- Volume 58, Issue 12, 2008
Volume 58, Issue 12, 2008
- Notification List
-
-
-
Notification that new names and new combinations have appeared in volume 58, part 9, 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
-
-
Mycetocola reblochoni sp. nov., isolated from the surface microbial flora of Reblochon cheese
Four Gram-positive, aerobic, non-sporulating, rod-shaped bacteria isolated from the surface microflora of Reblochon cheese at the late stage of ripening had chemotaxonomic properties characteristic of members of the family Microbacteriaceae. The isolates had virtually identical SDS-PAGE whole-organism protein patterns, shared many chemical and phenotypic characteristics and formed an independent branch in the Microbacteriaceae 16S rRNA gene tree that was most closely related to the type strains of Mycetocola species. The new isolates had chemotaxonomic properties consistent with their classification in the genus Mycetocola but were readily distinguished from recognized members of this taxon based on DNA–DNA relatedness, whole-organism protein and phenotypic data. The combined genotypic and phenotypic data indicate that the isolates should be classified in the genus Mycetocola as members of a novel species, for which the name Mycetocola reblochoni sp. nov. is proposed. The type strain is LMG 22367T (=R-20377T =BRB-1L41T =DSM 18580T).
-
-
-
Microlunatus panaciterrae sp. nov., a β-glucosidase-producing bacterium isolated from soil in a ginseng field
More LessA novel bacterial strain, designated Gsoil 954T, showing β-glucosidase activity was isolated from a soil sample from a ginseng field in Pocheon Province, South Korea. The isolate was a Gram-positive, aerobic, motile, coccus-shaped, non-endospore-forming bacterium. Comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil 954T belonged to the family Propionibacteriaceae, the highest levels of sequence similarity being found with the type strains of Microlunatus ginsengisoli (96.4 %) and Microlunatus phosphovorus (96.2 %). The strain showed <95.9 % similarity with respect to other species within the family Propionibacteriaceae. In addition, the presence of ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-9(H4) as the major menaquinone and anteiso-C15 : 0 and iso-C15 : 0 as the major cellular fatty acids suggested its affiliation with the genus Microlunatus. The G+C content of the genomic DNA was 65.1 mol%. On the basis of its phenotypic characteristics and phylogenetic distinctiveness, strain Gsoil 954T represents a novel species within the genus Microlunatus, for which the name Microlunatus panaciterrae sp. nov. is proposed. The type strain is Gsoil 954T (=KCTC 13058T=DSM 18662T).
-
-
-
Salinibacterium xinjiangense sp. nov., a psychrophilic bacterium isolated from the China No. 1 glacier
More LessA novel psychrophilic, Gram-positive, yellow-pigmented and aerobic bacterium, strain 0543T, was isolated from the China No. 1 glacier. Strain 0543T was able to grow at 4–23 °C, with optimum growth at 18–19 °C. The major fatty acids were anteiso-C15 : 0 (58.36 %), iso-C16 : 0 (21.13 %), iso-C14 : 0 (10.25 %) and anteiso-C17 : 0 (7.16 %). The genomic DNA G+C content was 63.5 mol% and the major menaquinone was MK-10. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 0543T represented a lineage within the family Microbacteriaceae, with the highest similarity of 97.4 % with Salinibacterium amurskyense KMM 3673T. On the basis of polyphasic, chemotaxonomic, physiological and biochemical evidence from this study, the novel species Salinibacterium xinjiangense sp. nov. is proposed; the type strain is 0543T(=CGMCC 1.5381T =JCM 13926T).
-
-
-
Mycobacterium llatzerense sp. nov., a facultatively autotrophic, hydrogen-oxidizing bacterium isolated from haemodialysis water
More LessSix mycobacterial isolates from haemodialysis water, conforming a homogeneous phylogenetic group in a previous multigenic analysis, were classified taxonomically. Physiological and biochemical characterization, as well as DNA–DNA hybridizations, demonstrated that the isolates were facultatively autotrophic, aerobic and hydrogen-oxidizing bacteria, representing a novel species in the rapid growing Mycobacterium group, for which the name Mycobacterium llatzerense sp. nov. is proposed. The type strain is MG13T (=CECT 7273T=CCUG 54744T).
-
-
-
Streptomyces lunalinharesii sp. nov., a chitinolytic streptomycete isolated from cerrado soil in Brazil
A novel chitinolytic actinomycete isolated from a Brazilian cerrado soil, designated strain RCQ1071T, was assigned to the genus Streptomyces on the basis of chemical and morphological characteristics. The almost-complete nucleotide sequence of the 16S rRNA gene of strain RCQ1071T was determined and also placed this strain in the genus Streptomyces. Phylogenetic analyses of 16S rRNA gene sequences showed that strain RCQ1071T formed a long branch in a group related to Streptomyces albulus, sharing approximately 98 % sequence similarity. Levels of DNA–DNA relatedness between strain RCQ1071T and members of this group, namely S. albulus DSM 40492T, Streptomyces noursei DSM 40635T and Streptomyces yunnanensis DSM 41793T, were 38.3, 27.8 and 46 %, respectively, strongly indicating that strain RCQ1071T was not a member of any of these species. The relatively long branch length within a stable clade together with the phenotypic data strongly supported that strain RCQ1071T represented a novel species. Based on the combination of physiological, phylogenetic and genomic data, strain RCQ1071T is suggested to represent a novel species of the genus Streptomyces, for which the name Streptomyces lunalinharesii sp. nov. is proposed. The type strain is RCQ1071T (=ATCC BAA-1231T =CIP 108852T =DSM 41876T).
