FEMS Yeast Research 4 (2003) 233^245
`
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`Phylogenetic circumscription of Saccharomyces, Kluyveromyces and
`other members of the Saccharomycetaceae, and the proposal of
`the new genera Lachancea, Nakaseomyces, Naumovia,
`Vanderwaltozyma and Zygotorulaspora
`Cletus P. Kurtzman
`
`Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service,
`U.S. Department of Agriculture, 1815 N. University Street, Peoria, IL 61604, USA
`
`Received 22 April 2003; received in revised form 23 June 2003; accepted 25 June 2003
`
`First published online
`
`Abstract
`
`Genera currently assigned to the Saccharomycetaceae have been defined from phenotype, but this classification does not fully
`correspond with species groupings determined from phylogenetic analysis of gene sequences. The multigene sequence analysis of
`Kurtzman and Robnett [FEMS Yeast Res. 3 (2003) 417^432] resolved the family Saccharomycetaceae into 11 well-supported clades. In
`the present study, the taxonomy of the Saccharomyctaceae is evaluated from the perspective of the multigene sequence analysis, which has
`resulted in reassignment of some species among currently accepted genera, and the proposal of the following five new genera: Lachancea,
`Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora.
`ß 2003 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.
`
`Keywords: Saccharomyces; Kluyveromyces; New ascosporic yeast genera; Molecular systematics; Multigene phylogeny
`
`1. Introduction
`
`The name Saccharomyces was proposed for bread and
`beer yeasts by Meyen in 1838 [1], but it was Reess in 1870
`[2] who ¢rst de¢ned the genus. As additional species were
`discovered and assigned to Saccharomyces, subgroups dif-
`fering in morphology and physiology were recognized. The
`presence of these subgroups led to the description of Zy-
`gosaccharomyces by Barker in 1901 [3] and to Torulaspora
`by Lindner in 1904 [4]. Stelling-Dekker [5] accepted Tor-
`ulaspora and recognized Zygosaccharomyces as a subgenus
`of Saccharomyces, but the distinction between these taxa
`was not always clear because some species have intermedi-
`ate phenotypes. Lodder and Kreger-van Rij [6], as well as
`van der Walt [7], argued that it was not possible to sepa-
`rate Torulaspora and Zygosaccharomyces from Saccharo-
`myces until additional taxonomic characters were found to
`
`* Corresponding author. Tel.: +1 (309) 681 6561;
`Fax: +1 (309) 681 6672.
`E-mail address: kurtzman@ncaur.usda.gov (C.P. Kurtzman).
`
`support the maintenance of three distinct genera. Yarrow
`[8^10] revived the concept of three genera and separated
`Torulaspora and Zygosaccharomyces from Saccharomyces,
`although species assignments were often di⁄cult. One of
`the most apparent morphological characters among spe-
`cies of the ‘Saccharomyces complex’ is the ascus. Some
`species have persistent asci whereas others have deliques-
`cent asci that release their ascospores at maturity. Van der
`Walt [11] described the genus Kluyveromyces based on
`K. polysporus,
`later expanding the genus to include all
`members of the ‘Saccharomyces complex’ that produce
`deliquescent asci [12].
`With the introduction of nuclear-DNA reassociation
`techniques, a number of studies demonstrated that species
`demarcation from phenotype was often incorrect. Apply-
`ing this method, Price et al. [13] found nine species vari-
`ously assigned to Torulaspora or Saccharomyces to be
`conspeci¢c with Torulaspora delbrueckii, and Vaughan-
`Martini and Kurtzman [14] showed that 16 previously
`described Saccharomyces species were conspeci¢c with
`S. cerevisiae. With the foregoing precedent, it is not sur-
`prising that gene sequence comparisons have shown that
`
`1567-1356 / 03 / $22.00 ß 2003 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.
`doi:10.1016/S1567-1356(03)00175-2
`
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`234
`
`C.P. Kurtzman / FEMS Yeast Research 4 (2003) 233^245
`
`species assignments among genera of the family Saccharo-
`mycetaceae are often incorrect. From 18S rDNA analyses,
`species of Kluyveromyces and Zygosaccharomyces were
`seen to be interspersed with Saccharomyces species [15].
`Comparisons from cytochrome oxidase II (COX II) [16]
`and from domains 1 and 2 (D1/D2) of large-subunit
`(26S) rDNA [17] showed the same heterogeneity. How-
`ever, none of these single-gene sequence analyses provided
`strong support for basal lineages, leaving in doubt rela-
`tionships among more divergent species. Kurtzman and
`Robnett [18] analyzed relationships among species of the
`‘Saccharomyces complex’ from sequences of 18S, ITS, 5.8S
`and 26S rDNAs, translation elongation factor 1-K (EF1-
`K), mitochondrial small-subunit rDNA and COX II. As
`with previous studies, single-gene phylogenies did not re-
`solve divergent lineages, but analysis of the combined se-
`quences resolved the ca. 80 species compared into 14 well-
`supported clades. Support for basal branches leading to
`these 14 clades was generally not strong, but was sugges-
`tive that the clades could be assigned to three families, the
`Saccharomycetaceae, the Eremotheciaceae, and the Sac-
`charomycodaceae.
