Candida pruni sp. nov. is a new yeast species with antagonistic potential against brown rot of peaches

Brown rot caused by Monilinia spp. is among the most important postharvest diseases of commercially grown stone fruits, and application of antagonistic yeasts to control brown rot is one promising strategy alternative to chemical fungicides. In this research, new yeast strains were isolated and tested for their activity against peach brown rot caused by Monilinia fructicola. Three yeast strains were originally isolated from the surface of plums (cv Chinese Angelino) collected in the north of China. In artificially wounded inoculation tests, the yeast reduced the brown rot incidence to 20 %. The population of the yeast within inoculated wounds on peaches significantly increased at 25 °C from an initial level of 5.0 × 10⁶ to 4.45 × 10⁷ CFU per wound after 1 day. The antagonistic strains were belonging to a new species of the genus Candida by sequence comparisons of 26 S rDNA D1/D2 domain and internal transcribed spacer region. The strains are most closely related to C. asparagi, C. musae and C. fructus on the basis of the phylogenetic trees based on the D1/D2 region of 26S rDNA. However, the strains are notably different from C. asparagi, C. musae and C. fructus, in morphological and physiological characteristics. Therefore, the name Candida pruni is proposed for the novel species, with sp-Quan (=CBS12814^T = KCTC 27526^T = GCMC 6582^T) as the type strain. Our study showed that Candida pruni is a novel yeast species with potential biocontrol against brown rot caused by M. fructicola on peaches.     

Inocybe praetervisa group – A clade of four closely related species with partly different geographical distribution ranges in Europe

Sequence data from a broad geographical region and different habitats show that the Inocybe praetervisa clade is comprised of four closely related species. These species of section Marginatae are characterized by having nodulose spores and a stipe that is abundantly pruinose only in the upper half. Inocybe praetervisa occurs in Southern Europe in mountainous mixed coniferous forests, and is not confirmed from Northern Europe. Inocybe rivularis occurs in northern boreal forests up to the lower alpine zone, associated with Betula in moist habitats, and is not confirmed from Southern Europe. Inocybe taxocystis is confirmed as a later synonym of I. favrei. The species has a wide geographical distribution range in Europe, mainly restricted to the alpine zone and moist soils, associated with Salix herbacea. Inocybe arctica is here described as a new species. It occurs in the arctic and higher alpine zones, associated with Dryas octopetala, Salix polaris, S. reticulata and S. herbacea. All species except I. arctica are shown to have an intercontinental distribution range and are confirmed from North America. Sequence data suggest the occurrence of one additional species in the alpine zone of China. A key to the species in the I. praetervisa group is provided.     

Yamadazyma ubonensis f.a., sp. nov., a novel xylitol-producing yeast species isolated in Thailand

Three hundred and thirty-seven xylose-utilizing yeast strains were isolated from various natural samples. Among these, 68 strains produced xylitol in the range of 0.1–0.69 g xylitol/g xylose. Thirty-nine xylitol-producing strains were identified to be Candida tropicalis. Ten strains were found belonging to 14 known species in the genus Candida, Cyberlindnera, Meyerozyma, Pichia, Wickerhamomyces, Yamadazyma and Cryptococcus. Two strains were identified to be two Candida species and two strains (DMKU-XE142^T and DMKU-XE332) were found to be a novel species. Strain DMKU-XE142^T was isolated from tree bark and DMKU-XE332 was obtained from decaying plant leaf collected in Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics and sequence analysis of the D1/D2 region of the large subunit rRNA gene (LSU) and the internal transcribed spacer (ITS) region, the two strains were determined to represent a novel Yamadazyma species although formation of ascospores was not observed. The sequences of the D1/D2 region of the LSU rRNA gene and the ITS region of the two strains were identical but differed from Yamadazyma phyllophila, the closest species in terms of pairwise sequence similarity of the D1/D2 region, by 1.7 % nucleotide substitutions and 3.5 % nucleotide substitutions in the ITS region. The name Yamadazyma ubonensis f.a., sp. nov. is proposed (type strain is DMKU-XE142^T = BCC 61020^T = CBS 12859^T).     