-
-
-
Klugiella xanthotipulae gen. nov., sp. nov., a novel member of the family Microbacteriaceae
More LessAn actinobacterium, designated strain 44C3T, was isolated in Michigan, USA, from the hindgut of the larvae of Tipula abdominalis, an aquatic crane fly, and was subjected to a polyphasic taxonomic investigation. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain represented a separate clade within the family Microbacteriaceae. It showed highest 16S rRNA gene sequence similarity with Cryobacterium psychrotolerans 0549T (96.5 %). Strain 44C3T had a novel B-type peptidoglycan. The peptidoglycan contained the diamino acid lysine, the peptide Gly–d-Glu was detected in the partial hydrolysate and alanine was the N terminus of the interpeptide bridge. No other amino acids found in other B-type peptidoglycans (including diaminobutyric acid, ornithine, homoserine and hydroxyglutamic acid) could be detected. The major menaquinones were MK-12 and MK-11, the major fatty acids were ai-C15 : 0, ai-C17 : 0 and i-C16 : 0 and the DNA G+C content was 60.9 mol%. Analysis of the chemotaxonomic and phylogenetic data suggested that strain 44C3T represented a novel species of a new genus within the family Microbacteriaceae, for which the name Klugiella xanthotipulae gen. nov., sp. nov. is proposed. The type strain of Klugiella xanthotipulae is 44C3T (=DSM 18031T =ATCC BAA-1524T).
-
-
-
Taxonomic study of a chromomycin-producing strain and reclassification of Streptomyces cavourensis subsp. washingtonensis as a later synonym of Streptomyces griseus
More LessA chromomycin-producing actinomycete, strain AP19, was isolated from a sample of faeces collected from Foping national nature reserve in China. Chemotaxonomic and morphological properties indicated that the novel isolate was a member of the genus Streptomyces. Phylogenetic analyses based on an almost complete 16S rRNA gene sequence of the strain and on the 120-nt nucleotide variable γ-region of this molecule revealed that it was closely related to Streptomyces griseus ISP 5236T and Streptomyces cavourensis subsp. washingtonensis ATCC 27732T. DNA–DNA relatedness values among these strains were above 70 %. Streptomyces cavourensis subsp. washingtonensis could be readily distinguished from Streptomyces cavourensis ATCC 14889T by differing BOX-PCR fingerprinting patterns, relatively low 16S rRNA gene sequence similarity and a low DNA–DNA relatedness value. It is proposed, therefore, that Streptomyces cavourensis subsp. washingtonensis is a later synonym of Streptomyces griseus.
-
-
-
Reclassification of Streptomyces caeruleus as a synonym of Actinoalloteichus cyanogriseus and reclassification of Streptomyces spheroides and Streptomyces laceyi as later synonyms of Streptomyces niveus
Previous studies have proposed that Streptomyces caeruleus is an earlier heterotypic synonym for Streptomyces niveus and Streptomyces spheroides. In this study, phylogenetic analysis of the almost complete 16S rRNA gene sequences of the Streptomyces caeruleus type strains NBRC 13344T, JCM 4014T and NRRL B-2194T revealed that S. caeruleus was closely related to Actinoalloteichus cyanogriseus and not to S. niveus, S. spheroides or any other species of the genus Streptomyces. Moreover, the diagnostic cell-wall diamino acid was found to be meso-diaminopimelic acid in S. caeruleus and DNA–DNA hybridization studies revealed that S. caeruleus NBRC 13344T was a member of the same species as A. cyanogriseus NBRC 14455T. Based on these chemotaxonomic and phylogenetic data, it is proposed that Streptomyces caeruleus ( Baldacci 1944 ) Pridham et al. 1958 be reclassified as a heterotypic synonym of Actinalloteichus cyanogriseus Tamura et al. 2000 . Furthermore, based on phylogenetic, morphological and MALDI-TOF MS analyses, it is proposed that the species Streptomyces laceyi Manfio et al. 2004 and Streptomyces spheroides Wallick et al. 1956 are reclassified as later heterotypic synonyms of Streptomyces niveus Smith et al. 1956 .
-
-
-
Mycobacterium stomatepiae sp. nov., a slowly growing, non-chromogenic species isolated from fish
Slowly growing, non-chromogenic mycobacteria were isolated from striped barombi mbo cichlids (Stomatepia mariae) maintained at the London Zoo Aquarium, UK. The isolates could be differentiated from other slowly growing, non-pigmented mycobacteria by a combination of phenotypic features including their inability to grow at 37 °C, positive tests for heat-stable catalase, tellurite reduction and arylsulfatase activity, and the absence of urease activity, Tween 80 hydrolysis, nitrate reductase, iron uptake and semiquantitative catalase. The almost full-length 16S rRNA gene sequence, together with partial sequences from the 65 kDa heat-shock protein (hsp65) and the β-subunit of the bacterial RNA polymerase (rpoB) genes and the 16S–23S internal transcribed spacer 1 (ITS 1) region were identical for all three novel strains, but distinct from those of all known mycobacterial species. Phylogenetic analysis based on 16S rRNA gene sequences placed the novel isolates within the slowly growing mycobacteria group in close proximity to Mycobacterium florentinum. Based on genotypic and phenotypic findings, it is proposed that these isolates represent a novel species of the genus Mycobacterium, for which the name Mycobacterium stomatepiae sp. nov. is proposed with strain T11T (=DSM 45059T=CIP 109275T=NCIMB 14252T) as the type strain.
