Species composition and toxicity of the genus Pseudo-nitzschia in Taiwan Strait,including P. chiniana sp. nov. and P. qiana sp. nov.

In a field survey in the Taiwan Strait during April 2016, the species composition and the domoic acid production of the diatom genus Pseudo-nitzschia were investigated. A total of 80 strains of Pseudo-nitzschia were established, and species identification was determined based on a combination of morphological and molecular data. Fourteen taxa were recognized, i.e., P. americana, P. brasiliana, P. calliantha, P. cuspidata, P. galaxiae, P. lundholmiae, P. multiseries, P. multistriata, P. pseudodelicatissima, P. pungens var. aveirensis, P. pungenus var. pungens and P. sabit, as well as two novel species P. chiniana C.X. Huang & Yang Li and P. qiana C.X. Huang & Yang Li. Morphologically, P. chiniana is characterized by striae comprising one or two rows of poroids, and valve ends that are normally dominated by two rows of poroids within each stria. Whereas P. qiana is unique by having a narrow valve width (1.3–1.5 μm) and sharply pointed valve ends. Both taxa constitute their own monophyletic lineage in the phylogenetic analyses inferred from LSU and ITS2 rDNA, and are well differentiated from other Pseudo-nitzschia species. Pseudo-nitzschia chiniana forms a group with P. abrensis and P. batesiana in LSU and ITS trees, whereas P. qiana is sister to P. lineola. When comparing ITS2 secondary structure, five CBCs and seven HCBCs are recognized between P. chiniana and P. abrensis, and four CBCs and ten HCBCs between P. chiniana and P. batesiana. Two CBCs and eight HCBCs are found between P. qiana with P. lineola. The ability of the strains to produce domoic acid was assessed, including a potential toxin induction by the presence of brine shrimps. Results revealed production of domoic acid in six strains belonging to three species. Without presence of brine shrimps, cellular DA (pDA) was detected in four P. multiseries strains (1.6 ± 0.3, 26.6 ± 2.7, 68.3 ± 4.2 and 56.9 ± 4.7 fg cell⁻¹, separately), one strain of P. pseudodelicatissima (0.8 ± 0.2 fg cell⁻¹) and one strain of P. lundholmiae (2.5 ± 0.4 fg cell⁻¹). In the presence of brine shrimps, pDA contents increased significantly (p < 0.05) in P. lundholmiae (strain MC4218) and P. multiseries (strain MC4177), from 2.5 ± 0.4 to 8.9 ± 0.7 and 1.6 ± 0.3 to 37.2 ± 2.5 fg cell⁻¹ respectively.     

Taxonomic revision of European Apium L. s.l.: Helosciadium W.D.J.Koch restored

European representatives of Apium sensu lato (Apiaceae), and Apium prostratum and Naufraga balearica, were studied with morphological, fruit anatomical, and palynological methods. Morphometric data were compared with phylogenetic results from previous molecular studies. This confirms that most of the European Apium species belong to a separate group corresponding to the previously named genus Helosciadium. All these species had previously been formally named as Helosciadium species, except for the new combination Helosciadium bermejoi, which is formally described here. Molecular studies place Apium prostratum and Naufraga balearica close to Apium graveolens, the type species of Apium. Our morphometric results show similarities of Naufraga with H. bermejoi, but fruit anatomy distinguishes it both from Helosciadium and from A. graveolens/prostratum. The placement of Cyclospermum leptophyllum in a separate genus is confirmed. Diagnostic keys to the genera and Helosciadium species, and an annotated checklist are given.     

