- Volume 61, Issue 7, 2011
Volume 61, Issue 7, 2011
- Validation List
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List of new names and new combinations previously effectively, but not validly, published
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors’ names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 61, part 4, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- Request For Opinion
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The status of the species Beijerinckia fluminensis Döbereiner and Ruschel 1958. Request for an Opinion
More LessIn a previous article [Oggerin M., Arahal, D. R., Rubio, V. & Marin, I. (2009). Int J Syst Evol Microbiol 59, 2323–2328], it has been shown that strain Beijerinckia fluminensis UQM 1685T and its derived equivalent B. fluminensis CIP 106281T do not conform to the description of the type strain of Beijerinckia fluminensis Döbereiner and Ruschel 1958. Indeed, both strains were identified as members of the species Rhizobium radiobacter and exhibited marked phenotypic and genotypic differences with members of the genus Beijerinckia. It was concluded that both strains, and any other equivalents derived from them, do not descend from the nomenclatural type. Since then, our attempts to find older deposits of the type strain, hopefully derived from the original isolate, or other existing strains of Beijerinckia fluminensis that could be proposed as a neotype strain, have been in vain. It is therefore proposed that the Judicial Commission should place the name Beijerinckia fluminensis Döbereiner and Ruschel 1958 on the list of rejected names if a suitable replacement type strain or a neotype cannot be found within two years following the publication of this Request (Rule 18c).
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- List Of Changes In Taxonomic Opinion
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Notification of changes in taxonomic opinion previously published outside the IJSEM
The Bacteriological Code deals with the nomenclature of prokaryotes. This may include existing names (the Approved Lists of Bacterial Names) as well as new names and new combinations. In this sense the Code is also dealing indirectly with taxonomic opinions. However, as with most codes of nomenclature there are no mechanisms for formally recording taxonomic opinions that do not involve the creation of new names or new combinations. In particular, it would be desirable for taxonomic opinions resulting from the creation of synonyms or emended descriptions to be made widely available to the public. In 2004, the Editorial Board of the International Journal of Systematic and Evolutionary Microbiology (IJSEM) agreed unanimously that it was desirable to cover such changes in taxonomic opinions (i.e. the creation of synonyms or the emendation of circumscriptions) previously published outside the IJSEM, and to introduce a List of Changes in Taxonomic Opinion [Notification of changes in taxonomic opinion previously published outside the IJSEM; Euzéby et al. (2004). Int J Syst Evol Microbiol 54, 1429–1430]. Scientists wishing to have changes in taxonomic opinion included in future lists should send one copy of the pertinent reprint or a photocopy or a PDF file thereof to the IJSEM Editorial Office or to the Lists Editor. It must be stressed that the date of proposed taxonomic changes is the date of the original publication not the date of publication of the list. Taxonomic opinions included in the List of Changes in Taxonomic Opinion cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission. The names that are to be used are those that are the ‘correct names’ (in the sense of Principle 6) in the opinion of the bacteriologist, with a given circumscription, position and rank. A particular name, circumscription, position and rank does not have to be adopted in all circumstances. Consequently, the List of Changes in Taxonomic Opinion must be considered as a service to bacteriology and it has no ‘official character’, other than providing a centralized point for registering/indexing such changes in a way that makes them easily accessible to the scientific community.
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- New Taxa
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- Actinobacteria
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Streptomyces sparsus sp. nov., isolated from a saline and alkaline soil
More LessA salt- and alkali-tolerant actinomycete strain, YIM 90018T, was isolated from a saline and alkaline soil sample collected from Qinghai, China. Aerial hyphae of strain YIM 90018T were only produced on YIM 82 agar. Vegetative hyphae were well developed and did not fragment. Straight or flexuous (rectiflexibiles) spore chains were produced. The isolate grew well with 25 % (w/v) MgCl2 . 6H2O and at pH 10. All of these characters indicated that strain YIM 90018T belonged to the genus Streptomyces. On the basis of phylogenetic analysis of the 16S rRNA gene sequence, DNA–DNA hybridization and phenotypic characteristics, strain YIM 90018T could be differentiated from all recognized species of the genus Streptomyces. A novel species, Streptomyces sparsus sp. nov., is proposed, with strain YIM 90018T ( = CCTCC AA204019T = DSM 41858T) as the type strain.
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Mycobacterium europaeum sp. nov., a scotochromogenic species related to the Mycobacterium simiae complex
Four strains isolated in the last 15 years were revealed to be identical in their 16S rRNA gene sequences to MCRO19, the sequence of which was deposited in GenBank in 1995. In a polyphasic analysis including phenotypic and genotypic features, the five strains (including MCRO19), which had been isolated in four European countries, turned out to represent a unique taxonomic entity. They are scotochromogenic slow growers and are genetically related to the group that included Mycobacterium simiae and 15 other species. The novel species Mycobacterium europaeum sp. nov. is proposed to accommodate these five strains. Strain FI-95228T ( = DSM 45397T = CCUG 58464T) was chosen as the type strain. In addition, a thorough revision of the phenotypic and genotypic characters of the species related to M. simiae was conducted which leads us to suggest the denomination of the ‘Mycobacterium simiae complex’ for this group.
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Marmoricola korecus sp. nov.
More LessA novel actinomycete, designated strain Sco-A36T, was isolated from volcanic ash. Cells were aerobic, Gram-stain-positive, oxidase-negative, catalase-positive, non-motile cocci; colonies were yellow-coloured, smooth, entire and convex. Phylogenetic analysis showed that the organism formed a distinct phyletic line within the radiation of the genus Marmoricola. Its closest phylogenetic neighbours were Marmoricola aurantiacus DSM 12652T (97.9 % 16S rRNA gene sequence similarity), Marmoricola scoriae Sco-D01T (97.9 %), Marmoricola aequoreus SST-45T (97.4 %) and Marmoricola bigeumensis MSL-05T (96.3 %). The diagnostic diamino acid in the cell walls was ll-diaminopimelic acid. The predominant menaquinone was MK-8(H4). The polar lipids contained phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and an unknown phospholipid. The predominant fatty acids were C16 : 0, C17 : 1ω8c, C18 : 1ω9c and C16 : 1ω7c and/or iso-C15 : 0 2-OH. The DNA G+C content of strain Sco-A36T was 71.0 mol%. Levels of DNA–DNA relatedness between the new isolate and the type strains of recognized species of the genus Marmoricola were 4.9–29.2 %. The phenotypic and DNA–DNA hybridization data presented here strongly suggest that strain Sco-A36T represents a novel species of the genus Marmoricola, for which the name Marmoricola korecus sp. nov. is proposed. The type strain is Sco-A36T ( = KCTC 19596T = DSM 22128T).
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Streptomyces sanyensis sp. nov., isolated from mangrove sediment
A novel strain, 219820T, whose metabolites were found to be active against tumour cells, was isolated and characterized. The isolate belonged to the genus Streptomyces and had white to grey aerial mycelium and long chains of smooth spores in the aerial mycelium. A phylogenetic tree based on 16S rRNA gene sequences showed that strain 219820T had highest similarity to members of the genus Streptomyces and was most closely, albeit loosely, associated with Streptomyces crystallinus NBRC 15401T (98.624 % similarity), Streptomyces melanogenes NBRC 12890T (98.565 %) and Streptomyces noboritoensis NBRC 13065T (98.564 %). However, DNA–DNA relatedness and phenotypic data readily distinguished strain 219820T from these phylogenetically related type strains. It is evident from the combination of genotypic and phenotypic data that strain 219820T represents a novel species of the genus Streptomyces, for which the name Streptomyces sanyensis sp. nov. is proposed; the type strain is 219820T ( = CGMCC 4.5626T = DSM 42014T).
