DNA barcoding in Mucorales: an inventory of biodiversity

Abstract

The order Mucorales comprises predominantly fast-growing saprotrophic fungi, some of which are used for the fermentation of foodstuffs but it also includes species known to cause infections in patients with severe immune or metabolic impairments. To inventory biodiversity in Mucorales ITS barcodes of 668 strains in 203 taxa were generated covering more than two thirds of the recognised species. Using the ITS sequences, Molecular Operational Taxonomic Units were defined by a similarity threshold of 99 %. An LSU sequence was generated for each unit as well. Analysis of the LSU sequences revealed that conventional phenotypic classifications of the Mucoraceae are highly artificial. The LSU- and ITS-based trees suggest that characters, such as rhizoids and sporangiola, traditionally used in mucoralean taxonomy are plesiomorphic traits. The ITS region turned out to be an appropriate barcoding marker in Mucorales. It could be sequenced directly in 82 % of the strains and its variability was sufficient to resolve most of the morphospecies. Molecular identification turned out to be problematic only for the species complexes of Mucor circinelloides, M. flavus, M. piriformis and Zygorhynchus moelleri. As many as 12 possibly undescribed species were detected. Intraspecific variability differed widely among mucorealean species ranging from 0 % in Backusella circina to 13.3 % in Cunninghamella echinulata. A high proportion of clinical strains was included for molecular identification. Clinical isolates of Cunninghamella elegans were identified molecularly for the first time. As a result of the phylogenetic analyses several taxonomic and nomenclatural changes became necessary. The genus Backusella was emended to include all species with transitorily recurved sporangiophores. Since this matched molecular data all Mucor species possessing this character were transferred to Backusella. The genus Zygorhynchus was shown to be polyphyletic based on ITS and LSU data. Consequently, Zygorhynchus was abandoned and all species were reclassified in Mucor. Our phylogenetic analyses showed, furthermore, that all non-thermophilic Rhizomucor species belong to Mucor. Accordingly, Rhizomucor endophyticus was transferred to Mucor and Rhizomucor chlamydosporus was synonymised with Mucor indicus. Lecto-, epi- or neotypes were designated for several taxa.

INTRODUCTION

The order Mucorales represents a phylogenetically ancient group of fungi comprising predominantly saprotrophs inhabiting soil, dung and dead plant material, as well as several parasites on plants and on other fungi. Mucoralean strains have been used for centuries in the fermentation of traditional Asian and African food such as tempeh or furu (fermented tofu) (Nout & Aidoo 2010), and they also play a role in the production of several kinds of cheese (Hermet et al. 2012). On the other hand, some members of the Mucorales are responsible for the spoilage of fresh and manufactured food (Pitt & Hocking 2009).

Mucoralean fungi are also known to be involved in human infection. Mucormycoses are still very rare, but their incidence is increasing in hosts with severe immune or metabolic impairment, e.g. due to hemomalignancy, hematopoietic stem cell transplantation or uncontrolled ketoacidotic diabetes mellitus (Skiada et al. 2011). Infections often take a dramatic course and have a high mortality rate. In risk group patients such as those with leukemia or allogenic bone marrow transplant an increase of 8 % and 2 %, respectively, has been noted (Greenberg et al. 2004). In part the clinical strains belong to the same species as the ones used in food fermentation. For example, Mucor circinelloides is used for starter cultures in Asian food (Hesseltine 1983, Nout & Aidoo 2010), but is also able to infect patients with an impaired immune system (e.g. Khan et al. 2009).

Mucorales are among the best represented groups in fungal culture collections. They easily grow in axenic culture and they have been used as model organisms since the late 19th century. A large share of all species described in the order are represented today by living cultures publicly available in fungal reference collections. For example, the Centraalbureau voor Schimmelcultures (www.cbs.knaw.nl) possesses 135 ex-type or authentic strains out of 227 currently accepted species. This is a unique situation, compared e.g. with dermatophytes which were described around the same period (Sabouraud 1910).

Problematic for the nomenclatural stability of the Mucorales is the practice of many early authors to designate a living strain as ‘type’ although this was permitted by the International Code of Botanical Nomenclature. Since 2000 Art. 8.4 of ICBN has allowed deposition of metabolically inactive cultures as types (Greuter et al. 2000). In order to link these original strains to the respective names we designated the vial with the lyophilised strain that was prepared at time of its accession as lectotypes. If the original strain was not lyophilized in the year of its accession we lectotypified the name by the original illustration and designated the original strain as epitype. In the case of Zygorhynchus exponens a neotype was chosen because the original figures were not specific and no other authentic material is known to exist.

Taxonomy of Mucorales has traditionally been based upon microscopic morphology and mating experiments. The classical works of Maria A.A. Schipper (Schipper 1973, 1975, 1976, 1978a, b, 1979, 1984, 1986, 1990, Schipper & Samson 1994, Schipper & Stalpers 1984, 2003) provided model studies and have long remained satisfactory for the identification of major species. A large number of names were synonymised. However, molecular phylogeny has revealed that diversity within and between species is much larger than anticipated, and this has led to a proliferation of the number of taxa recognised. Since the older, morphological synonyms were a priori omitted from most studies, the respective names remained obscure and were not included in nomenclatural comparisons. New names are being introduced today for species that do not match any of the known taxa deposited in GenBank. Verification of the ex-type strains of older, still valid names may prove that some of the new names are later synonyms, and that the historical names have to be re-installed.

DNA barcoding was originally aimed to allow faster and more precise species identification. However, the accuracy of this method strongly depends on completeness of taxon sampling and on taxonomic elaboration (Meyer & Pauley 2005). Since polyphyly was revealed with molecular data in many morphology-based families and genera (O’Donnell et al. 2001, Voigt & Wöstemeyer 2001), several groups have been revised using molecular phylogenetic analyses, e.g. Actinomucor (Zheng & Liu 2005, Khan et al. 2008), Apophysomyces (Álvarez et al. 2010b), Cunninghamella (Liu et al. 2001), Lentamyces (Hoffmann & Voigt 2009), Lichtheimia (Alastruey-Izquierdo et al. 2010), Pilobolus (Foos et al. 2011), Rhizopus (Abe et al. 2006, 2007, 2010, Liu et al. 2007, Gryganskyi 2010), Saksenaea (Álvarez et al. 2010a), Siepmannia (Kwaśna & Nirenberg 2008a, b) and Umbelopsis (Meyer & Gams 2003). However, some genera, e.g. Absidia s.str., Circinella and relatives, or Syncephalastrum have not been revised using molecular data. The largest mucorelean group, Mucor and its relatives, has been investigated only fragmentarily focusing on certain clades (Jacobs & Botha 2008, Budziszewska et al. 2010, Álvarez et al. 2011, Madden et al. 2011, Hermet et al. 2012). Only a few publications (Abe et al. 2007, Alastruey-Izquierdo et al. 2010, Gryganskyi 2010, Hermet et al. 2012) use at least two unlinked molecular markers and apply sufficient strain and taxon sampling to adopt concepts of genealogical concordance phylogenetic species recognition (GCPSR, Taylor et al. 2000) satisfactorily. As a consequence, the criteria of good taxonomy are insufficiently met, and many species in Mucorales are poorly delimited. It was, therefore, the primary aim of the present study to inventory the genetic diversity of Mucorales deposited in the CBS culture collection and to highlight critical groups that need to be studied by a multi-locus approach. Our paper provides DNA barcodes for all ex-type and authentic strains of Mucorales available in the CBS culture collection, and makes these data available by open access as reference for subsequent studies on biodiversity and taxonomy.

Recently, the Fungal Barcoding Consortium (Schoch et al. 2012) proposed the rDNA internal transcribed spacer (ITS) as a universal DNA barcode marker for fungi. In our study ITS was also applied because of its discriminative power in Mucorales (Meyer & Gams 2003, Kwaśna et al. 2006, Schwarz et al. 2006, Vitale et al. 2012). The ITS region is highly variable between members and is not alignable over the entire order. ITS sequences of some species differ to such an extent that they could not be aligned confidently with their putative sibling species. To establish the phylogenetic position of species and to acquire an overview of the entire order that includes all groups recognized on the basis of molecular data, the D1/D2 region of the large subunit (LSU) rDNA was sequenced from one strain of each Molecular Operational Taxonomic Unit (MOTU). A MOTU is defined by ITS similarities with mutual threshold values of > 99 %. Using this approach a species can be represented by a single or by several MOTUs depending on intraspecific variability.

Analyses of the ITS region as a single locus can not be used to define species boundaries, but, conversely, hypotheses on species limits can be developed by plotting morphospecies on the ITS trees. Therefore only those taxonomic rearrangements were made that did not require exact knowledge on species limits. These revisions will be discussed, and nomenclatural status of names analysed.

ITS barcodes of 668 strains in 203 taxa (178 species, 19 varieties, 6 forms) were generated for this study covering 78.4 % of the recognized species in Mucorales. Seventy-six percent of the species are represented by ex-type strains or other authentic material. LSU sequences were generated for 43.5 % of the strains. Special attention was paid to the inclusion of a high proportion of clinical strains predominantly provided by the Spanish National Center for Microbiology in Madrid (Spain) and the Postgraduate Institute of Medical Education and Research in Chandigarh (India). The paper focuses on the genera Actinomucor, Mucor and allies, Rhizomucor and Rhizopus because ITS trees have been published for the remaining medically important genera: Apophysomyces (Álvarez et al. 2010b), Cunninghamella (Liu et al. 2001), Lichtheimia (Alastruey-Izquierdo et al. 2010), Saksenaea (Álvarez et al. 2010a) and Syncephalastrum (Vitale et al. 2012).

In main traits we follow the nomenclature of the species provided by Species Fungorum (http://www.speciesfungorum.org) based largely on the 10th edition of the Dictionary of the Fungi. We adopted the family structure by Hoffmann et al. (2013).

MATERIALS AND METHODS

Strains

A total number of 668 mucoralean strains belonging to 178 species, 19 varieties and 6 formae and covering 78.4 % of the currently accepted species was studied. For 22.2 % of the taxa it was possible to include five or more strains per lowest taxonomic level (form, variety or species), 60.1 % of the taxa were represented by 2 or more isolates. Ex-type strains or other authentic material was available for 75.8 % of the studied species. In order to cover intraspecific variability, strains from the most distant localities and from a wide range of substrates were selected. Special attention was paid to the inclusion of clinical isolates. Studied strains originated from the reference collection of the CBS-KNAW Fungal Biodiversity Centre (CBS; Utrecht, The Netherlands), the Instituto de Salud Carlos III National Centre of Microbiology (CNM-CM; Madrid, Spain), the Departments of Medical Microbiology (PGIMER; Chandigarh, India) or the Belgian Co-ordinated Collections of Micro-organisms (IHEM; Brussels, Belgium). The studied strains, source information and GenBank accession numbers are listed in Table 1.

Table 1.

Source information and GenBank accession numbers of the studied strains. Strains marked with an asterisk belong to different genera based on their ITS- or LSU-sequences: * Absidia idahoensis CBS 103.91 belongs to Circinella; ** Circinella lacrymispora CBS 101757 belongs to Gongronella, *** Circinella simplex CBS 428.80 belongs to Mucor. Ex-type strains are designated by: T = ex-type strain, ET = ex-epitype strain, HT = ex-holotype strain, IT = ex-isotype strain, LT = ex-lectotype strain, NT = ex-neotype strain, PT = ex-paratype strain, ST = ex-syntype strain and AUT = authentic material. Type information was checked with original literature only for those taxa that are treated in the taxonomy part; the remaining data were derived from the CBS database.

