Molecular identification of Pseudozyma aphidis (Henninger & Windisch) Boekhout: first record from a Brazilian mangrove swamp

ABSTRACT

(Molecular identification of Pseudozyma aphidis (Henninger & Windisch) Boekhout: first record from a Brazilian mangrove swamp). Pseudozyma aphidis (Henninger & Windisch) Boekhout is an anamorph yeast-like basidiomycete commonly found as saprotroph in vegetable debris, such as leaves and flowers. However, there are also reports that this species is pathogenic in humans, usually occurring in patients with some type of immunosuppression, which predisposes to opportunistic infections. Specimens of P. aphidis were collected from water samples and Rhizophora mangle L. leaves at different salinities along the Perequê River, located in a mangrove swamp area at Parque Estadual da Ilha do Cardoso, Cananéia municipality, São Paulo State, Brazil. Aliquots of these samples were spread in Petri dishes. The samples baited with cataphylls of Allium cepa L. were incubated for seven days at 21 ºC. After incubation, the baits were observed under microscope and the specimens were isolated and purified. The identification of the specimens was made through the phylogenetic analysis of the ITS rDNA region. This is the first record of P. aphidis in São Paulo State.

Keywords:
Atlantic rainforest; Basidiomycota; ITS; yeast-like fungi

RESUMO

(Identificação molecular de Pseudozyma aphidis (Henninger & Windisch) Boekhout: primeira citação em um manguezal brasileiro). Pseudozyma aphidis (Henninger & Windisch) Boekhout é um basidiomiceto anamórfico leveduriforme comumente encontrado como sapróbio em detritos vegetais, como folhas e flores. No entanto, há relatos de que esta espécie é patogênica em seres humanos, geralmente ocorrendo em pacientes com algum tipo de imunossupressão que predispõe infecções oportunistas. Espécimes de P. aphidis foram coletados a partir de amostras de água e de folhas de Rhizophora mangle L. em diferentes salinidades ao longo do rio Perequê, localizado em um manguezal no Parque Estadual da Ilha do Cardoso, município de Cananéia, Estado de São Paulo, Brasil. No laboratório, alíquotas destas amostras foram colocadas separadamente em placas de Petri, iscadas com catafilos de Allium cepa L. e incubadas por sete dias a 21 ºC. Após incubação, as iscas foram observadas ao microscópio e os espécimes foram isolados e purificados. A identificação dos espécimes foi realizada através da análise filogenética da região ITS rDNA, sendo este o primeiro registro de P. aphidis no Estado de São Paulo.

Palavras-chave:
Basidiomycota; fungo leveduriforme; ITS; Mata Atlântica

Introduction

Pseudozyma Bandoni emend. Boekhout pro tempore comprises approximately 25 distinct anamorphic yeast species from the Ustilaginaceae, Basidiomycota (Index Fungorum 2016). Although a reliable connection with their teleomorph stages has not been established for many of these species (Boekhout 2011), recent studies have proposed to transfer anamorphic yeast species to their corresponding teleomorphic genera based on strongly supported phylogenetic affinities (Piatek et al. 2015, Wang et al. 2015). From these studies, many species of the genus Pseudozyma have been transferred to the genus Moesziomyces, as is the case of Pseudozyma aphidis (= Moesziomyces aphidis) and the use of the “pro tempore” was suggested by the authors to indicate that in Pseudozyma species names are temporarily remained. The results of these studies allowed the proposition of 16 new combinations for Pseudozyma (Index Fungorum 2016), however, the taxonomic status of five species still remains to be determined because of their uncertain phylogenetic positions (Bandoni 1985, Boekhout 1995, Sugita et al. 2003, Wang et al. 2006, Liou et al. 2009).

