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Submitted 18 May 2018, Accepted 12 June 2018, Published 11 July 2018
Corresponding Author: Ratchadawan Cheewangkoon – e-mail – ratchadawan.c@cmu.ac.th 769
Phaeosaccardinula coffeicola and Trichomerium chiangmaiensis, two
new species of Chaetothyriales (Eurotiomycetes) from Thailand
Maharachchikumbura SSN1,2, Haituk S1, Pakdeeniti P1, Al-Sadi AM2,
Hongsanan S3, Chomnunti P3, Cheewangkoon R1
1 Entomology and Plant Pathology Department, Faculty of Agriculture, Chiang Mai University
2 Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box 34,
123 Al-Khoud, Oman
3 Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
Maharachchikumbura SSN, Haituk S, Pakdeeniti P, Al-Sadi AM, Hongsanan S, Chomnunti P,
Cheewangkoon R 2018 – Phaeosaccardinula coffeicola and Trichomerium chiangmaiensis, two
new species of Chaetothyriales (Eurotiomycetes) from Thailand. Mycosphere 9(4), 769–778,
Doi 10.5943/mycosphere/9/4/5
Abstract
Two species of sooty mould-like taxa, were obtained from living leaves of Coffea arabica
plants collected in Chiang Mai Province, Thailand. Differences in phenotypic and phylogenetic
characteristics based on combined large subunit nuclear ribosomal DNA and internal transcribed
spacer sequences indicated that the two isolates represent two novel species (Phaeosaccardinula
coffeicola and Trichomerium chiangmaiensis) within the order Chaetothyriales. Phaeosaccardinula
coffeicola (Chaetothyriaceae) is distinguished morphologically from related species by its smaller
asci and ascospores. Trichomerium chiangmaiensis (Trichomeriaceae) is morphologically
distinguishable from its phylogenetically related species by its smaller conidial arms. Detailed
taxonomic descriptions and illustrations of the new species are provided.
Key words – Chaetothyriaceae – Coffea arabica – new species – sooty mould – Trichomeriaceae
Introduction
The order Chaetothyriales was introduced by Barr (1976) for Loculoascomycetes that
presence of with periphysoids (apical paraphyses) in the ascomata (Winka et al. 1998). Barr (1987)
accepted Chaetothyriaceae, Coccodiniaceae, Herpotrichiellaceae, Metacapnodiaceae,
Microtheliopsidaceae, Pyrenotrichaceae, Strigulaceae and Trichopeltidaceae as families of
Chaetothyriales. In the classification of Wijayawardene et al. (2018), ten families are accepted in
Chaetothyriales: Chaetothyriaceae, Coccodiniaceae, Cyphellophoraceae, Epibryaceae,
Herpotrichiellaceae, Lyrommataceae, Microtheliopsidaceae, Pyrenotrichaceae, Strelitzianaceae and
Trichomeriaceae. Members belonging to the order Chaetothyriales are morphologically highly
diverse both in their ascomycetous sexual morphs and dematiaceous hyphomycetous asexual
morphs (Gueidan et al. 2008, Chomnunti et al. 2012a, Dong et al. 2018). Species of Chaetothyriales
are common in tropical and temperate ecosystems and may cause plant diseases, have also been
recorded as an opportunistic human and animal pathogens, often isolated as saprobes, or occur as
lichenized taxa or epilithic fungi (Gueidan et al. 2008, Chomnunti et al. 2012a, Réblová et al. 2013,
Liu et al. 2015, Hongsanan et al. 2016, Hyde et al. 2016, Teixeira et al. 2017, Dong et al. 2018).
Mycosphere 9(4): 769–778 (2018) www.mycosphere.org ISSN 2077 7019
Article
Doi 10.5943/mycosphere/9/4/5
Copyright © Guizhou Academy of Agricultural Sciences
770
The Chaetothyriaceae was introduced by Hansford (1946) and members belonging to the
family are saprotrophic or biotrophic (Chomnunti et al. 2012a, 2014, Hongsanan et al. 2016). The
Chaetothyriaceae includes 16 genera, including the foliar epiphytic genus Phaeosaccardinula,
which has superficial ascomata, with a dark, non-setose pellicle, saccate, bitunicate asci and
muriform, hyaline to brownish ascospores (Batista et al. 1962, Hughes et al. 1976, Yang et al.
2014). Phaeosaccardinula was described by Hennings (1905) with P. diospyricolai as the type
species. Many of the species belonging to the Phaeosaccardinula were later transferred to the
genera Limacinula and Treubiomyces (Reynolds 1971, 1983) and it has an estimated 14 species
(Kirk et al. 2008, Yang et al. 2014, Wijayawardene et al. 2017).