Strain number	Species	Species name at the beginning of the study	Status	Country	Source	ITS	LSU
CBS 125.68	Absidia anomala		T	Cuba	soil	JN205815	JN206593
CBS 126.68	Absidia californica		T	USA	dung of rat		JN206583
CBS 314.78	Absidia californica			USA	dung of mouse	JN205816	JN206582
CBS 101.28	Absidia coerulea			USA	dung of rabbit	JN205818	JN206585
CBS 102.28	Absidia coerulea			USA	soil	JN205821	JN206584
CBS 104.08	Absidia coerulea			n.a.	soil	JN205811	HM849703
CBS 628.70B	Absidia coerulea			Denmark	forest soil	JN205812
CBS 101.59	Absidia cuneospora		T	USA	sandy soil		JN206580
CBS 102.59	Absidia cuneospora			USA	clay soil	JN205819	JN206579
CBS 100.08	Absidia cylindrospora var. cylindrospora			n.a.	n.a.	JN205822	JN206588
CBS 127.68	Absidia cylindrospora var. nigra		T	USA	soil of pastured hardwood		JN206589
CBS 153.63	Absidia cylindrospora var. rhizomorpha		T	Honduras	rhizosphere of Musa sapientum		JN206594
CBS 102.35	Absidia fusca		T	Germany	soil of pine forest	JN205814	HM849707
CBS 346.97	Absidia fusca	A. cylindrospora var. nigra		Netherlands	myxomycete	JN205817
CBS 100.48	Absidia glauca			Germany	manure, in asparagus field	JN205820	JN206581
CBS 101.08	Absidia glauca		T	n.a.	n.a.	JN205810	HM849705
CBS 101.29	Absidia heterospora		T	France	soil of pine forest		JN206595
CBS 103.91	Absidia idahoensis*		T	USA	brood chamber of Nomia melanderi	JN205847
CBS 697.68	Absidia macrospora		T	former Czechovakia	soil		HM849704
CBS 100.62	Absidia pseudocylindrospora		T	Tanzania	virgin soil		JN206591
CBS 128.68	Absidia psychrophilia		T	Canada	ambrosia beetle; gland		JN206587
CBS 115583	Absidia repens		IT	UK, England	wallpaper	JN205813	HM849706
CBS 187.64	Absidia spinosa var. biappendiculata		IT	USA	Comandra pallida; leaf		JN206592
CBS 106.08	Absidia spinosa var. spinosa			n.a.	n.a.	JN205809	JN206590
CBS 100.09	Actinomucor elegans			n.a.	n.a.	JN205827	JN206491
CBS 100.22	Actinomucor elegans			USA	n.a.	JN205828
CBS 111556	Actinomucor elegans					JN205826
CBS 154.86	Actinomucor elegans			Egypt	n.a.	JN205829	HM849686
CBS 338.72	Actinomucor elegans			Nepal	soil	JN205824
CBS 117697	Actinomucor elegans var. kuwaitiensis	A. kuwaitiensis	T	Kuwait	human; wound	JN205823	JN206493
CBS 111558	Actinomucor elegans var. meitauzae	A. taiwanensis		n.a.	n.a.	JN205825	JN206492
CBS 476.78	Apophysomyces elegans		T	India	soil of mango orchard	JN206279
CBS 477.78	Apophysomyces elegans			India	soil of grassy site	JN206280	JN206536
CBS 658.93	Apophysomyces variabilis	A. elegans	T	Netherlands Antilles	human; osteomyelitis	JN206281	HM849695
CBS 128.70	Backusella circina		T	USA	soil with lichens	JN206258	JN206529
CBS 129.70	Backusella circina		PT	USA	soil	JN206257
CBS 323.69	Backusella circina			Japan	n.a.	JN206259
CBS 382.95	Backusella circina			China	forest soil	JN206256
CBS 907.73	Backusella circina			Japan	n.a.	JN206260
CBS 786.70	Backusella indica	M. recurvus var. indicus	LT (designated here)	India	n.a.	JN206255	JN206526
CBS 107.09	Backusella lamprospora		T of Mucor dispersus	Norway	n.a.	JN206269
CBS 118.08	Backusella lamprospora		T	Switzerland	n.a.	JN206268	JN206531
CBS 195.28	Backusella lamprospora			USA	fallen leaf	JN206271	JN206530
CBS 244.67	Backusella lamprospora			France	moist wall	JN206270
CBS 568.70	Backusella oblongielliptica	Mucor oblongiellipticus	LT (designated here)	Japan	agaric	JN206278	JN206533
CBS 569.70	Backusella oblongispora	Mucor oblongisporus	NT (designated here)	Japan	soil	JN206251	JN206407
CBS 196.71	Backusella recurva	M. recurvus var. recurvus				JN206265	JN206523
CBS 317.52	Backusella recurva	M. recurvus var. recurvus		Macedonia	decaying wood	JN206262 (c1)
CBS 318.52	Backusella recurva	M. recurvus var. recurvus	ET (designated here)	USA	Fragaria; diseased root	JN206261	JN206522
CBS 673.75	Backusella recurva	M. recurvus var. recurvus		Australia	soil	JN206263 (c1)	JN206524
						JN206264 (c2)
CBS 538.80	Backusella sp.	M. recurvus var. recurvus		Egypt	Medicago sativa	HM999964	HM849692
CBS 562.66	Backusella tuberculispora	Mucor tuberculisporus	LT (designated here)	India	n.a.	JN206267
CBS 570.70	Backusella tuberculispora	Mucor tuberculisporus		Japan	cultivated soil	JN206266
CBS 564.66	Backusella variabilis	Mucor variabilis	LT (designated here)	India	excrements of human	JN206254 (c1)	JN206528
						JN206253 (c3)
CBS 421.70	Benjaminiella multispora		IT	India	humus-rich soil	JN206243	JN206410
CBS 158.60	Benjaminiella poitrasii		T	USA	dung of rat	JN206241	JN206411
CBS 103.89	Benjaminiella youngii		T	Spain	dung of lizard	JN206242	JN206409
CBS 130.59	Blakeslea trispora			Panama	soil	JN206227
CBS 137.49	Blakeslea trispora			Indonesia	Hibiscus rosa-sinensis; flower	JN206229
CBS 198.80	Blakeslea trispora			Sweden	n.a.	JN206228
CBS 564.91	Blakeslea trispora	B. sinensis	PT of B. sinensis	China	soil	JN206230	JN206515
CBS 116.24	Chaetocladium brefeldii			n.a.	n.a.	JN206020	JN206519
CBS 136.28	Chaetocladium brefeldii			n.a.	dung of horse	JN206019
CBS 156.74	Chaetocladium brefeldii			Netherlands	litter	JN206022	JN206520
CBS 162.82	Chaetocladium brefeldii			Netherlands	dung of rat	JN206021
CBS 811.69	Chaetocladium jonesiii			Norway	meadow soil	JN206023
CBS 172.67	Chlamydoabsidia padenii		T	USA	Pisum sativum; root	JN206294	JN206586
CBS 120.25	Choanephora cucurbitarum	C. infundibulifera f. cucurbitarum		n.a.	n.a.	JN206231
CBS 150.51	Choanephora cucurbitarum	C. infundibulifera f. cucurbitarum		n.a.	n.a.	JN206232
CBS 178.76	Choanephora cucurbitarum	C. infundibulifera f. cucurbitarum	T. of C. heterospora	India	dead insect	JN206235
CBS 445.72	Choanephora cucurbitarum	C. infundibulifera f. cucurbitarum		n.a.	n.a.	JN206234
CBS 674.93	Choanephora cucurbitarum	C. infundibulifera f. cucurbitarum		China	n.a.	JN206233	JN206514
CBS 153.51	Choanephora infundibulifera	C. infundibulifera f. infundibulifera		n.a.	n.a.	JN206236	JN206513
CBS 155.51	Choanephora infundibulifera	C. infundibulifera f. infundibulifera		n.a.	n.a.	JN206237
CBS 155.58	Choanephora infundibulifera	C. infundibulifera f. infundibulifera		Japan	n.a.	JN206238
CBS 172.62	Circinella angarensis			USA	dung of rodent	JN205848
CBS 173.62	Circinella angarensis		NT	USA	dung	JN205849	JN206551
CBS 140.28	Circinella chinensis		T	Japan	n.a.	JN205855	JN206549
CBS 101757	Circinella lacrymispora**		T	Argentina	soil	JN206289	JN206608
CBS 102.16	Circinella minor	C. umbellata		n.a.	n.a.	JN205860
CBS 142.81	Circinella minor			Netherlands	dung of mouse	JN205861	JN206552
CBS 143.56	Circinella minor			n.a.	n.a.	JN205862
CBS 107.13	Circinella muscae		T of C. sydowii	n.a.	gold mine, depth of 600 m	JN205854	JN206550
CBS 141.28	Circinella muscae			n.a.	n.a.	JN205853	JN206548
CBS 159.49	Circinella muscae			Indonesia	soil	JN205851
CBS 342.79	Circinella muscae			Netherlands	preserved meat	JN205852
CBS 720.76A	Circinella muscae			USA	n.a.	JN205850
CBS 428.80	Circinella simplex***			Colombia	paramo soil under undisturbed vegetation	JN206213	JN206445
CBS 101.16	Circinella umbellata			n.a.	dung of dog	JN205857	JN206553
CBS 160.49	Circinella umbellata			Italy	air	JN205858	HM849722
CBS 195.74	Circinella umbellata			Kuwait	soil	JN205856
CBS 837.97	Circinella umbellata			Germany	dung of mouse	JN205859
CBS 158.50	Cokeromyces recurvatus		T	USA	dung of rabbit	JN206244	HM849699
CBS 168.59	Cokeromyces recurvatus			USA	dung of rat	JN206245	JN206408
CBS 151.80	Cunninghamella bertholletiae	C. elegans		USA	human; lung (leukemic patient)	JN205875
CBS 182.84	Cunninghamella bertholletiae			USA	human	JN205877
CBS 186.84	Cunninghamella bertholletiae			USA	human; lung (leukemic patient)	JN205876
CBS 190.84	Cunninghamella bertholletiae			USA	human; heart, patient with lymphosarcoma	JN205878	HM849701
CBS 191.84	Cunninghamella bertholletiae			USA	human; tibia	JN205879
CBS 372.95	Cunninghamella bertholletiae	C. polymorpha		China	forest soil	JN205872
CBS 373.95	Cunninghamella bertholletiae	C. polymorpha		China	rotten log	JN205873
CBS 693.68	Cunninghamella bertholletiae	C. polymorpha	NT of C. polymorpha	former Yugoslavia	soil	JN205871	JN206600
CBS 779.68	Cunninghamella bertholletiae	C. polymorpha		n.a.	n.a.	JN205874	JN206599
CNM-CM3628	Cunninghamella bertholletiae			Spain	human; sputum	JN205881
CNM-CM3650	Cunninghamella bertholletiae			Spain	human; skin	JN205880
CBS 158.28	Cunninghamella binariae	C. elegans		n.a.	n.a.	JN205888	JN206602
CBS 481.66	Cunninghamella binariae	C. elegans		Brazil	soil	JN205889	JN206603
CBS 133.27	Cunninghamella blakesleeana		T	Switzerland	n.a.	JN205865
CBS 177.36	Cunninghamella blakesleeana			n.a.	n.a.	JN205868
CBS 224.64	Cunninghamella blakesleeana			Canada	Linum issitatissimum	JN205870
CBS 433.84	Cunninghamella blakesleeana			Kuwait	n.a.	JN205867
CBS 720.85	Cunninghamella blakesleeana	C. elegans		Croatia	decaying fruit	JN205866
CBS 782.68	Cunninghamella blakesleeana			n.a.	n.a.	JN205869	JN206601
CBS 100178	Cunninghamella clavata		T	n.a.	n.a.	JN205890	JN206604
CBS 362.95	Cunninghamella clavata			China	soil	JN205891
CBS 156.28	Cunninghamella echinulata		NT	n.a.	n.a.	JN205895	HM849702
CBS 656.85	Cunninghamella echinulata			Egypt	soil	JN205896	JN206598
CBS 766.68	Cunninghamella echinulata			n.a.	n.a.	JN205894
CBS 545.75	Cunninghamella echinulata var. antarctica	C. antarctica	T	Chile	soil	JN205893	JN206597
CBS 167.53	Cunninghamella elegans			Canada	Linum usitatissimum; seed	JN205882	HM849700
CBS 318.78	Cunninghamella elegans	C. phaeospora		Turkey	soil under shrub vegetation	JN205886
CBS 773.68	Cunninghamella elegans			former Czechoslovakia	n.a.	JN205887
CBS 781.68	Cunninghamella elegans	C. phaeospora		n.a.	n.a.	JN205885
CNM-CM5114	Cunninghamella elegans			Spain	human; lung, biopsy sample	JN205884
CBS 168.53	Cunninghamella homothallica		T	Japan	soil	JN205863	JN206605
CBS 347.69	Cunninghamella intermedia	C. phaeospora	T of C. brunnea	India	n.a.	JN205892	JN206606
CBS 692.68	Cunninghamella phaeospora		NT	Indonesia	soil	JN205864	HM849697
CBS 989.96	Cunninghamella vesiculosa		T	India	soil of Shorea robusta forest	JN205897	HM849693
CBS 695.76	Dichotomocladium elegans			USA	dung of rodent	JN205840	HM849715
CBS 714.74	Dichotomocladium elegans		T	USA	dung of mouse	JN205839	JN206555
CBS 164.61	Dichotomocladium hesseltinei		T	India	soil of a cultivated field	JN205841	JN206556
CBS 439.76	Dichotomocladium robustum			USA	dung of mouse	JN205842
CBS 440.76	Dichotomocladium robustum		T	USA	dung of mouse	JN205843	JN206557
CBS 243.57	Ellisomyces anomalus		T	USA	dung of lizard	JN205992	JN206423
CBS 697.76	Ellisomyces anomalus			USA	dung of mouse	JN205993
CBS 290.86	Fennellomyces heterothallicus		AUT	India	dung of house lizard	JN205844	JN206540
CBS 292.86	Fennellomyces heterothallicus		AUT	India	dung of shrew		JN206539
CBS 158.54	Fennellomyces linderi		T	USA	poplin	JN205846	HM849723
CBS 190.32	Gilbertella persicaria	G. persicaria var. persicaria	T	USA	Prunus persica; fruit	HM999958	HM849691
CBS 246.59	Gilbertella persicaria	G. persicaria var. persicaria		USA	trickling filter plant	JN206222
CBS 325.71A	Gilbertella persicaria	G. persicaria var. persicaria		Indonesia	Saccharum officinarum; leaf	JN206220
CBS 325.71D	Gilbertella persicaria	G. persicaria var. persicaria		Indonesia	wood	JN206225
CBS 403.51	Gilbertella persicaria	Rhizopus stolonifer		Japan	n.a.	JN206221
CBS 421.77	Gilbertella persicaria	G. persicaria var. persicaria		Pakistan	soil	JN206223
CBS 442.64	Gilbertella persicaria	G. persicaria var. indica	T of G. persicaria var. indica	India	n.a.	JN206219
CBS 532.77	Gilbertella persicaria	G. persicaria var. persicaria		India	dung of mouse		JN206517
CBS 565.91	Gilbertella persicaria	G. hainanensis	T of G. hainanensis	China	dung of swine	JN206226
CBS 785.97	Gilbertella persicaria	Mucor thermophilus		n.a.	n.a.	JN206218
CBS 102.44	Gongronella butleri			Italy	n.a.	JN206284
CBS 157.25	Gongronella butleri		T of G. urceolifera	Indonesia	Cocos nucifera; root		JN206607
CBS 179.28	Gongronella butleri			n.a.	n.a.	JN206286
CBS 216.58	Gongronella butleri		T of Mucor vesiculosus	UK	garden soil	JN206285	HM849698
CBS 415.67	Gongronella butleri			Brazil	soil	JN206288
CBS 969.73	Gongronella butleri			Chile	volcanic ash soil	JN206287
CBS 244.62	Gongronella lacrispora		T	USA	dooryard soil		JN206609
CBS 162.75	Halteromyces radiatus		T	Australia	mud from mangrove forest, contaminated with effluent	JN206290	JN206596
CBS 223.63	Helicostylum cordense		IT	India	forest soil	JN206193	JN206506
CBS 169.57	Helicostylum elegans			UK	dead isopod (woodlouse)		JN206471
CBS 107.23	Helicostylum pulchrum			n.a.	n.a.	JN206053
CBS 258.59	Helicostylum pulchrum		T of H. venustellum	UK, England	isopod, on the underside of a disturbed pine stump	JN206054
CBS 259.68	Helicostylum pulchrum			Germany	air-dried raw sausage	JN206052
CBS 639.69	Helicostylum pulchrum			USA	spoiled beef crackling	JN206055
CBS 197.68	Hesseltinella vesiculosa		IT	Brazil	rice-field soil		JN206610
CBS 254.85	Hyphomucor assamensis			Malaysia	Burmannia	JN206212	JN206440
CBS 415.77	Hyphomucor assamensis		T	India	n.a.	JN206211	JN206439
CBS 174.67	Lentamyces parricida		NT	UK	grassland soil, surface layer	JN206293	JN206535
CBS 100.17	Lichtheimia corymbifera	Mycocladus corymbifer		n.a.	n.a.	GQ342885	GQ342942
CBS 100.51	Lichtheimia corymbifera	Mycocladus corymbifer		n.a.	n.a.	GQ342886	GQ342939
CBS 102.48	Lichtheimia corymbifera	Mycocladus corymbifer		India	mouldy shoe	GQ342888	GQ342910
CBS 115811	Lichtheimia corymbifera	Mycocladus corymbifer		Germany	indoor air	GQ342887	GQ342932
CBS 429.75	Lichtheimia corymbifera	Mycocladus corymbifer	NT	Afghanistan	soil	GQ342878	GQ342903
CBS 100.31	Lichtheimia corymbifera	Mycocladus corymbifer		n.a.	aborted cow	GQ342879	GQ342914
CBS 101040	Lichtheimia corymbifera	Mycocladus corymbifer		France	human; keratomycosis	GQ342882	GQ342918
CBS 109940	Lichtheimia corymbifera	Mycocladus corymbifer		Norway	human; finger tissue	GQ342881	GQ342917
CBS 120580	Lichtheimia corymbifera	Mycocladus corymbifer		France	human; lung	GQ342884	GQ342919
CBS 120581	Lichtheimia corymbifera	Mycocladus corymbifer		France	human; bronchia	GQ342883	GQ342948
CBS 120805	Lichtheimia corymbifera	Mycocladus corymbifer		France	human; bone	GQ342880	GQ342915
CBS 519.71	Lichtheimia corymbifera	Absidia griseola	T of Absidia griseola	Japan	n.a.	GQ342889	GQ342904
CBS 100.28	Lichtheimia hyalospora	Mycocladus blakesleeanus; Absidia blakesleeana	T of Absidia blakesleeana	USA	Bertholletia excelsa; nut	GQ342896	GQ342902
CBS 100.36	Lichtheimia hyalospora	Mycocladus blakesleeanus; Absidia blakesleeana		n.a.	n.a.	GQ342898; GQ342897	GQ342943
CBS 102.36	Lichtheimia hyalospora	Mycocladus blakesleeanus; Absidia blakesleeana	T of Absidia cristata	Ghana	Manihot esculenta; stem	GQ342895	GQ342907
CBS 518.71	Lichtheimia hyalospora	Mycocladus blakesleeanus var. atrosporus; Absidia blakesleeana var. atrospora	T of Absidia blakesleeana var. atrospora	Japan	n.a.	GQ342894	GQ342944
CBS 173.67	Lichtheimia hyalospora	Mycocladus hyalosporus; Absidia hyalospora	NT	Philippines	fermented food taosi	GQ342893	GQ342905
CBS 291.66	Lichtheimia ornata	Mycocladus corymbifer	T of Absidia ornata	India	dung of bird	GQ342891	GQ342946
CNM-CM4978	Lichtheimia ornata			Spain	human; wound	GQ342892	JN206554
CBS 958.68	Lichtheimia ornata	Mycocladus corymbifer		n.a.	n.a.	GQ342890	GQ342936
CBS 100.24	Lichtheimia ramosa	Mycocladus corymbifer		n.a.	n.a.	GQ342876	GQ342941
CBS 100.49	Lichtheimia ramosa	Mycocladus corymbifer		Indonesia	dung of cow	GQ342858	GQ342940
CBS 100.55	Lichtheimia ramosa	Mycocladus corymbifer		n.a.	n.a.	GQ342851	GQ342938
CBS 101.51	Lichtheimia ramosa	Mycocladus corymbifer		Netherlands	Guinea pig; lung	GQ342859	GQ342945
CBS 101.55	Lichtheimia ramosa	Mycocladus corymbifer		Switzerland	human; cornea	GQ342865	GQ342947
CBS 103.35	Lichtheimia ramosa	Mycocladus corymbifer	T of Absidia gracilis	n.a.	Musa sapientum; fruit	GQ342847	GQ342908
CBS 124198	Lichtheimia ramosa	Mycocladus corymbifer		Netherlands	culture contaminant	GQ342848	GQ342906
CBS 223.78	Lichtheimia ramosa	Mycocladus corymbifer		n.a.	cocoa soil	GQ342877	GQ342934
CBS 271.65	Lichtheimia ramosa	Mycocladus corymbifer		n.a.	n.a.	GQ342875	GQ342937
CBS 582.65	Lichtheimia ramosa	Mycocladus corymbifer	NT	Ghana	Theobroma cacao; seed	GQ342874	GQ342909
CBS 649.78	Lichtheimia ramosa	Mycocladus corymbifer		India	cultivated field soil	GQ342849	GQ342912
CBS 713.74	Lichtheimia ramosa	Mycocladus corymbifer		n.a.	n.a.	GQ342856	GQ342935
CNM-CM2166	Lichtheimia ramosa	Mycocladus corymbifer		Spain	human; sputum	GQ342863	GQ342926
CNM-CM3590	Lichtheimia ramosa	Mycocladus corymbifer		Spain	human	GQ342869	GQ342924
CNM-CM4119	Lichtheimia ramosa	Mycocladus corymbifer		Spain	human; skin	GQ342862	GQ342923
CNM-CM4228	Lichtheimia ramosa	Mycocladus corymbifer		Spain	human; skin	GQ342861	GQ342922
CNM-CM4253	Lichtheimia ramosa	Mycocladus corymbifer		Spain	human; skin	GQ342860	GQ342921
CNM-CM4261	Lichtheimia ramosa	Mycocladus corymbifer		Spain	human; lung	GQ342854	GQ342953
CNM-CM4337	Lichtheimia ramosa	Mycocladus corymbifer		Spain	human; skin	GQ342852	GQ342920
CNM-CM4427	Lichtheimia ramosa	Mycocladus corymbifer		Spain	human; bronchoaspirate	GQ342853	GQ342931
CNM-CM4537	Lichtheimia ramosa	Mycocladus corymbifer		Spain	human; skin	GQ342873	GQ342930
CNM-CM4849	Lichtheimia ramosa	Mycocladus corymbifer		Spain	human; skin	GQ342855; GQ342868	GQ342929
CNM-CM5111	Lichtheimia ramosa	Mycocladus corymbifer		Spain	human; sputum	GQ342871	GQ342928
CNM-CM5171	Lichtheimia ramosa	Mycocladus corymbifer		Belgium	human	GQ342864	GQ342927
AS 3.4808	Lichtheimia ramosa	Mycocladus corymbifer	T of Absidia idahoensis var. thermophila	China	soil	GQ342867	GQ342955
CBS 112528	Lichtheimia ramosa	Mycocladus corymbifer		Germany	human; wound, double infection with Candida albicans	GQ342850	GQ342913
CBS 124197	Lichtheimia ramosa	Mycocladus corymbifer		Greece	human; abscess of the flank	GQ342870	GQ342951
CBS 269.65	Lichtheimia ramosa	Mycocladus corymbifer		n.a.	n.a.	GQ342857	GQ342949
CNM-CM1638	Lichtheimia ramosa	Mycocladus corymbifer		Spain	human; gastric juice	GQ342866	GQ342954
CNM-CM3148	Lichtheimia ramosa	Mycocladus corymbifer		Spain	human; corneal exudate	GQ342872	GQ342925
CBS 420.70	Lichtheimia sphaerocystis	Mycocladus aff. blakesleeanus		India	n.a.	GQ342900	GQ342933
CBS 647.78	Lichtheimia sphaerocystis	Mycocladus aff. blakesleeanus		India	dung of mouse	GQ342899	GQ342911
CBS 648.78	Lichtheimia sphaerocystis	Mycocladus aff. blakesleeanus		India	soil	GQ342901	GQ342916
