Clarifying the Taxonomic Identity of a Phylogenetically Important Group of Eukaryotes: Planomonas is a Junior Synonym of Ancyromonas

ABSTRACT. Ancyromonas was first described in 1882 by Saville Kent, with the modern concept of the genus dating from 1979 with the work of Hänel. Since then, organisms assigned to Ancyromonas have been found to be common in diverse ecosystems, and the group's isolated phylogenetic placement renders it of considerable evolutionary interest. However, in 2008 Cavalier‐Smith et al. concluded that all modern accounts of Ancyromonas were of a different organism from that described by Saville Kent, and erected the new genus Planomonas to encompass modern observations of Ancyromonas, and several new species. We critique the rationale for creating this new genus, reexamining the original sources and making additional observations using light and electron microscopy. We find that almost all the differences between the genera are mistaken or insubstantial. In particular, (1) Cavalier‐Smith et al. characterized Ancyromonas sensu Saville Kent as anchoring and Planomonas as gliding, while we find that each type of organism actually does both, and (2) it was claimed that Planomonas is flattened while Ancyromonas sensu Saville Kent is not, but this argument is inconsistent. We treat Planomonas as a junior synonym of Ancyromonas, and Planomonas mylnikovi as a junior synonym of Ancyromonas sigmoides. We transfer Planomonas cephalopora, Planomonas micra, Planomonas howeae and Planomonas limna to Ancyromonas. The genus Ancyromonas therefore includes: A. sigmoides, Ancyromonas cephalopora n. comb., Ancyromonas melba, Ancyromonas sinistra, Ancyromonas micra n. comb., Ancyromonas howeae n. comb., and Ancyromonas limna n. comb.     

Scale evolution,sequence phylogeny,and taxonomy of thaumatomonad Cercozoa: 11 new species and new genera Scutellomonas,Cowlomonas, Thaumatospina and Ovaloplaca

We describe 11 new species of Thaumatomonadida using light and electron microscopy and rDNA gene sequences (18S, ITS1, 5.8S, ITS2). We found clear distinctions between major clades in molecular and morphological traits that support now splitting Thaumatomastix into three genera: new marine genera Ovaloplaca (oval plate-scales) and Thaumatospina (triangular plate-scales), both with distinctive radially-symmetric bobbin-based spine-scales, restricting Thaumatomastix to freshwater species with putatively non-homologous eccentric-spine scales and thicker triangular plate-scales. New genus Scutellomonas lacks spine-scales, having oval plate-scales with deeply-dished upper tier as in Ovaloplaca, with which it forms a clade having short/absent anterior cilium. Cowlomonas gen. n. is possibly naked. We describe two new Allas species, two new Thaumatomonas, and one new Reckertia species, and transfer R. hindoni to Thaumatomonas. Triangular-scaled Reckertia has varied plate-scales and ciliary scales. Thaumatomonas rDNA trees reveal two clades: zhukovi/seravini (predominantly triangular scales); coloniensis/oxoniensis/lauterborni/constricta/solis (scales mostly oval). We hypothesise that the ancestor of Thaumatomonadidae had radially-symmetric bobbin-based spine-scales and triangular plate-scales, bobbin-based spine-scales being lost in one lineage and eccentric-spine scales evolving in Thaumatomastix. Bobbin-based spine-scales arguably evolved from triangular plate-scales and single-tier ciliary scales (Ovaloplaca and Reckertia only) from plate-scale rudiments. We present a unified scheme for scale evolution and development in Imbricatea.     

Planomonadida ord. nov. (Apusozoa): ultrastructural affinity with Micronuclearia podoventralis and deep divergences within Planomonas gen. nov

Gliding zooflagellates previously misidentified as Ancyromonas sigmoides, Metopion or Heteromita constitute a new genus Planomonas. Three new Planomonas species (marine P. micra and P. mylnikovi: freshwater P. limna) have extremely divergent 18S rRNA and subtly but consistently different light microscopic morphology, distinguishable from P. (=Ancyromonas) melba comb. nov. and P. (=Bodo) cephalopora comb. nov. Ultrastructurally, P. micra and P. mylnikovi have a sub-plasma membrane dense pellicular layer (except in the ventral feeding pocket whose rim is supported by microtubules), kinetocysts, and flat mitochondrial cristae. Centrioles, connected at approximately 80 degrees by short fibres, have a dense amorphous distal plate below a double axosome and four microtubular roots. Microbody, mitochondrion, and dictyosomes associate with the nucleus. Longitudinal cytokinesis is slow and peculiar; ciliary transformation is from anterior to posterior as in other bikonts. Planomonads, like the non-flagellate Micronuclearia (here grouped with planomonads as Hilomonadea cl. nov.), have an indistinguishable single dense pellicular layer, not a double layer like apusomonads (comprising emended class Thecomonadea, phylum Apusozoa). We also sequenced 18S rDNA for Planomonas howeae sp. nov. and Micronuclearia podoventralis, plus actin genes of P. micra, Micronuclearia, Amastigmonas marina. All were analysed phylogenetically; the Planomonas clade is ancient, diverse and robust: it sometimes groups weakly as sister to Micronuclearia.     

