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Komb Prod
Komb Prod
FEMS
Yeast Research
ELSEVIER FEMS Yeast Research I (2001) 133-138
www.fems-microbiology.org
Received I February 2001; received in revised form 4 April 2001; accepted 10 April 2001
Abstract
A new ascosporogenous yeast, Zygosaccharomyces kombuchaensis sp. n. (type strain RRL YB-4811, CBS 8849), is described; it was
isolated from Kombucha tea, a popular fermented tea-based beverage. The four known strains of the new species have identical nucleotide
sequences in domain 01/D2 of 265 rO A. Phylogenetic analysis of D 1/02 and 185 rO A sequences places Z. kombuchaensis near
Zygosaccharomyces lenlus. The two species are indistinguishable on standard physiological tests used for yeast identification, but can be
recognized from differences in restriction fragment length polymorphism patterns obtained by digestion of 18S-ITS I amplicons with the
restriction enzymes DdeI and MboI. © 200 I Federation of European Microbiological Societies. Published by Elsevier Science B. V. All
rights reserved.
Keywords: ew yeast; Molecular systematics; Ribosomal D A; Kombucha tea; Food microbiology; Zygosaccharomyces kombuchaensis
quences analyzed have been deposited with GenBank 3. Results and discussion
under the accession numbers given in Fig. 1.
3.1. Detection, phylogenetic placement and description of
2.3. Species separation by restriction fragment length the new species
polymorphisms (RFLPs)
Analysis of the variable ca. 600-nucleotide domain 01/
Amplicons were prepared from the following five re- D2 of 26S rD A showed that RRL YB-481I, and con-
gions of the rD A repeat: 18S+ITS 1 (primers S- specific strains, differ from all currently recognized asco-
I+ITS-2 (5'-GCT GCG TTC TTC ATC GAT GC)), mycetous yeasts [6]. The closest known species is Z. lentus,
18S (primers S-I + S-8A), ITS (primers S-7A + ITS-4 from which RRL YB-48 11 differs at nine of 585 nucle-
(5'-TCC TCC GCT TAT TGA TAT GC)), ITS2+5'-half otide positions (1.5%). Kurtzman and Robnett [6] demon-
of 26S (primers ITS-3 (5'-GCA TCG ATG AAG AAC strated for ascomycetous yeasts that strains differing by
GCA GC)+ L-I6IIAR (5'-CAC CTT GGA GAC CTG more than 1% substitutions in domain DI/D2 represent
CTG CGG)) and the 3'-half of 26S (primers L-I6IIAF separate species. The genus Zygosaccharomyces has been
(5' -CCG CAG CAG GTC TCC AAG GTG)+ L-ETS2- found to be polyphyletic from phylogenetic analysis of
IAR (5'-GGC TTA ATC TCA GCA GAT CG)). seq uences from domain D I/D2 [6], as well as from 18S
The amplicons were purified with Geneclean II (Bio 101, rO A [10,11]. Species that form a clade with Z. rouxii,
La Jolla, CA, USA) and digested for 24 h at 37°C with the the type species, are Z. bailii, Z. bisporus, Z. lentus, Zy-
restriction enzymes DdeI and MboI, either singly or in gosaccharomyces mellis, and the new species detected in
combination, using the manufacturer's (Stratagene, La the present study. Species currently assigned to Zygosac-
Jolla, CA, USA) protocol, except that the enzyme concen- charomyces that are not part of the Z. rouxii clade on the
trations were doubled. Aliquots of the enzyme digests were basis of rD A analysis are Z. cidri, Z. fermentati, z.
electrophoresed on 4% agarose gels (3: 1 uSieve-SeaKem, florentinus, z. microellipsoides and Z. mrakii. Conse-
FMC Corp., Rockland, ME, USA) in 1 X TAE buffer (40 quently, in view of the genetic isolation predicted for
mM Trizma base, 20 mM sodium acetate, 1 mM disodium RRL YB-4811 from rD A analysis and its phylogenetic
EOTA, pH 8.0). The molecular mass marker was ~XI74/ placement in the Z. rouxii clade (Fig. 1), the following new
HaeIII (Stratagene) with fragments ranging from 72 to species is proposed.
1353 bp. Gels were stained with ethidium bromide and
photographed under UV illumination.