CBS 388.35	Mucor abundans	M. hiemalis f. silvaticus	NT (designated here)	Germany	forest soil	JN206111
CBS 521.66	Mucor abundans			Russia	forest soil	JN206110	JN206457
CBS 244.58	Mucor aligarensis			UK	human; ear	JN206057
CBS 993.70	Mucor aligarensis		T	India	soil	JN206056	JN206461
CBS 185.77	Mucor amphibiorum			Central America	diseased Dendrobates sp.	JN206170
CBS 763.74	Mucor amphibiorum		T	Germany	amphibian	HM999957	HM849688
CNM-CM2934	Mucor amphibiorum			Germany	human	JN206171
CBS 210.80	Mucor ardhlaengiktus		ET (designated here)	India	garden soil	JN206172	JN206504
CBS 528.73	Mucor ardhlaengiktus			Mozambique	Gossypium; seed	JN206173
CBS 650.78	Mucor ardhlaengiktus	M. aff. variisporus		India	dung of lizard	JN206174	JN206499
CBS 292.63	Mucor azygosporus		IT	USA	dung of lizard	JN206187	JN206497
CBS 251.53	Mucor bacilliformis		T	USA	soil	JN206083	JN206451
CBS 573.70	Mucor bacilliformis			Japan	agaric	JN206084	JN206452
CBS 293.63	Mucor bainieri		IT	India	forest soil	JN205995	JN206424
CBS 129.41	Mucor brunneogriseus	M. plumbeus	T	Netherlands	aphid	JN205910
CBS 124110	Mucor circinelloides (non of the described formae)			Hawaii island, USA	Morinda citrifolia; fermented fruit juice	JN205996	JN206430
CBS 202.28	Mucor circinelloides (non of the described formae)	M. circinelloides f. janssenii		n.a.	n.a.	JN205994	JN206418
CBS 338.71	Mucor circinelloides (non of the described formae)	M. hiemalis f. hiemalis		Turkey	n.a.	JN205998
CBS 526.68	Mucor circinelloides (non of the described formae)	M. circinelloides f. janssenii		Armenia	soil	JN206015	JN206426
CBS 635.65	Mucor circinelloides (non of the described formae)	M. hiemalis f. hiemalis		UK, England	faeces of diseased Apis mellifera	JN205997	JN206428
CBS 846.73	Mucor circinelloides (non of the described formae)	M. flavus		Chile	soil	JN206014
CNM-CM5225	Mucor circinelloides (non of the described formae)			Austria	human	JN205999
CBS 108.16	Mucor circinelloides f. circinelloides			Japan	n.a.	JN205954	JN206413
CBS 111555	Mucor circinelloides f. circinelloides	M. hiemalis		China	sufu starter	JN205943
CBS 111560	Mucor circinelloides f. circinelloides	M. racemosus f. racemosus		Vietnam	sufu, chao	JN205957
CBS 121702	Mucor circinelloides f. circinelloides	M. ramosissimus		Spain	commercial honey	JN205966
CBS 123973	Mucor circinelloides f. circinelloides			Germany	human; thigh necrosis after trauma	JN205958
CBS 172.27	Mucor circinelloides f. circinelloides			n.a.	Artocarpus; fruit	JN205967
CBS 192.68	Mucor circinelloides f. circinelloides			Netherlands	dung of pig	JN205959
CBS 194.68	Mucor circinelloides f. circinelloides			South Africa	n.a.	JN205972
CBS 195.68	Mucor circinelloides f. circinelloides		NT	Netherlands	air	JN205961	HM849680
CBS 196.68	Mucor circinelloides f. circinelloides			Turkey	Triticum aestivum	JN205968
CBS 239.35	Mucor circinelloides f. circinelloides		T of M. griseoroseus	Germany	soil	JN205942
CBS 247.35	Mucor circinelloides f. circinelloides			Germany	air	JN205962
CBS 295.34	Mucor circinelloides f. circinelloides			Ukraine	n.a.	JN205955
CBS 384.95	Mucor circinelloides f. circinelloides	Rhizomucor variabilis var. regularior	T of Rhizomucor variabilis var. regularior	China	human; face	JN205933	HM849679
CBS 394.68	Mucor circinelloides f. circinelloides			Netherlands	thawing beef meat	JN205969
CBS 416.77	Mucor circinelloides f. circinelloides	M. rouxii		n.a.	fermenting rice, component of ‘Chinese yeast’	JN205934	JN206412
CBS 479.70	Mucor circinelloides f. circinelloides			Finland	soil	JN205973
CBS 480.70F	Mucor circinelloides f. circinelloides			India	garden soil	JN205956
CBS 480.70G	Mucor circinelloides f. circinelloides			n.a.	n.a.	JN205965
CNM-CM2437	Mucor circinelloides f. circinelloides			Spain	human; nail	JN205939
CNM-CM2541	Mucor circinelloides f. circinelloides			Spain	human; nail	JN205944	JN206414
CNM-CM2922	Mucor circinelloides f. circinelloides			Spain	human; wound exudate	JN205963
CNM-CM3112	Mucor circinelloides f. circinelloides			Spain	human; peritoneal dialysis	JN205945
CNM-CM3178	Mucor circinelloides f. circinelloides			Spain	human; urine	JN205946
CNM-CM3510	Mucor circinelloides f. circinelloides			Spain	human; reservoir	JN205947
CNM-CM3785	Mucor circinelloides f. circinelloides			Spain	human; catheter (low respiratory tract infection)	JN205948
CNM-CM3926	Mucor circinelloides f. circinelloides			Spain	human; arm wound (traumatism with arm amputation)	JN205949
CNM-CM4299	Mucor circinelloides f. circinelloides			Spain	human; skin (surgical wound)	JN205950
CNM-CM4366	Mucor circinelloides f. circinelloides			Spain	human; wound exudate (polytraumatism, esplenomectomy)	JN205974	JN206415
CNM-CM4526	Mucor circinelloides f. circinelloides			Spain, Canaries	human; otic exudate	JN205953
CNM-CM4569	Mucor circinelloides f. circinelloides			Spain	human; bronchioaspirate (acute lymphoblastic leukemia B cells)	JN205951
CNM-CM4621	Mucor circinelloides f. circinelloides			Spain	human; skin of arm (burned patient)	JN205970
CNM-CM4895	Mucor circinelloides f. circinelloides			Spain	human; exudate (traumatism)	JN205975
CNM-CM4974	Mucor circinelloides f. circinelloides			Spain	human; wound skin	JN205952
CNM-CM5071	Mucor circinelloides f. circinelloides			Spain	human; bronchioaspirate	JN205938
CNM-CM5169	Mucor circinelloides f. circinelloides			Belgium	human	JN205971
IHEM 16415	Mucor circinelloides f. circinelloides			Italy	human; skin of hand, trauma	JN205964
IHEM 20006	Mucor circinelloides f. circinelloides			Belgium	human; wound	JN205936
IHEM 21105	Mucor circinelloides f. circinelloides			France	human	JN205937
IHEM 21158	Mucor circinelloides f. circinelloides			Belgium	human; wound (burned patient)	JN205960
IHEM 21426	Mucor circinelloides f. circinelloides			Belgium	human (burned patient)	JN205935
IHEM 22323	Mucor circinelloides f. circinelloides			Belgium	human	JN205941
CBS 116.08	Mucor circinelloides f. griseocyanus		T	Norway	soil	JN206003	JN206421
CBS 198.28	Mucor circinelloides f. griseocyanus			n.a.	n.a.	HM999951	JN206420
CBS 223.56	Mucor circinelloides f. griseocyanus			Netherlands	n.a.	JN206000
CBS 366.70	Mucor circinelloides f. griseocyanus			Netherlands	canned strawberries	JN206001
CBS 698.68	Mucor circinelloides f. griseocyanus			South Africa	Zea mays	JN206002
CBS 144.93	Mucor circinelloides f. janssenii	M. aff. ramosissimus		USA?	human; thigh	JN206012
CBS 185.68	Mucor circinelloides f. janssenii		T of M. kurssanovii	Russia	grassland soil	JN206006
CBS 204.68	Mucor circinelloides f. janssenii			n.a.	iguana; lung	JN206010
CBS 205.68	Mucor circinelloides f. janssenii		NT (designated here)	South Africa	forest soil	HM999952	JN206425
CBS 206.68	Mucor circinelloides f. janssenii			India	n.a.	JN206004
CBS 227.29	Mucor circinelloides f. janssenii			n.a.	n.a.	JN206008
CBS 232.29	Mucor circinelloides f. janssenii		T of M. tenellus	France	n.a.	JN206007
CBS 243.67	Mucor circinelloides f. janssenii			South Africa	human	JN206005
CBS 365.70	Mucor circinelloides f. janssenii			n.a.	dung of Dixippus morosus	JN206009
CBS 762.74	Mucor circinelloides f. janssenii			Netherlands	milk powder	JN206011	JN206416
CBS 108.17	Mucor circinelloides f. lusitanicus		T	n.a.	n.a.	JN205980
CBS 111228	Mucor circinelloides f. lusitanicus	M. racemosus f. racemosus		China	sufu starter, from sufu factory	JN205991 (c1)	JN206429
						JN205989 (c3)
CBS 111229	Mucor circinelloides f. lusitanicus	M. indicus		China	sufu starter, from sufu factory	JN205983 (c2)
						JN205990 (c4)
CBS 236.35	Mucor circinelloides f. lusitanicus	M. fragilis		Germany	Tremella	JN205979	JN206422
CBS 242.33	Mucor circinelloides f. lusitanicus			n.a.	n.a.	JN205987
CBS 253.35	Mucor circinelloides f. lusitanicus			USA	Zea mays; grain	JN205988
CBS 276.49	Mucor circinelloides f. lusitanicus			n.a.	n.a.	JN205984
CBS 633.65	Mucor circinelloides f. lusitanicus			South Afrika	Zea mays	JN205986
CBS 847.72	Mucor circinelloides f. lusitanicus			Portugal	n.a.	JN205981
CBS 851.71	Mucor circinelloides f. lusitanicus			n.a.	n.a.	JN205982
CBS 968.68	Mucor circinelloides f. lusitanicus			Mexico	n.a.	HM999953	JN206419
CBS 969.68	Mucor circinelloides f. lusitanicus			Russia	forest soil	JN205985	JN206427
CBS 293.66	Mucor ctenidius	Backusella ctenidia		USA	desert soil	JN205976	JN206417
CBS 433.87	Mucor ctenidius	Backusella ctenidia		Kenya	dead plant material	JN205978
CBS 696.76	Mucor ctenidius	Backusella ctenidia		USA	dung of pack rat	JN205977
CBS 156.51	Mucor durus	Circinella rigida	ET (designated here)	UK, England	soil	JN206112	JN206456
CBS 484.66	Mucor durus	Circinella rigida		Ukraine	soil	JN206113
CBS 385.95	Mucor endophyticus	Rhizomucor endophyticus	HT	China	Triticum aestivum; leaves	JN206159	JN206448
CBS 141.20	Mucor exponens	Zygorhynchus exponens var. exponens	NT (designated here)	Germany	n.a.	JN206206	JN206441
CBS 404.58	Mucor exponens	Zygorhynchus exponens var. smithii	LT of Z. exponens var. smithii (designated here)	UK, England	ploughed field soil	JN206208
CBS 508.48	Mucor exponens	Zygorhynchus exponens var exponens		Germany	n.a.	JN206207
CBS 251.35	Mucor falcatus		HT	Germany	honeycomb	JN206250	JN206509
CBS 252.35	Mucor falcatus			Germany	dung of rabbit	JN206249
CBS 126.70	Mucor flavus		T of M. mephitis	USA	dung of mouse	JN206049	JN206469
CBS 182.90	Mucor flavus			Czech Republic	floor of room in cave, used for speleotherapy	JN206065	JN206472
CBS 197.71	Mucor flavus		T of M. meridionalis	Ukraine	dung of wood mouse	JN206066	JN206470
CBS 210.71	Mucor flavus		T of M. peacockensis	India	dung of peacock	JN206050	JN206462
CBS 230.35	Mucor flavus		T of M. attenuatus	Germany	dung of roe	JN206061	JN206464
CBS 234.35	Mucor flavus		NT	Germany	n.a.	JN206051	JN206468
CBS 664.67	Mucor flavus			Finland	forest litter	JN206064
CBS 681.73	Mucor flavus			Germany	wheat field soil	JN206069 (c2)	JN206473
						JN206070 (c3)
CBS 893.73	Mucor flavus		NT of M. sciurinus	Russia	forest soil	JN206062 (c1)	JN206465
						JN206063 (c2)
CBS 992.68	Mucor flavus			Antarctica	coastal gravel flat covered by Bryum argenteum	JN206067 (c1)	JN206467
						JN206068 (c3)
CBS 230.29	Mucor fuscus		T of M. petrinsularis var. echinosporus	France	n.a.	JN206204
CBS 254.48	Mucor fuscus		T of M. bedrchanii	Germany	n.a.	JN206203
CBS 282.78	Mucor fuscus			France	cheese	JN206201	JN206442
CBS 313.78	Mucor fuscus			France	cheese	JN206200
CBS 530.77	Mucor fuscus			India	dung of mouse	JN206202
CBS 336.68	Mucor fusiformis	Zygorhynchus psychrophilus	HT	Finland	Picea abies; brown needle	JN206157	JN206447
CBS 114.08	Mucor genevensis		T	Switzerland	soil	JN206041	JN206435
CBS 404.71	Mucor genevensis			Ukraine	dung of field-mouse	JN206042 (c1)
						JN206043 (c2)
CBS 535.78	Mucor genevensis			USA	n.a.	JN206045 (c1)
						JN206046 (c3)	JN206436
						JN206047 (c4)
CBS 564.75	Mucor genevensis			Netherlands	Malus sylvestris; fruit	JN206044 (c3)
CBS 383.95	Mucor gigasporus			China	soil	JN206246
CBS 566.91	Mucor gigasporus		T	China	soil	JN206247	JN206494
CBS 186.87	Mucor grandis		T	India	dung of mouse	JN206252	JN206527
CBS 174.27	Mucor guiliermondii		T	Russia	dung of Periplaneta americana	JN206082	JN206475
CBS 252.85	Mucor heterogamus	Zygorhynchus heterogamus		Netherlands	cattle feed	JN206161 (c1)	JN206490
						JN206162 (c4)
CBS 338.74	Mucor heterogamus	Zygorhynchus heterogamus		Sweden	sediment in drain pipe	JN206169 (c1)	JN206488
						JN206168 (c4)
CBS 405.58	Mucor heterogamus	Zygorhynchus heterogamus	ET (designated here)	n.a.	n.a.	JN206167	JN206487
CBS 580.83	Mucor heterogamus	Zygorhynchus heterogamus		Netherlands	sandy soil in potato field	JN206163	JN206486
CBS 594.83	Mucor heterogamus	Zygorhynchus heterogamus		Colombia	soil	JN206164 (c3)	JN206485
						JN206165 (c4)
CBS 115.18	Mucor hiemalis	M. hygrophilus		n.a.	n.a.	JN206127
CBS 118522	Mucor hiemalis			Denmark	agricultural soil	JN206138
CNM-CM2540	Mucor hiemalis			Spain	human; nail	JN206140
CNM-CM5229	Mucor hiemalis			Spain	human; nail	JN206141
Fungiscope AS72	Mucor hiemalis			Austria	human	JN206142
CBS 106.09	Mucor hiemalis f. corticola		T	Norway	n.a.	JN206130
CBS 362.68	Mucor hiemalis f. corticola			Russia	forest soil	JN206132	JN206449
CBS 365.68	Mucor hiemalis f. corticola			Austria	soil	JN206133
CBS 366.68	Mucor hiemalis f. corticola			Austria	soil	JN206139
CBS 532.78	Mucor hiemalis f. corticola			Netherlands	soil	JN206145
CBS 533.78	Mucor hiemalis f. corticola			Netherlands	greenhouse soil under Lycopersicon esculentum	JN206146
CBS 107.19	Mucor hiemalis f. hiemalis		T of M. vallesiacus	Switzerland	n.a.	JN206137
CBS 110.19	Mucor hiemalis f. hiemalis		T of M. hiemalis var. toundrae	Switzerland	n.a.	JN206136
CBS 117.08	Mucor hiemalis f. hiemalis		T of M. adventitius var. aurantiacus	Switzerland	n.a.	JN206143
CBS 123972	Mucor hiemalis f. hiemalis			Germany	human; sputum	JN206128
CBS 201.65	Mucor hiemalis f. hiemalis		NT	USA	n.a.	JN206125	HM849683
CBS 242.35	Mucor hiemalis f. hiemalis		IT of M. hiemalis var. griseus	Germany	forest soil	JN206134
CBS 328.92	Mucor hiemalis f. hiemalis			Italy	lake sediment, submerged	JN206135
CBS 337.71D	Mucor hiemalis f. hiemalis			Norway	soil	JN206131
CBS 454.71	Mucor hiemalis f. hiemalis			n.a.	dung of rabbit	JN206126
CBS 528.78	Mucor hiemalis f. hiemalis			Netherlands	agaric	JN206144
CBS 980.68	Mucor hiemalis f. hiemalis			Netherlands	Coccinella	JN206129
CBS 255.36	Mucor inaequisporus		T	Ghana	Spondias mombin; fruit	JN206177	JN206502
CBS 351.50	Mucor inaequisporus			Indonesia	Musa sapientum; fruit	JN206178	JN206500
CBS 496.66	Mucor inaequisporus			Japan	Diospyros kaki; immature fruit	JN206179	JN206501
CBS 120.08	Mucor indicus			n.a.	n.a.	JN206182
CBS 120585	Mucor indicus			India	human; muscle	JN206180
CBS 123974	Mucor indicus			Germany	human; gastrointestinal infection	JN206181
CBS 226.29	Mucor indicus		ET (designated here)	Switzerland	n.a.	HM999956	HM849690
CBS 414.77	Mucor indicus	Ascidiophora sp.		India	dung of berber goat	JN206185
CBS 422.71	Mucor indicus			Indonesia	Dioscorea; tuber	JN206186
CBS 535.80	Mucor indicus			South Africa	sorghum malt	JN206184
CBS 671.79	Mucor indicus			Indonesia	n.a.	JN206183
CBS 100164	Mucor irregularis	M. hiemalis f. luteus		China	human; nasolabial infection	JN206153
CBS 103.93	Mucor irregularis	Rhizomucor variabilis	T of Rhizomucor variabilis	China	human; hand	JN206150	HM849684
CBS 609.78	Mucor irregularis	M. hiemalis f. hiemalis		Nigeria	garden soil	JN206152
CBS 654.78	Mucor irregularis	M. aff. variosporus		India	owl pellet	JN206151
CBS 700.71	Mucor irregularis	M. hiemalis f. luteus	T	India	soil	JN206154	JN206450
CBS 977.68	Mucor irregularis	M. hiemalis f. hiemalis		India	n.a.	JN206155 (c1)
						JN206156 (c2)
CBS 154.69	Mucor japonicus	Zygorhynchus japonicus	NT (designated here)	Russia	forest soil	JN206158	JN206446
CBS 638.74	Mucor lanceolatus	M. fuscus		France	cheese	JN206205	JN206443
CBS 143.85	Mucor laxorrhizus		NT	UK	lake mud	JN206209	JN206444
CBS 237.66	Mucor laxorrhizus			Ukraine	peat	JN206210
CBS 243.35	Mucor luteus	M. hiemalis f. luteus	T	Germany	n.a.	HM999954	HM849685
CBS 244.35	Mucor luteus	M. hiemalis f. luteus		Germany	n.a.	JN206148
CBS 301.74	Mucor luteus	M. hiemalis f. luteus		Germany	n.a.	JN206149
CBS 567.70A	Mucor luteus	M. hiemalis f. luteus		Japan	agaric	JN206147
CBS 215.27	Mucor megalocarpus	Zygorhynchus macrocarpus	ET (designated here)	France	n.a.	JN206160	JN206489
CBS 204.28	Mucor microsporus		T of M. cylindrosporus	France	n.a.	JN206272	JN206521
CBS 245.35	Mucor microsporus			Austria	soil	JN206273
CBS 586.67	Mucor minutus		T of M. griseoochraceus var. minuta	India	n.a.	JN206048	JN206463
CBS 216.27	Mucor moelleri	Zygorhynchus moelleri		France	n.a.	JN206116
CBS 380.29	Mucor moelleri	Zygorhynchus moelleri		Netherlands	wood mixed with soil	JN206119
CBS 406.58	Mucor moelleri	Zygorhynchus moelleri	NT (designated here)	USA	soil	JN206121
CBS 444.65	Mucor moelleri	Zygorhynchus moelleri	LT of M. saximontensis (designated here)	USA	soil	JN206114	HM849682
CBS 460.51	Mucor moelleri	Zygorhynchus moelleri		UK, England	culture contaminant	JN206120
CBS 501.66	Mucor moelleri	Zygorhynchus moelleri		Austria	soil	JN206118
IHEM 21156	Mucor moelleri	Zygorhynchus moelleri		France	human	JN206115
CBS 402.58	Mucor moelleri f. californiensis	Zygorhynchus californiensis	ET (designated here)	USA	soil	JN206117
CBS 531.77	Mucor mousanensis			India	dung of mouse	JN206016
CBS 721.76	Mucor mousanensis			Taiwan	dung of Rattus norvegensis	JN206018
CBS 999.70	Mucor mousanensis		T	India	dung of mouse	JN206017	JN206434
CBS 228.29	Mucor mucedo		T of M. murorum	Russia	n.a.	JN206088
CBS 296.35	Mucor mucedo			Germany	dung of rabbit	JN206090
CBS 525.68	Mucor mucedo			Armenia	dung of field-mouse	JN206087
CBS 542.66	Mucor mucedo			Ukraine	water	JN206086
CBS 640.67	Mucor mucedo		NT	Netherlands	cow; nose effluent	JN206085	HM849687
CBS 834.73	Mucor mucedo			n.a.	dung of dog	JN206093 (c1)
						JN206091 (c2)
CBS 836.73	Mucor mucedo	M. piriformis		Germany	wheat field soil	JN206092 (c1)
CBS 987.68	Mucor mucedo			Netherlands	dung of rabbit	JN206089	JN206480
CBS 110662	Mucor multiplex	Zygorhynchus multiplex	HT	China	paddy field soil	JN206166	JN206484
CBS 735.70	Mucor nederlandicus			n.a.	n.a.	JN206176	JN206503
CBS 120.71	Mucor odoratus			USA	n.a.	JN206195
CBS 130.41	Mucor odoratus		T	Denmark	laboratory air	JN206197	JN206495
CBS 179.76A	Mucor odoratus			Germany	dung of cow	JN206196
CBS 201.71	Mucor odoratus			Netherlands	dung of horse	JN206198
CBS 572.70	Mucor odoratus			Japan	soil	JN206194
CBS 417.77	Mucor parviseptatus	M. laxorrhizus var. ovalisporus	T	Australia	sandy heath soil	JN206108	JN206453
CBS 522.79	Mucor parviseptatus	M. laxorrhizus var. ovalisporus		Austria	soil	JN206109
CBS 111230	Mucor piriformis			n.a.	n.a.	JN206030 (c1)
CBS 169.25	Mucor piriformis		NT	n.a.	Pyrus communis; decaying fruit	JN206028	HM849681
CBS 175.27	Mucor piriformis			France	n.a.	JN206029
CBS 256.85	Mucor piriformis			USA	soil and decaying pear fruit	JN206031
CBS 527.68	Mucor piriformis			Romania	river water	JN206034	JN206476
CBS 528.68	Mucor piriformis			Russia	ant hill	JN206032
CBS 177.46	Mucor plasmaticus			UK, England	dung of rabbit	JN206076 (c1)
						JN206077 (c4)
CBS 275.49	Mucor plasmaticus			Netherlands	dung of mouse	JN206078 (c2)	JN206483
						JN206079 (c4)
CBS 402.73	Mucor plasmaticus			Russia	dung of forest-mouse	JN206081 (c1)
						JN206080 (c4)
CBS 226.32	Mucor plumbeus			Canada	forest soil	JN205916
CBS 284.78	Mucor plumbeus			Netherlands	lettuce	JN205914