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Cellulomonas phragmiteti sp. nov., a cellulolytic bacterium isolated from reed (Phragmites australis) periphyton in a shallow soda pond
An alkalitolerant and moderately halophilic strain, designated KB23T, characterized by optimal growth at pH 8.0–9.0 and in the presence of 5–7 % (w/v) NaCl, was isolated from a reed (Phragmites australis) periphyton sample originating from an extremely shallow, alkaline soda pond located in Hungary. Cells of strain KB23T were Gram-stain-positive, motile straight rods. Strain KB23T was facultatively anaerobic, catalase-positive, oxidase-negative and contained peptidoglycan type A4β (l-Orn–d-Asp). MK-9(H4) was the predominant isoprenoid quinone and anteiso-C15 : 0, C16 : 0 and anteiso-C15 : 1 were the major cellular fatty acids. The DNA G+C content of strain KB23T was 74.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain belongs to the genus Cellulomonas and that it is related most closely to Cellulomonas flavigena DSM 20109T (97.35 % similarity), Cellulomonas terrae DB5T (96.81 %), Cellulomonas iranensis OT (96.75), Cellulomonas chitinilytica X.bu-bT (96.60 %), Cellulomonas persica IT (96.53 %), Cellulomonas composti TR7-06T (96.45 %), Cellulomonas biazotea DSM 20112T (96.34 %) and Cellulomonas fimi DSM 20113T (96.20 %). According to these results, together with DNA–DNA hybridization and physiological data, strain KB23T is considered to represent a novel species of the genus Cellulomonas, for which the name Cellulomonas phragmiteti sp. nov. is proposed. The type strain is KB23T ( = DSM 22512T = NCAIM B002303T).
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Isoptericola chiayiensis sp. nov., isolated from mangrove soil
More LessA novel actinomycete, designated strain 06182M-1T, was isolated from a mangrove soil sample collected from Chiayi County in Taiwan. Phylogenetic analysis based on 16S rRNA gene sequences revealed levels of similarity of 97.0–98.8 % to the type strains of recognized species of the genus Isoptericola. Chemotaxonomic data also supported the placement of strain 06182M-1T within the genus Isoptericola. However, the low levels of DNA–DNA relatedness between the novel strain and the type strains of recognized species of the genus Isoptericola, in combination with differential phenotypic data, demonstrate that strain 06182M-1T represents a novel species of the genus Isoptericola, for which the name Isoptericola chiayiensis sp. nov. is proposed. The type strain is 06182M-1T ( = BCRC 16888T = KCTC 19740T).
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Zhihengliuella aestuarii sp. nov., isolated from tidal flat sediment
A Gram-stain-positive, ovoid to short rod-shaped, yellow-pigmented bacterium, designated strain DY66T, was isolated from tidal-flat sediment collected from Deukryang Bay (Republic of Korea), and its taxonomic position was investigated by using a polyphasic approach. Strain DY66T grew optimally at 30 °C and pH 8–9 and in 2 % (w/v) NaCl. The peptidoglycan type was A4α, l-Lys–l-Ala–d-Glu, and tyvelose and glucose were the major cell-wall sugars. The predominant menaquinones were MK-10 and MK-9. Major cellular fatty acids (>10 % of total) were anteiso-C15 : 0 and iso-C15 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, an unknown aminophospholipid and three unknown aminolipids. The DNA G+C content was 59.1 mol%. This chemotaxonomic profile supported the assignment of strain DY66T to the genus Zhihengliuella. Phylogenetic analysis based on 16S rRNA gene sequences also indicated that strain DY66T belonged to the family Micrococcaceae and was related to the genus Zhihengliuella. On the basis of the evidence presented in this study, strain DY66T represents a novel species of the genus Zhihengliuella, for which the name Zhihengliuella aestuarii sp. nov. is proposed. The type strain is strain DY66T ( = KCTC 19557T = JCM 16364T).
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Actinopolyspora alba sp. nov. and Actinopolyspora erythraea sp. nov., isolated from a salt field, and reclassification of Actinopolyspora iraqiensis Ruan et al. 1994 as a heterotypic synonym of Saccharomonospora halophila
Three actinomycetal strains, designated YIM 90479, YIM 90480T and YIM 90600T, were isolated from a salt field in Xinjiang province, North-west China and subjected to polyphasic taxonomic study. All three strains were moderately halophilic and were able to grow on agar at NaCl concentrations of up to 20–25 % (w/v). No growth was observed in the absence of NaCl. Good growth occurred at 37 °C and 15 % (w/v) NaCl. The cell walls of the three strains were of the type IV variety and their phospholipid patterns were type PIII. MK-9 (H4) and MK-10 (H4) or MK-9 (H4) and MK-9 (H2) were the predominant menaquinones. iso-C16 : 0 and anteiso-C17 : 0 or anteiso-C15 : 0 and anteiso-C17 : 0 were the major fatty acids. The G+C contents of the genomic DNA were 66.4–68.3 mol%. Based on differential phenotypic, chemotaxonomic and phylogenetic characteristics and the results of DNA–DNA hybridization tests, the three novel stains represent two novel species, for which the names Actinopolyspora alba sp. nov. and Actinopolyspora erythraea sp. nov. are proposed. The type strains of the species are YIM 90480T ( = DSM 45004T = KCTC 19119T) and YIM 90600T ( = CCTCC M 208247T = KCTC 19372T). In addition, we propose that Actinopolyspora iraqiensis (Ruan et al., 1994) be transferred to the genus Saccharomonospora as a heterotypic synonym of Saccharomonospora halophila based on present research results.
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Agromyces flavus sp. nov., an actinomycete isolated from soil
A Gram-positive, non-motile strain, designated CPCC 202695T, was isolated from a soil sample collected from the Qinghai–Tibet plateau, north-west China. Strain CPCC 202695T contained rhamnose, glucose and galactose in the cell wall as diagnostic sugars and 2,4-diaminobutyric acid, alanine, glutamic acid and glycine in the peptidoglycan. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. MK-12 was the predominant menaquinone and anteiso-C15 : 0 (34.2 %), iso-C15 : 0 (19.8 %), iso-C16 : 0 (12.7 %) and anteiso-C17 : 0 (11.1 %) were the major fatty acids. 16S rRNA gene sequence similarities (94.2–97.1 %) between the isolate and the type strains of recognized species of the genus Agromyces indicated that strain CPCC 202695T was a member of the genus Agromyces. DNA–DNA relatedness clearly separated strain CPCC 202695T from its closest relatives. The phenotypic and genotypic data demonstrated that strain CPCC 202695T represents a novel species of the genus Agromyces, for which the name Agromyces flavus sp. nov. is proposed. The type strain is CPCC 202695T ( = KCTC 19578T = CCM 7623T).
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Modestobacter marinus sp. nov., a psychrotolerant actinobacterium from deep-sea sediment, and emended description of the genus Modestobacter
Jing Xiao, Yingxue Luo, Jing Xu, Shujie Xie and Jun XuThe taxonomic status of an actinobacterium that changed colour during growth, strain 42H12-1T, isolated from deep-sea sediment collected from the Atlantic Ocean, was established using a combination of genotypic and phenotypic data. Strain 42H12-1T formed a distinct branch in the 16S rRNA gene phylogenetic tree together with the type strains in the genus Modestobacter. The highest sequence similarity by blast analysis was to Modestobacter versicolor CP153-2T (98.5 %) and the second-highest sequence similarity was to Modestobacter multiseptatus AA-826T (97.5 %). DNA–DNA relatedness of only 12 % (sd 1.82 %) between strain 42H12-1T and M. versicolor DSM 16678T differentiated them as members of separate genomic species. Colonies of strain 42H12-1T were black on oligotrophic medium, but orange to red, turning black, on copiotrophic medium. The peptidoglycan contained meso-diaminopimelic acid. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and an unknown aminophospholipid. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0 and C17 : 1ω8c. The DNA G+C content was 72.3±1 mol%. Strain 42H12-1T ( = DSM 45201T = CGMCC 4.5581T) is assigned as the type strain of a novel species of the genus Modestobacter, for which the name Modestobacter marinus sp. nov. is proposed.
