Professional Documents
Culture Documents
016006-0
Cocoa beans, the principal raw material of chocolate, have to genotypic properties were isolated from malt extract agar
be fermented, dried and roasted to obtain the characteristic (Nielsen et al., 2007). Preliminary pheno- and genotypic
cocoa flavour and taste. The fermentation of cocoa is a results showed that the isolates clustered in three distinct
microbiologically complex process involving the activities of groups, all representing putatively novel yeast species. This
yeasts, lactic acid bacteria and acetic acid bacteria with yeasts study presents the morphological, biochemical and molecu-
being particularly important during the initial phases of the lar characterization of these isolates. Group A consisted of a
fermentation process (Schwan & Wheals, 2004; Jespersen single isolate (G3T5CBS 11009T5CCUG 56721T), group B
et al., 2005; Nielsen et al., 2007). During an investigation of comprised two isolates [G6T (5CBS 11010T5CCUG 56722T)
the micro-organisms involved in the fermentation of cocoa and G17] and group C contained four isolates [G15T(5CBS
beans, a number of yeast isolates with unusual pheno- and 11011T5CCUG 56723T), G68, G71 and G174]. All isolates
were isolated during the first 12 h of cocoa fermentation and
represented between 3 and 14 % of the total yeast biota at the
Abbreviation: Rep-PCR, repetitive palindromic polymerase chain
reaction.
time of sampling (Nielsen et al., 2007).
The GenBank/EMBL/DDBJ accession numbers for the 26S rRNA gene All isolates and reference strains were grown in YPG broth
sequences of Candida halmiae sp. nov. G3T, Geotrichum ghanense sp. [yeast extract 5 g l21 (Merck), glucose 10 g l21, peptone
nov. G6T and Candida awuaii sp. nov. G15T are DQ466525, DQ466527 10 g l21, pH 5.6] at 25 uC for 2–14 days. For long-term
and EU876854, respectively. storage, 20 % glycerol was added to the medium and
Supplementary figures showing (GTG)5-PCR fingerprints and corres- cultures were stored at 280 uC.
ponding dendrograms, derived from UPGMA linkage of correlation
coefficients, for the three novel species are available with the online The micro morphology of the isolates grown for 1–5 days
version of this paper. in YM (yeast extract 3 g l21, malt extract 3 g l21, peptone
5 g l21, glucose 10 g l21, pH 5.6) and YPG broth (25 uC) Table 1. Key phenotypic characteristics of Candida halmiae
was determined using phase-contrast microscopy (Fig. 1). sp. nov. and its closest phylogenetic relatives
Colony morphology was determined after 4–14 days of
Taxa: 1, Candida halmiae sp. nov.; 2, Candida diversa; 3, Candida
growth on YGP and MYGP agar (25 uC). Spore formation
silvae; 4, Saturnispora ahearnii; 5, Saturnispora besseyi; 6, Saturnispora
was examined on YM agar, V8 agar, 5 % malt agar and
dispora; 7, Saturnispora hagleri; 8, Saturnispora mendoncae; 9,
acetate agar (Robert et al., 2008) incubated for 4–28 days
Saturnispora saitoi; 10, Saturnispora zaruensis. +, Positive; 2,
(20 and 25 uC). Spore formation was determined using
negative; V, variable, strain dependent; S, slow; W, weak. Data partially
bright-field microscopy. None of the isolates investigated adopted from Kurtzman (1998a), Meyer et al. (1998), Morais et al.
produced ascospores. (2005) and Kurtzman (2006).
The carbohydrate assimilation and fermentation patterns
of the new isolates were determined following the protocol Characteristic 1 2 3 4 5 6 7 8 9 10
of Yarrow (1998) aided by use of the API ID32C Assimilation of:
identification system (bioMérieux). The results of these Cellobiose W2 2 2 2 2 2 2 2 2
analyses are presented in Tables 1, 2 and 3 and the species Glycerol 2V + 2 2 2 S V 2 2
descriptions. Maltose S 2 2 2 2 2 2 2 2 2
DL-Lactic acid + 2 V + + W/2 + + + +
Trehalose W 2 2 2 2 + + 2 + +
D-Xylose W V 2 2 2 2 2 2 2 2
http://ijs.sgmjournals.org 1461
D. S. Nielsen, M. Jakobsen and L. Jespersen
Table 2. Key phenotypic characteristics of Geotrichum Table 3. Key phenotypic characteristics of Candida awuaii sp.
ghanense sp. nov. and its closest phylogenetic relatives nov. and its closest phylogenetic relatives
Taxa: 1, Geotrichum ghanense sp. nov.; 2, Geotrichum silvicola; 3, Taxa; 1, Candida awuaii sp. nov.; 2, Candida rugopelliculosa; 3, Pichia
Geotrichum klebahnii; 4, Galactomyces geotrichum; 5, Dipodascus occidentalis; 4, Pichia exigua. +, Positive; 2, negative; V, variable,
albidus; 6, Dipodascus armillariae; 7, Dipodascus australiensis; 8, strain dependent; S, slow; W, weak. Data partially adopted from
Dipodascus geniculatus; 9, Dipodascus macrosporus. +, Positive; 2, Kurtzman (1998b) and Meyer et al. (1998).
negative; V, variable, strain dependent; W, weak; ND, not determined.
