Research Article
Print
Research Article
New species of Yamadazyma from rotting wood in China
expand article infoWan-Li Gao‡, Ying Li‡, Chun-Yue Chai‡, Zhen-Li Yan§, Feng-Li Hui‡
‡ Nanyang Normal University, Nanyang, China
§ State Key Laboratory of Motor Vehicle Biofuel Technology, Henan Tianguan Enterprise Group Co., Ltd, Nanyang, China

Corresponding author: Feng-Li Hui ( fenglihui@yeah.net )

Academic editor: Thorsten Lumbsch
© 2021 Wan-Li Gao, Ying Li, Chun-Yue Chai, Zhen-Li Yan, Feng-Li Hui.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation: Gao W-L, Li Y, Chai C-Y, Yan Z-L, Hui F-L (2021) New species of Yamadazyma from rotting wood in China. MycoKeys 83: 69-84. https://doi.org/10.3897/mycokeys.83.71156
Open Access

Abstract

Yamadazyma is one of the largest genera in the family Debaryomycetaceae (Saccharomycetales, Saccharomycetes) with species mainly found in rotting wood, insects and their resulting frass, but also recovered from flowers, leaves, fruits, tree bark, mushrooms, sea water, minerals, and the atmosphere. In the present study, several strains obtained from rotting wood in Henan and Yunnan Provinces of China were isolated. Based on morphology and a molecular phylogeny of the rDNA internal transcribed spacer region (ITS) and the D1/D2 domain of the large subunit (LSU) rDNA, these strains were identified as three new species: Yamadazyma luoyangensis, Y. ovata and Y. paraaseri; and three previously described species, Y. insectorum, Y. akitaensis, and Y. olivae. The three new species are illustrated and their morphology and phylogenetic relationships with other Yamadazyma species are discussed. Our results indicate a high undiscovered diversity of Yamadazyma spp. inhabiting rotting wood in China.

Keywords

Debaryomycetaceae, phylogeny, rotting wood-inhabiting yeast, taxonomy, Yamadazyma

Introduction

The genus Yamadazyma Billon-Grand (1989) was erected to accommodate 16 species previously assigned to the genus Pichia (Billon-Grand 1989). These species have coenzyme Q-9 as their main ubiquinone, form hat-shaped ascospores, produce pseudohyphae, ferment sugars, and require an exogenous source of vitamins for growth (Billon-Grand 1989; Kurtzman 2011). However, Yamadazyma was not initially accepted as genus due to a phylogenetic analysis of D1/D2 LSU rDNA strongly suggesting its polyphyletic nature (Kurtzman and Robnett 1998). Kurtzman and Suzuki (2010) analyzed phylogenetic relationships among species of Pichia and related genera based on combined sequences of the D1/D2 LSU rDNA and SSU rDNA, and proposed a new circumscription for Yamadazyma with six sexual species and 11 asexual species assigned to the genus Candida (Kurtzman and Suzuki 2010). Yamadazyma was later resolved as a well-supported monophyletic clade and a generally accepted genus in the family Debaryomycetaceae, order Saccharomycetales (Kurtzman and Suzuki 2010; Kurtzman 2011). The monophyly of the Yamadazyma clade was also supported by combined analysis of the ITS and D1/D2 LSU rDNA (Groenewald et al. 2011; Haase et al. 2017). In the fifth edition of The Yeasts: A Taxonomic Study, Yamadazyma philogaea, the type species of the genus, as well as Y. akitaensis, Y. mexicana, Y. nakazawae, Y. scolyti, Y. triangularis, and 23 Candida species were placed in the Yamadazyma clade (Kurtzman 2011; Lachance et al. 2011). Since then, a few novel Candida species have been described from this clade, including C. kanchanaburiensis (Nakase et al. 2008), C. khao-thaluensis, C. tallmaniae, C. oceani (Burgaud et al. 2011), and C. vaughaniae (Groenewald et al. 2011). In addition, many new species, e.g., Y. phyllophila, Y. paraphyllophila, Y. siamensis (Kaewwichian et al. 2013), Y. terventina (Ciafardini et al. 2013), Y. ubonensis (Junyapate et al. 2014), Y. dushanensis (Wang et al. 2015), Y. epiphylla, Y. insecticola (Jindamorakot et al. 2015), Y. riverae (Lopes et al. 2015), Y. barbieri (Burgaud et al. 2016), Y. endophytica (Khunnamwong and Limtong 2016), Y. kitorensis (Nagatsuka et al. 2016), Y. laniorum (Haase et al. 2017), and Y. cocois (Maksimova et al. 2020), have been proposed as part of the genus, and three have already been transferred to Yamadazyma as new combinations: Y. olivae, Y. tumulicola, and Y. takamatsuzukensis (Nagatsuka et al. 2016). The Yamadazyma clade currently consists of 24 species of the genus Yamadazyma and 38 asexual species still assigned to the genus Candida, making it one of the largest genera tentatively assigned to the family Debaryomycetaceae (Groenewald et al. 2011; Kurtzman 2011; Maksimova et al. 2020). Among 24 species included in this genus, 7 were sexual morphs, viz. Y. akitaensis, Y. mexicana, Y. nakazawae, Y. philogaea, Y. riverae, Y. scolyti, and Y. triangularis (Kurtzman 2011; Lopes et al. 2015).

