- Volume 56, Issue 8, 2006
Volume 56, Issue 8, 2006
- Notification List
-
-
-
Notification that new names and new combinations have appeared in volume 56, part 5, 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.
-
-
- New Taxa
-
- Actinobacteria
-
-
Catenulispora acidiphila gen. nov., sp. nov., a novel, mycelium-forming actinomycete, and proposal of Catenulisporaceae fam. nov.
A novel, Gram-positive bacterial strain was isolated from forest soil. Among species with validly published names, the 16S rRNA gene sequence is related most closely (approx. 93 % similarity) to that of Sporichthya polymorpha DSM 43042T. However, differently from this species, it forms both vegetative and aerial mycelia. The aerial hyphae are straight to slightly flexuous, starting to septate to form chains of more than 20 cylindrical spores with a rugose surface. The strain is acidophilic, with a pH range for robust growth between 4.3 and 6.8 and an optimum around 6.0. The peptidoglycan type is A3γ ll-Dpm–Gly. The polar lipids are phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and two unknown phospholipids. Predominant menaquinones are MK-9(H6) and -9(H4), and iso- and anteiso-branched C16 : 0 and C17 : 0 are the main cellular fatty acids. The DNA G+C content is 71.9 mol%. The distinct phylogenetic position and the unusual combination of chemotaxonomic characteristics justify the proposal of Catenulispora gen. nov., with the type species Catenulispora acidiphila sp. nov. (type strain, ID139908T =DSM 44928T=NRRL B-24433T). Catenulisporaceae fam. nov. is also proposed.
-
-
-
Actinospica robiniae gen. nov., sp. nov. and Actinospica acidiphila sp. nov.: proposal for Actinospicaceae fam. nov. and Catenulisporinae subord. nov. in the order Actinomycetales
Two novel Gram-positive, acidophilic bacterial strains were isolated from forest soil. According to their 16S rRNA gene sequences, these strains are related closely to each other and form a distinct cluster within the order Actinomycetales. They show the typical features of filamentous actinomycetes, with branched vegetative hyphae and production of aerial hyphae. The distinct phylogenetic positions and the combination of chemotaxonomic characteristics of these strains justify the proposal of Actinospica gen. nov. Both strains display 3-hydroxydiaminopimelic acid plus traces of meso-diaminopimelic acid, the phospholipids diphosphatidylglycerol, phosphatidylethanolamine, methylphosphatidylethanolamine and phosphatidylinositol, the predominant cellular fatty acids i-C15 : 0, i-C16 : 0 and ai-C15 : 0 and the whole-cell sugars mannose and rhamnose. They differ in the fatty acid profiles, in the quantitative ratios of the major menaquinones MK-9(H4), MK-9(H6) and MK-9(H8) and in the occurrence of additional whole-cell sugars (arabinose and xylose in strain GE134766T and galactose in strain GE134769T). Differences in the phenotypic characteristics and in the 16S rRNA gene sequences suggest the description of two species, Actinospica robiniae gen. nov., sp. nov. (the type species) and Actinospica acidiphila sp. nov., with the type strains GE134769T (=DSM 44927T=NRRL B-24432T) and GE134766T (=DSM 44926T=NRRL B-24431T), respectively. The DNA G+C contents of strains GE134769T and GE134766T are 70.8 and 69.2 mol%, respectively. Due to the large phylogenetic distance from known actinomycete genera, it is proposed to accommodate Actinospica gen. nov. in Actinospicaceae fam. nov. In addition, Catenulisporineae subord. nov. is proposed to harbour Actinospicaceae fam. nov. and the newly proposed family Catenulisporaceae, described in the accompanying paper.
-
-
-
Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium
More LessA Gram-positive, rod- or coccoid-shaped and N-hexanoyl-l-homoserine lactone-degrading bacterial strain, A2-4T, was isolated from a soil in Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain A2-4T grew optimally at pH 7.0–8.0 and 30 °C without NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain A2-4T is most closely related to members of the genus Nocardioides. Strain A2-4T possessed chemotaxonomic properties indicative of members of the genus Nocardioides; the cell-wall peptidoglycan type was based on ll-diaminopimelic acid, MK-8(H4) was the predominant menaquinone and iso-C16 : 0 was the predominant fatty acid. The DNA G+C content was 72.1 mol%. The 16S rRNA gene sequence of strain A2-4T was 98.3–99.1 % similar to those of the type strains of Nocardioides simplex, Nocardioides aromaticivorans and Nocardioides nitrophenolicus and 93.8–96.3 % similar to those of the type strains of other Nocardioides species. Strain A2-4T could be distinguished from the three phylogenetic relatives, N. nitrophenolicus, N. aromaticivorans and N. simplex, by DNA–DNA relatedness (25–42 %) and by differences in some phenotypic characteristics. On the basis of the phenotypic, phylogenetic and genetic data, the strain represents a novel species of the genus Nocardioides, for which the name Nocardioides kongjuensis sp. nov. is proposed. The type strain is A2-4T (=KCTC 19054T=JCM 12609T).
-
-
-
Actinocatenispora thailandica gen. nov., sp. nov., a new member of the family Micromonosporaceae
More LessTwo actinomycete strains, TT2-10T and TT2-3, which produced long spore chains (more than 10 spores per chain), were isolated from peat swamp forest soil in Pattaloong Province, Thailand. Their taxonomic positions were determined using a polyphasic approach. The chemotaxonomic characteristics of these strains coincided with those of the family Micromonosporaceae, i.e. cell-wall chemotype II, muramic acid of the N-glycolyl type, whole-cell sugar pattern D and type II phospholipids. Analysis of the 16S rRNA gene sequences also indicated that these strains constitute a distinct lineage within the family Micromonosporaceae, sharing 91.3–93.8 % sequence similarity with members of this family. On the basis of their phenotypic and genotypic characteristics and their phylogenetic position, these strains represent a novel genus and species, for which the name Actinocatenispora thailandica gen. nov., sp. nov. is proposed. The type strain of Actinocatenispora thailandica is strain TT2-10T (=JCM 12343T=PCU 235T=DSM 44816T).
-
-
-
Agrococcus lahaulensis sp. nov., isolated from a cold desert of the Indian Himalayas
More LessThe taxonomic position of a lemon-yellow-pigmented actinobacterium, strain K22-21T, isolated from a soil sample from Lahaul-Spiti Valley in the Indian Himalayas, was determined using a polyphasic approach. The strain had phenotypic and chemical properties that were consistent with its classification in the genus Agrococcus. Alignment of the 16S rRNA gene sequence of strain K22-21T with sequences from Agrococcus jenensis DSM 9580T, Agrococcus baldri DSM 14215T and Agrococcus citreus DSM 12453T revealed similarities of 98.5, 96.8 and 96.6 %, respectively. However, the level of DNA–DNA relatedness between strain K22-21T and A. jenensis was 55.1 %. The novel strain could be distinguished from type strains of the three species of the genus Agrococcus using DNA–DNA relatedness and phenotypic data. Based on these differences, strain K22-21T (=MTCC 7154T=DSM 17612T) should be classified as the type strain of a novel species of Agrococcus, for which the name Agrococcus lahaulensis sp. nov. is proposed.
-
-
-
Amycolatopsis taiwanensis sp. nov., from soil
More LessAn actinomycete strain (0345M-7T) was isolated from a soil sample from Yilan county, Taiwan. The isolate displayed substrate mycelia, upon which were borne short spore chains. The spore chains were composed of non-motile, smooth-surfaced, oval spores. Strain 0345M-7T had meso-diaminopimelic acid in its peptidoglycan. Whole-cell sugars were galactose, glucose, arabinose and ribose. The only phospholipid found was phosphatidylethanolamine. The predominant menaquinone was MK-9(H4). Mycolic acids were not detected. Major cellular fatty acids were iso-C16 : 0 (38.1 %) and C17 : 1 (25.4 %). The DNA G+C content of strain 0345M-7T was 68.9 mol%. On the basis of phenotypic and genotypic data, it is proposed that strain 0345M-7T (=BCRC 16802T=KCTC 19116T) should be classified as the type strain of a novel species of the genus Amycolatopsis, Amycolatopsis taiwanensis sp. nov.