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- Archaea
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Halolamina pelagica gen. nov., sp. nov., a new member of the family Halobacteriaceae
More LessTwo extremely halophilic archaeal strains, TBN21T and TBN49, were isolated from the Taibei marine solar saltern near Lianyungang city, Jiangsu province, China. Cells of the two strains were pleomorphic and Gram-negative and colonies were red. Strains TBN21T and TBN49 were able to grow at 25–50 °C (optimum 37 °C), at 1.4–5.1 M NaCl (optimum 3.4–3.9 M) and at pH 5.5–9.5 (optimum pH 7.0–7.5) and neither strain required Mg2+ for growth. Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). The major polar lipids of the two strains were phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and eight glycolipids; three of these glycolipids (GL3, GL4 and GL5) were chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1), galactosyl mannosyl glucosyl diether (TGD-1) and mannosyl glucosyl diether (DGD-1), respectively. Phylogenetic analysis revealed that strains TBN21T and TBN49 formed a distinct clade with their closest relative, Halobaculum gomorrense JCM 9908T (89.0–89.5 % 16S rRNA gene sequence similarity). The DNA G+C contents of strains TBN21T and TBN49 were 64.8 and 62.7 mol%, respectively. DNA–DNA hybridization between strains TBN21T and TBN49 was 90.1 %. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains TBN21T and TBN49 represent a novel species in a new genus within the family Halobacteriaceae, for which the name Halolamina pelagica gen. nov., sp. nov. is proposed. The type strain of Halolamina pelagica is TBN21T ( = CGMCC 1.10329T = JCM 16809T).
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- Bacteroidetes
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Mucilaginibacter myungsuensis sp. nov., isolated from a mesotrophic artificial lake
More LessA non-motile, pale-yellow bacterium, designated strain HMD1056T, was isolated from an artificial lake located within the campus of Hankuk University of Foreign Studies, Yongin, Korea. The major fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c; 49.1 %) and iso-C15 : 0 (22.4 %). The major respiratory quinone was MK-7. The DNA G+C content was 46.9 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD1056T formed a lineage within the genus Mucilaginibacter and was closely related to the type strains of Mucilaginibacter ximonensis (95.4 % sequence similarity), Mucilaginibacter kameinonensis (94.5 %) and Mucilaginibacter paludis (93.4 %). On the basis of the evidence presented in this study, strain HMD1056T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter myungsuensis sp. nov. is proposed. The type strain is HMD1056T ( = KCTC 22746T = CECT 7550T).
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Hymenobacter yonginensis sp. nov., isolated from a mesotrophic artificial lake
More LessA non-motile, red-pigmented bacterium, designated strain HMD1010T, was isolated from an artificial lake located within the campus of Hankuk University of Foreign Studies, Yongin, Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD1010T formed a lineage within the genus Hymenobacter and was closely related to the type strains of Hymenobacter rigui (96.7 % sequence similarity) and H. gelipurpurascens (95.6 %). The major fatty acids were C16 : 1ω5c (21.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c; 17.2 %), iso-C15 : 0 (14.5 %) and summed feature 4 (anteiso-C17 : 1 B and/or iso-C17 : 1 I; 11.9 %). The DNA G+C content was 60.4 mol%. On the basis of the evidence presented in this study, strain HMD1010T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter yonginensis sp. nov. was proposed. The type strain is HMD1010T ( = KCTC 22745T = CECT 7546T).
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Cesiribacter andamanensis gen. nov., sp. nov., isolated from a soil sample from a mud volcano
More LessA novel Gram-staining-negative, rod-shaped, non-motile bacterium, strain AMV16T, was isolated from a soil sample collected from a mud volcano located in the Andaman Islands, India. The cell suspension was pale orange. Cells of strain AMV16T were positive for catalase, oxidase, lipase, ornithine decarboxylase and lysine decarboxylase and negative for gelatinase and urease. The fatty acids present were anteiso-C11 : 0 (5.4 %), anteiso-C12 : 0 (4.1 %), C12 : 0 (7.0 %), iso-C15 : 0 (14.4 %), anteiso-C15 : 0 (3.4 %), anteiso-C16 : 0 (3.0 %), C16 : 0 (2.6 %), anteiso-C17 : 0 (3.7 %), iso-C19 : 0 (9.7 %), C13 : 1 (13.8 %), iso-C15 : 1 G (15.9 %), iso-C16 : 1 G (11.1 %) and summed feature 5 (anteiso-C18 : 0 and/or C18 : 2ω6,9c; 5.9 %). Strain AMV16T contained MK-4 as the major respiratory quinone and diphosphatidylglycerol and phosphatidylethanolamine made up the phospholipids. The G+C content of DNA of strain AMV16T was 50.9 mol%. blast sequence similarity searches based on the 16S rRNA gene sequence indicated that species of the genus Marivirga were the nearest phylogenetic neighbours, with pairwise sequence similarity ranging from 89.9 to 90.0 %. Phylogenetic analyses indicated that strain AMV16T clustered with the type strains of Marivirga tractuosa and Marivirga sericea at a phylogenetic distance of 14.6 % (85.4 % similarity), distinct from clades representing other genera of the family ‘Flammeovirgaceae’. Based on the above-mentioned phenotypic and phylogenetic characteristics, strain AMV16T is proposed as a representative of a new genus and novel species, Cesiribacter andamanensis gen. nov., sp. nov. The type strain of Cesiribacter andamanensis is AMV16T ( = DSM 22818T = CCUG 58431T).
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Winogradskyella lutea sp. nov., isolated from seawater, and emended description of the genus Winogradskyella
More LessA novel Gram-negative, orange-pigmented, rod-shaped, strictly aerobic, gliding, oxidase- and catalase-positive bacterial strain, A73T, was isolated from seawater collected off Jeju, South Korea. 16S rRNA gene sequence similarity between A73T and type strains of Winogradskyella species with validly published names ranged from 94.1 to 96.2 %. The dominant fatty acids of strain A73T were iso-C15 : 1 G (19.1 %), iso-C15 : 0 (13.3 %), iso-C17 : 0 3-OH (10.0 %) and iso-C15 : 0 3-OH (7.2 %). The DNA G+C content of strain A73T was 36.0 mol% and its major respiratory quinone was MK-6. On the basis of combined data from phenotypic and phylogenetic analyses, strain A73T represents a novel species of the genus Winogradskyella, for which the name Winogradskyella lutea sp. nov. is proposed. The type strain is A73T ( = KCTC 23237T = DSM 22624T). An emended description of the genus Winogradskyella is also provided.
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Mucilaginibacter boryungensis sp. nov., isolated from soil
More LessA Gram-stain-negative, non-motile, non-spore-forming bacterial strain, BDR-9T, was isolated from soil collected from Boryung on the west coast of the Korean peninsula, and its taxonomic position was investigated by using a polyphasic study. Strain BDR-9T grew optimally at 25 °C, at pH 6.0–7.5 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BDR-9T fell within the clade comprising species of the genus Mucilaginibacter within the phylum Bacteroidetes. 16S rRNA gene sequence similarity values between strain BDR-9T and the type strains of species of the genus Mucilaginibacter were in the range 94.0–95.6 %. Strain BDR-9T contained MK-7 as the predominant menaquinone and iso-C15 : 0 and C16 : 1ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The DNA G+C content was 44.3 mol%. Differential phenotypic properties and phylogenetic distinctiveness of strain BDR-9T demonstrated that this strain is distinguishable from species of the genus Mucilaginibacter. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain BDR-9T is considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter boryungensis sp. nov. is proposed. The type strain is BDR-9T ( = KCTC 23157T = CCUG 59599T).
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Flavitalea populi gen. nov., sp. nov., isolated from soil of a Euphrates poplar (Populus euphratica) forest
More LessA novel strain, designated HY-50RT, isolated from soil of a Euphrates poplar (Populus euphratica) forest in Xinjiang, China, was characterized using a polyphasic taxonomic approach. Cells of the isolate were Gram-reaction-negative, strictly aerobic, rod-shaped, non-motile, oxidase-negative and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate was a member of the phylum Bacteroidetes, its closest relatives being Niastella populi THYL-44T (93.6 % similarity), Flavisolibacter ginsengisoli Gsoil 643T (93.5 %), Terrimonas ferruginea IAM 15098T (93.3 %) and Flavisolibacter ginsengiterrae Gsoil 492T (93.2 %). The major fatty acids were iso-C15 : 1 G (11.7 %), iso-C15 : 0 (19.6 %) and iso-C17 : 0 3-OH (19.3 %). The predominant menaquinone of strain HY-50RT was MK-7 and the genomic DNA G+C content was 46.8 mol%. Flexirubin-type pigments were not produced. Based on phylogenetic evidence and the results of phenotypic, genotypic and chemotaxonomic analysis, strain HY-50RT represents a novel species of a novel genus, for which the name Flavitalea populi gen. nov., sp. nov. is proposed. The type strain is HY-50RT ( = CCTCC AB 208255T = NRRL B-59222T).
