Isolation and characterization of Trichoderma from Amazonian white-water river sediments with descriptions of five new species and new records from Brazil

Trichoderma is a cosmopolitan genus widely used in agriculture due to its beneficial traits that promote plant growth and provide sustainable crop protection. Over 450 valid Trichoderma species have been described, with increasing whole-genome data showing extensive enzymatic repertoires and biosynthetic potential. However, the Amazonian biome remains underexplored for Trichoderma diversity despite its megadiversity. In this study, 44 Trichoderma strains were isolated from sediments collected during a systematic expedition along three major white-water Amazonian rivers (Juruá, Madeira, and Purus). Initial molecular barcoding using tef1-α sequences identified 14 species, with Trichoderma lentiforme being ubiquitously distributed across all three river systems. Isolates exhibiting <97% sequence identity to known species underwent comprehensive polyphasic characterization, including multi-locus phylogenetic analyses ( tef1-α and rpb2 ), morphological studies, biocontrol assays, and comparative genomics. This approach led to the description of five novel species ( Trichoderma madeiraense , Trichoderma labreaense , Trichoderma tapauaense , Trichoderma submersum , and Trichoderma juburiaense ). It established the first records of Trichoderma cyanodichotomus and Trichoderma awajun for Brazil. All newly described species demonstrated strong antagonistic activity against major phytopathogens, with T. juburiaense TM67 achieving >95% mycelial growth inhibition against multiple Colletotrichum species. Comparative genomic analyses revealed diverse CAZyme arsenals enriched in glycoside hydrolases associated with mycoparasitism (GH16, GH18, GH72) and lignocellulose degradation, with T. labreaense TM26 exhibiting particularly high chitinase content and T. juburiaense TM67 showing elevated β-glucanase levels. Genome mining identified biosynthetic gene clusters encoding bioactive secondary metabolites, including verticillins, ilicicolins, chaetoglobosins, harzianopyridone, and brefeldin A, compounds with established antifungal, antibacterial, and cytotoxic activities. This study provides a taxonomic and genomic survey of Trichoderma from Amazonian white-water river sediments, describing five novel species and highlighting this frontier ecosystem as an important but undersampled source of fungal biodiversity.