CBS 295.63	Mucor plumbeus			Zaire	leaf litter	JN205912
CBS 312.78	Mucor plumbeus			Netherlands	horse meat	JN205915
CBS 630.74	Mucor plumbeus			France	cheese	JN205918
CBS 633.74	Mucor plumbeus			Switzerland	cat; subcutaneous tissue	JN205913
CBS 634.74	Mucor plumbeus			Germany	human; biopsy material	HM999955	HM849677
CBS 814.96	Mucor plumbeus			Sweden	wheat bran	JN205917
CBS 652.78	Mucor prayagensis	M. aff. variisporus		India	dung of shrew	JN206189 (c1)	JN206498
						JN206190 (c3)
CBS 816.70	Mucor prayagensis		T	India	n.a.	JN206188	JN206496
CBS 111557	Mucor racemosus f. racemosus	M. circinelloides f. circinelloides		China	sufu starter	JN205902
CBS 113.08	Mucor racemosus f. racemosus	M. racemosus f. sphaerosporus	IT of M. dimorphosporus	Switzerland	n.a.	JN205909
CBS 204.74	Mucor racemosus f. racemosus	M. sinensis	T of M. sinensis	China	soya cheese	JN205899
CBS 222.81	Mucor racemosus f. racemosus			Netherlands	Juglans regia; nut	JN205906
CBS 260.68	Mucor racemosus f. racemosus		NT (designated here)	Switzerland	n.a.	JN205898	HM849676
CBS 271.86	Mucor racemosus f. racemosus	M. racemosus f. sphaerosporus		Spain, Tenerife	dung	JN205900
CBS 369.71	Mucor racemosus f. racemosus			Finland	human; skin	JN205905
CBS 616.63	Mucor racemosus f. racemosus			n.a.	Agapornis; lung	JN205903
CBS 636.67	Mucor racemosus f. racemosus	M. racemosus f. chibinensis	NT (designated here) of M. racemosus f. chibinensis	Russia	grassland soil	JN205904
CBS 657.68	Mucor racemosus f. racemosus			Belgium	contaminated cheese	JN205901
CBS 660.66	Mucor racemosus f. racemosus	M. racemosus f. chibinensis		Ukraine	halva	JN205911
CBS 661.66	Mucor racemosus f. racemosus			Austria	soil	JN205908
CNM-CM2569	Mucor racemosus f. racemosus			Spain	human; nail	JN205929
CNM-CM3862	Mucor racemosus f. racemosus			Spain	human	JN205930
CBS 115.08	Mucor racemosus f. sphaerosporus		IT	Norway	n.a.	JN205919	JN206433
CBS 143.70	Mucor racemosus f. sphaerosporus			n.a.	storage rot of Cucurbita maxima	JN205925
CBS 238.35	Mucor racemosus f. sphaerosporus			Germany	wood	JN205920
CBS 347.87	Mucor racemosus f. sphaerosporus			USA	soil and litter	JN205924
CBS 538.78	Mucor racemosus f. sphaerosporus			Germany	sausage	JN205922
CBS 539.78	Mucor racemosus f. sphaerosporus			France	cheese	JN205923
CBS 571.70	Mucor racemosus f. sphaerosporus	M. plasmaticus		Japan	dung of horse	JN205926
CBS 574.70	Mucor racemosus f. sphaerosporus			Japan	steamed sweet potato	JN205921
CBS 634.78	Mucor racemosus f. sphaerosporus	M. racemosus f. racemosus		France	cheese	JN205927 (c2)
						JN205928 (c4)
CBS 135.65	Mucor ramosissimus		NT	Uruguay	human; nasal lesion	JN205932	HM849678
CBS 598.78	Mucor saturninus			Netherlands	fruit body of Hygrophoropsis aurantiaca	JN206074
CBS 599.78	Mucor saturninus			Netherlands	chicken leg	JN206073 (c3)
						JN206075 (c4)
CBS 974.68	Mucor saturninus		NT	Netherlands	soil	JN206072	JN206458
CBS 249.35	Mucor silvaticus	M. hiemalis f. silvaticus		Germany	soil of Picea forest	JN206122	JN206455
CBS 412.71	Mucor silvaticus	M. hiemalis f. silvaticus	NT (designated here)	Denmark	forest soil	JN206124
CBS 509.66	Mucor silvaticus	M. hiemalis f. silvaticus		Germany	forest soil	JN206123
CBS 122.23	Mucor sp.	M. plasmaticus		Germany	n.a.	JN206040	JN206479
CBS 125018	Mucor sp.			France	strawberries	JN206038 (c1)	JN206478
						JN206039 (c2)
CBS 334.71	Mucor sp.	M. hiemalis f. hiemalis		Benin	tropical vegetable	JN206248	JN206518
CBS 541.78	Mucor sp.	M. circinelloides f. griseocyanus		South Africa	Zea mays	JN206013	JN206431
CBS 608.78	Mucor sp.	M. circinelloides f. griseocyanus		USA	gymnosperm litter	JN205931	JN206432
CBS 837.73A	Mucor sp.	M. piriformis		Netherlands	Ribes rubrum	JN206033	JN206482
CBS 100.66	Mucor strictus		T of M. kanivcevii	Ukraine	grassland soil	JN206035	JN206477
CBS 368.71A	Mucor strictus			Norway	soil of dried up bog	JN206036
CBS 576.66	Mucor strictus		NT	Austria	soil at lake shore	JN206037
CBS 221.71	Mucor ucrainicus		T	Ukraine	dung of mouse	JN206191
CBS 674.88	Mucor ucrainicus			Germany	soil of litter layer	JN206192	JN206507
CBS 837.70	Mucor variisporus		T	India	n.a.	JN206175	JN206508
CBS 148.69	Mucor zonatus		T	Germany	soil	JN206104	JN206454
CBS 183.76	Mucor zonatus			Sweden	forest soil under Picea abies	JN206106 (c3)
						JN206107 (c4)
CBS 529.83	Mucor zonatus			Sweden	mould-infected Pinus wood	JN206105
CBS 416.67	Mucor zychae var. zychae		T	India	manured soil	JN206199
CBS 186.68	Mycotypha microspora			Germany	decaying wood	JN206215
CBS 230.32	Mycotypha microspora		T	Netherlands	Citrus aurantium; peel, contaminant	JN206217	JN206510
CBS 610.92	Mycotypha microspora			Germany	washroom in hospital	JN206216
CBS 109960	Mycotypha sp.	M. microspora		Thailand	human; pus of wound	JN206214	JN206511
CBS 412.66	Parasitella parasitica		T	USA	Paeonia	JN206027	JN206438
CBS 152.69	Parasitella sp.	P. parasitica		n.a.	n.a.	JN206024 (c1)	JN206437
						JN206025 (c3)
CBS 207.28	Parasitella sp.	P. parasitica		USA	n.a.	JN206026
CBS 113.76	Phascolomyces articulosus		T	Panama	dung of bat		JN206547
CBS 112.20	Phycomyces blakesleeanus	P. blakesleeanus var. piloboloides	T	Germany	n.a.	JN206303
CBS 188.27	Phycomyces blakesleeanus			USA	n.a.	JN206304
CBS 269.32	Phycomyces blakesleeanus	P. blakesleeanus var. piloboloides		Germany	n.a.	JN206309
CBS 270.32	Phycomyces blakesleeanus			Germany	n.a.	JN206305	HM849662
CBS 282.35	Phycomyces blakesleeanus			Netherlands	n.a.	JN206306
CBS 284.35	Phycomyces blakesleeanus			Germany	n.a.	JN206308
CBS 286.35	Phycomyces blakesleeanus	P. blakesleeanus var. piloboloides		Germany	n.a.	JN206307
CBS 131.23	Pilaira anomala			n.a.	n.a.	JN206097
CBS 396.71C	Pilaira anomala			UK, Scotland	dung of rabbit	JN206099
CBS 424.70	Pilaira anomala			UK	dung	JN206101
CBS 695.68	Pilaira anomala			Netherlands	dung	JN206098	JN206460
CBS 699.71	Pilaira anomala			Germany	dung of cow	JN206100
CBS 181.26	Pilaira moreaui			France	n.a.	JN206094	JN206459
CBS 411.67	Pilaira moreaui	Backusella lamprospora		India	n.a.	JN206095
CBS 496.71	Pilaira moreaui			Germany	dung of cow	JN206096
CBS 523.68	Pilaira moreaui var. caucasica	P. caucasica	T	Armenia	dung of mouse	JN206299	JN206532
CBS 302.83	Pilobolus umbonatus			Netherlands	dung of deer	JN206274	HM849665
CBS 425.50	Pilobolus umbonatus			Germany	n.a.	JN206275
CBS 962.68	Pirella circinans		T	India	soil	JN206102	JN206512
CBS 524.68	Pirella naumovi		T	Armenia	dung of mouse	JN206103	JN206474
CBS 588.88	Pirella sp.	P. circinans		USA	beneath Joshua trees	JN206071	JN206481
CBS 153.58	Poitrasia circinans		T	Trinidad and Tobago	soil	JN206239	JN206516
CBS 647.70	Poitrasia circinans			Sri Lanka	soil	JN206240
CBS 661.86	Protomycocladus faisalabadensis			India	dung of rodent		JN206558
CBS 205.77	Radiomyces embreei			USA	dung of lizard (?)	JN206291	HM849663
CBS 206.77	Radiomyces embreei			USA	dung of pack rat	JN206292
CBS 254.60	Radiomyces embreei		T	USA	dung of mouse		JN206538
CBS 255.60	Radiomyces spectabilis		T	USA	dung of lizard		JN206537
CBS 182.67	Rhizomucor miehei		T	USA	retting Parthenium argentatum	HM999959 (c1)	HM849717
						HM999960 (c2)
						HM999961 (c4)
CBS 209.77A	Rhizomucor miehei			USA	soil	JN206322 (c1)
						JN206321 (c2)
CBS 360.92	Rhizomucor miehei			Australia	human; kidney and liver (leukemic patient)	JN206318
CBS 429.70	Rhizomucor miehei			UK, England	Hordeum; stored grains	JN206319 (c1)
						JN206320 (c4)
CBS 179.69	Rhizomucor pusillus	R. tauricus	T of R. tauricus	Ukraine	forest soil	JN206310
CBS 219.31	Rhizomucor pusillus			n.a.	pig; kidney	JN206311
CBS 354.68	Rhizomucor pusillus		ET (designated here)	Netherlands	corn meal	JN206312	HM849716
CBS 425.78	Rhizomucor pusillus			USA	soil	HM999962
CNM-CM2752	Rhizomucor pusillus			Spain	human; sputum	JN206313
CNM-CM2935	Rhizomucor pusillus			n.a.	n.a.	JN206314
CNM-CM2974	Rhizomucor pusillus			Spain	human; peritoneal fluid	JN206315
CNM-CM4727	Rhizomucor pusillus			Spain	human; biopsy sample	JN206316
CNM-CM5124	Rhizomucor pusillus			Spain	human; lung, biopsy sample	JN206317
CBS 340.62	Rhizopus americanus	R. sexualis var. americanus	T	USA	air	HM999967 (c3)	HM849674
CBS 109939	Rhizopus arrhizus var. arrhizus	R. oryzae		Canada	human; dermal lesions of back	JN206330
CBS 110.17	Rhizopus arrhizus var. arrhizus	R. oryzae	T of R. maydis	Switzerland	n.a.	JN206327
CBS 112.07	Rhizopus arrhizus var. arrhizus	R. oryzae	T of R. oryzae	Netherlands	n.a.	JN206323	HM849659
CBS 118614	Rhizopus arrhizus var. arrhizus	R. oryzae		Turkey	human; palate	JN206326
CBS 125017	Rhizopus arrhizus var. arrhizus	R. oryzae		Greece	human; sinus (leukemic patient)	JN206332
CBS 146.90	Rhizopus arrhizus var. arrhizus	R. oryzae		Netherlands	human; palatum molle	JN206324
CBS 286.55	Rhizopus arrhizus var. arrhizus	R. oryzae		n.a.	rabbit brain	JN206328
CBS 330.53	Rhizopus arrhizus var. arrhizus	R. oryzae	T of R. boreas	Japan	n.a.	JN206331
CBS 438.76	Rhizopus arrhizus var. arrhizus	R. oryzae	NT of Amylomyces rouxii	Thailand	Look Pang (sweet fermented glutenous rice)	JN206329
CBS 515.94	Rhizopus arrhizus var. arrhizus	R. oryzae		Singapore	tempeh	JN206325
Chakrabarti710113	Rhizopus arrhizus var. arrhizus			India	human	JN206333
CBS 111231	Rhizopus arrhizus var. delemar	R. oryzae		n.a.	n.a.	JN206338
CBS 111760	Rhizopus arrhizus var. delemar	R. oryzae		Vietnam	starch-based rice wine starters	JN206334
CBS 120593	Rhizopus arrhizus var. delemar	R. oryzae		France	human; lung	JN206340
CBS 392.95	Rhizopus arrhizus var. delemar	R. oryzae	T of R. delemar var. multiplicisporus	n.a.	air	JN206336
CBS 402.51	Rhizopus arrhizus var. delemar	R. oryzae	T of R. javanicus var. kawasakiensis	Japan	n.a.	JN206339
CBS 544.80	Rhizopus arrhizus var. delemar	R. oryzae		South Africa	sorghum malt	JN206337
CBS 607.68	Rhizopus arrhizus var. delemar	R. oryzae		n.a.	spaghetti	JN206341
Chakrabarti710104	Rhizopus arrhizus var. delemar			India	human	JN206335
CBS 427.87	Rhizopus caespitosus		T	India	n.a.	HM999965	HM849671
CBS 111232	Rhizopus homothallicus			India	n.a.	JN206365	JN206404
CBS 336.62	Rhizopus homothallicus		T	Guatemala	tropical desert soil	HM999968	HM849670
CBS 117.43	Rhizopus lyococcus	R. stolonifer var. reflexus		Netherlands	Hordeum vulgare; grain	JN206375
CBS 320.35	Rhizopus lyococcus	R. stolonifer var. reflexus		n.a.	n.a.	JN206373	JN206534
CBS 398.95	Rhizopus lyococcus			n.a.	n.a.	JN206374
CBS 111563	Rhizopus microsporus			Vietnam	sufu starter: rice wine tablet	JN206363
CBS 357.93	Rhizopus microsporus var. azygosporus		T	Indonesia	tempeh	JN206343	HM849666
CBS 359.92	Rhizopus microsporus var. azygosporus			Australia	human; liver of premature infant, necrotising enterocolitis	JN206342
CBS 294.31	Rhizopus microsporus var. chinensis		T of R. bovinus	France	cow foetus	JN206351
CBS 344.29	Rhizopus microsporus var. chinensis		T of R. pypmaeus	Russia	n.a.	JN206360
CBS 388.34	Rhizopus microsporus var. chinensis		T of R. chinensis var. liquefaciens	Japan	n.a.	JN206354
CBS 394.34	Rhizopus microsporus var. chinensis		T of R. pseudochinensis var. thermosus	Japan	n.a.	JN206359
CBS 537.80	Rhizopus microsporus var. chinensis			South Africa	sorghum malt	JN206355
CBS 631.82	Rhizopus microsporus var. chinensis		T	China	bread	JN206344	HM849668
CBS 112285	Rhizopus microsporus var. microsporus			Mozambique	maize; ground nuts	JN206364	JN206403
CBS 308.87	Rhizopus microsporus var. microsporus			Australia	human; hand, necrotic tissue	JN206357
CBS 699.68	Rhizopus microsporus var. microsporus		NT	Ukraine	soil	HM999970	HM849669
CBS 112587	Rhizopus microsporus var. oligosporus			Indonesia	tempeh	JN206358
CBS 228.95	Rhizopus microsporus var. oligosporus			Indonesia	tempeh	JN206348
CBS 337.62	Rhizopus microsporus var. oligosporus		NT	Indonesia	probably from tempeh	JN206362
CBS 338.62	Rhizopus microsporus var. oligosporus			Indonesia	tempeh fermentation	JN206352
CBS 102277	Rhizopus microsporus var. rhizopodiformis			n.a.	human; rhinocerebral infection	JN206356
CBS 118987	Rhizopus microsporus var. rhizopodiformis			France	human; cutaneous lesion	JN206346
CBS 196.77	Rhizopus microsporus var. rhizopodiformis			USA	herbal tea from Borbonia cordata	JN206361
CBS 220.92	Rhizopus microsporus var. rhizopodiformis			Netherlands	human; lung	JN206347
CBS 258.79	Rhizopus microsporus var. rhizopodiformis			Sweden	dust in saw mill	JN206349
CBS 343.29	Rhizopus microsporus var. rhizopodiformis		T of R. pusillus	Russia	n.a.	JN206353
CBS 536.80	Rhizopus microsporus var. rhizopodiformis		NT	South Africa	sorghum malt	HM999971	JN206402
CBS 607.73	Rhizopus microsporus var. rhizopodiformis			former Yugoslavia	stored cereals	JN206345	HM849667
CBS 113206	Rhizopus microsporus var. tuberosus			China	koji in brewery	JN206350
CBS 138.95	Rhizopus schipperae		T	USA	human; bronchial wash of patient with myeloma	HM999969	HM849672
CBS 336.39	Rhizopus sexualis		T	UK	Fragaria; decaying fruit	HM999966	HM849673
CBS 126.83	Rhizopus sp.	R. stolonifer		n.a.	ragi	JN206368
CBS 442.74	Rhizopus sp.	R. stolonifer		Netherlands	coffee-ground	JN206367
CBS 926.87	Rhizopus sp.	R. stolonifer		Spain, Tenerife	Spartocytisus supranubius; stem	JN206366	JN206406
CBS 133.90	Saksenaea oblongispora	S. vasiformis		Brazil	rain forest soil	JN206282 (c1)	HM849694
						JN206283 (c3)
CBS 405.63	Spinellus fusiger			n.a.	n.a.	JN206298	HM849664
CBS 515.75	Spinellus fusiger			Netherlands	fruit bodies of Mycena galericulata	JN206297
CBS 633.80	Spinellus fusiger			Germany	fruit body of Mycena cf. leptocephala	JN206295
CBS 894.73	Spinellus fusiger			Switzerland	fruit body of Mycena pura	JN206296
CBS 195.77	Sporodiniella umbellata			Ecuador	Umbonia	JN206372	JN206405
CBS 122.12	Syncephalastrum monosporum	S. racemosum		Switzerland	n.a.	HM999977 (c1)	JN206575
						HM999976 (c2)
CBS 568.91	Syncephalastrum monosporum var.		T	China	soil	HM999975	HM849720
	cristatum
CBS 567.91	Syncephalastrum monosporum var.		T	China	soil	HM999974	HM849719
	monosporum
CBS 120811	Syncephalastrum racemosum			France	human; skin	HM999979 (c1)
						HM999980 (c4)
CBS 199.81	Syncephalastrum racemosum			Kuwait	tidal mud-flat soil	HM999972	HM849718
CBS 213.78	Syncephalastrum racemosum		T of S. verruculosum	India	air	HM999978	JN206578
CBS 302.65	Syncephalastrum racemosum			Brazil	soil	HM999981 (c2)	HM849721
						HM999984 (c4)
CBS 370.49	Syncephalastrum racemosum			Indonesia	air	HM999983
CBS 421.63	Syncephalastrum racemosum			Zaire	humose soil under Linum usitatissimum	HM999973	JN206576
CBS 440.59	Syncephalastrum racemosum			USA	soil	HM999982
CBS 441.59	Syncephalastrum racemosum			USA	dung of coyote	HM999985
CNM-CM2909	Syncephalastrum racemosum			Spain	environmental		JN206577
CBS 108947	Syzygites megalocarpus			Netherlands	Amanita rubescens; decaying fruit body	JN206371 (c1)
						JN206370 (c3)
CBS 372.39	Syzygites megalocarpus			n.a.	n.a.	JN206369 (c3)	JN206401
CBS 341.55	Thamnidium elegans			USA	n.a.	JN206060	JN206466
CBS 411.52	Thamnidium elegans			Poland	dung of bat	JN206058
CBS 641.69	Thamnidium elegans			USA	n.a.	JN206059
CBS 874.69	Thamnostylum lucknowense			USA	dung of pack rat	JN205837	JN206546
CBS 690.76	Thamnostylum nigricans		NT	Mexico	dung of lizard	JN205838	JN206541
CBS 170.57	Thamnostylum piriforme			USA	dung of rat	JN205835
CBS 182.28	Thamnostylum piriforme			USA	Bertholletia excelsa	JN205830	HM849724
CBS 233.28	Thamnostylum piriforme			USA	dung of rat	JN205832
CBS 316.66	Thamnostylum piriforme		T	France	n.a.	JN205836	JN206544
CBS 412.94	Thamnostylum piriforme			Cuba	dung of Capromys sp.	JN205834	JN206543
CBS 480.69	Thamnostylum piriforme			Canada	soil under Thuja occidentalis	JN205831
CBS 638.69	Thamnostylum piriforme			Brazil	dung of pig	JN205833
CBS 692.76	Thamnostylum repens		NT	USA	dung of mouse		JN206542
CBS 104.75	Thermomucor indicae seudaticae		T	India	municipal compost	JN206300	HM849661
CBS 446.78	Thermomucor indicae seudaticae			Nigeria	Zea mays	JN206302
CBS 447.78	Thermomucor indicae seudaticae			Germany	compost	JN206301
CBS 603.68	Umbelopsis angularis		HT	Netherlands	soil	JN206380	HM849710
CBS 212.72	Umbelopsis autotrophica			Sweden	forest soil		JN206561
CBS 110039	Umbelopsis dimorpha		HT	New Zealand	soil of basaltic parent material	JN206387	HM849709
CBS 117350	Umbelopsis dimorpha			USA	soil of native decidious forest	JN206388
CBS 385.85	Umbelopsis fusiformis		T	Australia	soil of forest of Eucalyptus regnans	JN206386	JN206560
CBS 919.85	Umbelopsis fusiformis			Australia	soil		JN206559
CBS 101745	Umbelopsis gibberispora			Japan	Pinus luchuensis; decaying needle		JN206565
CBS 109328	Umbelopsis gibberispora		T	Japan	Fagus crenata; leaf litter	JN206384	JN206564
CBS 100559	Umbelopsis isabellina			USA	soil	JN206396	JN206571
CBS 167.80	Umbelopsis isabellina			Colombia	fruit body of Panellus pusillus	JN206398
CBS 250.95	Umbelopsis isabellina			Netherlands	Varanus comodoensis; granulomatous ulcer	JN206399	JN206574
CBS 309.93	Umbelopsis isabellina			UK	soil	JN206397
CBS 560.63	Umbelopsis isabellina			Germany	soil of Larix forest	JN206400	JN206573
CBS 150.81	Umbelopsis nana		T of U. versiformis	USA	root	JN206389
CBS 309.52	Umbelopsis nana			Belgium	forest soil	JN206390
CBS 373.67	Umbelopsis nana			Georgia	forest soil	JN206394
CBS 444.68	Umbelopsis nana			USA	pine stump wood	JN206392
CBS 669.83	Umbelopsis nana			Canada	washed mycorrhizal root	JN206393
CBS 858.68	Umbelopsis nana		T of Mortierella alba	Poland	forest soil	JN206391
CBS 499.82	Umbelopsis ovata		IT	Australia	Isopogon ceratophyllus; rhizoplane	JN206395	JN206572
CBS 101226	Umbelopsis ramanniana			USA	soil, wood scraps and other debris	JN206383	JN206566
CBS 112976	Umbelopsis ramanniana			New Zealand	litter of ? Carex sp.	JN206382	JN206568
CBS 366.95	Umbelopsis ramanniana			China	forest soil	JN206385
CBS 913.85	Umbelopsis sp.	U. vinacea		Germany	Picea abies; root	JN206376	JN206562
CBS 914.85	Umbelopsis sp.	U. angularis		Germany	root	JN206377
CBS 559.86	Umbelopsis sp.	U. westeae		Australia	soil	JN206381	JN206563
CBS 868.85	Umbelopsis swartii		T	Australia	soil under Eucalyptus regnans	JN206378	JN206567
CBS 212.32	Umbelopsis vinacea		AUT	Australia	sandy loam		JN206570
CBS 236.82	Umbelopsis vinacea		T of U. multispora	Japan	Fragaria; root		JN206569
CBS 870.85	Umbelopsis westeae		T	Australia	soil of acid heathland	JN206379
CBS 329.73	Utharomyces epallocaulus			India	soil	JN206276	HM849660
CBS 342.73	Utharomyces epallocaulus			Mexico	dung of rat	JN206277
CBS 441.76	Zychaea mexicana		T	Mexico	dung of mouse	JN205845	JN206545