Vibrio taketomensis sp. nov. by genome taxonomy

Two novel strains C4III282^T and C4III291 were isolated from seawater collected a site off the Taketomi coral reef. Phylogenetic analysis based on the 16S rRNA sequences revealed that the two strains belong to the genus Vibrio. MLSA using eight protein-coding genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA) showed that C4III282^T and C4III291 are closely related to the members of the Ponticus clade, namely Vibrio panuliri JCM 19500^T, Vibrio ponticus DSM 16217^T, and “Vibrio rhodolitus” G98. ANI and in silico DDH values with members of the Ponticus clade were 77.6-78.7% and 22.2-23.1, respectively. The name Vibrio taketomensis sp. nov. is proposed with C4III282^T (CAIM 1928^T = DSM 106943^T = JCM 33434^T) as the type strain.     

Staphylococcus petrasii sp. nov. including S. petrasii subsp. petrasii subsp. nov. and S. petrasii subsp. croceilyticus subsp. nov., isolated from human clinical specimens and human ear infections

Thirteen coagulase-negative, oxidase-negative, and novobiocin-susceptible staphylococci were isolated from human clinical specimens. The isolates were differentiated from known staphylococcal species on the basis of 16S rRNA, hsp60, rpoB, dnaJ, tuf, and gap gene sequencing, automated ribotyping, (GTG)₅-PCR fingerprinting, and MALDI-TOF MS analysis. Phylogenetic analysis based on the 16S rRNA gene sequence indicated phylogenetic relatedness of the analyzed strains to Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus devriesei, and Staphylococcus lugdunensis. DNA–DNA hybridization experiments between representative strains CCM 8418^T, CCM 8421^T, and the closest phylogenetic neighbors confirmed that the isolates represent novel Staphylococcus species, for which the name Staphylococcus petrasii sp. nov. is proposed. Genotypic and phenotypic analyses unambiguously split the strains into two closely related subclusters. Based on the results, two novel subspecies S. petrasii subsp. petrasii subsp. nov. and S. petrasii subsp. croceilyticus subsp. nov. are proposed, with type strains CCM 8418^T (=CCUG 62727^T) and CCM 8421^T (=CCUG 62728^T), respectively.     

Fulvifomes hainanensis sp. nov. and F. indicus comb. nov. (Hymenochaetales,Basidiomycota) evidenced by a combination of morphology and phylogeny

Fulvifomes hainanensis sp. nov. is described from tropical China. The new species resembles Fulvifomes rimosus, but differs by uncracked pileal surface, the presence of a black cuticle between tomentum and lower context, and ellipsoid basidiospores. In nuclear large subunit rDNA (nLSU) and internal transcribed spacer (ITS) based phylogenies, F. hainanensis formed a distinct lineage from other sequenced taxa in the Fulvifomes clade. Aurificaria indica, the type of Aurificaria, has typical morphological characters for Fulvifomes, such as lack of setae and production of colored basidiospores. It was transferred to Fulvifomes based on additional evidence from molecular phylogeny, and F. indicus was redescribed according to Chinese collections. Aurificaria, posterior to Fulvifomes, was thus treated as a taxonomic synonym of Fulvifomes, and the concept of Fulvifomes was accordingly emended to include Aurificaria species. Inonotus luteoumbrinus and I. porrectus are similar to F. indicus in morphology, and they were also supported as lineages in the Fulvifomes clade. However, taxonomical adjustments for the two species were not proposed as the specimens yielding their nLSU and ITS sequences were not reexamined in morphology in this study.     

Four new species of Entoloma s.l. (Agaricales) from southern China

Four new Entoloma s.l. species (E. azureosquamulosum, E. caeruleoflavum, E. hainanense, and E. subtenuicystidiatum) are described from southern China. E. azureosquamulosum fits well within the section Rhamphocystotae, E. caeruleoflavum belongs to the section Entoloma, E. hainanense is placed in the section Calliderma, and E. subtenuicystidiatum is a species in the section Cyanula. Preliminary phylogenetic analyses for the four new species are provided based on ITS and LSU sequences in this paper.     

Mentzelia canyonensis (Loasaceae), a new species endemic to the Grand Canyon, Arizona, U.S.A.