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Flavobacterium banpakuense sp. nov., isolated from leaf-and-branch compost
A strictly aerobic, Gram-stain-negative, yellow-pigmented, non-spore-forming, motile (by gliding), rod-shaped bacterium, designated strain 15F3T, was isolated from leaf-and-branch compost. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 15F3T was most closely related to Flavobacterium reichenbachii WB 3.2-61T and formed a distinct phyletic lineage within the genus Flavobacterium, the type genus of the family Flavobacteriaceae. Growth was observed at 10–34 °C (optimum, 30 °C) and pH 6.0–8.0 (optimum, pH 7.0). No growth occurred in the presence of ≥2 % (w/v) NaCl. Strain 15F3T reduced nitrate to nitrogen and showed catalase activity but no oxidase activity. The predominant cellular fatty acids were iso-C15 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major isoprenoid quinone was menaquinone-6. The G+C content of the genomic DNA was 31.1 mol%. On the basis of data from this polyphasic study, strain 15F3T may be classified as a representative of a novel species within the genus Flavobacterium, for which the name Flavobacterium banpakuense sp. nov. is proposed; the type strain is 15F3T ( = KACC 14225T = JCM 16466T).
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- Firmicutes And Related Organisms
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Bacillus graminis sp. nov., an endophyte isolated from a coastal dune plant
More LessA Gram-stain-positive endophytic bacterium, designated strain YC6957T, was isolated from surface-sterilized roots of a halophyte (Elymus mollis Trin.) inhabiting coastal tidal flats of Namhae Island, located on the southern coast of Korea, and was subjected to a polyphasic taxonomic study. Cells were facultatively anaerobic, endospore-forming rods to coccoid rods, motile by a single flagellum. Strain YC6957T was catalase-positive, oxidase-negative and able to grow in the presence of 0–8 % (w/v) NaCl, with optimum growth at 4–5 % (w/v) NaCl. Growth occurred at 15–45 °C (optimal growth at 30–35 °C) and pH 6.0–8.5 (optimal growth at pH 7.0–8.0). The predominant isoprenoid quinone was menaquinone 7 (MK-7). The major cellular fatty acids were C16 : 0 (11.3 %), iso-C15 : 0 (19.2 %) and anteiso-C15 : 0 (36.4 %). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 41.6 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate belonged to the genus Bacillus. Strain YC6957T exhibited high 16S rRNA gene sequence similarity to its closest neighbours, Bacillus ruris LMG 22866T (96.14 %), Bacillus lentus NCIMB 8773T (95.97 %) and Bacillus galactosidilyticus LMG 17892T (95.91 %), and less than 95.84 % similarity to all other type strains in the genus Bacillus. On the basis of the phylogenetic, physiological and biochemical data, it is suggested that strain YC6957T represents a novel species of the genus Bacillus, for which the name Bacillus graminis sp. nov. is proposed. The type strain is YC6957T ( = KACC 13779T = DSM 22162T).
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Streptococcus porcorum sp. nov., isolated from domestic and wild pigs
More LessSeven isolates of an unidentified Gram-stain-positive, catalase-negative, coccus-shaped organism isolated from domestic and wild pigs were characterized by phenotypic and molecular-genetic methods. Based on cellular morphology and biochemical criteria, the isolates were tentatively assigned to the genus Streptococcus, although the organisms did not appear to correspond to any recognized species. Comparative 16S rRNA gene sequencing showed that the unknown bacterium was phylogenetically closely related to, but distinct from, Streptococcus suis (97.5 % 16S rRNA gene sequence similarity to the type strain). rpoB and sodA sequence analysis showed minimum interspecies divergence from phylogenetically close 16S rRNA gene sequence-based relatives of 13.8 and 18.6 %, respectively. DNA–DNA hybridization of a strain of the unidentified organism demonstrated 8–18 % reassociation with S. suis NCTC 10234T. The novel bacterium could be distinguished from S. suis and other Streptococcus species using biochemical tests. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from domestic and wild animals be assigned to a novel species of the genus Streptococcus, Streptococcus porcorum sp. nov. The type strain is 682-03T ( = CCUG 58479T = CECT 7593T).
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Pisciglobus halotolerans gen. nov., sp. nov., isolated from fish sauce
More LessTwo strains of Gram-stain-positive, catalase-negative, tetrad-forming cocci, C01T and C02, were isolated in Thailand from fish sauce. They were facultatively anaerobic, non-motile and non-spore-forming bacteria. These strains produced l-lactic acid from glucose. They grew at pH 5.0–9.0, at 15–40 °C and in the presence of 10 % (w/v) NaCl. The dominant fatty acid was C18 : 1ω9c. The DNA G+C contents of strains C01T and C02 were 38.6 and 38.7 mol%, respectively. Strain C01T was related most closely to Desemzia incerta DSM 20581T, with a 16S rRNA gene sequence similarity of 96.9 %. The strains could be distinguished clearly from D. incerta DSM 20581T based on cell morphology, physiological and biochemical characteristics and low levels of DNA–DNA relatedness. On the basis of the data presented, strains C01T and C02 are considered to represent a novel species of a new genus in the Bacillus–Lactobacillus cluster, for which the name Pisciglobus halotolerans gen. nov., sp. nov. is proposed. The type strain of Pisciglobus halotolerans is C01T ( = KCTC 13150T = TISTR 1958T = PCU 316T).
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Tumebacillus ginsengisoli sp. nov., isolated from soil of a ginseng field
A Gram-reaction-positive, rod-shaped, spore-forming bacterium, designated Gsoil 1105T, was isolated from soil of a ginseng field in Pocheon Province in South Korea and characterized in order to determine its taxonomic position. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the order Bacillales, showing the highest level of sequence similarity with respect to Tumebacillus permanentifrigoris Eur1 9.5T (94.6 %). The phylogenetic distances from other described species with validly published names within the order Bacillales were greater than 9.0 %. Strain Gsoil 1105T had a genomic DNA G+C content of 55.6 mol% and menaquinone 7 (MK-7) as the major respiratory quinone. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 1105T represents a novel species of the genus Tumebacillus, for which the name Tumebacillus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 1105T ( = KCTC 13942T = DSM 18389T).
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Jeotgalicoccus halophilus sp. nov., isolated from salt lakes
More LessTwo slightly halophilic bacterial strains, C1-52T and YD-9, were isolated from Daban and Aiding salt lakes in Xinjiang, China, respectively. The isolates were Gram-positive, non-endospore-forming, non-motile, facultatively anaerobic cocci. Colonies were pale yellow, and a light pink, diffusible pigment was produced after a few additional days of incubation. The isolates grew optimally with 2–3 % (w/v) NaCl, at pH 7.5 and at 30–35 °C. The peptidoglycan type was l-Lys–Gly3–4–l-Ala(Gly). The menaquinones were MK-7 (83.2 %) and MK-6 (16.8 %). The major fatty acids (>10 %) were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C content of strains C1-52T and YD-9 was 41.2 and 41.0 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains C1-52T and YD-9 were closely related to Jeotgalicoccus psychrophilus YKJ-115T (98.0 and 97.1 % 16S rRNA gene sequence similarity, respectively), followed by Jeotgalicoccus halotolerans YKJ-101T (97.1 and 96.8 %). Strains C1-52T and YD-9 shared, respectively, 20 and 11 % DNA–DNA relatedness with J. halotolerans JCM 11198T and 8 and 13 % with J. psychrophilus JCM 11199T. DNA–DNA relatedness between the isolates was 91 %. On the basis of phenotypic and phylogenetic distinctiveness, strains C1-52T and YD-9 belonged to the same species, which should be placed in the genus Jeotgalicoccus as a novel species. The name Jeotgalicoccus halophilus sp. nov. is proposed, with the type strain C1-52T ( = CGMCC 1.8911T = NBRC 105788T).