-
-
-
Gordonia araii sp. nov. and Gordonia effusa sp. nov., isolated from patients in Japan
Two bacterial strains, IFM 10211T and IFM 10200T, were isolated from the sputum of two Japanese patients, and were subjected to a polyphasic taxonomic study. The two strains were found to have morphological, physiological and chemotaxonomic properties that were consistent with their assignment to the genus Gordonia, except for a few chemotaxonomic characteristics. Almost complete 16S rRNA gene sequences of the two strains were determined; the data showed that they are related distantly to Gordonia amarae, Gordonia hirsuta, Gordonia hydrophobica and Gordonia sihwensis, showing 16S rRNA gene sequence similarities to the type strains of these species of 96.2–97.9 %. DNA–DNA relatedness data coupled with the combination of genotypic and phenotypic data indicated that the two strains are representatives of two novel, separate species. The names proposed to accommodate these two strains are Gordonia araii sp. nov. (type strain IFM 10211T=DSM 44811T=NBRC 100433T=JCM 12131T) and Gordonia effusa sp. nov. (type strain IFM 10200T=DSM 44810T=NBRC 100432T=JCM 12130T).
-
-
-
Brevibacterium samyangense sp. nov., an actinomycete isolated from a beach sediment
More LessA novel actinomycete, strain SST-8T, was isolated from sand sediment of Samyang Beach in Jeju, Korea, and subjected to a polyphasic taxonomic study. The organism, which produced opaque, circular, yellow colonies, with a coryneform morphology, showed the following chemotaxonomic characteristics: meso-diaminopimelic acid as the diamino acid in the peptidoglycan, MK-8(H2) as the major menaquinone, phosphatidylglycerol as the only polar lipid, anteiso-C15 : 0 and anteiso-C17 : 0 as major fatty acids and a DNA G+C content of 70.7 mol%. The combination of morphological and chemotaxonomic features supported its classification in the genus Brevibacterium. Phylogenetic analyses, based on 16S rRNA gene sequence studies, showed that strain SST-8T formed an intermediate branch between the Brevibacterium luteolum/Brevibacterium otitidis and Brevibacterium mcbrellneri/Brevibacterium paucivorans clusters. Sequence similarity calculations based on a neighbour-joining analysis revealed that the closest relatives of strain SST-8T were the type strains of B. paucivorans (96.6 %), B. luteolum (96.5 %), B. mcbrellneri (96.3 %), Brevibacterium avium (96.0 %) and B. otitidis (95.9 %). Based on a broad set of phenotypic and genetic data, it was evident that the strain represents a novel species of the genus Brevibacterium. The name Brevibacterium samyangense sp. nov. is proposed, with SST-8T (=NRRL B-41420T=KCCM 42316T) as the type strain.
-
-
-
A new genus of the family Micromonosporaceae, Polymorphospora gen. nov., with description of Polymorphospora rubra sp. nov.
More LessTwo actinomycete strains were isolated from soil surrounding mangrove roots. The isolates formed short spore chains with spores showing diverse shapes. The isolates contained glutamic acid, glycine, alanine and meso-diaminopimelic acid in the cell wall, 3-O-methylmannose, mannose, galactose and glucose as the whole-cell sugars and MK-10(H6), MK-10(H4), MK-9(H6) and MK-9(H4) as the predominant isoprenoid quinones. The isolates formed a distinct taxon in the phylogenetic tree of the Micromonosporaceae based on analysis of 16S rRNA gene sequences and showed chemical and phenotypic properties that were different from members of all of the other genera of this family. Based on these observations, it is proposed that the novel isolates belong to a new genus, Polymorphospora gen. nov. The type species of the genus is proposed as Polymorphospora rubra sp. nov., with strain TT 97-42T (=NBRC 101157T=DSM 44947T) as the type strain.
-
-
-
Rhodococcus imtechensis sp. nov., a nitrophenol-degrading actinomycete
More LessA Gram-positive actinobacterium, strain RKJ300T, capable of utilizing p-nitrophenol and 2,4-dinitrophenol, was isolated from a pesticide-contaminated site in India. The morphological and chemotaxonomic properties of the isolate were typical of members of the genus Rhodococcus. The DNA G+C content was 72 mol%. Strain RKJ300T exhibited the highest level of sequence similarity with Rhodococcus wratislaviensis NCIMB 13082T (99.3 %), followed by Rhodococcus opacus DSM 43205T (98.8 %), Rhodococcus percolatus MBS1T (98.6 %) and Rhodococcus koreensis DNP505T (98.1 %). The low levels of DNA–DNA relatedness (49–58 %) with the above micro-organisms, and the differences in the biochemical and physiological properties, suggest that strain RKJ300T should be classified within a novel species of the genus Rhodococcus, for which the name Rhodococcus imtechensis sp. nov. is proposed. The type strain is RKJ300T (=MTCC 7085T=JCM 13270T).
-
-
-
Kocuria himachalensis sp. nov., an actinobacterium isolated from the Indian Himalayas
More LessA reddish orange bacterium, strain K07-05T, was isolated from soil during a study of the bacterial diversity of a cold desert of the Indian Himalayas and was studied by using a polyphasic approach. The organism had morphological and chemotaxonomic properties consistent with its classification in the genus Kocuria. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain K07-05T was closely related to Kocuria rosea DSM 20447T and Kocuria polaris MTCC 3702T (98.1 and 97.8 % sequence similarity, respectively), whereas the sequence similarity values with respect to the other Kocuria species with validly published names were between 96.4 and 94.2 %. However, the genomic relatedness, as shown by DNA–DNA hybridization, of strain K07-05T and K. polaris MTCC 3702T is 49.5 % and that with K. rosea MTCC 2522T is 24.0 %. The DNA G+C content of the strain is 75.3 mol%. The above data in combination with the phenotypic distinctiveness of K07-05T clearly indicate that the strain represents a novel species, for which the name Kocuria himachalensis sp. nov. is proposed. The type strain is K07-05T (=MTCC 7020T=DSM 44905T=JCM 13326T).
-
-
-
Brooklawnia cerclae gen. nov., sp. nov., a propionate-forming bacterium isolated from chlorosolvent-contaminated groundwater
More LessTwo novel facultatively anaerobic bacterial strains, BL-34T and BL-35, isolated from groundwater contaminated by a mixture of chlorosolvents were characterized using a polyphasic approach. The two strains exhibited essentially identical taxonomic features except for a vitamin B12 requirement by strain BL-35 for optimal growth. Phylogenetically, the isolates were affiliated with members of the family Propionibacteriaceae and were placed in a phylogenetic branch adjacent to, but distinct from, those of the genera Propionimicrobium, Propionibacterium, Luteococcus, Propioniferax and Tessaracoccus. The cells of the novel strains were Gram-positive, non-motile, non-spore-forming pleomorphic rods. They produced catalase but not oxidase, and nitrate reduction did not occur in peptone/yeast extract/glucose medium. Propionate and acetate were the predominant products of glucose fermentation. Fermentation occurred in the presence of 1,2-dichloroethane and 1,1,2-trichloroethane at concentrations up to at least 9.8 mM. The genomic DNA G+C content was 67.5–67.9 mol%. Menaquinone MK-9(H4) was the predominant respiratory quinone and meso-diaminopimelic acid was present in the cell-wall peptidoglycan layer. The major cellular fatty acids were C15 : 0 and anteiso-C15 : 0. On the basis of the results obtained in this study, strains BL-34T and BL-35 should be classified within a novel taxon, for which the name Brooklawnia cerclae gen. nov., sp. nov. is proposed. The type strain of Brooklawnia cerclae is BL-34T (=LMG 23248T=NRRL B-41418T). An additional strain, BL-35 (=LMG 23249=NRRL B-41419), was also characterized.
