- Volume 65, Issue Pt_8, 2015
Volume 65, Issue Pt_8, 2015
- NEW TAXA
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- Bacteroidetes
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Risungbinella pyongyangensis gen. nov., sp. nov., a mesophilic member of the family Thermoactinomycetaceae isolated from an agricultural soil sample
A mesophilic strain, designed MC 210T, was isolated from an agricultural soil sample from Pyongyang, Democratic People's Republic of Korea, and its taxonomic position was investigated by using a polyphasic approach. The novel strain grew well on PYI medium, and no diffusible pigments were produced. The optimum temperature for growth was 37 °C. The aerial mycelium was well developed, but not fragmented. The strain was Gram-reaction-positive and non-motile and formed endospores on the aerial mycelium. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain MC 210T belongs to the family Thermoactinomycetaceae. Strain MC 210T showed 16S rRNA gene sequence similarities of 92.90 and 92.54 % to the type strains of Geothermomicrobium terrae and Shimazuella kribbensis, respectively. The cell wall of strain MC 210T contained meso-diaminopimelic acid, glutamic acid and alanine as the diagnostic amino acids, and whole-cell hydrolysates contained glucose, arabinose and galactose. Strain MC 210T contained anteiso-C13 : 0, iso-C14 : 0, C14 : 0, anteiso-C15 : 0, C16 : 0 and iso-C13 : 0 as the major cellular fatty acids. The main polar lipids were phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unknown aminophospholipids, an unknown aminolipid, three unknown phospholipids and five unknown polar lipids. The predominant menaquinone was MK-7.The G+C content of the genomic DNA was 42.1 mol%. On the basis of our phylogenetic, physiological and chemotaxonomic data, strain MC 210T is considered to represent a novel genus and species, for which we propose the name Risungbinella pyongyangensis gen. nov., sp. nov., in the family Thermoactinomycetaceae. The type strain of Risungbinella pyongyangensis is MC 210T (CCTCC AA 2013021T = NRRL B-59118T).
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Humibacter ginsengiterrae sp. nov., and Humibacter ginsengisoli sp. nov., isolated from soil of a ginseng field
Two novel Gram-staining-positive bacteria, designated DCY60T and DCY90T, were isolated from soil of a ginseng field in the Republic of Korea. 16S rRNA gene sequence comparisons showed the two novel strains were closely related to members of the genus Humibacter with greatest similarity to Humibacter antri KCTC 33009T (98.8 and 98.4 % for DCY60T and DCY90T, respectively). The predominant menaquinones present were MK-11 and MK-12. The major fatty acids were anteiso-C17 : 0 and summed feature 8 containing C18 : 1ω7c and/or C18 : 1ω6c. The DNA G+C contents of strains DCY60T and DCY90T were 62.8 and 66.8 mol%, respectively. The peptidoglycan of both strains contained the amino acids ornithine, 2,4-diaminobutyric acid, alanine, glutamic acid and glycine. The cell-wall sugars of strain DCY60T comprised glucose, galactose, rhamnose and xylose, while strain DCY90T contained glucose, galactose, rhamnose and ribose. The major polar lipids of both strains were phosphatidylglycerol, an unidentified glycolipid, and an unknown phospholipid. On the basis of the phenotypic analysis strains DCY60T and DCY90T represent novel species of the genus Humibacter, for which names Humibacter ginsengiterrae sp. nov. (type strain DCY60T = KCTC 33520T = JCM 30079T) and Humibacter ginsengisoli sp. nov. (type strain DCY90T = KCTC 33521T = JCM 30080T) are proposed.