-
-
-
Agrococcus versicolor sp. nov., an actinobacterium associated with the phyllosphere of potato plants
More LessThe taxonomic position of a group of actinobacterial strains isolated from the phyllosphere of potato plants was investigated by using a polyphasic approach. Although the similarity values for their 16S rRNA gene sequences suggested an intermediate position between Microbacterium and Agrococcus, the phylogenetic tree demonstrated a clear clustering of the representative strain, K 114/01T, within the genus Agrococcus. The presence of 2,4-diaminobutyric acid as the diagnostic diamino acid in the cell-wall peptidoglycan of strain K 114/01T substantiated the affiliation to the genus Agrococcus. An analysis performed using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry revealed highly similar spectral patterns for the isolated strains, which, together with their conformity regarding a multitude of phenotypic features, supported their affiliation to the same species. Differences in several physiological features, peptidoglycan and menaquinone composition and whole-cell fatty acid profiles enabled discrimination of the phyllosphere isolates with respect to recognized Agrococcus species. As the 16S rRNA gene sequence similarity values were below 97 %, the strains isolated from the phyllosphere of potato plants represent a novel species of the genus Agrococcus, for which the name Agrococcus versicolor sp. nov. is proposed. The type strain is K 114/01T (=DSM 19812T =LMG 24386T).
-
-
-
Corynebacterium sputi sp. nov., isolated from the sputum of a patient with pneumonia
More LessA coryneform bacterium isolated from the sputum of a patient with pneumonia was characterized by phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and short chain mycolic acids consistent with the genus Corynebacterium. Comparative 16S rRNA gene sequencing studies confirmed this assignment, with the organism forming a hitherto unknown subline within the genus associated with a subcluster containing Corynebacterium hansenii, Corynebacterium freneyi, Corynebacterium xerosis, Corynebacterium amycolatum and Corynebacterium sphenisci. Sequence divergence values of >2.7 % from established corynebacterial species suggested that the new isolate represented a novel species. This was also supported by the results of the biochemical tests. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown bacterium be classified as a novel species of the genus Corynebacterium, Corynebacterium sputi sp. nov. (type strain IMMIB L-999T=DSM 45148T=CCUG 55795T).
-
-
-
Cellulomonas aerilata sp. nov., isolated from an air sample
A Gram-positive, aerobic, motile, coccoid or short rod-shaped bacterium, 5420S-23T, was isolated from an air sample collected in the Republic of Korea. According to phylogenetic analysis based on 16S rRNA gene sequences, strain 5420S-23T revealed 97.5, 97.3, 97.3 and 97.2 % similarity, respectively, to Cellulomonas biazotea DSM 20112T, Cellulomonas cellasea DSM 20118T, Cellulomonas fimi DSM 20113T and Cellulomonas chitinilytica X.bu-bT. The peptidoglycan type of strain 5420S-23T was A4β, containing l-ornithine–d-glutamic acid. The cell-wall sugars were galactose, glucose and xylose. The major fatty acids were anteiso-C15 : 0 (49.7 %) and C16 : 0 (20.0 %). The major menaquinone was MK-9(H4) and major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content was 74 mol%. The results of DNA–DNA hybridization with strains of closely related Cellulomonas species, in combination with chemotaxonomic and physiological data, demonstrated that isolate 5420S-23T represents a novel Cellulomonas species, for which the name Cellulomonas aerilata sp. nov. is proposed, with strain 5420S-23T (=KACC 20692T =DSM 18649T) as the type strain.
-
-
-
Microbacterium profundi sp. nov., isolated from deep-sea sediment of polymetallic nodule environments
More LessA Gram-positive, aerobic, neutrophilic and rod-shaped bacterium, strain Shh49T, was isolated from a deep-sea sediment sample collected from the East Pacific polymetallic nodule region. The strain was able to grow within a temperature range of 4–35 °C and tolerated up to 7.5 % (w/v) NaCl. Strain Shh49T was characterized chemotaxonomically by having MK-12 and MK-13 as predominant isoprenoid quinones, anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major fatty acids and ornithine as cell-wall diamino acid. The genomic DNA G+C content was 66.8 mol%. On the basis of 16S rRNA gene sequence similarities, the closest phylogenetic neighbours were the type strains of Microbacterium phyllosphaerae (98.3 %) and Microbacterium keratanolyticum (98.0 %), but strain Shh49T could be clearly distinguished from its phylogenetic relatives with reference to a broad range of physiological and biochemical markers. DNA–DNA relatedness of strain Shh49T with M. phyllosphaerae DSM 13468T and M. keratanolyticum DSM 8606T was 56 and 31 %, respectively. On the basis of phenotypic and genotypic data presented in this study, strain Shh49T represents a novel species of the genus Microbacterium, for which the name Microbacterium profundi sp. nov. is proposed. The type strain is Shh49T (=CGMCC 1.6777T =JCM 14840T).