`Examination of the 11 clades that comprise the Saccha-
`romycetaceae shows that most presently accepted genera
`include species from other genera (Fig. 1). Most notably,
`Kluyveromyces species are found in six clades, demonstrat-
`ing that the key character for this genus, ascus deliques-
`cence, has no phylogenetic basis. This is not the ¢rst time
`that ascus deliquescence was shown to be phylogenetically
`incongruent. Species of Debaryomyces characteristically
`have persistent asci, but D. udenii is an exception, which
`has led to concerns of misclassi¢cation. Placement of
`D. udenii in Debaryomyces, however, has been supported
`by rDNA sequence analysis [17,19].
`A long-standing goal of yeast systematists has been to
`develop a classi¢cation system based on natural relation-
`ships, thus providing genetic homogeneity and predictive-
`ness to taxon names. This has not been possible when
`using phenotypic characters, but
`the opportunity to
`achieve this goal now appears attainable through phyloge-
`netic analysis of gene sequences. A major problem in uti-
`lizing this new information is determining the basis for
`de¢ning taxa. Avise and Johns [20] proposed a standar-
`dized scheme of biological classi¢cation based on temporal
`emergence of taxa. They acknowledged, however, that
`there is neither su⁄cient well-dated fossil evidence nor
`are there su⁄cient gene sequences to accurately date evo-
`lutionary events to provide the time scale necessary for
`this proposal. Another issue is that of missing taxa. The
`vast majority of yeast species, as well as other microorgan-
`isms, are yet to be discovered, and this limited sampling
`impacts the interpretation of present taxonomic groupings.
`One likely outcome is that somewhat divergent phyloge-
`netically de¢ned genera will be further divided as addi-
`tional species are discovered, and that monotypic genera
`established for isolated species will expand in size as more
`
`species are found. Consequently, genera de¢ned phyloge-
`netically from presently known species will be subject to
`future modi¢cation, but establishing a phylogenetic frame-
`work now will provide direction to future work.
`Kurtzman and Robnett [18] observed that the extent of
`resolution from di¡erent gene sequences varied among
`clades of the Saccharomycetaceae with the primary e¡ect
`being strength of branch support on phylogenetic trees
`rather than disparate evolutionary histories. Phylogenetic
`trees constructed from multiple genes have far greater
`bootstrap support than do single-gene trees, which indi-
`cates that each gene sequence is conveying the same evolu-
`tionary history and contributing to the strength of the
`signal. Combining data has been predicted to increase
`phylogenetic accuracy by increasing signal and dispersing
`noise [21], and any informational con£icts between genes
`are not expected to increase statistical support for a¡ected
`nodes [22]. An alternate approach would be to use whole-
`genome sequence comparisions to achieve more robust
`species phylogenies, which should be possible in the near
`future for taxonomic groups of the size compared here.
`However, because multigene phylogenies are likely to be
`an accurate re£ection of evolutionary history, whole-ge-
`nome comparisons would be expected to provide a re¢ne-
`ment of the present work rather than result in major
`changes.
`Analysis of the multigene dataset presented by Kurtz-
`man and Robnett [18] showed each of the 11 clades of the
`Saccharomycetaceae to be similarly diverged from one an-
`other. Some of the clades, such as Saccharomyces, Toru-
`laspora and Zygosaccharomyces, as well as Eremothecium
`from the Eremotheciaceae, are recognized from phenotype
`as well as from phylogenetic analysis. Using these genera
`as exemplars,
`the remaining phylogenetically de¢ned
`clades have been interpreted as genera. To apply the
`new gene sequence data to development of a phylogenetic
`system for classi¢cation, ¢ve new genera and various new
`combinations are proposed.
`
`2. Materials and methods
`
`2.1. Organisms
`
`The species compared are represented by their type
`strains or equivalent authentic strains when type material
`was a drawing or a herbarium specimen. The strains com-
`pared are listed in Table 1 with culture collection accession
`numbers.
`
`2.2. Phylogenetic analysis
`
`The phylogenetic analysis used for the taxonomic pro-
`posals presented is represented by ¢gure 9 of Kurtzman
`and Robnett [18] and reproduced here as Fig. 1. As de-
`scribed in that study, the phylogenetic tree was derived
`
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`C.P. Kurtzman / FEMS Yeast Research 4 (2003) 233^245
`
`235
`
`Fig. 1. Phylogenetic tree resolving species of the ‘Saccharomyces complex’ into clades, which are proposed as phylogenetically circumscribed genera.