Yamadazyma species can be originally found in tropical, subtropical, and temperate regions of different continents, but most known species appear to exist in Asia and South America (Nakase et al. 2008; Groenewald et al. 2011; Kurtzman 2011; Lachance et al. 2011; Kaewwichian et al. 2013; Junyapate et al. 2014; Jindamorakot et al. 2015; Lopes et al. 2015; Wang et al. 2015; Burgaud et al. 2016; Khunnamwong and Limtong 2016; Nagatsuka et al. 2016). The genus has been heavily studied in Asia, and 17 species of Yamadazyma were previously reported in Japan and Thailand (Nakase et al. 2008; Groenewald et al. 2011; Kurtzman 2011; Lachance et al. 2011; Kaewwichian et al. 2013; Junyapate et al. 2014; Jindamorakot et al. 2015; Wang et al. 2015; Khunnamwong and Limtong 2016; Nagatsuka et al. 2016). By contrast, little is known about Yamadazyma spp. in China. To date, only three Yamadazyma species have been described in China, namely C. diospyri, Y. dushanensis, and Y. paraphyllophila (Lachance et al. 2011; Kaewwichian et al. 2013; Wang et al. 2015). In this study, we collected rotting wood samples from Yunnan and Henan Provinces in China. After isolation and examination, three new species and three known species of Yamadazyma were identified based on phenotypic characteristics and phylogenetic analysis, increasing the species diversity of Yamadazyma in China.

Materials and methods

Sample collection and yeast isolation

Samples of rotting wood were collected in the Xishuangbanna Primeval Forest Park (Yunnan Province, China) and the Tianchi Mountain National Forest Park (Henan Province, China). The Xishuangbanna Primeval Forest Park (21°98'N, 100°88'E) is 500 m above sea level (MASL), with a hot and humid climate. The average annual temperature is between 16 °C and 28 °C, and the average annual rainfall is above 1,100 mm. The Tianchi Mountain National Forest Park (34°33'N, 112°28'E) is at 850 MASL, with a continental monsoon climate, average annual temperature of 14–16 °C, and average annual rainfall between 800 mm and 900 mm. Fifty decayed wood samples were collected during July and August in 2018–2020. The samples were stored in sterile plastic bags and transported under refrigeration to the laboratory over a period of no more than 24 h. The yeast strains were isolated from rotting wood samples in accordance with the methods described by Wang et al. (2015). Each sample (1 g) was added to 20 ml sterile yeast extract-malt extract (YM) broth (0.3% yeast extract, 0.3% malt extract, 0.5% peptone, 1% glucose, pH 5.0 ± 0.2) supplemented with 0.025% sodium propionate and 200 mg/L chloramphenicol in a 150 ml Erlenmeyer flask and then cultured for 3–10 days on a rotary shaker. Subsequently, 0.1 ml aliquots of the enrichment culture and appropriate decimal dilutions were spread on YM agar plates and then incubated at 25 °C for 3–4 days. Different yeast colony morphotypes were then isolated by repeated plating on YM agar and then stored on YM agar slants at 4 °C or in 15% glycerol at – 80 °C.

Phenotypic study

Morphological and physiological properties were determined according to those used by Kurtzman et al. (2011). The beginning of the sexual stage was determined by incubating single or mixed cultures of each of the two strains on cornmeal (CM) agar, 5% malt extract (ME) agar, dilute (1:9) V8 agar, or yeast carbon base plus 0.01% ammonium sulfate (YCBAS) agar at 15 and 25 °C for 6 weeks (Kurtzman 2011; Wang et al. 2015). The assimilation of carbon and nitrogen compounds and related growth requirements were tested at 25 °C. The effects of temperature from 25–40 °C were examined in liquid and agar plate cultures. Photomicrographs were taken using a Leica DM 2500 microscope (Leica Microsystems GmbH, Wetzlar, Germany) with a Leica DFC295 digital microscope color camera, with bright field, phase contrast, and DIC optics. Novel taxonomic descriptions and proposed names were deposited in MycoBank (http://www.mycobank.org; 8 June 2021) (Crous et al. 2004).

DNA extraction, PCR amplification, and sequencing

Genomic DNA was extracted from the yeast using an Ezup Column Yeast Genomic DNA Purification Kit, according to the manufacturer’s instructions (Sangon Biotech, Shanghai, China). The internal transcribed spacer (ITS) and the D1/D2 domain of the large subunit (LSU) rDNA were respectively amplified using ITS5/ITS4 (White et al. 1990) and NL1/NL4 (Kurtzman and Robnett 1998) primers with cycling conditions of 94 °C/30 s, 55 °C/50 s, 72 °C/60 s. All the PCR protocols had 35 cycles including 94 °C/5 min initial denaturation and 72 °C/10 min final extension.

The 25 µL total volume of PCR mixture contained 9.5 µL of ddH2O, 12.5 µL of 2X PCR Master Mix (TIANGEN Co., China), 1 µL of DNA template, and 1 µL of forward and reverse primers (10 µM each) in each reaction. PCR amplified products were checked on 1% agarose electrophoresis gels stained with GoldView I nuclear staining dye (1 µL/10 mL of agarose). Purification and sequencing of PCR products were done by Sangon Biotech (Shanghai) Co., Ltd., Shanghai, China. A consensus sequence for each gene region was assembled in SeqMan (DNAStar, Inc., Madison, WI, USA). The newly-generated sequences were deposited in GenBank (https://www.ncbi.nlm.nih.gov/genbank/ (accessed on 30 May 2021); Table 1).

Abbreviations:

CBS CBS-KNAW Collections, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands;

CECT the Spanish Type Culture Collection, Valencia, Spain;

VTCC Vietnam Type Culture Collection, Hanoi, Vietnam;

NYNU Microbiology Lab, Nanyang Normal University, Henan, China;

T type strain.