-
- Archaea
-
-
Halorubrum californiense sp. nov., an extreme archaeal halophile isolated from a crystallizer pond at a solar salt plant in California, USA
A motile, rod-shaped, pink-pigmented, extremely halophilic archaeon, strain SF3-213T, was isolated from a crystallizer pond at the Cargill Solar Salt Plant, Newark, California (USA). Analysis of the almost-complete 16S rRNA gene sequence showed that the isolate was phylogenetically related to species of the genus Halorubrum, with a close relationship to Halorubrum trapanicum NRC 34021T (98.6 % similarity), Halorubrum sodomense ATCC 33755T (98.3 %) and Halorubrum xinjiangense AS 1.3527T (98.2 %). The polar lipids of strain SF3-213T were C20C20 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a sulfated diglycosyl-diether. Strain SF3-213T grew in 2.5–5.0 M NaCl. The temperature and pH ranges for growth were 25–42 °C and 6.8–8.5, respectively. Optimal growth occurred at 3.5–4.5 M NaCl, 37 °C and pH 7.3. Mg2+ was required for growth. The DNA G+C content was 69.4 mol%. DNA–DNA hybridization values lower than 70 % were obtained between strain SF3-213T and the closely related species of the genus Halorubrum. Based on the data presented in this study, strain SF3-213T represents a novel species for which the name Halorubrum californiense sp. nov. is proposed; the type strain is SF3-213T (=CECT 7256T=DSM 19288T=JCM 14715T).
-
-
-
Haloterrigena salina sp. nov., an extremely halophilic archaeon isolated from a salt lake
More LessA novel extremely halophilic strain, designated XH-65T, isolated from the salt lake Xilinhot in Inner Mongolia, PR China, was subjected to a polyphasic taxonomic characterization. Strain XH-65T is neutrophilic, non-motile and requires at least 2.5 M NaCl for growth, with an optimum at 3.4 M NaCl, and grows at pH 6.0–9.0, with optimum growth at pH 7.5. Strain XH-65T grows at 25–50 °C, with optimal growth at 37 °C. Magnesium is not required for growth. On the basis of 16S rRNA gene sequence analysis, strain XH-65T was shown to belong to the genus Haloterrigena and was related to Haloterrigena turkmenica VKM B-1734T (98.1 % sequence similarity), Haloterrigena saccharevitans AB14T (96.9 %), Haloterrigena thermotolerans PR5T (96.3 %), Haloterrigena limicola AX-7T (95.8 %) and Haloterrigena hispanica FP1T (95.7 %). DNA–DNA hybridization revealed 37 % relatedness between strain XH-65T and Htg. turkmenica VKM B-1734T. The polar lipid composition revealed the presence of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and mannose-2,6-disulfate (1→2)-glucose glycerol diether (S2-DGD). The results of the DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain XH-65T from the six Haloterrigena species with validly published names. Therefore, strain XH-65T represents a novel species, for which the name Haloterrigena salina sp. nov. is proposed, with the type strain XH-65T (=CGMCC 1.6203T =JCM 13891T).
-
- Bacteroidetes
-
-
Lacinutrix algicola sp. nov. and Lacinutrix mariniflava sp. nov., two novel marine alga-associated bacteria and emended description of the genus Lacinutrix
Two heterotrophic, aerobic, yellow-pigmented, Gram-negative, non-gliding bacteria, designated AKS293T and AKS432T, isolated from a red alga, were analysed using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis revealed that the novel strains were affiliated to the genus Lacinutrix, a member of the family Flavobacteriaceae, showing sequence similarities of 96.1–96.4 % with respect to the type strain of Lacinutrix copepodicola. The two novel isolates shared 99.5 % 16S rRNA gene sequence similarity and 55.0 % DNA–DNA relatedness. They grew optimally at 17.5 °C and pH 6.5. The main cellular fatty acids of strain AKS293T were iso-C15 : 0, iso-C15 : 0 3-OH and iso-C16 : 0 3-OH, while those of strain AKS432T were anteiso-C15 : 0, iso-C15 : 0, iso-C15 : 1 and iso-C15 : 0 3-OH. In both cases, the major isoprenoid quinone was MK-6. The DNA G+C contents were 34.7 and 37.0 mol% for strains AKS293T and AKS432T, respectively. The phylogenetic evidence, phenotypic data and DNA–DNA hybridization results support the differentiation of strains AKS293T and AKS432T from each other and from their closest relative, L. copepodicola DJ3T. Therefore, strains AKS293T and AKS432T represent two novel species, for which the names Lacinutrix algicola sp. nov. and Lacinutrix mariniflava sp. nov. are proposed, respectively. The type strain of L. algicola sp. nov. is AKS293T (=KCCM 42313T=JCM 13825T) and the type strain of L. mariniflava sp. nov. is AKS432T (=KCCM 42306T=JCM 13824T). An emended description of the genus Lacinutrix is also proposed.
