Research Article
Print
Research Article
Five new additions to the genus Spathaspora (Saccharomycetales, Debaryomycetaceae) from southwest China
expand article infoShi-Long Lv, Chun-Yue Chai, Yun Wang, Zhen-Li Yan§, Feng-Li Hui
‡ Nanyang Normal University, Nanyang, China
§ Henan Tianguan Enterprise Group, Nanyang, China
Open Access

Abstract

Spathaspora is an important genus of d-xylose-fermenting yeasts that are poorly studied in China. During recent yeast collections in Yunnan Province in China, 13 isolates of Spathaspora were obtained from rotting wood and all represent undescribed taxa. Based on morphological and phylogenetic analyses (ITS and nuc 28S), five new species are proposed: Spathaspora elongata, Sp. mengyangensis, Sp. jiuxiensis, Sp. parajiuxiensis and Sp. rosae. Our results indicate a high species diversity of Spathaspora waiting to be discovered in rotting wood from tropical and subtropical southwest China. In addition, the two Candida species, C. jeffriesii and C. materiae, which are members of the Spathaspora clade based on phylogeny, are transferred to Spathaspora as new combinations.

Keywords

Five new species, Debaryomycetaceae, Saccharomycetales, yeast taxonomy, d-xylose-fermenting yeast

Introduction

Spathaspora N.H. Nguyen, S.O. Suh & M. Blackw (2006) (Saccharomycetales, Debaryomycetaceae) was introduced, based on a single species, Spathaspora passalidarum, which was isolated from a passalid beetle in Louisiana, USA (Nguyen et al. 2006). This species produces asci containing elongate ascospores with curved ends, a unique trait of this genus (Nguyen et al. 2006; Nguyen et al. 2011). Subsequently, Spathaspora arborariae, Sp. boniae, Sp. brasiliensis, Sp. girioi, Sp. gorwiae, Sp. hagerdaliae, Sp. piracicabensis, Sp. roraimanensis, Sp. suhii and Sp. xylofermentans were introduced. These were from rotting wood (Cadete et al. 2009, 2013; Lopes et al. 2016; Morais et al. 2017; Varize et al. 2018) and Sp. allomyrinae from insects (Wang et al. 2016). Spathaspora has been shown to be a polyphyletic group, containing members placed throughout the larger Spathaspora/Candida albicans/Lodderomyces clade of Debaryomycetaceae (Morais et al. 2017; Varize et al. 2018). Several Candida species, such as C. blackwellae, C. jeffriesii, C. lyxosophila, C. materiae, C. parablackwellae and C. subhashii, are closely related to Spathaspora, based on a phylogenetic analysis of the D1/D2 domain of the nuclear 28S rDNA (nuc 28S) sequences (Cadete et al. 2013; Daniel et al. 2014; Morais et al. 2017; Varize et al. 2018).

Most species of Spathaspora, including Sp. arborariae, Sp. brasiliensis, Sp. passalidarum, Sp. roraimanensis, Sp. suhii and Sp. xylofermentans, are economically important because of their ability to ferment d-xylose, the second most abundant sugar in lignocellulosic feedstocks (Nguyen et al. 2011; Cadete et al. 2013; Lopes et al. 2016; Morais et al. 2017). These xylose-fermenting species can be used directly for ethanol production or may provide a source of genes, enzymes and/or sugar transporters to engineer industrial strains for the efficient production of bioethanol from renewable biomass (Wohlbach et al. 2011; Cadete et al. 2013).

Spathaspora species are associated with rotting-wood substrates and the insects that occupy this ecological niche (Cadete et al. 2009, 2013; Nguyen et al. 2011; Lopes et al. 2016; Wang et al. 2016; Morais et al. 2017; Varize et al. 2018). They can be found in tropical, subtropical and temperate regions on different continents, but most species are presently known from Brazilian regions (Cadete et al. 2009, 2013; Lopes et al. 2016; Morais et al. 2017; Varize et al. 2018). In China, the genus is under-explored with only three published reports of the species Sp. allomyrinae, Sp. gorwiae and Sp. passalidarum (Ren et al. 2013; Wang et al. 2016). Here, we describe five new species of Spathaspora discovered in tropical and subtropical areas of southwest China, based on their morphological characters and molecular phylogenetic analyses.

Materials and methods

Sample collection and isolation

Rotting wood samples were collected in two areas of Yunnan Province, China. The areas are located in the Xishuangbanna Primeval Forest Park of Jinghong (21°98'N, 100°88'E) and Jiuxi Mountain Forest Park of Honghe (24°40'N, 103°68'E). The predominant vegetation is characterised as a tropical and subtropical forest biome. The climate is hot and humid, with annual precipitation between 1,100 to 1,600 mm and an average temperature that ranges from 17.2 to 26.4 °C. Sixty decayed wood samples were collected, thirty from each area, during July to August in 2016–2018. 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 Lopes et al. (2016). Each sample (1 g) was added to 20 ml sterile d-xylose medium (yeast nitrogen base 0.67%, d-xylose 0.5%, chloramphenicol 0.02%, pH 5.0 ± 0.2) 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 d-xylose agar plates and then incubated at 25 °C for 3–4 days. Different yeast colony morphotypes were then isolated by repeated plating on yeast extract-malt extract (YM) agar (1% glucose, 0.5% peptone, 0.3% yeast extract and 0.3% malt extract, pH 5.0 ± 0.2) and stored on YM agar slants at 4 °C or in 15% glycerol at –80 °C.

Morphological, physiological and biochemical studies

Morphological and physiological properties were determined according to Kurtzman et al. (2011). Induction of the sexual stage was tested by incubating single or mixed cultures of each of the two strains on cornmeal (CM) agar, 5% malt extract (ME) agar, dilute (1:9 and 1:19) V8 agar or yeast carbon base plus 0.01% ammonium sulphate (YCBAS) agar at 25 °C for 2 months (Cadete et al. 2013; Lopes et al. 2016). Assimilation of carbon and nitrogen compounds and growth requirements were tested at 25 °C. The effects of temperature from 25–40 °C were examined in liquid culture and on agar plates. Ethanol was determined with alcohol oxidase (Sangon Biotech, China) and peroxidase (Sangon Biotech, China), as described previously (Alves et al. 2007).