A new species and a new record of Helicomyces from Taiwan

Helicomyces geniculatus sp. nov. from decaying wood submerged in a freshwater stream at Juchi Town of Alishan area, Chiayi County, Taiwan, is described and illustrated. It differs from other Helicomyces species in having geniculate conidiophores arising from repent hyphae and also borne on erect setae. Abundant stalked sclerotia were also found in this species. Helicomyces torquatus is described in this paper as a new record for Taiwan, with new observation. The phylogenetic relationship of H. geniculatus, H. torquatus, and related taxa were sought by comparing the sequences of their ITS barcode of the nuc rDNA. A synopsis of the 13 accepted Helicomyces species is given.     

Phylogeny of Heterokonta: Incisomonas marina,a uniciliate gliding opalozoan related to Solenicola (Nanomonadea), and evidence that Actinophryida evolved from raphidophytes

Environmental rDNA sequencing has revealed many novel heterokont clades of unknown morphology. We describe a new marine heterotrophic heterokont flagellate, Incisomonas marina, which most unusually lacks an anterior cilium. It glides and swims with its cilium trailing behind, but is predominantly sedentary on the substratum, with or without a cilium. 18S rDNA sequence phylogeny groups Incisomonas strongly within clade MAST-3; with others it forms a robust sister clade to Solenicola, here grouped with it as new order Uniciliatida, placed within new class Nanomonadea encompassing MAST-3. Our comprehensive maximum likelihood heterokont phylogeny shows Nanomonadea as sister to MAST-12 plus Opalinata within Opalozoa, and that Actinophryida are not Opalozoa (previously suggested by distance trees), but highly modified raphidomonads, arguably related to Heliorapha (formerly Ciliophrys) azurina gen., comb. n. We discuss evolution of Actinophryida from photosynthetic raphidophytes. Clades MAST-4,6-11 form one early-branching bigyran clade. Olisthodiscus weakly groups with Hypogyristea not Raphidomonadea. Phylogenetic analysis shows that MAST-13 is all Bicosoeca. Some gliding uniciliates similar to Incisomonas marina seem to have been misclassified: therefore we establish Incisomonas devorata comb. n. for Rigidomastix devoratum, revise the genus Rigidomastix, transfer Clautriavia parva to Kiitoksia. We make 17 new familes (13 heterokont (three algal), two cercozoan, two amoebozoan).     

A new species of Pithoascus and first report of this genus as endophyte associated with Ferula ovina

A newly described species of Pithoascus from roots of Ferula ovina differs from other Pithoascus species by producing larger ascomata than all described species except P. exsertus. The shape of its ascospores is similar to that of P. lunatus, but differs from it by having an asexual state. This new species differs from P. ater by having a sexual state. Phylogenetic analyses based on concatenated ITS rDNA, LSU rDNA and partial translation elongation factor 1 alpha gene datasets also confirmed the generic placement in Pithoascus and showed its close phylogenetic relationships to P. ater and P. lunatus.     

A new species of the genus Trematosphaeria from China

A new species of the genus Trematosphaeria was isolated and identified from the soil in Jiuzhaigou Nature Reserve, southwestern China. The new taxon was studied based on morphological characters and phylogenetic analyses of three nuclear loci, i.e., the internal transcribed spacer rDNA operon (ITS), and large and small subunit nuclear ribosomal DNA (nuc28S rDNA, nuc18S rDNA). The analyzed Trematosphaeria species were clustered in several clades within the Pleosporales and the genus was shown to be polyphyletic. The new species is introduced as Trematosphaeria terricola, and it is characterized by short-papillate ascomata with suborbicular ostiolum, 3-septate, cinnamon-brown, fusiform ascospores with narrowly rounded ends, verruculose at maturity. Trematosphaeria terricola is compared with morphologically similar species T. confusa, T. mangrovis, and T. pertusa, which differ from the former species in the number of septa, and the shape and size of the ascospores with or without a sheath. This is the first report of a Trematosphaeria isolate from alpine soil in China.     