-
-
-
Chryseobacterium hungaricum sp. nov., isolated from hydrocarbon-contaminated soil
The taxonomic position of a strain isolated from kerosene-contaminated soil in Hungary and formerly misidentified as Brevundimonas vesicularis was examined using a polyphasic approach. The isolate, designated CHB-20pT, could be clearly assigned to the genus Chryseobacterium (family Flavobacteriaceae) on the basis of 16S rRNA gene sequence similarity. Strain CHB-20pT, a moderate oil degrader, was a Gram-negative, aerobic, mesophilic microbe with a temperature optimum of 28–30 °C. Predominant fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH) and iso-C17 : 0 3-OH. Menaquinone-6 (MK-6) was the predominant respiratory quinone; MK-5 was present as a minor component. The almost complete 16S rRNA gene sequence of strain CHB-20pT shared 94–97 % similarity with sequences of the type strains of species of the genus Chryseobacterium. DNA–DNA relatedness between strain CHB-20pT and its closest relative, Chryseobacterium caeni, was lower than 46 %. Moreover, several diagnostic phenotypic properties distinguished strain CHB-20pT from C. caeni. On the basis of biochemical, chemotaxonomic and genotypic data, isolate CHB-20pT represents a novel species within the genus Chryseobacterium, Chryseobacterium hungaricum sp. nov.; the type strain is CHB-20pT (=NCAIM B2269T=DSM 19684T).
-
- Other Bacteria
-
-
Spirochaeta cellobiosiphila sp. nov., a facultatively anaerobic, marine spirochaete
More LessA facultatively anaerobic, marine spirochaete, designated strain SIP1T, was isolated from interstitial water from a cyanobacteria-containing microbial mat. Cells of strain SIP1T were 0.3–0.4×10–12 μm in size, helical with a body pitch of approximately 1.4 μm and motile by means of two to four periplasmic flagella (one, or occasionally two, being inserted near each end of the cell). Cells were catalase-negative and used a variety of monosaccharides and disaccharides and pectin as energy sources, growing especially well on cellobiose. Neither organic acids nor amino acids were utilized as energy sources. One or more amino acids in tryptone and one or more components of yeast extract were required for growth. Growth was observed at 9–37 °C (optimally at or near 37 °C), at initial pH 5–8 (optimally at initial pH 7.5) and in media prepared with 20–100 % (v/v) seawater (optimally at 60–80 %) or 0.10–1.00 M NaCl (optimally at 0.30–0.40 M). The products of cellobiose fermentation were acetate, ethanol, CO2, H2 and small amounts of formate. Aerated cultures performed incomplete oxidation of cellobiose to acetate (and, presumably, CO2) plus small amounts of ethanol and formate, but exhibited a Y cellobiose that was only slightly greater than that of cellobiose-fermenting anoxic cultures. The G+C content of the genomic DNA of strain SIP1T was 41.4 mol%, the lowest among known spirochaetas. On the basis of its 16S rRNA gene sequence, strain SIP1T was grouped among other members of the genus Spirochaeta, but it bore only 89 % similarity with respect to its closest known relatives, Spirochaeta litoralis and Spirochaeta isovalerica, two marine obligate anaerobes. On the basis of its phenotypic properties and phylogenetic position, strain SIP1T represents a novel species of the genus Spirochaeta, for which the name Spirochaeta cellobiosiphila sp. nov. is proposed. The type strain is SIP1T (=ATCC BAA-1285T =DSM 17781T).
-
-
-
Deinococcus aquatilis sp. nov., isolated from water
More LessA pale-pink strain (CCUG 53370T) from water was investigated by a polyphasic taxonomic approach. The cells stained Gram-positive and were rod-shaped and non-spore-forming. Analyses using the 16S rRNA gene sequence of the isolate showed that the organism belongs to the genus Deinococcus, with the highest sequence similarities to the type strains of Deinococcus ficus (94.4 %), Deinococcus navajonensis (94.3 %) and Deinococcus mumbaiensis (94.3 %). Chemotaxonomic data revealed that CCUG 53370T contains exclusively menaquinone MK-8 as the respiratory quinone and a complex polar lipid profile consisting of different unidentified glycolipids and polar lipids, two unknown phospholipids and three unknown phosphoglycolipids. As in other deinococci, one of these phosphoglycolipids was predominant in the profile, and it was identified in Deinococcus radiodurans as 2′-O-(1,2-diacyl-sn-glycero-3-phospho)-3′-O-(α-galactosyl)-N-d-glyceroyl alkylamine. Predominant fatty acids were C16 : 1 ω7c, C17 : 1 ω8c and C17 : 1 ω9c. Biochemical and chemotaxonomic properties demonstrate that strain CCUG 53370T represents a novel species, for which the name Deinococcus aquatilis sp. nov. is proposed. The type strain is CCUG 53370T (=CCM 7524T).
