Diversity of Native Trichoderma spp. Associated with Theobroma cacao and Citrus sinensis Crops in Peruvian Amazon: First Report for San Martín Region

Trichoderma species are recognized biocontrol agents and plant growth promoters with applications in sustainable agriculture. Despite the economic importance of cacao and orange crops in the San Martín region of the Peruvian Amazon, the diversity of native Trichoderma associated with these crops remains undocumented. This study provides the first report of Trichoderma diversity in rhizospheric soil and plant tissues of Theobroma cacao and Citrus sinensis in this region. Sampling was conducted in 18 sectors across five districts (195–785 m a.s.l.). Molecular identification was performed using the translation elongation factor 1-alpha (tef1) gene marker, with NCBI BLAST analysis against GenBank and phylogenetic analysis using the Neighbor-Joining method. From 59 initial isolates, 18 strains were successfully identified. Seven putative species (T. koningiopsis, T. reesei, T. lentiforme, T. longibrachiatum, T. harzianum, T. spirale, and T. azevedoi) were found associated with cacao, while four putative species (T. erinaceum, T. parareesei, T. longibrachiatum, and T. virens) were identified from orange crops. Sequence identity ranged from 94.38% to 100%. BLAST comparison initially returned equal identity scores between T. harzianum and T. lentiforme for five strains (T-3, T-11, T-14, T-15, and T-16); subsequent phylogenetic placement using a broader GenBank reference panel resolved all five within the T. lentiforme clade. Phylogenetic placement also refined two further identifications beyond their initial BLAST match: strain T6-SR-B grouped with T. azevedoi rather than T. harzianum, and strain T12-R-A grouped with the sister species T. parareesei rather than T. reesei. These findings establish a baseline for Trichoderma biodiversity in the region and identify potential candidates for biocontrol applications.