Potential of fungi of the genus Trichoderma for biocontrol of Philaenus spumarius, the insect vector for the quarantine bacterium Xylella fastidosa.

BACKGROUND: The meadow spittlebug Philaenus spumarius L. is the vector for the bacterium Xylella fastidiosa subspecies pauca, involved in olive quick decline syndrome (OQDS) in Salento (Italy). Control of P. spumarius is key to limiting transmission of the bacterium, and an innovative approach can be based on effective natural compounds and biocontrol agents. Entomopathogenic fungi are an important source of bioactive natural molecules that play a role in the relationship between microorganisms and insects. RESULTS: Pathogenicity bioassays, performed by dipping adults of P. spumarius in either fungal culture suspension (120 mg mL-1 ) or cell-free culture supernatant of Trichoderma chlorosporum GJS 91-150, showed, respectively, 97% and 87% death within 24 h. The effect was dose-dependent. In laboratory bioassays, the powdered fungal culture of T. chlorosporum GJS 91-150 did not exhibit pathogenic activity when injected into nymph spittle. CONCLUSIONS: T. chlorosporum GJS 91-150 affected the survival of P. spumarius adults. The lethal effect was not associated with the development of mycelium on the cuticle, but seems due, at least partly, to fungal metabolites released in the culture medium. The fungus tested here has good potential for the development of effective low-environmental impact control strategies for P. spumarius and suppression of X. fastidiosa. © 2022 Society of Chemical Industry.

Growing plants on oily, nutrient-poor soil using a native symbiotic fungus.

The roots of land plants associate with microbes, including fungal symbionts that can confer abiotic stress tolerance. Bitumen extraction following oil-sand surface mining in the Athabasca region of Alberta, Canada removes plant nutrients but leaves a petrochemical residue, making the coarse tailings (CT) hostile to both plants and microbes. We isolated an endophyte strain of the Ascomycete Trichoderma harzianum we call TSTh20-1 (hereafter, TSTh) from a dandelion that was naturally growing on CT. TSTh colonization allowed tomato, wheat, and remediation seed mixtures to germinate and their seedlings to flourish on CT without the use of fertilizer. Compared to control plants, TSTh increased germination speed, percent germination, and biomass accumulation. TSTh also improved plant water use efficiency and drought recovery. TSTh-colonized plants secreted twice the level of peroxidase into CT as did plants alone. Over two months, plants colonized with TSTh doubled the petrochemical mobilization from CT over plants alone, suggesting a peroxide-mediated mechanism for petrochemical degradation. TSTh grew on autoclaved CT, bitumen, and other petrochemicals as sole carbon sources. Further, TSTh is a micro-aerobe that could metabolize 13C-phenanthrene to 13CO2 in 0.5% oxygen. TSTh has excellent potential for contributing to revegetating and remediating petrochemical contamination.

Epitypification of Fusisporium (Fusarium) solani and its assignment to a common phylogenetic species in the Fusarium solani species complex.

Fusisporium solani was described as the causal agent of a dry rot of potato in Germany in the mid 19th century. As Fusarium solani, the species became known as a plurivorous plant pathogen, endophyte, decomposer, and opportunistic pathogen of humans and nutritional symbiont of insects. In parallel, it became evident that the morphologically defined species F. solani represents a phylogenetically and biologically complex group of often morphologically cryptic species that has come to be known in part as the F. solani species complex (FSSC), accommodating several formae speciales and mating populations/biological species. The FSSC currently includes more than 60 phylogenetic species. Several of these have been named, but the majority remains unnamed and the identity of F. solani sensu stricto is unclear. To promote further taxonomic developments in the FSSC, lectoand epitypification is proposed for Fusisporium solani Although no type material for F. solani is known to exist, the species was abundantly illustrated in the protologue. Thus, a relevant illustration provided by von Martius is selected as the lectotype. The epitype selected here originates from a rotting potato collected in a field in Slovenia. This strain causes a dry rot of artificially inoculated potatoes. It groups in the heretofore unnamed phylogenetic species 5, which is nested within clade 3 of the FSSC (FSSC 5). Members of this phylogenetic species have a wide geographic distribution and include soil saprotrophs and plant and opportunistic human pathogens. This typification is consistent with the original description of Fusisporium solani and the concept of F. solani as a widely distributed soil inhabitant and pathogen.

Peptaibol, secondary-metabolite, and hydrophobin pattern of commercial biocontrol agents formulated with species of the Trichoderma harzianum complex.

