Taxonomic revisions in the Microstromatales: two new yeast species, two new genera, and validation of Jaminaea and two Sympodiomycopsis species

Kijpornyongpan, Teeratas; Aime, M. Catherine

doi:10.1007/s11557-017-1276-2

Cited by 24 publications

(24 citation statements)

References 29 publications

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“…Although less abundant than Malassezia and Cladosporium -related phylotypes, the exobasidiomycetous Pseudomicrostroma glucosiphilum also appeared to be numerically important in the hindgut of S. nudus . This species was originally isolated using a glucose air-exposed agar plate, and relevant ecological information is currently not available, except for physiological knowledge that it assimilates a range of carbon sources including cellobiose, trehalose, arabinose, and ribose and grows on vitamin-free medium ( 36 ). The present results add the gut environment as an additional ecological niche of this fungus.…”

Section: Discussionmentioning

confidence: 99%

Molecular Detection of Eukaryotic Diets and Gut Mycobiomes in Two Marine Sediment-Dwelling Worms, Sipunculus nudus and Urechis unicinctus

Wang

Shi

Huang

et al. 2018

Microbes and environments

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The present study aimed to reveal the eukaryotic diets of two economically important marine sediment-inhabiting worms, Sipunculus nudus (peanut worm) and Urechis unicinctus (spoon worm), using clone libraries and phylogenetic analyses of 18S rRNA genes. Fungal rDNA was also targeted and analyzed to reveal mycobiomes. Overall, we detected a wide range of eukaryotic phylotypes associated with the larvae of S. nudus and in the gut contents of both worms. These phylotypes included ciliates, diatoms, dinoflagellates, eustigmatophytes, placidids, oomycetes, fungi, nematodes, flatworms, seaweeds, and higher plants. Oomycetes were associated with the planktonic larvae of S. nudus. The composition of eukaryotic diets shifted greatly across the larval, juvenile, and adult stages of S. nudus, and among different gut sections in U. unicinctus, reflecting lifestyle changes during the ontogeny of the peanut worm and progressive digestion in the spoon worm. Malassezia-like fungi were prevalent in mycobiomes. Epicoccum and Trichosporon-related phylotypes dominated mycobiomes associated with larval individuals and in the gut contents of adults, respectively. The gut mycobiome of S. nudus was successively characterized through the midgut, aspiratory intestines, hindgut, and rectum as having a high proportion of Climacodon-Rhizochaete, Ceriporiopsis, Cladosporium-Pseudomicrostroma, and Malassezia-related species in the libraries. These results emphasize the dynamics of diets and gut mycobiomes in marine benthic animals.

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Section: Discussionmentioning

confidence: 99%

Molecular Detection of Eukaryotic Diets and Gut Mycobiomes in Two Marine Sediment-Dwelling Worms, Sipunculus nudus and Urechis unicinctus

Wang

Shi

Huang

et al. 2018

Microbes and environments

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“…Ustilaginomycotinous yeasts are commonly detected from very diverse habitats, using both culture dependent and culture-independent methods (e.g., Boekhout et al 2003;Inácio et al 2008;Sipiczki and Kajdacsi 2009;Bourret et al 2013;Nasr et al 2014;Nasanit et al 2015Nasanit et al , 2016Tantirungkij et al 2015;Wang et al 2015;Kijpornyongpan and Aime 2017;Kruse et al 2017). The links between asexual and sexual morphs were demonstrated only for a few species, for example between Pseudozyma prolifica Bandoni and Mycosarcoma maydis (DC.)…”

Section: Discussionmentioning

confidence: 99%

Pattersoniomyces tillandsiae gen. et comb. nov.: linking sexual and asexual morphs of the only known smut fungus associated with Bromeliaceae

et al. 2017

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The enigmatic species Ustilago tillandsiae is the only known smut fungus associated with Bromeliaceae. Its generic position is evaluated by morphological, physiological, and molecular phylogenetic analyses using large subunit rDNA sequences. Phylogenetic analyses resolved U. tillandsiae as a member of the Ustilaginales in a sister relationship to the lineage containing Tranzscheliella species. However, U. tillandsiae differs from Tranzscheliella species by the development of sori in flowers, a different structure of sori and a different type of spore ornamentation. Consequently, a new genus Pattersoniomyces is described to accommodate U. tillandsiae. The new combination Pattersoniomyces tillandsiae is substantiated. In the sexual stage (teleomorph), this species infects bromeliads: Tillandsia flabellata, Tillandsia leiboldiana, and Tillandsia sp. in Central America between southern Mexico and Costa Rica. The yeast stage (anamorph) of P. tillandsiae was found associated with the phylloplane of Canistrum improcerum and in water tanks (phytotelmata) of Vriesea minarum, two bromeliads occurring in northeast and southeast Brazil, respectively. The link between the teleomorph and anamorphic strains is supported by identical sequences of the D1/D2 domains of the large subunit rDNA. Pattersoniomyces represents the tenth endemic smut genus to the Americas, but the only one that occurs in both North and South America, being a truly neotropical genus. The host plant families of Ustilaginales are extended to the Bromeliaceae. As far as we know, Pattersoniomyces represents the single event of a host jump from Cyperaceae or Poaceae to Bromeliaceae, apparently without further species radiation on multiple bromeliad species and genera growing in South America.