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- Other Bacteria
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Rubritalea halochordaticola sp. nov., a carotenoid-producing verrucomicrobial species isolated from a marine chordate
More LessA Gram-negative-staining, obligately aerobic, non-motile, rod-shaped and chemoheterotrophic bacterium, designated strain MN1-1006T, was isolated from an ascidian (sea squirt) sample, and was studied using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the new isolate shared approximately 93–99% sequence similarity with recognized species of the genus Rubritalea within the phylum ‘Verrucomicrobia’. DNA–DNA hybridization values between strain MN1-1006T and Rubritalea squalenifaciens HOact23T and Rubritalea sabuli YM29-052T were 57% and 14.5%, respectively. Strain MN1-1006T produced carotenoid compounds that rendered the cell biomass a reddish pink colour. The strain also contained squalene. The cell-wall peptidoglycan of the novel strain contained muramic acid and meso-diaminopimelic acid. The DNA G+C content of strain MN1-1006T was 51.4 mol%. The major cellular fatty acids were iso-C14:0, iso-C16:0 and anteiso-C15:0. The major isoprenoid quinone was MK-9. On the basis of these data, it was concluded that strain MN1-1006T represents a novel species of the genus Rubritalea, for which the name Rubritalea halochordaticola sp. nov. is proposed. The type strain is MN1-1006T ( = KCTC 23186T = NBRC 107102T).
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Lactococcus fujiensis sp. nov., a lactic acid bacterium isolated from vegetable matter
More LessThree strains of lactic acid bacteria, designated NJ 317T, NJ 414 and NJ 415, were isolated from the outer leaves of Chinese cabbages (Brassica rapa L. var. glabra Regel) and characterized taxonomically. The strains were Gram-reaction-positive, catalase-negative, facultatively anaerobic cocci that did not produce gas from glucose and formed l-lactic acid. The major fatty acids were C18 : 1ω9c, C16 : 0, C14 : 0 and summed feature 10. Morphological, physiological and phylogenetic data indicated that the strains belonged to the genus Lactococcus. These strains shared similar phenotypic characteristics and exhibited DNA relatedness values >96.6 % to each other, indicating that they represent a single species. The DNA G+C contents of the three strains were 42.1–42.5 mol%. 16S rRNA gene sequences of the novel strains were determined and aligned with those of other species of the genus Lactococcus. On the basis of phylogenetic analysis the three strains grouped with other members of the genus Lactococcus. Lactococcus lactis and Lactococcus garvieae were the most closely related species, sharing a sequence similarity value of 94.4 % with the three strains. Ribotyping patterns, however, revealed that these strains were well-separated from reference strains of species of the genus Lactococcus and DNA–DNA hybridization studies indicated that the novel strains had low levels (<20.2 %) of DNA relatedness with reference strains of L. lactis, L. garvieae and other type strains of previously described species, showing that they represent a different species. Based on this evidence, strains NJ 317T, NJ 414 and NJ 415 represent a novel species of the genus Lactococcus, for which the name Lactococcus fujiensis sp. nov. is proposed. The type strain is NJ 317T ( = JCM16395T = CGMCC 1.10453T).
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Thermosipho globiformans sp. nov., an anaerobic thermophilic bacterium that transforms into multicellular spheroids with a defect in peptidoglycan formation
More LessAn anaerobic rod-shaped thermophile was isolated from a hydrothermal vent at Suiyo Seamount, Izu-Bonin Arc, western Pacific Ocean, and was named strain MN14T. The rods were Gram-negative-staining, non-motile without flagella, 2–4 µm long and 0.5 µm wide, and divided by binary fission in the mid-exponential phase. The cells were surrounded by a sheath-like structure (toga) and occurred singly or in chains. Spheroids containing multiple cells were observed not only in the stationary phase, as previously observed for species of the order Thermotogales, but also from the early exponential phase. Transmission electron microscopy revealed that the peptidoglycan in rods partly disintegrated in the early growth phases and that the outer membrane of the spheroids was not completely lined with peptidoglycan. These findings suggested that the spheroids were formed from rods by the disintegration of peptidoglycan and subsequent inflation of the outer membrane. The spheroids eventually generated tiny cells in the periplasmic space, indicating a viviparous mode of proliferation in addition to binary fission. Strain MN14T grew at 40–75 °C, pH 5.0–8.2 and with 0.25–5.20 % (w/v) NaCl, with optimal growth occurring at 68 °C, pH 6.8 and with 2.5 % NaCl. The shortest doubling time was 24 min, assuming that the strain propagated only by binary fission. Elemental sulfur enhanced growth, but was not essential. Thiosulfate was not an electron acceptor for growth. The strain was a chemo-organotroph that grew on yeast extract as the sole growth substrate. Tryptone and starch supported its growth in the presence of yeast extract. The G+C content of the genomic DNA was 31.7 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Thermosipho. No significant DNA–DNA hybridization was observed between the genomic DNA of strain MN14T and phylogenetically related species of the genus Thermosipho. Based on this evidence, strain MN14T is proposed to represent a novel species, named Thermosipho globiformans sp. nov. The species epithet globiformans reflects the formation of multicellular and reproductive spheroids by the novel strain. The type strain of this species is MN14T ( = JCM 15059T = DSM 19918T).
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- Proteobacteria
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Revision of the genus Massilia La Scola et al. 2000, with an emended description of the genus and inclusion of all species of the genus Naxibacter as new combinations, and proposal of Massilia consociata sp. nov.
More LessA Gram-stain-negative, rod-shaped, non-spore-forming bacterium originating from a human clinical specimen was studied for its taxonomic position. 16S rRNA gene sequence similarity studies clearly allocated this strain (CCUG 58010T) to the class Betaproteobacteria, closely related to members of the genera Massilia and Naxibacter. Naxibacter varians was shown to be the most closely related species on the basis of 16S rRNA gene sequence similarity (97.5 %), followed by Massilia niastensis (96.8 %) and Massilia aerilata (96.4 %). Similarities to all other species of the genera Naxibacter and Massilia were in the range 93.9–96.2 %. Chemotaxonomic data (major ubiquinone: Q-8; major polar lipids: phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol; and major fatty acids: summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c and C12 : 0, with C10 : 0 3-OH as hydroxylated fatty acid) supported the affiliation of the isolate to these genera, which share these chemotaxonomic traits. DNA–DNA hybridization of strain CCUG 58010T with the type strain of N. varians CCUG 35299T resulted in a relatedness value of 39.2 % (reciprocal, 50 %) and physiological and biochemical tests also allowed phenotypic differentiation of the isolate from the most closely related species. There is currently no justification for a division of the genera Massilia and Naxibacter and for this reason a proposal is made to transfer all species of the genus Naxibacter to the genus Massilia, as Massilia alkalitolerans comb. nov., Massilia varians comb. nov., Massilia haematophila comb. nov. and Massilia suwonensis comb. nov. Strain CCUG 58010T represents a novel species, for which the name Massilia consociata sp. nov. is proposed, with the type strain CCUG 58010T ( = CCM 7792T).