DNA extraction, PCR amplification and nucleotide sequencing

Genomic DNA was extracted from the yeasts using the Ezup Column Yeast Genomic DNA Purification Kit, according to the manufacturer’s protocol (Sangon Biotech, China). The nuc rDNA ITS1-5.8S-ITS2 (ITS) region was amplified using the primer pair ITS1/ITS4 (White et al. 1990). The D1/D2 domain of the nuc 28S rDNA was amplified using the primer pair NL1/NL4 (Kurtzman and Robnett 1998). The following thermal profile was used to amplify the ITS and nuc 28S regions: an initial denaturation step of 2 min at 95 °C, followed by 35 cycles of 30 s at 95 °C, 30 s at 51 °C and 40 s at 72 °C, with a final extension of 10 min at 72 °C (Liu et al. 2016). PCR products were directly purified and sequenced by Sangon Biotech Inc. (Shanghai, China). We determined the identity and accuracy of the newly-obtained sequences by comparing them to sequences in GenBank and assembled them using BioEdit (Hall 1999). Newly-obtained sequences were then submitted to GenBank (https://www.ncbi.nlm.nih.gov/genbank/; Table 1).

Phylogenetic analyses

The sequences obtained from this study and the reference sequences downloaded from GenBank (Table 1) were aligned using MAFFT v. 6 (Katoh and Toh 2010) and manually edited using MEGA v. 7 (Kumar et al. 2016). The best-fit nucleotide substitution models for each gene were selected using jModelTest v2.1.7 (Darriba et al. 2012), according to the Akaike Information Criterion.

Phylogenetic analyses of the combined gene regions (ITS and nuc 28S) were performed using the Maximum Likelihood (ML) and Bayesian Inference (BI) methods. Candida argentea CBS 12358 was chosen as the outgroup. ML analysis was performed using MEGA v7 with the GTR+I+G model (Nei and Kumar 2000) and 1,000 rapid bootstrap replicates to estimate branch confidence. BI analysis was performed using a Markov Chain Monte Carlo (MCMC) algorithm in MrBayes v. 3.0b4 (Ronquist and Huelsenbeck 2003). Two MCMC chains, started from random trees for 1,000,000 generations and trees, were sampled every 100th generation, resulting in a total of 10,000 trees. The first 25% of the trees were discarded as burn-in of each analysis. Branches with significant Bayesian Posterior Probabilities (BPP) were estimated in the remaining 7,500 trees. The phylogenetic trees from the ML and BI analyses were displayed using Mega 7 and FigTree v1.4.3 (Rambaut 2016), respectively.

Table 1.

DNA sequences used in the molecular phylogenetic analysis. Entries in bold are newly generated in this study.

Species Strain ITS D1/D2
Candida albicans NRRL Y-12983T HQ876043 U45776
Candida argentea CBS 12358T JF682350/ JF682353
Candida baotianmanensis CBS 13915T KM586743 KM586733
Candida blackwellae CBS 10843T EU402940/ EU402939
Candida bohiensis NRRL Y-27737T FJ172255 AY520317
Candida buenavistaensis NRRL Y-27734T FJ623627 AY242341
Candida cetoniae CBS 12463 T KC118129 KC118128
Candida chauliodes NRRL Y-27909 T FJ623621 DQ655678
Candida coleopterorum CBS 14180 T KU128707 KU128722
Candida corydalis NRRL Y-27910T FJ623622 DQ655679
Candida dubliniensis NRRL Y-17841T KY102055 U57685
Candida frijolesensis NRRL Y-48060T EF658666 EF120596
Candida hyderabadensis NRRL Y-27953T AM180949 AM159100
Candida jeffriesii CBS 9898 T NR_111398 NG_042498
Candida jiufengensis CBS 10846 T EU402936 EU402935
Candida kantuleensis CBS 15219T LC317101 LC317097
Candida labiduridarum NRRL Y-27940 T EF658664 DQ655687
Candida lyxosophila NRRL Y-17539 T KY102184 HQ263370
Candida maltosa NRRL Y-17677 T NR_138346 U45745
Candida margitis CBS 14175 T KU128708 KU128721
Candida materiae CBS 10975T FJ154790 FJ154790
Candida metapsilosis CBS 10907T FJ872019 DQ213057
Candida morakotiae NBRC 105009 T AB696987 DQ400364
Candida neerlandica NRRL Y-27057T EF658662 AF245404
Candida oleophila NRRL Y-2317 T AJ539374/ U45793
Candida orthopsilosis ATCC MYA-96139T FJ545241 DQ213056
Candida oxycetoniae CBS 10844T KY102281 EU402933
Candida parablackwellae NYNU 17763T MG255731 MG255702
Candida parachauliodis CBS 13928 T KP054272 KP054271
Candida parapsilosis NRRL Y-12969T AJ635316 U45754
Candida pseudojiufengensis CBS 10847 T EU402938 EU402937
Candida pseudoviswanathii CBS 13916 T KM586736 KM586735
Candida sanyaensis CBS 12637T JQ647915 JQ647914
Candida sakaeoensis CBS 12318 T AB696985 AB617978
Candida sojae NRRL Y-17909T KJ722419 U71070
Candida subhashii CBS 10753 T NR_073356 EU836708
Candida tetrigidarum NRRL Y-48142 T FJ623630 EF120599
Candida theae ATCC MYA-4746T JQ812707 JQ812701
Candida tropicalis NRRL Y-12968T AF287910 U45749
Candida verbasci CBS 12699T JX515982 JX515981
Candida viswanathii CBS 4024T KY102515 U45752
Candida xiaguanensis CBS 13923T KM586732 KM586731
Candida yunnanensis NYNU 17948 T MG255721 MG255709
Lodderomyces beijingensis CBS 14171 T KU128709 KU128720
Lodderomyces elongisporus NRRL YB-4239 T AY391848 U45763
Nematodospora anomalae CBS 13927T KP054270 KP054269
Nematodospora valgi CBS 12562 T KM386993 HM627112
Scheffersomyces stipitis NRRL Y-7124T JN943257/ U45741
Spathaspora allomyrinae CBS 13924T KP054268 KP054267
Spathaspora arborariae ATCC MYA-4684T NR_111592 NG_042574
Spathaspora boniae CBS 13262T NR_158910 KT276332
Spathaspora brasiliensis CBS 12679 T JN099271 JN099271
Spathaspora elongata NYNU 18115T MK682770 MK682796
Spathaspora elongata NYNU 181112 MT276033 MT274662
Spathaspora elongata NYNU 181120 MT276034 MT276036
Spathaspora elongata NYNU 181158 MT276035 MT276032
Spathaspora girioi CBS 13476T NR_155783 NG_059955
Spathaspora gorwiae CBS 13472 T NR_155784 NG_059956
Spathaspora hagerdaliae CBS 13475T NR_155800 KU556168
Spathaspora jiuxiensis NYNU 17416 T MG255706 MG255718
Spathaspora jiuxiensis NYNU 17417 MT276035 MT276032
Spathaspora mengyangensis NYNU 17741T KY213816 KY213819
Spathaspora mengyangensis NYNU 17705 MT272353 MT272351
Spathaspora parajiuxiensis NYNU 16747 T MG255728 MG255705
Spathaspora parajiuxiensis NYNU 16632 MT272352 MT272350
Spathaspora passalidarum NRRL Y-27907T NR_111397 DQ109807
Spathaspora piracicabensis CBS 15054T KR864907 KR864906
Spathaspora rosae NYNU 17934T MG255725 MG255701
Spathaspora rosae NYNU 17903 MT274659 MT274661
Spathaspora rosae NYNU 17909 MT274664 MT274663
Spathaspora roraimanensis CBS 12681T JN099269 JN099269
Spathaspora suhii CBS 12680T JN099270 JN099270
Spathaspora xylofermentans CBS 12682T JN099268 JN099268
Wickerhamia fluorescens JCM 1821T NR_111311/ NG_054831