Trichomeriaceae was introduced by Chomnunti et al. (2012a) and placed in Chaetothyriales
based on analysis of LSU and ITS sequence data. The family comprises a single genus,
Trichomerium, with its type species T. coffeicola. Chomnunti et al. (2012a) proposed T. foliicola as
the type species of Trichomerium, since it has been impossible to obtain the holotype specimen of
T. coffeicola and also no molecular data exists in worldwide databases for this species or genus.
The foliar epiphyte genus Trichomerium occurs superficially on living leaves of a variety of plants
(Chomnunti et al. 2012a). It is estimated that the genus includes 23 species (Kirk et al. 2008),
however, only seven species have sequence data. Trichomeriaceae was synonymized under
Chaetothyriaceae by Réblová et al. (2013) based on ITS-β-tubulin-LSU-SSU-RPB2-mcm7
phylogeny and assessment of ITS secondary structures. However, Trichomeriaceae was accepted as
a distinct family in most subsequent studies based on multi-gene phylogenetic analysis (Gueidan et
al. 2014, Liu et al. 2015, Hyde et al. 2016).
We have been carrying out a taxonomic survey of foliar epiphytes on Coffea arabica (coffee)
plants in Thailand and in the present study, two new species, Phaeosaccardinula coffeicola and
Trichomerium chiangmaiensis, are introduced. Evidence for the new species is based on their
unique morphological characters, as well as the support from phylogenetic analyses of combined
LSU and ITS sequence data.
Materials & Methods
Isolation and identification of fungi
Fungi with sooty mould-like colonization were collected in 2014 from coffee leaves in
Chiang Mai Province, Thailand. Specimens were taken to the laboratory in envelopes.
Measurements and descriptions of sections of the ascomata/conidiomata, asci and
ascospores/condia were carried out by immersing ascomata/conidiomata in water or in Shear’s
reagent. Unless otherwise stated, all photographs and measurements were made from material
mounted in water and 95% lactic acid. Slides were viewed under a Nikon SMZ745T stereo
microscope and (Axiovision Zeiss Scope-A1) microscope where diagnostic morphological features
were recorded photomicrographs and measurements were taken. The fungal species present on the
substrate were isolated using a single spore culture technique. In short, an ascomata/ conidiomata
was immersed in 300 μl of sterile distilled water on a slide and left for a few minutes, so that the
ascospores were discharged. An ascospore suspension was made, small drops were placed on water
agar (WA) in Petri-dishes and kept at room temperature for 8–12 h for ascospores to germinate;
single germinating ascospores were transferred to potato dextrose agar (PDA) plates. The plates
were incubated at 25 °C for 15 to 20 days. After a month, the growing cultures were used for
molecular work. Holotype specimens are deposited in herbarium of Chiang Mai University and
living cultures are deposited in Sultan Qaboos University culture collection (SQUCC).
Facesoffungi and Index Fungorum numbers are registered as outlined in Jayasiri et al. (2015),
Index Fungorum (2018).
DNA isolation, amplification and Sequencing
Total genomic DNA was extracted directly using a DNA extraction kit (E.Z.N.A. Forensic
DNA Kit), following the protocols in the manufacturer’s instructions. For nucleotide sequence
771
comparisons, the internal transcribed spacer region (ITS) and a segment of the large subunit rDNA
(LSU) regions were amplified using primer pairs ITS4/ITS5 (White et al. 1990) and LROR/LR5
(Vilgalys & Hester 1990), respectively. The thermal cycling program followed
Maharachchikumbura et al. (2014). Sequencing of the PCR amplicons was conducted using the
same primers used for the amplification reactions. The PCR products were verified by staining with
ethidium bromide on 1 % agarose electrophoresis gels. DNASTAR Lasergene SeqMan Pro v.8.1.3
was used to obtain consensus sequences from sequences generated from forward and reverse
primers and these were subsequently lodged in GenBank (Table 1).