The production of bioactive polypeptides (peptaibiotics) in vivo is a sophisticated adaptation strategy of both mycoparasitic and saprotrophic Trichoderma species for colonizing and defending their natural habitats. This feature is of major practical importance, as the detection of peptaibiotics in plant-protective Trichoderma species, which are successfully used against economically relevant bacterial and fungal plant pathogens, certainly contributes to a better understanding of these complex antagonistic interactions. We analyzed five commercial biocontrol agents (BCAs), namely Canna(®) , Trichosan(®) , Vitalin(®) , Promot(®) WP, and TrichoMax(®) , formulated with recently described species of the Trichoderma harzianum complex, viz. T. afroharzianum, T. simmonsii, and T. guizhouense. By using the well-established, HPLC/MS-based peptaibiomics approach, it could unequivocally be demonstrated that all of these formulations contained new and recurrent peptaibols, i.e., peptaibiotics carrying an acetylated N-terminus, the C-terminus of which is reduced to a 1,2-amino alcohol. Their chain lengths, including the amino alcohol, were 11, 14, and 18 residues, respectively. Peptaibols were also to be the dominating secondary metabolites in plate cultures of the four strains obtained from four of the Trichoderma- based BCAs, contributing 95% of the UHPLC-UV/VIS peak areas and 99% of the total ion count MS peak area from solid media. Furthermore, species-specific hydrophobins, as well as non-peptaibiotic secondary metabolites, were detected, the latter being known for their antifungal, siderophore, or plant-growth-promoting activities. Notably, none of the isolates produced low-molecular weight mycotoxins.

Systematics of the Cosmospora viliuscula species complex.

The genus Cosmospora includes nectrioid fungi that grow on polypores and xylariaceous fungi. The collections growing on xylariaceous fungi have been identified recently as Cosmospora viliuscula. In this paper the phylogeny and taxonomy of C. viliuscula are investigated. A phylogeny was generated with maximum likelihood and Bayesian inference methods applied to a three-partition dataset (ITS, 28S, MCM7-RPB1-TUB2). Based on these results, we demonstrate that Cosmospora viliuscula represents a diverse species complex comprising more than 10 species. Seven new species are described, including three single-strain lineages, and the sexual states of C. arxii and C. khandalensis are described for the first time. The sexual states of these fungi tend to have a high degree of morphological homoplasy, making it difficult to differentiate among them based on morphological characters alone. However, the apparent host specificity of species in this complex aide in the diagnosis of these fungi. In addition, the RPB1 marker provides sufficient resolution to distinguish these fungi.

Systematics of the Trichoderma harzianum species complex and the re-identification of commercial biocontrol strains.

Trichoderma harzianum is known as a cosmopolitan, ubiquitous species associated with a wide variety of substrates. It is possibly the most commonly used name in agricultural applications involving Trichoderma, including biological control of plant diseases. While various studies have suggested that T. harzianum is a species complex, only a few cryptic species are named. In the present study the taxonomy of the T. harzianum species complex is revised to include at least 14 species. Previously named species included in the complex are T. guizhouense, T. harzianum, and T. inhamatum. Two new combinations are proposed, T. lentiforme and T. lixii. Nine species are described as new, T. afarasin, T. afroharzianum, T. atrobrunneum, T. camerunense, T. endophyticum, T. neotropicale, T. pyramidale, T. rifaii and T. simmonsii. We isolated Trichoderma cultures from four commercial biocontrol products reported to contain T. harzianum. None of the biocontrol strains were identified as T. harzianum s. str. In addition, the widely applied culture 'T. harzianum T22' was determined to be T. afroharzianum. Some species in the T. harzianum complex appear to be exclusively endophytic, while others were only isolated from soil. Sexual states are rare. Descriptions and illustrations are provided. A secondary barcode, nuc translation elongation factor 1-α (TEF1) is needed to identify species in this complex.

Accepted Trichoderma names in the year 2015.