-
- Archaea
-
-
Haloterrigena longa sp. nov. and Haloterrigena limicola sp. nov., extremely halophilic archaea isolated from a salt lake
More LessHalophilic archaeal strains ABH32T and AX-7T were isolated from Aibi salt lake in Xin-Jiang, China, and were subjected to taxonomic studies. The cells of both strains were rod-shaped, and growth required at least 10 % (w/v) NaCl. The cellular polar lipids were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and mannose-2,6-disulfate (1→2)-glucose glycerol diether (S2-DGD). The isolates were different in that strain ABH32T did not require magnesium and had strong ability to assimilate sugars for growth, whereas strain AX-7T required magnesium and did not assimilate glucose, sucrose or maltose for growth. Both strain ABH32T and strain AX-7T were most closely related to members of the genera Haloterrigena and Natrinema. On the basis of phenotypic and genotypic characteristics, especially their cellular polar lipids, the two isolates were assigned to the genus Haloterrigena. Moreover, the DNA relatedness values for strains ABH32T and AX-7T with respect to members of the genus Haloterrigena were found to be well below 70 %. Thus, strains ABH32T and AX-7T represent two novel species within the genus Haloterrigena, for which the names Haloterrigena longa sp. nov. (type strain ABH32T=CGMCC 1.5334T=JCM 13562T) and Haloterrigena limicola sp. nov. (type strain AX-7T=CGMCC 1.5333T=JCM 13563T) are proposed.
-
- Bacteroidetes
-
-
Chryseobacterium taiwanense sp. nov., isolated from soil in Taiwan
More LessAmong a large collection of Taiwanese soil isolates, a novel Gram-negative, rod-shaped, non-spore-forming, yellow-pigmented bacterial strain, Soil-3-27T, was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequencing, DNA–DNA hybridization, fatty acid analysis and comparative phenotypic characterization. The 16S rRNA gene sequence analysis indicated that the organism belongs to the genus Chryseobacterium. The organism contains menaquinone MK-6 as the predominant isoprenoid quinone and 15 : 0 iso (43 %), 17 : 1 isoω9c (17.5 %) and 17 : 0 iso 3-OH (16.6 %) as the major fatty acids. Phylogenetically, the closest relatives of strain Soil-3-27T are Chryseobacterium daecheongense, Chryseobacterium defluvii and Chryseobacterium taichungense with 96.7–97.2 % sequence similarity. DNA–DNA hybridization showed relatedness values of 8.5–24.2 % with these species. The DNA G+C content is 36.8 mol%. Strain Soil-3-27T is clearly distinguishable from other Chryseobacterium species and represents a novel species, for which the name Chryseobacterium taiwanense sp. nov. is proposed. The type strain is strain Soil-3-27T (=BCRC 17412T=IAM 15317T=LMG 23355T).
-
-
-
Niastella koreensis gen. nov., sp. nov. and Niastella yeongjuensis sp. nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng
Two novel strains, GR20-10T and GR20-13T, were isolated from soil using R2A medium. The soil sample was collected from a field in the Yeongju region of Korea that was cultivated with Korean ginseng. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains formed a cluster with several uncultured bacterial clones and with Flexibacter filiformis, Flexibacter sancti, Flexibacter japonensis, Cytophaga arvensicola and Flavobacterium ferrugineum (recently reclassified as Terrimonas ferruginea) in the phylum Bacteroidetes. The level of 16S rRNA gene sequence similarity between the two novel strains was 98.9 %. Isolates GR20-10T and GR20-13T showed the highest sequence similarities to Flexibacter japonensis IFO 16041T (91.8 and 91.9 %, respectively) and T. ferruginea ATCC 13524T (90.4 and 90.6 %, respectively). The whole-cell fatty acid profiles of the two isolates were similar and their major fatty acids were 15 : 0 iso, 17 : 0 iso 3-OH and 15 : 1 iso G. The major isoprenoid quinone of both strains was MK-7. The G+C contents of GR20-10T and GR20-13T were 45.8 and 44.3 mol%, respectively. DNA–DNA hybridization (57 % DNA–DNA hybridization value) and phenotypic data indicated that strains GR20-10T and GR20-13T each belong to a separate species. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains GR20-10T and GR20-13T represent two novel species in a novel genus in the phylum Bacteroidetes; the names Niastella koreensis gen. nov., sp. nov. (the type species; type strain GR20-10T=KACC 11465T=DSM 17620T) and Niastella yeongjuensis sp. nov. (type strain GR20-13T=KACC 11466T=DSM 17621T) are proposed.
-
-
-
Gillisia myxillae sp. nov., a novel member of the family Flavobacteriaceae, isolated from the marine sponge Myxilla incrustans
A yellow-pigmented, Gram-negative, rod-shaped, strictly aerobic bacterium (strain UST050418-085T) was isolated from the surface of a marine sponge, Myxilla incrustans, at Friday Harbor, WA, USA. The DNA G+C content of this strain was 34.6 mol%. The predominant fatty acids were i15 : 0, a15 : 0, i15 : 1, i16 : 0, i17 : 0 3-OH, 17 : 0 2-OH and summed feature 3, comprising i15 : 0 2-OH and/or 16 : 1ω7c (altogether representing 69.0 % of the total fatty acids). MK-6 was the only respiratory quinone detected. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the closest relatives of UST050418-085T were members of the genus Gillisia, with sequence similarities of 93.2–96.6 %. Strain UST050418-085T differed from its closest relatives by 11 to 18 phenotypic traits. Molecular evidence and phenotypic characteristics suggest that strain UST050418-085T represents a novel species within the genus Gillisia. The name Gillisia myxillae sp. nov. is proposed, with UST050418-085T (=JCM 13546T=NRRL B-41416T) as the type strain.
-
-
-
Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter
More LessA Gram-negative, pink-coloured, rod-shaped, non-flagellated bacterium, designated CL-GP80T, was isolated from a hypertrophic pond located within the campus of Seoul National University, Korea. Analysis of its 16S rRNA gene sequence revealed that strain CL-GP80T belongs to the family Sphingobacteriaceae and is closely related to Pedobacter heparinus ATCC 13125T (95.8 % sequence similarity) and to other members of the genus Pedobacter (90.8–95.3 % similarity). Temperature and pH ranges for growth were 5–33 °C and pH 6–8, respectively. The DNA G+C content was 41.3 mol%. The major fatty acids were iso-C15 : 0 (37.0 %), iso-C15 : 0 2-OH and/or C16 : 1 ω7c (24.5 %), and iso-C17 : 0 3-OH (11.3 %). Phenotypic, chemotaxonomic and phylogenetic analyses indicated that strain CL-GP80T could be assigned to the genus Pedobacter, but distinguished from recognized species of the genus. Strain CL-GP80T (=KCCM 42272T=JCM 13399T) is therefore proposed as the type strain of a novel species, for which the name Pedobacter roseus sp. nov. is proposed.
-
-
-
Pedobacter aquatilis sp. nov., isolated from drinking water, and emended description of the genus Pedobacter
More LessA Gram-negative, rod-shaped, non-spore-forming bacterium (strain AR107T) was isolated from the drinking water distribution system of Seville (Spain). A polyphasic taxonomic study of the isolate resulted in its identification as a member of the genus Pedobacter. On the basis of 16S rRNA gene sequence comparisons, strain AR107T was shown to belong to the phylum Bacteroidetes, being related to members of the genus Pedobacter. It showed 95.2 % sequence similarity with respect to the type strains of Pedobacter heparinus and Pedobacter piscium, and 94.1 % similarity with respect to the type strain of Pedobacter himalayensis. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c), which supports the affiliation of strain AR107T to the genus Pedobacter. The DNA G+C content of this strain was 38 mol%. On the basis of the phenotypic, phylogenetic and genotypic results, strain AR107T represents a novel species, for which the name Pedobacter aquatilis sp. nov. is proposed. The type strain is AR107T (=CCM 7347T=CECT 7114T=JCM 13454T).
-
-
-
Balneola vulgaris gen. nov., sp. nov., a member of the phylum Bacteroidetes from the north-western Mediterranean Sea
More LessA novel aerobic, Gram-negative bacterium, named 13IX/A01/164T, was isolated from surface waters in the coastal north-western Mediterranean Sea. Cells were motile, straight rods, 2.5 μm long and 0.2 μm wide, and formed orange colonies on marine agar medium. The G+C content of the genomic DNA of strain 13IX/A01/164T was 42 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the phylum Bacteroidetes within the family Crenotrichaceae. On the basis of 16S rRNA gene sequence comparison and physiological and biochemical characteristics, this isolate represents a novel species of a new genus, for which the name Balneola vulgaris gen. nov., sp. nov. is proposed. The type strain of Balneola vulgaris is 13IX/A01/164T (=DSM 17893T=CIP 109092T=OOB 256T).
