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.

Host jumps by microbial symbionts are often associated with bursts of species diversification driven by the exploitation of new adaptive zones. The objective of this study was to infer the evolution of habitat preference (decaying plants, soil, living fungi, and living plants), and nutrition mode (saprotrophy and mycoparasitism) in the fungal genus Trichoderma to elucidate possible interkingdom host jumps and shifts in ecology. Host and ecological role shifts were inferred by phylogenetic analyses and ancestral character reconstructions. The results support several interkingdom host jumps and also show that the preference for a particular habitat was gained or lost multiple times. Diversification analysis revealed that mycoparasitism is associated with accelerated speciation rates, which then suggests that this trait may be linked to the high number of species in Trichoderma. In this study it was also possible to infer the cryptic roles that endophytes or soil inhabitants play in their hosts by evaluating their closest relatives and determining their most recent ancestors. Findings from this study may have implications for understanding certain evolutionary processes such as species radiations in some hyperdiverse groups of fungi, and for more applied fields such as the discovery and development of novel biological control strategies.

Although fungi contribute significantly to the microbial biomass in terrestrial ecosystems, little is known about their contribution to biogeochemical nitrogen cycles. Agricultural soils usually contain comparably high amounts of inorganic nitrogen, mainly in the form of nitrate. Many studies focused on bacterial and archaeal turnover of nitrate by nitrification, denitrification and assimilation, whereas the fungal role remained largely neglected. To enable research on the fungal contribution to the biogeochemical nitrogen cycle tools for monitoring the presence and expression of fungal assimilatory nitrate reductase genes were developed. To the ~100 currently available fungal full-length gene sequences, another 109 partial sequences were added by amplification from individual culture isolates, representing all major orders occurring in agricultural soils. The extended database led to the discovery of new horizontal gene transfer events within the fungal kingdom. The newly developed PCR primers were used to study gene pools and gene expression of fungal nitrate reductases in agricultural soils. The availability of the extended database allowed affiliation of many sequences to known species, genera or families. Energy supply by a carbon source seems to be the major regulator of nitrate reductase gene expression for fungi in agricultural soils, which is in good agreement with the high energy demand of complete reduction of nitrate to ammonium.