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- Other bacteria
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Characterization of the microaerophilic, bacteriochlorophyll a-containing bacterium Gemmatimonas phototrophica sp. nov., and emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca
A red-pigmented, bacteriochlorophyll (BChl) a-producing strain, AP64T, was isolated previously from the freshwater Swan Lake located in the western Gobi Desert. Based on its 16S rRNA gene sequence identity (96.1 %) to the type strain Gemmatimonas aurantiaca T-27T, the new isolate was tentatively classified as a member of the bacterial phylum Gemmatimonadetes. Here, we report its formal description and polyphasic characterization. Strain AP64T grew best on agar media under 9.8–15.2 % atmospheric oxygen. The cells were rods, dividing by symmetrical or asymmetrical binary fission. Budding structures were also observed. Its genomic DNA G+C content was 64.4 % (from the draft genome sequence). Phylogenetic analysis based on the 16S rRNA gene sequence clearly separated AP64T from related species. Its genotypic differentiation from phylogenetically close relatives was further supported by performing in silico DNA–DNA hybridization and calculating average nucleotide identity, whereas the high percentage (67.3 %) of shared conserved proteins between strain AP64T and Gemmatimonas aurantiaca T-27T supports the classification of the two strains into the same genus. Strain AP64T contained C16 : 1, C14 : 1 and C18 : 1ω9c as predominant fatty acids. The main respiratory quinone was menaquinone 8 (MK-8). The most distinctive feature of strain AP64T was the presence of fully functional purple bacterial photosynthetic reaction centres. The main CO2-fixation pathways were absent. Strain AP64T was capable of growth and BChl production in constant darkness. Thus, strain AP64T is a facultatively photoheterotrophic organism. It represents a novel species of the genus Gemmatimonas, for which the name Gemmatimonas phototrophica sp. nov. is proposed. The type strain is AP64T ( = DSM 29774T = MCCC 1K00454T). Emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca are also provided.
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Thermus amyloliquefaciens sp. nov., isolated from a hot spring sediment sample
A Gram-stain-negative, aerobic bacterium, designated strain YIM 77409T, was isolated from the Niujie hot spring in the Eryuan county of Dali, Yunnan province, south-west China. Cells of the strain were rod-shaped and colonies were yellow and circular. The strain grew at pH 6.0–8.0 (optimum, pH 7.0) and 50–70°C (optimum, 60–65°C). The predominant menaquinone was MK-8 and the DNA G+C content was 66.4 mol%. Major fatty acids (>10 %) were iso-C15 : 0 and iso-C17 : 0.The polar lipids consisted of one aminophospholipid, one phospholipid and two glycolipids. 16S rRNA gene sequence analysis showed that strain YIM 77409T formed a cluster with Thermus scotoductus DSM 8553T, Thermus antranikianii DSM 12462T, Thermus caliditerrae YIM 77925T and Thermus tengchongensis YIM 77924T, with highest 16S rRNA gene sequence similarity to T. scotoductus DSM 8553T (97.57 %). However, DNA–DNA hybridization indicated that strain YIM 77409T should be viewed as a representative of a novel species, as there was only 30.6 ± 1.6 % reassociation with T. scotoductus DSM 8553T. On the basis of the morphological and chemotaxonomic characteristics, as well as the genotypic data, it is proposed that strain YIM 77409T represents a novel species of the genus Thermus, with the name Thermus amyloliquefaciens sp. nov. The type strain is YIM 77409T ( = DSM 25898T = KCTC 32024T).
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Leuconostoc rapi sp. nov., isolated from sous-vide-cooked rutabaga
More LessA Gram-stain-positive, ovoid, lactic acid bacterium, strain LMG 27676T, was isolated from a spoiled sous-vide-cooked rutabaga. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the genus Leuconostoc, with Leuconostoc kimchii and Leuconostoc miyukkimchii as the nearest neighbours (99.1 and 98.8 % 16S rRNA gene sequence similarity towards the type strain, respectively). Phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of the pheS, rpoA and atpA genes, and biochemical and genotypic characteristics allowed differentiation of strain LMG 27676T from all established species of the genus Leuconostoc. Strain LMG 27676T ( = R-50029T = MHB 277T = DSM 27776T) therefore represents the type strain of a novel species, for which the name Leuconostoc rapi sp. nov. is proposed.
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- Eukaryotic micro-organisms
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Isaria takamizusanensis is the anamorph of Cordyceps ryogamimontana, warranting a new combination, Purpureocillium takamizusanense comb. nov.
More LessThe entomogenous anamorphic fungus Isaria takamizusanensis has not been resolved clearly in its teleomorphic state. We succeeded in inducing ascostroma formation by incubating conidiomata of I. takamizusanensis on cicada adults in a moist chamber. We observed the ascostroma and conducted a phylogenetic analysis based on ITS rDNA and EF-1α genes. The morphology of the ascostroma was identical to that of Cordyceps ryogamimontana. In the phylogenetic tree inferred from EF-1α, the isolate from the partspores grouped with nine strains derived from conidia of I. takamizusanensis, which was distinct from a clade including Purpureocillium lilacinum. Moreover, a conidial structure identical to that of I. takamizusanensis was rediscovered on the holotype specimen of C. ryogamimontana. As a result, we propose a new name, Purpureocillium takamizusanense, which is a combination of the teleomorph–anamorph connection of C. ryogamimontana–I. takamizusanensis, in accordance with the ‘one fungus, one name’ concept of the International Code of Nomenclature for Algae, Fungi, and Plants (ICN).