Data partially adopted from de Hoog et al. (1998a, b, c) and Pimenta Characteristic 1 2 3 4
et al. (2005).
Fermentation of maltose + 2 2 2
Assimilation of:
Characteristic 1 2 3 4 5 6 7 8 9
Cellobiose + 2 2 2
Fermentation of: Maltose V 2 2 2
Glucose + 2 + V 2 2 2 W/2 2 Ribitol V 2 2 2
Galactose + ND W/2 V 2 2 2 2 2 Sucrose S 2 2 2
Trehalose V 2 2 2
Assimilation of: W 2 2 +
D-Xylose
Cellobiose + 2 2 2 2 + 2 2 +
Maltose +/W 2 2 2 2 2 2 + 2
D-Mannitol + + + V + + + + +
Ribitol + 2 V V 2 2 V 2 V observed in the new isolate, the novel species must belong
Sucrose W 2 2 2 2 2 2 2 2 to the anamorphic ascomycetous yeasts. The name
Trehalose W 2 2 2 2 2 2 2 2 Candida halmiae sp. nov. is proposed for the new isolate,
+ + + + + + + + +
D-Xylose with strain G3T (5CBS 11009T5CCUG 56721T) being the
type strain.
using BioNumerics version 4.5 (Applied Maths). Unknown Isolates G6T and G17 formed a genetically and phenotyp-
bases were discarded for the analysis. The statistical ically distinct group that was most closely related to D.
reliability of the topology of the phylogenetic trees was albidus, D. geniculatus and D. australiensis but as ascospore
evaluated using bootstrap resampling of the data (1000 formation was not observed, the isolates belong to the
resamplings) (Figs 2, 3 and 4). anamorphic ascomycetous yeasts. Phenotypically, the
ability to ferment galactose and assimilate sucrose and
Additionally, the isolates and their closest phylogenetic trehalose differentiated strains G6T and G17 from their
neighbours were genotypically investigated by Repetitive closest phylogenetic neighbours (Table 2). The results
Element Palindromic (rep)-PCR using the primer GTG5 obtained in the present study clearly indicate that isolates
(59-GTGGTGGTGGTGGTG-39) as previously described G6T and G17 represent a novel species in the anamorphic
(Andrade et al., 2006; Nielsen et al., 2007). Isolate G3T genus Geotrichum, for which we propose the name
(group A) was clearly separated (r¡68 %) from type Geotrichum ghanense sp. nov. with strain G6T (5CBS
strains representing the phylogenetically closest relatives 11010T5CCUG 56722T) being the type strain.
(see Supplementary Fig. S1 in IJSEM Online). Isolates G6T
and G17 (group B) clustered closely together (r.90 %) and Isolates G15T, G68, G71 and G174 formed a genetic and
were only distantly related (r¡52 %) to type strains phenotypic distinct group phylogenetically closest related
representing the phylogenetically closest relatives (see to C. rugopelliculosa, P. occidentalis and P. exigua.
Supplementary Fig. S2). Isolates G15T, G68, G71 and Phenotypically, the ability to ferment maltose and
G174 (group C) formed two closely related (r582 %) but assimilate cellobiose and ribitol clearly differentiated
distinct groups with the four isolates clearly clustering strains G15T, G68, G71 and G174 from their closest
(r561 %) away from the closest phylogenetic relatives (see phylogenetic neighbours (Table 3). In conclusion, the
Supplementary Fig. S3). results obtained in the present study clearly indicate that
isolates G15T, G68, G71 and G174 represent a novel species
Based on the above data, it can be concluded that strain in the genus Candida, for which we propose the name
G3T is genetically and phenotypically distinct from all Candida awuaii sp. nov. with strain G15T (5CBS
currently recognized species with S. mendoncae and S. 11011T5CCUG 56723T) being the type strain.
ahearnii being the closest phylogenetic relatives.