A list of 254 names of species and two names of varieties in Trichoderma with name or names against which they are to be protected, following the ICN (Melbourne Code, Art. 14.13), is presented for consideration by the General Committee established by the Congress, which then will refer them to the Nomenclature Committee for Fungi (NCF). This list includes 252 species, one variety and one form. Two new names are proposed: T. neocrassum Samuel (syn. Hypocrea crassa P. Chaverri & Samuels), T. patellotropicum Samuels (syn. Hypocrea patella f. tropica Yoshim. Doi). The following new combinations in Trichoderma are proposed: T. brevipes (Mont.) Samuels, T. cerebriforme (Berk.) Samuels, T. latizonatum (Peck) Samuels, and T. poronioideum (A. Möller) Samuels. The following species are lectotypified: T. americanum (Canham) Jaklitsch & Voglmayr, Gliocladium flavofuscum J.H. Miller, Giddens & A.A. Foster, T. inhamatum Veerkamp & W. Gams, T. konilangbra Samuels, O. Petrini & C.P. Kubicek, T. koningii Oudem., T. pezizoides (Berk. & Broome) Jaklitsch & Voglmayr, T. sulphureum (Schwein.) Jaklitsch & Voglmayr and T. virens (J.H. Miller, Giddens & A.A. Foster) Arx. Epitypes are proposed for the following species: T. albocorneum (Yoshim. Doi) Jaklitsch & Voglmayr, T. albofulvum (Berk. & Broome) Jaklitsch & Voglmayr, T. atrogelatinosum (Dingley) Jaklitsch & Voglmayr, T. corneum (Pat.) Jaklitsch & Voglmayr, T. cornu-damae (Pat.) Z.X. Zhu & W.Y. Zhuang, T. flaviconidium (P. Chaverri, Druzhinina & Samuels) Jaklitsch & Voglmayr, T. hamatum (Bonord.) Bain., T. hunua (Dingley) Jaklitsch & Voglmayr, T. patella (Cooke & Peck) Jaklitsch & Voglmayr, Hypocrea patella f. tropica Yoshim. Doi, T. polysporum (Link) Rifai, T. poronioideum (A. Möller) Samuels T. semiorbis (Berk.) Jaklitsch & Voglmayr, T. sulphureum (Schwein.) Jaklitsch & Voglmayr, and T. tropicosinense (P.G. Liu) P.G. Liu, Z.X. Zhu & W.Y. Zhuang.

Evolution of habitat preference and nutrition mode in a cosmopolitan fungal genus with evidence of interkingdom host jumps and major shifts in ecology.

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.

Pseudocosmospora, a new genus to accommodate Cosmospora vilior and related species.

Cosmospora sensu Rossman accommodated nectroid fungi with small, reddish, smooth, thin-walled perithecia but recently was found to be polyphyletic and has been segregated into multiple genera. Not all cosmospora-like fungi have been treated systematically. Some of these species include C. vilior and many specimens often labeled "Cosmospora sp." The objectives of this research were to establish the identity of C. vilior through epitypication using a recent collection that agrees with the type specimen in morphology, host and geography and to determine its phylogenetic position within Cosmospora sensu lato and the Nectriaceae. A multilocus phylogeny was constructed based on six loci (ITS, LSU, MCM7, rpb1, tef1, tub) to estimate a phylogeny. Results from the phylogenetic analyses indicated that C. vilior forms a monophyletic group with other cosmospora-like fungi that have an acremonium-like anamorph and that parasitize Eutypa and Eutypella (Ascomycota, Sordariomycetes, Xylariales, Diatrypaceae). The group is phylogenetically distinct from other previously segregated genera. A new genus, Pseudocosmospora, is described to accommodate the type species, P. eutypellae, and nine additional species in this clade.

Genera in Bionectriaceae, Hypocreaceae, and Nectriaceae (Hypocreales) proposed for acceptance or rejection.

With the recent changes concerning pleomorphic fungi in the new International Code of Nomenclature for algae, fungi, and plants (ICN), it is necessary to propose the acceptance or protection of sexual morph-typified or asexual morph-typified generic names that do not have priority, or to propose the rejection or suppression of competing names. In addition, sexual morph-typified generic names, where widely used, must be proposed for rejection or suppression in favour of asexual morph-typified names that have priority, or the latter must be proposed for conservation or protection. Some pragmatic criteria used for deciding the acceptance or rejection of generic names include: the number of name changes required when one generic name is used over another, the clarity of the generic concept, their relative frequencies of use in the scientific literature, and a vote of interested mycologists. Here, twelve widely used generic names in three families of Hypocreales are proposed for acceptance, either by conservation or protection, despite their lack of priority of publication, or because they are widely used asexual morph-typified names. Each pair of generic names is evaluated, with a recommendation as to the generic name to be used, and safeguarded, either through conservation or protection. Four generic names typified by a species with a sexual morph as type that are younger than competing generic names typified by a species with an asexual morph type, are proposed for use. Eight older generic names typified by species with an asexual morph as type are proposed for use over younger competing generic names typified by a species with a sexual morph as type. Within Bionectriaceae, Clonostachys is recommended over Bionectria; in Hypocreaceae, Hypomyces is recommended over Cladobotryum, Sphaerostilbella over Gliocladium, and Trichoderma over Hypocrea; and in Nectriaceae, Actinostilbe is recommended over Lanatonectria, Cylindrocladiella over Nectricladiella, Fusarium over Gibberella, Gliocephalotrichum over Leuconectria, Gliocladiopsis over Glionectria, Nalanthamala over Rubrinectria, Nectria over Tubercularia, and Neonectria over Cylindrocarpon.