-
-
-
Rubidibacter lacunae gen. nov., sp. nov., a unicellular, phycoerythrin-containing cyanobacterium isolated from seawater of Chuuk lagoon, Micronesia
More LessA unicellular cyanobacterium, designated KORDI 51-2T, was isolated from surface seawater of Chuuk lagoon, Micronesia. The cells were wine-coloured rods and emitted red fluorescence under green excitation of an epifluorescence microscope. Thus, morphologically, the strain resembled Synechococcus species. However, based on 16S rRNA gene sequence similarities between strain KORDI 51-2T and related strains belonging to cyanobacteria, the novel strain was distantly related to members of the ‘Halothece’ cluster. However, sequence similarities between strain KORDI 51-2T and members of the ‘Halothece’ cluster were very low, ranging from 90.7 to 92.1 %, and phylogenetic analyses showed that the strain formed a distinct branch. Therefore, a polyphasic characterization including morphology, physiology and pigment composition was conducted to elucidate the taxonomic position of strain KORDI 51-2T. The strain grew within a temperature range of 25–35 °C and a salinity range of 2–7 %. The optimal temperature and salinity were about 30 °C and 5 %, respectively. Strain KORDI 51-2T contained phycoerythrin, and the dominant carotenoid pigments were zeaxanthin, β-carotene and echinenone. The DNA G+C content was 60.5 mol%. Based on phylogenetic analysis of the 16S rRNA gene sequence, and the physiological data and pigment compositions, strain KORDI 51-2T is considered to represent a new genus and novel species of cyanobacteria for which the name Rubidibacter lacunae gen. nov., sp. nov. is proposed. The type strain is KORDI 51-2T (=KCTC 40015T=UTEX L2944T).
-
-
-
Megamonas rupellensis sp. nov., an anaerobe isolated from the caecum of a duck
More LessWe report here the identification, characterization and culture of a Gram-negative to Gram-variable, rod-shaped, non-spore-forming anaerobic bacterium (strain FM1025T) isolated from the caecum of a duck. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that this strain clustered with species of the family ‘Acidaminococcaceae’, with 94.9 % similarity to Megamonas hypermegale DSM 1672T and less than 91 % similarity with type strains of Pectinatus species. Sequence similarities of at least 98–99 % were observed with numerous sequences deposited in GenBank of uncultured strains from human and chicken caecal contents, but this strain is the first isolate of this taxon to be cultivated and described. On the basis of morphological, physiological and phylogenetic features, this strain should be assigned to a novel species in the genus Megamonas, for which the name Megamonas rupellensis sp. nov. is proposed. The type strain is strain FM1025T (=DSM 19944T =CIP 109788T).
-
- Proteobacteria
-
-
Vogesella perlucida sp. nov., a non-pigmented bacterium isolated from spring water
More LessA transparent, non-pigmented, Gram-negative, rod-shaped bacterium, designated strain DS-28T, was isolated from water samples collected from a spring located in Tainan County, Taiwan. 16S rRNA gene sequence analysis indicated that the novel strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Vogesella; the only sole close neighbour of the novel strain was Vogesella indigofera ATCC 19706T (97.4 % 16S rRNA gene sequence similarity). The isolate was distinguished from V. indigofera on the basis of genotypic data, several phenotypic properties and an inability to produce characteristic blue-pigmented colonies on peptone agar. The fatty acid profile was slightly different from that reported for V. indigofera ATCC 19706T. It was evident from the genotypic and phenotypic data that strain DS-28T represents a novel species of the genus Vogesella, for which the name Vogesella perlucida sp. nov. is proposed. The type strain is DS-28T (=BCRC 17730T=LMG 24214T).
-
-
-
Amorphus coralli gen. nov., sp. nov., a marine bacterium isolated from coral mucus, belonging to the order Rhizobiales
More LessA bacterial strain, designated RS.Sph.026T, was isolated from mucus of the coral Fungia granulosa collected from the northern Red Sea (Gulf of Eilat, Israel). The bacterium was found to be Gram-negative, non-motile, halotolerant and heterotrophic. Comparative 16S rRNA gene sequence analyses showed that strain RS.Sph.026T belonged to the order Rhizobiales, with the highest levels of 16S RNA gene sequence similarity with Rhodobium orientis (92 %). Strain RS.Sph.026T grew optimally at a salinity of 3–4 %, pH 7.5–8 and 25–30 °C. The major cellular fatty acids were cis-7-octadecenoic acid (C18 : 1 ω7с; 57.2 %) and C19 : 0 cyclo ω8с (15.5 %). The DNA G+C content of strain RS.Sph.026T was 67.1 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain RS.Sph.026T represents a novel genus and species in the order Rhizobiales, for which the name Amorphus coralli gen. nov., sp. nov. is proposed. The type strain is RS.Sph.026T (=LMG 24307T=DSM 19760T).
-
-
-
Ruegeria scottomollicae sp. nov., isolated from a marine electroactive biofilm
Seventy isolates were obtained from a marine electroactive biofilm that was generated on a cathodically polarized stainless steel electrode (Genoa, Italy). The genetic diversity was investigated by means of BOX-PCR fingerprinting and two clusters of isolates with similar BOX-PCR profiles were delineated. Whole-cell fatty acid methyl ester analysis and 16S rRNA gene sequence analysis showed that the isolates belonged to the Roseobacter lineage of the class Alphaproteobacteria. DNA–DNA hybridization experiments and a biochemical analysis demonstrated that four isolates belonged to the species Ruegeria mobilis. However, 66 isolates from the second BOX-PCR cluster constituted a novel species within the genus Ruegeria, for which the name Ruegeria scottomollicae sp. nov. is proposed. The DNA G+C content was 61.0±0.4 %. The type strain is LMG 24367T (=CCUG 55858T).