`This is one of three most parsimonious trees derived from maximum-parsimony analysis of a dataset comprised of nucleotide sequences from 18S, 5.8S/
`alignable ITS, and 26S (three regions) rDNAs, EF-1K, mitochondrial small-subunit rDNA and COX II [18]. Branch lengths, based on nucleotide substi-
`tutions, are indicated by the bar. Bootstrap values v 50% are given. Pichia anomala is the outgroup species, and all species are analyzed from type
`strains.
`
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`Table 1 (Continued).
`
`Speciesa
`
`T. pha⁄i
`Torulaspora delbrueckii
`T. franciscae
`T. globosa
`T. pretoriensis
`Zygosaccharomyces bailii
`Z. bisporus
`Z. cidri
`Z. fermentati
`Z. £orentinus
`Z. kombuchaensis
`Z. lentus
`Z. mellis
`Z. microellipsoides
`Z. mrakii
`Z. rouxii
`Reference species
`Pichia anomala
`
`Accession numbersb;c
`
`NRRL
`
`Y-8282T
`Y-866T
`Y-17532T
`Y-12650T
`Y-17251T
`Y-2227T
`Y-12626T
`Y-12634T
`Y-1559T
`Y-1560T
`YB-4811T
`Y-27276T
`Y-12628T
`Y-1549T
`Y-12654T
`Y-229T
`
`Other
`
`CBS 4417
`CBS 1146
`CBS 2926
`CBS 764
`CBS 2187
`CBS 680
`CBS 702
`CBS 4575
`CBS 707
`CBS 746
`CBS 8849
`CBS 8574
`CBS 736
`CBS 427
`CBS 4218
`CBS 732
`
`Y-366NT
`
`CBS 5759
`
`aCommonly recognized synonym names are given in parentheses.
`bT = type strain, NT = neotype strain, A = authentic strain, the reference
`strain used when there is no living type or ex-type strain.
`cNRRL = ARS Culture Collection, National Center for Agricultural Uti-
`lization Research, Peoria, IL, USA; CBS = Centraalbureau voor Schim-
`melcultures, Utrecht, The Netherlands; JCM = Japan Collection of Mi-
`croorganisms, Saitama, Japan; IFO = Institute for Fermentation, Osaka,
`Japan; NCYC = National Collection of Yeast Cultures, Norwich, UK.
`
`from maximum-parsimony analysis of a dataset comprised
`of nucleotide sequences from 18S, 5.8S/alignable ITS, and
`26S (three regions) rDNAs, translation elongation factor
`EF-1K, mitochondrial small-subunit rDNA and COX II.
`Analyses were made using PAUP* 4.063a [23], and boot-
`strap values were based on 1000 replications. GenBank
`accession numbers for all nucleotide sequences analyzed
`were previously reported [18].
`Three recently described species of Saccharomyces, i.e.
`S. humaticus, S. naganishii, and S. yakushimaensis were
`not included in the work of Kurtzman and Robnett [18],
`but are included in the present study. Phylogenetic place-
`ment of these three new species near Saccharomyces trans-
`vaalensis and Kluyveromyces sinensis was determined from
`maximum-parsimony analysis of D1/D2 26S rDNA se-
`quences that were provided in the original descriptions
`of these species [24].
`
`3. Results and discussion
`
`The 11 clades of the Saccharomycetaceae resolved from
`multigene phylogenetic analysis are shown in Fig. 1 with
`proposed species assignments to phylogenetically circum-
`scribed genera. Table 2 is a compilation of intra- and in-
`tergeneric divergence among the species compared. Not
`unexpectedly, the clades vary in size with intrageneric dis-
`tances often re£ecting the number of species in each clade.
