- Volume 66, Issue 7, 2016

A novel Gram-stain-negative, aerobic, motile by gliding and filamentous strain, designated 772T,was isolated from surface-sterilized root tissue of maize planted in the Fangshan District of Beijing, China. 16S rRNA gene sequence analysis indicated that strain 772T was closely related to Filimonas endophytica SR2-06T and Filimonas lacunae YT21T of the family Chitinophagaceae with sequence similarities of 99.0 and 96.9 %, respectively. However, the new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to Filimonas. endophytica KCTC 42060T (18.7±1.8 %) and Filimonas. lacunae DSM 21054T (17.9±2.0%). The DNA G+C content of strain 772T was 44.9 mol%. The respiratory quinone was menaquinone-7 and the polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and one unidentified lipid. The major fatty acids were iso-C15 : 0 and iso-C15 : 1 G. The results of the physiological and biochemical tests and minor differences in the fatty acid profiles allowed the clear phenotypic differentiation of strain 772T from the closely related species Filimonas. endophytica andF. lacunae. Strain 772T thus represents a novel species within the genus Filimonas , for which the name Filimonas zeae sp. nov. is proposed. The type strain is 772T (=CGMCC 1.15290T=DSM 100760T).

Five closely related yeast strains were isolated from soil in Kharg Island, Persian Gulf, Iran, and from fallen fruits in Galle, Sri Lanka, during separate projects. Morphologically, the strains produced white-coloured yeast colonies, with cells that were ovoid to ellipsoidal, making branched, true hyphae and pseudohyphae. Ascospore formation was not observed. Biochemically, the strains were able to ferment d-glucose and weakly ferment d-galactose. The strains could use a wide variety of carbon sources except methanol and hexadecane. Phylogenetic analyses using combined sequences of the small ribosomal subunit and the D1/D2 domains of the LSU, as well as the internal transcribed spacer regions, suggested that these strains belong to the Wickerhamomyces clade and that together they form one strongly supported phylogenetic clade. Differences in their sequences, biochemistry and morphology suggest they are representatives of distinct species of the genus Wickerhamomyces. Therefore, the name Wickerhamomyces orientalis f.a., sp. nov. is proposed to accommodate these novel strains; the type strain is IBRC-M 30103T (=CBS 13306T). The MycoBank number is MB 807323.

Five strains (CCY 058-007-001T, CCY 058-007-002, CCY 058-007-003, CCY 058-007-004 and CCY 058-007-005) of a novel parasitic yeast belonging to the genus Taphrina were isolated from leaf tissues of Geum montanum L. (Rosaceae), collected from the Vysoké Tatry Mountains, Slovakia. Genetic analyses revealed that these isolates differ by 15 unique substitutions in the ITS region and by six substitutions in the rns gene from all other species of the genus Taphrina analysed hitherto. The novel strains are also distinguished from all other species of the genus Taphrina by their morphology, biochemical properties and ecology. These strains represent a novel species, for which the name Taphrina gei-montani sp. nov. is proposed. The type strain is CCY 058-007-001T (=CBS 14159=BU001). The MycoBank number is MB815677. The present study also demonstrates that two distinct species of the genus Taphrina parasitize the herbaceous Rosaceae: Taphrina gei-montani sp. nov. on Geum montanum and Taphrina tormentillae on Potentilla species.

Four strains alternating between yeast and filamentous growth morphologies were isolated from flowers in two regions of Laos. In liquid environment the isolates propagated by budding and developed irregularly shaped pseudohyphae. On solid media, their yeast cells switched to hyphal growth which could return to the yeast phase by developing lateral blastoconidia. The sequences of the D1/D2 domains of the large subunit (LSU) 26S rRNA genes, the internal transcribed spacer (ITS) regions and the small subunit (SSU) 18S rRNA genes were identical in the four strains and differed from the corresponding sequences of other yeast species available in databases by at least 11 % (D1/D2), 13 % (ITS) and 7 % (SSU). In an independent project, two strains with D1/D2 and ITS sequences very similar to those of the Laotian strains were found in bark samples collected in Brazil. The six strains also differed from the closest yeast species in physiological properties, indicating that they represented a hitherto undescribed species. Phylogenetic analysis of the D1/D2 sequences, and the concatenated sequences of the SSU rRNA genes, D1/D2 domains of LSU rRNA genes as well as the protein-encoding genes ACT1 and TEF1 placed thestrains close to Hyphopichia. To reflect this position, the novel genus name Metahyphopichia gen. nov. and the novel species name Metahyphopichia laotica gen. nov., sp. nov. are proposed for them. The type strain of the type species is 11-1006T(=CBS 13022T=CCY 092-001-001T=NCAIM Y.02126T) and was isolated in Luang Prabang (Laos). MycoBank registration numbers are MB 808253 (Metahyphopichia) and MB 808254 (Metahyphopichia laotica).