Phylogenetic analysis

The sequences obtained in this study and the reference sequences downloaded from GenBank (Table 1) were aligned using MAFFT v 7(https://mafft.cbrc.jp/alignment/server/large.html;) (Katoh et al. 2019) and manually edited using MEGA7 (Kumar et al. 2016). The best-fit nucleotide substitution models for individual and combined datasets were selected using jModelTest v2.1.7 (Darriba et al. 2012) according to the Akaike information criterion. Phylogenetic analyses of combined gene regions (ITS and D1/D2 LSU) were performed using MEGA7 for maximum parsimony (MP) analysis (Kumar et al. 2016) and PhyML v3.0 for maximum likelihood (ML) analysis (Guindon et al. 2010). Scheffersomyces coipomoensis (CBS 8178) and Babjeviella inositovora (CBS 8006) were used as the outgroup taxa based on Haase et al. (2017) and Nagatsuka et al. (2016).

Table 1.
Download as
CSV
XLSX

Sequences used in molecular phylogenetic analysis. Entries in bold are newly generated in this study.

Species Strain no. Locality Sample GenBank accession numbers
ITS D1/D2
Candida aaseri CBS 1913T Norway Sputum AY821838 U45802
C. amphixiae CBS 9877T Panama Beetle EU491501 AY520327
C. andamanensis CBS 10859T Thailand Estuarine water AB525239 AB334210
C. atlantica CBS 5263T Portugal Shrimp egg AJ539368 U45799
C. atmosphaerica CBS 4547T Spain Atmosphere AJ539369 U45779
C. blattariae CBS 9876T Panama Cockroach FJ715435 AY640213
C. buinensis CBS 6796T Papua New Guinea Gelatinous exudate HQ283376 U45778
C. cerambycidarum CBS 9879T Panama Beetle AY964669 AY520299
C. conglobata CBS 2018T – Tubercular lung AJ539370 U45789
C. dendronema CBS 6270T South Africa Frass HQ283365 U45751
C. diddensiae CBS 2214T USA Shrimp AY580315 U45750
C. diospyri CBS 9769T China Kaki fruit AY450919 AY450918
C. endomychidarum CBS 9881T Panama Beetle AY964672 AY520330
C. friedrichii CBS 4114T Germany D-glucitol solution HQ283377 U45781
C. germanica CBS 4105T Germany Atmosphere HQ283366 AF245401
C. gorgasii CBS 9880T Panama Beetle AY964670 AY520300
C. insectorum CBS 6213T South Africa Frass HQ283372 U45791
C. insectorum NYNU 1672 China Rotten wood MZ314279 MZ314278
C. jaroonii CBS 10790T Thailand Frass AB360437 DQ404493
C. kanchanaburiensis CBS 11266T Thailand Mushroom NR_137581 KY106534
C. keroseneae CECT 13058T UK Aircraft fuel FJ235128 FJ357698
C. khao-thaluensis CBS 8535T Thailand Leaf HQ283374 HQ283383
C. koratica CBS 10789T Thailand Frass AB360443 AB354232
C. lessepsii CBS 9941T Panama Beetle AY964671 AY640214
C. membranifaciens CBS 1952T India Urine AJ606465 U45792
C. michaelii CBS 9878T Panama Beetle AY964673 AY520329
C. naeodendra CBS 6032T South Africa Frass AY580316 U45759
C. oceani CBS 11857T Atlantic Ocean Deep-sea coral NR_156008 GU002284
C. pseudoaaseri CBS 11170T Germany Blood culture JN241686 JN241689
C. sinolaborantium CBS 9940T Panama Beetle NR_111343 NG_055206
C. songkhlaensis CBS 10791T Thailand Frass AB360438 DQ404499
C. spencermartinsiae CBS 10894T Seawater Florida FJ008050 FJ008044
C. tallmaniae CBS 8575T French Guiana Flower HQ283378 HQ283385
C. tammaniensis CBS 8504T USA Frass HQ283375 AF017243
C. taylori CBS 8508T Belize Sea water FJ008051 FJ008045
C. temnochilae CBS 9938T Panama Beetle AY964678 AY242344
C. trypodendroni CBS 8505T Canada Beetle FJ153212 AF017240
C. vaughaniae CBS 8583T French Guiana Flower HQ283364 HQ283381
C. vrieseae CBS 10829T Brazil Bromeliad FJ755905 EU200785
Yamadazyma akitaensis CBS 6701T Japan Exudate DQ409164 U45766
Y. akitaensis NYNU 16719 China Rotten wood MZ314281 MZ314280
Y. barbieri CBS 14301T Brazil Sea water LT547714 LT547716
Y. cocois VTCC 920004T Vietnam Fruits of the coconut palm MN764369 MN764369
Y. dushanensis CBS 13914T China Rotten wood KM272249 KM272248
Y. endophytica CBS 14163T Thailand Corn leaf KT307981 KT307981
Y. epiphylla CBS 13384T Thailand Rice leaf LC006082 LC006026
Y. insecticola CBS 13382T Thailand Frass LC006081 DQ400379
Y. kitorensis CBS 14158T Japan Red viscous gel LC060995 LC060995
Y. laniorum CBS 14780T USA Bark KY588337 KY588136
Y. luoyangensis NYNU 201023T China Rotting wood MW365549 MW365545
Y. luoyangensis NYNU 201035 China Rotting wood MZ318445 MZ318422
Y. mexicana CBS 7066T Mexico Agria cactus AB054110 U45797
Y. nakazawae CBS 6700T Japan Exudate EU343867 U45748
Y. olivae CBS 11171T Greece Fermenting olive FJ715432 FJ715430
Y. olivae NYNU 167106 China Rotting wood MZ314288 MZ314282
Y. olivae NYNU 209116 China Rotting wood MZ318443 MZ318444
Y. ovata NYUN 191125T China Rotting wood MT990560 MT990559
Y. ovata NYUN 19130 China Rotting wood MZ318424 MZ318425
Y. ovata NYUN 19116 China Rotting wood MZ318442 MZ318423
Y. paraaseri NYNU 1811114T China Rotting wood MK682794 MK682805
Y. paraaseri NYNU 181033 China Rotting wood MZ318421 MZ318460
Y. paraphyllophila CBS 9928T China, Taiwan Pencil wood leaf AY559447 AY562397
Y. philogaea CBS 6696T South Africa Soil AB054107 U45765
Y. phyllophila CBS 12572T Thailand Corn leaf AB734050 AB734047
Y. riverae CBS 14121T Brazil Rotting wood KP900044 KP900043
Y. scolyti CBS 4802T USA Frass EU343807 U45788
Y. siamensis CBS 12573T Thailand Sugarcane leaf AB734049 AB734046
Y. takamatsuzukensis CBS 10916T Japan Air AB365470 AB365470
Y. tenuis CBS 615T Russia Beetle HQ283371 U45774
Y. terventina CBS 12510T Italy Olive oil JQ247717 JQ247717
Y. triangularis CBS 4094T Japan Tamari soya EU343869 U45796
Y. tumulicola CBS 10917T Japan Stone chamber AB365463 AB365463
Y. ubonensis CBS 12859T Thailand Tree bark NR_155998 AB759913
Scheffersomyces coipomoensis CBS 8178T – – NR_111424 U45747
Babjeviella inositovora CBS 8006T – – NR_111018 U45848