`
`Accession numbersb;c
`
`NRRL
`
`YB-4302T
`Y-17070T
`Y-65T
`Y-17074T
`Y-1363A
`Y-12970T
`Y-17582A
`Y-1056A
`Y-17231T
`Y-1625T
`Y-7946T
`Y-1613T
`Y-1614T
`Y-1626T
`Y-17529T
`Y-27206T
`Y-17531T
`YB-4510T
`Y-8276T
`Y-17846T
`Y-10934T
`Y-2379T
`Y-1974T
`Y-8279T
`Y-8280T
`Y-8281T
`Y-27343T
`Y-17977T
`Y-8283T
`Y-27222T
`Y-8284T
`Y-8285T
`Y-8286T
`Y-17763T
`Y-27223T
`Y-12624T
`Y-27203T
`Y-27337T
`Y-12630T
`Y-12632NT
`Y-12639T
`Y-12640NT
`
`Y-12651T
`Y-27339T
`Y-27209T
`Y-409T
`Y-27341T
`
`Y-17217NT
`Y-27171NT
`Y-17919T
`Y-12661T
`Y-17920T
`Y-17245T
`Y-27345T
`Y-1556T
`
`Y-12793T
`Y-27308T
`Y-27309T
`Y-27310T
`
`Other
`
`CBS 2685
`CBS 4332
`CBS 138
`CBS 5658
`
`CBS 2608
`CBS 270.75
`CBS 109.51
`CBS 8199
`CBS 465
`CBS 2592
`CBS 313
`CBS 314
`CBS 479
`CBS 2171
`CBS 6463
`CBS 285
`CBS 4438
`CBS 2517
`CBS 7720
`CBS 6284
`CBS 2170
`CBS 2104
`CBS 683
`CBS 2757
`CBS 712
`JCM 10232
`CBS 7738
`CBS 2163
`CBS 7660
`CBS 6340
`CBS 6430
`CBS 2745
`CBS 8242
`CBS 6946
`CBS 380
`CBS 8638
`NCYC 2890
`CBS 4309
`CBS 1171
`CBS 421
`CBS 379
`IFO 10673T
`CBS 3082
`IFO 1802
`CBS 7662
`CBS 6334
`IFO 1815
`IFO 10181T
`CBS 432
`CBS 1538
`CBS 7127
`CBS 4311
`CBS 3019
`CBS 2186
`CBS 8665
`CBS 398
`IFO 1889T
`CBS 821
`IFO 10925
`IFO 10929
`IFO 10899
`
`236
`
`Table 1
`Species compared
`
`Speciesa
`
`Arxiozyma telluris
`Candida castellii
`C. glabrata
`C. humilis
`Eremothecium ashbyi
`E. (Nematospora) coryli
`E. cymbalariae
`E. (Ashbya) gossypii
`E. (Holleya) sinecaudum
`Hanseniaspora guilliermondii
`H. (Kloeckeraspora) occidentalis
`H. (Kloeckeraspora) osmophila
`H. uvarum
`H. valbyensis
`H. (Kloeckeraspora) vineae
`Kazachstania viticola
`Kloeckera lindneri
`Kluyveromyces aestuarii
`K. africanus
`K. bacillisporus
`K. blattae
`K. delphensis
`K. dobzhanskii
`K. lactis var. lactis
`K. lodderae
`K. marxianus
`K. nonfermentans
`K. piceae
`K. polysporus
`K. sinensis
`K. thermotolerans
`K. waltii
`K. wickerhamii
`K. yarrowii
`Saccharomyces barnettii
`S. bayanus
`S. bulderi
`S. cariocanus
`S. castellii
`S. cerevisiae
`S. dairenensis
`S. exiguus
`S. humaticus
`S. kluyveri
`S. kudriavzevii
`S. kunashirensis
`S. martiniae
`S. mikatae
`S. naganishii
`S. paradoxus
`S. pastorianus
`S. rosinii
`S. servazzii
`S. spencerorum
`S. (Pachytichospora) transvaalensis
`S. turicensis
`S. unisporus
`S. yakushimaensis
`Saccharomycodes ludwigii
`Tetrapisispora arboricola
`T. iriomotensis
`T. nanseiensis
`
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`237
`
`The proposed genus Zygotorulaspora has just two species,
`which are separated by 52 nucleotide di¡erences, whereas
`Zygosaccharomyces has six species with a divergence of
`154 nucleotides and Eremothecium has ¢ve species with a
`divergence of 331 nucleotides. Do these clades represent
`genera? When phylogenetically circumscribed, the genera
`Saccharomyces, Torulaspora, Zygosaccharomyces and Ere-
`mothecium can also be recognized from phenotype. Several
`of the other clades are less easily recognized from available
`phenotypic data, but genetically, they are just as well de-
`¢ned as Saccharomyces. Consequently, these clades, al-
`though phenotypically somewhat heterogenous, appear
`to be phylogenetically circumscribed genera. The following
`proposals of phylogenetically circumscribed genera also
`include a phenotypic description of the taxa. Because
`some of the genera are di⁄cult to recognize from pheno-
`type, a key is provided. Individual species descriptions that
`include known synonyms are given in The Yeasts, A
`Taxonomic Study, 4th edition [25^32] and in Yeasts of
`the World [33].
`
`3.1. Accepted taxa and proposed new genera and new
`combinations for species of the Saccharomycetaceae
`
`3.1.1. Kazachstania Zubkova (1971)
`
`reproduction.
`description. Vegetative
`3.1.1.1. Genus
`Asexual reproduction is by multilateral budding on a nar-
`row base. Cells are spheroidal, ovoidal or elongate. Pseu-
`
`dohyphae may be formed, but true hyphae are not pro-
`duced.