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Litorimonas taeanensis gen. nov., sp. nov., isolated from a sandy beach
More LessA heterotrophic, Gram-negative, prosthecate bacterium, designated strain G5T, was isolated from a sandy beach of Taean in South Korea. Cells of strain G5T were aerobic, catalase- and oxidase-positive, straight to slightly curved motile rods with a single flagellum and formed yellow–orange colonies on agar. Growth occurred at 15–40 °C (optimum 25–30 °C) and pH 6–9 (optimum pH 7–8). The major cellular fatty acids were C18 : 1ω7c, C17 : 0, C16 : 0, 11-methyl C18 : 1ω7c, C17 : 1ω8c and C17 : 1ω6c. The polar lipid pattern indicated the presence of phosphatidylglycerol, monoglycosyldiglyceride, glucuronopyranosyldiglyceride and two unidentified glycolipids. The G+C content of the genomic DNA was 63.6 mol% and the major quinone was Q-10. Comparative 16S rRNA gene sequence analysis showed that strain G5T belonged to the branch containing the genera Hellea, Robiginitomaculum and Hypomonas within the family Hyphomonadaceae. Within this group, strain G5T was most closely related to Hellea balneolensis 26III/A02/215T with 95.8 % 16S rRNA gene sequence similarity. Based on its phylogenetic position and its phenotypic, chemotaxonomic and molecular properties, strain G5T represents a novel species of a novel genus of the family Hyphomonadaceae, for which the name Litorimonas taeanensis gen. nov., sp. nov. is proposed. The type strain is G5T ( = KACC 13701T = DSM 22008T).
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Jhaorihella thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring
A beige-coloured, Gram-staining negative, aerobic, non-motile, moderately thermophilic, rod-shaped bacterium, CC-MHSW-1T, was isolated on Marine Agar 2216 from a water sample from a coastal hot spring on Green Island (Lutao), located off Taituang, Taiwan. 16S rRNA gene sequence analysis demonstrated that the novel strain shared <94 % sequence similarity with members of the genera Lutimaribacter, Maritimibacter and Oceanicola. Ubiquinone (Q-10) was the major respiratory quinone and C18 : 1ω7c was the predominant fatty acid. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and unidentified phospholipids and aminolipids. The DNA G+C content of strain CC-MHSW-1T was 64.7 mol%. On the basis of 16S rRNA gene sequence analysis and the chemotaxonomic and physiological data, strain CC-MHSW-1T represents a new genus and species in the family Rhodobacteraceae for which the name Jhaorihella thermophila gen. nov., sp. nov., is proposed. The type strain of the type species is CC-MHSW-1T ( = JCM 15068T = CCM 7767T).
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Methylopila jiangsuensis sp. nov., an aerobic, facultatively methylotrophic bacterium
The taxonomic status was determined of an aerobic, facultatively methylotrophic strain, JZL-4T, isolated from activated sludge. The cells were Gram-negative, asporogenous, colourless, motile, short rods. The strain utilized methanol, methylamine, formate and a variety of polycarbon compounds, but not methane, dichloromethane or CO2/H2, as carbon and energy sources. C1 compounds were assimilated via the isocitrate lyase-negative serine pathway. Optimal growth occurred at 30 °C, pH 6.5–7.5 and 0.5 % (w/v) NaCl. The major cellular fatty acids were C18 : 1ω7c and C18 : 0. The major phospholipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and phosphatidylmonomethylethanolamine (PME); PME, the main phospholipid of strain JZL-4T, was absent or present in only minor amounts in Methylopila capsulata IM1T, Methylopila helvetica DM9T and Albibacter methylovorans DM10T. The major ubiquinone was Q-10. The DNA G+C content of strain JZL-4T was 70.4 mol% (T m). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain showed high sequence similarities to M. capsulata IM1T (97.2 %), A. methylovorans DM10T (94.9 %) and M. helvetica DM9T (94.1 %), and showed less than 94 % similarity to strains of other species with validly published names. Strain JZL-4T had a low level of DNA–DNA relatedness (34 %) with M. capsulata IM1T. On the basis of phenotypic, genetic and phylogenetic data, strain JZL-4T is proposed to represent a novel species of the genus Methylopila, with the name Methylopila jiangsuensis sp. nov. The type strain is strain JZL-4T ( = ACCC 05406T = DSM 22718T = VKM B-2555T).
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Primorskyibacter sedentarius gen. nov., sp. nov., a novel member of the class Alphaproteobacteria from shallow marine sediments
More LessTwo Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria, strains KMM 9015 and KMM 9018T, were isolated from a sample of shallow sediment collected from the Sea of Japan. An analysis of the nearly complete 16S rRNA gene sequences showed that the isolates were very close to each other phylogenetically (99.9 % sequence similarity) and their close relatives were Marinovum algicola FF3T (95.8 and 95.9 %, respectively) and members of the genera Leisingera (95.7–95.1 and 95.8–95.2 %), Phaeobacter (95.0–94.2 and 95.1–94.2 %) and Thalassobius (96.3–94.8 and 96.2–94.7 %) of the class Alphaproteobacteria. In phylogenetic trees based on 16S rRNA gene sequences, strains KMM 9015 and KMM 9018T were positioned as a distinct phylogenetic line adjacent to Marinovum algicola. The major isoprenoid quinone was Q-10, the polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown lipid and the major fatty acid was C18 : 1ω7c, followed by 11-methyl C18 : 1ω7c, in both strains. The DNA G+C contents of strains KMM 9015 and KMM 9018T were 60.2 and 61.9 mol%, respectively. Based on distinctive phenotypic characteristics and phylogenetic analysis, strains KMM 9015 and KMM 9018T represent a novel species in a novel genus, for which the name Primorskyibacter sedentarius gen. nov., sp. nov. is proposed. The type strain of Primorskyibacter sedentarius is strain KMM 9018T ( = NRIC 0784T = JCM 16874T).
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Photobacterium aphoticum sp. nov., isolated from coastal water
A facultatively anaerobic marine gammaproteobacterium, designated strain M46T, was isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. The strain was characterized by using a polyphasic approach and was found to be situated within the genus Photobacterium in the family Vibrionaceae. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain M46T was closely related to P. rosenbergii CECT 7644T, P. halotolerans CECT 5860T and P. ganghwense CECT 7641T, showing sequence similarities of 96.8, 96.4 and 96.2 %, respectively. According to the results of phylogenetic analyses based on recA and gyrB gene sequences, the most closely related taxon was P. ganghwense CECT 7641T with 87.4 and 85.0 % sequence similarity, respectively. Regardless of the gene used in phylogenetic analysis, strain M46T always formed a separate and stable clade containing these three species of the genus Photobacterium. Strain M46T was not luminescent and produced a diffusible brown pigment. It required NaCl to grow, reduced nitrate to nitrite and oxidized a small number of substrates in Biolog GN plates. Strain M46T was positive for arginine dihydrolase (ADH), β-galactosidase, aesculin hydrolysis and DNase activity. In API ZYM tests, the novel strain was positive for alkaline phosphatase, leucine arylamidase and acidic phosphatase activities. The major cellular fatty acids were unsaturated C18 and C16, as in other members of the genus Photobacterium, but their relative amounts and the presence or absence of other fatty acids differentiated strain M46T from its closest relatives. Based on the results of this polyphasic taxonomic study, strain M46T represents a novel species of the genus Photobacterium, for which the name Photobacterium aphoticum is proposed. The type strain is M46T ( = CECT 7614T = KCTC 23057T).
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Halomonas daqiaonensis sp. nov., a moderately halophilic, denitrifying bacterium isolated from a littoral saltern
More LessTwo novel Gram-negative, oxidase- and catalase-positive, rod-shaped bacterial strains, designated YCSA28T and YCSA39, were isolated from sediment of Daqiao saltern, Jimo, Qingdao, on the east coast of China. The two strains grew optimally at 28–30 °C, at pH 7.5 and in the presence of 7–8 % (w/v) NaCl. They were assigned to the genus Halomonas, class Gammaproteobacteria, based on 16S rRNA gene sequence analysis. The major cellular fatty acids of the two strains were C18 : 1ω7c (42.9 %), C16 : 0 (23.1 %) and C16 : 1ω7c/ω6c (18.0 %), and Q-9 was the major ubiquinone. The G+C content of the DNA of strains YCSA28T and YCSA39 was 63.7 and 63.9 mol%, respectively. The predominant respiratory lipoquinone, cellular fatty acid profiles and DNA G+C content of strains YCSA28T and YCSA39 were consistent with those of recognized species of the genus Halomonas. Levels of DNA–DNA relatedness between strains YCSA28T and YCSA39, between YCSA28T and Halomonas ventosae Al12T, and between YCSA39 and H. ventosae Al12T were 95, 45 and 50 %, respectively. Together, these data indicated that strains YCSA28T and YCSA39 represent a single novel species of the genus Halomonas, for which the name Halomonas daqiaonensis sp. nov. is proposed. The type strain is YCSA28T ( = CGMCC 1.9150T = NCCB 100305T = MCCC 1B00920T).