DNA extraction, PCR amplification, cloning and sequencing

Genomic DNA was extracted in most cases from 2d-old cultures grown on malt extract agar (MEA 5 %, Oxoid, Badhoevedorp, The Netherlands) following the protocol given by Möller et al. (1992) with diverse modifications described in detail by Alastruey-Izquierdo et al. (2010). The primer pair V9G (de Hoog & Gerrits van den Ende 1998) and LR3 (Vilgalys & Hester 1990) was used to amplify a DNA segment consisting of the complete ITS region and the D1/D2 region of the LSU. The PCR reaction mixture (25 μl) contained 0.4 μM of each primer, 0.185 mM of each deoxynucleoside triphosphate (GC Biotech, Alphen aan den Rijn, The Netherlands), 10× NH₄ BioTaq Reaction buffer (GC Biotech), 1.5 mM MgCl₂, 0.8 U BioTaq DNA polymerase (GC Biotech), and about 20 ng DNA. PCR reactions were conducted on a Thermal cycler 2720 (Applied Biosystems, Nieuwerkerk a/d IJssel, The Netherlands) as follows: one initial cycle at 94 °C for 5 min, followed by 35 cycles of 1 min at 94 °C, 1 min at 53 °C and 2 min at 72 °C, and one final cycle of 7 min at 72 °C. PCR products were analysed in 1 % agarose gels. Direct cycle-sequencing was performed for both strands of the PCR products using the Big dye sequencing kit (Applied Biosystems) and the primer set ITS1 and ITS4 (White et al. 1990) for the complete ITS region, and NL1 and LR3 for the D1/D2 region of the LSU (O’Donnell 1993). Cycle-sequencing products were analysed on an ABI 3730XL automatic sequencer (Applied Biosystems).

In cases where direct sequencing failed or double bands were detected in the agarose gels PCR products were ligated into pGEM-T Easy Vector (Promega, Leiden, The Netherlands) and cloned in E. coli JM109 competent cells (Promega) following the manufacturer’s instructions. Colony-PCRs were performed using the primer pair M13f (5’-GTAAAACGACGGCCAGT-3’) and M13r (5’-GGAAACAGCTATGACCATG-3’).

Sequence analyses

Consensus sequences were constructed by means of the SeqMan program v. 7.2.2 (DNASTAR, Lasergene) and deposited in GenBank. A total of 592 ITS sequences (GenBank accession numbers JN205809 to JN206400) and 210 LSU sequences (GenBank accession numbers JN206401 to JN206610) were newly generated for this study. Ninety-two ITS sequences and 113 LSU sequences of strains included in this study were published in previous papers (Alastruey-Izquierdo et al. 2010, Vitale et al. 2012).

The highly diverse ITS sequences were divided in subsets of alignable sequences for phylogenetic analyses. Additionally, a set of LSU sequences was generated representing every MOTU detected in the ITS alignments. The MOTUs were defined by a ≥ 99 % similarity threshold. Similarity values based on the uncorrected distances were calculated with BioNumerics (v. 0.4.61) software (Applied Maths, Sint-Martens-Latem, Belgium).

ITS and LSU sequences were aligned using the server version of the MAFFT program (www.ebi.ac.uk/Tools/mafft) and manually corrected using the program Se-Al v. 2.0a11 (Rambaut 2002; http://tree.bio.ed.ac.uk/software/seal/). All alignments are lodged in TreeBASE (www.treebase.org/). Mortierella parvispora, a member of the Mortierellales, was selected as outgroup of the LSU tree because the Mortierellales is the sibling order of the Mucorales (e.g. O’Donnell et al. 2001, Voigt & Wöstemeyer 2001). The ITS trees were rooted by the nearest neighbours of the respective group in the LSU tree. The maximum likelihood algorithm with the server version of RAxML-VI-HPC v. 7.0.0 (Stamatakis et al. 2008) as implemented on the Cipres portal was used to estimate phylogenetic relationships. The robustness of all phylogenetic trees was assessed by bootstrap analyses with 1 000 replicates. ITS trees were only calculated for Actinomucor, Mucor (4 trees), Rhizomucor and Rhizopus, but all of the taxa are included in the LSU tree.

Morphology

Strains with a position in the phylogenetic tree that was in conflict with their original classification were verified microscopically. These strains were cultivated on MEA at 24 °C. After 2 and 7 d colonies were observed using a stereomicroscope (SMZ 1500; Nikon) and slides for microscopic examination were made. Fungal material was mounted in lactic acid with cotton blue (2 mg cotton blue/mL lactic acid) and in lactic acid only and examined using a Nikon eclipse 80i microscope (Nikon, Amstelveen, The Netherlands). Measurements were performed using the software NIS-Elements D 3.0 (Nikon). For a few strains mounts from slide cultures were photographed using a Nikon 05SM digital camera.

RESULTS AND DISCUSSION

Performance of ITS and LSU sequencing

Direct sequencing was possible in 82 % of the strains for the ITS and in all strains for the LSU region. ITS sequences of strains that failed direct sequencing could be obtained by cloning in most taxa, while cloning did not solve the problem in the group of Rhizopus stolonifer; this was probably due to extended poly-A- and poly-T-regions. In the majority of cloned strains ITS copies differed only by a single basepair. However, in Syncephalastrum we found ITS sequences of two types forming two clades in the ITS tree (illustrated in Vitale et al. 2012). Divergent copies of ITS have been found in Fusarium (O’Donnell & Cigelnik 1997) and Laetiporus (Lindner & Banik 2011). The proportion of strains that had to be cloned was especially high in Absidia, Umbelopsis and Syncephalastrum.

Phylogenetic relationships inferred from LSU data

The family structure of the Mucorales revealed by the LSU cladogram in main traits corresponds with that given by Hoffmann et al. (2013), although the Lichtheimiaceae and the Mucoraceae do not form clades (Fig. 1), probably because our analysis is based on a single locus. Some remaining taxonomic inconsistencies between phenotypic and sequence-based classifications were found, particularly in the upper part of the LSU cladogram (Fig. 1). The Mycotyphaceae and the Choanephoraceae are nested within the Mucoraceae and these families together with the Backusellaceae, the Pilobolaceae and the Rhizopodaceae compose a well-supported clade (Mucorineae clade; bootstrap 75 %). The Mucorineae clade is dominated by the polyphyletic genus Mucor (Fig. 2a), which comprises many groups that are intermingled by other sporangia-forming genera such as Circinella p.p. (Fig. 2h), Parasitella, Pilaira, Pirella (Fig. 2f), Rhizomucor p.p. (Fig. 2b), and Zygorhynchus (Fig. 2d), sporangia- and sporangiola-forming genera such as Backusella (Fig. 8) and Thamnidium (Fig. 2i), as well as exclusively sporangiola-forming genera such as Chaetocladium, Ellisomyces (Fig. 2g), Helicostylum and Kirkomyces. Based on the LSU (Fig. 1) and ITS trees (Fig. 3 to 6), the genera Backusella, Circinella, Mucor, Rhizomucor and Zygorhynchus appear to be polyphyletic. The lower part of the LSU tree shows a more resolved taxonomy. The majority of genera here are clearly defined and appear to be monophyletic based on our sampling. Exceptions were the paraphyletic genus Absidia that includes Halteromyces and Chlamydoabsidia, and the polyphyletic genera Circinella and Rhizomucor that are addressed in more detail below.

Fig. 1.

RAxML phylogram of the Mucorales based on the D1/D2 region of the LSU. Each LSU sequence covers for a MOTU in ITS defined by a similarity threshold of 99 %. Branches with bootstrap values of 75 % or higher are printed in bold. Morphological groups according to sporangiophore branching and diameter of the sporangium: Mucor mucedo group, M. flavus group, M. hiemalis group, M. racemosus group, M. amphibiorum group, M. recurvus group. Black bar highlights the Mucor circinelloides complex. Ex-type strains are designated by: T = ex-type strain, ET = ex-epitype strain, HT = ex-holotype strain, IT = ex-isotype strain, LT = ex-lectotype strain, NT = ex-neotype strain, PT = ex-paratype strain, ST = ex-syntype strain, AUT = authentic material, c = clone, clinical strains are highlighted by red strain and GenBank accession numbers, strains representing MOTUs that comprise clinical strains are marked by red squares. Clinically relevant species are indicated by a red circle if no ITS sequence of a clinical isolate was available for the assignment to a MOTU. Potentially undescribed taxa are indicated by bold blue font.

Fig. 2.

Morphological diversity of Mucoraceae. a. CBS 243.35 Mucor luteus, sporangiophore and sporangium with collar, columella and sporangiospores; b. CBS 385.95 Rhizomucor endophyticus (recombined into Mucor endophyticus in this paper), sporangiophore with columella and collar; c. CBS 243.35 Mucor luteus, rhizoids formed on glass slides; d. CBS 110662 Zygorhynchus multiplex (recombined into Mucor multiplex in this paper), zygospore; e. CBS 385.95 Rhizomucor endophyticus (recombined into Mucor endophyticus in this paper), zygospore; f. CBS 588.88 Pirella circinans, lateral sporangium; g. CBS 243.57 Ellisomyces anomalus, multispored sporangiola; h. Circinella rigida (recombined into Mucor durus in this paper), circinate sporangiophore branch with apophysate sporangium; i. CBS 341.55 Thamnidium elegans, multispored sporangiola. — Scale bars = 10 μm, except c = 100 μm.

Fig. 8.

Morphology of the genus Backusella. a, b. CBS 128.70 Backusella circina, a. unispored sporangiola; b. transitorily recurved sporangiophore; c. CBS 318.52 Mucor recurvus var. recurvus (Backusella recurva here), transitorily recurved sporangiophore; d. CBS 564.66 Mucor variabilis (Backusella variabilis here), transitorily recurved sporangiophore. — Scale bar: a = 10 μm, b–d = 50 μm.

Fig. 3.

RAxML phylogram of the Mucor mucedo group, M. flavus group, M. hiemalis group and related taxa based on the ITS region. Branches with bootstrap values of 75 % or higher are printed in bold. Ex-type strains are designated by: T = ex-type strain, ET = ex-epitype strain, HT = ex-holotype strain, IT = ex-isotype strain, LT = ex-lectotype strain, NT = ex-neotype strain. Ex-type strains of currently accepted taxa are printed in bold. Clones are specified by a ‘c’ followed by the clone number. Clinical strains are highlighted by red strain and GenBank accession numbers, non-human hosts are given in brackets. Potentially undescribed taxa are indicated by bold blue font. Morphological identifications are given in quotation marks.

Although the polyphyly of Mucor is indisputable, only few clear lineages within Mucor are recognisable. Some of these lineages show a characteristic combination of sporangium size and the branching of the tall sporangiophores: in the Mucor mucedo group (Fig. 1), consisting, in addition to the name-giving species M. mucedo, of M. piriformis, M. plasmaticus and M. strictus, all form unbranched tall sporangiophores and large sporangia often exceeding 200 μm diam. The morphology of Mucor strictus is strongly temperature-dependent. The species develops the typical group morphology only at low temperatures (Schipper 1975: 24). The Mucor flavus group, comprising M. aligarensis, M. minutus and M. saturninus in addition to M. flavus consists of species developing sympodially branched tall sporangiophores and medium-sized sporangia that are over 80 μm but not exceeding 200 μm diam. A clade including M. hiemalis, M. irregularis, M. luteus, Rhizomucor endophyticus and Zygorhynchus psychrophilus, the Mucor hiemalis group, is characterised by poorly sympodially branched tall sporangiophores and small sporangia not exceeding 80 μm diam. The Mucor racemosus group contains M. circinelloides with the formae circinelloides, griseocyanus, lusitanicus and janssenii, Mucor bainieri, M. plumbeus, M. racemosus, M. ramosissimus and Backusella ctenidia. The characteristics of this group are repeatedly sympodially branched sporangiophores and small sporangia not exceeding 80 μm diam. Species of the Mucor amphibiorum group, namely M. amphibiorum, M. ardhlaengiktus, M. azygosporus, M. falcatus, M. inaequisporus, M. indicus, M. nederlandicus, M. odoratus, M. prayagensis, M. ucrainicus, M. variosporus and M. zychae form − with the exception of M. indicus and M. falcatus − usually unbranched tall sporangiophores that bear, unlike species of the M. mucedo group, small- to medium-sized sporangia (maximum diameter between 70 and 175 μm). The Mucor recurvus group comprises Mucor and Backusella species with transitorily recurved sporangiophores and is discussed below in more detail. All of these groups were recognised, to a large extent, by Schipper (1973, 1975, 1976, 1978a).

Phenotypic characters with restricted taxonomic relevance

Genera preferably are defined as monophyletic. This may be in conflict with phenotypic definitions when single characters are concerned. For example, sporangiola-forming taxa such as Backusella, Chaetocladium, Ellisomyces, Helicostylum, Kirkomyces and Thamnidium, appear sporadically among Mucor species (Fig. 1, 3, 5, 6) and only the clade consisting of the sporangiola-forming genera Benjaminiella and Cokeromyces (Fig. 1) possess phylogenetic support. Hence we consider the potential to develop sporangiola in addition to or instead of sporangia as a plesiomorphic character in the Mucoraceae that is genetically fixed but not revealed in all species. Consequently, the presence of sporangiola should not be used to define new genera, as was done recently in the newly described genus Isomucor (de Souza et al. 2012) with sporangiola as the only distinctive trait. A classical generic criterion is the presence or absence of rhizoids. Our finding of rhizoids in Mucor species (Fig. 2c), the genus originally separated from Rhizomucor by the absence of rhizoids, and the reclassification of Rhizomucor species such as R. regularior, R. variabilis (Álvarez et al. 2010a), R. chlamydosporus and R. endophyticus (this paper) into Mucor suggests that the potential to form rhizoids might be plesiomorphic in Mucorales as well. Homo- and heterothallic species cluster randomly in our trees demonstrating the reduced taxonomic value of this trait. Circinate sporangiophores branches (Fig. 2h), considered to be a characteristic of the genus Circinella, evolved at least three times.

Fig. 5.

RAxML phylogram of the Mucor racemosus group and related taxa based on the ITS region. Branches with bootstrap values of 75 % or higher are printed in bold. Ex-type strains are designated by: T = ex-type strain, ET = ex-epitype strain, IT = ex-isotype strain, NT = ex-neotype strain. Ex-type strains of currently accepted taxa are printed in bold. Clones are specified by a ‘c’ followed by the clone number. Clinical strains are highlighted by red strain and GenBank accession numbers, non-human hosts are given in brackets. Potentially undescribed taxa are indicated by bold blue font. Morphological identifications are given in quotation marks. Black bars indicate groups within Mucor circinelloides f. circinelloides including a large number of clinical strains.