`Ascospore formation. Asci may be unconjugated or
`show conjugation between independent cells or between
`a cell and its bud. Asci may be deliquescent or persistent
`and produce 1^16 or more ascospores that are spherical,
`ovoidal or elongate. Ascospore surfaces may be roughened
`or smooth.
`Physiology/biochemistry. Glucose is fermented and most
`species ferment and assimilate galactose. Cadaverine, L-
`lysine and ethylamine are seldom utilized as nitrogen sour-
`ces. Nitrate is not utilized. Coenzyme Q-6 is produced.
`The diazonium blue B reaction is negative.
`Comments on the genus. The Kazachstania clade,
`although moderately well supported basally, has a rela-
`tively large number of poorly supported internal nodes.
`Besides the genes analyzed for Fig. 1, Kurtzman and Rob-
`nett [18] also sequenced actin-1 and RNA polymerase II in
`an unsuccessful attempt to better resolve internal lineages.
`The species Kluyveromyces africanus, Kazachstania vitico-
`la and Saccharomyces martiniae are particularly subject to
`movement within the clade, depending on the outgroup
`used in phylogenetic analysis. For this reason, the entire
`clade is treated as a single genus, but it seems likely that
`the clade will resolve into three main lineages if a larger
`number of gene sequences are included in the phylogenetic
`analysis.
`The genus Kazachstania was validly described by Zub-
`kova in 1971 [34] and therefore has taxonomic priority
`
`Table 2
`Extent of intrageneric and intergeneric nucleotide changes among members of the Saccharomycetaceae, Eremotheciaceae and Saccharomycodaceae from
`analysis of a multigene dataseta
`
`Genus
`
`Intrageneric
`nucleotide changes
`
`Intergeneric nucleotide changes
`
`Kaz. Nau.
`
`Nak.
`
`Tet.
`
`Van.
`
`Zyg.
`
`Z’tor. Tor.
`
`Lac.
`
`Klu.
`
`Ere. Han.
`
`S’my.
`
`101
`
`104
`75
`
`96
`115
`118
`
`181
`200
`203
`155
`
`160
`179
`182
`134
`77
`
`166
`185
`188
`140
`181
`160
`
`206
`225
`228
`180
`221
`200
`138
`
`177
`196
`199
`151
`192
`171
`109
`69
`
`Saccharomyces (7)b
`88
`412
`Kazachstania (21)
`345
`431
`Naumovia (2)
`106
`434
`Nakaseomyces (4)
`197
`386
`340c
`Tetrapisispora (5)
`427
`Vanderwaltozyma (2)
`99
`406
`Zygosaccharomyces (6)
`154
`344
`Zygotorulaspora (2)
`52
`350
`Torulaspora (5)
`105
`321
`Lachancea (5)
`115
`274
`Kluyveromyces (6)
`129
`266
`Eremothecium (5)
`331
`242
`297d
`Hanseniaspora (7)
`150
`Saccharomycodes (1)
`(1 sp.)
`(1 sp.)
`aThe multigene dataset used is comprised of nucleotide sequences from 18S, 5.8S/alignable ITS, and 26S (three regions) rDNAs, EF-1K, mitochondrial
`small-subunit rDNA and COX II. The dataset was pruned of all potentially ambiguously aligned regions resulting in 4962 characters of which 929 were
`parsimony informative. Distances are summations of branch lengths given on a phylogenetic tree derived from maximum-parsimony analysis (dataset
`used for ¢gure 9 of Kurtzman and Robnett [18]). Intrageneric distances are based on the two most distantly related species of each genus. Intergeneric
`distances are the sum of nucleotide changes separating the basal nodes of the genera compared. All species are represented by type, neotype, or authen-
`tic strains as listed in Table 1.
`bNumber of recognized species is given in parentheses and includes associated anamorphic species (Candida, Kloeckera).
`cIntrageneric divergence in Tetrapisispora was 107 nucleotide changes with the exclusion of T. blattae.
`dDivergence in the H. valbyensis clade is 65 nucleotide changes, and 54 changes in the H. vineae clade.
`
`194
`213
`216
`168
`209
`188
`126
`132
`103
`
`232
`251
`254
`206
`247
`226
`164
`170
`141
`94
`
`270
`289
`292
`244
`285
`264
`202
`208
`179
`132
`124
`
`416
`435
`438
`390
`431
`410
`348
`354
`325
`278
`270
`246
`
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`Basionym: Saccharomyces barnettiiVaughan-Martini.
`Antonie van Leeuwenhoek 68, 116. 1995.
`(Middelhoven, Kurtzman p
`3. Kazachstania bulderi
`Vaughan-Martini) Kurtzman comb. nov.
