Fungal endophytes: invisible crusaders of green agriculture

Dr. Kanika Chowdhary (DST-WOS B Scientist, CRDT, IIT-Delhi

2021-07-29 05:36:35

Credit: Kanika Chowdhary

Credit: Kanika Chowdhary

Nature’s many ironical ways have never cease to excite, inspire and challenge human brains. Amongst many such intriguing revelations is the benign presence of microbes (particularly fungi and bacteria) in almost every plant organelle investigated till date, collectively called “endophytes”.

To dig more into the reason and thrust that lets these two evolutionarily contrasting organisms (microbe that is invisible and miniscule in a multifunctional macro-organism plant) stay together, we need to first understand the fundamental nature of symbiosis. In technical terms the phenomenon is described as living together of two any different species leading to a close and long-term relationships between different. It is a harmonious, purposeful and calculated arrangement for which numerous scientific basis have now been documented. 

Symbiosis has been recognised as the central drive of evolution of various life forms on earth. It is an engineered mechanism with which inputs are divided while the positive outputs get amplified. It saves much effort and energy of both the partners. For instance, plants absorb nutrients such as potassium, phosphate, zinc and sulphur for growth and have roots to do the job. But, upon symbiotic facilitation by nutrient solubilising microbes this entire process gets faster and consumes lesser energy. Therefore, by creating such juxtaposed and interconnected pathways “symbiosis” largely works on two interfaces. The first interface is to provide chemical novelties. The manipulation both the partners have to do in their regular metabolic pathways for sustaining symbiotic relationship leads to some of the unexpected and reportedly functional secondary metabolites. The other interface that it caters to is enhanced vigor. The various fitness benefitting factors (higher growth rates, defense elements and nutrient allocation) which host receives through trusted symbionts are unprecedented in quantum and quality.

Literature documents that every eukaryote has myriad of microbial associations. Likewise, as against the outmoded assumption a plant is considered as a “phytosphere”, it is no longer an isolated unit of life rather a “Holobiont”, dynamically functioning with its associated microbes. Amongst these various symbiotic interactions, the phenomenon of microbes residing inside plants without causing any disease or any imbalance is known as “endophytism”. Endophytologists have specifically advised to strategically bioprospect endophytes of unexplored medicinal plants. Nature has hidden in itself myriad opportunities abound that can provide natural products with significant therapeutic/industrial potential which might contribute to solving plant, animal and human health problems in response to the increasing threats from drug resistant strains of plant and human pathogens. Endophytic microbes are functional partner (symbiont) in a dynamic phytosphere.

Fungi and fungal-like organisms such as Pythium sp. and Phytophthora sp. are responsible for causing highest number of plant diseases. Fungal plant pathogens account for around 8,000 different species. Plant diseases impede quantity and quality of food, fibre and biofuel crops. The environmental drawbacks of chemical pesticides have led to enhanced usage and awareness of botanical pesticides for crop protection. It has been well understood after about a century of heavy chemical use in agriculture both in theory and practice that pesticidal plant products serve as a viable, much needed and cheaper option for disease management in sustainable agriculture. It has also been estimated that utilisation of microbial biopesticides would precipitously lower the future investments in agriculture.

Our research group investigated two categories of host plants i.e. essential oil producing plant species such as Ocimum sanctum (Tulsi) and Mentha piperita (Pudina) and saponins containing plant species such as Chlorophytum borivilianum (Safed Musli) and Asparagus racemosus (Shatavari). Also it was a one of its kind of work wherein temporal and spatial assemblages of fungal endophytes were examined.All four medicinal host plants and their tissues have resembled as distinctive microhabitats. Every plant part was an unique ecological niche in itself. Every sampling differed in its fungal population both in function and structure. The resulted divergence between distribution patterns by geographical locations was related to differences in geological, ecological and climatic conditions immediately before collection of samples. The outcomes achieved had indicated towards a degree of host preference and specificity among endophytic assemblages. As for the novelty, this study led to identification of a fungus mentioned in the published article as endophytic Macrophomina phaseolina strain which was found to produce an antifungal compound 2H-pyran-2-one 5, 6 dihydro-6-pentyl. This novel metabolite was responsible for pesticidal action of the endophytic fungus M. phaseolina.

In another recent study, we investigated fungal endophytes associated with aromatic plants such as Cassia fistula (Amaltas), Ocimum basicilium (Babui tulsi), Murraya koenigii (kadi patta), Aloe vera and Plectranthus amboinicus (ajwain poddha) for plant growth promotion and biocontrol potential.  Trichoderma harzanium was the most dominant species in A. vera. T. harzanium tested positive for numerous plant growth promoting traits. Also, the strain was tested to withstand stressful conditions such as high temperature, cold stress and UV-B exposure. T. harzanium showed its potential as a promising biocontrol agent and exhibited antagonism against plant pathogenic fungus Sclerotinia sclerotiorum. Gas chromatography- mass spectroscopy (GC-MS) analysis of its hexane concentrate detected abundant presence antifungal compounds such as palmitic and linoleic acid. In my quest for antifungal compounds from isolated endophytes, I have been able to characterise few novel metabolites such as GC-MS analysis of hexane extract of another biocontrol endophyte Colletotrichum sp. isolated from Cassia fistula depicted essential oil components (monoterpenes) β-citronellol (25.05% ) and Geraniol (11.5% ). Essential oils are basically plant produced metabolites and their presence in endophytic fungi gives enough direction towards genetic evolution of both the symbiotic partners.


Exploring agriculturally beneficial endophytes is quite a prospective field of research. The practical usage of endophytes as ‘bio-supplements’ in conventional agriculture requires immediate attention.  With appropriate strategy and management, these beneficial microbes can be exploited for control of present and emerging pests and pathogens and also for various biotic stressors.


1. Chowdhary K., & Kaushik, N. (2015). Fungal endophyte diversity and bioactivity in the Indian medicinal plant Ocimum sanctum Linn. PloS one, 10(11), e0141444.

2. Chowdhary K., & Kaushik, N (2017) Biodiversity and In Vitro Inhibition Study of Fungal Endophytes of Chlorophytum borivilianum Against Selected Phytopathogens. Proceedings of the National Academy of Sciences, India Section B: Biological Sciences. 89(1): 113-121.