98 100
Z. bailii U72161 Z. bailii X91083
92 65
Table 2
Responses of Z. kombuchaensis on fermentation, assimilation and other growth test a.b
Fermentation:
Glucose + Maltose Trehalose
Galactose Lactose
Sucrose + Raffinose
Assimilation:
Glucose + L-Ara binose a-Methyl-o-glucoside
Galactose + o-Arabinose Salicin
L-Sorbose v o-Ribose o-Gluconate
Sucrose v L-Rhamnose 2-Keto-o-gluconate
Maltose v o-Glucosamine 5-Keto-o-gluconate
Cellobiose N-Acetyl-o-glucosamine Saccharate
Trehalose Methanol oL-Lactate
Lactose Ethanol + Succinate
Melibiose Glycerol Citrate
Raffinose Erythritol Inositol
elezitose Ribitol Hexadecane
Inulin Galactitol . itrate
Soluble starch o-Mannitol v Vitamin-free
o-Xylose o-Glucitol v
Additional growth tests:
10% NaCl/5% glucose v Cycloheximide, 100 !lg ml-\ Gelatin liquefaction w/-
Starch formation Cadaverine + Growth at 37°C
aCombined test results from RRL YB-4810, YB-4811, Y-27162, and Y-27163.
b_ negative, + positive, w weak, v variable, i.e. + or -.
c.P. Kurtzman et al./FEMS Yeast Research 1 (2001) 133 138 137
ellipsoidal (3.0-6.7 X 3.8-8.7 Ilm), and occur singly, in galactose and assimilate raffinose, and can be separated
pairs, and in small clusters (Fig. 2A). Growth is white to from the sensu stricto group by these reactions. Earlier
tannish-white, dull to semi-glistening and butyrous. work [12,13] showed that Z. rouxii and Z. mellis did not
grow on media containing 1% acetic acid and could be
3.1.2.2. Growth on the surface of assimilation media. separated from Z. bailii and Z. bisporus by this test.
Pellicles are not formed. Z. kombuchaensis grows in the presence of 1% acetic
acid, but some strains of Z. lentus do not ([7], this study).
3.1.2.3. Dalmau plate culture on yeast morphology However, Z. lentus does grow in the presence of 0.9%
agar. After 7 days at 25°C, neither pseudohyphae nor acetic acid, and this allows separation of Z. bailii, Z. bis-
true hyphae are formed under the coverglass. Aerobic porus, Z. kombuchaensis and Z. lentus from Z. mellis and
growth is semi-glistening, white to tannish-white, butyr- Z. rouxii. The latter two species can be separated from
ous, and raised, but with a central depression. Colony each other on sodium chloride media [12]. Of the four
margins may be entire or with small, irregular lobes. acetic acid tolerant species, Z. bailii assimilates trehalose,
whereas the other three taxa do not. Z. bisporus does not
3.1.2.4. Ascosporulation. Ascospores were produced ferment sucrose and thereby can be separated from
on YM and 5% ME agar media after 3-7 days at 25°C. Z. kombuchaensis and Z. lentus. However, there appear
Asci are conjugated and many show the 'dumbbell' con- to be no fermentation or assimilation reactions on stan-
figuration typical of Zygosaccharomyces species in which dard tests that will separate Z. kombuchaensis from
the equally sized rounded conjugants are joined by a con- Z. lentus. Steels et al. [7] reported that Z. lentus did not
jugation tube. In this configuration, each conjugant forms assimilate galactose, L-sorbose and sucrose, but these three
one to two spherical ascospores (Fig. 2B). Other asci lack sugars permitted growth of Z. lentus in our tests, and
this configuration and form two to four ascospores in just strains of Z. kombuchaensis gave variable growth reactions
one of the conjugating cells, which is larger than the other on the sugars.
conjugant (Fig. 2C). Species showing the type of conjuga- To provide a rapid diagnostic method for separation of
tion described are ordinarily homothallic. Ascospores were Z. kombuchaensis and Z. lentus, we examined RFLPs for
observed in all four known strains of Z. kombuchaensis, five regions of the rD A repeat using the enzymes DdeI
but RRL YB-4810 failed to form ascospores in the and MboI, either singly or in combination. RFLP patterns
present study, although ascosporulation was observed on from ITS, I8S, ITS2+5' -half of 26S and 3'-half of 26S
two earlier occasions.
en en
>- >-
I
failed to resolve the two species either due to failure to cut quently, it appears that all of these species share an ability
or to a lack of uniformity of patterns among strains of a to grow in high sugar media at low pH. In view of this,
species. The amplicon comprised of I8S and ITS 1 pro- Z. kombuchaensis could potentially occur as a spoilage
vided resolution of Z. kombuchaensis and Z. lentus, with organism in acidic high sugar foods and beverages.
all strains giving species-specific patterns. Either enzyme
alone was adequate for separation of the two species,
but when DdeI and MboI were used in combination, mi- Acknowledgements
nor bands present in single enzyme digests disappeared
leaving a uniform pattern of major bands (Fig. 3). A dou- Larry W. Tjarks is gratefully acknowledged for skillful
ble enzyme digest of the I8S-ITS 1 amplicon also resolved operation of the nucleic acid sequencer. The mention of
the type strains of Z. bailii and Z. bisporus from each firm names or trade products does not imply that they are
other and from Z. kombuchaensis and Z. lentus, but addi- endorsed or recommended by the U.S. Department of
tional strains of Z. bailii and Z. bisporus were not tested Agriculture over other firms or similar products not men-
because these two species can be separated using growth tioned.
tests. Amplicons that were treated with the Geneclean
procedure gave much clearer RFLP patterns, but species
could be recognized from digests made using the unpuri-
fied PCR reaction mixtures. References