The Longibrachiatum Clade of Trichoderma: a revision with new species.

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.

Multigene phylogenetic analyses of the Thelonectria coronata and T. veuillotiana species complexes.

Thelonectria is a recently established genus of common and ubiquitous fungi on woody hosts, previously placed in the genus Neonectria. Thelonectria coronata and T. veuillotiana occur sympatrically in tropical, subtropical and temperate regions. Previous taxonomic studies including T. coronata and T. veuillotiana suggested these fungi could represent species complexes; however, the morphological features used to define species exhibited few differences useful for testing this hypothesis. To assess the status of T. coronata and T. veuillotiana, phylogenetic analyses of six genomic regions were combined with a morphological examination of specimens. A multi-gene phylogeny reconstructed with maximum parsimony, maximum likelihood and Bayesian approaches identified five phylogenetic groups in T. coronata and six in T. veuillotiana. As is common for cryptic species, unequivocal diagnostic morphological characters could not be identified; however, average values of morphological traits correspond to the phylogenetic groups. An increased number of non-synonymous/synonymous substitutions in the ß-tubu-lin gene and a decreased or absent production of conidia were detected within the T. coronata complex, possibly indicating the homothallic nature of these isolates. T. coronata and T. veuillotiana and related species are described and illustrated here; a dichotomous key to all species is provided.

Molecular phylogeny and species delimitation in the section Longibrachiatum of Trichoderma.

The phylogenetically most derived group of the genus Trichoderma - section Longibrachiatum, includes some of the most intensively studied species, such as the industrial cellulase producer T. reesei (teleomorph Hypocrea jecorina), or the facultative opportunistic human pathogens T. longibrachiatum and H. orientalis. At the same time, the phylogeny of this clade is only poorly understood. Here we used a collection of 112 strains representing all currently recognized species and isolates that were tentatively identified as members of the group, to analyze species diversity and molecular evolution. Bayesian phylogenetic analyses based on several unlinked loci in individual and concatenated datasets confirmed 13 previously described species and 3 previously recognized phylogenetic species all of which were not yet described formally. When the genealogical concordance criterion, the K/θ method and comparison of frequencies of pairwise nucleotide differences were applied to the data sample, 10 additional new phylogenetic species were recognized, seven of which consisted only of a single lineage. Our analysis thus identifies 26 putative species in section Longibrachiatum, what doubles the currently estimated taxonomic diversity of the group, and illustrates the power of combining genealogical concordance and population genetic analysis for dissecting species in a recently diverged group of fungal species.

Vascular Streak Dieback of cacao in Southeast Asia and Melanesia: in planta detection of the pathogen and a new taxonomy.

Vascular Streak Dieback (VSD) disease of cacao (Theobroma cacao) in Southeast Asia and Melanesia is caused by a basidiomycete (Ceratobasidiales) fungus Oncobasidium theobromae (syn. =Thanatephorus theobromae). The most characteristic symptoms of the disease are green-spotted leaf chlorosis or, commonly since about 2004, necrotic blotches, followed by senescence of leaves beginning on the second or third flush behind the shoot apex, and blackening of infected xylem in the vascular traces at the leaf scars resulting from the abscission of infected leaves. Eventually the shoot apex is killed and infected branches die. In susceptible cacao the fungus may grow through the xylem down into the main stem and kill a mature cacao tree. Infections in the stem of young plants prior to the formation of the first 3-4 lateral branches usually kill the plant. Basidiospores released from corticioid basidiomata developed on leaf scars or along cracks in the main vein of infected leaves infect young leaves. The pathogen commonly infects cacao but there are rare reports from avocado. As both crops are introduced to the region, the pathogen is suspected to occur asymptomatically in native vegetation. The pathogen is readily isolated but cultures cannot be maintained. In this study, DNA was extracted from pure cultures of O. theobromae obtained from infected cacao plants sampled from Indonesia. The internal transcribed spacer region (ITS), consisting of ITS1, 5.8S ribosomal RNA and ITS2, and a portion of nuclear large subunit (LSU) were sequenced. Phylogenetic analysis of ITS sequences placed O. theobromae sister to Ceratobasidium anastomosis groups AG-A, AG-Bo, and AG-K with high posterior probability. Therefore the new combination Ceratobasidium theobromae is proposed. A PCR-based protocol was developed to detect and identify C. theobromae in plant tissue of cacao enabling early detection of the pathogen in plants. A second species of Ceratobasidium, Ceratobasidium ramicola, identified through ITS sequence analysis, was isolated from VSD-affected cacao plants in Java, and is widespread in diseased cacao collected from Indonesia.

