Grapevines (
Vitis vinifera
) are colonized by ubiquitous microorganisms known as endophytes, which may have advantageous or neutral effects without causing disease symptoms. Certain endophytes are ...uncultivable, so culture-independent approaches such as next generation sequencing (NGS) can help for a better understanding of their ecology and distribution. To date, there are no studies which directly link NGS results with taxa derived from a culturing approach, integrating morphological and multi-gene phylogenetic analysis of endophytes. In this study, a culture-dependent and high-resolution culture-independent approach (next generation sequencing) were used to identify endophytes in grapevine stems. In the culture-dependent approach, a total of 94 isolates were recovered from 84 of 144 healthy grapevine stem fragments (colonization rate = 58.3%). The study is unique as we used subsets of combined multi-gene regions to identify the endophytes to species level. Based on each multi-gene phylogenetic analysis, 28 species belong to 19 genera (
Acremonium
,
Alternaria
,
Arthrinium
,
Ascorhizoctonia
,
Aspergillus
,
Aureobasidium
,
Bipolaris
,
Botryosphaeria
,
Botrytis
,
Chaetomium
,
Cladosporium
,
Curvularia
,
Hypoxylon
,
Lasiodiplodia
,
Mycosphaerella
,
Nigrospora
,
Penicillium
,
Phoma
,
Scopulariopsis
) were identified. A higher number of culturable fungi were obtained from 13 year-old vines, followed by eight and three year-old vines. In the culture-independent approach, a fungal richness of 59 operational taxonomic units (OTU) was detected, being highest in 13 year-old grapevines, followed by eight and three years. Even though the cultivation approach detected lower fungal richness, the results related to stem are consistent for fungal community composition and richness. Comparison of the fungal taxa identified by the two approaches resulted in an overlap of 53% of the fungal genera. Due to interspecific variability of the sequences from NGS, in many cases the OTUs (even with the highly abundant ones) were only assignable to order, family or genus level. Incorporating multi-gene phylogenies we successfully identified many of the NGS derived OTUs with poor taxonomic information in reference databases to the genus or species levels. Hence, this study signifies the importance of applying both culture-dependent and culture-independent approaches to study the fungal endophytic community composition in
Vitis vinifera
. This principle could also be applied to other host species and ecosystem level studies.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene cluster is widely used in fungal taxonomy and phylogeographic studies. The medicinal and edible mushroom Agaricus ...subrufescens has a worldwide distribution with a high level of polymorphism in the ITS region. A previous analysis suggested notable ITS sequence heterogeneity within the wild French isolate CA487. The objective of this study was to investigate the pattern and potential mechanism of ITS sequence heterogeneity within this strain. Using PCR, cloning, and sequencing, we identified three types of ITS sequences, A, B, and C with a balanced distribution, which differed from each other at 13 polymorphic positions. The phylogenetic comparisons with samples from different continents revealed that the type C sequence was similar to those found in Oceanian and Asian specimens of A. subrufescens while types A and B sequences were close to those found in the Americas or in Europe. We further investigated the inheritance of these three ITS sequence types by analyzing their distribution among single-spore isolates from CA487. In this analysis, three co-dominant markers were used firstly to distinguish the homokaryotic offspring from the heterokaryotic offspring. The homokaryotic offspring were then analyzed for their ITS types. Our genetic analyses revealed that types A and B were two alleles segregating at one locus ITSI, while type C was not allelic with types A and B but was located at another unlinked locus ITSII. Furthermore, type C was present in only one of the two constitutive haploid nuclei (n) of the heterokaryotic (n+n) parent CA487. These data suggest that there was a relatively recent introduction of the type C sequence and a duplication of the ITS locus in this strain. Whether other genes were also transferred and duplicated and their impacts on genome structure and stability remain to be investigated.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
, a genus within the phylum Ascomycota (Fungi) and family Glomerellaceae are important plant pathogens globally. In this paper, we detail four
species found in mangrove ecosystems. Two new species,
...and
, and a new host record for
were identified in Thailand.
was collected from Taiwan's mangroves and is a new record for
. These identifications were established through a combination of molecular analysis and morphological characteristics. This expanded dataset for
enhances our understanding of the genetic diversity within this genus and its associations with mangrove ecosystems. The findings outlined herein provide data on our exploration of mangrove pathogens in Asia.