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Burkholderia bannensis sp. nov., an acid-neutralizing bacterium isolated from torpedo grass (Panicum repens) growing in highly acidic swamps
More LessTwo strains of acid-neutralizing bacteria, E25T and E21, were isolated from torpedo grass (Panicum repens) growing in highly acidic swamps (pH 2–4) in actual acid sulfate soil areas of Thailand. Cells of the strains were Gram-negative, aerobic, non-spore-forming rods, 0.6–0.8 µm wide and 1.6–2.1 µm long. The strains showed good growth at pH 4.0–8.0 and 17–37 °C. The organisms contained ubiquinone Q-8 as the predominant isoprenoid quinone and C16 : 0, C17 : 0 cyclo and C18 : 1ω7c as the major fatty acids. Their fatty acid profiles were similar to those reported for other Burkholderia species. The DNA G+C content of the strains was 65 mol%. On the basis of 16S rRNA gene sequence similarity, the strains were shown to belong to the genus Burkholderia. Although the calculated 16S rRNA gene sequence similarity of E25T to strain E21 and the type strains of Burkholderia unamae, B. tropica, B. sacchari, B. nodosa and B. mimosarum was 100, 98.7, 98.6, 97.6, 97.4 and 97.3 %, respectively, strains E25T and E21 formed a group that was distinct in the phylogenetic tree; the DNA–DNA relatedness of E25T to E21 and B. unamae CIP 107921T, B. tropica LMG 22274T, B. sacchari LMG 19450T, B. nodosa LMG 23741T and B. mimosarum LMG 23256T was 90, 42, 42, 42, 45 and 35 %, respectively. The results of physiological and biochemical tests including whole-cell protein pattern analysis allowed phenotypic differentiation of these strains from previously described Burkholderia species. Therefore, strains E25T and E21 represent a novel species, for which the name Burkholderia bannensis sp. nov. is proposed. The type strain is E25T ( = NBRC 103871T = BCC 36998T).
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Sulfuritalea hydrogenivorans gen. nov., sp. nov., a facultative autotroph isolated from a freshwater lake
More LessA novel facultatively autotrophic bacterium, designated strain sk43HT, was isolated from water of a freshwater lake in Japan. Cells of the isolate were curved rods, motile and Gram-reaction-negative. Strain sk43HT was facultatively anaerobic and autotrophic growth was observed only under anaerobic conditions. The isolate oxidized thiosulfate, elemental sulfur and hydrogen as sole energy sources for autotrophic growth and could utilize nitrate as an electron acceptor. Growth was observed at 8–32 °C (optimum 25 °C) and 6.4–7.6 (optimum pH 6.7–6.9). Optimum growth of the isolate occurred at NaCl concentrations of less than 50 mM. The G+C content of genomic DNA was around 67 mol%. The fatty acid profile of strain sk43HT when grown on acetate under aerobic conditions was characterized by the presence of C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as the major components. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was a member of the class Betaproteobacteria showing highest sequence similarity with Georgfuchsia toluolica G5G6T (94.7 %) and Denitratisoma oestradiolicum AcBE2-1T (94.3 %). Phylogenetic analyses were also performed using genes involved in sulfur oxidation. On the basis of its phylogenetic and phenotypic properties, strain sk43HT ( = DSM 22779T = NBRC 105852T) represents a novel species of a new genus, for which the name Sulfuritalea hydrogenivorans gen. nov., sp. nov. is proposed.
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Phaeospirillum oryzae sp. nov., a spheroplast-forming, phototrophic alphaproteobacterium from a paddy soil
More LessTwo strains (JA317T and JA559) of spiral shaped, spheroplast-forming, anaerobic, Gram-negative, motile purple non-sulfur bacteria were isolated from rhizosphere soils of paddy and were characterized by a polyphasic taxonomic approach. Bacteriochlorophyll a and carotenoids, rhodopin, lycopene and rhodopin glucoside, were present as photosynthetic pigments. Intracellular photosynthetic membranes were of stacked type. The major fatty acids were C18 : 1ω7c, C16 : 0 and C16 : 1ω6c/C16 : 1ω7c in both strains. The genomic DNA G+C content was 63.3±0.8 mol%. The two strains were closely related (mean DNA–DNA hybridization >85 %). Phylogenetic analysis showed that the strains clustered with the species of the genus Phaeospirillum, which belongs to the family Rhodospirillaceae within the class Alphaproteobacteria. Based on 16S rRNA gene sequence analysis, strains JA317T and JA559 showed highest sequence similarity with the type strains of Phaeospirillum chandramohanii (98.2 %), Phaeospirillum molischianum (97.4 %) and Phaeospirillum fulvum (97.1 %) of the family Rhodospirillaceae. Strain JA317T can be clearly distinguished from P. chandramohanii with respect to spheroplast formation and several other morphological and physiological properties. DNA–DNA relatedness of strain JA317T with its closest relatives of the genus Phaeospirillum was less than 55 %. It is evident from the phenotypic, chemotaxonomic and molecular genetic evidence that strain JA317T represents a novel species of the genus Phaeospirillum, for which the name Phaeospirillum oryzae sp. nov., is proposed. The type strain of the species is JA317T ( = NBRC 104938T = KCTC 5704T).
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Eionea nigra gen. nov., sp. nov., a gammaproteobacterium from the Mediterranean Sea
More LessA novel aerobic, Gram-negative bacterial strain, designated 17X/A02/237T, was isolated from waters of the coastal north-western Mediterranean Sea. Cells were motile straight rods and formed dark-grey colonies on marine agar medium. Strain 17X/A02/237T contained ubiquinone Q-8 and its major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C18 : 1ω7c, C16 : 0, C18 : 0 and C10 : 0 3-OH. The G+C content of the genomic DNA was 47.5 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria. Based on 16S rRNA gene sequence data, as well as physiological and biochemical characteristics, this isolate represents a novel species of a new genus, for which the name of Eionea nigra gen. nov., sp. nov. is proposed. The type strain is 17X/A02/237T ( = DSM 19752T = CIP 109759T = MOLA 288T).
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Thiocystis chemoclinalis sp. nov. and Thiocystis cadagnonensis sp. nov., motile purple sulfur bacteria isolated from the chemocline of a meromictic lake
Two isolates, designated CadH11T and Cad448T, representing uncultured purple sulfur bacterial populations H and 448, respectively, in the chemocline of Lake Cadagno, a crenogenic meromictic lake in Switzerland, were obtained using enrichment and isolation conditions that resembled those used for cultured members of the genus Thiocystis. Phenotypic, genotypic and phylogenetic analyses of these isolates confirmed their assignment to the genus Thiocystis. However, 16S rRNA gene sequence similarities of 98.2 % between CadH11T and Cad448T, and similarities of 97.7 and 98.5 %, respectively, with their closest cultured relative Thiocystis gelatinosa DSM 215T, as well as differences in DNA G+C content and carbon source utilization suggested that the isolates belonged to two distinct species. DNA–DNA hybridization of CadH11T and Cad448T with T. gelatinosa DSM 215T showed relatedness values of 46.4 and 60.8 %, respectively; the relatedness value between CadH11T and Cad448T was 59.2 %. Based on this evidence, strains CadH11T and Cad448T represent two novel species within the genus Thiocystis, for which the names Thiocystis chemoclinalis sp. nov. and Thiocystis cadagnonensis sp. nov. are proposed, respectively. The type strains of T. chemoclinalis sp. nov. and T. cadagnonensis sp. nov. are CadH11T ( = JCM 15112T = KCTC 5954T) and Cad448T ( = JCM 15111T = KCTC 15001T), respectively.