Results

Phylogenetic analyses

The combined nuclear dataset (ITS and nuc 28S) was analysed to infer the interspecific relationships within the larger Spathaspora/Candida albicans/Lodderomyces clade of Debaryomycetaceae. The dataset consisted of 72 sequences including the outgroup, Candida argentea (culture CBS 12358). A total of 944 characters including gaps (391 for ITS and 553 for nuc 28S) were included in the phylogenetic analysis. The best nucleotide substitution model for ITS and nuc 28S was GTR+I+G. ML and BI analyses of the combined dataset resulted in phylogenetic reconstructions with similar topologies and the average standard deviation of split frequencies was 0.011210 (BI). In the ML phylogenetic tree (Figure 1), thirteen strains formed five single clades with high to full support (100% in ML and 0.99 or 1.00 in BI) and clustered in the clade that comprised most species of Spathaspora. Phylogenetically, S. elongata and S. mengyangensis clustered together with high support (84% in ML and 0.91 in BI), while S. jiuxiensis and S. parajiuxiensis clustered together with strong support (100% in ML and 1.00 in BI). Two strains of S. rosae formed a unique lineage with S. allomyrinae, but with low support.

Figure 1. 

Phylogenetic tree, based on an ML analysis of a combined DNA dataset of ITS and nuc 28S rDNA sequences for Spathaspora species and related taxa in the Debaryomycetaceae. Numbers above the branches indicate ML bootstraps (left, MLBS ≥ 50%) and Bayesian Posterior Probabilities (right, BPP ≥ 0.90). The tree is rooted with sequences from Candida argentea CBS 12358. Isolates from the current study are shown in bold letters. “-” indicates MLBS < 50% or BPP < 0.90. The scale bar indicates the number of substitutions per site.

Taxonomy

Spathaspora elongata C.Y. Chai & F.L. Hui, sp. nov.

MycoBank No: 836444
Figure 2

Type

China, Yunnan Province, Jinghong City, Mengyang Town, in rotting wood from a tropical rainforest, August 2018, K.F. Liu & Z.W. Xi (holotype, NYNU 18115T preserved in a metabolically-inactive state), ex-holotype: CICC 33353; CBS 16002.

Etymology

Elongata refers to the elongate ascospores of this yeast.

Description

After 3 days of culture in YM broth at 25 °C, the cells are ovoid (3–4 × 3–7 μm) and occur singly or in pairs (Fig. 2a). Budding is multilateral. Sediment is formed after a month, but a pellicle is not observed. After 3 days of growth on YM agar at 25 °C, colonies are white to cream-coloured, butyrous and smooth with entire margins. After 14 days at 25 °C, on Dalmau plate culture on CM agar, pseudohyphae are present, but true hyphae are not formed (Fig. 2b). Sporulation occurs on dilute (1:19) V8 agar after 14 days at 25 °C. Unconjugated asci are formed from single cells with one elongated ascospore which are tapered and curved at the ends (Fig. 2c). Glucose, galactose, maltose and sucrose are weakly fermented. Xylose fermentation is absent using Durham tubes, but ethanol is produced from xylose when determined with alcohol oxidase and peroxidase tests. Glucose, d-ribose, d-xylose, d-arabinose, sucrose, maltose, trehalose, methyl α-d-glucoside, cellobiose, salicin, arbutin, inulin, ribitol, d-glucitol, d-mannitol, 2-keto-d-gluconate, succinate, citrate and ethanol are assimilated. No growth occurs with galactose, l-sorbose, d-glucosamine, l-arabinose, l-rhamnose, melibiose, lactose, raffinose, melezitose, glycerol, erythritol, xylitol, galactitol, myo-inositol, d-glucono-1, 5-lactone, 5-keto-d-gluconate, d-gluconate, d-glucuronate, dl-lactate or methanol. For the assimilation of nitrogen compounds, growth on ethylamine, l-lysine, glucosamine or d-tryptophan is present, whereas growth on nitrate, nitrite, cadaverine, creatine, creatinine or imidazole is absent. Growth is observed at 37 °C but not at 40 °C. Growth in the presence of 1% acetic acid is present, but growth in the presence of 10% sodium chloride (NaCl) plus 5% glucose and 0.01% cycloheximide is absent. Starch-like compounds are not produced. Urease activity and diazonium blue B reactions are negative.

