Certain Trichoderma isolates provide biofertilizer, biocontrol, and other plant-beneficial activities while inhabiting the soil or internal plant issues; and their use in agricultural systems could contribute to sustainable food production. It is thought that this colonization of soil and internal plant tissues is fundamental for biocontrol and biofertilizer applications. Our collective analyses of prior surveys, where the tef1 sequence was almost exclusively used to identify Trichoderma species, showed that isolates from the Harzianum Complex Clade, the T. asperellum/T. asperelloides group, T. virens, T. hamatum, and T. atroviride were prevalent in soil and/or as endophytes. Population structure and genetic diversity of these species were investigated, and new lineages with geo-graphic significance within T. atroviride, T. asperellum, T. hamatum, and T. virens populations were found. The nearest relatives of some species were also revealed. Choosing isolates from among more than 500 known Trichoderma species for use in non-targeted evaluation screens for biocontrol or biofertilizer applications is time-consuming and expensive. Preferentially selecting species from T. atroviride, T. asperellum/T. asperelloides, T. hamatum, species from the T. harzianum Complex Clade, T. virens, and possibly nearest relatives, may speed the identification of candidates for commercialization due to the demonstrated ability of these species to successfully inhabit the soil and endorhizosphere. To our knowledge, this is the first report where dominant soil- and en-dophyte-inhabiting Trichoderma species were identified from past survey data and population structure and genetic diversity analyses conducted.

As environmental and health concerns increase, the trend of sustainable agriculture moves toward using biological agents. About 60% of all biological fungicides have Trichoderma species as the active ingredient, with T. harzianum as the most common species in these products. However, the name T. harzianum has often been incorrectly used in culture collections, databases, and the scientific literature due to the division of the Harzianum Complex Clade (HCC) into more than 95 cryptic species with only one being named T. harzianum. In this study, 49 strains previously identified as T. harzianum in three surveys of Trichoderma species from soils in South and Central America were re-identified using phylogenetic analyses based on tef1α, rpb2, and ITS loci and were combined with the corresponding species in two other studies, where the species were correctly identified. Based on the results of the five surveys of the total 148 strains in HCC, 11 species were identified and T. afroharzianum, T. lentiforme, T. endophyticum followed by T. azedevio and T. harzianum were detected as the dominant species of the HCC in South and Central America. This is the first report of identifying dominant Trichoderma species within the HCC in South and Central American soil based on multiple studies, which will be useful in selecting strains within the complex clade for formulation of biocontrol and biofertilizer products in the continent.

As environmental and health concerns increase, the trend of sustainable agriculture moves toward using biological agents. About 60% of all biological fungicides have Trichoderma species as the active ingredient, with T. harzianum as the most common species in these products. However, the name T. harzianum has often been incorrectly used in culture collections, databases, and the scientific literature due to the division of the Harzianum Complex Clade (HCC) into more than 95 cryptic species with only one being named T. harzianum. In this study, strains previously identified as T. harzianum in three surveys of Trichoderma species from soils in South and Central America were reanalyzed using phylogeny based on tef1α, rpb2, and ITS loci and combined with the corresponding species in two other studies, where the species were correctly identified. Based on the results of the five surveys, T. afroharzianum, T. lentiforme, T. endophyticum followed by T. azedevio and T. harzianum were found to be the dominant species of the HCC in South and Central America. This is the first report of identifying dominant Trichoderma species within the HCC in South and Central American soil based on multiple studies, which will be useful in selecting strains within the complex clade for formulation of biocontrol and biofertilizer products in the continent.