MP analysis was run using a heuristic search option of 1,000 search replicates with random-addition of sequences and tree bisection and reconnection (TBR) as the branch-swapping algorithm. Gaps were treated as missing data. Bootstrapping with 1,000 replicates was performed to determine branch support (Felsenstein 1985). Parsimony scores of tree length (TL), consistency index (CI), retention index (RI), and rescaled consistency (RC) were calculated for each generated tree. ML analysis was performed using a GTR site substitution model, including a gamma-distributed rate heterogeneity and a proportion of invariant sites (Guindon et al. 2010). Branch support was evaluated using a bootstrapping method of 1,000 bootstrap replicates (Hillis and Bull 1993). The phylogenies from MP and ML analyses were displayed using Mega7 and FigTree v1.4.3 (Rambaut 2016), respectively. ML and MP bootstrap support values above 50% are shown as first and second positionS above nodes, respectively.

Results

Molecular phylogeny

The alignment based on the combined nuclear dataset (ITS and D1/D2 LSU) included 65 taxa and two outgroup taxa (Scheffersomyces coipomoensis and Babjeviella inositovora), and was comprised of 1,103 characters including gaps (576 for ITS and 527 for D1/D2 LSU) in the aligned matrix. Of these characters, 351 were constant, 455 variable characters were parsimony-uninformative, and 297 characters were parsimony-informative. The heuristic search using MP analysis generated the most parsimonious tree (TL = 979, CI = 0.297, RI = 0.653, RC = 0.248). The best model applied in the ML analysis was GTR+I+G. The ML analysis yielded a best scoring tree with a final optimization likelihood value of –11,006.61. Both methods for phylogenetic tree inference resulted in a similar topology. Therefore, only the best scoring PhyML tree is shown with BS and BT values simultaneously in Figure 1.

Figure 1. 

Maximum likelihood phylogenetic tree of Yamadazyma inferred from the combined ITS and D1/D2 LSU dataset and rooted with Scheffersomyces coipomoensis (CBS 8178) and Babjeviella inositovora (CBS 8006). ML and MP bootstrap support values above 50% are respectively shown at the first and second positions. Newly sequenced collections are in blue boldface.

According to the phylogenetic tree (Figure 1), three known species, Y. insectorum, Y. akitaensis, and Y. olivae, were part of Yamadazyma. Yamadazyma luoyangensis, Y. ovata, and Y. paraaseri are new to science based on the distinct and well-supported molecular phylogenetic placement and morphological differences with their closest described relatives (Table 2). Phylogenetically, Y. luoyangensis clustered together with Y. ovata and other species, including Y. mexicana, Y. terventina, Y. dushanensis, and C. trypodendroni, while Y. paraaseri was closely related to C. aaseri with high bootstrap support (98% ML/98% MP).

Table 2.
Download as
CSV
XLSX

Physiological characteristics of the new Yamadazyma species and their closely related taxa.

Characteristics Y. luoyangensis Y. mexicana Y. ovata C. trypodendroni Y. paraaseri C. aaseri
Fermentation of
d-Glucose + + + + - v
Assimilation of
l-Sorbose – – + – + s
d-Glucosamine + + + – + –
l-Rhamnose + + – + – –
Melibiose – v + – – –
Lactose – + – – + v
Raffinose – + – – – –
Inulin + – – – + –
Xylitol + + – – +
Galactitol + v + – – –
2-Keto-d-Gluconate – s + + – –
Cadaverine – n – + – +
Growth tests
10%Nacl/5%glucose + + + v – +
Growth at 37 °C – + + – + +

+, positive reaction; –, negative reaction; s, slow positive reaction; v, variable reaction; n, data not available.

Taxonomy

Yamadazyma luoyangensis C.Y. Chai & F.L. Hui, sp. nov.

MycoBank No: 840099
Figure 2

Type

China, Henan Province, Luoyang City, Song County, in rotting wood from a forest park, September 2020, J.Z. Li & Z.T Zhang (holotype NYNU 201023T, culture ex-type CBS 16666, CICC 33509).