Figure 2. 

Morphology of Spathaspora elongata (NYNU 18115, holotype) a budding cells on YM broth after 3 d b Pseudohyphae on CM agar after 14 d c ascus and ascospore (arrow) on dilute V8 agar after 14 d. Scale bars: 10 μm.

Additional isolates examined

China, Yunnan Province, Jinghong City, Mengyang Town, in rotting wood from a tropical rainforest, August 2018, K.F. Liu & Z.W. Xi, NYNU 181112, NYNU 181120 and NYNU 181158.

Notes

Four strains, representing Sp. elongata, clustered in a well-supported phylogenetic clade that is closely related to Sp. mengyangensis, another new species proposed in this paper and C. subhashii. The nucleotide differences between Sp. elongata and Sp. mengyangensis were 2.5% substitutions in the D1/D2 domain and 5.2% substitutions in the ITS region (Groenewald et al. 2016). Similarly, Sp. elongata and C. subhashii showed differences of 3.9% substitutions in the D1/D2 domain and 5.9% substitutions in the ITS region (Groenewald et al. 2016). Physiologically, Sp. elongata can be differentiated from its close relative, Sp. mengyangensis, based on its growth in citrate and the presence of 1% acetic acid, which are present for Sp. elongata and absent for Sp. mengyangensis. Moreover, Sp. elongata weakly ferments glucose, galactose, maltose and sucrose and grows at 37 °C, but Sp. mengyangensis does not.

Spathaspora mengyangensis C.Y. Chai & F.L. Hui, sp. nov.

MycoBank No: 836445
Figure 3

Type

China, Yunnan Province, Jinghong City, Mengyang Town, in rotting wood from a tropical rainforest, July 2017, K.F. Liu & L. Zhang (holotype, NYNU 17741T preserved in a metabolically-inactive state), ex-holotype: CICC 33267; CBS 15227.

Etymology

Mengyangensis refers to the geographical origin of the type strain of this species.

Description

In YM broth after 3 days at 25 °C, cells are ovoid (3–7 × 5–7.5 μm) and occur singly or in pairs (Fig. 3a). Budding is multilateral. Sediment is formed after a month, but a pellicle is not observed. After 3 days of growth on YM agar at 25 °C, colonies are white to cream-coloured, butyrous and smooth with entire margins. After 14 days at 25 °C on Dalmau plate culture on CM agar, pseudohyphae are present, but true hyphae are not formed (Fig. 3b). Sporulation occurs on CM agar after 14 days at 25 °C. Unconjugated asci are formed from single cells with one elongated ascospore which are tapered and curved at the ends (Fig. 3c). Xylose fermentation is negative using Durham tubes, but ethanol is produced from xylose when determined with alcohol oxidase and peroxidase tests. Glucose, d-ribose, d-xylose, sucrose, maltose, trehalose, methyl α-d-glucoside, cellobiose, salicin, arbutin, inulin, ribitol, d-glucitol, d-mannitol, 2-keto-d-gluconate, succinate and ethanol are assimilated. No growth occurs with galactose, l-sorbose, d-glucosamine, l-arabinose, d-arabinose, l-rhamnose, melibiose, lactose, raffinose, melezitose, glycerol, erythritol, xylitol, galactitol, myo-inositol, d-glucono-1, 5-lactone, 5-keto-d-gluconate, d-gluconate, d-glucuronate, dl-lactate, citrate or methanol. For the assimilation of nitrogen compounds, growth on ethylamine, l-lysine, glucosamine or d-tryptophan is present, whereas growth on nitrate, nitrite, cadaverine, creatine, creatinine or imidazole is absent. Growth is observed at 30 °C, but not at 35 °C. Growth in the presence of 10% NaCl plus 5% glucose, 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. 

Spathaspora mengyangensis (NYNU 17741, holotype) a budding cells on YM broth after 3 d b simple pseudohyphae on CM agar after 14 d c ascus and ascospore (arrow) on CM agar after 14 d. Scale bars: 10 μm.

Additional isolate examined

China, Yunnan Province, Jinghong City, Mengyang Town, in rotting wood from a tropical rainforest, July 2017, K.F. Liu & L. Zhang, NYNU 17705.

Notes

Phylogenetic analyses show that Sp. mengyangensis is closely related to Sp. elongata and C. subhashii; however, the independent phylogenetic position and different physiological characters can distinguish Sp. mengyangensis from its sister species Sp. elongata (as mentioned above). Similarly, Sp. mengyangensis differed from C. subhashii by 2.8% substitutions in the D1/D2 domain and 7.8% substitutions in the ITS region (Groenewald et al. 2016). Physiologically, Sp. mengyangensis can be differentiated from C. subhashii by the ability to assimilate d-ribose, trehalose, d-glucitol and d-mannitol and the inability to assimilate galactose, l-arabinose and melezitose. In addition, C. subhashii can grow at 40 °C, but Sp. mengyangensis cannot.

Spathaspora jiuxiensis C.Y. Chai & F.L. Hui, sp. nov.