Marinomonas profundimaris sp. nov., isolated from deep-sea sediment sample of the Arctic Ocean

A taxonomic study was carried out on strain D104^T, which was isolated from deep-sea subsurface sediment sample from the Arctic Ocean. The bacterium was found to be Gram-negative, oxidase negative and catalase weakly positive, rod shaped, motile by means of polar flagellum. The organism grows between 4 and 37 °C (optimum 25–28 °C) and 0.5–6 % NaCl (optimum 3 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain D104^T belongs to the genus Marinomonas, with highest sequence similarities of 97.7 % to Marinomonas ushuaiensis DSM 15871^T, followed by M. dokdonensis DSW10-10^T (96.9 %), M. arenicola KMM 3893^T (96.7 %), M. arctica 328^T (96.6 %) and other 18 species of the genus Marinomonas (94.4–96.5 %). The average nucleotide identity and estimated DNA–DNA hybridization values between strain D104^T and M. ushuaiensis DSM 15871^T were 84.24 % and 20.80 ± 2.33 % respectively. The principal fatty acids were C_16:0, sum in feature 3 (C_16:1 ω7c/C_16:1 ω6c), sum in feature 8 (C_18:1 ω7c/C_18:1 ω6c) and C_12:1 3OH. The G + C content of the chromosomal DNA was determined to be 44.8 mol%. The respiratory quinone was found to be Q8 (100 %). Polar lipids include phosphatidylglycerol and phosphatidylethanolamine as major phospholipids and aminolipid and phospholipid as minor components. The results of the genotypic and phenotypic analyses indicate that strain D104^T represents a novel species of the genus Marinomonas, for which the name Marinomonas profundimaris sp. nov. is proposed, with the type strain D104^T (=MCCC 1A07573^T = LMG 27696^T).     

Yarrowia porcina sp. nov. and Yarrowia bubula f.a. sp. nov., two yeast species from meat and river sediment

Eleven yeast strains representing two hitherto undescribed species were isolated from different kinds of meat samples in Hungary and one from the sediment of a tropical freshwater river in Southeastern Brazil. The analysis of the sequences of their large subunit rRNA gene D1/D2 domain and the internal transcribed spacer (ITS) regions placed the two new species in the Yarrowia clade. Some of the seven strains representing the first new species can mate and give rise to asci and form ascospores embedded in capsular material, which qualifies it as the third teleomorph species of the Yarrowia clade. The name Yarrowia porcina sp. nov. (type strain: NCAIM Y.02100^T = CBS 12935^T = NRRL Y-63669^T, allotype strain UFMG-RD131^A = CBS 12932^A) is proposed for this new yeast species, which, based on physiological characters, is indistinguishable from Yarrowia lipolytica and some other species of the genus. Considerable intraspecific variability was detected among the sequences of the large subunit rRNA gene D1/D2 domains of the seven strains. The variability among the D1/D2 sequences exceeded the divergence observed among the ITS sequences and in some cases more than 1 % substitution among the D1/D2 sequences was detected. The conspecificity of these strains was supported by the low (0–3 substitutions) sequence divergence among their ITS sequences, the result of a parsimony network analysis utilizing the concatenated ITS and D1/D2 sequences and also by the fingerprint patterns generated by microsatellite primed PCR. No ascospore formation was observed in the group of the other five strains representing the second new species. These strains shared identical D1/D2 and ITS sequences. Yarrowia bubula f.a., sp. nov. (type strain: NCAIM Y.01998^T = CBS 12934^T = NRRL Y-63668^T) is proposed to accommodate these strains.     