Etymology

The species name luoyangensis refers to the geographical origin of the type strain of this species.

Description

The cells are ovoid to ellipsoid (2–4 × 3.5–7 μm) and occur singly or in pairs after being placed in YM broth for three days at 25 °C (Figure 2A). Budding is multilateral. After three days of growth on YM agar at 25 °C, the colonies are white to cream-colored, buttery, and smooth, with entire margins. After seven days at 25 °C on a Dalmau plate culture with CM agar, pseudohyphae are formed, but true hyphae are not (Figure 2B). Asci or signs of conjugation are not observed on sporulation media. Glucose, galactose, trehalose, and cellobiose are fermented, but maltose, sucrose, melibiose, lactose, melezitose, raffinose, d-xylose, and inulin are not. Glucose, galactose, d-glucosamine, d-ribose, d-xylose, l-arabinose, d-arabinose, l-rhamnose, sucrose, maltose, trehalose, methyl α-d-glucoside, cellobiose, salicin, arbutin, melezitose, inulin, glycerol, erythritol, ribitol, d-glucitol, d-mannitol, galactitol, d-glucono-1, 5-lactone, 5-keto-d-gluconate, d-gluconate, succinate, citrate, and ethanol are assimilated. No growth is observed in l-sorbose, melibiose, lactose, raffinose, myo-inositol, 2-keto-d-gluconate, d-glucuronate, dl-lactate, or methanol. In nitrogen-assimilation tests, growth is present on ethylamine, l-lysine, glucosamine, and d-tryptophan, while growth is absent on nitrate, nitrite, cadaverine, creatine, creatinine, and imidazole. Growth is observed at 35 °C but not at 37 °C. Growth in the presence of 10% NaCl with 5% glucose is present, but growth in the presence of 0.01% cycloheximide and 1% acetic acid is absent. Starch-like compounds are not produced. Urease activity and diazonium blue B reactions are negative.

Figure 2. 

Yamadazyma luoyangensis (NYNU 201023, holotype) A budding cells after three days in YM broth at 25 °C B pseudohyphae on cornmeal agar after seven days at 25 °C. Scale bars: 10 μm.

Additional isolate examined

China, Henan Province, Luoyang City, Song County, in rotting wood from a forest park, September 2020, J.Z. Li & Z.T Zhang, NYNU 201035.

GenBank accession numbers

Holotype NYNU 201023T (ITS: MW365549; D1/D2 LSU: MW365545); additional isolate NYNU 201035 (ITS: MZ318445; D1/D2 LSU: MZ318422).

Notes

Two isolates representing Y. luoyangensis were resolved in a well-supported clade and are most closely related to Y. mexicana (Figure 1). Yamadazyma luoyangensis can be distinguished from Y. mexicana based on ITS and D1/D2 LSU loci (4/592 in ITS and 10/531 in D1/D2 LSU). Physiologically, Y. luoyangensis differs from Y. mexicana by its ability to assimilate inulin and 5-keto-d-gluconate and its inability to assimilate lactose, raffinose, and 2-keto-d-gluconate. Additionally, Y. mexicana grows at 37 °C, while Y. luoyangensis does not (Table 2) (Kurtzman 2011).

Yamadazyma ovata C.Y. Chai & F.L. Hui, sp. nov.

MycoBank No: 840100
Figure 3

Type

China, Henan Province, Luoyang City, Song County, in rotting wood from a forest park, September 2019, J.Z. Li & Z.T Zhang (holotype NYNU 191125T, culture ex-type CBS 16655, CICC 33500).

Etymology

The species name ovata refers to the ovoid cell morphology of the type strain.

Description

The cells are ovoid to ellipsoid (2–3 × 3–6.5 μm) and occur singly or in pairs after growth in a YM broth for three days at 25 °C (Figure 3A). Budding is multilateral. After three days of growth on YM agar at 25 °C, the colonies are white to cream-colored, buttery, and smooth with entire margins. After nine days at 25 °C, on a Dalmau plate culture with CM agar, pseudohyphae consisting of elongated cells with lateral buds are formed (Figure 3B). True hyphae are not observed. Asci or signs of conjugation are not observed on sporulation media. Glucose, galactose, and trehalose are fermented, but maltose, sucrose, melibiose, lactose, cellobiose, melezitose, raffinose, d-xylose, and inulin are not. Glucose, galactose, l-sorbose, d-glucosamine, d-ribose, d-xylose, l-arabinose, d-arabinose, sucrose, maltose, trehalose, methyl α-d-glucoside, cellobiose, salicin, melibiose, melezitose, glycerol, erythritol, ribitol, xylitol, d-glucitol, d-mannitol, d- galactitol, d-glucono-1, 5-lactone, 2-keto-d-gluconate, d-gluconate, succinate, citrate, and ethanol are assimilated. No growth is observed in l-rhamnose, lactose, raffinose, inulin, myo-inositol, d-glucuronate, dl-lactate, or methanol. In nitrogen-assimilation tests, growth is present on l-lysine, creatine, glucosamine, and d-tryptophan, while growth is absent on nitrate, nitrite, ethylamine, cadaverine, creatinine, or imidazole. Growth is observed at 37 °C, but not at 40 °C. Growth in the presence of 16% NaCl with 5% glucose is present, but growth in the presence of 0.01% cycloheximide and 1% acetic acid is absent. Starch-like compounds are not produced. Urease activity and diazonium blue B reactions are negative.

Figure 3. 

Yamadazyma ovata (NYNU 191125, holotype) A budding cells after three days in YM broth at 25 °C B pseudohyphae on cornmeal agar after nine days at 25 °C. Scale bars: 10 μm.