This genus has been isolated from different types of materials such as leaves (Golubev et al. 2007, Chamnanpa et al. 2013), flowers (Wei et al. 2005, Liou et al. 2009), blood samples (Sugita et al. 2003, Mekha et al. 2014) and even associated with coral reefs and insects (Henninger & Windisch 1975, Statzell-Tallman et al. 2010, Oliveira et al. 2014). Pseudozyma aphidis (Henninger & Windisch) Boekhout was firstly described as Sterigmatomyces aphidis Henninger & Windisch in Germany and isolated from Aphididae secretions on leaves of Solanum pseudocapsieum (Henninger & Windisch 1975). This species is commonly found as a saprotroph on leaves and flowers (Han et al. 2015, Limtong & Kaewwichian 2015, Nasanit et al. 2015, Tantrungkij et al. 2015), although it is not pathogenic to plants. However, there are reports of this species as pathogenic in humans (Prakash et al. 2014, Herb et al. 2015, Joo et al. 2015, Orecchini et al. 2015), usually occurring in patients with some type of immunosuppression that predisposes opportunistic infections.

In Latin America, the first report of P. aphidis was in Brazil when Costa (2006) reported the presence of this species, through molecular identification of the region D1/D2 of 26S rDNA, in semi-arid soil from Mucugê municipality, Bahia State. Tristão et al. (2012) reported an association of P. aphidis with pineapple fruits sampled from the Central Region of Tocantins State. As a human pathogen, the first case was reported from a public pediatric oncology center in Recife, Pernambuco State, causing pulmonary infection in a patient with Burkitt lymphoma (Parahym et al. 2013).

The occurrence and activity of yeasts in marine waters have been observed worldwide since first reported by Fischer & Brebeck (1894) and is well established due to their role in the decomposition of organic substrates, nutrient cycling, hydrocarbon biodegradation, and as pathogenic for a variety of marine organisms (Vogel et al. 2007, Kutty & Philip 2008). Species of Pseudozyma, including P. aphidis, have commonly been reported in marine and mangrove environments (Gadanho et al. 2003, Statzell-Tallman et al. 2010, Fell et al. 2011).

Several papers have also shown the potential of this species for inducing systemic resistance and as a biocontrol agent against plant pathogens of different crops (Tristão et al. 2012, Buxdorf et al. 2013a, b, Gafni et al. 2015). They are also reported as a potential source of squalene (Chang et al. 2008), lipase (Dimitrijevic et al. 2011) and biosurfactant mannosylerythritol lipids (Morita et al. 2007, Fan et al. 2014, Lorenz et al. 2014, Gunther et al. 2015).

Molecular methods are useful tools for the accurate positioning of yeasts within the Kingdom Fungi, being the classic methods of limited value due to the low morphological variation between species and the existence of a significant yet undescribed diversity (Hoog et al. 1998). The use of nucleotide sequences of internal transcribed spacer (ITS) of the rDNA region is considered the best tool for rapid and accurate identification of yeast isolates (White et al. 1990).

During a survey at the Parque Estadual da Ilha do Cardoso (PEIC), we identified four isolates of P. aphidis based on the phylogenetic analysis of the ITS rDNA region. Thus, the aim of this study is to present the phylogeny of the genus with the inclusion of specimens collected in this mangrove area of Brazilian Atlantic Rainforest.

Material and methods

The Pseudozyma specimens used in this study were isolated from water samples and Rhizophora mangle L. leaves collected (in sterile plastic bottle) in the months of August and November 2012 at different salinities (1.5 to 3%) along the Perequê River. The study area is located in a mangrove swamp from Parque Estadual da Ilha do Cardoso (PEIC), 25°03'05"-25°18'18"S; 47°53'48"-48°05'42"W, situated in Cananéia municipality, São Paulo State, Brazil. This island is a preserved fragment of Atlantic Rainforest that contains different types of vegetation, including tropical forest, “restinga”, dunes and mangrove swamps, with several water bodies like waterfalls, streams and rivers (Barros et al. 1991). During the sampling, the surface water temperature of the estuary was lower in August, about 20 ºC and higher in November, about 27 ºC.

