ORIGINAL ARTICLE Inhibition of the collar rot fungus, Sclerotium rolfsii Sacc. by an endophytic fungus Alternaria sp.: implications for biocontrol P. Rajani 1,2 • H. Aiswarya 1 • M. M. Vasanthakumari 1 • Shreyans K. Jain 3 • Sandip B. Bharate 3 • C. Rajasekaran 2 • G. Ravikanth 4 • R. Uma Shaanker 1,4,5 Received: 7 November 2019 / Accepted: 22 November 2019 Ó Indian Society for Plant Physiology 2019 Abstract Sclerotium rolfsii is a necrotrophic, soil-borne pathogenic fungus responsible for serious crop losses worldwide. It is one of the major phytopathogens infecting chilli and causes yield losses ranging from 16 to 80%. Among the various approaches to manage S. rolfsii, bio- logical control is an environmentally acceptable alternative over other chemical methods. In this study, 120 endophytic fungal isolates obtained from a medicinal plant, Nothapo- dytes nimmoniana were evaluated for their in vitro and in vivo antagonism towards S. rolfsii. Among these, one isolate, Alternaria sp. exhibited 46.62% inhibition against S. rolfsii in dual culture assay on PDA. The inhibition was found to be mediated by the mycotoxin, tenuazonic acid, produced by the endophyte. Pre-germinated chilli seeds treated with mycelial suspension of Alternaria sp. reduced the seedling mortality due to S. rolfsii infection. Pretreat- ment with the endophyte also enhanced seedling growth and biomass compared to untreated seedlings under greenhouse conditions. These results suggest that the endophytic fungus, Alternaria sp. has potential implication for use as a biocontrol against S. rolfsii as well as for promoting growth of chilli. Keywords Collar rot Á Chilli Á Sclerotium rolfsii Á Alternaria sp. Á Endophytic fungus Á Tenuazonic acid Á Biological control Introduction Chilli (Capsicum annuum L., Family: Solanaceae) is one of the important cash crops cultivated as an important spice and vegetable crop. Native to South America, Chilli was introduced into India by the end of fifteenth century. India is considered as the secondary centre of diversity of chilli as it is one of the most widely cultivated crops with large number of varieties (Dhaliwal et al. 2014). With a total production of 3.59 million MT of green chillies and 2.14 million MT of dry chillies in 2017–2018, India is the world’s largest producer, consumer and exporter of chillies (NHB, 2017–2018). The chilli fruit is a reservoir of numerous chemicals including steam-volatile oils, fatty oils, capsaicinoids, carotenoids, vitamins, proteins, fibres and mineral elements (Saranakumar et al. 2011). Chillies are rich in vitamin A, vitamin C, vitamin E and are a good source of potassium and folic acid (Perva-Uzunalic ´ et al. 2004). Chilli is susceptible to a wide array of fungal as well as bacterial diseases and this has been a major constraint in Electronic supplementary material The online version of this article (https://doi.org/10.1007/s40502-019-00484-6) contains sup- plementary material, which is available to authorized users. & P. Rajani rajanirajpijakala@gmail.com & C. Rajasekaran drcrs70@gmail.com 1 School of Ecology and Conservation, University of Agricultural Sciences, GKVK Campus, Bangalore 560065, India 2 Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu 632014, India 3 CSIR - Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India 4 Ashoka Trust for Research in Ecology and the Environment, Royal Enclave, Srirampura, Jakkur Post, Bangalore 560064, India 5 Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore 560065, India 123 Plant Physiol. Rep. https://doi.org/10.1007/s40502-019-00484-6