Additional isolates examined

China, Henan Province, Luoyang City, Song County, in rotting wood from a forest park, September 2019, J.Z. Li & Z.T Zhang, NYNU 19116, NYNU 19130.

GenBank accession numbers

Holotype NYNU 191125T (ITS: MT990560; D1/D2 LSU: MT990559); additional isolates NYNU 19116 (ITS: MZ318442; D1/D2 LSU: MZ318423), and NYNU 19130 (ITS: MZ318424; D1/D2 LSU: MZ318425).

Notes

We generated sequences for three isolates of Y. ovata, NYNU 191125, NYNU 19116, and NYNU 19130. This new species is phylogenetically most closely related to C. trypodendroni (Figure 1). Yamadazyma ovata can be distinguished from C. trypodendroni based on ITS and D1/D2 LSU loci (15/565 in ITS and 8/532 in D1/D2 LSU). Physiologically, Y. ovata can be differentiated from C. trypodendroni based on growth in l-sorbose, d-glucosamine, melibiose, and d-glucono-1, 5-lactone, all of which are positive for Y. ovata and negative for C. trypodendroni (Table 2) (Lachance et al. 2011).

Yamadazyma paraaseri C.Y. Chai & F.L. Hui, sp. nov.

MycoBank No: 840101
Figure 4

Type

China, Yunnan Province, Jinghong City, Mengyang Town, in rotting wood from a tropical rainforest, July 2018, K.F. Liu & Z.W. Xi (holotype NYNU 1811114T, culture ex-type CBS 16010, CICC 33365).

Etymology

The species name paraaseri refers to its phylogenetic similarity to C. aaseri.

Description

The cells are ovoid to elongate (2–2.5 × 3–8.5 μm) and occur singly or in pairs after being placed in YM broth for three days at 25 °C (Figure 4A). Budding is multilateral. After three days of growth on YM agar at 25 °C, the colonies are white to cream-colored, buttery, and smooth, with entire margins. After two weeks at 25 °C on a Dalmau plate culture with CM agar, pseudohyphae consisting of elongated cells with lateral buds are formed (Figure 4B). True hyphae are not observed. Asci or signs of conjugation are not observed on sporulation media. Fermentation of sugars is absent. Glucose, galactose, l-sorbose, d-glucosamine, d-ribose, d-xylose, l-arabinose, d-arabinose, sucrose, maltose, trehalose, methyl α-d-glucoside, cellobiose, salicin, arbutin, lactose, melezitose, inulin, glycerol, erythritol, ribitol, d-glucitol, d-mannitol, d-gluconate, dl-lactate, succinate, citrate, and ethanol are assimilated. No growth is observed in l-rhamnose, melibiose, raffinose, xylitol, galactitol, myo-inositol, d-glucono-1, 5-lactone, 2-keto-d-gluconate, d-glucuronate, or methanol. In nitrogen-assimilation tests, growth is present on ethylamine, l-lysine, glucosamine, and d-tryptophan, while growth is absent on nitrate, nitrite, cadaverine, creatine, creatinine, and imidazole. Growth is observed at 37 °C but not at 40 °C. Growth in the presence of 0.01% cycloheximide, 10% NaCl with 5% glucose and 1% acetic acid is absent. Starch-like compounds are not produced. Urease activity and diazonium blue B reactions are negative.

Figure 4. 

Yamadazyma paraaseri (NYNU 1811114, holotype) A budding cells after three days in YM broth at 25 °C B pseudohyphae on cornmeal agar after two weeks at 25 °C. Scale bars: 10 μm.

Additional isolate examined

China, Yunnan Province, Jinghong City, Mengyang Town, in rotting wood from a tropical rainforest, July 2018, K.F. Liu & Z.W. Xi, NYNU 181033.

GenBank accession numbers

Holotype NYNU 1811114T (ITS: MK682794; D1/D2 LSU: MK682805); additional isolate NYNU 181033 (ITS: MZ318421; D1/D2 LSU: MZ318460).

Notes

Two strains representing Y. paraaseri were clustered in a well-supported clade and were phylogenetically related to C. aaseri [7]. Yamadazyma paraaseri can be distinguished from C. aaseri based on ITS and D1/D2 LSU loci (8/573 in ITS and 8/531 in D1/D2 LSU). Physiologically, the ability to assimilate d-glucosamine and inulin and the inability to assimilate xylitol and d-glucono-1, 5-lactone are the primary differences between Y. paraaseri and its closest relative, C. aaseri. Additionally, C. aaseri can grow in 10% NaCl with 5% glucose, while Y. paraaseri cannot (Table 2) (Lachance et al. 2011).

Discussion

In this work, six Yamadazyma species were identified based on morphology and molecular phylogeny. All species were isolated from rotting wood collected in Henan and Yunnan Provinces, China. Yamadazyma luoyangensis, Y. ovata, and Y. paraaseri are proposed as new species in Yamadazyma due to their well-supported phylogenic positions and distinctive physiological traits. Also, three known species of Yamadazyma, Y. insectorum, Y. akitaensis, and Y. olivae, were clearly identified by both morphological and molecular approaches.