-
-
-
Myroides pelagicus sp. nov., isolated from seawater in Thailand
More LessAn aerobic, Gram-negative, non-motile, yellow-to-orange pigmented and rod-shaped bacterium, designated strain SM1T, was isolated from seawater in Thailand and subjected to a polyphasic taxonomic study. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the novel isolate shared 93–95 % sequence similarity with species of the genus Myroides. The DNA–DNA relatedness values of strain SM1T with Myroides odoratimimus JCM 7460T and Myroides odoratus JCM 7458T were below 70 %. The DNA G+C content of strain SM1T was 33.6 mol%, the major menaquinone was MK-6 and the major fatty acids were C15 : 0 iso, C17 : 1 ω9c iso and C17 : 0 iso 3-OH. Based on its phenotypic and chemotaxonomic characteristics, strain SM1T was classified as representing a novel species of the genus Myroides, for which the name Myroides pelagicus sp. nov. is proposed. The type strain is SM1T (=IAM 15337T=KCTC 12661T).
-
-
-
Dyadobacter ginsengisoli sp. nov., isolated from soil of a ginseng field
More LessA Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterium, strain Gsoil 043T, was isolated from soil from a ginseng field in Pocheon province, South Korea. The novel isolate was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 043T was shown to belong to the family ‘Flexibacteraceae’ and was related to Dyadobacter fermentans (96.7 %), Dyadobacter crusticola (96.3 %) and Dyadobacter hamtensis (95.8 %). The 16S rRNA gene sequence similarity of the novel strain to other recognized species within the family ‘Flexibacteraceae’ was less than 87.0 %. The G+C content of genomic DNA was 48 mol%. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, C16 : 1 ω7c, iso-C15 : 0 and C16 : 0) supported the affiliation of strain Gsoil 043T to the genus Dyadobacter. The results of physiological and biochemical tests enabled strain Gsoil 043T to be differentiated genotypically and phenotypically from the three Dyadobacter species with validly published names. The novel isolate therefore represents a novel species for which the name Dyadobacter ginsengisoli sp. nov. is proposed, with the type strain Gsoil 043T (=KCTC 12589T=LMG 23409T).
-
-
-
Alistipes onderdonkii sp. nov. and Alistipes shahii sp. nov., of human origin
More LessTwo groups of previously unknown Gram-negative, strictly anaerobic, pigment-producing, rod-shaped bacteria, which phenotypically and phylogenetically displayed a close association with the recently described species Alistipes finegoldii, were characterized using phenotypic and molecular taxonomic methods. A 16S rRNA gene sequence divergence of approximately 3 % between the two unknown bacteria and A. finegoldii, as well as distinguishable biochemical characteristics, demonstrates that these organisms are genotypically and phenotypically distinct and that each group represents a previously unknown subline within the genus Alistipes. Chromosomal DNA–DNA reassociation studies further confirmed the separateness of the unidentified bacteria and A. finegoldii. On the basis of the phenotypic and phylogenetic findings, two novel species, Alistipes onderdonkii sp. nov. and Alistipes shahii sp. nov., are proposed. The type strains of A. onderdonkii and A. shahii are WAL 8169T (=CCUG 48946T=ATCC BAA-1178T) and WAL 8301T (=CCUG 48947T=ATCC BAA-1179T), respectively; their DNA G+C contents are 58 and 56 mol%, respectively.
-
- Proteobacteria
-
-
Sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. and emended description of the genus Sulfurimonas
A novel mesophilic bacterium, strain GO25T, was isolated from a nest of hydrothermal vent polychaetes, Paralvinella sp., at the Iheya North field in the Mid-Okinawa Trough. Cells were motile short rods with a single polar flagellum. Growth was observed between 4 and 35 °C (optimum 30 °C; 13–16 h doubling time) and between pH 5.4 and 8.6 (optimum pH 6.1). The isolate was a facultatively anaerobic chemolithoautotroph capable of growth using molecular hydrogen, elemental sulfur or thiosulfate as the sole energy source, carbon dioxide as the sole carbon source, ammonium or nitrate as the sole nitrogen source and elemental sulfur, thiosulfate or yeast extract as the sole sulfur source. Strain GO25T represents the first deep-sea epsilonproteobacterium capable of growth by both hydrogen and sulfur oxidation. Nitrate or molecular oxygen (up to 10 % partial pressure) could serve as the sole electron acceptor to support growth. Metabolic products of nitrate reduction shifted in response to the electron donor provided. The G+C content of genomic DNA was 37.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate belonged to the genus Sulfurimonas and was most closely related to Sulfurimonas autotrophica OK10T (96.3 % sequence similarity). DNA–DNA hybridization demonstrated that the novel isolate could be differentiated genotypically from Sulfurimonas autotrophica OK10T. On the basis of the physiological and molecular properties of the novel isolate, the name Sulfurimonas paralvinellae sp. nov. is proposed, with strain GO25T (=JCM 13212T=DSM 17229T) as the type strain. Thiomicrospira denitrificans DSM 1251T (=ATCC 33889T) is phylogenetically associated with Sulfurimonas autotrophica OK10T and Sulfurimonas paralvinellae GO25T. Based on the phylogenetic relationship between Thiomicrospira denitrificans DSM 1251T, Sulfurimonas autotrophica OK10T and Sulfurimonas paralvinellae GO25T, we propose the reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. (type strain DSM 1251T=ATCC 33889T). In addition, an emended description of the genus Sulfurimonas is proposed.
-
-
-
Rhodanobacter spathiphylli sp. nov., a gammaproteobacterium isolated from the roots of Spathiphyllum plants grown in a compost-amended potting mix
Three Gram-negative, yellow-pigmented strains were isolated from the rhizospheres of Spathiphyllum plants grown in a compost-amended potting mix. The strains showed biological control activity towards the root-rot plant pathogen Cylindrocladium spathiphylli, and were characterized to determine their taxonomic position. Cells of the strains were non-motile rods, and the strains were oxidase- and catalase-positive and unable to ferment most sugars tested. The three strains showed differences in growth temperature range, optimal growth temperature and some biochemical reactions. The majority of the fatty acids were branched, and large amounts of 15 : 0 iso and 17 : 1 iso ω9c were present. The 16S rRNA gene sequence (1497 bp) of strain B39T showed the highest level of similarity (98.5 %) to that of Rhodanobacter fulvus IAM 15025T, followed by Rhodanobacter lindaniclasticus LMG 18385T (96.0 %; strain no longer extant), Dyella koreensis CCUG 50883T (96.4 %), Dyella japonica DSM 16301T (96.3 %), Frateuria aurantia LMG 1558T (96.2 %) and Fulvimonas soli LMG 19981T (95.9 %). Less than 90 % 16S rRNA gene sequence similarity was observed for other members of the Gammaproteobacteria. The mean DNA–DNA reassociation value for the three strains was 100 % and was 25 % when the strains were compared with DNA from R. fulvus LMG 23003T. The strains had a mean DNA G+C content of 67.6 mol%. On the basis of their phylogenetic, genomic and phenotypic properties, the three strains represent a novel species within the genus Rhodanobacter, for which the name Rhodanobacter spathiphylli sp. nov. is proposed. The type strain is strain B39T (=LMG 23181T=DSM 17631T).
-
-
-
Chitinimonas koreensis sp. nov., isolated from greenhouse soil in Korea
Strain R2A43-10T was isolated from a greenhouse soil in Korea. Cells were Gram-negative rods, motile by means of a single flagellum. Growth occurred at 10–40 °C and at pH 5–8. Ubiquinone-8 (Q-8) was the only respiratory lipoquinone. Major fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. 16S rRNA gene sequence analysis revealed that strain R2A43-10T was closely related to Chitinimonas taiwanensis cfT (sequence similarity of 94.8 %), but it exhibited low sequence similarities (<92 %) to other members of the Betaproteobacteria. The G+C content of the genomic DNA of strain R2A43-10T was 65.0 mol%. The novel isolate could be differentiated from C. taiwanensis cfT by several physiological properties. On the basis of genomic and phenotypic data, it is concluded that R2A43-10T (=KACC 11467T=DSM 17726T) is the type strain of a novel species of the genus Chitinimonas, for which the name Chitinimonas koreensis sp. nov. is proposed.