Phylogenetic analysis
The sequences generated in this study were supplemented by additional sequences obtained
from GenBank, based on BLAST searches and the literature. Multiple sequence alignments were
generated with MEGA v.7.0.26 (Kumar et al. 2016) and the alignment was visually improved
where necessary. Phylogenetic analyses of the sequence data consisted of Maximum Parsimony
(MP) and Maximum Likelihood (ML) analyses of the aligned datasets. A maximum likelihood
analysis was performed using RAxMLGUI v. 1.3 (Silvestro & Michalak 2012). The optimal ML
tree search was conducted with 1,000 separate runs, using the default algorithm of the program
from a random starting tree for each run. The final tree was selected among suboptimal trees from
each run by comparing likelihood scores under the GTR+GAMMA substitution model evolution by
MrModeltest 2.2 (Nylander 2004). The MP analysis was performed with PAUP v.4.0b10 (Swofford
2003). Trees were inferred by using the heuristic search option with TBR branch swapping and
1,000 random sequence additions. The maximum number of retained trees was limited to 5,000,
branches of zero length were collapsed and all multiple equally most parsimonious trees were
saved. Tree length (TL), consistency index (CI), retention index (RI), rescaled consistency index
(RC), homoplasy index (HI), and log likelihood (−ln L) (HKY model) values were calculated. The
robustness of the equally most parsimonious trees was evaluated by 1,000 bootstrap replications
(Felsenstein 1985) resulting from a maximum parsimony analysis, each with 10 replicates of
random stepwise addition of taxa. The resulting trees were printed with MEGA v.7.0.26 (Kumar et
al. 2016) and the layout was made with Adobe Illustrator CS v.6.
Table 1 Details of the strains included for molecular study and newly generated sequences are
indicated in bold
Taxon
Isolate
GenBank accessions
LSU
ITS
Aphanophora eugeniae
CBS 124105
FJ839652
NR_132829
Bradymyces alpinus
CCFEE 5493
GU250396
NR_132844
Brycekendrickomyces acaciae
CBS 124104
FJ839641
NR_132828
Camptophora hylomeconis
CBS 113311
-
NR_132881
Capronia mansonii
CBS 101.67
NR_121262
AY004338
Ceramothyrium ficus
MFLUCC 15-0229
KT588600
KT588602
Ceramothyrium ficus
MFLUCC 15-0228
KT588599
NR_154800
Ceramothyrium menglunense
MFLUCC 16-1874
KX524146
NR_154813
Ceramothyrium podocarpi
CPC 19826
KC005795
NR_120227
Ceramothyrium thailandicum
MFLUCC 10-0008
KP324930
NR_137768
Cladophialophora minourae
CBS 556.83
FJ358235
AY251087
Cyphellophora fusarioide
MUCL 44033
KC455252
NR_132879
Cyphellophora guyanensis
MUCL 43737
KC455253
NR_132880
Cyphellophora olivacea
CBS 122.74
KC455260
KC455247
Cyphellophora oxyspora
CBS 698.73
KC455262
NR_132883
772
Table 1 Continued.
Taxon
Isolate
GenBank accessions
LSU
ITS
Cyphellophora reptans
CBS 113.85
JQ766493
NR_121346
Epibryon diaphanum
M122
EU940101
-
Epibryon hepaticola
M10
EU940091
JX298885
Epibryon interlamellare
M223
EU940135
-
Epibryon plagiochilae
M187
EU940124
-
Exophiala eucalyptorum
CBS 121638
KC455258
KC455245
Exophiala xenobiotica
CBS 115831
FJ358246
AY857539
Fonsecaea monophora
CBS 102243
FJ358247
EU938579
Knufia cryptophialidica
DAOM 216555
JN040500
JN040500
Knufia epidermidis
CBS 120353
NG_042475
NR_111330
Knufia perforans
CBS 885.95
JN040506
NG_042586
Leptoxyphium madagascariense
CBS 124766
GQ303308
GQ303277
Metulocladosporiella musae
CBS 161.74
DQ008161
DQ008137
Metulocladosporiella musicola
CBS 113873
DQ008135
DQ008159
Minimelanolocus aquaticus
MFLUCC 15-0414
KR215612
NR_154181
Minimelanolocus submersus
KUMCC 15-0206
KX789215
KX789212
Phaeococcomyces aloes
CPC 21873
KF777234
NR_132069
Phaeococcomyces catenatus
CBS 650.76
-
AF050277
Phaeosaccardinula coffeicola
COF25
MH345729
MH345730
Phaeosaccardinula dendrocalami
IFRDCC 2649
KF667244
NR_132894
Phaeosaccardinula dendrocalami
IFRDCC 2663
KF667246
KF667243
Phaeosaccardinula ficus
MFLUCC 10-0009
HQ895837
NR_132850
Phaeosaccardinula multiseptata
IFRDCC 2639
KF667246
KF667243
Strelitziana malaysiana
CPC 24874
KR476766
KR476731
Trichomerium bambusae
MFLU 16-2286
-
KX845435
Trichomerium deniqulatum
MFLUCC 10-0884
JX313660
JX313654
Trichomerium chiangmaiensis
COF18
MH345728
MH345731
Trichomerium eucalypti
CBS 143443
MG386121
MG386068
Trichomerium foliicola
MFLUCC10-0078
JX313661
NR_144963
Trichomerium gleosporum
MFLUCC10-0087
JX313662
JX313656
Trichomerium siamensis
MFLUCC 12-0105
-
KP744468
Vonarxia vagans
CPC 15152
FJ839673
FJ839637
Vonarxia vagans
CBS 123533
FJ839672
NR_132830
Results
Phylogenetic analyses
New nucleotide sequences generated in this study were deposited in GenBank (Table 1).