`Basionym:
`Saccharomyces
`bulderi Middelhoven,
`Kurtzman p Vaughan-Martini. Antonie van Leeu-
`wenhoek 77, 224. 2000.
`4. Kazachstania exigua (Reess ex E.C. Hansen) Kurtz-
`man comb. nov.
`Basionym: Saccharomyces exiguus Reess ex E.C.
`Hansen. C.R. Trav. Lab. Carlsberg 2, 146. 1888.
`5. Kazachstania humatica (Mikata p Ueda-Nishimura)
`Kurtzman comb. nov.
`Basionym: Saccharomyces humaticus Mikata p
`Ueda-Nishimura. Int. J. Syst. Evol. Microbiol. 51,
`2193. 2001.
`6. Kazachstania kunashirensis (James, Cai, Roberts p
`Collins) Kurtzman comb. nov.
`Basionym: Saccharomyces kunashirensis James, Cai,
`Roberts p Collins. Int. J. Syst. Bacteriol. 47, 458.
`1997.
`7. Kazachstania lodderae (van der Walt p Tscheuschner)
`Kurtzman comb. nov.
`Basionym: Saccharomyces lodderae (as S. lodderi) van
`der Walt p Tscheuschner. Antonie van Leeuwenhoek
`23, 188. 1957.
`8. Kazachstania martiniae (James, Cai, Roberts p Col-
`lins) Kurtzman comb. nov.
`Basionym: Saccharomyces martiniae James, Cai, Rob-
`erts p Collins. Int. J. Syst. Bacteriol. 47, 458. 1997.
`9. Kazachstania naganishii (Mikata, Ueda-Nishimura p
`Hisatomi) Kurtzman comb. nov.
`Basionym: Saccharomyces naganishii Mikata, Ueda-
`Nishimura p Hisatomi. Int. J. Syst. Evol. Microbiol.
`51, 2191. 2001.
`10. Kazachstania piceae (Weber p Spaaij) Kurtzman
`comb. nov.
`Basionym: Kluyveromyces piceae Weber p Spaaij. An-
`tonie van Leeuwenhoek 62, 240. 1992.
`11. Kazachstania rosinii (Vaughan-Martini, Barcaccia p
`Pollacci) Kurtzman comb. nov.
`Basionym: Saccharomyces rosinii Vaughan-Martini,
`Barcaccia p Pollacci. Int. J. Syst. Bacteriol. 46, 616.
`1996.
`12. Kazachstania servazzii (Capriotti) Kurtzman comb.
`nov.
`Basionym: Saccharomyces servazzii Capriotti. Ann.
`Microbiol. Enzimol. 17, 83. 1967.
`13. Kazachstania sinensis (Li, Fu p Tang) Kurtzman
`comb. nov.
`Basionym: Kluyveromyces sinensis Li, Fu p Tang.
`Acta Microbiol. Sin. 30, 96. 1990.
`14. Kazachstania spencerorum (Vaughan-Martini) Kurtz-
`man comb. nov.
`spencerorum Vaughan-
`Basionym: Saccharomyces
`Martini. Antonie van Leeuwenhoek 68, 116. 1995.
`
`Fig. 2. Phylogenetic tree showing placement of Saccharomyces humati-
`cus, S. naganishii and S. yakushimaensis with representative species of
`the Kazachstania clade. Represented by one of three most parsimonious
`trees derived from maximum-parsimony analysis of D1/D2 26S rDNA
`sequences. Tree length = 104, consistency index = 0.923, retention in-
`dex = 0.917 and rescaled consistency index = 0.846. Type strains were an-
`alyzed for all species. GenBank accession numbers follow species names.
`Branch lengths, based on nucleotide substitutions, are the lower num-
`bers and bootstrap values v 50% are given above the branches. Kluy-
`veromyces polysporus was the outgroup species in the analysis.
`
`over Arxiozyma van der Walt p Yarrow (1984) [35] and
`Pachytichospora van der Walt (1978) [36], two closely re-
`lated monotypic genera also included in this clade. Species
`of this clade that are currently assigned to Saccharomyces
`or Kluyveromyces must be transferred to Kazachstania as
`new combinations because they are not members of either
`Saccharomyces or Kluyveromyces as now de¢ned. Recog-
`nition of the genus Kazachstania from phenotype alone is
`di⁄cult because the species assigned have little de¢nitive
`group-speci¢c morphology and their restricted responses
`on the standard tests used in yeast taxonomy do not reli-
`ably separate them from certain species in other genera.