Pseudozyma vetiver sp. nov., a novel anamorphic ustilaginomycetous yeast species isolated from the phylloplane in Thailand

Three strains representing one novel yeast species were isolated from the phylloplanes of the vetiver grasses (DMKU-LV90 and DMKU-LV99^T) and sugarcane (DMKU-SP260) collected in Thailand by leaf washing followed by a plating technique. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics and the sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer region (ITS), the three strains were found to represent a single novel anamorphic ustilaginomycetous yeast species in the genus Pseudozyma. The name Pseudozyma vetiver sp. nov. is proposed for this novel species. The type strain is DMKU-LV99^T (BCC 61021 = CBS 12824). The novel species showed phylogenetic relationships to the other members of the genus Pseudozyma and to teleomorphic fungal genera, namely Ustilago, Sporisorium and Anomalomyces in Ustilaginaceae, Ustilaginales. The three strains showed identical sequences both in the D1/D2 and ITS regions. The Pseudozyma species closest to the novel species in terms of pairwise sequence similarity in the D1/D2 region was Pseudozyma pruni but with 2.3 % nucleotide substitutions (14 nucleotide substitutions and no gaps out of 606 nt). The novel species and P. pruni differed by 10.9 % nucleotide substitutions (75 nucleotide substitutions and 31 gaps out of 691 nt) in the ITS region. The phylogenetic analysis based on the combined sequences of the ITS region and the D1/D2 region of the LSU rRNA gene showed that the novel species was found to be most closely related to Pseudozyma fusiformata but with 2.9 % nucleotide substitutions in the D1/D2 region and 7.4 % nucleotide substitutions in the ITS region.     

Articulospora – Phylogeny vs morphology

The taxonomy of the aquatic hyphomycete genus Articulospora (Ascomycota, Pezizomycotima, Leotiales, Helotiaceae) is based on the morphology of the generative phase of its lifecycle. The type species is Articulospora tetracladia, which is distributed worldwide. Its most frequent populations in nature have dimorphic conidia, differing by the extent of conidial branching (i.e., one or two levels of branching). Some strains, stable in culture, produce exclusively conidia of one type. With the molecular analyses employed here and the relatively low number of available isolates (20), separation based on branching of conidia has not been fully supported. Therefore we propose to retain the broad concept of A. tetracladia with dimorphic conidia. Among the three gene sequences tested as potential barcodes, the internal transcribed spacer (ITS) gene was the most promising region. All strains yielded amplifiable DNA which provided adequate resolution, according to accepted ranges in inter/intraspecific differences, to differentiate among the three Articulospora and two Fontanospora species that were tested (Articulospora atra, Articulospora proliferata, A. tetracladia, Fontanospora eccentrica, Fontanospora fusiramosa). D1/D2 primers also permitted amplification in all strains, however without much resolution. Amplification of the COX1 gene sequence was least consistent.     

Cryptococcus lacticolor sp. nov. and Rhodotorula oligophaga sp. nov., novel yeasts isolated from the nasal smear microbiota of Queensland koalas kept in Japanese zoological parks

A total of 515 yeast strains were isolated from the nasal smears of Queensland koalas and their breeding environments in Japanese zoological parks between 2005 and 2012. The most frequent species in the basidiomycetous yeast biota isolated from koala nasal passages was Cryptococcus neoformans, followed by Rhodotorula minuta. R. minuta was the most frequent species in the breeding environments, while C. neoformans was rare. Seven strains representing two novel yeast species were identified. Analyses of the 26S rDNA (LSU) D1/D2 domain and nuclear ribosomal DNA internal transcribed spacer region sequences indicated that these strains represent new species with close phylogenetic relationships to Cryptococcus and Rhodotorula. A sexual state was not found for either of these two novel yeasts. Key phenotypic characters confirmed that these strains could be placed in Cryptococcus and Rhodotorula. The names Cryptococcus lacticolor sp. nov. (type strain TIMM 10013^T = JCM 15449^T = CBS 10915^T = DSM 21093^T, DDBJ/EMBL/Genbank Accession No.; AB375774 (ITS) and AB375775 (26S rDNA D1/D2 region), MycoBank ID; MB 802688, Fungal Barcoding Database ID; 3174), and Rhodotorula oligophaga sp. nov. (type strain TIMM 10017^T = JCM 18398^T = CBS 12623^T = DSM 25814^T, DDBJ/EMBL/Genbank Accession No.; AB702967 (ITS) and AB702967 (26S rDNA D1/D2 region), MycoBank ID; MB 802689, Fungal Barcoding Database ID; 3175) are proposed for these new species.     