Aliquots (30 mL) of water samples and disks (1 cm diameter) of R. mangle leaves (washed in sterilized seawater) together with 30 mL of a dilution of 50% reverse osmosis and 50% seawater, were placed separately in Petri dishes. These samples were baited with cataphylls of Allium cepa L. (Sparrow 1960, Milanez 1989) and incubated for seven days at 21 ºC. After incubation, the baits were observed under microscope and the specimens were isolated and purified onto PYGs culture medium (Fuller & Jaworski 1987) prepared with a dilution of 50% sterile seawater, penicillin G 0.4 g L^-1 and streptomycin sulphate 0.4 g L^-1.

The specimens were preserved by the Castellani’s method (50% sterile reverse osmosis water and 50% sterile seawater) and posteriorly deposited at the CCIBt culture collection (Coleção de Culturas de Algas, Cianobactérias e Fungos do Instituto de Botânica, São Paulo, SP, Brazil).

Biomass for DNA extraction was obtained by cultivating each isolate onto PYGs culture medium, prepared with a dilution of 50% sterile seawater, penicillin G 0.4 g L^-1 and streptomycin sulphate 0.4 g L^-1, for seven days at 21 ºC. After incubation, the cells were harvested using a platinum loop. The DNA extraction followed the protocol described in the PureLink Genomic DNA kit (Invitrogen^®). The ITS1-5.8S-ITS2 region was amplified using the primers UN-up18S42 and UN-lo28S22 (Robideau et al. 2011). PCR amplification was performed with the PCR SuperMix kit (Invitrogen^®) for a final volume of 25 µl in a C1000 Touch™ Thermal Cycler Bio-Rad following the conditions described by Marano et al. (2014). Amplicons were purified with AxyPrep PCR Clean-up kit (Axygen^®). Sequencing was performed using the same PCR primers in an ABI 3730 DNA Analyser (Life Technologies™). Assembly of contigs and correction of ambiguous bases were manually edited using Sequencher^™ version 4.1.4.

The ITS sequences obtained were compared against BLASTn (Basic Local Alignment Search Tool). For phylogenetic reconstruction, we used ITS rDNA sequences of our isolates and of the other isolates of Pseudozyma available at GenBank (table 1). We analysed 42 sequences from 23 species, using Cintractia axicola (Berk.) Cornu and Trichocintractia utriculicola (Henn.) M. Piepenbr. as outgroups. Sequences were aligned using MAFFT version 7 (Kazutaka & Daron 2013), the ambiguously aligned characters were removed manually using Geneious version 8 (Kearse et al. 2012) and the alignment was deposited in the Treebase (Boettinger & Lang 2011). The best fitting model of evolution was selected using the Akaike Information Criterion in jModeltest version 0.1.1 (Posada 2008). The Maximum Likelihood (ML) phylogenies were reconstructed with PhyML version 3.1 (Guindon & Gascuel 2003) using the TPm2uf + G substitution model, branch swapping by best of NNI and SPR, and support for nodes obtained by 1,000 bootstrap pseudo-replicates. Bayesian inferences (BI) were generated using MrBayes version 3.2.1 (Ronquist & Huelsenbeck 2003) with Markov Chain Monte Carlo (MCMC) methodology to calculate posterior probabilities of the phylogenetic trees. The program was run for 5 millions generations with the TPm2uf + G substitution model. The first 10% of the interactions were discarded as burn-in.

Table 1
Taxa, strain numbers and GenBank accession numbers of the species considered in this study.