-
-
-
Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium
An arsenite-oxidizing bacterium, designated strain ULPAs1T, was isolated from industrial sludge heavily contaminated with arsenic. Cells of this isolate were Gram-negative, curved rods, motile by means of a polar flagellum. The strain was positive for oxidase and catalase activities, was able to reduce nitrate to nitrite, used acetate, lactate and peptone as organic carbon sources under aerobic conditions and was able to oxidize arsenite (As[III]) to arsenate (As[V]). 16S rRNA gene sequence analysis and the absence of dodecanoic fatty acids suggested that this strain represents a member of the genus Herminiimonas of the family Oxalobacteraceae, order Burkholderiales in the Betaproteobacteria. Genomic DNA–DNA hybridization between strain ULPAs1T and Herminiimonas fonticola S-94T and between strain ULPAs1T and Herminiimonas aquatilis CCUG 36956T revealed levels of relatedness of <10 %, well below the recommended 70 % species cut-off value. Thus, strain ULPAs1T (=CCM 7303T=DSM 17148T=LMG 22961T) is the type strain of a novel species of Herminiimonas, for which the name Herminiimonas arsenicoxydans sp. nov. is proposed.
-
-
-
Classification of Centers for Disease Control Group Eugonic Fermenter (EF)-4a and EF-4b as Neisseria animaloris sp. nov. and Neisseria zoodegmatis sp. nov., respectively
More LessA polyphasic taxonomic study was performed on isolates classified as Centers for Disease Control Group Eugonic Fermenter (EF)-4a and EF-4b. Comparative 16S rRNA gene sequence analysis confirmed that group EF-4a and EF-4b belong to the genus Neisseria with Neisseria canis and Neisseria dentiae as the nearest phylogenetic neighbours. DNA–DNA hybridizations and biochemical analyses demonstrated that isolates of group EF-4a and EF-4b represent two novel species within this sublineage of the genus Neisseria. Based on the results of the present study, isolates of group EF-4a and EF-4b are classified as Neisseria animaloris sp. nov. (type strain LMG 23011T=NCTC 12228T) and Neisseria zoodegmatis sp. nov. (type strain LMG 23012T=NCTC 12230T), respectively.
-
-
-
Description of Pseudochrobactrum gen. nov., with the two species Pseudochrobactrum asaccharolyticum sp. nov. and Pseudochrobactrum saccharolyticum sp. nov.
Two Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacteria (CCUG 46016T and CCUG 33852T), isolated from a knee aspirate of a 66-year-old man and an industrial glue, respectively, were studied for their taxonomic position. On the basis of chemotaxonomic data [i.e. major ubiquinone (Q-10), major polar lipids (phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine) and major fatty acids (C18 : 1 ω7c and C19 : 0 cyclo ω8c)] and 16S rRNA gene sequence similarity, both strains belong to the Alphaproteobacteria. The presence of spermidine and putrescine as the predominant polyamines in CCUG 46016T were in agreement with its phylogenetic affiliation in the vicinity of the genus Ochrobactrum. 16S rRNA gene sequence similarities between both strains and established species within the genera Bartonella, Ochrobactrum and Brucella were less than 95 %. Although both organisms showed highest 16S rRNA gene sequence similarity to members of Brucella, phenotypic features (including chemotaxonomic features) were more like those of members of the genus Ochrobactrum. Sequence comparison of the recA genes confirmed the separate phylogenetic position of the two strains. On the basis of DNA–DNA pairing results and physiological and biochemical data, the two strains can be clearly differentiated from each other and from all known Ochrobactrum species. It is evident that these organisms represent two novel species in a new genus, Pseudochrobactrum gen. nov., for which the names Pseudochrobactrum asaccharolyticum sp. nov. (the type species, type strain CCUG 46016T=CIP 108977T) and Pseudochrobactrum saccharolyticum sp. nov. (type strain CCUG 33852T=CIP 108976T) are proposed.
-
-
-
Burkholderia mimosarum sp. nov., isolated from root nodules of Mimosa spp. from Taiwan and South America
Fourteen strains were isolated from nitrogen-fixing nodules on the roots of plants of the genus Mimosa growing in Taiwan, Brazil and Venezuela. On the basis of 16S rRNA gene sequence similarities, all of the strains were previously shown to be closely related to each other and to belong to the genus Burkholderia. A polyphasic approach, including DNA–DNA reassociation, whole-cell protein analysis, fatty acid methyl ester analysis and extensive biochemical characterization, was used to clarify the taxonomic position of these strains: all 14 strains were classified as representing a novel species, for which the name Burkholderia mimosarum sp. nov. is proposed. The type strain, PAS44T (=LMG 23256T =BCRC 17516T), was isolated from Mimosa pigra nodules in Taiwan.
-
-
-
Meganema perideroedes gen. nov., sp. nov., a filamentous alphaproteobacterium from activated sludge
More LessAn industrial wastewater treatment plant at Grindsted, Denmark, has suffered from bulking problems for several years caused by filamentous bacteria. Five strains were isolated from the sludge by micromanipulation. Phylogenetic analysis of the 16S rRNA gene sequences showed that the strains formed a monophyletic cluster in the Alphaproteobacteria, and they were phenotypically different from their closest relatives and from all hitherto known filamentous bacteria described (closest relative Brevundimonas vesicularis ATCC 11426T, 89.8 % sequence similarity). In pure culture, the cells (1.5–2.0 μm) in filaments are Gram-negative and contain polyphosphate and polyhydroxyalkanoates. The optimum temperature for growth is 30 °C and the strains grow in 2 % NaCl and are oxidase- and catalase-positive. Ubiquinone 10 is the major quinone. The major fatty acid (C18 : 1 ω7c) and smaller amounts of unsaturated fatty acids, 3-hydroxy fatty acids with a chain length of 16 and 18 carbon atoms and small amounts of 10-methyl-branched fatty acids with 18 carbon atoms (C19 : 0 10-methyl) affiliated the strains with the Methylobacterium/Xanthobacter group in the Alphaproteobacteria. The G+C content of the DNA is 42.9 mol% (for strain Gr1T). The two most dissimilar isolates by 16S rRNA gene comparison (Gr1T and Gr10; 97.7 % identical) showed 71.5 % DNA–DNA relatedness. Oligonucleotide probes specific for the pure cultures were designed for fluorescence in situ hybridization and demonstrated that two filamentous morphotypes were present in the Grindsted wastewater treatment plant. It is proposed that the isolates represent a new genus and species, Meganema perideroedes gen. nov., sp. nov. The type strain of Meganema perideroedes is strain Gr1T (=DSM 15528T=ATCC BAA-740T).
-
-
-
Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm
More LessA rod-shaped marine bacterium, CL-TA03T, isolated from a biofilm in a coastal fish farm in Tongyeong, Korea, was characterized for physiological and biochemical features, fatty acid profile and phylogenetic position based on 16S rRNA gene sequences. Analysis of the 16S rRNA gene sequence revealed a clear affiliation with the family Rhodobacteraceae. Phylogenetic analysis of the 16S rRNA gene sequence showed that the closest relatives of CL-TA03T were Thalassobius gelatinovorus and Thalassobius mediterraneus (95.6 % similarity). The sequence similarities between CL-TA03T and other type species of the Roseobacter lineage ranged from 92.4 to 95.4 %. Strain CL-TA03T is motile and grows on marine agar as colourless or beige colonies. The strain is able to grow optimally in the range of 3–5 % sea salts. It grows within a temperature range of 15–35 °C and at pH 6–10. The fatty acids are dominated by 18 : 1ω7c (64.1 %) and 11-methyl 18 : 1ω7c (10.6 %). The DNA G+C content is 57.2 mol%. According to physiological data, fatty acid composition and phylogenetic analysis of the 16S rRNA gene sequence, CL-TA03T is considered to represent a new genus in the family Rhodobacteraceae and the name Shimia marina gen. nov., sp. nov. is proposed. The type strain of Shimia marina is CL-TA03T (=KCCM 42117T=JCM 13038T).