The family liolopidae (Digenea) including a new genus and two new species from crocodilians

Two new species of liolopid digeneans infecting crocodilians are described and the classification of the family slightly revised. Liolope copulans from the salamander Megalobatrachus japonicus in Japan actually possesses an internal rather than external seminal vesicle and tegumental spines, and the generic diagnosis is emended to include those features. Liolopids paratisitizing crocodilians are removed from Harmotrema and placed in a separate new genus characterized by the possession of a relatively short body with gonads in the posterior rather than middle third of the body. Liolopids infecting Neotropical lizards and turtles remain in Helicotrema and those parasitizing freshwater and marine snakes remain in Harmotrema. The first new species, from Alligator mississipiensis in the southeastern United States, most closely resembles the species described as Harmotrema rudolphii from a saltwater crocodile in the Philippines, but differs from it by having a shorter cirrus sac, stouter and shorter cirrus, and slightly smaller eggs; it differs from all crocodilian liolopids by possessing a more extensively folded metraterm. The second new species, from Crocodylus cataphractis in the Congo (Belgian), differs from all others in crocodilians by having a relatively larger pharynx and smaller acetabulum. Diagnoses of all crocodilian liolopids are presented. Harmotrema laticaudae, previously known from Laticauda laticaudata in Okinawa only, is reported from Aipysurus laevis, Hydrophis major, and a ‘black and white-ringed sea snake’ in Queensland, Australia.     

Pseudo-nitzschia pungens (Bacillariophyceae): A cosmopolitan diatom species?

Genetic, reproductive and morphological variation were studied in 193 global strains of the marine diatom species Pseudo-nitzschia pungens (Grunow ex Cleve) Hasle to assess potential intraspecific variation and biogeographic distribution patterns. Genetic differentiation between allo- and sympatric strains was investigated using the ITS1–5.8S–ITS2 rDNA region. Three ITS clades were found. Clones of opposite mating type were sexually compatible within clades I or II, and viable F1 hybrid offspring were produced in crosses between them. The molecular differences between these clades were correlated with slight but consistent morphological differences. At present, nothing can be said about morphology and mating behavior for clade III clones because only ITS data were available. The three ITS clades showed different geographic distributions. Clade II was restricted to the NE Pacific, whereas clones belonging to clade III originated from geographically widely separated areas (Vietnam, China and Mexico). ITS clade I was recovered in all locations studied: the North Sea (Belgium, The Netherlands, France), the eastern and western N Atlantic (Spain, Canada), the NW and S Pacific (Japan, New Zealand) and the NE Pacific (Washington State). Clade I thus appears to be globally distributed in temperate coastal areas and provides the first strong evidence to date for the global distribution of a biologically, genetically and morphologically defined diatom species.     

An integrative taxonomic study of Susanlimocotyle narina n. gen. n. sp. (Monogenoidea,Dactylogyridae) from the nasal cavities of a marine catfish (Siluriformes,Ariidae) from the Atlantic Amazon Coast of Brazil and new molecular data of Chauhanellus spp.

Based on a taxonomic approach, combining morphological characters with DNA sequences (i.e.,18S rDNA, ITS1, 5.8S rDNA and ITS2), Susanlimocotyle n. gen. is proposed to accommodates Susanlimocotyle narina n. sp. from the nostrils of the ariid Sciades herzbergii (Bloch) from the coast of the state of Pará, Brazil. Susanlimocotyle n. gen. is characterized by species possessing: an intestinal ceca confluent posteriorly; a male copulatory organ, comprising a variable tube, articulated with the accessory piece; a sclerotized vagina, vaginal aperture dextro-ventral; an onchium; a robust ventral bar; two dorsal bars; a ventral anchor with elongated shaft and a dorsal anchor with deep root expanding into wings. In addition, new molecular data of Chauhanellus spp. are also provided and used for the evaluation of the phylogenetic relationships among monogenoids parasitizing siluriforms. Susanlimocotyle n. gen. exhibited a higher genetic divergence level for 18S rDNA (4.6 to 7.2% [83–130 bp]) with respect to Chauhanellus spp. despite sharing S. herzbergii as a host, than Hamatopeduncularia spp., (4.1 to 5.8% [75–110 bp]) from Oriental ariids. For the 18S rDNA, 5.8S rDNA, ITS1 and ITS2 regions, C. boegeri and C. susamlimae were observed to have the smallest interspecific distances, and C. velum was revealed to be the most genetically distant species to Chauhanellus. The proposal for Susanlimocotyle n. gen. is also supported by phylogenetic analysis based on the 18S rDNA gene, which supports the close relationship between the new genus and Hamatopeduncularia and Chauhanellus from ariids from the South America and Oriental regions. Moreover, the patterns towards the shared diversification between monogenoids and their ariid hosts were addressed.     