Results of the individual LSU and ITS trees (results not shown) indicated that there was no
significant conflict between the topologies and respective clades in each loci. Therefore, the LSU
and ITS loci were concatenated into a single dataset for analysis. After exclusion of ambiguously
aligned regions, the final dataset included 48 isolates with an alignment length of 1724 characters
(including gaps). With parsimony analysis, 942 characters were constant and 595 parsimony-
informative. The parsimony analysis of the data matrix resulted in 12 equally parsimonious trees
and the first tree (TL = 3,370 steps, CI = 0.396, RI = 0.609, HI = 0.604, RC = 0.241). A best
773
scoring RAxML tree resulted with the value of Likelihood: –16510.941529. The ML analyses
showed similar tree topologies and was congruent to those obtained in MP analysis and the
phylogenetic tree resulting from the analysis of two loci concatenated is rooted using Leptoxyphium
madagascariense (CBS 124766) (Fig. 1). The phylogenetic tree of the partial LSU and ITS loci
produced by using ML and MP analysis shows that the families of the order Chaetothyriales
generally resolved into well supported clades. Trichomerium chiangmaiensis sp. nov. formed a
distinct clade which is sister to species including Trichomerium foliicola, Trichomerium
gleosporum and Trichomerium eucalypti. Phylogenetic analysis observation that
Phaeosaccardinula coffeicola is distinct evolutionary entity and was recognized as basal lineage for
all other Phaeosaccardinula isolates.
Figure 1 – Consensus tree resulting from a maximum likelihood analysis of a combined LSU and
ITS sequence alignment for taxa of Chaetothyriaceae, Trichomeriaceae and other species in
Chaetothyriales. Families are indicated in coloured blocks. RAxML bootstrap support values (MLB
above 70 %) and maximum parsimony bootstrap support values (MPB above 70 %) are given at the
nodes (MLB/MPB). The scale bar represents the expected number of changes per site. The tree is
rooted to Leptoxyphium madagascariense (CBS 124766). The new sequences used in this study are
in blue and type sequences are indicate by T.
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Taxonomy
Phaeosaccardinula coffeicola Maharachch., Haituk & Cheew., sp. nov. Fig. 2
Index Fungorum number: IF554763; Facesoffungi number: FoF04392
Etymology – coffeicola referring to the host on which the taxon was found.
Foliar epiphytes growing on the upper surface of living leaves forming a soot-like coating. Sexual
morph: Mycelium superficial, black, hyphae-like, dark brown to black, reticulate to branched,
constricted at the septa. Ascomata 171–215 × 134–172 μm (x
̄ = 193 × 153 μm, n = 10), scattered on
upper surface of living leaves of Coffea arabica, superficial, globose, dull black, lacking setae,
thick-walled, inwardly of hyaline of textura prismatica, dark brown to brown towards the outside,
comprised 3−4 layers of textura angularis. Asci 37–54 × 10–26 μm (x
̄ = 46 × 18 μm, n = 10), 4–6-
spored, bitunicate, oblong-ellipsoid when young, subglobose to oval when mature, with short
pedicel, ocular chamber not visible in mature asci. Ascospores 24–33 × 8–12 μm (x
̄ = 29 × 10 μm,
n = 10) overlapping 2–4-seriate, hyaline, olivaceous green at the septa of mature ascospores,
oblong-ellipsoid, muriform, with 5–7 transversal septa and 3–5 longitudinal septa, constricted at the
septum, with mucilaginous sheath (absent in some mature ascospores) germ tubes developing from
numerous cells. Asexual morph: Undetermined.
Culture characters – Conidia germinating on PDA at 25 °C for 24 h, Colonies on PDA
growing 2 cm diam after 60 days, surface brown, spreading, velvety, dense floss on the surface,
pale brown and rough at the margin. No asexual state produced on PDA after 60 days.
Material examined – Thailand, Chiang Mai Province, Khun Chang Khian Highland Research
Station, on living leaves of Coffea arabica L. (Rubiaceae), 21 December 2014, S.S.N
Maharachchikumbura (COF25, holotype), – ex-type culture in SQUCC 12166.