We describe Mentzelia canyonensis, a new species endemic to the Grand Canyon. Based on floral and fruit forms, shoot system architecture, and phylogenetic analyses of nuclear ribosomal DNA, we infer that M. canyonensis belongs to the ‘subshrubby’ clade of Mentzelia section Bartonia, which includes the morphologically similar M. hualapaiensis, M. oreophila, M. puberula, and M. tiehmii. The new species is most similar to M. hualapaiensis, which is also known only from the Grand Canyon. These two species share leaf shape, subshrubby habits, corolla color, and fruit shape, although they differ in staminode presence and especially in leaf and corolla size. Principal component analyses of variation among floral and vegetative traits demonstrates that M. canyonensis and M. hualapaiensis share highly overlapping floral character space, but M. canyonensis occupies unique vegetative character space compared to similar species. A dichotomous key is provided to assist with identification of, and differentiation among, species of Mentzelia section Bartonia that occur in the Grand Canyon region.     

Phaseolus vulgaris seed-borne endophytic community with novel bacterial species such as Rhizobium endophyticum sp. nov.

The bacterial endophytic community present in different Phaseolus vulgaris (bean) cultivars was analyzed by 16S ribosomal RNA gene sequences of cultured isolates derived from surface disinfected roots and immature seeds. Isolated endophytes from tissue-macerates belonged to over 50 species in 24 different genera and some isolates from Acinetobacter, Bacillus, Enterococcus, Nocardioides, Paracoccus, Phyllobacterium, and Sphingomonas seem to correspond to new lineages. Phytate solubilizing bacteria were identified among Acinetobacter, Bacillus and Streptomyces bean isolates, phytate is the most abundant reserve of phosphorus in bean and in other seeds. Endophytic rhizobia were not capable of forming nodules. A novel rhizobial species Rhizobium endophyticum was recognized on the basis of DNA–DNA hybridization, sequence of 16S rRNA, recA, rpoB, atpD, dnaK genes, plasmid profiles, and phenotypic characteristics. R. endophyticum is capable of solubilizing phytate, the type strain is CCGE2052 (ATCC BAA-2116; HAMBI 3153) that became fully symbiotic by acquiring the R. tropici CFN299 symbiotic plasmid.     

Polystichum lilianae sp. nov. (Dryopteridaceae) and its relationships to P. fournieri and P. turrialbae

Morphological, isozyme, and cytological analyses of the small, pale-scaled polystichums from oakdominated montane rain forests in Costa Rica and Mexico reveal the presence of a separable undescribed species endemic to the Cordillera de Talamanca of Costa Rica. The new taxon,Polystichum lilianae, is an allotetraploid hypothesized to have the sympatricP. turrialbae as one diploid progenitor based on isozyme characters. The isozyme and morphometric data also support the inclusion ofP. smithii, described from southern Mexico, inP. turrialbae, described from Costa Rica. The namePolystichum fournieri, formerly used for all of these plants, applies to species endemic to Oaxaca and Chiapas, Mexico. It is not a progenitor ofP. lilianae.     

Novelties in the Corticiales: Vuilleminia nilsii sp. nov. and Dendrominia gen. nov. (Basidiomycota)

Vuilleminia nilsii sp. nov. is described based on collections made in Argelès-sur-Mer communal forest, France. It is characterized by a resupinate, smooth, whitish, decorticating basidiocarp, cylindrical cystidia, heavily crystallized matrix, and guttulate, allantoid spores. It can be distinguished from V. coryli by basidiospore size, substrate preferences, abundance of dendrohyphidia, and crystal in the context. Phylogenetic analyses place Vuilleminia ericae, Dendrothele dryina (= V. dryina) and Dendrothele maculata in a distinct, well-defined clade. The new genus Dendrominia is proposed for this clade. The new combinations Dendrominia dryina, D. ericae, and D. maculata are proposed. Dendrothele corticola is regarded as a synonym of D. maculata. A lectotype is selected for V. macrospora. An updated key to the genus Vuilleminia and a key to Dendrominia species are provided.     