MycoBank No: 836446
Figure 4

Type

China, Yunnan Province, Honghe Prefecture, Luxi County, in rotting wood in Jiuxi Mountain Forest Park, July 2017, K.F. Liu & L. Zhang (holotype, NYNU 17416T preserved in a metabolically-inactive state), ex-holotype: CICC 33264; CBS 15226.

Etymology

Jiuxiensis refers to Jiuxi Mountain, the mountain from which it was collected.

Description

In YM broth after 3 days at 25 °C, cells are ovoid to elongate (3–6 × 3.5–9 μm) and occur singly or in pairs (Fig. 4a); pseudohyphae are present. Budding is multilateral. Sediment is formed after a month, but a pellicle is not observed. After 3 days of growth on YM agar at 25 °C, colonies are white to cream-coloured, butyrous and smooth with entire margins. After 12 days at 25 °C on Dalmau plate culture on CM agar, pseudohyphae and true hyphae are formed (Fig. 4b). Asci or signs of conjugation were not seen on the sporulation media used. Glucose and maltose are weakly fermented. Xylose fermentation is negative using Durham tubes, but ethanol is produced from xylose when determined with alcohol oxidase and peroxidase tests. Glucose, d-glucosamine, d-ribose, d-xylose, sucrose, maltose, trehalose, methyl α-d-glucoside, cellobiose, salicin, arbutin, melezitose, inulin, ribitol, d-glucitol, d-mannitol, 2-keto-d-gluconate, dl-lactate, succinate and ethanol are assimilated. No growth occurs with galactose, l-sorbose, l-arabinose, d-arabinose, l-rhamnose, melibiose, lactose, raffinose, glycerol, erythritol, xylitol, galactitol, myo-inositol, d-glucono-1, 5-lactone, 5-keto-d-gluconate, d-gluconate, d-glucuronate, citrate, l-arabinitol or methanol. For the assimilation of nitrogen compounds, growth on l-lysine, glucosamine or d-tryptophan is present, whereas growth on nitrate, nitrite, ethylamine, cadaverine, creatine, creatinine or imidazole is absent. Growth is observed at 35 °C, but not at 37 °C. Growth in the presence of 0.01% cycloheximide is present, but growth in the presence of 0.1% cycloheximide, 10% NaCl plus 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. 

Morphology of Spathaspora jiuxiensis (NYNU 17416, holotype) a budding cells and pseudohyphae on YM broth after 3 d b true hyphae with blastoconidia on CM agar after 14 d. Scale bars: 10 μm.

Additional isolate examined

China, Yunnan Province, Honghe Prefecture, Luxi County, in rotting wood in Jiuxi Mountain Forest Park, July 2017, K.F. Liu & L. Zhang, NYNU 17417.

Notes

The two strains, both representing Sp. jiuxiensis, cluster in a well-supported clade in the phylogenetic analysis and are closely related to Sp. parajiuxiensis. The nucleotide differences between these two new species were 1.4% substitutions in the D1/D2 domain and 4.6% substitutions in the ITS region (Groenewald et al. 2016). These two sister species can also be differentiated by a few physiological characteristics; Sp. jiuxiensis can assimilate dl-lactate and Sp. parajiuxiensis can grow at 37 °C.

Spathaspora parajiuxiensis C.Y. Chai & F.L. Hui, sp. nov.

836447 Figure 5

Type

China, Yunnan Province, Honghe Prefecture, Luxi County, in rotting wood in Jiuxi Mountain Forest Park, July 2016, R.C. Ren & L. Zhang (holotype, NYNU 16747T preserved in a metabolically-inactive state), ex-holotype: CICC 33162; CBS 14691.

Etymology

Paraluxiensis refers to its close phylogenetic relationship to Sp. luxiensis.

Description

In YM broth after 3 days at 25 °C, cells are ovoid to elongate (3.5–4 × 7–15 μm) and occur singly or in pairs (Fig. 5a); pseudohyphae are present. Budding is multilateral. Sediment is formed after a month, but a pellicle is not observed. After 3 days of growth on YM agar at 25 °C, colonies are white to cream-coloured, butyrous and smooth with entire margins. After 12 days at 25 °C on Dalmau plate culture on CM agar, pseudohyphae and true hyphae are formed (Fig. 5b). Sporulation occurs on 5% ME agar after 14 days at 25 °C. Unconjugated asci are formed from single cells with one elongated ascospores which are tapered and curved at the ends (Fig. 5c) Glucose and maltose are weakly fermented. Xylose fermentation is negative using Durham tubes, but ethanol is produced from xylose when determined with alcohol oxidase and peroxidase tests. Glucose, d-glucosamine, d-ribose, d-xylose, sucrose, maltose, trehalose, methyl α-d-glucoside, cellobiose, salicin, arbutin, melezitose, inulin, ribitol, d-glucitol, d-mannitol, 2-keto-d-gluconate, succinate and ethanol are assimilated. No growth occurs with galactose, l-sorbose, l-arabinose, d-arabinose, l-rhamnose, melibiose, lactose, raffinose, glycerol, erythritol, xylitol, galactitol, myo-inositol, d-glucono-1, 5-lactone, 5-keto-d-gluconate, d-gluconate, d-glucuronate, dl-lactate, citrate, l-arabinitol or methanol. For the assimilation of nitrogen compounds, growth on l-lysine, glucosamine or d-tryptophan is present, whereas growth on nitrate, nitrite, ethylamine, cadaverine, creatine, creatinine or imidazole is absent. Growth is observed at 37 °C, but not at 40 °C. Growth in the presence of 0.01% cycloheximide is present, but growth in the presence of 0.1% cycloheximide, 10% NaCl plus 5% glucose and 1% acetic acid is absent. Starch-like compounds are not produced. Urease activity and diazonium blue B reactions are negative.

Figure 5. 

Morphology of Spathaspora parajiuxiensis (NYNU 16747, holotype) a budding cells and pseudohyphae on YM broth after 3 d b true hyphae with blastoconidia on CM agar after 14 d c ascus and ascospore (arrow) on 5% ME agar after 14 d. Scale bars: 10 μm.

