The family structure of the Mucorales: a synoptic revision based on comprehensive multigene-genealogies

Abstract

The Mucorales (Mucoromycotina) are one of the most ancient groups of fungi comprising ubiquitous, mostly saprotrophic organisms. The first comprehensive molecular studies 11 yr ago revealed the traditional classification scheme, mainly based on morphology, as highly artificial. Since then only single clades have been investigated in detail but a robust classification of the higher levels based on DNA data has not been published yet. Therefore we provide a classification based on a phylogenetic analysis of four molecular markers including the large and the small subunit of the ribosomal DNA, the partial actin gene and the partial gene for the translation elongation factor 1-alpha. The dataset comprises 201 isolates in 103 species and represents about one half of the currently accepted species in this order. Previous family concepts are reviewed and the family structure inferred from the multilocus phylogeny is introduced and discussed. Main differences between the current classification and preceding concepts affects the existing families Lichtheimiaceae and Cunninghamellaceae, as well as the genera Backusella and Lentamyces which recently obtained the status of families along with the Rhizopodaceae comprising Rhizopus, Sporodiniella and Syzygites. Compensatory base change analyses in the Lichtheimiaceae confirmed the lower level classification of Lichtheimia and Rhizomucor while genera such as Circinella or Syncephalastrum completely lacked compensatory base changes.

Keywords: Mucorales; families; phylogeny.

Fig. 1.

General life cycle, important fields of scientific research and main applications of Mucorales. Exemplary and prominent species are given.

Fig. 2.

a. Syzygites megalocarpus on Pleurotus ostreatus (artificially infected); b. Parasitella parasitica on Mucor circinelloides. Galls (g) and sikyotic cells (s) are marked; c. Choanephora cucurbitarum on yellow summer squash. d. Rhizopus stolonifer on strawberries. — Scale bar = 20 μm.

Fig. 3.

a. Cunninghamella sp. Sporangiophore with apical vesicle and sporangiola on stalks; b. apophysate sporangia of Absidia sp.; c. columella of Absidia sp. with typical apical projection and subsporangial septae; d, e. sporangium of Gilbertella persicaria: d. ruptured sporangial wall and released spores; f. branching sporangiophore of Blakeslea trispora with apical vesicles bearing few spored sporangiola. — Scale bars: a = 5 μm; b, c = 20 μm; d–f = 50 μm.

Fig. 4.

a. Umbelopsidaceae. Sporangium and sporangiophore with the highly reduced columella (arrow). — b, c. Lentamycetaceae. b. Warty zygospore, species are homothallic; c. sporangium. — d–f. Dichotomocladium. d. Zygospores; e, f. dichotomous branched sporangiophores. — g. Syncephalastrum racemosum, merosporangia. — h–j. Lichtheimia. h. Columella; i, j. apophysate sporangia. — k. Mycotypha sp., cylindrical vesicle covered with sporangiola. — l, m. Chaetocladium sp., branched fertile head with sporangiola. Branches often terminate in sterile spines. — n, o. Thamnidium elegans. n. Dichotomous branched sporangiophores with sporangiola; o. main multi-spored sporangia. — p, q. Columella and sporangia borne on circinate sporangiophores of Circinella sp. — Scale bars: all = 20 μm.

Fig. 5.

Pilobolaceae. a. Substrate mycelium with trophocysts; b. sporangium of Utharomyces epallocaulus with subsporangial swelling; c. colony morphology of Pilobolus sp. on horse dung. Sporangia are phototrophic; d. sporangiophores with subsporangial swelling and the black sporangium. Light is focused through the swelling towards carotenoids at the base of the vesicle, the ocellus (orange colour); e. colony morphology of Pilaira sp. Sporangiophores are also light sensitive; f. sporangium and columellae of Pilaira sp. — Scale bar = 50 μm.

Fig. 6.

Schematic fungal tree and important data about the fungal groups. The topology resembles the current understanding of the relationships of the fungal groups according to Hibbett et al. (2007), James et al. (2006) and Schoch et al. (2012) (data retrieved April 2012).

Fig. 7.

Chronology of sequences submitted to GenBank since 1993 for the Mucorales (data retrieved April 2012).

Fig. 8.

Number of publications predominantly focused on mucoralean phylogeny retrieved from NCBI and ISI Web of Science by searching ‘Zygomycota/ Mucorales AND phylogeny’. Publications are separated by the molecular marker applied for phylogeny. Nearly half of all published studies included more than one molecular marker. Published combinations of molecular markers are indicated by different colours (data retrieved April 2012).

Fig. 9.

Distribution of available sequences in GenBank for the Mucoromycotina. Also the total number of available sequences for all basal fungal linages are given (data retrieved April 2012).

Fig. 10.

Bayesian analysis of combined sequences coding for actin, translation elongation factor 1-alpha, 18S rDNA and 28S rDNA. Bootstrap values and posterior probabilities are given for branches supported with equal or higher than 75 % in maximum likelihood (RAxML) and Bayesian analysis (see legend within figure for explanation of the symbols). Strain numbers are given in parts to distinguish different isolates (compare with Table 5). Furthermore, a rough outline about the historical family structures and changes are given on the right site including benchmark studies since 1969 (Zycha et al. 1969, Hesseltine & Ellis 1973, Benjamin 1979, Benny 1982, von Arx 1982, Benny et al. 2001, Voigt & Wöstemeyer 2001, O’Donnell et al. 2001, Kirk et al. 2008). Families accepted here, are colour coded over the whole tree branches.

Fig. 10.

Bayesian analysis of combined sequences coding for actin, translation elongation factor 1-alpha, 18S rDNA and 28S rDNA. Bootstrap values and posterior probabilities are given for branches supported with equal or higher than 75 % in maximum likelihood (RAxML) and Bayesian analysis (see legend within figure for explanation of the symbols). Strain numbers are given in parts to distinguish different isolates (compare with Table 5). Furthermore, a rough outline about the historical family structures and changes are given on the right site including benchmark studies since 1969 (Zycha et al. 1969, Hesseltine & Ellis 1973, Benjamin 1979, Benny 1982, von Arx 1982, Benny et al. 2001, Voigt & Wöstemeyer 2001, O’Donnell et al. 2001, Kirk et al. 2008). Families accepted here, are colour coded over the whole tree branches.

Fig. 11.

Distance matrices for all applied loci based on nucleic acid and amino acid sequences. The range of distances is given for each locus. Families are coded according to Fig. 10.

Fig. 12.

CBC analyses of ITS2 sequences from the genus Rhizomucor. Numbers of detected CBCs are given.

Fig. 13.

CBC analyses of ITS2 sequences from the genus Lichtheimia. Numbers of detected CBCs are given.

Fig. 14.

CBC analyses of ITS2 sequences from the genus Dichotomocladium. Numbers of detected CBCs are given.

Fig. 15.

CBC analyses of ITS2 sequences from the clade Circinella / Phascolomyces / Zychaea / Fennellomyces / Thamnostylum. Numbers of detected CBCs are given.