Phenotypically, strain G3T can be differentiated from the
Latin diagnosis of Candida halmiae Nielsen,
closest phylogenetic neighbours on the basis of its ability to
Jakobsen et Jespersen sp. nov.
assimilate cellobiose, D-xylose and maltose (slow reaction)
as seen from Table 1. The results obtained in the present In liquido YM, post dies 1–3 ad 25 uC, cellulae vegetativae
study clearly indicate that strain G3T represent a novel ovoidae (2.5–5.0 mm63.8–7.5 mm), singulae aut binae. Per
species that is genetically closely related to the genus gemmationem multipolarem reproducentes. In agaro MYGP
Saturnispora. However, as ascospore production was not post dies 4–6 ad 25 uC cultura 2–3 mm, candida et cremea,
butyrosa, glabra, infima-convexa et margo integra. diameter of 2–3 mm, tannish-white, butyrous, smooth,
Ascosporae non formantur. Glucosum et maltosum fermen- glistering, low convex and with an entire margin. Formation
tatur. Sucrosum, D-galactosum, D-trehalosum, D-lactosum, of ascospores is not observed. Glucose and maltose are
D-raffinosum non fermentatur. Assimilantur D-glucosum, fermented. Sucrose, D-galactose, trehalose, lactose and
ribitolum (exigue), D-xylosum (exigue), cellobiosum (exigue), raffinose are not fermented. Glucose, ribitol (weak),
D-mannitolum, maltosum (exigue), trehalosum (exigue), et D-xylose (slow), cellobiose (slow), D-mannitol, maltose
DL-acidum lacticum. Non assimalatur L-sorbosum, sucrosum, (slow), trehalose (weak) and DL-lactic acid are assimilated.
D-galactosum, D-sorbitolum, D-ribosum, N-acetylglucosami- L-Sorbose, sucrose, D-galactose, D-sorbitol, D-ribose,
num, L-rhamnosum, L-arabinosum, erythritolum, D-raffino- N-acetylglucosamine, L-rhamnose, L-arabinose, erythritol,
sum, D-melibiosum, D-melezitosum, 2-ketogluconatum, raffinose, melibiose, melezitose, 2-ketogluconate, gluconate,
gluconatum, methyl D-pyranosidium, D-lactosum, inositolum methyl D-glucopyranoside, D-lactose, inositol and glycerol
et glycerolum. Non assimalatur nitratum. Aesculinum are not assimilated. Aesculin is hydrolysed. Nitrate is not
hydrolysatur. Crescentiae (exigue) 37 uC. Typus G3T assimilated. No growth in the presence of 0.01 % cyclohex-
(5CBS 11009T5CCUG 56721T). imide. Grows at 37 uC, but growth is weak and delayed.
The type strain, G3T (5CBS 11009T5CCUG 56721T), was
Description of Candida halmiae Nielsen, isolated from cocoa fermentations in Tafo, Ghana. The
Jakobsen & Jespersen sp. nov. description of the type strain corresponds to the descrip-
tion of the species.
Candida halmiae (hal9mi.ae. N.L. fem. gen. n. halmiae of
Halm, named in honour of Dr Mary Halm, a Ghanaian
microbiologist who has contributed significantly to our Latin diagnosis of Geotrichum ghanense Nielsen,
understanding of the importance of yeasts in indigenous Jakobsen et Jespersen sp. nov.
African fermented foods).
In liquido YM, post dies 1–5 ad 25 uC pellicula formantur et
In YM and YGP broth after 1–3 days at 25 uC, cells are cellulae ovoidae aut elongatae (3.5–6.366.3–12.5 mm),
ovoidal (2.5–5.0 mm63.8–7.5 mm), occur singly and in singulae authyphae. Hyphae ramosae cum arthroconidiis
pairs, and divide by multilateral budding. On YPG and formantur. In agaro MYGP post dies 4 ad 25 uC cultura 5–
MYGP agar (4–6 days, 25 uC) colonies are circular with a 10 mm, candida, farinosus, margine ciliata. Ascosporae non
http://ijs.sgmjournals.org 1463
D. S. Nielsen, M. Jakobsen and L. Jespersen
cosamine, L-rhamnose, L-arabinose, erythritol, raffinose, Jespersen, L., Nielsen, D. S., Hønholt, S. & Jakobsen, M. (2005).
melibiose, melezitose, 2-ketogluconate, gluconate, methyl D- Occurrence and diversity of yeasts involved in fermentation of West
African cocoa beans. FEMS Yeast Res 5, 441–453.
glucopyranoside, lactose, inositol and glucosamine are not
assimilated. Assimilation of maltose (slow), ribitol, D- Kurtzman, C. P. (1998a). Saturnispora Liu & Kurtzman. In The Yeasts
– a Taxonomic Study, pp. 387–390. Edited by C. P. Kurtzman & J. W.
mannitol (slow) and trehalose (slow) are strain dependent.
Fell. Amsterdam: Elsevier.