Saccharomonospora oceani sp. nov. isolated from marine sediments in Little Andaman, India

Two actinomycete strains, designated YIM M11168^T and YIM M11177, were isolated from marine sediment samples from Little Andaman, Indian Ocean, and their taxonomic position was determined by a polyphasic approach. The two Gram-positive, aerobic strains were observed to produce branched substrate mycelium and aerial hyphae but did not fragment, and no diffusible pigment was produced on the media tested. At maturity, spores were formed singly or in pairs on aerial hyphae and substrate mycelium, and occasionally the single ones were borne on long sporophores. The optimum growth was determined to occur at 28 °C, 0–4 % (w/v) NaCl and pH 7.0–8.0. Whole-cell hydrolysates of both strains contained meso-diaminopimelic acid and the diagnostic sugars were determined to be galactose, glucose and arabinose. Their predominant menaquinone was found to be MK-9(H₄). The polar lipids detected in the two strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, phosphatidylmethylethanolamine, phosphatidylethanolamine and two unknown phosphoglycolipids. The major fatty acids (>10 %) identified were iso-C_16:0, iso-C_16:1 H, iso-C_16:0, C_17:1 ω6c for strain YIM M11168^T, iso-C_16:0 and Summed Feature 3 for strain YIM M11177. The G + C contents of the genomic DNAs of both strains were determined to be 71.4 %. DNA–DNA hybridization relatedness values (78.4 ± 3.7 %) of these two isolates supported the conclusion that they belong to the same species. Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the two isolates belong to a novel species of the genus Saccharomonospora of the family Pseudonocardiaceae. The name Saccharomonospora oceani sp. nov. (Type strain YIM M11168^T = DSM 45700^T = JCM 18128^T) is proposed for the novel species.     

Yamadazyma siamensis sp. nov., Yamadazyma phyllophila sp. nov. and Yamadazyma paraphyllophila sp. nov., three novel yeast species isolated from phylloplane in Thailand and Taiwan

Four strains representing three novel anamorphic yeast species were isolated from the external surface of sugarcane leaves (DMKU-RK254^T), corn leaves (DMKU-RK548^T), bean leaves (K129) in Thailand and hengchun pencilwood leaves (TrB1-1^T) in Taiwan. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, the sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene, the internal transcribed spacer (ITS) region, the actin gene (ACT1) and the elongation factor 2 gene (EF2), the four strains were determined to represent novel Yamadazyma species although formation of ascospores was not observed. Strain DMKU-RK254^T was determined to be related to Candida diddensiae, Candida naeodendra and Candida kanchanaburiensis but with 1.8, 1.8 and 2.0 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene, respectively. It was assigned to Yamadazyma siamensis sp. nov. (type strain DMKU-RK254^T = BCC 50730^T = NBRC 108901^T = CBS 12573^T). The sequences of the D1/D2 region of the LSU rRNA gene, the ITS region, ACT1 gene and EF2 gene of two strains (DMKU-RK548^T and K129) were identical but differed from that of strain TrB1-1^T by 0.6, 1.0, 3.3 and 5.9 % nucleotide substitutions, respectively. Therefore, the two strains (DMKU-RK548^T and K129) and strain TrB1-1^T were assigned to be two separate species. The closest species in terms of pairwise sequences similarity of the D1/D2 region to the two novel species was Yamadazyma philogaea but with 1.1–1.7 % nucleotide substitutions. The two strains (DMKU-RK548^T and K129) were assigned to Yamadazyma phyllophila sp. nov. (type strain DMKU-RK548^T = BCC 50736^T = NBRC 108906^T = CBS 12572^T) and the strain TrB1-1^T was named Yamadazyma paraphyllophila sp. nov. (type strain TrB1-1^T = BCRC 23030^T = CCTCC AY 204005^T = CBS 9928^T).     