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“…The authors apparently ignore the fundamental principles of multiple alignment-based phylogenetic analyses and quantitative species recognition methods now routinely applied to delimit clades, whether based on single or multiple markers, methods used by themselves on multiple occasions (e.g. Peršoh et al 2009 , Thines & Kummer 2013 , Choi et al 2015 , Liu et al 2016 , Kijpornyongpan & Aime 2017 , Hongsanan et al . 2017 , Raja et al .…”

Section: Responsesmentioning

confidence: 99%

Sequence-based nomenclature: a reply to Thines et al. and Zamora et al. and provisions for an amended proposal “from the floor” to allow DNA sequences as types of names

2018

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We reply to two recently published, multi-authored opinion papers by opponents of sequence-based nomenclature, namely Zamora et al. (IMA Fungus 9: 167–175,2018) and Thines et al. (IMA Fungus 9: 177–183, 2018). While we agree with some of the principal arguments brought forward by these authors, we address misconceptions and demonstrate that some of the presumed evidence presented in these papers has been wrongly interpreted. We disagree that allowing sequences as types would fundamentally alter the nature of types, since a similar nature of abstracted features as type is already allowed in the Code (Art. 40.5), namely an illustration. We also disagree that there is a high risk of introducing artifactual taxa, as this risk can be quantified at well below 5 %, considering the various types of high-throughput sequencing errors. Contrary to apparently widespread misconceptions, sequence-based nomenclature cannot be based on similarity-derived OTUs and their consensus sequences, but must be derived from rigorous, multiple alignment-based phylogenetic methods and quantitative, single-marker species recognition algorithms, using original sequence reads; it is therefore identical in its approach to single-marker studies based on physical types, an approach allowed by the Code. We recognize the limitations of the ITS as a single fungal barcoding marker, but point out that these result in a conservative approach, with “false negatives” surpassing “false positives”; a desirable feature of sequence-based nomenclature. Sequence-based nomenclature does not aim at accurately resolving species, but at naming sequences that represent unknown fungal lineages so that these can serve as a means of communication, so ending the untenable situation of an exponentially growing number of unlabeled fungal sequences that fill online repositories. The risks are outweighed by the gains obtained by a reference library of named sequences spanning the full array of fungal diversity. Finally, we elaborate provisions in addition to our original proposal to amend the Code that would take care of the issues brought forward by opponents to this approach. In particular, taking up the idea of the Candidatus status of invalid, provisional names in prokaryote nomenclature, we propose a compromise that would allow valid publication of voucherless, sequence-based names in a consistent manner, but with the obligate designation as “nom. seq.” (nomen sequentiae). Such names would not have priority over specimen- or culture-based names unless either epitypified with a physical type or adopted for protection on the recommendation of a committee of the International Commission on the Taxonomy of Fungi following evaluation based on strict quality control of the underlying studies based on established rules or recommendations.

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Taxonomic revisions in the Microstromatales: two new yeast species, two new genera, and validation of Jaminaea and two Sympodiomycopsis species

Cited by 24 publications

References 29 publications

Molecular Detection of Eukaryotic Diets and Gut Mycobiomes in Two Marine Sediment-Dwelling Worms, <i>Sipunculus nudus</i> and <i>Urechis unicinctus</i>

Molecular Detection of Eukaryotic Diets and Gut Mycobiomes in Two Marine Sediment-Dwelling Worms, <i>Sipunculus nudus</i> and <i>Urechis unicinctus</i>

Pattersoniomyces tillandsiae gen. et comb. nov.: linking sexual and asexual morphs of the only known smut fungus associated with Bromeliaceae

Sequence-based nomenclature: a reply to Thines et al. and Zamora et al. and provisions for an amended proposal “from the floor” to allow DNA sequences as types of names

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