The dual face of biocontrol in the phytobiome: between the impact of cyclic lipopeptides and the trichoderma paradox

Role and fate of cyclic lipopeptides in phytobiomes and consequences for biocontrol

Prof. Monica  Höfte

Abstracts

A phytobiome is a complex ecological system consisting of a plant, its surrounding abiotic environment, and all associated microorganisms and macroorganisms living in, on, or around it. Among the key players in this ecosystem are plant-associated members of the bacterial genera Bacillus and Pseudomonas. Multiple species within these genera produce cyclic lipopeptides (CLiPs), amphiphilic molecules with biosurfactant activity composed of a fatty acid tail and a cyclic oligopeptide lactone ring.  CLiPs are encoded by nonribosomal peptide synthetases and show a remarkable chemical diversity that drastically impacts key functionalities. They are important in sliding motility, root colonization, biofilm formation, and nutrient uptake, but also as mediators of ecological interactions. With potent antimicrobial activity, they ward off competitors and predators. Some CLiPs act as virulence factors for plant pathogens, while others induce systemic resistance in plants, resulting in protection against pathogens and pests. Expression of CLiPs is modulated by abiotic factors and exogenous signals from the biotic environment.  Some pathogens and competitors co-occurring with CLiP producers in the phytobiome linearize  CLiPs for detoxification or breakdown CliPs to sustain growth. Depending on the role of the CLiP in the pathobiome, this may result in reduced virulence or biocontrol collapse. For biocontrol to be effective, the focus must shift from microbial metabolite production alone to understanding and managing the ecological interactions that shape their fate and activity within the phytobiome.

The paradox of Trichoderma: beneficial biocontrol agent or emerging threat?

Prof. Sabrina Sarocco

Abstract

Plant diseases are estimated to reduce agricultural productivity by 20–40% and making the search for environmentally friendly alternatives to chemical pesticides a top priority. Among the most successful biocontrol agents are fungi belonging to the genus Trichoderma, which have been used since the 1930s and now dominate the global biocontrol market owing to their multiple direct and indirect modes of action. However, the recent identification of species such as Trichoderma afroharzianum as the causal agent of Maize Ear Rot outbreaks in Europe has revealed a "dual-identity paradox", leading to its inclusion on the EPPO Alert List and highlighting the urgent need for a deeper understanding of the genetic and environmental factors that determine whether a species acts as a beneficial ally or a pathogen. To address this complexity, our research has focused on Trichoderma gamsii T6085 as a specialized biocontrol agent for the management of Fusarium Head Blight (FHB). T6085 exhibits remarkable ecological fitness, effectively competing for natural substrates and maintaining growth even in the presence of high concentrations of the mycotoxin deoxynivalenol (DON). Its biocontrol efficacy is further enhanced by its endophytic lifestyle, which enables colonization of wheat roots and spikes and modulates host defense response. Transcriptomic analyses have revealed a sophisticated "stealth mode" of molecular cross-talk during long-distance interactions with pathogens, in which T6085 down-regulates a large portion of its own transcriptome while sensing and responding to its competitor. Furthermore, high-throughput phenotyping has demonstrated that T6085-treated plants maintain significantly greater photosynthetic performance during infection, supporting its development as a next-generation biofungicide in line with global strategies aimed at reducing chemical pesticide use.

The speakers

Prof. Monica Höfte, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Belgium
Monica Höfte is a professor at Ghent University in Belgium and serves as the head of the Department of Plants and Crops. She is a plant pathologist with a broad expertise in both fundamental and applied aspects of plant-pathogen interactions. Her work focuses on the biological and integrated management of fungal and bacterial pathogens affecting a wide range of tropical and temperate crops. Her research group specializes in studying fungal and bacterial rice pathogens and their interactions with rice plants, as well as soilborne pathogens such as Pythium, Phytophthora, Fusarium, Verticillium, and Rhizoctonia. In the field of biocontrol, the main focus is on cyclic lipopeptides produced by Pseudomonas and Bacillus strains with an emphasis on their natural function, regulation by abiotic and biotic factors, and fate in the environment. https://orcid.org/0000-0002-0850-3249.

Prof. Sabrina Sarrocco is Associate Professor of Plant Pathology at the Department of Agriculture, Food and Environment of the University of Pisa. Her research focuses on plant pathology, mycology, and the biological control of plant diseases, with particular emphasis on beneficial fungi of the genus Trichoderma. She obtained her PhD in Plant Pathology in 2004 and has been visiting researcher at the University of Copenhagen, Aalborg, Paris Saclay and Piracicaba. Her scientific activity combines molecular biology, genomics, transcriptomics, and ecophysiology to investigate plant–microbe interactions and sustainable disease management strategies. She is involved in several national and international research projects, including the Trichoderma Whole Genus Genomics initiative. She has authored more than 100 peer-reviewed publications and serves on the editorial boards of several international journals in plant pathology and microbiology. Since 2026, she has been an Ordinary Member of the Accademia dei Georgofili and actually Vice-President of the Italian Phytopathological Society (SIPaV). Her current research is aimed at developing innovative biocontrol solutions to support sustainable agriculture and reduce reliance on chemical pesticides.