Two new species of Melanoleuca (Agaricales,Basidiomycota) from northeastern China,supported by morphological and molecular data

Two new species, Melanoleuca leucopoda and M. porphyropoda, are described based on collections made from Shenyang City, Liaoning Province, China. Melanoleuca leucopoda is mainly characterized by its whitish stipe with fibrils and oblong spores with elongated warts. Melanoleuca porphyropoda differs from all other Melanoleuca species in lacking cystidia and in having decurrent gills and a purplish stipe. The sequences of internal transcribed spacer regions (ITS1-5.8S-ITS2) of Melanoleuca species were analyzed and the results indicated that two new species clustered into two clades and differed from the other species of the genus. The combination of morphological and molecular data confirmed that the two fungi are new species. The morphological similarity of the new species to other species of Melanoleuca and the systematic position of the two species based on molecular data are also discussed.     

Simplicillium spumae (Cordycipitaceae,Hypocreales), a new hyphomycetes from aquarium foam in Japan

Five Simplicillium isolates were obtained from foam generated in an aquarium in Minato-ku, Tokyo, Japan. Using a combination of micro-morphological characteristics and multigene (ITS, SSU, LSU, TEF) phylogenics, the isolates were identified as S. subtropicum and a new species which were previously undescribed. Simplicillium spumae, which is a new species, differs from known Simplicillium species in the morphology of their conidia and conidiophores.     

Pseudoidium javanicum,a new species of powdery mildew on Acalypha spp. from Indonesia

Pseudoidium javanicum is proposed as a new species based on analyses of 28S, ITS and IGS rDNA sequences, and morphological data. This new species was found on Acalypha wilkesiana var. marginata, A. argentea, and A. cristata collected from Cibodas Botanical Garden, Bogor (West Java Province, Indonesia). Our analyses showed that all these specimens have identical rDNA sequences and similar morphological characteristics. They form a distinct clade separated from other species of Erysiphaceae. Pseudoidium javanicum differs from Erysiphe acalyphae by having shorter conidiophores and foot cells 1–3 times as long as the 0–2 following cells. The conidial size of Ps. javanicum is also smaller than that of E. jatrophae.     

Five new species of <Emphasis Type="Italic">Conocybe</Emphasis> (Agaricomycetes,Bolbitiaceae) from Russia

Five new Conocybe species are described from Russia based on collections made in different parts of the country. One species (C. olivaceopileata) belongs to sect. Conocybe, two species (C. praticola and C. coniferarum) to sect. Mixtae. The ornamented basidiospores of C. confundens and C. incerta is characteristic for sect. Ochromarasmius. All new species are described based on morphology and, in some cases, on DNA sequencing (ITS rDNA). Photos of basidiocarps, illustrations of microstructures and a comparison with similar taxa are given.     

Cyst‐motile stage relationship and molecular phylogeny of a new freshwater dinoflagellate Gymnodinium plasticum from Plastic Lake,Canada

The dinophyceaen genus Gymnodinium was established with the freshwater species G. fuscum as type. According to Thessen et al. (2012), there are 268 species, with the majority marine species. In recently published molecular phylogenies based on ribosomal DNA sequences, Gymnodinium is polyphyletic. Here, a new freshwater Gymnodinium species, G. plasticum, is described from Plastic Lake, Ontario, Canada. Two strains were established by incubating single cysts, and their morphology was examined with light microscopy and scanning electron microscopy. The cyst had a rounded epicyst and hypocyst with a wide cingulum and smooth surface. Vegetative cells were characterized by an elongated nucleus running vertically and a deep sulcal intrusion. The apical structure complex was horseshoe‐shaped and consisted of two pronounced ridges with a deep internal groove, encircling 80% of the apex. Small subunit ribosomal DNA (SSU rDNA), large subunit ribosomal DNA (LSU rDNA) and internal transcribed spacer (ITS) sequences were obtained from cultured strains. Molecular phylogeny based on concatenated SSU, LSU and ITS sequences supports the monophyly of the Gymnodiniales sensu stricto clade but our results suggest that many Gymnodinium species might need reclassification. Gymnodinium plasticum is closest to Dissodinium pseudolunula in our phylogeny but distant from the type species G. fuscum, as are the other gymnodiniacean taxa.     