New species from the Fusarium solani species complex derived from perithecia and soil in the old World tropics.

A large collection of strains belonging to the Fusarium solani species complex (FSSC) was isolated from soil and perithecia in primary forests in Sri Lanka (from fallen tree bark) and tropical Australia (Queensland, from fallen tree fruits and nuts). Portions of the translation elongation factor 1-alpha (tef1) gene, the nuclear large subunit (NLSU) and internal transcribed spacer regions (ITS) of the nuclear ribosomal RNA genes were sequenced in 52 isolates from soil and perithecia. The FSSC was divided previously into three clades with some biogeographic structure, termed Clades 1, 2 and 3. All Sri Lankan and Australian soil isolates were found to be members of Clade 3, most grouping with the cosmopolitan soil-associated species F. falciforme. All but two Sri Lankan perithecial isolates were associated with a set of five divergent phylogenetic lineages that were associated with Clade 2. Australian perithecial isolates resided in a subclade of Clade 3 where most of the previously defined mating populations of the FSSC reside. Isolates from perithecia and those cultured from soil were always members of different species lineages, even when derived from proximal locations. The previous biogeographic assignment of Clade 2 to South America is now expanded to the worldwide tropics. Sri Lanka appears to be an important center of diversity for the FSSC. Nectria haematococca is epitypified with a collection from the type locality in Sri Lanka; its anamorph is described as a new species, Fusarium haematococcum. Neocosmospora E.F. Smith is adopted as the correct genus for Nectria haematococca. These new species are described: F. kurunegalense/Neo. kurunegalensis, F. rectiphorus/Neo. rectiphora/, F. mahasenii/Neo. mahasenii/, F. kelerajum/Neo. keleraja.

Species diversity of Trichoderma in Poland.

In the present study, we reinvestigate the diversity of Trichoderma in Poland utilizing a combination of morphological and molecular/phylogenetic methods. A total of 170 isolates were collected from six different substrata at 49 sites in Poland. These were divided among 14 taxa as follows: 110 of 170 Trichoderma isolates were identified to the species level by the analysis of their ITS1, ITS2 rDNA sequences as: T. harzianum (43 isolates), T. aggressivum (35), T. citrinoviride (11), T. hamatum (9), T. virens (6), T. longibrachiatum (4), T. polysporum (1), and T. tomentosum (1); 60 isolates belonging to the Viride clade were identified based on a fragment of the translation-elongation factor 1-alpha (tef1) gene as: T. atroviride (20 isolates), T. gamsii (2), T. koningii (17), T. viridescens (13), T. viride (7), and T. koningiopsis (1). Identifications were made using the BLAST interface in TrichOKEY and TrichoBLAST ( http://www.isth.info ). The most diverse substrata were soil (nine species per 22 isolates) and decaying wood (nine species per 75 isolates). The most abundant species (25%) isolated from all substrata was T. harzianum.

Hypocrea peltata: a mycological Dr Jekyll and Mr Hyde?

Hypocrea peltata (Pezizomycotina, Hypocreales, Hypocreaceae) is a common, widespread essentially subtropical species, with an uncharacteristically large stroma and asci containing four large and four small bicellular ascospores. Its only anamorph consists of indehiscent aleuriospores; it does not form a Trichoderma anamorph, which is typical of most Trichoderma/Hypocrea species. Hypocrea peltata grows very well at 37 C. The large stromata and failure to form a Trichoderma anamorph could lead one to doubt its generic placement. However sequences of the internal transcribed spacer region (ITS), 28S nuclear large subunit (LSU) of rDNA and RNA polymerase subunit II (rpb2) regions indicate that it represents a unique lineage within Trichoderma/Hypocrea. ITS and rbp2 sequences derived from cultures of H. peltata are identical to the "unidentified Hypocreaceae" reported in the literature as being isolated from lung of a patient with non-fatal pulmonary fibrosis.