`Lack of phenotypic identity is not peculiar to Kazachsta-
`nia species, but is characteristic of many species in the
`‘Saccharomyces complex’, which has led to past uncertain-
`ties about genus assignments. Assignment to Kazachstania
`of the three newly described species Saccharomyces huma-
`ticus, S. naganishii and S. yakushimaensis was made from
`phylogenetic analysis of D1/D2 26S rDNA sequences,
`which places these three species near ‘Saccharomyces
`transvaalensis’ and ‘Kluyveromyces sinensis’ in the Kazach-
`stania clade (Fig. 2).
`
`3.1.1.2. Species accepted.
`1. Kazachstania africana (van der Walt) Kurtzman comb.
`nov.
`Basionym: Kluyveromyces africanus van der Walt. An-
`tonie van Leeuwenhoek 22, 325. 1956.
`2. Kazachstania barnettii
`(Vaughan-Martini) Kurtzman
`comb. nov.
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`
`15. Kazachstania turicensis (Wyder, Meile p Teuber)
`Kurtzman comb. nov.
`Basionym: Saccharomyces turicensis Wyder, Meile p
`Teuber. Syst. Appl. Microbiol. 22, 423. 1999.
`16. Kazachstania telluris (van der Walt) Kurtzman comb.
`nov.
`Basionym: Saccharomyces telluris (as S. tellustris) van
`der Walt. Antonie van Leeuwenhoek 23, 27. 1957.
`17. Kazachstania transvaalensis (van der Walt) Kurtzman
`comb. nov.
`transvaalensis van der
`Basionym: Saccharomyces
`Walt. Antonie van Leeuwenhoek 22, 192. 1956.
`18. Kazachstania unispora (Jo«rgensen) Kurtzman comb.
`nov.
`Basionym: Saccharomyces unisporus Jo«rgensen. Die
`Mikroorganismen der Ga«rungsindustrie, 5te Au£., p.
`371, 1909. P. Parey, Berlin.
`19. Kazachstania viticola Zubkova (1971) (type species of
`the genus Kazachstania).
`20. Kazachstania yakushimaensis (Mikata p Ueda-Nishi-
`mura) Kurtzman comb. nov.
`Basionym: Saccharomyces yakushimaensis Mikata p
`Ueda-Nishimura. Int. J. Syst. Evol. Microbiol. 51,
`2194. 2001.
`
`3.1.2. Kluyveromyces Kurtzman, Lachance, Nguyen p
`Prillinger nom. cons. (2001)
`
`reproduction.
`description. Vegetative
`3.1.2.1. Genus
`Asexual reproduction is by multilateral budding on a nar-
`row base. Cells are spheroidal, ovoidal or elongate. Pseu-
`dohyphae may be formed, but true hyphae are not pro-
`duced.
`Ascospore formation. Asci may be unconjugated or
`show conjugation between independent cells or between
`a cell and its bud. Asci are deliquescent at maturity
`and produce 1^4 spherical, ovoidal or reniform ascospores.
`Physiology/biochemistry. With the exception of one spe-
`cies, glucose is fermented and all species assimilate galac-
`tose. Cadaverine, L-lysine and ethylamine are generally
`utilized as nitrogen sources. Nitrate is not utilized. Coen-
`zyme Q-6 is produced. The diazonium blue B reaction is
`negative.
`Comments on the genus. Species previously described as
`Kluyveromyces are distributed among six clades (Fig. 1),
`demonstrating the polyphyly of this genus when de¢ned
`from the character of ascus deliquescence. Lachance [28]
`has reviewed the history of the genus and discussed pos-
`sible species groupings based on phenotype, genotype and
`habitat speci¢city. In view of molecular, physiological,
`ecological and biotechnological considerations, Kurtzman
`et al.
`[37] proposed to conserve Kluyveromyces with
`K. marxianus as the conserved type species. This resulted
`in assignment of the six known species of the K. marx-
`ianus clade to the newly conserved Kluyveromyces. Nau-
`mov [38] and Naumov and Naumova [39] have argued
`
`that these six species should be placed in the genus Zygo-
`fabospora, but
`the proposal of Kurtzman et al.
`[37]
`pointed out that the genus Zygofabospora was ambigu-
`ously conceived, and that changing the genus name of
`the widely known and biotechnologically important spe-
`cies K. marxianus and K. lactis after more than 30 years
`assignment to Kluyveromyces is incompatible with Article
`14.2 of the International Code of Botanical Nomenclature
`[40], which proposes nomenclatural stability for well-
`known species.
`
`(Dombrowski) van der Walt
`
`3.1.2.2. Species accepted.
`1. Kluyveromyces aestuarii (Fell) van der Walt (1971).
`2. Kluyveromyces dobzhanskii (Shehata, Mrak p Pha¡)
`van der Walt (1971).
`Kluyveromyces
`lactis
`(1971).
`3.1. Kluyveromyces lactis (Dombrowski) van der
`Walt var. lactis (1986).