In sampling fungi from the built environment, two isolates that could not confidently be placed in described species were encountered. Phenotypic analysis suggested that they belonged in Aspergillus sect. Usti. In order to verify the sectional placement and to assure that they were undescribed rather than phenotypically aberrant isolates, DNA was isolated and sequenced at the beta-tubulin, calmodulin, internal transcribed spacer and RNA polymerase II loci and sequences compared with those from other species in the genus Aspergillus. At each locus, each new isolate was distant from existing species. Phylogenetic trees calculated from these data and GenBank data for species of the section Usti excluded the placement of these isolates in existing species, with statistical support. Because they were excluded from existing taxa, the distinct species Aspergillus asper (type strain NRRL 35910T) and Aspergillus collinsii (type strain NRRL 66196T) in sect. Usti are proposed to accommodate these strains.

Myrmecridium hiemale sp. nov. was isolated from snow-covered alpine bare soil and is described as the first eurypsychrophilic species of this genus of filamentous fungi. Colony growth temperature experiments were carried out in the range 4–37 °C. Morphological characteristics and colony appearance were in accordance with characteristics typical for Myrmecridium, but M. hiemale does not grow at temperatures of 25 °C and above. Sequence analyses of the internal transcribed spacer and LSU rRNA D1/D2 regions indicated that the strain in question represents a distinct taxon within the genus Myrmecridium (Myrmecridiaceae, Sordariomycetes, Ascomycota). The type strain of M. hiemale is CBS 141017T(=JMRC 12083T). A morphological description is provided, and a key is presented for the currently known taxa of Myrmecridium, a group of interesting fungi that are either saprobes or plant endophytes.

Strain DMKU-CE23T representing a novel yeast species was isolated from tissue of a corn leaf (Zea may L.) collected in Thailand. A phylogenetic analysis based on the combined sequences of the internal transcribed spacer (ITS) region and the D1/D2 region of the LSU rRNA gene indicated that strain DMKU-CE23T belongs to the Yamadazyma clade and is clearly distinct from other related species. It therefore represents a novel species of the genus Yamadazyma although the formation of ascospores was not observed. The strain of novel species was most closely related to the type strain of Yamadazyma epiphylla but with 5.1 % nucleotide substitutions in the ITS region and 3.7 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene. The name Yamadazyma endophytica f.a., sp. nov. is proposed. The type strain is DMKU-CE23T (=CBS 14163T=TBRC 5174T).

The ample genetic diversity and variability of Helicobater pylori, and therefore its phenotypic evolution, relate not only to frequent mutation and selection but also to intra-specific recombination. Webb and Blaser applied a mathematical model to distinguish the role of selection and mutation for Lewis antigen phenotype evolution during long-term gastric colonization in infected animal hosts (mice and gerbils). To investigate the role of recombination in Lewis antigen phenotype evolution, we have developed a prior population dynamic by adding recombination term to the model. We simulate and interpret the new model simulation's results with a comparative analysis of biological aspects. The main conclusions are as follows: (i) the models and consequently the hosts with higher recombination rate require a longer time for stabilization; and (ii) recombination and mutation have opposite effects on the size of H. pylori populations with phenotypes in the range of the most-fit ones (i.e. those that have a selective advantage) due to natural selection, although both can increase phenotypic diversity.

Actinobaculum massiliense (Euzéby, 2006) was isolated from the urine of an elderly woman in 2001. Unfortunately, the strain deposited as the type strain was, by error, an Actinobaculum schaalii strain ( Yassin et al., 2015 ). In 2015, we isolated a new strain of A. massiliense , FC3, from the urine of a 12-year-old patient with acute cystitis. We herein present the characteristics of strain FC3 (=CSUR P1982=DSM 100580) and formally propose it as the neotype strain of A. massiliense.