In the past, methods of species identification of Yamadazyma were based only on morphology and physiological characters such as the shape of ascospores and reactions in standard growth and fermentation tests (Billon-Grand 1989). Recent molecular phylogenetic analyses demonstrate that determining species boundaries using only morphology and physiological characters is not possible due to their variability under changing environmental conditions (Kurtzman 2011; Lachance et al. 2011). D1/D2 LSU sequence is an appropriate marker to identify species of Yamadazyma species through phylogenetic analysis, as revealed by Kurtzman and Robnett (1998). Many Yamadazyma species are described based on a polyphasic approach together with morphological and physiological characterization (Suh et al. 2005; Kurtzman 2007; Imanishi et al. 2008; Nagatsuka et al. 2009; Am-In et al. 2011). However, none to only two substitutions are present in D1/D2 LSU sequences of the ex-type strains of the closest related species within Yamadazyma, such as C. diddensiae and C. naeodendra, Y. akitaensis and Y. nakazawae as well as C. jaroonii and C. songkhlaensis (Groenewald et al. 2011; Wang et al. 2015). The ITS sequences show more variation between these closely related well-defined species in contrast to the low nucleotide differences in D1/D2 LSU sequences (Groenewald et al. 2011). Although D1/D2 LSU sequence is still an appropriate region to use for higher level taxon delimitations, it is clear that this sequence alone is not sufficient for species delimitation in the Yamadazyma clade. The ITS sequence is thus a good additional marker to obtain a better understanding of relatedness among Yamadazyma species.

Yamadazyma species have a worldwide distribution and are isolated from diverse substrates. They can be found in flowers, leaves, fruits, tree bark, mushrooms, sea water, mineral and atmosphere, but most known species appear to exist in rotting wood, insects and their resulting frass (Groenewald et al. 2011; Kurtzman 2011). This clade also includes the clinically significant species C. aaseri, C. conglobata, C. pseudoaaseri, and Y. triangularis (Kurtzman 2011; Lachance et al. 2011). These studies expanded our knowledge on the substrates where Yamadazyma species can occur, but on the other hand demonstrated the complicated ecological function of this genus. In this study, three known species and three new species were identified from rotting wood in China. Further research will focus on Yamadazyma diversity from a wide range of substrates.

Acknowledgements

We sincerely thank Dr. Jing-Zhao Li, Dr. Zheng-Tian Zhang, Dr. Kai-Fang Liu, and Dr. Zhi-Wen Xi for their help with collecting specimens. This project was supported by Grant No. 31570021 from the National Natural Science Foundation of China, China, No. 2018001 from the State Key Laboratory of Motor Vehicle Biofuel Technology, Henan Tianguan Enterprise Group Co., Ltd., China.

