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The Family Structure of the Mucorales: a Synoptic Revision Based on Comprehensive Multigene-Genealogies

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The Family Structure of the Mucorales: a Synoptic Revision Based on Comprehensive Multigene-Genealogies Persoonia 30, 2013: 57–76 www.ingentaconnect.com/content/nhn/pimj RESEARCH ARTICLE http://dx.doi.org/10.3767/003158513X666259 The family structure of the Mucorales: a synoptic revision based on comprehensive multigene-genealogies K. Hoffmann1,2, J. Pawłowska3, G. Walther1,2,4, M. Wrzosek3, G.S. de Hoog4, G.L. Benny5*, P.M. Kirk6*, K. Voigt1,2* Key words 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 Mucorales classification scheme, mainly based on morphology, as highly artificial. Since then only single clades have been families investigated in detail but a robust classification of the higher levels based on DNA data has not been published phylogeny 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. Article info Received: 29 September 2012; Accepted: 1 January 2013; Published: 13 March 2013. INTRODUCTION compatible mating types of heterothallic species results in the formation of zygospores. Zygospores often display a specific The fungal order Mucorales – exospore ornamentation (smooth, rough, warty) and protect- evolutionary position and characterisation ing appendages (finger-like, antler-like) born on the supporting As a member of the Mucoromycotina, the Mucorales belong cells (suspensors) (Zycha et al. 1969). Some species of the to the early diverging, ancient fungi along with the Kickxel­ Mucorales exhibit dimorphism, possessing the ability to switch lomycotina, Zoopagomycotina, Entomophthoromycotina, between a filamentous, multi-cellular state to a yeast-like state Mortiellomycotina, Chytridiomycota, Neocallimastigomycota, (Bartnicki-Garcia & Nickerson 1962). Blastocladiomycota, and Cryptomycota and Microsporidia with the latter two still highly discussed (Schüßler et al. 2001, James Life styles and applications — Fig. 1 et al. 2006, Hibbett et al. 2007, Hoffmann et al. 2011, Jones et al. Mucoralean fungi are ubiquitous, predominantly saprobic soil 2011a, b, Benny 2012). The Entomophthoromycotina were later organisms on decaying organic material but parasites of plants, elevated to the phylum Entomophthoromycota (Humber 2012). fungi and animals also are known. As one of the largest or- Mucorales are characterised by a usually abundant, rapidly ders in the basal Fungi, the Mucorales is also one of the most growing mycelium as well as anamorph structures usually studied groups in the early diverging fungi. These studies on formed in large quantities. The mycelium is typically unseptate mucoralean fungi encompass physiology and biochemistry, as or irregularly septate. Anamorphic sporangiospores are pro- well as taxonomy and systematics, and potential applications in duced in multi-spored sporangia, few-spored sporangiola or industry. In general, mucoralean fungi reproduce anamorphically merosporangia. Chlamydospores, arthrospores and yeast cells via non-motile sporangiospores released from variously shaped are, in most species, rarely formed. Sporangia are characterised sporangia. If not homothallic, a compatible mating partner is by the inclusion of a variously shaped columella. This well- needed for the formation of the zygospore, where meiosis occurs. developed columella counts as a synapomorphic character for The different sexual modality of either homo- or heterothally in the Mucorales. Conjugation in homothallic species or between the Mucorales was discovered more than 100 yr ago, with most 1 Institute of Microbiology, Department of Microbiology and Molecular Biology, species found to be heterothallic (Blakeslee 1904). Volatiles are University of Jena, Jena, Germany; responsible for the formation of sexual reproductive structures corresponding author e-mails: [email protected], [email protected]. (Burgeff 1924). These volatiles were identified as trisporoids, 2 Leibniz-Institute for Natural Product Research and Infection Biology – Hans- Knöll-Institute, Jena Microbial Resource Collection, Jena, Germany. derivatives of beta-carotene (van den Ende 1967, Gooday 1968). 3 Department of Systematics and Plant Geography, University of Warsaw, The trisporic acid precursors are mutually processed by the Warsaw, Poland. compatible mating partners, resulting in the formation of a mature 4 CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands. zygospore (Werkman 1976). Although the composition of the 5 Department of Plant Pathology, 1453 Fifield Hall, University of Florida, compounds is species specific to allow only intra-species matings Gainesville Florida 32611-0680, USA. 6 Royal Botanic Gardens, Mycology Section, Kew, Surrey TW9 3AF, UK. (Sutter et al. 1989), inter-species zygospores are also described * Shared senior authors in alphabetical order. with some impact on systematics (Blakeslee & Cartledge 1927, © 2013 Naturalis Biodiversity Center & Centraalbureau voor Schimmelcultures You are free to share - to copy, distribute and transmit the work, under the following conditions: Attribution: You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). Non-commercial: You may not use this work for commercial purposes. No derivative works: You may not alter, transform, or build upon this work. For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode. Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights. 58 Persoonia – Volume 30, 2013 general life cycle, single cultures, crossed cultures Table 1 Morphological featured observable in mucoralean fungi. spores spores Feature/character Criteria sporangium mycelium mating mycelium sporangium Mycelium Height, colour, rhizoids, arthrospores, chla- - carotenoid metabolism Phycomyces blakesleeanus mydospores, giant cells - gravity- / phototropism Mucor mucedo parasitism - trisporic acid pathway Blakeslea trispora Syzygites megalocarpus Sporangia incl. sporangiophore Height, origin, branching pattern, size, - mating type loci spores - horizontal gene transfer Parasitella parasitica shape, colour, number of spores, septation, mycelium sporangium Absidia glauca dissolving of the wall, release of spores, biotechnology agriculture medical response to light - fermentation - plant & animal pathogens - human pathogens (e.g. food, steroles) - spoilage - chitosan production Sporangiospores Shape, size, ornamentation, colour, append- - aditives to food, feed, (biomedical applications) ages cosmetics , pharmaceuticals Lichtheimia spp. Lichtheimia spp. (e.g. carotenoids, lycopene) Rhizopus spp. Mucor circinelloides Zygospores Homo-/heterothallism, air-borne or sub- Mucor spp. Rhizopus arrhizus Rhizopus microsporus Saksenaea vasiformis merged, relative placement and size of Apophysomyces spp. Blakeslea trispora suspensors, shape, size, colour, ornamenta- Absidia cylindrospora Rhizomucor miehei Absidia caerulea Cunninghamella bertholletiae tion, appendages 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. Stalpers & Schipper 1980). Combining an order-wide trisporoid Although a general trisporic acid biosynthesis pathway (Schacht- profiling with the current knowledge on phylogenetic relationships schabel et al. 2005) is widely accepted, the genetic background would most likely reveal the ‘languages’ of the different clades is resolved only in parts. The synthesis and degradation of and their potentials for interspecific mutual recognition. But cur- beta-carotene is well studied and understood (Almeida & rently, only profiles for few species are known: e.g. Phycomyces Cerdá-Olmedo 2008, Polaino et al. 2010, Tagua et al. 2012) blakesleeanus (Miller & Sutter 1984) and Blakeslea trispora but most enzymes responsible for trisporic acid production (Caglioti et al. 1966). remain undiscovered. So far, only 4-dihydro-methyltrisporate K. Hoffmann et al.: DNA barcoding in Mucorales 59 dehydrogenase and 4-dihydrotrisporin dehydrogenase are 2c, d) (Dennis 1983).
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