Fig. 6.

RAxML phylogram of the Mucor amphibiorum group and related taxa based on the ITS region. Branches with bootstrap values of 75 % or higher are printed in bold. Ex-type strains are designated by: T = ex-type strain, ET = ex-epitype strain, HT = ex-holotype strain, IT = ex-isotype strain, LT = ex-lectotype strain, NT = ex-neotype strain, PT = ex-paratype strain. Ex-type strains of currently accepted taxa are printed in bold. Clones are specified by a ‘c’ followed by the clone number. Clinical strains are highlighted by red strain and GenBank accession numbers, non-human hosts are given in brackets. Potentially undescribed taxa are indicated by bold blue font. Morphological identifications are given in quotation marks.

Species identification by DNA barcoding

In our study the ITS region turned out to be an appropriate DNA barcoding marker in Mucorales because of its power to discriminate the currently accepted species, including predominantly morphologically defined species (morphospecies), and also all species in Mucor (Hermet et al. 2012), Lichtheimia (Alastruey-Izquierdo et al. 2010) and Rhizopus (Abe et al. 2007) recognized by GCPSR studies. The statement of Schwarz et al. (2006) that ITS is able to discriminate most but not all clinically relevant members of Mucorales was due to the fact that the authors treated R. azygosporus as a separate species, while now it is classified as a variety of R. microsporus (Zheng et al. 2007). Indeed the taxonomy of the Mucoraceae is unsatisfactory according to current molecular characteristics and consequently identification by DNA barcoding is reliable only for species that form clearly delimited clades in the ITS trees. In Rhizomucor (Fig. 11) and Rhizopus (Fig. 10), all species can be identified by their ITS sequence, and even two varieties of Rp. arrhizus proved to be distinguishable (see sections on Rhizomucor or Rhizopus, respectively). ITS data also separate a surprisingly high number of species of Mucor and its allies as monophyletic groups (Fig. 2–5), allowing reliable species identification despite unclear generic boundaries. Problematic for molecular identification are the species complexes of Mucor circinelloides, M. flavus, M. piriformis and Zygorhynchus moelleri. The complex of Mucor circinelloides constitutes a supported clade (bootstrap support 88 %) in the LSU phylogram (Fig. 1) and comprises all formae of M. circinelloides but also other species such as M. bainieri and M. ramosissimus, Ellisomyces anomalus and Backusella ctenidia that cannot be separated by ITS and LSU data from M. circinelloides (Fig. 5). All formae of M. circinelloides described by Schipper (1976) can be discriminated by their ITS sequences, but there are several strains in the complex with a M. circinelloides morphology that do not group in any of these formae (see sections Mucor and Backusella).

Fig. 11.

RAxML phylogram of the genus Rhizomucor based on the ITS region. Branches with bootstrap values of 75 % or higher are printed in bold. Ex-type strains are designated by: T = ex-type strain, LT = ex-lectotype strain, ET = ex-epitype strain. The identifying ex-type strain of a clade is printed in bold. Clones are specified by a ‘c’ followed by the clone number. Clinical strains are highlighted by red strain and GenBank accession numbers.

Fig. 10.

RAxML phylogram of the genus Rhizopus based on the ITS region. Branches with bootstrap values of 75 % or higher are printed in bold. Ex-type strains are designated by: T = ex-type strain, NT = ex-neotype strain. Ex-type strains of currently accepted taxa are printed in bold. Clones are specified by a ‘c’ followed by the clone number. Clinical strains are highlighted by red strain and GenBank accession numbers, non-human hosts are given in brackets. Potentially undescribed taxa are indicated by bold blue font. Morphological identifications are given in quotation marks.

Criteria for taxonomic changes based on ITS and LSU data

In general, multilocus studies are needed to establish boundaries between taxa forming sister clades in single-locus trees. However, in this stage of research we consider ITS and LSU data sufficient to justify taxonomic changes in the following cases: 1) synonymy if the ex-type strains have identical ITS sequences (in case the ITS sequences are identical but large morphological differences have been reported we maintain varieties or formae); 2) attribution of the species rank to varieties or formae if they appear distant to the type variety or forma in ITS and LSU trees; 3) reclassifications based on polyphyly shown by ITS and LSU data (e.g. Zygorhynchus); and 4) extension of a genus based on ITS and LSU analyses and morphological synapomorphies (e.g. Backusella).

Species concepts: conflicts between grouping in the ITS trees and mating results

The broad species concepts in Mucor maintained by Schipper (1973, 1975, 1976, 1978a), based on positive matings, are partly in conflict with the grouping in our ITS trees. Species in the sense of Schipper, e.g. Mucor circinelloides, M. hiemalis (including M. luteus) and M. flavus are not monophyletic. Their clades include other species or even other genera showing that the simple presence of zygospores is not a sufficient marker for conspecifity. However, a detailed study of their size, shape, colour and number may allow to differentiate between inter- and intraspecific zygospores, as shown for Mucor irregularis (Schell et al. 2011) and Lichtheimia (Alastruey-Izquierdo et al. 2010). Consequently, the study of zygospores should not be devaluated by our results but is ideally combined with multi-locus studies to recognize species.

Detection of undescribed species by DNA barcoding

Twelve MOTUs are revealed by ITS sequencing that deviate considerably from species included in this study and might represent undescribed taxa (indicated by bold blue font in all trees). The species to which they had previously been assigned, on the basis of morphological features, are given in quotation marks. In order to establish whether these MOTUs deserve species rank we have initiated multilocus-analyses and detailed morphological studies, which will be published in subsequent papers. Regardless of the question if these MOTUs represent undescribed species, our results suggest that the used phenotypic criteria for species recognition in the Mucorales underestimated existing diversity.

The ITS sequences of numerous strains of Absidia and Umbelopsis could not be obtained by direct sequencing and not all of them could be cloned. Our ITS dataset is therefore incomplete for these genera.

ITS barcoding detected cryptic species, but conversely revealed growth-reduced mutants of existing taxa that had been maintained incorrectly as separate species. Examples include Mucor sinensis, which is synonymised with M. racemosus f. racemosus below, alleged Mucor ramosissimus strains that proved to belong to M. circinelloides f. circinelloides or f. janssenii, and Rhizomucor tauricus which is a synonym of Rm. pusillus.

Intraspecific variability

Intraspecific variability differs widely among mucorealean species and genera. The following dissimilarity values were obtained for the ITS region of species represented by at least 5 strains: Backusella circina (0 %), Choanephora cucurbitarum (0.5 %), Circinella muscae (1.6 %), Cunninghamella bertholletiae (1.0 %), C. blakesleeana (0.9 %), C. echinulata (13.3 %), Gilbertella persicaria (1.2 %), Gongronella butleri (1.1 %), Lichtheimia corymbifera (2.0 %), L. hyalospora (6.3 %), L. ramosa (7.6 %), Mucor circinelloides (5.3 %), M. fuscus (0.2 %), M. hiemalis (4.1 %), M. indicus (0.9 %), M. irregularis (2.6 %), M. mucedo (3.5 %), M. odoratus (0.3 %), M. piriformis (0.6 %), M. plumbeus (0.2 %), M. racemosus (2.1 %), Phycomyces blakesleeanus (0 %), Pilaira anomala (0 %), Rhizomucor pusillus (0.2 %), Rhizopus arrhizus incl. var. delemar (1.2 %), R. lyococcus (0.7 %), R. microsporus (2.8 %), Thamnostylum piriforme (1.6 %), Umbelopsis nana (0 %) and Zygorhynchus moelleri (0 %). Complete identity might be the result of undersampling. High dissimilarity values of morphologically defined species such as Cunninghamella echinulata could be caused by the inclusion of more than one species. However, the taxonomically well-elaborated genus Lichtheimia also contains species with more than 5 % dissimilarity suggesting that intraspecific variability can be comparatively high in Mucorales.

In agreement with Nilsson et al. (2006) we did not find a unifying threshold for intraspecific variability, a result that should caution against formal ITS-based species delimitation. On the other hand, the ≥ 99 % identity threshold given by Balajee et al. (2009) for comparative ITS sequence identification using GenBank in Mucorales is not covering the intraspecific variability of several clinically important species. Our data suggest that a distinct identity threshold has to be defined for every species for a reliable ITS-based identification. GCPSR studies will be required beforehand to define species boundaries in species with conflicting morphological and ITS data especially in those that are part of a species complex.

Clinically relevant taxa

Clinical strains are highlighted by red strain numbers and GenBank accession numbers in all figures. Strains representing a clinically relevant MOTU are marked either by a red square (assignment to the respective MOTU by ITS comparison) or by a red circle (assignment to the respective MOTU by morphology) in the LSU tree (Fig. 1). The following genera contain species that are involved in human opportunistic infections: Actinomucor, Apophysomyces, Cokeromyces, Cunninghamella, Lichtheimia, Mucor, Rhizomucor, Rhizopus, Saksenaea, Syncephalastrum, and possibly Mycotypha, Thamnostylum (Xess et al. 2012) and Zygorhynchus, the latter genus being synonymised with Mucor below. The recently described clinically relevant species of Apophysomyces, viz. A. ossiformis and A. trapeziformis (Álvarez et al. 2010b) and of Saksenaea, viz. S. erythrospora as well as the pathogenic S. vasiformis (Álvarez et al. 2010a) were not included in our study.

No clinical strains of the following species were included in the present study, but clinical relevance of the species, resp. strains originating from clinical samples were reported by other authors: Cokeromyces recurvatus (e.g. Ryan et al. 2011), Cunninghamella blakesleeana (García Rodríguez et al. 2012), C. echinulata (Lemmert et al. 2002), Mucor ardhlaengiktus (as M. ellipsoideus), M. circinelloides f. lusitanicus (as M. lusitanicus) (Álvarez et al. 2011), Rhizopus homothallicus (Chakrabarti et al. 2010), Rhizopus stolonifer (de Hoog et al. 2000) and Thamnostylum lucknowense (Xess et al. 2012). A clinical strain treated as Mucor fragilis by Álvarez et al. (2011) is assigned to M. circinelloides below.

The involvement of Zygorhynchus moelleri and a possibly undescribed Mycotypha species in human mucormycoses has not been proven: strain IHEM 21156 of Zygorhynchus moelleri was isolated by J.P. Bouchara at the University Hospital Angers (France) in 2004 but the exact source is unknown, and Mycotypha strain CBS 109960 was isolated by N. Poonwan from pus of a wound in the RMSC Pitsunalok (Thailand) in 2002. There is also no case report on Mucor plumbeus but the source of isolation of strain CBS 634.74 (human biopsy material) and CBS 633.74 (subcutaneous tissue of a cat) suggest a pathogenic potential of this species. Mucor aligariensis was isolated in 1958 from human and M. saturninus in 1978 from chicken, but no proven case reports have been published. Based on their maximum growth temperatures (< 30 °C, Schipper 1978a) the involvement of these species in infections is questionable.

The clinical strain CNM-CM 5114 (JN205884) isolated in 2008 from a lung biopsy specimen in Barcelona (Spain) was diagnosed as Cunninghamella elegans by a 99.2 % similarity of the ITS region with the ex-neotype strain of this species CBS 160.28 (AF254928). This is the first time that the involvement of C. elegans in human infection has been documented molecularly.

The recent detection of species with clinical relevance, such as Cunninghamella echinulata (Lemmert et al. 2002), Lichtheimia ornata (Alastruey-Izquierdo et al. 2010), Mucor ardhlaengiktus (as M. ellipsoideus, Álvarez et al. 2011) or Rhizopus homothallicus (Chakrabarti et al. 2010) shows that basically all mucorealean taxa, including species regarded as strictly environmental, should be included in the database for molecular identification of clinical strains. Molecular identification by BLAST searches of GenBank may lead to wrong conclusions because of incomplete sampling, inconsistent nomenclature and a high percentage of misidentified taxa (Bridge et al. 2003, Nilsson et al. 2006, Bidartondo et al. 2008, Lian et al. 2011).

The following taxa have been reported from proven case studies (de Hoog et al. 2000, Gomes et al. 2011): Actinomucor elegans, Apophysomyces variabilis, A. trapeziformis (Weddle et al. 2012), Cokeromyces recurvatus, Cunninghamella bertholletiae, C. elegans, Lichtheimia corymbifera, L. ramosa, Mucor amphibiorum, M. ardhlaengiktus (Sugui et al. 2011), M. circinelloides (f. circinelloides, f. janssenii, f. lusitanicus), M. hiemalis, M. irregularis (syn. Rhizomucor variabilis), M. luteus (syn. M. hiemalis f. luteus), M. indicus, M. racemosus f. racemosus, M. ramosissimus, Rhizopus microsporus, Rp. arrhizus, Rp. homothallicus, Rp. schipperae, Rp. stolonifer, Rhizomucor miehei, Rm. pusillus, Saksenaea vasiformis, S. erythrospora (Hospenthal et al. 2011) and Syncephalastrum racemosum.

The forma circinelloides of Mucor circinelloides contains the highest number of clinical isolates in Mucor and forms a well-supported clade (bootstrap 95 %). Two groups within forma circinelloides (highlighted by black bars in Fig. 5) contain a large number of clinical strains, which might be explained to high frequency in the human environment, or to an increased virulence. Interestingly, the forma griseocyanus, being the only forma of Mucor circinelloides that is not able to grow at 37 °C, does not comprise any clinical isolate. In Mucor racemosus we found a similar picture: only the forma racemosus appears to be involved in human infections, while the forma sphaerosporus contains strains only isolated from food and environmental samples. The maximum growth temperature of forma sphaerosporus is distinctly lower (28 °C > T_max < 25 °C) than that of the clinically relevant forma racemosus (37 °C > T_max < 30 °C) (Schipper 1976).

Many thermotolerant or thermophilic species (Schipper 1973, 1975, 1976, 1978a, b, 1979, 1984, 1986, 1990, Schipper & Stalpers 1984, Schipper & Samson 1994, de Hoog et al. 2000, Zheng & Chen 2001, Hoffmann et al. 2007, Alastruey-Izquierdo et al. 2010, Álvarez et al. 2010a, b) in the Mucorales are opportunistic pathogens of vertebrates, but there is no direct correlation between thermotolerance and pathogenicity. Several taxa including species of Backusella, Cunninghamella and Mucor, as well as Protomycocladus faisalabadensis and Thermomucor indicae-seudaticae are thermotolerant or even thermophilic, but have never been reported to cause infections.

TAXONOMY

Mucor

Mucor mucedo group, M. flavus group, M. hiemalis group and related taxa

In our ITS tree (Fig. 3) Mucor flavus is divided in several small clades that are intermingled with M. aligarensis, Helicostylum pulchrum and Thamnidium elegans. Several ex-type strains of species that were synonymised by Schipper (1975) with M. flavus based on positive matings and morphological similarity are placed in other clades than the neotype strain CBS 234.35. Their correct taxonomic status needs to be assessed by more detailed studies.

Only two of the four formae established by Schipper (1973) for Mucor hiemalis, viz. f. hiemalis and f. corticola, constitute a clade in the ITS tree (Fig. 3). This clade is divided into two subclades both composed of strains morphologically assigned to f. hiemalis and f. corticola. However, the ex-type strains of both formae are located in the same subclade (Fig. 3). For that reason we consider the small differences in the shape of the spores between the formae as taxonomically insignificant. Strains of Mucor hiemalis f. silvaticus are not part of the well-supported Mucor hiemalis clade, not in the ITS (Fig. 3) nor in the LSU tree (Fig. 1). Therefore we treat this taxon as a discrete species. The same applies to Mucor hiemalis f. luteus that recently was reclassified as Mucor luteus (Budziszewska et al. 2010).

No authentic material is known to exist of Mucor abundans. The protologue (Povah 1917) describes M. abundans as a species with slightly branched sporangiophores, sporangia with a diameter below 100 μm, subglobose to pyriform columellae and small globose to short ellipsoidal sporangiospores. The strains CBS 388.35 (Fig. 4) and CBS 521.66, the latter deposited as M. abundans in the CBS collection, match these microscopic characters including the typical size and shape of the sporangiospores. They only differ by features that may have changed during prolonged cultivation such as the colour of the colony or the colour of the young sporangia that are hyaline with a slight yellow tinge in the studied strains instead of yellowish. Schipper (1973) noted the similarity of both strains with M. abundans but she considered them too similar to M. hiemalis f. corticola to recognise a separate species. Our ITS tree (Fig. 3) however, supports the separate position of these strains and therefore we here designate CBS 388.35 (preserved in a metabolically inactive state by lyophilization, batch nr. 472) as the neotype of Mucor abundans.

Fig. 4.

CBS 388.35 Mucor abundans. a, c. Sporangiophore with columella and collar; b. sporangiospores; d. chlamydospores. — Scale bars = 50 μm.

On MEA at room temperature strain CBS 388.35 shows the following features: colonies expanding, cottony, at first white later depending on the intensity of sporulation grey beige or pale grey; reverse uncoloured; sporangiophores slightly sympodially branched, up to 15 μm diam; sporangiophore branches straight; sporangia dark greyish, young hyaline or with a slight yellow tinge, small, up to 70 μm diam; columellae subglobose, ellipsoidal or slightly pyriform (as illustrated by Povah 1917) (Fig. 4a, c), up to 39 by 46 μm in size, often purplish grey; collars distinct; sporangiospores hyaline, smooth, subglobose (3.5–6 μm diam), short ellipsoidal to short cylindrical (4.5–7 by 3.5–5.5 μm) (Fig. 4b); chlamydospores globose, ellipsoidal or pyriform, intercalary, terminally and laterally formed mainly in the submerged mycelium (Fig. 4d); zygospores absent.

Mucor racemosus group and related taxa

Based on our analyses (Fig. 1, 5) Mucor circinelloides represents a species complex, which also includes other Mucor species and sporangiola-forming taxa. The backbone of the M. circinelloides part of the ITS tree is poorly resolved, hampering a decision on the rank of the taxa included. Based on positive matings, Schipper (1976) reduced four species related to Mucor circinelloides to formae, namely f. circinelloides, f. griseocyanus, f. janssenii and f. lusitanicus. Recently Álvarez et al. (2011) proposed species status for f. lusitanicus without considering the positive mating results obtained by Schipper (1976). Strains morphologically assigned to the various formae of M. circinelloides form well-supported clades in the ITS tree (Fig. 5), but several additional strains that morphologically belong to M. circinelloides are located outside these clades. The strains CBS 338.71 and CBS 635.65, for example, are placed basally to the forma lusitanicus clade in the ITS tree (Fig. 5) and develop predominantly globose columellae characteristic of forma lusitanicus, but occasionally they develop obovoid columellae typical of forma circinelloides. Schipper’s (1976) mating results, the presence of intermediate strains and the absence of compensatory base changes (CBC) between f. circinelloides, f. lusitanicus, and f. janssenii (Pawłowska et al. In press) lead us to regard M. circinelloides as a single species that consists of several still interbreeding lineages which result in a high intraspecific ITS variability of 5.3 %.

Some confusion exists because of misapplied names for important model strains. Strain CBS 416.77, deposited in the CBS collection by S. Bartnicki-García as Mucor rouxii, belongs to Mucor circinelloides according to its ITS sequence, a fact that has been noted by several authors (Abe et al. 2006, Schwarz et al. 2006, Liu et al. 2007). Ellis et al. (1976) proposed NRRL 5866 = CBS 438.76 as the neotype for Amylomyces rouxii (Calmette 1892) and found it to be conspecific with that of Rhizopus arrhizus. Wehmer (1900) incorrectly believed that the strains he isolated represented Calmette’s Amylomyces rouxii and proposed the name Mucor rouxii (Calmette) Wehmer for them. However, he probably studied strains of Mucor indicus (Schipper 1978a: 10). Consequently Mucor rouxii sensu Wehmer is a synonym of Mucor indicus, whereas Mucor rouxii (Calmette) Wehmer is Rhizopus arrhizus. Strains of M. indicus are very similar morphologically to Mucor circinelloides at some stages in the life cycle (Schipper 1978a: 10), but the molecular differences between the two species are unambiguous.