References

  • Am-In S, Limtong S, Yongmanitchai W, Jindamorakot S (2011) Candida andamanensis sp. nov., Candida laemsonensis sp. nov. and Candida ranongensis sp. nov., anamorphic yeast species isolated from estuarine waters in a Thai mangrove forest. International Journal of Systematic and Evolutionary Microbiology 61: 454–461. https://doi.org/10.1099/ijs.0.022038-0
  • Billon-Grand GA (1989) A new ascosporogenous yeast genus: Yamadazyma gen. nov. Mycotaxon 35: 201–204.
  • Burgaud G, Arzur D, Sampaio JP, Barbier G (2011) Candida oceani sp. nov., a novel yeast isolated from a mid-atlantic ridge hydrothermal vent (-2300 meters). Antonie van Leeuwenhoek 100: 75–82. https://doi.org/10.1007/s10482-011-9566-1
  • Burgaud G, Coton M, Jacques N, Debaets S, Maciel NOP, Rosa CA, Gadanho M, Sampaio JP, Casaregola S (2016) Yamadazyma barbieri f.a. sp. nov., an ascomycetous anamorphic yeast isolated from a Mid-Atlantic Ridge hydrothermal site (-2300 m) and marine coastal waters. International Journal of Systematic and Evolutionary Microbiology 66: 3600–3606. https://doi.org/10.1099/ijsem.0.001239
  • Ciafardini G, Zullo BA, Antonielli L, Corte L, Roscini L, Cardinali G (2013) Yamadazyma terventina sp. nov., a yeast species of the Yamadazyma clade from Italian olive oils. International Journal of Systematic and Evolutionary Microbiology 63: 372–376. https://doi.org/10.1099/ijs.0.045898-0
  • Crous PW, Gams W, Stalpers JA, Robert V, Stegehuis G (2004) MycoBank: An online initiative launch mycology into the 21st century. Studies in Mycology 50: 19–22.
  • Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: e772. https://doi.org/10.1038/nmeth.2109
  • Groenewald M, Robert V, Smith MT (2011) The value of the D1/D2 and internal transcribed spacers (ITS) domains for the identification of yeast species belonging to the genus Yamadazyma. Persoonia 26: 40–46. https://doi.org/10.3767/003158511X559610
  • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology 59: 307–321. https://doi.org/10.1093/sysbio/syq010
  • Haase MAB, Kominek J, Langdon QK, Kurtzman CP, Hittinger CT (2017) Genome sequence and physiological analysis of Yamadazyma laniorum f.a. sp. nov. and a reevaluation of the apocryphal xylose fermentation of its sister species, Candida tenuis. FEMS Yeast Research 17: fox019. https://doi.org/10.1093/femsyr/fox019
  • Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology 42: 182–192. https://doi.org/10.1093/sysbio/42.2.182
  • Imanishi Y, Jindamorakot S, Mikata K, Nakagiri A, Limtong S, Potacharoen W, Tanticharoen M, Nakase T (2008) Two new ascomycetous anamorphic yeast species related to Candida friedrichii-Candida jaroonii sp. nov., and Candida songkhlaensis sp. nov. isolated in Thailand. Antonie van Leeuwenhoek 94: 267–276. https://doi.org/10.1007/s10482-008-9242-2
  • Jindamorakot S, Am-In S, Kaewwichian R, Limtong S (2015) Yamadazyma insecticola f.a., sp. nov. and Yamadazyma epiphylla f.a., sp. nov., two novel yeast species. International Journal of Systematic and Evolutionary Microbiology 65: 1290–1296. https://doi.org/10.1099/ijs.0.000100
  • Junyapate K, Jindamorakot S, Limtong S (2014) Yamadazyma ubonensis f.a., sp. nov., a novel xylitol-producing yeast species isolated in Thailand. Antonie van Leeuwenhoek 105: 471–480. https://doi.org/10.1007/s10482-013-0098-8
  • Kaewwichian R, Yongmanitchai W, Kawasaki H, Wang PH, Yang SH, Limtong S (2013) Yamadazyma siamensis sp. nov., Yamadazyma phyllophila sp. nov. and Yamadazyma paraphyllophila sp. nov., three novel yeast species isolated from phylloplane in Thailand and Taiwan. Antonie van Leeuwenhoek 103: 777–788. https://doi.org/10.1007/s10482-012-9860-6
  • Katoh K, Rozewicki J, Yamada KD (2019) MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20: 1160–1166. https://doi.org/10.1093/bib/bbx108
  • Khunnamwong P, Limtong S (2016) Yamadazyma endophytica f.a. sp. nov., an ascomycetous yeast species isolated from leaf tissue. International Journal of Systematic and Evolutionary Microbiology 66: 2717–2723. https://doi.org/10.1099/ijsem.0.001113
  • Kurtzman CP (2007) New anamorphic yeast species: Candida infanticola sp. nov., Candida polysorbophila sp. nov., Candida transvaalensis sp. nov. and Trigonopsis californica sp. nov. Antonie van Leeuwenhoek 92: 221–231. https://doi.org/10.1007/s10482-007-9150-x
  • Kurtzman CP, Robnett CJ (1989) Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek 73: 331–371. https://doi.org/10.1023/A:1001761008817
  • Kurtzman CP, Suzuki M (2010) Phylogenetic analysis of ascomycete yeasts that form coenzyme Q-9 and the proposal of the new genera Babjeviella, Meyerozyma, Millerozyma, Priceomyces, and Scheffersomyces. Mycoscience 51: 2–14. https://doi.org/10.1007/S10267-009-0011-5
  • Kurtzman CP, Fell JW, Boekhout T, Robert V (2011) Methods for isolation, phenotypic characterization and maintenance of yeasts. In: Kurtzman CP, Fell JW, Boekhout T (Eds) The Yeasts – a Taxonomic Study, 5th edn, vol. 1. Elsevier, Amsterdam, 87–110. https://doi.org/10.1016/B978-0-444-52149-1.00007-0
  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33: 1870–1874. https://doi.org/10.1093/molbev/msw054
  • Lopes MR, Ferreira MC, Carvalho TFC, Pagnocca FC, Chagas RA, Morais PB, Rosa LH, Lachance MA, Rosa CA (2015) Yamadazyma riverae sp. nov., a yeast species isolated from plant materials. International Journal of Systematic and Evolutionary Microbiology 65: 4469–4473. https://doi.org/10.1099/ijsem.0.000597
  • Lachance MA, Boekhout T, Scorzetti G, Fell JW, Kurtzman CP (2011) Candida Berkhout (1923). In: Kurtzman CP, Fell JW, Boekhout T (Eds) The Yeasts – a Taxonomic Study, 5th edn, vol. 2. Elsevier, Amsterdam, 987–1279. https://doi.org/10.1016/B978-0-444-52149-1.00090-2
  • Maksimova IA, Glushakova AM, Thanh VN, Kachalkin AV (2020) Yamadazyma cocois f.a., sp. nov., an ascomycetous yeast isolated from coconuts. International Journal of Systematic and Evolutionary Microbiology 70: 3491–3496. https://doi.org/10.1099/ijsem.0.004203
  • Nagatsuka Y, Kiyuna T, Kigawa R, Sano C, Miura S, Sugiyama J (2009) Candida tumulicola sp. nov. and Candida takamatsuzukensis sp. nov., novel yeast species assignable to the Candida membranifaciens clade, isolated from the stone chamber of the Takamatsu-zuka tumulus. International Journal of Systematic and Evolutionary Microbiology 59: 186–194. https://doi.org/10.1099/ijs.0.65830-0
  • Nagatsuka Y, Ninomiya S, Kiyuna T, Kigawa R, Sano C, Sugiyama J (2016) Yamadazyma kitorensis f.a., sp. nov. and Zygoascus biomembranicola f.a., sp. nov., novel yeasts from the stone chamber interior of the Kitora tumulus, and five novel combinations in Yamadazyma and Zygoascus for species of Candida. International Journal of Systematic and Evolutionary Microbiology 66: 1692–16704. https://doi.org/10.1099/ijsem.0.000930
  • Nakase T, Jindamorakot S, Ninomiya S, Imanishi Y, Kawasaki H, Potacharoen W (2008) Candida kanchanaburiensis sp. nov., a new ascomycetous yeast species related to Pichia nakazawae isolated in Thailand. Journal of General and Applied Microbiology 54: 259–265. https://doi.org/10.2323/jgam.54.259
  • Rambaut A (2016) FigTree, version 1.4.3. University of Edinburgh, Edinburgh.
  • Wang Y, Ren YC, Li Y, Hui FL (2015) Molecular phylogeny and taxonomy of Yamadazyma dushanensis f.a., sp. nov., a cellobiose-fermenting yeast species from China. Current Microbiology 71: 268–273. https://doi.org/10.1007/s00284-015-0847-1
  • White TJ, Bruns TD, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (Eds) PCR protocols, a guide to methods and applications. Academic, San Diego, 315–322. https://doi.org/10.1016/B978-0-12-372180-8.50042-1
login to comment