-
-
-
Pseudomonas peli sp. nov. and Pseudomonas borbori sp. nov., isolated from a nitrifying inoculum
More LessSixteen Gram-negative, rod-shaped, non-spore-forming isolates were obtained from a nitrifying inoculum. Analysis of repetitive sequence-based PCR and SDS-PAGE banding patterns, 16S rRNA gene sequence analysis and DNA–DNA hybridizations showed that the isolates belonged to various groups within the genus Pseudomonas. One group of isolates could be assigned to Pseudomonas migulae and a second to Pseudomonas veronii. Two groups could be differentiated genotypically from each other and from all other currently known Pseudomonas species. Analysis of the fatty acid composition and physiological and biochemical tests allowed differentiation of these groups from their closest phylogenetic neighbours and they therefore represent two novel species within the genus Pseudomonas, for which the names Pseudomonas peli sp. nov. and Pseudomonas borbori sp. nov. are proposed, with strains LMG 23201T (=DSM 17833T=R-20805T) and LMG 23199T (=DSM 17834T=R-20821T), respectively, as the type strains.
-
-
-
Novel nitrogen-fixing Acetobacter nitrogenifigens sp. nov., isolated from Kombucha tea
More LessThe four nitrogen-fixing bacteria so far described in the family Acetobacteraceae belong to the genera Gluconacetobacter and Acetobacter. Nitrogen-fixing bacterial strain RG1T was isolated from Kombucha tea and, based on the phylogenetic analysis of 16S rRNA gene sequence which is supported by a high bootstrap value, was found to belong to the genus Acetobacter. Strain RG1T differed from Acetobacter aceti, the nearest member with a 16S rRNA gene sequence similarity of 98.2 %, and type strains of other Acetobacter species with regard to several characteristics of growth features in culture media, growth in nitrogen-free medium, production of γ-pyrone from glucose and dihydroxyacetone from glycerol. Strain RG1T utilized maltose, glycerol, sorbitol, fructose, galactose, arabinose and ethanol, but not methanol as a carbon source. These results, along with electrophoretic mobility patterns of nine metabolic enzymes, suggest that strain RG1T represents a novel nitrogen-fixing species. The ubiquinone present was Q-9 and DNA G+C content was 64.1 mol%. Strain RG1T exhibited a low value of 2–24 % DNA–DNA relatedness to the type strains of related acetobacters, which placed it as a separate taxon. On the basis of this data, the name Acetobacter nitrogenifigens sp. nov. is proposed, with the type strain RG1T (=MTCC 6912T=LMG 23498T).
-
-
-
Aeromonas sharmana sp. nov., isolated from a warm spring
More LessA Gram-negative, facultatively anaerobic bacterial strain designated GPTSA-6T was isolated from a water sample collected from a warm spring in Assam, India. Preliminary analysis of the 16S rRNA gene sequence of this isolate revealed its affiliation to the family Aeromonadaceae. Detailed characterization using a polyphasic approach indicated that strain GPTSA-6T is most closely related to Aeromonas sobria but differs significantly from existing members of the genus Aeromonas. Analysis of the almost-complete (1430 nt) 16S rRNA gene sequence of this strain revealed that its closest relative (99.23 % similarity) is an uncultured bacterial clone, A-8, isolated from an algal bloom. Of the taxa with validly published names, Aeromonas sobria ATCC 43979T showed the highest level of sequence similarity (95.13 %) with respect to strain GPTSA-6T, followed by Aeromonas molluscorum 848TT and Aeromonas popoffii LMG 17541T (95.04 % similarity in both cases). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, it can be concluded that strain GPTSA-6T represents a novel species of the genus Aeromonas, for which the name Aeromonas sharmana sp. nov. is proposed. The type strain is GPTSA-6T (=MTCC 7090T=DSM 17445T).
-
-
-
Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean
A novel marine bacterial strain, PV-4T, isolated from a microbial mat located at a hydrothermal vent of Loihi Seamount in the Pacific Ocean, has been characterized. This micro-organism is orangey in colour, Gram-negative, polarly flagellated, facultatively anaerobic and psychrotolerant (temperature range, 0–42 °C). No growth was observed with nitrate, nitrite, DMSO or thiosulfate as the electron acceptor and lactate as the electron donor. The major fatty acid detected in strain PV-4T was iso-C15 : 0. Strain PV-4T had ubiquinones consisting mainly of Q-7 and Q-8, and possessed menaquinone MK-7. The DNA G+C content of the strain was 53.8 mol% and the genome size was about 4.5 Mbp. Phylogenetic analyses based on 16S rRNA gene sequences placed PV-4T within the genus Shewanella. PV-4T exhibited 16S rRNA gene sequence similarity levels of 99.6 and 97.5 %, respectively, with respect to the type strains of Shewanella aquimarina and Shewanella marisflavi. DNA from strain PV-4T showed low mean levels of relatedness to the DNAs of S. aquimarina (50.5 %) and S. marisflavi (8.5 %). On the basis of phylogenetic and phenotypic characteristics, the bacterium was classified in the genus Shewanella within a distinct novel species, for which the name Shewanella loihica sp. nov. is proposed. The type strain is PV-4T (=ATCC BAA-1088T=DSM 17748T).
-
-
-
Sulfurivirga caldicuralii gen. nov., sp. nov., a novel microaerobic, thermophilic, thiosulfate-oxidizing chemolithoautotroph, isolated from a shallow marine hydrothermal system occurring in a coral reef, Japan
Novel thermophilic bacteria, designated strains VW1 and MM1T, were isolated from hydrothermal fluid and microbial mat samples, respectively, collected from a shallow marine hydrothermal system (water depth 22 m) occurring in coral reefs off Taketomi Island, Okinawa, Japan. Cells of the two novel strains were motile rods with a single polar flagellum in the exponential growth phase. In a medium that included elemental sulfur, cells of the two strains became non-motile with oval to spherical cell shapes. For both strains, growth occurred at between 30 and 60 °C (optimum temperature of 50–55 °C; 60–80 min doubling time) and between pH 5.5 and 7.1 (optimum pH 6.0). The isolates were microaerobic chemolithoautotrophs capable of using thiosulfate or tetrathionate as the sole energy source, O2 as the sole electron acceptor and CO2 as the sole carbon source. Organic substrates, such as yeast extract and tryptone, inhibited growth of both strains. The G+C contents of genomic DNA were 51.3 and 49.5 mol% for strains VW1 and MM1T, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains were closely related to each other (99.9 % sequence similarity) and were distantly related to other previously described genera within the Gammaproteobacteria. The novel isolates could also be differentiated from other gammaproteobacterial genera on the basis of their physiological properties. It is suggested that the novel isolates represent the type species of a new genus, for which the name Sulfurivirga caldicuralii gen. nov., sp. nov. (type strain MM1T=JCM 13439T=DSM 17737T) is proposed.
-
-
-
Burkholderia silvatlantica sp. nov., a diazotrophic bacterium associated with sugar cane and maize
In a previous study, nitrogen-fixing isolates were recovered from the rhizosphere of maize and from surface-sterilized leaves of sugar cane cultivated in Rio de Janeiro, Brazil. On the basis of 16S rRNA gene sequence similarities, these isolates were identified as belonging to the genus Burkholderia, and whole-cell-protein profiles demonstrated that they are closely related to each other. In the present study, novel isolates were recovered from the roots of different sugar-cane varieties cultivated in diverse geographical regions of Brazil. Twenty-one nitrogen-fixing isolates were analysed using polyphasic taxonomy criteria, including DNA–DNA relatedness, 16S rRNA gene sequence similarities, fatty acid profiles, whole-cell-protein patterns and multilocus enzyme electrophoresis profiles, as well as morphological, physiological and biochemical characterization. The analysis confirmed that these isolates belong to a novel species within the genus Burkholderia, for which the name Burkholderia silvatlantica sp. nov. is proposed. The type strain, SRMrh-20T (=LMG 23149T=ATCC BAA-1244T), was isolated from the rhizosphere of maize var. Avantis A2345 cultivated in Seropédica, Rio de Janeiro.