Nitrate is not assimilated. No growth in the presence of
Kurtzman, C. P. (1998b). Issatchenkia Kudryavtsev emend.
0.01 % cycloheximide. Growth occurs at 37 uC.
Kurtzmann, Smiley & Johnson. In The Yeasts – a Taxonomic Study,
The type strain, G15T (5CBS 11011T5CCUG 56723T), and pp. 221–226. Edited by C. P. Kurtzman & J. W. Fell. Amsterdam:
all other known strains of the species have been isolated Elsevier.
from cocoa fermentations in Tafo, Ghana. The description Kurtzman, C. P. (2006). New species and new combinations in the
of the type strain corresponds to the description the species yeast genera Kregervanrija gen. nov., Saturnispora and Candida. FEMS
except that ribitol (slow) and trehalose (slow) are Yeast Res 6, 288–297.
assimilated and D-mannitol is not assimilated. Kurtzman, C. P., Robnett, C. J. & Basehoar-Powers, E. (2008).
Phylogenetic relationships among species of Pichia, Issatchenkia and
Williopsis determined from multigene sequence analysis, and the
Acknowledgements proposal of Barnettozyma gen. nov., Lindnera gen. nov and
Wickerhamomyces gen. nov. FEMS Yeast Res 8, 939–954.
The work performed was partly financed through the EU INCO Meyer, S. A., Payne, R. W. & Yarrow, D. (1998). Candida Berkhout. In
project: ‘Developing biochemical and molecular markers for deter- The Yeasts – a Taxonomic Study, pp. 454–573. Edited by C. P.
mining quality assurance in the primary processing of cocoa in West Kurtzman & J. W. Fell. Amsterdam: Elsevier.
Africa – COCOQual’ (ICA4-CT-2002-10040). The cooperation of the
Cocoa Research Institute of Ghana (Dr J. S. Takrama) and the Morais, P. B., Lachance, M. A. & Rosa, C. A. (2005). Saturnispora
excellent technical assistance of Janne Benjaminsen are highly hagleri sp. nov., a yeast species isolated from Drosophila flies in
appreciated. Atlantic rainforest in Brazil. Int J Syst Evol Microbiol 55, 1725–
1727.
Nielsen, D. S., Teniola, O. D., Ban-Koffi, L., Owusu, M., Andersson, T.
References & Holzapfel, W. H. (2007). The microbiology of Ghanaian cocoa
fermentations analysed using culture dependent and culture inde-
Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., pendent methods. Int J Food Microbiol 114, 168–186.
Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new Pimenta, R. S., Alves, P. D. D., Corrêa, A., Jr, Lachance, M. A.,
generation of protein database search programs. Nucleic Acids Res 25, Prasad, G. S., Rajaram, Sinha, B. R. R. P. & Rosa, C. A. (2005).
3389–3402. Geotrichum silvicola sp. nov., a novel asexual arthroconidial yeast
Andrade, M. J., Rodriguez, M., Sánchez, B., Aranda, E. & Córdoba, J. J. species related to the genus Galactomyces. Int J Syst Evol Microbiol 55,
(2006). DNA typing methods for differentiation of yeasts related to 497–501.
dry-cured meat products. Int J Food Microbiol 107, 48–58. Robert, V., Groenewald, G., Epping, W., Boekhout, T., Smith, M. &
de Hoog, G. S., Smith, M. T. & Guého, E. (1998a). Dipodascus de Stalpers, J. (2008). CBS Yeasts Database. Utrecht, The Netherlands:
Lagerheim. In The Yeasts – a Taxonomic Study, pp. 181–193. Edited Centraalbureau voor Schimmelcultures.
by C. P. Kurtzman & J. W. Fell. Amsterdam: Elsevier. Schwan, R. F. & Wheals, A. E. (2004). The microbiology of cocoa
de Hoog, G. S., Smith, M. T. & Guého, E. (1998b). Galactomyces fermentation and its role in chocolate quality. Crit Rev Food Sci Nutr
Redhead & Malloch. In The Yeasts – a Taxonomic Study, pp. 209–213. 44, 205–222.
Edited by C. P. Kurtzman & J. W. Fell. Amsterdam: Elsevier. Yarrow, D. (1998). Methods for the isolation, maintenance and
de Hoog, G. S., Smith, M. T. & Guého, E. (1998c). Geotrichum Link: identification of yeasts. In The Yeasts – a Taxonomic Study, 4th edn,
Fries. In The Yeasts – a Taxonomic Study, pp. 574–579. Edited by C. P. pp. 77–100. Edited by C. P. Kurtzman & J. W. Fell. Amsterdam:
Kurtzman & J. W. Fell. Amsterdam: Elsevier. Elsevier.
http://ijs.sgmjournals.org 1465