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Bullera vrieseae sp. nov., a tremellaceous yeast species isolated from bromeliads
Two independent surveys of yeasts associated with different bromeliads in different Brazilian regions led to the proposal of a novel yeast species, Bullera vrieseae sp. nov., belonging to the Tremellales clade (Agaricomycotina, Basidiomycota). Analysis of the sequences in the internal transcribed spacer (ITS) region and D1/D2 domain of the LSU rRNA gene suggested affinity to a phylogenetic lineage that includes Bullera miyagiana and Bullera sakaeratica. Six isolates of the novel species were obtained from different bromeliads and regions in Brazil. Sequence analysis of the D1/D2 domains of the large subunit of the rRNA gene showed that the novel species differs from B. miyagiana and B. sakaeratica by 85 and 64 nt substitutions, respectively and by more than 75 nt substitutions in the ITS region. Phenotypically, Bullera vrieseae sp. nov. can be distinguished from both species based on the assimilation of meso-erythritol, which was negative for B. vrieseae sp. nov. but positive for the others, assimilation of d-glucosamine, which was positive for B. vrieseae sp. nov. but negative for B. miyagiana and of l-sorbose, which was negative for B. vrieseae sp. nov. but positive for B. sakaeratica. The novel species Bullera vrieseae sp. nov. is proposed to accommodate these isolates. The type strain of Bullera vrieseae sp. nov. is UFMG-CM-Y379T (BRO443T; ex-type CBS 13870T).
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Pythium kandovanense sp. nov., a fungus-like eukaryotic micro-organism (Stramenopila, Pythiales) isolated from snow-covered ryegrass leaves
More LessPythium kandovanense sp. nov. (ex-type culture CCTU 1813T = OPU 1626T = CBS 139567T) is a novel oomycete species isolated from Lolium perenne with snow rot symptoms in a natural grassland in East-Azarbaijan province, Iran. Phylogenetic analyses based on sequence data from internal transcribed spacer (ITS)-rDNA, coxI and coxII mitochondrial genes clustered our isolates in Pythium group E as a unique, well supported clade. Pythium kandovanense sp. nov. is phylogenetically and morphologically distinct from the other closely related species in this clade, namely Pythium rostratifingens and Pythium rostratum. Pythium kandovanense sp. nov. can be distinguished from these two species by its cylindrical sporangia and lower temperatures for optimum and maximum growth rate. The development of zoospores released through a shorter discharge tube is an additional morphological feature which can be used to differentiate Pythium kandovanense sp. nov. from Pythium rostratifingens. Laboratory inoculation tests demonstrated the pathogenicity of Pythium kandovanense sp. nov. to L. perenne under wet cold (0–3 °C) conditions.
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New record of Apoholosticha sinica (Ciliophora, Urostylida) from the UK: morphology, 18S rRNA gene phylogeny and notes on morphogenesis
More LessThe benthic urostylid ciliate Apoholosticha sinica Fan et al., 2014 was isolated from a salt marsh at Blakeney, UK, and reinvestigated using light microscopy and small-subunit rRNA gene sequencing. Morphologically, it corresponds well with the original description. Several stages of divisional morphogenesis and physiological reorganization were also observed from which the following could be deduced: (i) the oral apparatus is completely newly built in the proter; (ii) frontal-ventral-transverse cirral anlage II does not produce a buccal cirrus; (iii) each of the posteriormost three or four anlagen contributes one transverse cirrus at its posterior end; (iv) a row of frontoterminal cirri originates from the rearmost frontal-ventral-transverse cirral anlage; (v) the last midventral row is formed from the penultimate frontal-ventral-transverse cirral anlage. Based on new data, two diagnostic features were added to the genus definition: (i) the midventral complex is composed of midventral pairs and midventral row and (ii) pretransverse ventral cirri are absent. Based on a combination of morphological and morphogenetic data, the genus Apoholosticha is assigned to the recently erected subfamily Nothoholostichinae Paiva et al., 2014 , which is consistent with sequence comparison and phylogenetic analyses based on SSU rRNA gene data. It is also concluded that this benthic species, previously reported only from China, is not an endemic form.