-
-
-
Thiorhodococcus mannitoliphagus sp. nov., a purple sulfur bacterium from the White Sea
More LessA novel purple sulfur bacterium, strain WST, was isolated from a microbial mat from an estuary of the White Sea. Individual cells are coccoid shaped, motile by flagella and do not contain gas vesicles. The mean cell diameter is 1.85 μm (range 1.5–2.0 μm). Cell suspensions exhibit a purple–violet colour. They contain bacteriochlorophyll a and carotenoids of the rhodopinal series as photosynthetic pigments. The novel bacterium is an anoxygenic photoautotroph, using sulfide, thiosulfate, sulfite and elemental sulfur as electron donors for photosynthesis and is capable of photoassimilating several organic carbon sources in the presence of carbonate and a reduced sulfur source (sulfide and/or thiosulfate). Sulfur globules, formed during oxidation of sulfide, are stored transiently inside the cells. Optimal salinity and pH for growth are at 0.5–2.0 % NaCl and pH 7.0–7.5. The DNA base composition of strain WST is 61.8 mol% G+C. 16S rRNA gene sequence analysis showed that the new isolate belongs to the genus Thiorhodococcus, with Thiorhodococcus minor CE2203T as the nearest relative (sequence similarity of 97.3 %). Several distinct differences from described species necessitate the description of a novel species. Thiorhodococcus mannitoliphagus sp. nov. is the proposed name, with strain WST (=ATCC BAA-1228T=VKM B-2393T) as the type strain.
-
-
-
Reclassification of Pseudomonas beijerinckii Hof 1935 as Chromohalobacter beijerinckii comb. nov., and emended description of the species
Pseudomonas beijerinckii (type strain DSM 7218T=ATCC 19372T=NCIMB 9041T) was isolated from salted beans and was first described by Hof in 1935. 16S rRNA gene sequence comparisons demonstrated its close relatedness (>97–99 %) to species of the genus Chromohalobacter. A recent isolate from salted herrings originating from the Baltic Sea, strain 3b, also clustered phylogenetically within this genus. Phenotypic features, substrate utilization, fatty acid profile, quinone and polar lipid composition and whole-cell protein patterns supported the similarity of strain 3b to P. beijerinckii DSM 7218T and confirmed its relatedness to members of the genus Chromohalobacter. The G+C content of the DNA from strain 3b and P. beijerinckii DSM 7218T was 60.4 and 60.7 mol%, respectively. DNA–DNA hybridization data showed that the two strains represent the same species, but are separated from Chromohalobacter canadensis, the closest species from a phylogenetic point of view. Therefore, the reclassification of Pseudomonas beijerinckii as Chromohalobacter beijerinckii comb. nov. (type strain DSM 7218T=ATCC 19372T=NCIMB 9041T) is proposed. The species description has been emended considering the new data on both the type strain and strain 3b.
-
-
-
Hoeflea alexandrii sp. nov., isolated from the toxic dinoflagellate Alexandrium minutum AL1V
More LessA Gram-negative, aerobic, non-symbiotic bacterium (AM1V30T) was isolated from the toxic dinoflagellate Alexandrium minutum AL1V. On the basis of 16S rRNA gene sequence similarity, strain AM1V30T was most closely related (97.4 % similarity) to the type strain of Hoeflea marina, which belongs to the family Phyllobacteriaceae within the order Rhizobiales of the class Alphaproteobacteria. A polyphasic approach was used to clarify the taxonomic position of strain AM1V30T. During the course of this study, a second species was described by others as belonging to the genus Hoeflea, namely Hoeflea phototrophica; it showed a somewhat higher level of 16S rRNA gene sequence similarity with respect to strain AM1V30T (98.2 %) and was also taken into account. The fatty acid profiles, physiological and biochemical data and DNA G+C content (59.7 mol%) support the classification of strain AM1V30T as a member of the genus Hoeflea. The characteristics of the novel strain were sufficiently distinct to indicate that it represents a separate species. To confirm this conclusion, DNA–DNA hybridizations were performed: low values (between 15.8 and 29.8 %) were obtained in all cases. Thus, AM1V30T represents a novel species within the genus Hoeflea, for which the name Hoeflea alexandrii sp. nov. is proposed. Strain AM1V30T (=CECT 5682T=DSM 16655T) is the type strain.
-
- Eukaryotic Micro-Organisms
-
-
Molecular-genetic diversity of the ascomycetous yeast genus Arthroascus: Arthroascus babjevae sp. nov., Arthroascus fermentans var. arxii var. nov. and geographical populations of Arthroascus schoenii
More LessUsing molecular and genetic analyses, 28 Arthroascus strains were analysed, isolated from widely different geographical localities in Europe, North America, Far-East Asia and Hawaii. Most of the strains have been assigned to the species Arthroascus schoenii. PCR-RAPD revealed two Japanese Arthroascus strains (UCD 67-278 and IFO 10138) to have peculiar patterns. Comparative rDNA (D1/D2 26S, ITS1 and ITS2) sequence analysis showed that the two strains respectively represent a novel species and a novel variety. Based on the results of sequence analysis, genetic hybridization and DNA–DNA reassociation, two new members of the genus Arthroascus are formally described, Arthroascus babjevae sp. nov. (type strain UCD 67-278T=CBS 9167T) and Arthroascus fermentans var. arxii var. nov. (type strain IFO 10138T=CBS 9168T). These results show that A. schoenii has a worldwide distribution, while the species Arthroascus javanensis is represented only by the type culture CBS 2555T, isolated in Indonesia. Cluster analysis revealed a correlation between PCR-RAPD fingerprints and geographical origin of the A. schoenii strains. Despite this molecular differentiation, A. schoenii strains collected in different regions of the world formed predominantly fertile hybrids, with normal recombination of control markers.
-
-
-
Lipomyces orientalis sp. nov., a yeast species isolated from soil in Vietnam
More LessFive strains of the novel ascogenous yeast species Lipomyces orientalis sp. nov. were isolated from soil samples collected in Vietnam. The yeast forms asci containing one to four ascospores. The ascospores of L. orientalis have warty surfaces and differ from the characteristic striated ascospores of Lipomyces tetrasporus. Phylogenetic analyses of D1/D2 26S rDNA and ITS sequences indicate that L. orientalis and L. tetrasporus are closely related, but they differ from each other by 6 nucleotides in the D1/D2 region and 16 nucleotides in the ITS region. The type culture is strain Lip 95T (=CBS 10300T=NRRL Y-27927T).
-
-
-
Candida floccosa sp. nov., a novel methanol-assimilating yeast species
More LessTwo methanol-assimilating yeast strains were isolated from a flux of a sessile oak (Quercus petrea) in Hungary and one genetically and phenotypically very similar strain from a flux of a red oak (Quercus rubra) in Canada. The strains exhibited ascomycetous affinity but ascospore formation was not observed. On the basis of the sequence of their D1/D2 domain of the large subunit rDNA, as well as of their physiological characteristics, they represent a novel yeast species of the genus Candida. Therefore Candida floccosa sp. nov. is proposed, with NCAIM Y.01581T (=CBS 10307T=NRRL Y-27951T) as the type strain.
-
- Other Gram-Positive Bacteria
-
-
Lactobacillus durianis Leisner et al. 2002 is a later heterotypic synonym of Lactobacillus vaccinostercus Kozaki and Okada 1983
The taxonomic status of the species Lactobacillus durianis and Lactobacillus vaccinostercus is briefly summarized and experimental evidence concerning their similarity is presented. Highly similar 16S rRNA gene sequences (99.8 % similarity over 1523 bp), partial recA gene sequences (99.5 % similarity over 600 bp) and partial hsp60 gene sequences (99.1 % similarity over 924 bp) suggest that the two species are closely related. Moreover, a high DNA–DNA binding level (87 %) and similar genomic DNA G+C contents (41–44 mol% for both species) as well as similar biochemical characteristics support the evidence that they constitute a single species. Consequently, according to Rules 38 and 42 of the Bacteriological Code, the name Lactobacillus vaccinostercus, the oldest legitimate name, must be maintained and the name Lactobacillus durianis should be considered a later heterotypic synonym.