Metschnikowia henanensis sp. nov., a new anamorphic yeast species isolated from rotten wood in China

Four yeast strains were isolated from rotting wood samples collected from two sites in the Baotianman Nature Reserve and the Laojieling Nature Reserve in China. DNA sequence comparison and other taxonomic characteristics identified the strains as a single novel species of the genus Metschnikowia. The name Metschnikowia henanensis sp. nov. is proposed to accommodate these highly divergent organisms with the type strain BY-97^T (= CICC 1982^T = CBS 12677^T). The novel species produced chlamydospores, but it did not exhibit ascospore formation in sporulation media for 4 weeks. Molecular phylogeny from the D1/D2 domains of the large subunit (LSU) rRNA gene sequences placed this new species in a basal position to the Metschnikowia viticola/Candida kofuensis/Metschnikowia noctiluminum subclade, and an undescribed Candida species namely strains IMB-EMP4 and IMB-EMP5 was a close sister to M. henanensis.     

Cryptococcus nanyangensis sp. nov., A New Basidiomycetous Yeast Isolated from the Gut of Wood-Boring Larvae

Two strains of a novel basidiomycetous yeast species were isolated from the gut of wood-boring larvae collected in the Baotianman Nature Reserve, the central China. Sequence analysis of the D1/D2 domains of the large subunit (LSU) rRNA gene and internal transcribed spacer (ITS) regions showed that these yeasts belong to the Bulleromyces clade and formed a cluster together with eleven undescribed Cryptococcus species. The novel species differed from its closest known species, Cryptococcus rajasthanensis, by 3.3 % divergence (15 substitutions and 6 gaps over 630 bases) in the D1/D2 domains, and by 13.4 % divergence (41 substitutions and 27 gaps over 508 bases) in the ITS regions. Physiologically, the fermentation of glucose, galactose, sucrose, trehalose, and raffinose in Durham tubes was observed for the strains of this new yeast. Based on the phenotypical and molecular characteristics presented, the two strains are proposed as a new species, Cryptococcus nanyangensis sp. nov., with the type strain KCY-1^T (=CICC 1976^T = CBS 12474^T).     

Natural diversity of nodular microsymbionts of Myrica rubra

Myrica is often considered a promiscuous actinorhizal genus. However, there are large differences in diversity among Myrica spp., and M. gale does not exhibit such promiscuity in its natural environment. In order to understand the diversity of nodular microsymbionts of M. rubra in natural environments and whether or not the M. rubra is a `promiscuous' host, we studied the natural diversity of nodular microsymbionts of different cultivars of M. rubra. 15 nodules from nine horticultural cultivars of M. rubra were collected in 7 sites of eastern, southeastern, central and northern part of Zhejiang province, China. Unisolated strains were compared by sequence analyses of their nifD-nifK intergenic spacers and PCR amplification protocol on nodules. Phylogenetic relationships among nodular Frankia strains were analyzed by comparing sequences of their nifD-nifK intergenic spacers and reference strains. There is a high degree of diversity among nodular Frankia symbionts of M. rubra. Frankia strains from cluster I and cluster III were found in nodules from many different cultivars of M. rubra. Furthermore, there were sometimes two strains which belong to different infective clusters of Frankia in the same nodule, and Frankia strains of cluster I were often dominant strains when there were two strains. M. rubra can thus be considered to be promiscuous in nature. Identical sequences in nodules from different plants at widely separated sites were commonly found, indicating that some strains are cosmopolitan. Geographic separation, host selectivity for Frankia symbionts and soil environment may account for the diversity of Frankia strains and differences in Frankia populations found in M. rubra nodules. Several very closely related local Frankia populations in M. rubra nodules could be distinguished from one another by our approach.     

Ogataea kanchanaburiensis sp. nov. and Ogataea wangdongensis sp. nov., two novel methylotrophic yeast species from phylloplane in Thailand