-
-
-
Marinomonas basaltis sp. nov., a marine bacterium isolated from black sand
A Gram-negative, aerobic, slightly halophilic, rod-shaped bacterium was isolated from black sand in Soesoggak, Jeju island, Korea. The strain, designated J63T, was oxidase- and catalase-positive and arginine dihydrolase-negative. The isolate required Na+ for growth and differed from phenotypically related species by being able to utilize sucrose and d-galactose as a carbon source. Phylogenetic analysis based on the sequence of the 16S rRNA gene revealed that strain J63T belongs to the genus Marinomonas. It exhibited 16S rRNA gene sequence similarities of 97.6–98.7 % to the closely related species Marinomonas communis, Marinomonas ostreistagni, Marinomonas aquimarina and Marinomonas vaga. The phylogenetic analysis revealed that strain J63T comprised a relatively long subline of descent, shared a branch point with the outlying species Marinomonas communis and occupied a phylogenetically distant position on the main Marinomonas branch. Based on DNA–DNA hybridization, the levels of relatedness between strain J63T and M. communis NBRC 102224T, M. aquimarina CIP 108405T and M. vaga JCM 20774T were 56.2, 45.1 and 51.3 %, respectively. On the basis of the phenotypic, genetic and phylogenetic data, strain J63T should be placed in the genus Marinomonas as representing a novel species, for which the name Marinomonas basaltis sp. nov. is proposed. The type strain is J63T (=KCTC 22118T=JCM 14948T).
-
-
-
Leisingera aquimarina sp. nov., isolated from a marine electroactive biofilm, and emended descriptions of Leisingera methylohalidivorans Schaefer et al. 2002, Phaeobacter daeponensis Yoon et al. 2007 and Phaeobacter inhibens Martens et al. 2006
More LessStrain LMG 24366T was isolated from a marine electroactive biofilm grown on a stainless steel cathode (Genova, Italy) and was investigated by using a polyphasic taxonomic approach. This study demonstrated that strain LMG 24366T represents a novel species within the genus Leisingera, which shared 98.9 % 16S rRNA gene similarity with its nearest phylogenetic neighbour, Leisingera methylohalidivorans. Strain LMG 24366T grew on betaine (1 mM) as a sole carbon source, whereas no growth was observed on l-methionine (10 mM). The phenotypic and genotypic analyses showed that strain LMG 24366T could be differentiated from established Leisingera species and that it represented a novel species, for which the name Leisingera aquimarina sp. nov. is proposed. The type strain is LMG 24366T (=CCUG 55860T) and has a DNA G+C content of 61.4 mol%.
-
-
-
Characterization of ‘Candidatus Neoehrlichia lotoris’ (family Anaplasmataceae) from raccoons (Procyon lotor)
Recently, a novel ehrlichial organism was isolated from a raccoon (Procyon lotor) and the isolate (RAC413) was infectious to two naïve raccoons but not laboratory mice, rats or rabbits. In this study, amplification and sequencing of four gene targets (16S rRNA gene, groESL, gltA and rpoB) confirmed that the novel ehrlichial organism was a member of the family Anaplasmataceae and was most closely related to, but distinct from, ‘Candidatus Neoehrlichia mikurensis’ TK4456R and IS58. RAC413 shared the highest sequence similarity with members of the genus Ehrlichia (94.2–95.1, 80.9–83.1, 67.9–71.9 and 39.9–40.7 % similarity for the 16S rRNA gene, groESL, gltA and rpoB, respectively). No sequence variation in three sequences (16S rRNA gene, groESL and gltA) was observed between the RAC413 isolate and five additional sequences amplified from blood of naturally infected raccoons from several geographically isolated populations in the south-eastern USA. Serum samples from four experimentally infected raccoons did not react to Ehrlichia canis, Ehrlichia chaffeensis, Anaplasma marginale or Anaplasma phagocytophilum antigens in an immunofluorescence assay or an Ehrlichia ewingii peptide in an ELISA format. On the basis of the distinctive molecular and serological characteristics and apparent host specificity of this ehrlichial organism, it is proposed that this organism be designated ‘Candidatus Neoehrlichia lotoris’ (reference strain RAC413R).
-
-
-
Amphritea japonica sp. nov. and Amphritea balenae sp. nov., isolated from the sediment adjacent to sperm whale carcasses off Kagoshima, Japan
Two novel species were isolated from the sediment adjacent to sperm whale carcasses off Kagoshima, Japan, at a depth of about 230 m. The isolated strains, JAMM 1866T, JAMM 1548 and JAMM 1525T, were Gram-negative, rod-shaped, non-spore-forming and motile by means of a single polar or bipolar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences of strains JAMM 1866T and JAMM 1548 indicated a relationship to the symbiotic bacterial clone R21 of Osedax japonicus (100 % sequence similarity) and all three isolates were closely related to Amphritea atlantica (97.7–97.8 % similarity) within the class Gammaproteobacteria. The novel isolates were able to produce isoprenoid quinone Q-8 as the major component. The predominant fatty acids were C16 : 0, C16 : 1 and C18 : 1, with C12 : 1 3-OH present in smaller amounts. The DNA G+C contents of the three isolated strains were about 47 mol%. Based on differences in taxonomic characteristics, the three isolated strains represent two novel species of the genus Amphritea for which the names Amphritea japonica sp. nov. (type strain JAMM 1866T=JCM 14782T=ATCC BAA-1530T; reference strain JAMM 1548) and Amphritea balenae sp. nov. (type strain JAMM 1525T=JCM 14781T=ATCC BAA-1529T) are proposed.
