The genus Trichoderma has been studied for production of enzymes and other metabolites, as well as for exploitation as effective biological control agents. The biodiversity of Trichoderma has seen relatively limited study over much of the neotropical region. In the current study we assess the biodiversity of 183 isolates from Mexico, Guatemala, Panama, Ecuador, Peru, Brazil and Colombia, using morphological, metabolic and genetic approaches. A comparatively high diversity of species was found, comprising 29 taxa: Trichoderma asperellum (60 isolates), Trichoderma atroviride (3), Trichoderma brevicompactum (5), Trichoderma crassum (3), Trichoderma erinaceum (3), Trichoderma gamsii (2), Trichoderma hamatum (2), Trichoderma harzianum (49), Trichoderma koningiopsis (6), Trichoderma longibrachiatum (3), Trichoderma ovalisporum (1), Trichoderma pubescens (2), Trichoderma rossicum (4), Trichoderma spirale (1), Trichoderma tomentosum (3), Trichoderma virens (8), Trichoderma viridescens (7) and Hypocrea jecorina (3) (anamorph: Trichoderma reesei), along with 11 currently undescribed species. T. asperellum was the prevalent species and was represented by two distinct genotypes with different metabolic profiles and habitat preferences. The second predominant species, T. harzianum, was represented by three distinct genotypes. The addition of 11 currently undescribed species is evidence of the considerable unresolved biodiversity of Trichoderma in neotropical regions. Sequencing of the internal transcribed spacer regions (ITS) of the ribosomal repeat could not differentiate some species, and taken alone gave several misidentifications in part due to the presence of nonorthologous copies of the ITS in some isolates.

ABSTRACT A chronology is presented that charts the development of a genus and species concept in Trichoderma. Eighty-nine species of Trichoderma have been named, and several species of Hypocrea have been linked to unnamed Trichoderma anamorphs. Eighty-three taxa of Trichoderma and their teleomorphs, Hypocrea spp., have been included in phylogenetic analyses, including 11 species of Hypocrea with unnamed Trichoderma anamorphs. Phylogenetic analyses show that Trichoderma and Hypocrea are congeneric. Trichoderma species not linked to Hypocrea teleomorphs are derived from among species that are linked to teleomorphs, indicating sexual and asexual lineages are not independent of each other. Many more species remain to be discovered and described. Molecular phylogenetic analyses have revealed the existence of more species than have been recognized on the basis of morphology alone. A suggestion is made to modify the International Code of Botanical Nomenclature to enable adoption of a single generic name for Trichoderma/Hypocrea, with Trichoderma being the older and more utilitarian name. As increasing numbers of species are studied, the few morphological characters of anamorph and teleomorph have reached their limit for defining species. DNA-based characters have assumed an indispensable role. Exploration of new niches, such as within tree trunks and new geographic locations, have resulted in a substantial increase in the number of species of Trichoderma. Trichoderma is usually considered a genus of free-living soil fungi but evidence suggests that Trichoderma species may be opportunistic, avirulent plant symbionts as well as parasites of other fungi. Members of the genus Trichoderma are universally present in soils, although individual species may be either cosmopolitan (e.g., T. harzianum) or limited (e.g., T. viride) in their geographic distribution. To facilitate identification of species, a list of correctly identified strains of Trichoderma and their GenBank numbers for sequences of translation-elongation factor EF-1alpha and internal transcribed spacer rDNA is provided.

The first large-scale survey of sexual and asexual Trichoderma morphs collected from plant and fungal materials conducted in Southern Europe and Macaronesia including a few collections from French islands east of Africa yielded more than 650 specimens identified to the species level. Routine sequencing of tef1 revealed a genetic variation among these isolates that exceeds previous experience and ca. 90 species were recognized, of which 74 are named and 17 species newly described. Aphysiostroma stercorarium is combined in Trichoderma. For the first time a sexual morph is described for T. hamatum. The hitherto most complete phylogenetic tree is presented for the entire genus Trichoderma, based on rpb2 sequences. For the first time also a genus-wide phylogenetic tree based on acl1 sequences is shown. Detailed phylogenetic analyses using tef1 sequences are presented in four separate trees representing major clades of Trichoderma. Discussions involve species composition of clades and ecological and biogeographic considerations including distribution of species.