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Molecular systematics of marine gregarine apicomplexans from Pacific tunicates, with descriptions of five novel species of Lankesteria
More LessThe eugregarines are a group of apicomplexan parasites that mostly infect the intestines of invertebrates. The high level of morphological variation found within and among species of eugregarines makes it difficult to find consistent and reliable traits that unite even closely related lineages. Based mostly on traits observed with light microscopy, the majority of described eugregarines from marine invertebrates has been classified into a single group, the Lecudinidae. Our understanding of the overall diversity and phylogenetic relationships of lecudinids is very poor, mainly because only a modest amount of exploratory research has been done on the group and very few species of lecudinids have been characterized at the molecular phylogenetic level. In an attempt to understand the diversity of marine gregarines better, we surveyed lecudinids that infect the intestines of Pacific ascidians (i.e. sea squirts) using ultrastructural and molecular phylogenetic approaches; currently, these species fall within one genus, Lankesteria. We collected lecudinid gregarines from six ascidian host species, and our data demonstrated that each host was infected by a different species of Lankesteria: (i) Lankesteria hesperidiiformis sp. nov., isolated from Distaplia occidentalis, (ii) Lankesteria metandrocarpae sp. nov., isolated from Metandrocarpa taylori, (iii) Lankesteria halocynthiae sp. nov., isolated from Halocynthia aurantium, (iv) Lankesteria herdmaniae sp. nov., isolated from Herdmania momus, (v) Lankesteria cf. ritterellae, isolated from Ritterella rubra, and (vi) Lankesteria didemni sp. nov., isolated from Didemnum vexillum. Visualization of the trophozoites with scanning electron microscopy showed that four of these species were covered with epicytic folds, whereas two of the species were covered with a dense pattern of epicytic knobs. The molecular phylogenetic data suggested that species of Lankesteria with surface knobs form a clade that is nested within a paraphyletic assemblage species of Lankesteria with epicytic folds.
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- Evolution Phylogeny and Biodiversity
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Occurrence, distribution and possible functional roles of simple sequence repeats in phytoplasma genomes
More LessPhytoplasmas are unculturable, cell-wall-less bacteria that parasitize plants and insects. This transkingdom life cycle requires rapid responses to vastly different environments, including transitions from plant phloem sieve elements to various insect tissues and alternations among diverse plant hosts. Features that enable such flexibility in other microbes include simple sequence repeats (SSRs) — mutation-prone, phase-variable short DNA tracts that function as ‘evolutionary rheostats’ and enhance rapid adaptations. To gain insights into the occurrence, distribution and potentially functional roles of SSRs in phytoplasmas, we performed computational analysis on the genomes of five completely sequenced phytoplasma strains, ‘Candidatus Phytoplasma asteris’-related strains OYM and AYWB, ‘Candidatus Phytoplasma australiense’-related strains CBWB and SLY and ‘Candidatus Phytoplasma mali’-related strain AP-AT. The overall density of SSRs in phytoplasma genomes was higher than in representative strains of other prokaryotes. While mono- and trinucleotide SSRs were significantly overrepresented in the phytoplasma genomes, dinucleotide SSRs and other higher-order SSRs were underrepresented. The occurrence and distribution of long SSRs in the prophage islands and phytoplasma-unique genetic loci indicated that SSRs played a role in compounding the complexity of sequence mosaics in individual genomes and in increasing allelic diversity among genomes. Findings from computational analyses were further complemented by an examination of SSRs in varied additional phytoplasma strains, with a focus on potential contingency genes. Some SSRs were located in regions that could profoundly alter the regulation of transcription and translation of affected genes and/or the composition of protein products.
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Detection and identification of a novel 16SrXIII subgroup phytoplasma associated with strawberry red leaf disease in Argentina
Strawberry red leaf phytoplasma was found in strawberry plants from production fields in Lules (Tucumán province) and Bella Vista (Corrientes province), Argentina. Characteristic strawberry red leaf symptoms were stunting, young leaves with yellowing at the edges, mature leaves which curled and were reddish at the abaxial face, flower and fruit deformation and death. The pathogen was detected with phytoplasma-universal primer pairs P1/P7 followed by R16F2n/R16R2 as nested primers in 13 diseased plants. Based on RFLP and sequence analysis of the amplified 16S rRNA gene, the phytoplasma was related to the 16SrXIII group (Mexican periwinkle virescence). In silico the RFLP profile of all the samples analysed revealed the presence of a unique pattern, showing that the novel phytoplasma is different from all the phytoplasmas currently composing the 16SrXIII group. The phylogenetic analysis was consistent with RFLP analysis as the strawberry red leaf phytoplasma was grouped within the 16SrXIII group, but formed a particular cluster. On this basis, the Strawberry red leaf phytoplasma associated with strawberry red leaf disease was assigned to a new subgroup, 16SrXIII-F.
