Trichoderma koningii Oudem. is one of the most commonly cited species of Trichoderma Pers., the anamorph genus of Hypocrea Fr. (Hypocreales, Hypocreaceae). Literally hundreds of publications report the involvement of this species in the biological control of plant diseases caused by other fungi. Among these, T. koningii is reported to produce 6-pentyl alpha pyrone, a spore germination inhibitor (Worasatit et al. 1994). Song et al. (2006) characterized trichokonins, which are peptaibols that have antimicrobial activity, in T. koningii. A search of the literature reveals a role of T. koningii in many activities in addition to biological control of fungus-induced plant disease. For example, culture filtrates of T. koningii and T. harzianum killed 100 % of root-knot nematodes in Sri Lanka (Sankaranarayanan et al. 1997). Trichoderma koningii also benefits plant health and nutrient uptake when it was determined to be highly active in biomineralizing calcium oxalate crystals in soil (Oyarbide et al. 2001), the first reference to indicate this species as a biomineral-producing agent.
What is T. koningii? Despite the fact that the genus Trichoderma Pers. was proposed late in the 18th century, prior to 1984 only 35 species were included in the genus, and before 1969 very few of these were reported in the literature subsequent to their original description. Trichoderma koningii, described in 1902 (Oudemans & Koning 1902), was included by Rifai (1969) as one of the nine "aggregate" or "morphological" species that he recognized. Bissett (1991a) included it in Trichoderma sect. Trichoderma, which includes the type of the genus, T. viride Pers., on the basis of the morphology of the conidiophore. Lieckfeldt et al. (1998) confirmed membership of T. koningii in sect. Trichoderma using ITS1 and 2 sequences of the rDNA gene cluster, and PCR fingerprinting, a result that has been affirmed in additional publications with other genes (e.g. Kullnig-Gradinger et al. 2002). Lübeck et al. (2004) showed that infra-species variation was greater than inter-species in ITS in the T. koningii aggregate species. Essentially, in that study ITS1 and 2 were not helpful in separating closely related species of sect. Trichoderma, but the authors found that UP-PCR fingerprinting could distinguish T. koningii from T. viride and other members of Trichoderma sect. Trichoderma. The first version of an oligonucleotide barcode based on ITS1 and 2 implemented in TrichOKEY program (Druzhinina et al. 2005) is able to identify the T. koningii/T. ovalisporum/H. muroiana species triplet and attribute it to the "Pachybasium A" clade after Kullnig-Gradinger et al. (2002).
Bissett (1991a) divided Trichoderma species among several sections. Among them was sect. Trichoderma, which included T. viride. Chaverri & Samuels (2004) proposed a move towards the classification based on phylogenetic clades rather than dividing the genus into sections. They referred to the "Rufa Clade," named for Hypocrea rufa, the type species of the genus, which included members of sections Trichoderma and species from the "Pachybasium A" Clade. The latter group includes T. hamatum (Bonord.) Bainier, the type species of Pachybasium Sacc., and other species. It was refered to as the "Hamatum clade" by Jaklitsch et al. (2006a). In the present work we refer to the combined "Rufa Clade" and the "Pachybasium A" Clade as the "Viride Clade." Trichoderma koningii and the species discussed in the current paper belong to that clade.
Lieckfeldt et al. (1998) narrowly defined the morphology of T. koningii and linked it to a teleomorph, Hypocrea koningii Lieckfeldt et al. Lieckfeldt et al. (1998) and Lübeck et al. (2004) demonstrated genetic diversity within the T. koningii aggregate species. Lieckfeldt et al. (1998) noted four additional, morphologically similar and phylogenetically closely related species that they identified as H. cf. muroiana or Hypocrea sp. One of the strains identified by Lieckfeldt et al. (1998) as H. cf. muroiana has since been described as H. stilbohypoxyli B.S. Lu & Samuels (Lu & Samuels 2003). Later, in a revision of T. viride, Lieckfeldt et al. (1999) found nine ITS haplotypes among isolates that conformed to the broadly defined morphospecies T. koningii, of which one was true T. koningii in the narrow sense of Lieckfeldt et al. (1998). Holmes et al. (2004) distinguished T. ovalisporum Samuels & Schroers from T. koningii s. str. and other members of the T. koningii morphological aggregate on the basis of sequences of the protein-encoding gene translation-elongation factor 1- (tef1) and conidium morphology. In addition to these T. koningii-like species, Holmes et al. (2004) designated four clades of Trichoderma collections that have the T. koningii morphology as "Tkon 20," "Tkon 21," "Tkon 22," and "Tkon 3."
Since the study of Lieckfeldt et al. (1999) we have received many additional collections from geographically and biologically diverse sources that can be assigned generally to sect. Trichoderma and specifically to the T. koningii aggregate species. In the present work we examine the phenotypic and phylogenetic diversity found within the T. koningii aggregate species, and develop a taxonomy for those fungi by combining results of morphological, cultural, and molecular-phylogenetic analyses.