Mucor ramosissimus is another member of the Mucor circinelloides complex. Its ITS sequence clusters in the well-supported clade of Mucor circinelloides f. lusitanicus. However, the sequence differs considerably (19 out of 585 basepairs, 3.2 % dissimilarity) from the remaining sequences of M. circinelloides f. lusitanicus. This is expressed by a long branch in Fig. 5. We therefore retain the species rank for this taxon and await studies on other loci. Other strains that had been identified morphologically as M. ramosissimus are positioned distantly in different groups: CBS 144.93 clusters in the Mucor circinelloides f. janssenii clade and CBS 121702 in the M. circinelloides f. circinelloides clade. These strains differ by slow growth and possibly represent growth-reduced mutants of these formae.

CBS 236.35, the only strain listed as Mucor fragilis in the CBS database, is positioned basally in the Mucor circinelloides f. lusitanicus clade. As far as we are aware no type material exists for M. fragilis. Bainier’s (1884) original description assigns the fungus to the Mucor hiemalis group because the zygospores are black and bear characteristically roughened stellate spines. Schipper (1976) treated Mucor fragilis as a doubtful species because strain CBS 236.35, received as Mucor fragilis from Zycha in 1935, deviated from Bainier’s description. In agreement with Schipper (1976) we are not using this name and reidentify strain CBS 236.35 as Mucor circinelloides f. lusitanicus.

Mucor circinelloides f. janssenii splits in two groups in the ITS tree (Fig. 5): a first group containing the ex-type strain, and a second group consisting of CBS 144.93, CBS 204.68 and CBS 762.74 at 0.7 % distance. Considering the high degree of sequence diversity in Mucorales, expressed for example in an ITS sequence dissimilarity of 2.6 % between Mucor circinelloides f. janssenii and f. lusitanicus, these groups within jansenii are being treated as taxonomically insignificant. The ITS sequence of the ex-type strain of the recently described Mucor velutinosus (FN650646; Álvarez et al. 2011) is identical to that of CBS 762.74 of f. janssenii (data not shown). According to their ITS sequences (data not shown) isolates ATCC1209b (HM754254) and UIC-1 (HQ154609) of M. circinelloides forming an unknown group in the phylogenetic analyses of Li et al. (2011) also belong to f. janssenii but type material of this form was not included in the study of Li et al. (2011).

The ITS sequence deposited in GenBank (EF203698) for the newly described species Mucor renisporus (Jacobs & Botha 2008) is identical to that of CBS 480.70F (data not shown) of Mucor circinelloides f. circinelloides. However, according to the description given by Jacobs & Botha (2008) the taxa differ significantly in the sizes of sporangia, columellae and sporangiospores. A microscopical study of the ex-type strain of Mucor renisporus, and repeated ITS sequencing are necessary to verify conspecifity.

The morphological distinction of f. racemosus and f. sphaerosporus of M. racemosus is ambiguous while they can be clearly differentiated based on ITS data. Some strains of f. racemosus such as CBS 271.86 and CBS 113.08 produce a high proportion of spherical sporangiospores.

Mucor racemosus f. chibinensis is grouped with M. racemosus f. racemosus and represents a synonym of the latter. To our knowledge no type material is available for f. chibinensis. Schipper (1976) concluded that CBS 636.67 and CBS 660.66 strains matched the protologue of Mucor chibinensis (Neophytova 1955) and proposed the name Mucor racemosus f. chibinensis. Here we designate CBS 636.67 (preserved in a metabolically inactive state by lyophilization, batch nr. 768) as neotype of Mucor racemosus f. chibinensis because it matches the description of the basionym M. chibinensis and it is well described and illustrated (Schipper 1976); in addition the strain was isolated in Russia, corresponding which the geographic origin of the type.

Mucor sinensis is considered to be conspecific with M. racemosus f. racemosus because it groups with the ex-neotype CBS 260.68 of the latter in the ITS tree. It appears to represent a morphological variant or a growth-reduced mutant rather than a separate species.

Mucor amphibiorum group and related taxa

The ITS sequence of the ex-type strain of the recently described Mucor ellipsoideus (FN650647, Álvarez et al. 2011) is identical to that of CBS 210.80, the ex-type strain of Mucor ardhlaengiktus, except of an A missing at the 3’ terminus probably due to low sequence quality (data not shown). The characteristic azygospores described in M. ardhlaengiktus (Mehrotra & Mehrotra 1978) appear to be a variable feature that was absent from the strain studied by Álvarez et al. (2011) and from strain CBS 650.78. Mucor ardhlaengiktus is the older name (Mehrotra & Mehrotra 1978) and we therefore consider M. ellipsoideus as a synonym. The varieties of Mucor laxorrhizus, var. laxorrhizus and var. ovalisporus, appear distantly positioned in the ITS (Fig. 6) and LSU (Fig. 1) trees and as a result we recognize them as separate species.

Mucor ardhlaengiktus B.S. Mehrotra & B.M. Mehrotra, Sydowia 31: 94. 1979 [1978]. — MycoBank MB317921

= Mucor ellipsoideus E. Álvarez, Stchigel, Cano, D.A. Sutton & Guarro, in Álvarez et al., Med. Mycol. 49: 67. 2011.

Lectotype. Fig. 1 (Mehrotra & Mehrotra, Sydowia 31: 95. 1979 [1978]), designated here.

Epitype. CBS 210.80 (preserved in a metabolically inactive state by lyophilization, batch nr. 968), designated here.

Specimens examined. CBS 210.80, CBS 528.73, CBS 650.78.

Mucor circinelloides f. janssenii (Lendn.) Schipper, Stud. Mycol. 12: 13. 1976. — MycoBank MB348491

Basionym. Mucor janssenii Lendn. (as ‘janseni’), Bull. Herb. Boissier 2, Sér. 7: 251. 1908.

≡ Mucor griseocyanus Hagem f. janssenii (Lendn.) Schipper, Antonie van Leeuwenhoek 36: 486. 1970.

≡ Circinomucor janssenii (Lendn.) Arx, Sydowia 35: 18.1982.

= Mucor tenellus Y. Ling, Rev. Gén. Bot. 42: 736. 1930.

≡ Circinella tenella (Y. Ling) Zycha, Krypt.-Fl. Brandenburg (Leipzig) 6a: 99. 1935.

= Mucor stagnalis Novot., Notul. Syst. Inst. Cryptog. Horti Bot. Petropol. 6: 158. 1950.

= Mucor kurssanovii Milko & Beliakova, Mikrobiologija 36: 118. 1967.

= Mucor velutinosus E. Álvarez, Stchigel, Cano, D.A. Sutton & Guarro, in Álvarez et al., Med. Mycol. 49: 64. 2011.

Neotype. CBS 205.68 (preserved in a metabolically inactive state by lyophilization, batch nr. 605), designated here.

Specimens examined. CBS 144.93, CBS 185.68, CBS 204.68, CBS 205.68, CBS 206.68, CBS 227.29, CBS 232.29, CBS 243.67, CBS 365.70, CBS 762.74.

Notes — Schipper (1970) described Mucor griseocyanus f. janssenii based on strain CBS 205.68 because no authentic material of M. janssenii existed. However, she did not designate CBS 205.68 as the neotype though it was considered as such in the following years. Here we designate strain CBS 205.68 (in a lyophilized state) as neotype of M. janssenii because it fits the description of this species morphologically and it is well described (Schipper 1970).

Mucor parviseptatus G. Walther & de Hoog, nom. nov. — MycoBank MB800447

≡ Mucor laxorrhizus Y. Ling var. ovalisporus Schipper, Stud. Mycol. 31: 154. 1989, non Mucor ovalisporus (G. Sm.) Pidopl. & Milko, Atlas Mukor. Grib. (Kiev): 61. 1971.

Etymology. The epithet parviseptatus refers to the few septa that are formed unconnected with branching of the sporangiophores.

Specimens examined. CBS 417.77 ex-type strain of Mucor laxorrhizus var. ovalisporus, CBS 522.79.

Mucor racemosus Fresen. f. racemosus Beitr. Mykol. 1: 12. 1850. — MycoBank MB427116

≡ Circinomucor racemosus (Fresen.) Arx, Sydowia 35: 18. 1982.

= Mucor racemosus f. brunneus Morini, Malpighia 10: 88. 1896.

= Mucor dimorphosporus Lendn., Mat. Fl. Crypt. Suisse 3, 1: 93. 1908.

= Mucor christianensis Hagem, Ann. Mycol. 8: 268. 1910.

= Mucor racemosus var. christianensis (Hagem) Naumov, Opred. Mukor. (Mucorales): 46. 1935.

= Mucor varians Povah, Bull. Torrey Bot. Club 44: 297. 1917.

= Mucor pispekii Naumov, Encycl. Mycol. 9: 47. 1939.

= Mucor chibinensis Neophyt., Notul. Syst. Inst. Cryptog. Horti Bot. Petropol. 10: 160. 1955.

= Mucor racemosus f. chibinensis (Neophyt.) Schipper, Stud. Mycol. 12: 24. 1976.

= Mucor oudemansii VÁňová, Česka Mykol. 45: 25. 1991.

= Mucor sinensis Milko & Beliakova, in Pidopl. & Milko, Atlas Mukor. Grib. (Kiev): 53. 1971.

Neotype. CBS 260.68 (preserved in a metabolically inactive state by lyo-philization, batch nr. 87.1018), designated here.

Specimens examined. CBS 113.08 ex-lectotype strain of Mucor dimorphosporus (lectotype: Fig. 34 (Lendner, Mat. Fl. Crypt. Suisse 3, 1: 93. 1908), designated here; epitype: CBS 113.08, preserved in a metabolically inactive state by lyophilization, batch nr. 479, designated here), CBS 204.74 ex-type strain of Mucor sinensis, CBS 222.81, CBS 260.68, CBS 271.86, CBS 369.71, CBS 616.63, CBS 636.67 ex-neotype strain of Mucor racemosus f. chibinensis, CBS 657.68, CBS 660.66, CBS 661.66, CBS 111557, CNM-CM 2569, CNM-CM 3862.

Notes — Strain CBS 260.68 was used by Schipper (1970) for the description of Mucor racemosus f. racemosus but not designated as neotype. Here we designate strain CBS 260.68 (in a lyophilized state) as neotype of this species because it is well characterized (Schipper 1970) and because its morphology fully complies with the original description.

Mucor silvaticus Hagem, Skr. Vidensk.-Selsk. Christiana, Math.-Naturvidensk. Kl. 7: 31. 1908. — MycoBank MB182519

≡ Mucor hiemalis f. silvaticus (Hagem) Schipper, Stud. Mycol. 4: 31. 1973.

Neotype. CBS 412.71 (preserved in a metabolically inactive state by lyophilization, batch nr. 853), designated here.

Specimens examined. CBS 249.35, CBS 412.71, CBS 509.66.

Notes — To our knowledge, authentic material of this species has been lost. Schipper (1973) studied five strains that matched the description of Hagem (CBS 249.35, CBS 250.35, CBS 508.66, CBS 509.66 and CBS 412.71). Schipper’s description and drawings are based on CBS 412.71. It was isolated in Denmark, while the remaining strains originated in Germany. Here we designate CBS 412.71 as the neotype of Mucor silvaticus, because it was well described and illustrated as M. hiemalis f. silvaticus in Schipper (1973). Compared to the strains available in international fungal culture collections, it was isolated closest to the locality of the type, Norway.

Mucor recurvus group and Backusella

The LSU phylogram (Fig. 1) resolved a clade (Mucor recurvus group) consisting of Mucor grandis, M. oblongiellipticus, M. oblongisporus, M. recurvus, M. tuberculisporus, M. variabilis, two potentially undescribed species as well as Backusella circina and B. lamprospora that exclusively unifies taxa with transitorily recurved sporangiophores (Fig. 8). In this clade the sporangiophores are curved during maturation of the sporangium and become upright afterwards. Schipper (1978a) recognised the Mucor portion of this group on morphological grounds. The type species of Backusella, B. circina (Ellis & Hesseltine 1969: 865) (Fig. 8a, b), as well as B. lamprospora (Benny & Benjamin 1975: 320) also have been described to form transitorily recurved sporangiophores.

The genus Backusella differs from Mucor only by the formation of sporangiola in addition to sporangia. However, sporangiola, though in low frequency, have also been described in Mucor recurvus var. indicus and in M. tuberculisporus (Schipper 1978a). In our opinion the clade in the LSU phylogram including Mucor and Backusella species represents a natural group characterised by transitorily recurved sporangiophores. Consequently, we transfer all Mucor species belonging to that clade to the genus Backusella. The two varieties of Mucor recurvus (var. recurvus and var. indicus) are located in different supported subclades of our ITS tree (Fig. 7) and likely represent separate species.

Fig. 7.

RAxML phylogram of the Mucor recurvus group and Backusella based on the ITS region. Branches with bootstrap values of 75 % or higher are printed in bold. Ex-type strains are designated by: T = ex-type strain, ET = ex-epitype strain, LT = ex-lectotype strain, PT = ex-paratype strain. Ex-type strains of currently accepted taxa are printed in bold. Clones are specified by a ‘c’ followed by the clone number. Potentially undescribed taxa are indicated by bold blue font. Morphological identifications are given in quotation marks.

Sequence diversity is high in the emended genus Backusella. ITS sequences of M. oblongisporus CBS 569.70, M. oblongiellipticus CBS 568.70, and a contaminant strain of CBS 523.68 deviate significantly from the remaining members of the group and cannot be aligned with confidence. However, their LSU sequences and the formation of transitorily recurved sporangiophores clearly assign these taxa to the emended genus Backusella.

Backusella ctenidia is positioned inside the Mucor circinelloides complex (Fig. 1, 5) and does not belong in Backusella. For that reason we propose transferring it to Mucor.

We propose the following emendation for Backusella:

Backusella Ellis & Hesseltine emend. Walther et al.

Type species. Backusella circina J.J. Ellis & Hesselt.

Sporophores arising directly from the substrate mycelium, simple or sympodially branched, recurved when young, erect at maturity (transitorily recurved), smooth or roughened, producing terminal sporangia and in some species few to many lateral, pedicellate sporangiola. Terminal sporangia columellate, multispored, globose to subglobose, size ranging from 90 to 375 μm diam, nonapophysate, wall encrusted, deliquescent; columellae subglobose, ellipsoidal, slightly pyriform or conical, smooth. Collars small or consisting of needle-shaped spines. Sporangiolar pedicels straight, curved, or recurved, simple or branched, smooth or encrusted. Sporangiola columellate, multi- or unispored; wall verrucose or spinulose or both, persistent. Sporangiospores of sporangia and multispored sporangia identical, large, subglobose, ellipsoidal or irregularly polyhedral, smooth. Columellae, hyphae and sporangiospores in some species with yellowish or brownish content. Zygospores globose to subglobose; wall dark, opaque or translucent, ornamented with conical or rounded projections; suspensors opposed, smooth or roughened, equal or unequal.

Notes — The emended genus Backusella includes the following species: Backusella circina, B. grandis, B. indica, B. lamprospora, B. oblongielliptica, B. oblongispora, B. recurva, B. tuberculispora and B. variabilis.

Backusella grandis (Schipper & Samson) G. Walther & de Hoog, comb. nov. — MycoBank MB800453

Basionym. Mucor grandis Schipper & Samson, Mycotaxon 50: 479. 1994.

Specimen examined. CBS 186.87 ex-type strain of Mucor grandis.

Notes — The ITS sequence of Mucor grandis differs by only 6 basepairs from that of M. variabilis, while different clones of M. variabilis vary at four positions. The small sequence differences suggest conspecifity but the diameter of the sporangia varies significantly between the species. More detailed taxonomic studies are needed to clarify species limits.

Backusella indica (Baijal & B.S. Mehrotra) G. Walther & de Hoog, comb. nov. — MycoBank MB800449

Basionym. Mucor recurvus var. indicus Baijal & B.S. Mehrotra, Sydowia 19: 207. 1965.

Lectotype. CBS 786.70 (preserved in a metabolically inactive state by lyophilization, batch nr. 344), designated here.

Specimen examined. CBS 786.70.

Backusella oblongielliptica (H. Nagan., Hirahara & Seshita ex Pidopl. & Milko) G. Walther & de Hoog, comb. nov. — MycoBank MB800451

Basionym. Mucor oblongiellipticus H. Nagan., Hirahara & Seshita, Essays Stud. Fac. Hiroshima Jogakuin College 18: 167. 1969, nom. inval., Art. 36.1

≡ Mucor oblongiellipticus H. Nagan., Hirahara & Seshita ex Pidopl. & Milko, Atlas Mukor. Grib. (Kiev): 81. 1971.

Lectotype. CBS 568.70 (preserved in a metabolically inactive state by lyophilization, batch nr. 113), designated here.

Specimen examined. CBS 568.70.

Backusella oblongispora (Naumov) G. Walther & de Hoog, comb. nov. — MycoBank MB800452

Basionym. Mucor oblongisporus Naumov, Mater. Mykol. Fitopatol. Rossii 1(4): 12. 1915.

Neotype. CBS 569.70 (preserved in a metabolically inactive state by lyophilization, batch nr. 55), designated here.

Specimen examined. CBS 569.70.

Backusella recurva (E.E. Butler) G. Walther & de Hoog, comb. nov. — MycoBank MB800448; Fig. 8c

Basionym. Mucor recurvus E.E. Butler, Mycologia 44: 561. 1952.

Lectotype. Fig. 1 (Butler, Mycologia 44: 562. 1952).

Epitype. CBS 318.52 (preserved in a metabolically inactive state by lyophilization, batch nr. 717), designated here.

Specimens examined. CBS 196.71, CBS 317.52, CBS 318.52, CBS 673.75.

Backusella tuberculispora (Schipper) G. Walther & de Hoog, comb. nov. — MycoBank MB800450

Basionym. Mucor tuberculisporus Schipper, Stud. Mycol. 17: 23. 1978.

Lectotype. CBS 562.66 (preserved in a metabolically inactive state by lyophilization, batch nr. 88.1007), designated here.

Specimens examined. CBS 562.66, CBS 570.70.

Backusella variabilis (A.K. Sarbhoy) G. Walther & de Hoog, comb. nov. — MycoBank MB800454; Fig. 8d

Basionym. Mucor variabilis A.K. Sarbhoy, Trans. Brit. Mycol. Soc. 48: 559. 1965.

Lectotype. CBS 564.66 (preserved in a metabolically inactive state by lyophilization, batch nr. 22), designated here.

Specimen examined. CBS 564.66.

Mucor ctenidius (Durrell & M. Fleming) G. Walther & de Hoog, comb. nov. — MycoBank MB800455

Basionym. Thamnidium ctenidium Durrell & M. Fleming, Mycologia 58: 797. 1966.

≡ Backusella ctenidia (Durrell & M. Fleming) Pidopl. & Milko, Atlas Mukor. Grib. (Kiev): 85. 1971, ex Benny & R.K. Benj., Aliso 8: 325. 1975.

Specimens examined. CBS 293.66 ex-isotype strain of Thamnidium ctenidium, CBS 433.87, CBS 696.76.

Pilaira

Recently, Zheng & Liu (2009a) studied the genus Pilaira morphologically and reclassified P. caucasica as a variety of P. moreaui. The variety differed from var. moreaui in the size of sporangiophores and sporangiospores (Zheng & Liu 2009a). We found identical ITS sequences for both varieties supporting conspecifity (Fig. 3). We retain both varieties despite of identical ITS sequences because of the clear morphological distinction.

Zygorhynchus

Phenotypically Zygorhynchus and Mucor differ in the following features. First, species of Zygorhynchus are exclusively homothallic, while the majority of Mucor species is heterothallic (Watanabe 1994). Second, the suspensors of the zygospores are unequal in Zygorhynchus and equal in Mucor. Third, the two suspensors originate from the same hypha in Zygorhynchus, the ‘Zygorhynchus pattern’, while they arise from different hyphae in Mucor, the ‘Mucor pattern’ (Hesseltine et al. 1959, Schipper 1986). However, these differences are gradual (Schipper 1986). Zygorhynchus exponens may develop equal but Mucor plumbeus more or less unequal suspensors (Schipper 1986). In Zygorhynchus exponens (Hesseltine et al. 1959), Z. japonicus (Schipper 1986) and Z. moelleri (Green 1927) zygospores are also produced between different hyphae.

Based on our LSU (Fig. 1) and ITS (Fig. 3, 6) data, Zygorhynchus is polyphyletic. Our analyses indicate that unequal suspensors and the Zygorhynchus pattern of zygospore production do not represent synapomorphies in the genus Zygorhynchus, but appear to be convergent characters within Mucor. Therefore we recombine all Zygorhynchus species in Mucor.

The ex-type strains of Zygorhynchus moelleri and Z. californiensis have identical ITS sequences suggesting conspecifity. However, Z. californiensis has regularly globose spores, while the spores of Z. moelleri are oblong to ovoidal in shape, 2.0–3.3 × 3.0–6.5 μm (Hesseltine et al. 1959). For that reason we propose reclassifying Z. californiensis as a forma of Z. moelleri.

The two varieties described in Zygorhynchus exponens, var. exponens and var. smithii differ by only a single basepair in their ITS sequences. Also small morphological differences such as the lighter and browner sporangia and columellae in var. smithii, do not justify the maintenance of a separate variety and consequently we consider both varieties as synonymous.

Mucor exponens (Burgeff) G. Walther & de Hoog, comb. nov. — MycoBank MB800461

Basionym. Zygorhynchus exponens Burgeff, Bot. Abh. 4: 34. 1924.

= Zygorhynchus exponens Burgeff var. smithii Hesselt., C.R. Benj. & B.S. Mehrotra, Mycologia 51: 179. 1959.

Neotype. CBS 141.20 (preserved in a metabolically inactive state by lyophilization, batch nr. 563), designated here.

Specimens examined. CBS 141.20, CBS 404.58 ex-lectotype strain of Zygorhynchus exponens var. smithii (lectotype: CBS 404.58, preserved in a metabolically inactive state by lyophilization, batch nr. 40, designated here), CBS 508.48.

Mucor fusiformis G. Walther & de Hoog, nom. nov. — MycoBank MB800459

≡ Zygorhynchus psychrophilus Schipper & Hintikka, Antonie van Leeuwenhoek 35: 29. 1969, non Mucor psychrophilus Milko, in Pidopl. & Milko, Atlas Mukor. Grib. (Kiev): 73. 1971.

Etymology. The epithet refers to the shape of the sporangiospores.

Specimens examined. CBS 336.68 ex-type strain of Zygorhynchus psychrophilus.

Mucor heterogamus Vuill., Bull. Séanc. Soc. Sci. Nancy 8: 50. 1887. — MycoBank MB249261

≡ Zygorhynchus heterogamus (Vuill.) Vuill., Bull. Trimestriel. Soc. Mycol. France 19: 117. 1903.

Lectotype. Pl. II, f. 27-48 (Vuill., Bull. Séanc. Soc. Sci. Nancy 8. 1887), designated here.

Epitype. CBS 405.58 (preserved in a metabolically inactive state by lyophilization, batch nr. 658), designated here.

Specimens examined. CBS 252.85, CBS 338.74, CBS 405.58, CBS 580.83, CBS 594.83.

Notes — The original material of this species consists of slides labelled as “Mucor heterogamus P.V. Zygospores Mis de pain 17-3-86” (Hesseltine et al. 1959). Hesseltine et al. (1959) studied five strains: NRRL 1489, NRRL 1490, NRRL 1491, NRRL 1616 (= CBS 405.58) and a fresh isolate without an NRRL number designated as ‘No. 1957’ and compared these strains with the original material. The authors found remarkable intraspecific variation in colony appearance, but micromorphologically Vuillemin’s material was almost identical with their living cultures except for some differences in lengths of the zygospore projections. Therefore they considered the type material and their strains as conspecific. Here we designate CBS 405.58 (NRRL 1616, preserved in a lyophilized state) verified by Hesseltine et al. (1959) as epitype of Mucor heterogamus.

Isolates of M. heterogamus vary considerably in their ITS sequences (maximum dissimilarity of 10 %) and might represent a complex of several species. Isolates that were morphologically assigned to M. heterogamus form a well-supported group with Z. multiplex and Z. macrocarpus, but at distances to the designated ex-epitype strain of 10.8 % and 7.7 %, respectively. The precise definition of species boundaries awaits detailed multilocus DNA sequence-based analyses.

Mucor japonicus (Komin.) G. Walther & de Hoog, comb. nov. — MycoBank MB800458

Basionym. Zygorhynchus japonicus Komin., Mykol. Zentbl. 5: 3. 1915 (1914).

Neotype. CBS 154.69 (preserved in a metabolically inactive state by lyophilization, batch nr. 409), designated here.

Specimen examined. CBS 154.69.

Notes — The authentic strain of Zygorhynchus japonicus studied by Kominami (1915) has been lost (Schipper 1986). Strain CBS 154.69 (preserved in a lyophilized state) is selected as neotype of Z. japonicus because it resembles the original strain and it is well described and illustrated (Schipper 1986).

Mucor megalocarpus G. Walther & de Hoog, nom. nov. — MycoBank MB800456

≡ Zygorhynchus macrocarpus Y. Ling, Rev. Gén. Bot. 42: 150. 1930, non Mucor macrocarpus Corda, Icon. Fungorum 2: 21. 1838.

Lectotype. Fig. 1 (Ling, Rev. Gén. Bot. 42: 152. 1930), designated here.

Epitype. CBS 215.27 (preserved in a metabolically inactive state by lyophilization, batch nr. 748), designated here.

Specimen examined. CBS 215.27.

Mucor moelleri (Vuill.) Lendn. f. moelleri, Mat. Fl. Crypt. Suisse 3, 1: 72. 1908.

Basionym. Zygorhynchus moelleri Vuill., Bull. Trimestriel Soc. Mycol. France 19: 117. 1903.

= Zygorhynchus vuilleminii Namysl., Ann. Mycol. 8: 154. 1910.

= Zygorhynchus vuilleminii race agamus Namysl., Bull. Int. Acad. Sci. Cracovie, Cl. Sci. Math., Ser. B, Sci. Nat. 6: 479. 1911.

= Zygorhynchus dangeardii Moreau, Bull. Soc. Bot. France 59: 717. 1912.

= Mucor saximontensis Rall, Mycologia 57: 874. 1965.

Neotype. CBS 406.58 (preserved in a metabolically inactive state by lyophilization, batch nr. 656), designated here.

Specimens examined. CBS 216.27, CBS 380.29, CBS 406.58, CBS 444.65 ex-lectotype strain of Mucor saximontensis (lectotype: CBS 444.65, preserved in a metabolically inactive state by lyophilization, batch nr. 803, designated here), CBS 460.51, CBS 501.66, IHEM 21156.

Notes — No authentic material of this species is known to be preserved. Hesseltine et al. (1959) reported NRRL 2660 (= CBS 406.58) as the type of Z. moelleri but the strain studied by Vuillemin was isolated in Eberswalde (Germany) while NRRL 2660 originated from soil in Wisconsin (USA).

Mucor moelleri f. californiensis (Hesselt., C.R. Benj. & B.S. Mehrotra) G. Walther & de Hoog, comb. nov. — MycoBank MB800460

Basionym. Zygorhynchus californiensis Hesselt., C.R. Benj. & B.S. Mehrotra, Mycologia 51: 185. 1959.

Lectotype. Fig. 8–10 (Hesseltine, Benjamin & Mehrotra, Mycologia 51: 176. 1959), designated here.

Epitype. CBS 402.58 (preserved in a metabolically inactive state by lyophilization, batch nr. 90.0055), designated here.

Specimen examined. CBS 402.58.

Mucor multiplex (R.Y. Zheng) G. Walther & de Hoog, comb. nov. — MycoBank MB800457

Basionym. Zygorhynchus multiplex R.Y. Zheng, Mycotaxon 84: 370. 2002.

Specimen examined. CBS 110662 ex-type strain of Zygorhynchus multiplex.

Actinomucor

Currently there are three varieties in Actinomucor: A. elegans var. elegans, var. meitauzae (syn. A. taiwanensis, Zheng & Liu 2005) and var. kuwaitiensis (Khan et al. 2008). Characters distinguishing the varieties are shape, size and ornamentation of the sporangiospores (Zheng & Liu 2005, Khan et al. 2008). The var. meitauzae and var. kuwaitiensis show reduced growth on Czapek’s agar. In contrast to earlier reports (Jong & Yuan 1985), the maximum growth temperature does not discriminate the varieties (Zheng & Liu 2005, Khan et al. 2008). However, the relationships deduced from our ITS data (Fig. 9) contradict current taxonomic concepts. Strains with the characteristics of var. meitauzae are scattered over nearly all parts of the tree, and only a part of the strains belonging to var. elegans is included in a well-supported clade around the ex-type strain of var. elegans. A detailed taxonomic revision is required.

Fig. 9.

RAxML phylogram of the genus Actinomucor based on the ITS region. Branches with bootstrap values of 75 % or higher are printed in bold. Ex-type strains are designated by: T = ex-type strain, NT = ex-neotype strain. Ex-type strains are printed in bold. Clinical strains are highlighted by red strain and GenBank accession numbers.

Rhizopus

Based on our phylogenetic trees the genus Rhizopus is para-phyletic because Sporodiniella umbellata and Syzygites megalocarpus cluster among Rhizopus species. All currently accepted Rhizopus species are well recognizable in the ITS tree. However, three strains of Rhizopus stolonifer, CBS 126.83, CBS 442.74 and CBS 926.87, exhibit widely deviating ITS sequences, forming a separate group that may represent a new species. In agreement with our results, Vágvölgyi et al. (2004) found strains morphologically assigned to R. stolonifer with strongly deviating randomly amplified polymorphic DNA (RAPD) patterns and consequently the authors suspected an undescribed variety or even species. The varieties arrhizus and delemar of Rhizopus arrhizus are also recognized in the ITS tree, in accordance with Abe et al. (2007) and Gryganskyi (2010) who treated them as separate species. Strains identified morphologically as R. arrhizus var. tonkinensis by Zheng et al. (2007) do not form a separate cluster but are distributed in var. arrhizus and var. delemar clades. However, by using short tandem repeat motives of IGS rDNA sequences Liu et al. (2008) were able to characterize all three varieties of R. arrhizus.

The morphological varieties described in Rhizopus microsporus are not supported genetically; a single, supported clade includes strains representing the varieties microsporus, chinensis and oligosporus. ITS sequences of the remaining R. microsporus strains that had been assigned morphologically to the varieties azygosporus, chinensis, oligosporus, rhizopodiformis and tuberosus are all identical. The ITS identities imply in agreement with Liu et al. (2008), Abe et al. (2010) and Dolatabadi et al. (In press) that enlarged size and indistinct ornamentation of sporangiospores have no genetic basis in R. microsporus.

Circinella

The genus Circinella was erected by van Tieghem & le Monnier (1873) in order to accommodate strains differing from Mucor by circinate sporangiophore branches that terminate in globose sporangia with persistent walls (Hesseltine & Fennell 1955). Based on our LSU tree (Fig. 1) Circinella is polyphyletic, resolved in a well-supported group around the type species C. umbellata within the Lichtheimiaceae, and two separate species, C. simplex and C. rigida, positioned distantly within different clades of Mucor. As a consequence, we propose assigning C. rigida to Mucor. No type material is known to have been preserved of C. simplex. We studied five strains of this species but we only obtained good sequence data for CBS 428.80. More detailed taxonomic studies on the numerous strains of this species that are available in public collections are necessary to test its monophyly and to select a neotype. Excluding the unrelated species C. rigida and C. simplex, the genus Circinella is restricted to species that develop sporangiophores either with sterile spines or umbels with circinate branches.

The ex-type strain of Circinella lacrymispora clusters with the ex-type strain of Gongronella lacrispora in the Gongronella clade of the LSU phylogram (Fig. 1). Based on this finding Circinella lacrymispora should be reclassified in Gongronella. The LSU sequences of C. lacrymispora and G. lacrispora differ only in 3 basepairs and conspecifity cannot be excluded. We defer recombination until we obtain the ITS sequences of both taxa and until we perform a detailed morphological study.

Mucor durus G. Walther & de Hoog, nom. nov. — MycoBank MB800462

≡ Circinella rigida G. Sm., Trans. Brit. Mycol. Soc. 34: 19. 1951, non Mucor rigidus Léger, Rech. Struct. Mucor (Thèse, Paris): 71. 1895.

Lectotype. Pl. 2, Fig. 7–8 (Smith, Trans. Brit. Mycol. Soc. 34: 17–22. 1951), designated here.

Epitype. CBS 156.51 (preserved in a metabolically inactive state by lyophilization, batch nr. 389), designated here.

Etymology. Named after the rigid wall of the sporangium.

Specimens examined. CBS 156.51, CBS 484.66.

Notes — The species differs markedly from other Mucor species by the extremely rigid sporangial walls, the often curved branches of the sporangiophores, the common formation of subsporangial septa and the frequent presence of distinct apophyses (Fig. 2h).

Rhizomucor

All non-thermophilic Rhizomucor species, namely Rm. chlamydosporus, Rm. endophyticus, Rm. regularior and Rm. variabilis belong to Mucor based on our LSU tree (Fig. 1). Rhizomucor regularior and Rm. variabilis have recently been reclassified: Rm. variabilis has been renamed as Mucor irregularis, whereas Rm. regularior has been synonymised with M. circinelloides (Álvarez et al. 2011). Our ITS data (Fig. 3) indicate that Rhizomucor endophyticus represents a discrete species closely related to Mucor luteus. The ITS sequence of the ex-type strain of Rm. chlamydosporus (GenBank EF583634) is identical to that of Mucor indicus (data not shown); the morphological description of the species (Zheng & Liu 2009b) fully matches with that of M. indicus.

Mucor hiemalis and M. luteus develop distinct rhizoids when they grow over glass slides (Fig. 2c). These findings demonstrate that not only Rhizomucor, but also Mucor species have the ability to produce rhizoids, at least under certain conditions. Consequently, this feature should not be used as sole criterion for the distinction of Mucor and Rhizomucor.

After removal of the above species, Rhizomucor with its type species Rhizomucor parasiticus (which is a synonym of Rm. pusillus) is monophyletic. The genus is restricted to thermophilic species with predominantly subglobose spores, as was recognized previously by Schipper (1978b) applying only phenotypic characters. Currently four thermophilic Rhizomucor species are accepted: Rm. miehei, Rm. nainitalensis, Rm. pakistanicus and Rm. pusillus. Rhizomucor tauricus is considered to be conspecific with Rm. pusillus because their ITS sequences are identical (Fig. 11). Analysis of its carbon source utilization, isoenzyme patterns and PCR-coupled RFLP of the ITS suggested that Rm. tauricus represented a heterothallic mutant strain of Rm. pusillus (Vágvölgyi et al. 1999).

Rhizomucor nainitalensis forms sporangiospores of different shapes, varying from subglobose to irregularly shaped (Joshi 1982). The sporangiospores of Rhizomucor pakistanicus are globose or ovoidal (Mirza et al. 1979). The following description of Rhizomucor is slightly modified from Schipper (1978b: 53):

Rhizomucor Lucet & Costantin (1900)

Thermophilic; sporangiophores originating from aerial mycelium, either from short aerial hyphae or from distinct stolons, both with simple or weakly branched rhizoids; sporangiophores branched, each branch bearing a multispored terminal sporangium; sporangia borne in an upright position, globose, dark (coloured), distinctly columellate, non-apophysate; sporangiospores consistently or partly subglobose; zygospores globose, covered with blunt projections, and formed in the aerial mycelium between non-ornamented, isogamous opposed suspensors.

Mucor endophyticus (R.Y. Zheng & H. Jiang) J. Pawłowska & G. Walther, comb. nov. — MycoBank MB800463

Basionym. Rhizomucor endophyticus R.Y. Zheng & H. Jiang, Mycotaxon 56: 456. 1995.

Specimens examined. CBS 385.95 ex-type strain of Rhizomucor endophyticus.

Mucor indicus Lendn., Bull. Soc. Bot. Genève, Ser. 2, 21: 258. 1930. — MycoBank MB267842

≡ Zygorhynchus indicus (Lendn.) Arx, Sydowia 35: 16. 1982.

= Rhizomucor chlamydosporus R.Y. Zheng, X.Y. Liu & R.Y. Li, Sydowia 61: 142. 2009.

Lectotype. Fig. 1–3 (Lendner, Bull. Soc. Bot. Genève, Ser. 2, 21: 258–260. 1930), designated here.

Epitype. CBS 226.29 (preserved in a metabolically inactive state by lyophilization, batch nr. 679), designated here.

Specimens examined. CBS 120.08, CBS 226.29, CBS 414.77, CBS 422.71, CBS 535.80, CBS 671.79, CBS 120585, CBS 123974.

Rhizomucor pusillus (Lindt) Schipper, Stud. Mycol. 17: 54. 1978. — MycoBank MB322484

Basionym. Mucor pusillus Lindt, Arch. Exp. Path. Pharmacol. 21: 272. 1886.

= Mucor septatus Bezold, Schimmelmyc. Menschl. Ohres: 97. 1889.

≡ Rhizomucor septatus (Bezold) Lucet & Costantin, Archs Parasitol. 4: 362. 1901.

= Mucor parasiticus Lucet & Costatin, Compt. Rend. Hebd. Séances Acad. Sci. 129: 1033. 1899.

≡ Rhizomucor parasiticus (Lucet & Costantin) Lucet & Costantin, Rev. Gén. Bot. 12: 81. 1900.

≡ Rhizopus parasiticus (Lucet & Costantin) Lendn., Mat. Fl. Crypt. Suisse 3: 115. 1908.

= Mucor buntingii Lendn., Bull. Soc. Bot. Genève, Ser. 2, 21: 260. 1930.

= Mucor tauricus Milko & Schkur., Novosti Sist. Nizsh. Rast. 7: 139. 1970.

≡ Rhizomucor tauricus (Milko & Schkur.) Schipper, Stud. Mycol. 17: 62. 1978.

≡ Rhizomucor pusillus var. tauricus (Milko & Schkur.) R.Y. Zheng, X.Y. Liu & R.Y. Li, Sydowia 61: 144. 2009.

Lectotype. Pl. II.III, Fig. 1–6 (Lindt, Arch. Exp. Path. Pharmacol. 21: 269–298. 1886), designated here.

Epitype. CBS 354.68 (preserved in a metabolically inactive state by lyophilization, batch nr. 85.0901), designated here.

Specimens examined. CBS 179.69 ex-lectotype strain of Rhizomucor tauricus (lectotype: CBS 179.69, preserved in a metabolically inactive state by lyophilization, batch nr. 87.3168, designated here), CBS 219.31, CBS 354.68, CBS 425.78, CBS 120586, CBS 120587, CNM-CM 2752, CNM-CM 2935, CNM-CM 2974, CNM-CM 4727, CNM-CM 5124.

Umbelopsis

Our ITS dataset is incomplete for Umbelopsis because of the high proportion of strains that needed to be cloned. For that reason, we refrain from taxonomic changes. The ex-type strains of Umbelopsis dimorpha and Umbelopsis nana possess identical ITS sequences and it is likely that these species are conspecific. The ITS sequences of the ex-type strains of U. swartii and U. westeae, as well as those of U. gibberosa and U. ramanniana are very similar necessitating a critical revision of Umbelopsis taxonomy.