Cronisia and its two species,C. fimbriata and C. weddellii

The systematic position of Riccia fimbriata Nees, a species formerly known only in sterile condition and tentatively placed in the genus Exormotheca, is reexamined in the light of the recently discovered reproductive structures. The species proved to be a member of the genus Cronisia, identical to Cronisia mexicana Hicks, described in 1993. A key is provided to the two known species of Cronisia, C. fimbriata and C. weddellii, and they are described and illustrated.     

Xiphidorus amazonensis n. sp. (Nematoda: Longidoridae) from the Brazilian Amazon Basin

Xiphidorus amazonensis n. sp. was found in the rhizospheres of Jatropha curcas, Musa sp., Anona muricata, Cassia tora, Panicum laxum, Paspalum fasciculatum, Aeschynomene sensitiva, Saccharum officinarum, Manihot esculenta, Abelmoschus esculentus, Tamarindus indica, Mangifera indica, Vigna unguiculata, Zea mays, Commelina sp., Cyperus rotundus, Fimbristylis miliacea, Citrus sinensis, and Eichhornia crassipes on the Amazon River island of Xiborena, approximately 40 km southeast of Manaus, capital of the State of Amazonas. The type habitat is flooded annually for about 6 months by the Amazon River. Xiphidorus amazonensis n. sp. differs from the closely related species Xiphidorus yepesara Monteiro, 1976 by the larger size, by a, b, and c values, and by the rounded tail terminus. It also resembles Xiphidorus tucumanensis Chaves and Coomans, 1984, but can be distinguished by its larger size, larger a, b, and c values, more conical female tail, bilobed amphidial pouch, and the presence of a spermatheca full of sperm.     

Pungentus porosus n.sp. (Nematoda:Dorylaimoidea) from Canada with a Key to the Species of Pungentus

Pungentus porosus n. sp. is described and illustrated. The differential characters are a short odontostyle of 6-8 μm or slightly less than one head width, vulva at 44-50%, goblet-shaped amphids, presence of a prevulval uterine sac, and a hemispherical tail with a variable number of pores. Pungenlus sublatum, P. vesiculosus, P. orthocephalus, P. granosus, and P. parvus sensu Eroshenko are considered to be incertae sedis. A key is provided to the 21 valid species of Pungentus. The following species are new Canadian records: P. angulosus, P. clavatus, P. engradinensis, P. marietani, P. microdentatus, P. monohystera, P. obscurus, P. parvus, P. pungens and P. silvestris.     

Nimbya and Embellisia revisited, with nov. comb for Alternaria celosiae and A. perpunctulata

Previous phylogenetic analyses revealed that species within the genera Nimbya and Embellisia reside within a large monophyletic clade that also includes the genera Alternaria, Ulocladium, Undifilum, Sinomyces, and Crivellia with Stemphylium as the sister taxon. This study expands upon previous work by including many contemporary species of each genus and utilizes molecular and morphological characters to further examine relationships. Maximum parsimony and Bayesian analysis reveals that Nimbya is not a monophyletic genus but is split into two phylogenetically distant clades, which have different and distinct conidial morphologies. One of these clades resides completely within Alternaria. Phylogenetic analyses also reveals that Embellisia does not form a monophyletic genus but is split into four monophyletic lineages. Moreover, several species of Embellisia cluster individually with clades that are predominantly Alternaria, Ulocladium, or Stemphylium, yet these Embellisia spp. possess morphological characters that are diagnostically Embellisia. Thus, these data reveal that both Nimbya and Embellisia are polyphyletic as currently defined and taxonomic restructuring is necessary in order to resolve conflict between historical morphological and contemporary molecular-based phylogenies.     