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Mannheimia caviae sp. nov., isolated from epidemic conjunctivitis and otitis media in guinea pigs
More LessStrains T138021-75T, Pg19 and Pg20 (taxon 25 of Bisgaard) were isolated from guinea pigs and characterized. Strains T138021-75T and Pg20 showed identical 16S rRNA gene sequences and were distantly related to the published strain P224 with the highest 16S rRNA similarity of 98.6 %. These two strains showed 97.8 % sequence similarity with the type strain and other strains of Mannheimia glucosida and 97.3 % similarity with the type strain of Mannheimia varigena, but <97 % similarity with all other type strains of the genus Mannheimia, including Mannheimia haemolytica (96.9 %). Phylogenetic analysis of rpoB gene sequences showed that strain P224 had a distant position (89.9 % gene sequence similarity) compared with the three other strains (T138021-75T, Pg20 and Pg19), which had identical gene sequences. These three novel strains also shared identical recN gene sequences. Phylogenetic analysis of the recN gene sequences showed a close relationship between the three novel strains and strain P224. The DNA–DNA reassociation value between strain T138021-75T and P224 was 81.6 % and 40.3 % between strain T138021-75T and the type strain of M. glucosida. Based on the DNA–DNA reassociation data, strain T138021-75T belonged to a separate species that was closely related to strain P224. Strain P224 differed from strains T138021-75T, Pg20 and Pg19 in the following phenotypic characteristics: activity of ornithine carboxylase, hydrolysis of glycosides, and acid formation from maltose, dextrin, melibiose and raffinose, as well as reactions for α-galactosidase and β-xylosidase. Whole genome similarity calculations based on recN gene sequences showed that strains T138021-75T and P224 were related at the species level (0.932), whereas 16S rRNA and partial rpoB gene sequence comparisons showed a more divergent position of strain P224 compared with the novel strains, including a different host of isolation. The results showed that the three strains of taxon 25 represent a novel species for which the name Mannheimia caviae sp. nov. is proposed. The type strain, T138021-75T ( = CCUG 59995T = DSM 23207T) was isolated from purulent conjunctivitis in guinea pigs. Previous publications have documented both ubiquinones and demethylmenaquinone to be present in the type strain. The G+C content of the DNA of the type strain has been found to be 41.4 mol% (T m).
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- Eukaryotic Micro-Organisms
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Dioszegia rishiriensis sp. nov., a novel yeast species from soil collected on Rishiri Island, Hokkaido, Japan
More LessAnamorphic basidiomycetous yeast strains RS090T and RS092 were isolated from a soil sample collected on Rishiri Island in the Rishiri, Rebun, Sarobetsu National Park, Hokkaido, Japan. As the sequences of the D1/D2 domains of their large-subunit rRNA genes were identical and those of the internal transcribed spacer regions differed in only four bases, we conclude that they belong to a single species with intraspecific diversity. Phylogenetically, this species was related to Dioszegia buhagiarii and Dioszegia hungarica, in the Tremellales, Tremellomycetes, Basidiomycota, but was clearly distinct from them. Based on the results of sequence analyses and phenotypic characteristics, we conclude that they belong to a novel species in the genus Dioszegia, for which the name Dioszegia rishiriensis sp. nov. is proposed, with the type strain RS090T ( = JCM 16282T = CBS 11844T).
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Characterization of two urostylid ciliates, Metaurostylopsis flavicana spec. nov. and Tunicothrix wilberti (Lin & Song, 2004) Xu et al., 2006 (Ciliophora, Stichotrichia), from a mangrove nature protection area in China
More LessTwo marine stichotrich ciliates, Metaurostylopsis flavicana spec. nov. and Tunicothrix wilberti (Lin & Song, 2004) Xu et al., 2006, isolated from the Shenzhen Mangrove Protection Area on the coast of the South China Sea, were investigated using live observation and protargol impregnation techniques. Metaurostylopsis flavicana is characterized by its elongate body shape, yellowish body colour and bright-yellow cortical granules that are either grouped around the cirri and the dorsal cilia or aligned between the rows of cirri and dorsal cilia. It has four to eight frontal, two frontoterminal, one buccal and seven to ten transverse cirri, a mid-ventral complex comprising 13–17 midventral cirral pairs in a row that extends about three-fifths of the body length, four left and three right marginal rows and three complete dorsal kineties. The small subunit rRNA gene of this species was sequenced and phylogenetic trees were constructed in which M. flavicana does not group with its congeners, suggesting that the genus Metaurostylopsis is paraphyletic. Some supplementary morphological and morphogenetic traits for Tunicothrix wilberti are also documented.
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Yeasts in the Sugiyamaella clade associated with wood-ingesting beetles and the proposal of Candida bullrunensis sp. nov.
More LessDuring a survey of yeasts associated with wood-ingesting insects, six strains of the Sugiyamaella clade were isolated from the gut of passalid and tenebrionid beetles and the decayed wood inhabited by them. Phylogeny based on rRNA gene sequences placed these yeasts as members of Sugiyamaella smithiae, Sugiyamaella americana, Candida lignohabitans and a novel species closely related to Su. americana. The only strain of the novel species, EH008T, could be unquestionably distinguished from its relatives by DNA sequences and other taxonomic characteristics. Ascospore production was not observed under the laboratory conditions tested. Therefore, this novel species is proposed as Candida bullrunensis sp. nov. (type strain EH008T = ATCC MYA-4660T = CBS 11840T).
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- Evolution, Phylogeny And Biodiversity
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Phylogenetic analysis of the genera Proteus, Morganella and Providencia by comparison of rpoB gene sequences of type and clinical strains suggests the reclassification of Proteus myxofaciens in a new genus, Cosenzaea gen. nov., as Cosenzaea myxofaciens comb. nov.
Phylogenetic analysis of partial rpoB gene sequences of type and clinical strains belonging to different 16S rRNA gene-fingerprinting ribogroups within 11 species of enterobacteria of the genera Proteus, Morganella and Providencia was performed and allowed the definition of rpoB clades, supported by high bootstrap values and confirmed by ≥2.5 % nucleotide divergence. None of the resulting clades included strains belonging to different species and the majority of the species were confirmed as discrete and homogeneous. However, more than one distinct rpoB clade could be defined among strains belonging to the species Proteus vulgaris (two clades), Providencia alcalifaciens (two clades) and Providencia rettgeri (three clades), suggesting that some strains represent novel species according to the genotypes outlined by rpoB gene sequence analysis. Percentage differences between the rpoB gene sequence of the type strain of Proteus myxofaciens and other members of the same genus (17.3–18.9 %) were similar to those calculated amongst strains of the genus Providencia (16.4–18.7 %), suggesting a genetic distance at the genus-level between Proteus myxofaciens and the rest of the Proteus–Providencia group. Proteus myxofaciens therefore represents a member of a new genus, for which the name Cosenzaea gen. nov., is proposed.
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Microbial evolution of sulphate reduction when lateral gene transfer is geographically restricted
More LessLateral gene transfer (LGT) is an important mechanism by which micro-organisms acquire new functions. This process has been suggested to be central to prokaryotic evolution in various environments. However, the influence of geographical constraints on the evolution of laterally acquired genes in microbial metabolic evolution is not yet well understood. In this study, the influence of geographical isolation on the evolution of laterally acquired dissimilatory sulphite reductase (dsr) gene sequences in the sulphate-reducing micro-organisms (SRM) was investigated. Sequences on four continental blocks related to SRM known to have received dsr by LGT were analysed using standard phylogenetic and multidimensional statistical methods. Sequences related to lineages with large genetic diversity correlated positively with habitat divergence. Those affiliated to Thermodesulfobacterium indicated strong biogeographical delineation; hydrothermal-vent sequences clustered independently from hot-spring sequences. Some of the hydrothermal-vent and hot-spring sequences suggested to have been acquired from a common ancestral source may have diverged upon isolation within distinct habitats. In contrast, analysis of some Desulfotomaculum sequences indicated they could have been transferred from different ancestral sources but converged upon isolation within the same niche. These results hint that, after lateral acquisition of dsr genes, barriers to gene flow probably play a strong role in their subsequent evolution.
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- Erratum
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- Retraction
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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)