Taxa	Strain number	GenBank accession number
Cintractia axicola	HUV17460	AY344967
Trichocintractia utriculicola	MP 2075	DQ875354
Pseudozyma abaconensis	CBS8380	FJ008053
Pseudozyma alboarmeniaca	DMST17135	AB117961
Pseudozyma antarctica	JCM10317	AB089358
Pseudozyma antarctica	JCM3941	JN942669
Pseudozyma aphidis*	CCIBt 4253	KY288985
Pseudozyma aphidis*	CCIBt 4254	KY288982
Pseudozyma aphidis*	CCIBt 4255	KY288981
Pseudozyma aphidis*	CCIBt 4256	KY288984
Pseudozyma aphidis	CBS51783	AF294699
Pseudozyma aphidis	IMUFRJ51941	FN424100
Pseudozyma aphidis	JCM10318	AB089362
Pseudozyma aphidis	LH59	HQ832804
Pseudozyma brasiliensis	GHG001	KF737866
Pseudozyma churashimaensis	OK96	AB548947
Pseudozyma churashimaensis	OK99	AB548950
Pseudozyma crassa	DMST17136	AB117062
Pseudozyma flocculosa	JCM10321	AB089364
Pseudozyma fusiformata	JCM3931	AB089366
Pseudozyma fusiformata	AP6	FJ919774
Pseudozyma graminicola	LI20	AB180728
Pseudozyma hubeiensis	AS2.2493	DQ008954
Pseudozyma hubeiensis	LH146	HQ832814
Pseudozyma jejuensis	CBS10454	EF079966
Pseudozyma jejuensis	IMUFRJ52021	FN428892
Pseudozyma parantarctica	JCM11752	NR130693
Pseudozyma parantarctica	M9932	AB089356
Pseudozyma prolifica	JCM10319	AB089368
Pseudozyma prolifica	CBS31987	AF294700
Pseudozyma pruni	BCRC34227	EU379942
Pseudozyma rugulosa	M12	FJ464594
Pseudozyma rugulosa	JCM10323	AB089370
Pseudozyma rugulosa	CBS17088	AF294697
Pseudozyma shanxiensis	AS2.2523	DQ008956
Pseudozyma shanxiensis	SN37	FJ515182
Pseudozyma siamensis	DMST17137	AB117963
Pseudozyma thailandica	M9933	AB089354
Pseudozyma tsukubaensis	JCM10324	AB089372
Pseudozyma tsukubaensis	KM160	AB855769
Pseudozyma vetiver	DMKU-LV99	AB809652
Pseudozyma vetiver	DMKU-LV90	AB809651

• ^*
  Taxa, strain numbers and GenBank accession numbers of the isolates of Pseudozyma aphidis sequenced in this study.

Results and Discussion

The specimens grew abundantly on Allium cepa L. used as bait and later onto PYGs (figure 1a), with a great number of cells produced in one week (figures 1b, 1c).

Figure 1
a-c. Pseudozyma aphidis. a. One-week old culture onto PYGs culture medium. b-c. Yeast-like fungi cells obtained from colonies growing onto PYGs culture medium. Bars = 10 µm.

The BLASTn query showed that these specimens belong to Pseudozyma aphidis (alignment in the Treebase, http://purl.org/phylo/treebase/phylows/study/TB2:S21546). Our isolates of P. aphidis are well supported and clustered together with other isolates of the same species (90% of bootstrap support with high values of posterior probability (0.98), as shown in figure 2. This species has a close phylogenetic affinity with P. rugulosa (80% of bootstrap support and 0.98 of posterior probability), as previously demonstrated (Chang et al. 2008).

Figure 2
Maximum likelihood tree of internal transcribed spacer (ITS) rDNA sequences of Pseudozyma spp. Maximum likelihood bootstrap support and posterior probability values large than 50% are indicated numerically, those under 50% are marked with (-). Those clades that were not present in the Bayesian trees are marked as (0). The scale bar represent the average number of substitutions per site

The culture collection numbers of the isolates obtained in this study and their respective sequences deposited in GenBank database are shown in table 1.

Although P. aphidis has been already reported in Brazil (Costa 2006, Tristão et al. 2012, Parahym et al. 2013) and worldwide, this is the first report from a mangrove area in São Paulo State.

• †
  (in memoriam)

Acknowledgements

We are indebted to “Instituto Florestal” for the permission given to collect samples at PEIC. Also, we would like to thank FAPESP (“Fundação de Amparo à Pesquisa do Estado de São Paulo”) for the financial support given to C.L.A. Pires-Zotarelli (process nº 2012/50222-7) and CNPq (“Conselho Nacional de Desenvolvimento Científico e Tecnológico”) is also acknowledged for the grant given to C.L.A. Pires-Zottarelli (process nº 304411/2012-4).

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Publication Dates

• Publication in this collection
  Oct-Dec 2017

History

• Received
  11 Jan 2017
• Accepted
  17 Oct 2017