Description of the new phototrophic dinoflagellate Alexandrium pohangense sp. nov. from Korean coastal waters

The planktonic phototrophic dinoflagellate Alexandrium pohangense sp. nov. isolated from the coastal waters off Korea is described from living and fixed cells by light and scanning electron microscopy (SEM). DNA sequence data were collected from the small subunit (SSU), the large subunit (LSU), internal transcribed spacer regions (ITS1 and ITS2), and 5.8S of the ribosomal DNA (rDNA). The SSU and LSU rDNA sequences of the new dinoflagellate were 4–7% and 14–17%, respectively, different from those of Alexandrium minutum, Alexandrium ostenfeldii, Alexandrium tamutum, Alexandrium margalefii, and Alexandrium pseudogonyaulax, the most closely related species. In addition, the 5.8S rDNA sequence of the new dinoflagellate was also 12% different from those of A. minutum, A. ostenfeldii, A. tamutum, and Alexandrium peruvianum. In a phylogenetic tree based on LSU rDNA sequences, A. pohangense formed a clade with A. margalefii, and this clade was clearly distinct from the clade of A. minutum, Alexandrium diversaporum, A. tamutum, Alexandrium leei, A. ostenfeldii, and Alexandirum andersoni. Moreover, in a phylogenetic tree based on SSU rDNA sequences, A. pohangense was positioned at the base of the clade containing A. leei and A. diversaporum. Morphological analysis showed that A. pohangense has a Kofoidian plate formula of Po, 4′, 6′′, 6c, 8s, 5′′′, and 2′′′′, which confirmed its assignment to the genus Alexandrium. This dinoflagellate has a wide rectangular 1′ plate, the upper left side of which is slightly bent, protruding, and touching the 2′ plate, unlike A. margalefii, which has a wide rectangular 1′ plate that does not touch the 2′ plate, or A. pseudogonyaulax and Alexandrium camurascutulum, which have a narrower elongated pentagonal 1′ plate that touches the 2′ plate. Furthermore, the 1′ plate of A. pohangense meets the 1′′ plate as a straight vertical line, whereas that of A. camurascutulum meets the 1′′ plate as an inclined line because it is lifted by the intrusion of the 1′′ plate. In addition, A. pohangense had a relatively small ventral pore whose majority was located on the 4′ plate, unlike A. margalefii or A. pseudogonyaulax, which have a relatively large ventral pore whose majority is located on the 1′ plate. Furthermore, A. pohangense had pores of two different sizes on the cell surface, unlike A. margalefii and A. pseudogonyaulax, which have similar pores of only one size. On the basis of morphological and phylogenetic criteria, it is proposed that this is a new species of the genus Alexandrium.     

Acetatifactor muris gen. nov., sp. nov., a novel bacterium isolated from the intestine of an obese mouse

We used selective agar media for culturing bacteria from the caecum of mice fed a high calorie diet. In addition to the isolation of Enterobacteriaceae growing on a medium containing cholesterol and bile salts, we focused on the characterization of strain CT-m2^T, which, based on 16S rDNA analysis, did not appear to correspond to any currently described organisms. The isolate belongs to the Clostridium cluster XIV and is most closely related to members of the Lachnospiraceae, including the genera Anaerostipes, Blautia, Butyrivibrio, Clostridium, Coprococcus, Eubacterium, Robinsoniella, Roseburia, Ruminococcus and Syntrophococcus (≤90?% similarity). Strain CT-m2^T is a non-motile Gram-positive rod that does not form spores and has a G?+?C content of DNA of 48.5?%. Cells grow under strictly anoxic conditions (100?% N₂) and produce acetate and butyrate after growth in reduced WCA broth. In contrast to related species, the new bacterium does not metabolize glucose and is positive for phenylalanine arylamidase, and its major cellular fatty acid is C_14:0. Based on phylogenetic and phenotypic studies, the isolate merits recognition as a member of a novel genus and species, for which the name Acetatifactor muris is proposed. The type strain is CT-m2^T (=?DSM 23669^T?=?ATCC BAA-2170^T).