Notes – Phaeosaccardinula coffeicola forms a separate cluster in the combined phylogeny, as
basal sister to a group including P. dendrocalami, P. ficus and P. multiseptata which were isolated
from on living leaf of Dendrocalamus brandisii, on living leaf of Ficus sp. and on living leaf of
Dillenia pentagyna respectively (Chomnunti et al. 2012b, Yang et al. 2014). It differs from its
closest phylogenetic neighbours; P. dendrocalami (asci = 57−70 × 27−41 μm; ascospores = 37−49
× 11−15 μm), P. ficus (asci = 120–185 3 49–64 μm; ascospores = 33–56 × 10–17 μm) and P.
multiseptata (asci = 55–69 × 30–40 μm; ascospores = 38–47 × 13–16 μm) by its smaller asci and
ascospores (asci = 37−54 × 10−26 μm; ascospores = 24−33 × 8−12 μm).
Trichomerium chiangmaiensis Maharachch., Pakdeeniti & Cheew., sp. nov. Fig. 3
Index Fungorum number: IF554764; Facesoffungi number: FoF04393
Etymology – named after the region where it was isolated.
Epiphytic or saprobic on the upper surface of leaves. Superficial hyphae, branched, septate,
slightly constricted at the septa, pale brown to dark brown, hyphal networks cover the surface of
hosts.Foliar epiphytes growing on the upper surface of living leaves forming a soot-like coating
Asexual morph: Stroma none. Setae and hyphopodia absent. Conidiophore micronematous,
mononematous; usually very short, pale brown, thick denticles develop from swollen hyphal cells
but are not cut off by septa. Conidiogenous cells monoblastic, integrated, intercalary, determinate,
cylindrical, denticulate; denticles stout, cylindrical. Conidia arms 39–58 × 7–9 μm (x
̄ = 50 × 8 μm,
n = 10), solitary, dry, pleurogenous, branched, with usually 4 arms, sometime up to 5 arms,
3−5-septate, pale olivaceous or brown, smooth; arms subulate, multiseptate, tapering to the apex,
with rounded ends; conidia also have a fifth branch of 1–2 cells tapering to a subobtuse apex.
Sexual morph: Undetermined.
Culture characters – Conidia germinating on PDA at 25 °C for 18 hours, germ tubes
appearing from each branch of conidia, hyaline to bluish, but becoming dark brown to black.
Colonies reaching 1 cm diameter after 7 days on PDA at 25 °C, colonies, velvety surface, dark
775
brown pale brown at the margin, dark brown sparse aerial hyphae outer region. Conidia produced
in PDA after 15 days incubation.
Figure 2 – Phaeosaccardinula coffeicola (COF25, holotype). a−b Sooty molds on leaf surface.
c Vertical sections of ascoma. d−e Asci. f Colonies on media. g Ascospores. Scale bars: c−e, = 30
μm, g = 5 μm.
776
Material examined – Thailand, Chiang Mai Province, Mae Rim, Nong Hoi Royal Project, on
living leaves of Coffea arabica L. (Rubiaceae), 15 December 2014, S.S.N Maharachchikumbura
(COF18, holotype) – ex-type culture in SQUCC 12167.
Notes – Trichomerium chiangmaiensis is introduced as a new species based on its asexual
morphs isolated from the living leaves of Coffea arabica. Trichomerium chiangmaiensis
phylogenetically closely related to T. eucalypti, T. foliicola and T. gleosporum. The genus
Trichomerium has Tripospermum asexual morphs (Crous et al. 2014) and the asexual morph of T.
chiangmaiensis is comparable with T. eucalypti and T. gloeosporum. Trichomerium chiangmaiensis
can be distinguished from T. eucalypti (conidial arms size = 30–80 × 8–10 µm) by its smaller
conidial arms (size = 39−58 × 7−9 μm). Furthermore, the microconidia present on the T. eucalypti
(Crous et al. 2017) were not observed on the T. chiangmaiensis. Trichomerium gloeosporum is
distinct from T. chiangmaiensis by its smaller conidial arms (size = 29−35 × 5−7 μm), longer basal,
and apical appendages.
Figure 3 – Trichomerium chiangmaiensis. a–b Sooty molds on host. c Conidia and conidiophore.
d–g Immature conidia at various stages of development attached to the prostrate mycelium.
h Denticulate. i–f Conidia. j Colonies on media. Scale bars: c, i–k = 30 μm, d–h = 10 μm.
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Acknowledgements
We would like to acknowledge financial support from Sultan Qaboos University and Oman
Animal and Plant Genetic Resources Center through the project EG/AGR/CROP/16/01. We also
received support from the Chiang Mai University Postdoctoral Fellowship (2017).
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