`3.2. Kluyveromyces lactis var. drosophilarum (Sheha-
`ta, Mrak p Pha¡) Sidenberg p Lachance
`(1986).
`4. Kluyveromyces marxianus (E.C. Hansen) van der Walt
`(1971) (type species of the genus Kluyveromyces nom.
`cons.).
`5. Kluyveromyces nonfermentans Nagahama, Hamamo-
`to, Nakase p Horikoshi (1999).
`6. Kluyveromyces wickerhamii (Pha¡, M. W. Miller p
`Shifrine) van der Walt (1971).
`
`3.1.3. Lachancea Kurtzman gen. nov.
`
`3.1.3.1. Latin diagnosis of Lachancea Kurtzman gen.
`nov.. Asci conjugati vel
`inconjugati, habentes 1^4 asco-
`sporae globosae et rumpuntur vel non rumpuntur. Cellulae
`vegetativae globosae, ellipsoideae aut elongatae. Pseudohy-
`phae ¢unt raro; non ¢unt hyphae verae. Glucosum et alius
`saccharas fermentantur. Cadaverinum, L-lysinum et ethyla-
`minum plerumque assimilantur. Nitras kalicus non assimi-
`lantur. Systema coenzymatis Q-6 adest. Diazonium caeruli-
`an B non
`respondens. Species
`typica: Lachancea
`thermotolerans (Filippov) Kurtzman comb. nov.
`
`reproduction.
`description. Vegetative
`3.1.3.2. Genus
`Asexual reproduction is by multilateral budding on a nar-
`row base. Cells are spheroidal, ovoidal or elongate. Pseu-
`dohyphae may be formed, but true hyphae are not pro-
`duced.
`Ascospore formation. Asci may be unconjugated or
`show conjugation between independent cells or between
`a cell and its bud. Asci may be deliquescent or persistent
`and produce 1^4 spherical ascospores.
`Physiology/biochemistry. Glucose and at least one other
`sugar are fermented. Galactose is assimilated by nearly all
`species. Cadaverine, L-lysine and ethylamine are generally
`utilized as nitrogen sources, but nitrate is not utilized.
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`
`Coenzyme Q-6 is produced. The diazonium blue B reac-
`tion is negative.
`Comments on the genus. The ¢ve species assigned to
`this newly described genus were formerly members of
`Kluyveromyces, Saccharomyces and Zygosaccharomyces.
`Despite di¡erences in the morphology of their ascosporic
`states, the species share many similarities in physiology
`and habitat. The somewhat low bootstrap support for
`the basal node of this genus results from inclusion of the
`former Saccharomyces kluyveri, which may eventually
`serve as type species for a sister genus.
`The genus is named in honor of Dr. Marc-Andre¤ La-
`chance, University of Western Ontario, London, Ontario,
`Canada, for his many contributions to yeast systematics
`and ecology.
`
`3.1.3.3. Species accepted.
`1. Lachancea cidri (Legakis) Kurtzman comb. nov.
`Basionym: Saccharomyces cidri Legakis. A contribu-
`tion to the study of the yeast £ora of apples and apple
`wine. Thesis. University of Athens, Greece. 1961 (cf.
`van der Walt, p. 609, 1970 [7]).
`2. Lachancea fermentati (H. Naganishi) Kurtzman comb.
`nov.
`Basionym: Zygosaccharomyces fermentati H. Naga-
`nishi. J. Zymol. 6, 1. 1928.
`3. Lachancea kluyveri (Pha¡, M. W. Miller p Shifrine)
`Kurtzman comb. nov.
`Basionym: Saccharomyces kluyveri Pha¡, M. W. Miller
`p Shifrine. Antonie van Leeuwenhoek 22, 159. 1956.
`4. Lachancea thermotolerans (Filippov) Kurtzman comb.
`nov. (type species of the genus Lachancea).
`Basionym: Zygosaccharomyces
`thermotolerans Filip-
`pov. Arb. Zentr. Biochem. Forsch. Inst. Nahrungs-u.
`Genussmittel-Ind. 2, 26. 1932.
`5. Lachancea waltii (K. Kodama) Kurtzman comb. nov.
`Basionym: Kluyveromyces waltii K. Kodama. J. Ferm.
`Technol. 52, 609. 1974.
`
`3.1.4. Nakaseomyces Kurtzman gen. nov.
`
`3.1.4.1. Latin diagnosis of Nakaseomyces Kurtzman gen.
`nov.. Asci conjugati vel inconjugati, rumpuntur, habentes
`1^8 ascosporae reniformes aut bacilliformes. Cellulae vege-
`tativae globosae, ellipsoideae aut elongatae. Non ¢unt pseu-
`dohyphae et hyphae verae. Glucosum fermentantur. Cadav-
`erinum, L