Setoidium castanopsidis,a new species of anamorphic Cystotheca (Ascomycota,Erysiphales) from Indonesia

A powdery mildew fungus belonging to the genus Setoidium (anamorph of Cystotheca) was found on Castanopsis javanica in Cibodas Botanical Garden and mount Tangkuban Perahu, West Java, Indonesia. The fungus is considered as a new species, namely, Setoidium castanopsidis. Phylogenetic analyses of the 28S and ITS rDNA regions showed that S. castanopsidis formed a distinct lineage separated from Cy. tjibodensis, Cy. lanestris, and Cy. wrightii. Setoidium castanopsidis also differs morphologically from Cy. tjibodensis in having distinct appressoria (nipple-shaped), longer conidiophores with longer foot-cells, larger conidia, and being found on Ca. javanica. The teleomorphic state has not been found during the collection.     

Morphological and molecular phylogenetic analysis of <Emphasis Type="Italic">Melampsora</Emphasis> species on poplars in China

Many species of Melampsora on Populus have been reported in China, based on morphological characteristics of both uredial and telial states, and on host species, but their morphology and taxonomy are still poorly defined. In this study, 196 specimens representing Melampsora species on poplars and collected from various areas of China were used for morphological observations. The morphological characteristics of urediniospores and teliospores were examined with light and scanning electron microscopy. The specimens could be classified into five groups based on their morphology. For the sequencing of the nuclear large subunit rDNA (D1/D2), 5.8S rDNA and their internal transcribed spacers, ITS1 and ITS2 region, 54 specimens were selected from the specimens used in morphological observations. These specimens were separated into six clades by phylogenetic analyses of the D1/D2 and ITS regions. Correlations among morphological groups and phylogenetic clades based on these results suggest a revision of these species. In particular, no evidence to discriminate specimens of M. acedioides, M. magnusiana, and M. rostrupii was found from either morphological characteristics or sequence analysis.Contribution no. 185 Laboratory of Plant Parasitic Mycology, Institute of Agriculture and Forestry, University of Tsukuba, Japan     

Morphological and molecular data reveal a new species of Neoechinorhynchus (Acanthocephala: Neoechinorhynchidae) from Dormitator maculatus in the Gulf of Mexico

Neoechinorhynchus (Neoechinorhynchus) mexicoensis sp. n. is described from the intestine of Dormitator maculatus (Bloch 1792) collected in 5 coastal localities from the Gulf of Mexico. The new species is mainly distinguished from the other 33 described species of Neoechinorhynchus from the Americas associated with freshwater, marine and brackish fishes by having smaller middle and posterior hooks and possessing a small proboscis with three rows of six hooks each, apical hooks longer than other hooks and extending to the same level as the posterior hooks, 1 giant nucleus in the ventral body wall and females with eggs longer than other congeneric species. Sequences of the internal transcribed spacer (ITS) and the large subunit (LSU) of ribosomal DNA including the domain D2 + D3 were used independently to corroborate the morphological distinction among the new species and other congeneric species associated with freshwater and brackish water fish from Mexico. The genetic divergence estimated among congeneric species ranged from 7.34 to 44% for ITS and from 1.65 to 32.9% for LSU. Maximum likelihood and Bayesian inference analyses with each dataset showed that the 25 specimens analyzed from 5 localities of the coast of the Gulf of Mexico parasitizing D. maculatus represent an independent clade with strong bootstrap support and posterior probabilities. The morphological evidence, plus the monophyly in the phylogenetic analyses, indicates that the acanthocephalans collected from intestine of D. maculatus from the Gulf of Mexico represent a new species, herein named N. (N.) mexicoensis sp. n.     

A new species of Leptobacillim,L. symbioticum,isolated from mites and sori of soybean rust

A verticillium-like fungus forming a whitish colony and mainly solitary phialides that produced fusiform to cylindrical conidia in chains was isolated from uredinia of Phakopsora pachyrhizi, a causal agent of soybean rust. In addition, two similar looking isolates were obtained from Prostigmata mites. Our taxonomic study based on morphology and phylogenetic analysis using ITS rDNA and LSU rDNA D1/D2 region sequences revealed that the three isolates were the same species and assigned to the genus Leptobacillium. These isolates represent a new species, morphologically and phylogenetically distinguished from the type species, L. leptobactrum, and we propose L. symbioticum sp. nov. In addition, Simplicillium chinense and S. coffeanum are assigned to the genus Leptobacillium.