Three strains (KM03^T, KM13 ^T and KM15) representing two novel methylotrophic yeast species were isolated from the external surface of plant leaves, which were collected from Kanchanaburi province, Thailand, by three-consecutive enrichments in methanol broth. Strain KM03^T was isolated from phylloplane of a mango tree (Mangifera indica) and two strains, KM13^T and KM15, were obtained from phylloplane of different wine grapes (Vitis vinifera). The sequences of the D1/D2 region of the large subunit (LSU) rRNA gene of the two strains (KM13^T and KM15) were identical and differed markedly from that of strain KM03^T. In terms of pairwise sequence similarity of the D1/D2 region the closest species to the strains KM13^T and KM15 were Candida suzukii (CBS 9253^T) and Candida nitratophila (CBS 2027^T) but with 2.1 % nucleotide substitutions. Strain KM03^T differed from Ogataea wickerhamii (CBS 4307^T), its closest relative, by 2.3 % nucleotide substitutions. Phylogenetic analysis based on the D1/D2 sequences placed the three strains in the Ogataea clade. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, the sequence analyses of the D1/D2 and the internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA gene (nrRNA) operon, the three strains represent two novel Ogataea species although formation of ascospores was not observed. Ogataea kanchanaburiensis sp. nov. is proposed for strain KM03^T (=BCC 47626^T = NBRC 108603^T = CBS 12673^T). Two strains, KM13^T and KM15, were assigned to Ogataea wangdongensis sp. nov. (type strain KM13^T = BCC 42664^T = NBRC 107778^T = CBS 12674^T). GenBank/EMBL/DDBJ accession numbers for the sequences of the D1/D2 and the ITS regions of O. kanchanaburiensis KM03^T are AB734090 and AB734093, respectively, of O. wangdongensis KM13^T are AB734091 and AB734094, respectively, and of O. wangdongensis KM15 are AB734092 and AB734095, respectively.     

Haloplanus litoreus sp. nov. and Haloplanus ruber sp. nov., from a marine solar saltern and an aquaculture farm,respectively

Two halophilic archaea, strains GX21^T and R35^T, were isolated from a marine solar saltern and an aquaculture farm in China, respectively. Cells of the two strains were observed to be pleomorphic, flat, to contain gas vesicles, stain Gram-negative and produce red-pigmented colonies. Strain GX21^T was found to be able to grow at 25–50 °C (optimum 37 °C), at 2.6–4.8 M NaCl (optimum 3.4 M NaCl), at 0.05–1.0 M MgCl₂ (optimum 0.1 M MgCl₂) and at pH 6.0–8.5 (optimum pH 6.5) while strain R35^T was found to be able to grow at 25–45 °C (optimum 37 °C), at 2.1–4.8 M NaCl (optimum 3.1 M NaCl), at 0–0.7 M MgCl₂ (optimum 0.03 M MgCl₂) and at pH 5.5–9.5 (optimum pH 6.5–7.0). The cells of both isolates were observed to lyse in distilled water. The minimum NaCl concentrations that prevented cell lysis were determined to be 15 % (w/v) for strain GX21^T and 12 % (w/v) for strain R35^T. The major polar lipids of the two strains were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, one major glycolipid and a minor lipid chromatographically identical to sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. 16S rRNA gene sequence analysis revealed that strains GX21^T and R35^T show 97.1 % sequence similarity to each other and are closely related to Haloplanus aerogenes TBN37^T (96.8 and 95.8 %), Haloplanus vescus RO5-8^T (96.7 and 96.1 %), Haloplanus salinus YGH66^T (96.4 and 95.8 %) and Haloplanus natans JCM 14081^T (96.3 and 95.4 %). The rpoB′ gene similarity between strains GX21^T and R35^T is 90.5 % and show 88.5–90.8 % similarity to the Haloplanus species with validly published names. The DNA G+C content of strain GX21^T and R35^T were determined to be 65.8 and 66.0 mol%, respectively. The DNA–DNA hybridization values between strain GX21^T and strain R35^T, and the two strains with the Haloplanus species with validly published names, showed less than 50 % DNA–DNA relatedness. It was concluded that strain GX21^T (=CGMCC 1.10456^T = JCM 17092^T) and strain R35^T (=CGMCC 1.10594 ^T = JCM 17271^T) represent two new species of Haloplanus, for which the names Haloplanus litoreus sp. nov. and Haloplanus ruber sp. nov. are proposed.     