Trichoderma amazonicum, a new endophytic species on Hevea brasiliensis and H. guianensis from the Amazon basin.

A new species of Trichoderma (teleomorph Hypocrea, Ascomycota, Sordariomycetes, Hypocreales, Hypocreaceae), T. amazonicum, endophytic on the living sapwood and leaves of Hevea spp. trees is described. Trichoderma amazonicum is distinguished from closely related species in the Harzianum clade (e.g. Hypocrea alni, H. brunneoviridis, H. epimyces, H. parepimyces, T. aggressivum, T. harzianum, T. pleuroticola and T. pleuroti) by morphological and ecological characteristics and phylogenetic analysis of three loci (ITS nrDNA, tef1 and rpb2). The closest relatives of this species are the facultatively fungicolous species T. pleuroticola and T. pleuroti.

Colletotrichum gloeosporioides s.l. associated with Theobroma cacao and other plants in Panama: multilocus phylogenies distinguish host-associated pathogens from asymptomatic endophytes.

Colletotrichum interacts with numerous plant species overtly as symptomatic pathogens and cryptically as asymptomatic endophytes. It is not known whether these contrasting ecological modes are optional strategies expressed by individual Colletotrichum species or whether a species' ecology is explicitly pathogenic or endophytic. We explored this question by inferring relationships among 77 C. gloeosporioides s.l. strains isolated from asymptomatic leaves and from anthracnose lesions on leaves and fruits of Theobroma cacao (cacao) and other plants from Panamá. ITS and 5'-tef1 were used to assess diversity and to delineate operational taxonomic units for multilocus phylogenetic analysis. The ITS and 5'-tef1 screens concordantly resolved four strongly supported lineages, clades A-D: Clade A includes the ex type of C. gloeosporioides, clade B includes the ex type ITS sequence of C. boninense, and clades C and D are unidentified. The ITS yielded limited resolution and support within all clades, in particular the C. gloeosporioides clade (A), the focal lineage dealt with in this study. In contrast the 5'-tef1 screen differentiated nine distinctive haplotype subgroups within the C. gloeosporioides clade that were concordant with phylogenetic terminals resolved in a five-locus nuclear phylogeny. Among these were two phylogenetic species associated with symptomatic infections specific to either cacao or mango and five phylogenetic species isolated principally as asymptomatic infections from cacao and other plant hosts. We formally describe two new species, C. tropicale and C. ignotum, that are frequent asymptomatic associates of cacao and other Neotropical plant species, and epitypify C. theobromicola, which is associated with foliar and fruit anthracnose lesions of cacao. Asymptomatic Colletotrichum strains isolated from cacao plants grown in China included six distinct C. gloeosporioides clade taxa, only one of which is known to occur in the Neotropics.

Trichoderma asperellum sensu lato consists of two cryptic species.

Analysis of a worldwide collection of strains of Trichoderma asperellum sensu lato using multilocus genealogies of four genomic regions (tef1, rpb2, act, ITS1, 2 and 5.8s rRNA), sequence polymorphism-derived (SPD) markers, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) of the proteome and classical mycological techniques revealed two morphologically cryptic sister species within T. asperellum, T. asperellum, T. asperelloides sp. nov. and a third closely related but morphologically distinct species. T. yunnanense. Trichoderma asperellum and T. asperelloides have wide sympatric distribution on multiple continents; T. yunnanense is represented by a single strain from China. Several strains reported in the literature or represented in GenBank as T. asperellum are re-identified as T. asperelloides. Four molecular SPD typing patterns (I-IV) were found over a large geographic range. Patterns I-III were produced only by T. asperellum and pattern IV by T. asperelloides and T. yunnanense. Pattern I was found in North America, South America, Africa and Europe and Asia (Saudi Arabia). Pattern III was found in Africa, North America, South America and Asia, not in Europe. Pattern II was found only in Cameroon (central Africa) and Peru. Pattern IV was found in all continents. All SPD II pattern strains formed a strongly supported subclade within the T. asperellum clade in the phylogenetic tree based on rpb2 and MLS (combined multilocus sequence). The diversity of DNA sequences, SPD markers and polypeptides in T. asperellum suggests that further speciation is under way within T. asperellum. MALDI-TOF MS distinguished T. yunnanense from related taxa by UPGMA clustering, but separation between T. asperellum and T. asperelloides was less clear.