-
-
-
Bacillus safensis sp. nov., isolated from spacecraft and assembly-facility surfaces
More LessThirteen strains of a novel spore-forming, Gram-positive, mesophilic heterotrophic bacterium were isolated from spacecraft surfaces (Mars Odyssey Orbiter) and assembly-facility surfaces at the Jet Propulsion Laboratory in California and the Kennedy Space Center in Florida. Phylogenetic analysis of 16S rRNA gene sequences has placed these novel isolates within the genus Bacillus, the greatest sequence similarity (99.9 %) being found with Bacillus pumilus. However, these isolates share a mere 91.2 % gyrB sequence similarity with Bacillus pumilus, rendering their 16S rRNA gene-derived relatedness suspect. Furthermore, DNA–DNA hybridization showed only 54–66 % DNA relatedness between the novel isolates and strains of B. pumilus. rep-PCR fingerprinting and previously reported matrix-assisted laser desorption/ionization time-of-flight mass spectrometry protein profiling clearly distinguished these isolates from B. pumilus. Phenotypic analyses also showed some differentiation between the two genotypic groups, although the fatty acid compositions were almost identical. The polyphasic taxonomic studies revealed distinct clustering of the tested strains into two distinct species. On the basis of phenotypic characteristics and the results of phylogenetic analyses of 16S rRNA and gyrB gene sequences, repetitive element primer-PCR fingerprinting and DNA–DNA hybridization, the 13 isolates represent a novel species of the genus Bacillus, for which the name Bacillus safensis sp. nov. is proposed. The type strain is FO-36bT (=ATCC BAA-1126T=NBRC 100820T).
-
-
-
Paucisalibacillus globulus gen. nov., sp. nov., a Gram-positive bacterium isolated from potting soil
More LessA Gram-positive bacterium, designated B22T, was isolated from potting soil produced in Portugal. This organism is a catalase-positive, oxidase-negative, motile, spore-forming, aerobic rod that grows optimally at 37 °C and pH 8.0–8.5. Optimal growth occurs in media containing 1 % (w/v) NaCl, although the organism can grow in 0–8 % NaCl. The cell wall peptidoglycan is of the A4α type with a cross-linkage containing d-Asp. The major respiratory quinone is menaquinone 7 and the major fatty acids are anteiso-15 : 0, anteiso-17 : 0 and iso-15 : 0. The DNA G+C content is 37.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain B22T formed a new branch within the family Bacillaceae. The novel isolate is phylogenetically closely related to members of genera of moderately halophilic bacilli and formed a coherent cluster with species of the genera Salinibacillus, Virgibacillus, Oceanobacillus and Lentibacillus, supported by bootstrap analysis at a confidence level of 71 %. Strain B22T exhibited 16S rRNA gene pairwise sequence similarity values of 94.7–94.3 % with members of the genus Salinibacillus, 95.1–92.8 % with members of the genus Virgibacillus, 94.7–93.2 % with members of the genus Oceanobacillus and 93.1–92.3 % with members of the genus Lentibacillus. On the basis of phylogenetic analysis and physiological and biochemical characteristics, it is proposed that strain B22T represents a novel species in a new genus, Paucisalibacillus globulus gen. nov., sp. nov. Strain B22T (=LMG 23148T=CIP 108857T) is the type strain of Paucisalibacillus globulus.
-
-
-
Lentibacillus halophilus sp. nov., from fish sauce in Thailand
More LessFifteen strains of extremely halophilic bacteria were isolated from fish sauce (nam-pla) collected in Thailand at various stages of the fish-fermentation process. The isolates were strictly aerobic, spore-forming, Gram-positive rods. They grew optimally in the presence of 20–26 % NaCl. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. Polar lipid analysis revealed the presence of phosphatidylglycerol, diphosphatidylglycerol and two unidentified glycolipids. The DNA G+C content was 42.1–43.1 mol%. On the basis of the 16S rRNA gene sequence, a representative strain, PS11-2T, was found to be closely related to Lentibacillus juripiscarius JCM 12147T (97.3 % similarity). The 15 strains were included in the same species on the basis that the levels of DNA–DNA relatedness with strain PS11-2T were greater than 70 %. They could be distinguished from L. juripiscarius and other Lentibacillus species on the basis of several phenotypic characteristics and low levels of DNA–DNA relatedness (⩽19.4 %). Therefore, the strains represent a novel species of the genus Lentibacillus, for which the name Lentibacillus halophilus sp. nov. is proposed. The type strain is PS11-2T (=JCM 12149T=TISTR 1549T=PCU 240T).
-
-
-
Bacillus seohaeanensis sp. nov., a halotolerant bacterium that contains l-lysine in its cell wall
More LessA halotolerant, round-endospore-forming, aerobic, Gram-positive bacterium, designated BH724T, was isolated from a solar saltern at Taean in Korea. Cells of this strain were rod-shaped and found to be non-motile. Strain BH724T grew at salinities of 0–10 % (w/v) NaCl with an optimum of 3 % (w/v) NaCl and at temperatures of 15–50 °C with an optimum of 40 °C. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BH724T belonged to the genus Bacillus and that Bacillus aquimaris TF-12T, Bacillus marisflavi TF-11T and Bacillus vietnamensis JCM 11124T were its closest neighbours, sharing 97.3, 97.2 and 97.0 % 16S rRNA gene sequence similarity, respectively. The genomic DNA G+C content was 39 mol% and the predominant menaquinone was MK-7. Its major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and iso-C14 : 0. The peptidoglycan type was A1α, linked directly through l-lysine. On the basis of morphological, chemotaxonomic, physiological and phylogenetic properties, strain BH724T represents a novel species of the genus Bacillus, for which the name Bacillus seohaeanensis sp. nov. is proposed. The type strain is BH724T (=KCTC 3913T=DSM 16464T).
-
- International Committee On Systematics Of Prokaryotes
-
- Minutes
- Errata
-
Volumes and issues
-
Volume 74 (2024)
-
Volume 73 (2023)
-
Volume 72 (2022 - 2023)
-
Volume 71 (2020 - 2021)
-
Volume 70 (2020)
-
Volume 69 (2019)
-
Volume 68 (2018)
-
Volume 67 (2017)
-
Volume 66 (2016)
-
Volume 65 (2015)
-
Volume 64 (2014)
-
Volume 63 (2013)
-
Volume 62 (2012)
-
Volume 61 (2011)
-
Volume 60 (2010)
-
Volume 59 (2009)
-
Volume 58 (2008)
-
Volume 57 (2007)
-
Volume 56 (2006)
-
Volume 55 (2005)
-
Volume 54 (2004)
-
Volume 53 (2003)
-
Volume 52 (2002)
-
Volume 51 (2001)
-
Volume 50 (2000)
-
Volume 49 (1999)
-
Volume 48 (1998)
-
Volume 47 (1997)
-
Volume 46 (1996)
-
Volume 45 (1995)
-
Volume 44 (1994)
-
Volume 43 (1993)
-
Volume 42 (1992)
-
Volume 41 (1991)
-
Volume 40 (1990)
-
Volume 39 (1989)
-
Volume 38 (1988)
-
Volume 37 (1987)
-
Volume 36 (1986)
-
Volume 35 (1985)
-
Volume 34 (1984)
-
Volume 33 (1983)
-
Volume 32 (1982)
-
Volume 31 (1981)
-
Volume 30 (1980)
-
Volume 29 (1979)
-
Volume 28 (1978)
-
Volume 27 (1977)
-
Volume 26 (1976)
-
Volume 25 (1975)
-
Volume 24 (1974)
-
Volume 23 (1973)
-
Volume 22 (1972)
-
Volume 21 (1971)
-
Volume 20 (1970)
-
Volume 19 (1969)
-
Volume 18 (1968)
-
Volume 17 (1967)
-
Volume 16 (1966)
-
Volume 15 (1965)
-
Volume 14 (1964)
-
Volume 13 (1963)
-
Volume 12 (1962)
-
Volume 11 (1961)
-
Volume 10 (1960)
-
Volume 9 (1959)
-
Volume 8 (1958)
-
Volume 7 (1957)
-
Volume 6 (1956)
-
Volume 5 (1955)
-
Volume 4 (1954)
-
Volume 3 (1953)
-
Volume 2 (1952)
-
Volume 1 (1951)