Diversity of culturable yeasts in phylloplane of sugarcane in Thailand and their capability to produce indole-3-acetic acid

Yeasts were isolated by the enrichment technique from the phylloplane of 94 samples of sugarcane leaf collected from seven provinces in Thailand. All sugarcane leaf samples contained yeasts and 158 yeast strains were obtained. On the basis of the D1/D2 domain of the large subunit rRNA gene sequence analysis, 144 strains were identified to 24 known species in 14 genera belonging to the Ascomycota viz. Candida akabanensis, Candida dendronema, Candida mesorugosa, Candida michaelii, Candida nivariensis, Candida rugosa, Candida orthopsilosis, Candida quercitrusa, Candida tropicalis, Candida xylopsoci, Cyberlindnera fabianii, Cyberlindnera rhodanensis, Debaryomyces nepalensis, Hannaella aff. coprosmaensis, Hanseniaspora guilliermondii, Kluyveromyces marxianus, Lachancea thermotolerans, Lodderomyces elongisporus, Metschnikowia koreensis, Meyerozyma caribbica, Millerozyma koratensis, Pichia kudriavzevii, Torulaspora delbrueckii and Wickerhamomyces edaphicus, and 12 species in six genera of the Basidiomycota viz . Cryptococcus flavescens, Cryptococcus laurentii, Cryptococcus rajasthanensis, Kwoniella heveanensis, Rhodosporidium fluviale, Rhodosporidium paludigenum, Rhodotorula mucilaginosa, Rhodotorula sesimbrana, Rhodotorula taiwanensis, Sporidiobolus ruineniae, Sporobolomyces carnicolor and Sporobolomyces nylandii. Seven strains were identical or similar to four undescribed species. Another seven strains represented four novels species in the genus Metschnikowia, Nakazawaea, Wickerhamomyces and Yamadazyma. The results revealed 69 % of the isolated strains were ascomycete yeasts and 31 % were basidiomycete yeast. The most prevalent species was M. caribbica with a 23 % frequency of occurrence followed by Rh. taiwanensis (11 %) and C. tropicalis (10 %). All strains were assessed for indole-3-acetic acid (IAA) producing capability showing that 69 strains had the capability of producing IAA when cultivated in yeast extract peptone dextrose broth supplemented with 1 g/L l-tryptophan. The highest IAA concentration of 565.1 mg/L was produced by R. fluviale DMKU-RK253.     

Candida species in tchapalo and bangui, two traditional alcoholic beverages from Côte d'Ivoire

The increase of infections due to non-Candida albicans species made it very necessary to conduct adequate characterization to be able to identify the species of Candida isolated from traditional fermented foods. In this study, based on their hue on Candida Chromogenic Agar medium, a total of 136 yeast strains were isolated from tchapalo and bangui. Molecular identification based on PCR-RFLP of internal transcribed spacers of rDNA (ITS) and sequencing of the ITS and the D1/D2 regions allowed us to assign these isolates to seven species: Candida tropicalis, Candida inconspicua, Candida rugosa, Saccharomyces cerevisiae, Kluyveromyces marxianus, Hanseniaspora guilliermondii, Trichosporon asahii. With the respect to each beverage, six species were found among with four species are regarded as opportunistic pathogens. From these, C. tropicalis, C. inconspicua and K. marxianus were the most commonly encountered. The enzyme activities of the potential pathogens assessed using API ZYM system showed that almost strains had esterase, esterase lipase, valine and cystine arylamidase, alpha chymotrypsin, alkaline phosphatase and naphthol phosphohydrolase activities. The activity of α-glucosidase was found only in C. tropicalis and C. inconspicua strains isolated from tchapalo while β-glucosidase activity was found in all strains from tchapalo and only in C. inconspicua isolated from bangui.     