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A novel subgroup 16SrVII-D phytoplasma identified in association with erigeron witches' broom
Erigeron sp. plants showing symptoms of witches' broom and stunting were found near orchards of passion fruit in São Paulo state, Brazil. These symptoms were indicative of infection by phytoplasmas. Thus, the aim of this study was to detect and identify possible phytoplasmas associated with diseased plants. Total DNA was extracted from symptomatic and asymptomatic plants and used in nested PCR conducted with the primer pairs P1/Tint and R16F2n/16R2. Amplification of genomic fragments of 1.2 kb from the 16S rRNA gene confirmed the presence of phytoplasma in all symptomatic samples. The sequence identity scores between the 16S rRNA gene of the phytoplasma strain identified in the current study and those of previously reported ‘Candidatus Phytoplasma fraxini’-related strains ranged from 98 % to 99 % indicating the phytoplasma to be a strain affiliated with ‘Candidatus Phytoplasma fraxini’. The results from a phylogenetic analysis and virtual RFLP analysis of the 16S rRNA gene sequence with 17 restriction enzymes revealed that the phytoplasma strain belongs to the ash yellows phytoplasma group (16SrVII); the similarity coefficient of RFLP patterns further suggested that the phytoplasma represents a novel subgroup, designated 16SrVII-D. The representative of this new subgroup was named EboWB phytoplasma (Erigeron bonariensis Witches' Broom).
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- TAXONOMIC NOTE
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Updating Rule 15 of the International Code of Nomenclature of Bacteria
More LessThe wording of Rule 15 as originally published in the 1975 and 1990 revisions of the International Code of Nomenclature of Bacteria with regard to the definition of
nomenclatural typeswas not clearly expressed and was modified by the Judicial Commission in 2008. However, there is a difference between the wording as proposed and that accepted. On reflection there is justification for re-examining both the proposed and the accepted wording.
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Reclassification of Bacillus invictae as a later heterotypic synonym of Bacillus altitudinis
More LessThe aim of this study was to reclarify the taxonomic status of strain Bacillus invictae Bi.FFUP1 T by performing comparative analyses with the other four type strains within the Bacillus pumilus group. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains B. invictae Bi.FFUP1 T ( = DSMZ 26896T = MCCC 1A07089T), B. altitudinis 41KF2bT ( = DSMZ 21631T = MCCC 1A06452T), B. safensis FO-36bT ( = DSMZ 19292T = MCCC 1A6451T), B. pumilus ATCC 7061T ( = DSMZ 27T = MCCC 1A06453T) and B. xiamenensis HYC-10T ( = MCCC 1A00008T) were, respectively, 82.90 % and 98.10 %, which are greater than the thresholds for bacterial species delineation, suggesting that they should belong to the same species, while the dDDH and ANI values between strain B. invictae DSMZ 26896T and the other three type strains within the B. pumilus group were below the respective thresholds of 70 % and 95 %. Meanwhile, B. invictae DSMZ 26896T and B. altitudinis 41KF2bT shared 98.7 % gyrB gene sequence similarity based on resequencing, whereas strain B. invictae DSMZ 26896T shared low similarities ( < 95 %) with the other three type strains. In addition, in comparison with those from the other three type strains, phenotypic data of B. invictae DSMZ 26896T and B. altitudinis 41KF2bT, including API 20NE, API ZYM, Biolog GN2 and API 50CHB tests, showed slight differences. The data from these combined genotypic and phenotypic analyses suggest that Bacillus invictae Branquinho et al. 2014 should be regarded as a later heterotypic synonym of Bacillus altitudinis Shivaji et al. 2006 .
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- LETTER TO THE EDITOR
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The status of the species Shewanella irciniae Lee et al. 2006. Request for an opinion
More LessDuring a taxonomic study in describing a novel species of the genus Shewanella from a mangrove ecosystem, it was found that the type strain Shewanella irciniae was not available from the Japan Collection of Microorganisms (JCM) and the type strain received from the Agricultural Research Service (ARS) culture collection and from the author who described this species were found to be members of the genus Brevibacillus based on 16S rRNA gene sequence analysis. Therefore, this species cannot be included in any further scientific studies. It is therefore proposed that the Judicial Commission of the International Committee of Systematics of Prokaryotes place the name Shewanella irciniae on the list of rejected names, if a suitable replacement for the type strain is not found or a neotype strain is not proposed within two years following the publication of this Request for an Opinion.
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- ERRATUM
Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)