Additional isolate examined

China, Yunnan Province, Honghe Prefecture, Luxi County, in rotting wood in Jiuxi Mountain Forest Park, July 2016, R.C. Ren & L. Zhang, NYNU 16632.

Spathaspora rosae C.Y. Chai & F.L. Hui, sp. nov.

MycoBank No: 836448
Figure 6

Type

China, Yunnan Province, Jinghong City, Mengyang Town, in rotting wood in a tropical rainforest, July 2017, Z.W. Xi & L. Zhang (holotype, NYNU 17934T preserved in a metabolically-inactive state), ex-holotype: CICC 33271; CBS 15231.

Etymology

Rosae was named in honour of Carlos A. Rosa for his contributions in yeast taxonomy.

Description

In YM broth after 3 days at 25 °C, cells are ovoid to elongate (4–7 × 5–16 μm) and occur singly or in pairs (Fig. 6a). Budding is multilateral. Sediment is formed after a month, but a pellicle is not observed. After 3 days of growth on YM agar at 25 °C, colonies are white to cream-coloured, butyrous and smooth with entire margins. After 7 days at 25 °C, on Dalmau plate culture on CM agar, pseudohyphae and true hyphae are formed (Fig. 6b). Asci or signs of conjugation are not seen on sporulation media used. Xylose fermentation is negative using Durham tubes, but ethanol is produced from xylose when determined with alcohol oxidase and peroxidase tests. Glucose, d-glucosamine, d-xylose, sucrose, maltose, trehalose, methyl α-d-glucoside, cellobiose, salicin, arbutin, inulin, ribitol, d-glucitol, d-mannitol, 2-keto-d-gluconate, dl-lactate, succinate, citrate and ethanol are assimilated. No growth occurs with galactose, l-sorbose, d-ribose, l-arabinose, d-arabinose, l-rhamnose, melibiose, lactose, raffinose, melezitose, glycerol, erythritol, xylitol, galactitol, myo-inositol, d-glucono-1, 5-lactone, 5-keto-d-gluconate, d-gluconate, d-glucuronate, l-arabinitol or methanol. For the assimilation of nitrogen compounds, growth on ethylamine, l-lysine, glucosamine or d-tryptophan is present, whereas growth on nitrate, nitrite, cadaverine, creatine, creatinine or imidazole is absent. Growth is observed at 35 °C, but not at 37 °C. Growth in the presence of 0.01% cycloheximide is present, but growth in the presence of 0.1% cycloheximide, 10% NaCl plus 5% glucose and 1% acetic acid is absent. Starch-like compounds are not produced. Urease activity and diazonium blue B reactions are negative.

Figure 6. 

Morphology of Spathaspora rosae (NYNU 17934, holotype) a budding cells and elongated vegetative cells on YM broth after 3 d b true hyphae with blastoconidia on CM agar after 14 d. Scale bars: 10 μm.

Additional isolates examined

China, Yunnan Province, Jinghong City, Mengyang Town, in rotting wood in a tropical rainforest, July 2017, Z.W. Xi & L. Zhang NYNU 17903, NYNU 17909.

Notes

Three strains, representing Sp. rosae, grouped in a well-supported clade and appear to be most closely related to Sp. allomyrinae (Wang et al. 2016). The nucleotide differences between Sp. rosae and its close relative, Sp. allomyrinae, were 10.2% substitutions in the D1/D2 domain and 11% substitutions in the ITS region (Groenewald et al. 2016). Physiologically, Sp. rosae can be differentiated from Sp. allomyrinae, based on growth in galactose, melezitose, xylitol and 5-keto-d-gluconate, which are positive for Sp. allomyrinae and negative for Sp. rosae. Moreover, Sp. allomyrinae weakly ferments glucose, galactose, maltose and cellobiose, but Sp. rosae does not.

Two new combinations

In addition to the previously-described taxa, two new combinations are proposed herein and their descriptions refer to relevant protologues.

Spathaspora materiae (Barbosa, Cadete, Gomes, Lachance & Rosa) C.Y. Chai & F.L. Hui, comb. nov.

836449

Basionym

Candida materiae Barbosa, Cadete, Gomes, Lachance & Rosa, International Journal of Systematic and Evolutionary Microbiology 59(8): 2015 (2009).

Spathaspora jeffriesii (N.H. Nguyen, S.-O. Suh & M. Blackwell) C.Y. Chai & F.L. Hui, comb. nov.

836450

Basionym

Candida jeffriesii N.H. Nguyen, S.-O. Suh & M. Blackwell, Mycological Research 110(10): 1239 (2006).

Discussion

Spathaspora is distributed worldwide with 12 species identified from rotting wood and insects. In China, three species of Spathaspora have been previously reported (Ren et al. 2013; Wang et al. 2016). In the present study, five additional species, Sp. elongata, Sp. jiuxiensis, Sp. mengyangensis, Sp. parajiuxiensis and Sp. rosae (Fig. 1), were recorded in addition to previously-known species. Thus, to our knowledge, eight species of Spathaspora are currently known from China. Of these eight species, only two species, Sp. gorwiae and Sp. passalidarum, were reported in China up until 2013 (Ren et al. 2013). The remaining six species, namely Sp. allomyrinae, Sp. elongata, Sp. jiuxiensis, Sp. mengyangensis, Sp. parajiuxiensis and Sp. rosae, were recorded from 2016 to 2018. Given this history, it is most likely that more species will be found. Nonetheless, this number is significant when compared to the total diversity of 11 species of Spathaspora reported for South America (Cadete et al. 2009, 2013; Lopes et al. 2016; Morais et al. 2017; Varize et al. 2018). Further studies are needed to document the overall diversity of species of Spathaspora in China, especially in the southwest regions.

