A pycnidium of Phoma. Pycnidia are often spherical or inversely pearshaped (obpyriform) and their internal cavity is lined with conidiophores. When ripe, an opening generally appears at the top, through which the pycnidiospores escape. Pycnidia are not to be confused with perithecia which produce ascospores.

A class of conidial fungi where the conidia are formed within a cavity lined by fungal or host tissue.

The fruiting stuructres may be spherical with an apical openig (pynidia) or saucer shaped (acervuli). The production of conidia within a fruiting body distinguishes this group from the hyphomycetes which have "naked" conidia.

Pycnidia may be confused with ascocarps so its important to make the distinction between an acsospore and a conidium.

Species descriptions

  • Colletotrichum coccodes

    Over 500 Colletotrichum species have been reported. C. coccodes is a common soil and plant pathogen widely distributed in Africa, Asia, Australasia, Europe, and the Americas. It has been reported from a case of human mycotic keratitis.

    RG-1 organism.

    Colletotrichum sclerotia

    Sclerotia with setae of Colletotrichum coccodes.

    Morphological description: 
    Colonies usually darkly pigmented with white aerial mycelium, consisting of numerous black sclerotia and light brown-coloured conidial masses, reverse is dark brown. Sclerotia are usually abundant, setose, spherical and are often confluent. Conidia are straight, fusiform, attenuated at the ends, 16-22 x 3-4 µm. Appressoria are common, clavate, brown, 11-16.5 x 6-9.5 µm, variable in shape.

    Colletotrichum culture

    Culture, conidia and appressoria of Colletotrichum coccodes.

    Molecular identification: 
    ITS and/or D1/D2 sequencing may be used for species identification (Cano et al. 2004).


    Antifungal susceptibility: Colletotrichum species (Australian national data); MIC µg/mL.
      No ≤0.03 0.06 0.125 0.25 0.5 1 2 4 8 ≥16
    AmB 15   1 3 5 3 2 1      
    ISAV 5       2 2         1
    VORI 15     1 1 4 6   2   1
    POSA 15   1   2 5 5 1     1
    ITRA 15     1 2 2 3 1     6



    Domsch et al. (1980), McGinnis (1980), de Hoog et al. (2000, 2015).

  • Lasiodiplodia theobromae

    Botryosphaeria rhodina; Botryodiplodia theobromae

    Lasiodiplodia theobromae is a well known plant pathogen reported from about 500 host plants, mainly confined to an area 40 degrees north to 40 degrees south of the equator. It has also been associated with ulcerated human cornea, lesions on nail and subcutaneous tissue.

    RG-1 organism.

    Lasiodiplodia culture

    Lasiodiplodia theobromae pycnidia growing on carnation leaf agar.

    Morphological description: 
    Colonies are greyish sepia to mouse grey to black, fluffy with abundant aerial mycelium; reverse fuscous to black. Pycnidia are simple or compound, often aggregated, stromatic, ostiolate, frequently setose, up to 5 mm wide. Conidiophores are hyaline, simple, sometimes septate, rarely branched cylindrical, arising from the inner layers of cells lining the pycnidial cavity. Conidiogenous cells are hyaline, simple, cylindrical to sub-obpyriform, holoblastic, annellidic. Conidia are initially unicellular, hyaline, granulose, sub-ovoid to ellipsoid-oblong, thick-walled, base truncate; mature conidia one-septate, cinnamon to fawn, often longitudinally striate, 20-30 x 10-15 µm. Paraphyses when present are hyaline, cylindrical, sometimes septate, up to 50 µm long.

    Lasiodiplodia microscopy

    Lasiodiplodia theobromae mature two-celled dark brown conidia with typical longitudinal striations.

    Key features: 
    Coelomycete, with pycnidia producing characteristic two-celled, dark brown, striated conidia.

    Molecular identification: 
    Recommended genetic marker: EF-1α (de Hoog et al. 2015). ITS sequencing is useful for identifying clinically important species (Bagyalakshmi 2008).

    Antifungal susceptibility: Lasiodiplodia theobromae (Australian national data); MIC µg/mL
      No <0.016 0.03 0.06 0.125 0.25 0.5 1 2 4 8 16 32 ≥64
    AmB 4 1       1 1 1            
    ISAV 1                   1      
    VORI 4         1   2   1        
    POSA 3               1   2      
    ITRA 4             1       3    

    de Hoog et al. (2000, 2015), Liu et al. (2012), Phillips et al. (2013).

  • Microsphaeropsis arundinis

    Microsphaeropsis arundinis is an ascomycetous fungus that produces conidia within a pycnidium (an asexual fruiting body containing conidia). It is ubiquitous in soil and fresh water and typically inhabits terrestrial plant hosts. It typically inhabits terrestrial plant hosts and has a well-known association with Aruno donax, a garden escape weed known as ‘giant reed’ or ‘elephant grass’. M. arundinis is an emerging cause of phaeohyphomycosis in cats and immunosuppressed humans.

    RG-1 organism.

    Microsphaeropsis culture

    Culture of Microsphaeropsis arundinis.

    Morphological description: 
    Colonies growing slowly, with dense aerial mycelium, initially greenish-grey, later becoming dark brown to grey-brown. Hyphae are septate, pigmented, and irregularly shaped, with swollen segments up to 4 μm in diameter. Pycnidia are subspherical, 250-350 μm in diameter; with a pseudoparenchymatous wall composed of very densely packed cells that appear angular in cross section (textura angularis). Conidiogenous cells ampulliform, up to 5 μm long. Conidia brown, thick- and smooth-walled, cylindrical, 3.5-4.5 × 1.0-1.5 μm.