is a species-rich order of fungi that includes endophytes, saprobes, and pathogens associated with forest plants and crops. They may also occur as parasites or secondary invaders of plant tissues ...injured or infected by other organisms or inhabit living animal and human tissues, as well as soil. Meanwhile, some severe pathogens wipe out large-scale cultivations of profitable crops, timber monocultures, and forests. Based on morphological and phylogenetic analyses of combined ITS, LSU,
, and
sequence data, generated using maximum likelihood (ML), maximum parsimony (MP), and MrBayes (BI), we introduce two new genera of
found in
in Thailand, namely
and
.
is characterized by solitary, subglobose, pycnidial, unilocular conidiomata with the internal layers convex and pulvinate at the base; hyaline, unbranched, septate conidiophores; hyaline, phialidic, cylindrical to ampulliform, determinate conidiogenous cells and hyaline, cylindrical, straight, unicellular, and aseptate conidia with obtuse ends.
has clavate to broadly fusoid, short pedicellate asci with an indistinct J- apical ring; biturbinate to subellipsoidal, hyaline to pale brown, smooth, guttulate ascospores that are 1-septate and slightly constricted at the septa. Detailed morphological and phylogenetic comparisons of these two new genera are provided in this study.
Fungi have been often neglected, despite the fact that they provided penicillin, lovastatin and many other important medicines. They are an understudied, but essential, fascinating and ...biotechnologically useful group of organisms. The study of fungi in northern Thailand has been carried out by us since 2005. These studies have been diverse, ranging from ecological aspects, phylogenetics with the incorportation of molecular dating, taxonomy (including morphology and chemotaxonomy) among a myriad of microfungi, to growing novel mushrooms, and DNA-based identification of plant pathogens. In this paper, advances in understanding the biodiversity of fungi in the region are discussed and compared with those further afield. Many new species have been inventoried for the region, but many unknown species remain to be described and/or catalogued. For example, in the edible genus
Agaricus
, over 35 new species have been introduced from northern Thailand, and numerous other taxa await description. In this relatively well known genus, 93% of species novelty is apparent. In the microfungi, which are relatively poorly studied, the percentage of novel species is, surprisingly, generally not as high (55
–
96%). As well as Thai fungi, fungi on several hosts from Europe have been also investigated. Even with the well studied European microfungi an astounding percentage of new taxa (32
–
76%) have been discovered. The work is just a beginning and it will be a daunting task to document this astonishingly high apparent novelty among fungi.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Cancellidium
is a remarkable fungal genus which has been collected from wood submerged in freshwater and has unique conidia that are important in dispersal in running streams. With such a remarkable ...morphology, one would have expected it to be a distinct family or order. However, due to the dearth of molecular evidence in related taxa, this genus has previously been placed in the order
Hypocreales
, subclass Hypocreomycetidae of Sordariomycetes. In this study, we made three new collections of this remarkable aquatic genus from streams in China and Thailand, isolated them into culture, extracted DNA and carried out multigene phylogenetic analysis and divergence time estimation which placed the genus in Diaporthomycetidae. This is one of the seven subclasses of Sordariomycetes and contains 30 lineages that are only known from freshwater. The subclass is therefore of interest when considering the evolution of freshwater fungi. Several lineages of Diaporthomycetidae are morphologically unique and taxa cluster with strong support, but have weak support at the base of the trees. The phylogenetic and MCC trees generated in this study indicate that
Aquapteridospora
,
Barbatosphaeriaceae
,
Bullimyces
,
Cancellidium
,
Ceratolenta
,
Conlarium
,
Phialemoniopsis
,
Pseudostanjehughesia
and
Rhamphoriaceae
are distinct genera/families that evolved in the family/order time frame. The new orders
Barbatosphaeriales
(177 MYA),
Cancellidiales
(137 MYA),
Ceratolentales
(147 MYA),
Conlariales
(138 MYA) and
Rhamphoriales
(133 MYA) and six new families,
Aquapteridosporaceae
(110 MYA),
Cancellidiaceae
(137 MYA),
Ceratolentaceae
(81 MYA),
Bullimycetaceae
(81 MYA),
Phialemoniopsaceae
(59 MYA), and
Pseudostanjehughesiaceae
(111 MYA) are introduced with evidence from phylogenies, divergence estimates and distinct morphologies. Of these families,
Aquapteridosporaceae
,
Cancellidiaceae
,
Bullimycetaceae
, and
Pseudostanjehughesiaceae
are only known from freshwater.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Ophioceras is accommodated in the monotypic family Ophioceraceae (Magnaporthales, Sordariomycetes), and the genus is delimited based on molecular data. During an ongoing survey of bambusicolous fungi ...in southwest China, we collected a submerged decaying branch of bamboo from Sichuan Province, China and an Ophioceras species occurring on this substrate was observed and isolated. An Ophioceras taxon was delimited based on morphological characteristics and combined LSU, RPB1 and ITS sequence analyses and is described as Ophioceras sichuanense sp. nov. The species formed a well-supported clade basal to Ophioceras (100% ML, 1.00 PP). Based on the updated phylogenetic tree of Magnaporthales, Ceratosphaerella castillensis (generic type) and C. rhizomorpha formed a clade within Ophioceras and morphologically resemble Ophioceras. Therefore, Ceratosphaerella is synonymized under Ophioceras. The phylogenetic relationships of Ophioceras are discussed in relation to morphological similarities of genera in Magnaporthales. The generic circumscription of Ophioceras is emended.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
This study deals with an extensive evaluation focusing on phylogenetic and chemotaxonomic infrageneric relationships of the genus
Annulohypoxylon
(Xylariaceae, Ascomycota), whose species are ...ubiquitously associated with seed plants as endophytes and saprotrophs in all forested areas of the world. Using evidence from phylogenetic, chemotaxonomic and morphological data, various varieties within the genus are raised to species level, leading to the new combinations for
A. areolatum
(≡
A. bovei
var
. microsporum
),
A. macrosporum
(≡
A. leptascum
var.