The phylogenetic relationship of Spathaspora has been unclear until now, mainly due to its polyphyletic nature (Daniel et al. 2014; Morais et al. 2017; Varize et al. 2018). In this article, we used more available type strains to revise this genus, based on a phylogenetic analysis of the combined ITS and nuc 28S rDNA sequences. As shown in Figure 1, three main groups were reconstructed and the results showed that Spathaspora is not a monophyletic group, but rather is polyphyletic with several Candida species included. Sp. passalidarum, the type species of the genus, C. jeffriesii, C. materiae, Sp. arborariae, Sp. brasiliensis, Sp. girioi and Sp. suhii form a core group that is well supported by phylogeny. This result is similar to the results of previous phylogenetic analyses of nuc 28S rDNA sequences (Morais et al. 2017; Varize et al. 2018). Therefore, two Candida species, C. materiae and C. jeffriesii, are transferred to Spathaspora as new combinations because of their phylogenetic placement within that genus.

The second group is composed of ten distinct species, including the four species Sp. elongata, Sp. mengyangensis, Sp. jiuxiensis and Sp. parajiuxiensis described in this study. Typical ascospores are formed by Sp. elongata, Sp. mengyangensis, Sp. parajiuxiensis and Sp roraimanensis, but other members of the group are known from their asexual cycle only.

The species Sp. allomyrinae, which shares the unique ascospore morphology of the genus, fell outside a larger Spathaspora clade, as in the nuc 28S-based phylogeny proposed by Morais et al. (2017). However, this species is joined by Sp. rosae, which is described in the current study, in a third cluster consisting of Spathaspora in our phylogenetic analysis (Fig. 1). Placement of Sp. allomyrinae and Sp. rosae is only weakly supported and continued assignment to the genus will require verification from more robust datasets, such as whole genome sequences.

Morais et al. (2017) described the species Sp. boniae, based on two strains producing asci containing elongate ascospores with curved ends typical of the genus Spathaspora. Our phylogenomic analysis showed that Sp. boniae clusters with C. blackwellae and C. parablackwellae to form a distinct clade outside a larger Spathaspora clade. This result was also supported by previous phylogenetic analyses on this clade using nuc 28S rDNA sequences (Morais et al. 2017; Varize et al. 2018; Zhai et al. 2019). These results suggest that the genus Spathaspora should be limited to species in the group comprising the type species Sp. passalidarum. This clade, which has been treated previously as members of Spathaspora, may represent a separate genus, despite the morphological characteristics of the included species and isolates are similar to Spathaspora. Therefore, whole genome sequencing of all Spathaspora species and those of related genera, combined with the discovery of new species of the clade, is needed to clarify the possible heterogeneity of this genus.

Spathaspora is a cosmopolitan genus, but most known species have relatively-distinct habitats or regional locations. Currently, most Spathaspora species are known from East Asia (mainly in China) and South America. Although the taxonomy of Spathaspora has received much attention in recent years, many regions in the world are under-sampled and more under-described indigenous Spathaspora species will undoubtedly be discovered in the future as with most microfungal genera (Hyde et al. 2020). Our study indicates that there is a high species diversity of Spathaspora waiting to be discovered in rotting wood in tropical and subtropical southwest China and nearby areas as with other genera (Hyde et al. 2018).

Acknowledgements

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

References

  • Alves Jr SL, Herberts RA, Hollatz C, Miletti LC, Stambuk BU (2007) Maltose and maltotriose active transport and fermentation by Saccharomyces cerevisiae. Journal of the American Society of Brewing Chemists 65: 99–104. https://doi.org/10.1094/ASBCJ-2007-0411-01
  • Barbosa AC, Cadete RM, Gomes FC, Lachance MA, Rosa CA (2009) Candida materiae sp. nov., a yeast species isolated from rotting wood in the Atlantic Rain Forest. International Journal of Systematic and Evolutionary Microbiology 59: 2104–2106. https://doi.org/10.1099/ijs.0.009175-0
  • Cadete RM, Santos RO, Melo MA, Mouro A, Goncalves DL, Stambuk BU, Gomes FCO, Lachance MA, Rosa CA (2009) Spathaspora arborariae sp. nov., a d-xylose-fermenting yeast species isolated from rotting wood in Brazil. FEMS Yeast Research 9: 1338–1342. https://doi.org/10.1111/j.1567-1364.2009.00582.x
  • Cadete RM, Melo MA, Dussán KJ, Rodrigues RCLB, Silva SS, Zilli JE, Vital MJS, Gomes FCO, Lachance MA, Rosa CA (2012) Diversity and physiological characterization of d-xylose-fermenting yeasts isolated from the Brazilian Amazonian Forest. PLoS One 7: e43135. https://doi.org/10.1371/journal.pone.0043135
  • Cadete RM, Melo MA, Zilli JE, Vital MJ, Mouro A, Prompt AH, Gomes FCO, Stambuk BU, Lachance MA, Rosa CA (2013) Spathaspora brasiliensis sp. nov., Spathaspora suhii sp. nov., Spathaspora roraimanensis sp. nov. and Spathaspora xylofermentans sp. nov., four novel d-xylose-fermenting yeast species from Brazilian Amazonian forest. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology 103: 421–431. https://doi.org/10.1007/s10482-012-9822-z
  • Cadete RM, de Las Heras AM, Sandström AG, Ferreira C, Gírio F, Gorwa-Grauslund MF, Rosa CA (2016) Exploring xylose metabolism in Spathaspora species: XYL1.2 from Spathaspora passalidarum as the key for efficient anaerobic xylose fermentation in metabolic engineered Saccharomyces cerevisiae. Biotechnology Biofuels 9: e167. https://doi.org/10.1186/s13068-016-0570-6
  • Daniel HM, Lachance MA, Kurtzman CP (2014) On the reclassification of species assigned to Candida and other anamorphic ascomycetous yeast genera based on phylogenetic circumscription. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology 106: 67–84. https://doi.org/10.1007/s10482-014-0170-z
  • Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772–772. https://doi.org/10.1038/nmeth.2109
  • Groenewald DVM, Szöke S, Cardinali G, Eberhardt U, Stielow B, Vries M de, Verkleij MJM, Crous PW, Boekhout T, Robert V (2016) DNA barcoding analysis of more than 9 000 yeast isolates contributes to quantitative thresholds for yeast species and genera delimitation. Studies in Mycology 85: 91–105. https://doi.org/10.1016/j.simyco.2016.11.007
  • Hall TA (1999) Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic acids symposium series 41: 95–98.
  • Hyde KD, Norphanphoun C, Chen J, Dissanayake AJ, Doilom M, Hongsanan S, Jayawardena RS, Jeewon R, Perera RH, Thongbai B, Wanasinghe DN, Wisitrassameewong K, Tibpromma S, Stadler M (2018) Thailand’s amazing diversity: up to 96% of fungi in northern Thailand are novel. Fungal Diversity 93: 215–239. https://doi.org/10.1007/s13225-018-0415-7
  • Hyde KD, Jeewon R, Chen YJ, Bhunjun CS, Calabon MS, Jiang HB, Lin CG, Norphanphoun C, Sysouphanthong P, Pem D, Tibpromma S, Zhang Q, Doilom M, Jayawardena RS, Liu JK, Maharachchikumbura SSN, Phukhamsakda C, Phookamsak R, Al-Sadi AM, Naritsada Thongklang N, Wang Y, Gafforov Y, Jones EBG, Lumyong S (2020) The numbers of fungi: is the descriptive curve flattening? Fungal Diversity 103: 219–271. https://doi.org/10.1007/s13225-020-00458-2
  • 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
  • Kurtzman CP, Robnett CJ (1998) Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology 73: 331–371. https://doi.org/10.1023/A:1001761008817
  • 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. Amsterdam, Elsevier, 87–110. https://doi.org/10.1016/B978-0-444-52149-1.00007-0
  • 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. Amsterdam, Elsevier, 987–1278. https://doi.org/10.1016/B978-0-444-52149-1.00090-2
  • Lopes MR, Morais CG, Kominek J, Cadete RM, Soares MA, Uetanabaro APT, Fonseca C, Lachance MA, Hittinger CT, Rosa CA (2016) Genomic analysis and d-xylose fermentation of three novel Spathaspora species: Spathaspora girioi sp. nov., Spathaspora hagerdaliae fa, sp. nov. and Spathaspora gorwiae fa, sp. nov. FEMS Yeast Research 16: 1–12. https://doi.org/10.1093/femsyr/fow044
  • Morais CG, Batista TM, Kominek J, Borelli BM, Furtado C, Moreira RG, Franco GR, Rosa LH, Fonseca C, Hittinger CT, Lachance MA, Rosa CA (2017) Spathaspora boniae sp. nov., a d-xylose-fermenting species in the Candida albicansLodderomyces clade. International Journal of Systematic and Evolutionary Microbiology 67: 3798–3805. https://doi.org/10.1099/ijsem.0.002186
  • Nei M, Kumar S (2000) Molecular Evolution and Phylogenetics. Oxford University Press, New York.
  • Nguyen NH, Suh SO, Marshall CJ, Blackwell M (2006) Morphological and ecological similarities: wood-boring beetles associated with novel xylose-fermenting yeasts, Spathaspora passalidarum gen. sp. nov. and Candida jeffriesii sp. nov. Mycological Research 110: 1232–1241. https://doi.org/10.1016/j.mycres.2006.07.002
  • Nguyen NH, Suh S-O, Blackwell M (2011) Spathaspora N.H. Nguyen, S.-O. Suh & M. Blackwell. In: Kurtzman CP, Fell JW, Boekhout T (Eds) The Yeasts – a Taxonomic Study, 5th edn, vol. 2. Amsterdam, Elsevier, 795–797. https://doi.org/10.1016/B978-0-444-52149-1.00068-9
  • Rambaut A (2016) FigTree, version 1.4.3. University of Edinburgh, Edinburgh.
  • Ren YC, Chen L, Niu QH, Hui FL (2013) Description of Scheffersomyces henanensis sp. nov., a new d-xylose-fermenting yeast species isolated from rotten wood. PLoS One 9: e92315. https://doi.org/10.1371/journal.pone.0092315
  • Varize CS, Cadete RM, Lopes LD, Christofoleti-Furlan RM, Lachance MA, Rosa CA, Basso LC (2018) Spathaspora piracicabensis f. a., sp. nov., a d-xylose fermenting yeast species isolated from rotting wood in Brazil. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology 111: 525–531. https://doi.org/10.1007/s10482-017-0974-8
  • Wang Y, Ren YC, Zhang ZT, Ke T, Hui FL (2016) Spathaspora allomyrinae sp. nov., a d-xylose-fermenting yeast species isolated from a scarabeid beetle Allomyrina dichotoma. International Journal of Systematic and Evolutionary Microbiology 66: 2008–2012. https://doi.org/10.1099/ijsem.0.000979
  • 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
  • Wohlbach DJ, Kuo A, Sato TK, Potts KM, Salamov AA, Labutti KM, Sun H, Clum A, Pangilinan JL, Lindquist EA, Lucas S, Lapidus A, Jin M, Gunawan C, Balan V, Dale BE, Jeffries TW, Zinkel R, Barry KW, Grigoriev IV, Gasch AP (2011) Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. Proceedings of the National Academy of Sciences of the United States of America 108: 13212–13217. https://doi.org/10.1073/pnas.1103039108
  • Zhai YC, Huang LN, Xi ZW, Chai CY, Hui FL (2019) Candida yunnanensis sp. nov. and Candida parablackwellae sp. nov., two yeast species in the Candida albicans/Lodderomyces clade. International Journal of Systematic and Evolutionary Microbiology 69: 2775–2780. https://doi.org/10.1099/ijsem.0.003552