    Microsphaeropsis micro

    Microsphaeropsis arundinis showing pigmented septate hyphae, with swollen segments.

    Key features: 
    Coelomycete, with ostiolate pycnidia, ampulliform conidiogenous cells, and small, smooth-walled, brown, cylindrical conidia.

    Molecular identification: 
    ITS and D1/D2 sequencing is recommended, especially as it may take many weeks before pycnidia are produced in culture (Reppas et al. 2015). Note: ITS and D1/D2 sequencing alone cannot discriminate between Microsphaeropsis arundinis and Paraconiothyrium cyclothyrioides, additional sequencing of ACT and b-tubulin is required (Gordon et al., 2012).

    Kluger et al. (2004), Pendle et al. (2004), Krockenberger et al. (2010), Hall et al. (2013), Reppas et al. (2015), de Hoog et al. (2015).

  • Neoscytalidium dimidiatum

    Hendersonula toruloidea; Scytalidium dimidiatum; Scytalidium hyalinum.

    Neoscytalidium dimidiatum is a coelomycete and recognised agent of onychomycosis and superficial skin infections, especially in tropical regions. The primary isolation of this fungus from clinical specimens may be difficult as isolates are sensitive to cycloheximide (actidione), which is commonly added to primary isolation media used for culturing skin scrapings.

    The taxonomy of this species has been very confusing; the conidial state of S. dimidiatum was originally described under the name Hendersonula toruloidea. However it is phylogenetically remote from Scytalidium and has now been placed into Neoscytalidium (Crous et al. 2006, Machouart et al. 2012). Colourless mutants (previously known as Scytalidium hyalinum) often occur and have now been listed as variety N. dimidiatum var. hyalinum (Madrid et al. 2009).

    Nattrassia mangiferae, previously considered the teleomorph form of S. dimidiatum, is now considered a distinct species, and has been placed in the genus Neofusicoccum, based on the lack of an arthoconidial anamorph (Crous et al. 2006, Machouart et al. 2012).

    RG-2 organism.

    Neoscytalidium microscopy

    Microscopic morphology of the Neoscytalidium dimidiatum showing chains of one- to two-celled, darkly pigmented arthroconidia.

    Morphological description: 
    Cultures are effuse, hairy, dark grey to blackish-brown, or white to greyish, with a cream-coloured to deep ochraceous-yellow reverse. Colourless mutants often occur. Arthroconidia are typically present in chains of one to two-cells, darkly pigmented, 3.5-5 x 6.5-12 µm, produced by the holothallic fragmentation of undifferentiated hyphae. Pycnidia, only occasionally formed in older cultures are black, ostiolate and contain numerous hyaline, flask-shaped phialides. Phialoconidia are at first one-celled and hyaline, later becoming three-celled, brown, with the centre cell darker than the end cells and are ovoid to ellipsoidal in shape.

    Molecular identification: 
    ITS and D1/D2 sequencing may be used for accurate species identification (Halliday et al. 2015).

    Alshawa et al. (2012) developed a spectral database for 12 different species of dermatophytes which also included Neoscytalidium dimidiatum and N. dimidiatum var. hyalinum. Correct identification of the species was obtained for 18/21 Neoscytalidium isolates (85.7%).

    McGinnis (1980), Moore (1986), Rippon (1988), Frankel and Rippon (1989), Sutton and Dyko (1989) Madrid et al. (2009), de Hoog et al. (2000, 2015), Crous et al. (2006), Machouart et al. (2012), Alshawa et al. (2012).

    Antifungal susceptibility: Neoscytalidium dimidiatum limited data (Australian national data); MIC µg/mL.
    Antifungal No ≤0.016 0.03 0.06 0.125 0.25 0.5 1 2 4 8
    AMB 12     1   1 3 5 2    
    VORI 12 1 2 1 1 3 1 3      
    POSA 12   1 1 2 1   1 1   5
    ITRA 12     1 2   1 1     7
  • Phoma spp.

    Members of the genus Phoma have a worldwide distribution and are ubiquitous in nature, with over 200 species having been described from soil, as saprophytes on various plants, and as pathogens to plants and humans.

    RG-1 organism.

    Phoma pycnidium

    Pycnidium of Phoma.

    Morphological description: 
    Colonies are spreading, greyish-brown, powdery or suede-like and produce large, globose, membranous to leathery, darkly pigmented, ostiolate pycnidia. Conidia are produced in abundance within the pycnidia on narrow thread-like phialides, which are hardly differentiated from the inner pycnidial wall cells. Conidia are globose to cylindrical, one-celled, hyaline, and are usually extruded in slimy masses from the apical ostiole.

    Molecular identification: 
    ITS, D1/D2, β-tubulin and 18S sequencing has been used to identify Phoma species (de Gruyter et al. 2009, Aveskamp et al. 2010). Note: Public sequence databases, particularly GenBank, contain many sequences from incorrectly identified species, making identifications of coelomycetous fungi very difficult, without confirmatory morphological studies.

    Key features: 
    Coelomycete, ostiolate pycnidia producing masses of slimy, hyaline, single-celled conidia.

    Punithalingam (1979), McGinnis (1980), Sutton (1980), Rippon (1988), Montel et al. (1991), Samson et al. (1995), de Hoog et al. (2000, 2015).

A list of Mycology references cited for the identification of medically important fungi is available for viewing.