers conclude, the fungal communities associated with A. mexicana roots, shoots, and rhizospheric soil were identified for the first time in the northeastern region of India using next-generation sequencing. Every sample contained Trichoderma species, and Ascomycota dominated across all compartments. The plant’s pharmaceutically important secondary metabolites, including sanguinarine, berberine, jatrorrhizine, protopine, and columbamine, may be shaped by the fungi that live with it. This revelation transforms our view of a common weed from a simple botanical entity into a complex holobiont, where plant and fungus collaborate in ways that science is only beginning to decipher. The next chapter in this story will likely involve controlled experiments to confirm whether specific fungal species can enhance or suppress the production of tick-killing compounds, potentially leading to microbiome-based approaches for tick management in livestock systems.

Subject of Research: Fungal microbiome diversity and Trichoderma ubiquity in Argemone mexicana across Assam, India

Article Title: Dominance of ascomycota and ubiquity of Trichoderma in Argemone mexicana microbiomes across Assam, India

Article References: Dominance of ascomycota and ubiquity of Trichoderma in Argemone mexicana microbiomes across Assam, India. (n.d.). https://doi.org/10.3389/ffunb.2026.1868321

Image Credits: AI Generated

DOI: 10.3389/ffunb.2026.1868321

Keywords: Argemone mexicana, Ascomycota, Trichoderma, metagenomics, fungal diversity, rhizosphere, endophytes, Assam, acaricidal compounds, sanguinarine, berberine, ITS2 sequencing