BackgroundThe mitosporic fungus Trichoderma harzianum (Hypocrea, Ascomycota, Hypocreales, Hypocreaceae) is an ubiquitous species in the environment with some strains commercially exploited for the biological control of plant pathogenic fungi. Although T. harzianum is asexual (or anamorphic), its sexual stage (or teleomorph) has been described as Hypocrea lixii. Since recombination would be an important issue for the efficacy of an agent of the biological control in the field, we investigated the phylogenetic structure of the species.ResultsUsing DNA sequence data from three unlinked loci for each of 93 strains collected worldwide, we detected a complex speciation process revealing overlapping reproductively isolated biological species, recent agamospecies and numerous relict lineages with unresolved phylogenetic positions. Genealogical concordance and recombination analyses confirm the existence of two genetically isolated agamospecies including T. harzianum sensu stricto and two hypothetical holomorphic species related to but different from H. lixii. The exact phylogenetic position of the majority of strains was not resolved and therefore attributed to a diverse network of recombining strains conventionally called 'pseudoharzianum matrix'. Since H. lixii and T. harzianum are evidently genetically isolated, the anamorph - teleomorph combination comprising H. lixii/T. harzianum in one holomorph must be rejected in favor of two separate species.ConclusionsOur data illustrate a complex speciation within H. lixii - T. harzianum species group, which is based on coexistence and interaction of organisms with different evolutionary histories and on the absence of strict genetic borders between them.

The Longibrachiatum Clade of Trichoderma is revised. Eight new species are described (T. aethiopicum, T. capillare, T. flagellatum, T. gillesii, T. gracile, T. pinnatum, T. saturnisporopsis, T. solani). The twenty-one species known to belong to the Longibrachiatum Clade are included in a synoptic key. Trichoderma parareesei and T. effusum are redescribed based on new collections or additional observations. Hypocrea teleomorphs are reported for T. gillesii and T. pinnatum. Previously described species are annotated.

Abstract:One of the biggest threats to coffee growers in East Africa are emerging vascular wilt diseases (tracheomycosis) caused by Fusarium spp. Many Trichoderma species are known to be natural antagonists of these pathogens and are widely used in biological control of fungal plant diseases. More recently, several Trichoderma spp., which exhibited high antifungal activity have been isolated as endophytes. Consequently, we have investigated the presence and the antagonistic activity of endophytic Trichoderma isolated from roots of healthy coffee plants (Coffea arabica) from the major coffee growing regions of Ethiopia. Our results showed that community of Trichoderma spp. in roots of C. arabica contains fungi from coffee rhizosphere, as well as putatively obligate endophytic fungi. The putatively -true‖ endophytic species, until now, isolated only from coffee plant ecosystems in Ethiopia and recently described as T. flagellatum and novel T. sp. C.P.K. 1812 were able to antagonize Fusarium spp., which cause coffee tracheomycosis. Moreover, we found that strains of these species are also highly antagonistic against other phytopathogenic fungi, such as Alternaria alternata, Botryotinia fuckeliana (anamorph: Botrytis cinerea), and Sclerotinia sclerotiorum.

The southwestern highlands forests of Ethiopia are the origin of the coffee plant Coffea arabica. The production of coffee in this area is affected by tracheomycosis caused by a soil-born fungus Gibberella xylarioides. The use of endemic antagonistic strains of mycoparasitic Trichoderma species would be a nature conserving means to combat this disease. We have used molecular methods to reveal that the community of Trichoderma in the rhizosphere of C. arabica in its native forests is highly diverse and includes many putatively endemic species. Among others, the putative new species were particularly efficient to inhibit growth of G. xylarioides

Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas.