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Centraalbureau voor Schimmelcultures, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
Correspondence
Maudy Th. Smith
smith{at}cbs.knaw.nl
| ABSTRACT |
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Published online ahead of print on 3 December 2004 as DOI 10.1099/ijs.0.63277-0.
The GenBank/EMBL/DDBJ accession numbers for the 26S and ITS rRNA gene sequences determined in this study are given in Table 1
.
| INTRODUCTION |
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. C. inositophila and C. steatolytica were placed into synonymy with C. hellenica, since that name has priority, and the nomenclaturally independent teleomorph name Zygoascus hellenicus was modelled after the accepted anamorph name.
In earlier studies, Meyer et al. (1984)
reported that, of four strains previously identified as being representatives of C. steatolytica [Centraalbureau voor Schimmelcultures (CBS catalogues; CBS, 1972
)], only one showed a DNADNA relatedness of 98 % with the type strain. Therefore, the remaining strains were excluded from this species and remained unclassified. Furthermore, Meyer et al. (1984)
kept C. steatolytica and C. inositophila as separate taxa, because the DNADNA reassociation value between the type strains of these species was around 57 %, as determined by the DNA filter reassociation technique (S. A. Meyer, personal communication), a value considered by Meyer to be low enough to keep the species apart. However, the observation of mating among the three unclassified isolates and the type strains of the three aforementioned species, resulting in asci with ascospores, was considered sufficient to conclude that they all belonged to the species Z. hellenicus (Smith, 1986
). Accepting the presence of mating as an indicator of conspecificity, Meyer et al. (1998)
excluded these three species from the list of purely anamorphic Candida species in a later revision of this genus.
As these species concepts based on sexual compatibility and DNADNA relatedness values were discrepant and, as we had obtained some new and difficult-to-place Z. hellenicus-like isolates, we undertook a revision of this group. In this study, physiological characters and mating behaviour were studied, and genome-level differences were examined by means of PCR-randomly amplified polymorphic DNA (RAPD) analyses, DNADNA reassociation studies and sequencing of the D1/D2 domain of the large-subunit (LSU) rRNA gene, as well as the internal transcribed spacer (ITS) regions ITS1 and ITS2 and the intervening 5·8S rRNA gene.
| METHODS |
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PCR-RAPD analysis.
For fingerprinting analyses, a decamer primer, OPA13 (Operon Technologies) and the microsatellite primers M13 (Vassart et al., 1987
) and (ATG)5 (Garbelotto et al., 1993
) were used in PCRs. The final reaction mixtures of 50 µl containing 50 ng genomic DNA, 10 mM Tris/HCl (pH 9·5), 50 mM KCl, 1·5 mM MgCl2, 0·01 % gelatin, 200 µM of each of the dNTPs (Roche), 10 pM of primer and 0·5 U of Supertherm polymerase (ITK Diagnostics) were processed in a Biomed thermocycler (model 60; Theres). The programmes of 40 cycles of the thermocycler were: 94 °C for 60 s, 34 °C for 60 s and 72 °C for 120 s for OPA13; 94 °C for 20 s, 60 °C for 60 s and 72 °C for 120 s for M13; and 94 °C for 60 s, 48 °C for 60 s and 72 °C for 120 s for (ATG)5. The PCR products were separated on 1·7 % agarose gels in 1x Tris/acetate/EDTA buffer (40 mM Tris/HCl and 2 mM EDTA; pH 8·0), chilled to 14 °C. The PCR-RAPD profiles for each strain obtained with the three primers were combined in a composite fingerprint by using GelCompar 3.1 (Applied Maths). Similarities between combined fingerprints were calculated by using the Pearson product-moment correlation coefficient. A dendrogram was generated by using the UPGMA method.
Mol% G+C content and DNADNA relatedness.
Mol% G+C content and DNADNA relatedness values were calculated according to previously described procedures (Smith et al., 1995
).
rRNA gene sequencing and sequence analysis.
The primers NL-1 and NL-4 (O'Donnell, 1993
) were used to amplify the D1/D2 region of the LSU rRNA gene, and the primers ITS1 and ITS4 (White et al., 1990
) were used to amplify the whole ITS region, including ITS1, ITS2 and the intervening 5·8S rRNA gene. The compositions and final volumes of the reaction mixtures were as for the PCR-RAPD analysis. An initial denaturation step at 94 °C for 5 min was followed by 35 cycles of 94 °C for 45 s, 52 °C for 30 s and 72 °C for 2 min for the D1/D2 amplification, or 35 cycles of 94 °C for 60 s, 55 °C for 60 s and 72 °C for 2 min for the ITS amplification, followed in both cases by final extension at 72 °C for 6 min. The amplified DNA was stored at 20 °C and was purified before use by using GFX columns (27-9602-01; Amersham Biosciences), according to the manufacturer's instructions. For the sequencing of both strands of the D1/D2 and ITS regions, the primers used were the same as those for the PCRs. The final sequence reaction mixture of 10 µl contained 2 µl Dyenamic (Amersham Biosciences), 1 µl primer (final concentration 0·4 pmol µl1), 1 µl buffer, 5 µl Milli-Q-water (Millipore) and 1 µl PCR product. Purified sequencing reactions were loaded on an ABI 3700 capillary sequencer (PE Biosystems). Sequences were edited and assembled by using the SeqMan package (DNAStar) and aligned using CLUSTAL W software (Thompson et al., 1994
). No manual adjustments were done, except that the ends were trimmed. Phylogenetic relationships were inferred by a combined analysis of the D1/D2 and the ITS regions, by using the maximum-likelihood optimality criterion and the general heuristic search option of PAUP* software, version 4.0 beta 10 (Swofford, 1993
). Bootstrap values of less than 50 % were not reported.
| RESULTS AND DISCUSSION |
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Molecular analysis
PCR-RAPD results.
Individual OPA13, M13 and (ATG)5 patterns and the dendrogram derived from the combined fingerprints are shown in Fig. 1
. At a similarity level of 40 %, the 15 strains could be separated into two major groups, Group I and Group II. At a similarity level of 80 %, however, each group could be further subdivided. Group Ia was represented by a single strain (CBS 6736T), Group Ib contained six strains (CBS 4028, CBS 5839T CBS 6726, CBS 6779, CBS 7652, CBS 8424), Group IIa included five strains (CBS 4075, CBS 4099T, CBS 6360, CBS 7521T, CBS 8426) and Group IIb comprised three strains (CBS 6173, CBS 7115T, CBS 8425).
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The separation into groups as observed by PCR-RAPD fingerprinting was further examined by determining DNADNA relatedness values calculated from reassociation rates (Table 2
, upper triangle). Two main reassociation groups could be distinguished, which were identical to the major groups observed following PCR-RAPD fingerprint analysis (Fig. 1
). The reassociation values obtained when Group I isolates were paired with Group II isolates ranged from 19 to 38 % (Table 2
). Detailed examination revealed a further subdivision similar to that obtained in the fingerprint analyses (Fig. 1
). Reassociation values of strains of Group Ia, represented by CBS 6736T (the type strain of C. inositophila), with strains of Group Ib ranged from 66 to 76 %. The values obtained in pairings among the six strains of Group Ib (including the type strain of C. steatolytica) ranged from 91 to 100 %. Within Group IIa, reassociation values ranging from 93 to 100 % were observed. This group included the type strains of C. hellenica (CBS 4099T) and P. hangzhouana (CBS 7521T), which by this way of measuring appeared to share 100 % of their DNA. The name P. hangzhouana, though pertaining to the teleomorphic genus Pichia, was originally given to material that did not contain true teleomorphic elements; ascospores that were ostensibly seen appear to have been oil droplets or artefacts. According to article 59.3 of the International Code of Botanical Nomenclature (Greuter et al., 2000
), this name is therefore considered to be that of an anamorph. On the basis of the reassociation results obtained, P. hangzhouana can be considered to be conspecific with C. hellenica. Reassociation values among the three strains of Group IIb, CBS 6173, CBS 7115T and CBS 8425, originally identified as Z. hellenicus, ranged from 99 to 100 %. The DNADNA reassociation values between strains of groups IIa and IIb ranged from 65 to 79 %.
Sequence analyses.
Analysis of the D1/D2 and ITS regions showed the separation of the strains into two well-supported main clades (100 % bootstrap), which could be further divided into two subclades (Fig. 2
) The groupings based on the phylogenetic analysis were identical to those obtained from the PCR-RAPD fingerprints (Fig. 1
) and DNADNA reassociation analyses (Table 2
and Fig. 3
), except for strain CBS 5839T, which was closer to CBS 6736T than to the other members of clade Ib. The latter topology was also found in the phylogenetic analysis of the actin gene (Daniel, 2002
).
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-D-glucoside, L-arabinitol, DL-lactate and 1,2-propanediol. The two teleomorphic species newly distinguished below, Zygoascus meyerae sp. nov. and Z. hellenicus, could not be distinguished physiologically. Among the four anamorphic varieties newly distinguished below, only Candida hellenica var. hellenica and Candida steatolytica var. steatolytica showed different assimilation properties for DL-lactate, whereas Candida steatolytica var. inositophila differed from Candida hellenica var. acidophila in the assimilation of methyl
-D-glucoside and 2-keto-D-gluconate.
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. The predicted relatedness of P. hangzhouana with Z. hellenicus on the basis of the D1/D2 rRNA gene sequences (Kurtzman & Robnett, 1998
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In addition, the division of the Zygoascus isolates into four clusters is supported by the actin gene-sequencing study of Daniel (2002
; and unpublished data). Each of the four groups could be distinguished by differences of more than 20 nucleotides. H.-M. Daniel (personal communication) considered this value to be high enough to support the hypothesis that these groups represented separate taxa.
On the basis of the results summarized in Fig. 3
and the above cited data, it seems warranted to propose two novel teleomorphic species within the genus Zygoascus, namely, Z. hellenicus and Z. meyerae sp. nov. These species correspond to Group I and Group II, respectively. To deal with the two molecular genetic subgroups found within each of these Zygoascus species, we propose C. steatolytica var. steatolytica and C. steatolytica var. inositophila as two novel anamorphic varieties connected to Z. hellenicus, and C. hellenica var. hellenica and C. hellenica var. acidophila as two novel anamorphic varieties linked to Z. meyerae. The varieties are proposed only at the anamorphic level, because the level of DNADNA relatedness (71 %) between varietal subgroups within each species appears sufficient to predict fully compatible mating; thus, the organisms at the teleomorphic level represent (at least potentially) unified biological species. This matter needs to be further investigated with studies on actual introgression levels among the groups and subgroups within the genus Zygoascus. In the meantime, because strong consistency was observed among all the molecular characters studied, we feel confident to propose the two teleomorphic species. Because all the observations (DNADNA reassociation, D1/D2, ITS and actin gene sequences, and PCR-RAPD fingerprints) consistently suggest that two subgroups can be distinguished within each teleomorphic species, but not to the point where we could describe them as separate species, we propose to consider them as four anamorphic varieties.
Taxonomy
The following species and varieties within the Zygoascus clade are proposed.
I. Zygoascus hellenicus M. Th. Smith.
Antonie van Leeuwenhoek (1986) 52, 27.
Teleomorph of C. steatolytica var. steatolytica and C. steatolytica var. inositophila.
Type specimen: a dried specimen of mixed sporulating culture of CBS 5839TxCBS 6736T is preserved at the CBS.
Ia. Candida steatolytica Yarrow var. inositophila (Nakase) M. Th. Smith & V. Robert comb. nov., stat. nov.
Basionym: C. inositophila Nakase
Antonie van Leeuwenhoek (1975) 41, 206.
Anamorph of Z. hellenicus.
Type strain: ex-type isolate CBS 6736T (=IFO 1575T) is a living strain in the CBS yeast collection.
Ib. Candida steatolytica Yarrow var. steatolytica.
Antonie van Leeuwenhoek (1969) 35, 24.
Anamorph of Z. hellenicus.
Type strain: ex-type isolate CBS 5839T (=IFO 10184T) is a living strain in the CBS yeast collection.
II. Zygoascus meyerae M. Th. Smith & V. Robert sp. nov.
Etymology: the epithet meyerae is chosen in honour of S. A. Meyer, who played a great role in the establishment of DNADNA reassociation methods in yeast taxonomy.
Teleomorph of C. hellenica var. hellenica and C. hellenica var. acidophila.
Type specimen: a dried specimen of a mating culture of CBS 4099TxCBS 7521T with ascospores is preserved at the CBS as Herb. CBS 6599T.
Latin diagnosis of Zygoascus meyerae M. Th. Smith et V. Robert sp. nov.
Species heterothallica. Coloniae in agaro maltoso post 7 dies 25 °C 710 mm diametro, elevatae, restrictae, tenaces, rugosae vel crispatae, pubescentes vel floccosae, albae vel cremeae, margine fimbriate circumdatae. Cellulae gemmantes ovoideae, elongatae vel cylindricae, (2·25·4)x(5·410·2) µm, saepe catenulatae et pseudohyphae formantes. Hyphae septatae, ramosae, 2·03·5 µm latae. Microsporus singulus in centro septum. Blastosporae ellipsoidae, ovoideae vel elongatae, cylindricae. Asci ovoidei vel globosi, parietibus persitentibus, plerumque unispori, sed etiam 4-spori (4·16·2)x(5·27·4) µm. Ascosporaehemisphericae ad galeatae, ad basim margine prominente praeditae, (1·53·5)x(2·54·5) µm. Glucosum, galactosum, maltosum, sucrosum, trehalosum, cellobiosum, raffinosum (variabile) fermentur, at non methyl
-D-glucosidum, melibiosum, lactosum, melezitosum, inulinum, amylum nec xylosum. Glucosum, galactosum, sorbosum, glucosaminum, xylosum, L-arabinosum, rhamnosum, sucrosum, trehalosum, cellobiosum, salicinum, glycerolum, ribitolum, xylitolum, glucitolum, mannitolum, galactitolum, inositolum, 5-ketogluconatum, glucuronatum, galacturonatum et ethanolum assimilantur, at non melibiosum, lactosum, inulinum, erythritolum, methanolum, butane-2,3-diolum, acidum quinicum, glucaratum nec galactonatum. Ribosum, D-arabinosum, maltosum, methyl
-D-glucosidum, arbutinum, raffinosum, melezitosum, amylum, L-arabinitolum, glucono-1,5-lactonum, 2-ketogluconatum, gluconatum, acidum DL-lacticum, acidum succinicum, acidum citricum, propane-1,2-diolum variabile assimilantur. Lysinum, cadaverinum, glucosaminum assimilantur at non kalium nitricum, kalium nitrosum, creatinum, ceatininum nec imidazolum. Ad crescentiam vitaminae necessariae sunt. Diazonium caeruleum B negativum. Augmentum ad 37 °C. Holotypus cultura conjugate ascigera CBS 4099TxCBS 7521T, exsiccate in collectione CBS, Utrecht, praeservatur.
IIa. Candida hellenica (Verona & Picci) D. S. King & S.-C. Jong var. hellenica.
Mycotaxon (1977) 6, 413.
Basionym: Trichosporon hellenicum Verona & Picci, Ann Microbiol Enzimol (1958) 8, 106.
Synonym: Pichia hangzhouana X.-H. Lu & M.-X. Li, Acta Mycol Sin (1989) 8, 253.
Anamorph of Z. meyerae.
Type strain: ex-type isolate CBS 4099T (=IFO 10246T) is a living strain in the CBS yeast collection.
IIb. Candida hellenica var. acidophila M. Th. Smith & V. Robert nov. var.
Etymology: the epithet acidophilus is chosen because some strains were isolated from acidic source material.
Anamorph of Z. meyerae.
Type strain: ex-type isolate CBS 7115T (=NCYC 2544T) is a living strain in the CBS yeast collection.
Latin diagnosis of Candida hellenica var. acidophila M. Th. Smith et V. Robert nov. var.
Caractera morfologica similes Candida hellenica var. hellenica. Glucosum fermentur et galactosum, maltosum, sucrosum, trehalosum, cellobiosum, raffinosum variabile fermentur, at non methyl
-D-glucosidum, melibiosum, lactosum, melezitosum, inulinum, amylum nec xylosum. Glucosum, galactosum, sorbosum, glucosaminum, amylum, glucono-1,5-lactonum, acidum succinicum, acidum citricum, xylosum, L-arabinosum, rhamnosum, sucrosum, trehalosum, cellobiosum, salicinum, glycerolum, ribitolum, xylitolum, glucitolum, mannitolum, galactitolum, inositolum, 5-ketogluconatum, glucuronatum, galacturonatum et ethanolum assimilantur, at non melibiosum, D-arabinosum, methyl
-D-glucosidum, 2-ketogluconatum, lactosum, inulinum, erythritolum, methanolum, butane-2,3-diolum, acidum quinicum, glucaratum nec galactonatum. Ribosum, maltosum, arbutinum, raffinosum, melezitosum, L-arabinitolum, gluconatum, acidum DL-lacticum, propane-1,2-diolum variabile assimilantur. Lysinum, cadaverinum, glucosaminum assimilantur at non kalium nitricum, kalium nitrosum, creatinum, ceatininum nec imidazolum. Diazonium caeruleum B negativum. Ad crescentiam vitaminae necessariae sunt. Augmentum ad 37 °C. Typus CBS 7115T lyophilus depositus in collectione zymotica CBS, Utrecht.
As mentioned above, a dried, sporulated specimen from a cross between the two mating strains, C. steatolytica CBS 5839TxC. inositophila CBS 6736T was originally deposited by Smith (1986)
as the holotype of Z. hellenicus. This specimen was selected because asci with ascospores were abundantly present. In crossings with the ex-type isolate of C. hellenica, reduced ascospore formation was seen, but Smith considered this isolate to be conspecific with the isolates used in making the holotype. This then made the basionym T. hellenicum the oldest available name for the anamorphic species involved, and Smith (1986)
selected hellenica as the epithet for the species as revised. The epithet of the teleomorph name Z. hellenicus was adopted as an echo, at another taxonomic level, of the established anamorph epithet, following examples such as the echoing of the anamorph name Cryptococcus neoformans in the teleomorph name Filobasidiella neoformans. Our current application of molecular criteria has somewhat inconveniently shown that the type strain of Candida hellenica differs at the species level from both allotype isolates of Z. hellenicus. Therefore, in the present study, we were obliged to redispose C. hellenica as the anamorph of a novel teleomorph species, which in this case bears the quite different name Z. meyerae.
It should be noted that the practice of echoic designation of teleomorph epithets automatically carries with it the potential disadvantage that the anamorph and teleomorph epithets may later become separated. Though superficially it may seem sensible to apply a one yeast-one epithet policy in order to simplify nomenclature when a new teleomorph species is being described, the separate rooting of each epithet to its own type material needs to be borne in mind. The potential for later separation of the two identical epithets is, of course, minimized when the ex-type isolate of the anamorph name is a vigorously mating isolate used in preparing the holotype of the teleomorph name. It seems sensible to suggest that reuse of currently valid anamorph epithets for newly obtained teleomorphs should be restricted to cases where this condition holds.
| ACKNOWLEDGEMENTS |
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