macrosporum
), and
A. microdiscum
(≡
A. moriforme
var.
microdiscum
).
Annulohypoxylon substygium
nom. nov. is applied for
A. stygium
var
. annulatum
and the four new tropical and subtropical species
A. massivum
,
A. violaceopigmentum
,
A. viridistratum
and
A. yungensis
are introduced. Furthermore,
A. leucadendri
is excluded from the genus as its morphological characters disagree with the generic concept, the recently erected
A. palmicola
is synonymized with
A. leptascum
and
A. austrobahiense
has been reassigned to the genus
Hypoxylon
. In addition, the key taxa
A. annulatum
and
A. truncatum
have been reinvestigated and epitypes have been defined. For the first time, a dichotomous key to the genus is provided. A phylogenetic β-tubulin tree in conjunction with stromatal HPLC profiles clearly shows that
Annulohypoxylon
comprises two distinct lineages. The
A. cohaerens
/
multiforme
group might eventually warrant segregation into a new genus as further molecular data become available.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
This article provides morphological descriptions and illustrations of microfungi associated with the invasive weed,
Chromolaena odorata
, which were mainly collected in northern Thailand. ...Seventy-seven taxa distributed in ten orders, 23 families (of which Neomassarinaceae is new), 12 new genera (
Chromolaenicola
,
Chromolaenomyces
,
Longiappendispora
,
Pseudocapulatispora
,
Murichromolaenicola
,
Neoophiobolus
,
Paraleptospora
,
Pseudoroussoella
,
Pseudostaurosphaeria
,
Pseudothyridariella
,
Setoarthopyrenia
,
Xenoroussoella
), 47 new species (
Aplosporella chromolaenae
,
Arthrinium chromolaenae
,
Chromolaenicola chiangraiensis
,
C. lampangensis
,
C. nanensis
,
C. thailandensis
,
Chromolaenomyces appendiculatus
,
Diaporthe chromolaenae
,
Didymella chromolaenae
,
Dyfrolomyces chromolaenae
,
Leptospora chromolaenae
,
L. phraeana
,
Longiappendispora chromolaenae
,
Memnoniella chromolaenae
,
Montagnula chiangraiensis
,
M. chromolaenae
,
M. chromolaenicola
,
M. thailandica
,
Murichromolaenicola chiangraiensis
,
M. chromolaenae
,
Muyocopron chromolaenae
,
M. chromolaenicola
,
Neomassarina chromolaenae
,
Neoophiobolus chromolaenae
,
Neopyrenochaeta chiangraiensis
,
N. chromolaenae
,
N. thailandica
,
N. triseptatispora
,
Nigrograna chromolaenae
,
Nothophoma chromolaenae
,
Paraleptospora chromolaenae
,
P. chromolaenicola
,
Patellaria chromolaenae
,
Pseudocapulatispora longiappendiculata
,
Pseudoroussoella chromolaenae
,
Pseudostaurosphaeria chromolaenae
,
P. chromolaenicola
,
Pseudothyridariella chromolaenae
,
Pyrenochaetopsis chromolaenae
,
Rhytidhysteron chromolaenae
,
Setoarthopyrenia chromolaenae
,
Sphaeropsis chromolaenicola
,
Tremateia chiangraiensis
,
T. chromolaenae
,
T. thailandensis
,
Xenoroussoella triseptata
,
Yunnanensis chromolaenae
), 12 new host records, three new taxonomic combinations (
Chromolaenicola siamensis
,
Pseudoroussoella elaeicola
,
Pseudothyridariella mahakashae
), and two reference specimens (
Torula chromolaenae
,
T. fici
) are described and illustrated. Unlike some other hosts, e.g. bamboo (Poaceae) and Pandanaceae, the dominant group of fungi on Siam weed were Dothideomycetes. Only 15 species previously recorded from northern Thailand were found in this study. Most of the taxa are likely to have jumped hosts from surrounding plants and are unlikely to be a specialist to Siam weed. Most fungal families found on Siam weed had divergence estimates with stem ages in the Cretaceous, which coincided with the expected origin of the host family (Asteraceae). This further indicates that the species have jumped hosts, as it is unlikely that the taxa on the alien Siam weed came from the Americas with its host. They may, however, have jumped from other Asteraceae hosts. In a preliminary screening 40 (65%) of the 62 species tested showed antimicrobial activity and thus, the fungi associated with