Halorubrum rubrum sp. nov., an extremely halophilic archaeon from a Chinese salt lake

Two halophilic archaeal strains, YC87^T and YCA11, were isolated from Yuncheng salt lake in Shanxi, China. Cells of the two strains were observed to be pleomorphic rod-shaped, stained Gram-negative and produced red-pigmented colonies. Strain YC87^T was able to grow at 20–50 °C (optimum 37 °C), at 1.4–4.8 M NaCl (optimum 2.1 M NaCl), at 0.05–1.0 M MgCl₂ (optimum 0.3 M MgCl₂) and at pH 6.0–9.0 (optimum pH 7.0) while strain YCA11 was able to grow at 20–50 °C (optimum 37 °C), at 2.1–4.8 M NaCl (optimum 3.1 M NaCl), at 0.01–0.7 M MgCl₂ (optimum 0.1 M MgCl₂) and at pH 6.0–9.0 (optimum pH 7.5). The cells of both isolates were observed to lyse in distilled water. The minimum NaCl concentrations that prevented cell lysis were determined to be 8 % (w/v) for strain YC87^T and 12 % (w/v) for strain YCA11. The major polar lipids of the two strains were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and one major glycolipid chromatographically identical to sulfated mannosyl glucosyl diether; another major glycolipid and trace amounts of several unidentified lipids were also detected. The 16S rRNA gene sequences of the two strains were 99.8 % identical, showing 93.2–98.2 % similarity to members of the genus Halorubrum of the family Halobacteriaceae. The rpoB′ gene similarity between strains YC87^T and YCA11 was 99.3 % and showed 87.5–95.2 % similarity to the closest relative members of the genus Halorubrum. The DNA G+C content of strains YC87^T and YCA11 were determined to be 64.9 and 64.5 mol%, respectively. The DNA–DNA hybridization value between strain YC20^T and strain YC77 was 87 % and the two strains showed low DNA–DNA relatedness with Halorubrum cibi JCM 15757^T and Halorubrum aquaticum CGMCC 1.6377^T, the most related members of the genus Halorubrum. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains YC87^T and YCA11 represent a novel species of the genus Halorubrum, for which the name Halorubrum rubrum sp. nov. is proposed. The type strain is YC87^T (=CGMCC 1.12124^T = JCM 18365^T).     

Candida sanyaensis sp. nov., an ascomycetous yeast species isolated from soil

Strains representing a novel ascomycetous yeast species, Candida sanyaensis, were isolated from soil samples collected on Hainan Island and Taiwan Island in China. Analysis of the D1/D2 domains of the large subunit (LUS) rRNA gene and internal transcribed spacer (ITS) regions of these strains showed that this species was related to Candida tropicalis and Candida sojae, their closest relatives. C. sanyaensis differed by three substitutions and one gap from C. tropicalis, and by four substitutions and one gap from C. sojae, in the D1/D2 domain sequences. However, the ITS sequences of C. sanyaensis were quite divergent from the latter two species, showing that it is a genetically separate species. The novel strains were also found to have very similar PCR-fingerprinting profiles which were quite distinct from those of C. tropicalis and C. sojae strains. The type strain of C. sanyaensis is HN-26^T (= CICC 1979^T = CBS 12637^T).     

The limit of the genetic adaptation to copper in freshwater phytoplankton

Copper is one of the most frequently used algaecides to control blooms of toxic cyanobacteria in water supply reservoirs. Among the negative impacts derived from the use of this substance is the increasing resistance of cyanobacteria to copper toxicity, as well as changes in the community structure of native phytoplankton. Here, we used the ratchet protocol to investigate the differential evolution and maximum adaptation capacity of selected freshwater phytoplankton species to the exposure of increasing doses of copper. Initially, a dose of 2.5 μM CuSO₄·5H₂O was able to completely inhibit growth in three strains of the toxic cyanobacterium Microcystis aeruginosa, whereas growth of the chlorophyceans Dictyosphaerium chlorelloides and Desmodesmus intermedius (represented by two different strains) was completely abolished at 12 μM. A significant increase in resistance was achieved in all derived populations during the ratchet experiment. All the chlorophyceans were able to adapt to up to 270 μM of copper sulfate, but 10 μM was the highest concentration that M. aeruginosa strains were able to cope with, although one of the replicates adapted to 30 μM. The recurrent use and increasing doses of copper in water reservoirs could lead to the selection of copper-resistant mutants of both chlorophyceans and cyanobacteria. However, under high concentrations of copper, the composition of phytoplankton community could undergo a drastic change with cyanobacteria being replaced by copper-resistant chlorophyceans. This result stems from a distinct evolutionary potential of these species to adapt to this substance.