C. odorata
may be promising sources of novel bioactive compound discovery. We provide a checklist of fungi associated with
C. odorata
based on the USDA Systematic Mycology and Microbiology Laboratory (SMML) database, relevant literature and our study. In total, 130 taxa (116 identified and 14 unidentified species) are distributed in 20 orders, 48 families, and 85 genera.
Pseudocercospora
is the most commonly encountered genus on Siam weed.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Species with relatively small, membraneous, black ascomata, with or without long necks, unitunicate, cylindrical asci with apical rings and fusiform, hyaline ascospores with or without mucilaginous ...sheaths are common in freshwater habitats in tropical and temperate regions. Many of these taxa have originally been recorded as
Annulatascaceae
-like taxa. Twenty genera have been included in the family
Annulatascaceae
, mostly based on morphological characters, while molecular work and phylogenetic analyses are lacking for many genera. In this study, nine new
Annulatascaceae
-like taxa collected from Thailand were morphologically examined. Pure cultures obtained from single ascospores were used in molecular studies. The nine new strains and several other strains of Annulatascaceae-like Sordariomycetes species were used to establish phylogenetic and evolution relationships among the taxa, based on combined LSU, SSU, ITS and RPB2 sequence data. Phylogenetic analyses provide evidence to introduce one new order and six new families, to accommodate taxa excluded from
Annulatascaceae
sensu stricto. A new order
Atractosporales
is established based on the molecular study, including three new introduced families
Conlariaceae
,
Pseudoproboscisporaceae
and
Atractosporaceae
.
Conlariaceae
is introduced for the genus
Conlarium
which comprises two species,
Conlarium duplumascosporun
and a new Hyphomycetous asexual morph taxon
Conlarium aquaticum
which has subglobose or irregular, brown, clathrate, muriform conidia.
Pseudoproboscisporaceae
includes
Pseudoproboscispora
and
Diluviicola
, while
Atractosporaceae
includes the genera
Rubellisphaeria
and
Atractospora. Barbatosphaeria
,
Xylomelasma
and
Ceratostomella
form a distinct stable lineage which is introduced as a new family
Barbatosphaeriaceae
in Diaporthomycetidae families
incertae sedis.
A new family
Lentomitellaceae
is introduced in Diaporthomycetidae families
incertae sedis
, to accommodate the genus
Lentomitella. Woswasiaceae
is introduced to accommodate
Woswasia
,
Xylochrysis
and
Cyanoannulus
in Diaporthomycetidae families
incertae sedis
. Three new species of
Fluminicola
viz.
F. saprophytica
,
F. thailandensis
and
F. aquatica
are introduced. A new sexual morph,
Dictyosporella thailandensis,
is reported and
Dictyosporella
is excluded from
Annulatascaceae
and placed in Diaporthomycetidae genera
incertae sedis
. The first sexual morph of
Sporidesmium
,
S. thailandense
is also described. The new species
Atractospora thailandensis
,
Diluviicola aquatica
and
Pseudoproboscispora thailandensis
are also introduced.
Platytrachelon
is added to
Papulosaceae
based on phylogenetic analysis and morphological characters.
Aquaticola
,
Fusoidispora
and
Pseudoannulatascus
are excluded from
Annulatascaceae
and placed in Diaporthomycetidae genera
incertae sedis
.
Mirannulata
is accommodated in Sordariomycetes, genera
incertae sedis
.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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