-
-
-
Halomonas salifodinae sp. nov., a halophilic bacterium isolated from a salt mine in China
More LessA Gram-negative, aerobic, motile, halophilic bacterium, designated strain BC7T, was isolated from a salt mine in north-western China and was subjected to a polyphasic taxonomic characterization. The isolate was able to grow in the presence of 0.5–20 % (w/v) NaCl and at pH 6.0–9.0 and 4–48 °C; optimum growth was observed with 3 % (w/v) NaCl and at pH 7.0 and 30 °C. Cells were long rods, 0.8–1.2 μm wide and 4.0–6.0 μm long. The major fatty acids were C18 : 1 ω7c, C16 : 0 and C16 : 0 ω7c. The DNA G+C content was 65.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BC7T belonged to the genus Halomonas and showed highest sequence similarity to the type strain of Halomonas pacifica (99.2 %). Levels of DNA–DNA relatedness between strain BC7T and H. pacifica CGMCC 1.2314T and Halomonas taeanensis DSM 16463T were 51 and 38 %, respectively. On the basis of phenotypic and genotypic data, strain BC7T is considered to represent a novel species of the genus Halomonas, for which the name Halomonas salifodinae sp. nov. is proposed. The type strain is BC7T (=CGMCC 1.6774T =JCM 14803T).
-
-
-
Halomonas daqingensis sp. nov., a moderately halophilic bacterium isolated from an oilfield soil
A Gram-negative, moderately halophilic, short rod-shaped, aerobic bacterium with peritrichous flagellae, strain DQD2-30T, was isolated from a soil sample contaminated with crude oil from the Daqing oilfield in Heilongjiang Province, north-eastern China. The novel strain was capable of growth at NaCl concentrations of 1–15 % (w/v) [optimum at 5–10 % (w/v)]. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel strain belonged to the genus Halomonas in the class Gammaproteobacteria; the highest 16S rRNA gene sequence similarities were with Halomonas desiderata DSM 9502T (98.8 %), Halomonas campisalis A4T (96.6 %) and Halomonas gudaonensis CGMCC 1.6133T (95.1 %). The major cellular fatty acids of strain DQD2-30T were C18 : 1 ω7c (43.97 %), C19 : 0 cyclo ω8c (23.37 %) and C16 : 0 (14.83 %). The predominant respiratory lipoquinone was ubiquinone with nine isoprene units (Q9). The DNA G+C content was 67.0 mol%. The DNA–DNA hybridization values of strain DQD2-30T with the most closely related species of the genus Halomonas were 51.8 %, 28.4 % and 23.5 % for H. desiderata, H. campisalis and H. gudaonensis, respectively. Based on these analyses, strain DQD2-30T (=CGMCC 1.6443T=LMG 23896T) is proposed to represent the type strain of a novel species, Halomonas daqingensis sp. nov.
-
-
-
Marinobacter goseongensis sp. nov., from seawater
A Gram-negative marine bacterium, designated strain En6T, was isolated from seawater of the East Sea of Korea. The organism grew in 1–25 % (w/v) NaCl and at 10–37 °C and pH 5.3–9.3, with optimal growth occurring in 4–5 % NaCl and at 25–30 °C and pH 7.5. Phylogenetic analysis of the 16S rRNA gene sequence of strain En6T placed this bacterium in the clade Marinobacter within the class Gammaproteobacteria. The 16S rRNA gene sequence similarity between strain En6T and Marinobacter lipolyticus SM19T, the most closely related species, was 98.4 %, and the level of DNA–DNA relatedness between the two strains was 22 %. On the basis of the phylogenetic analysis and phenotypic and chemotaxonomic data, strain En6T is considered to represent a novel species of the genus Marinobacter. The name Marinobacter goseongensis sp. nov. is proposed, with strain En6T (=KCTC 12515T=DSM 19471T) as the type strain.
-
-
-
Rhizobium fabae sp. nov., a bacterium that nodulates Vicia faba
Six strains were isolated from root nodules of Vicia faba grown in Nanchang, Yifeng, Taihu, Huaibei, Bengbu and Lujiang, in the middle and lower reaches of the Yangtze River. According to phylogenetic analyses of 16S rRNA gene, atpD and recA sequences, these strains belong to the genus Rhizobium, with Rhizobium etli and Rhizobium leguminosarum as the closest related species. CCBAU 33202T, a representative of these novel isolates, showed sequence similarity to its closest relatives R. etli CFN 42T and R. leguminosarum USDA 2370T of 99.5 and 99.1 % for the 16S rRNA gene, 91.9 and 91.9 % for atpD and 90.3 and 93.2 % for recA. The strains from this study could also be differentiated from R. etli CFN 42T and R. leguminosarum USDA 2370T by 16S–IGS RFLP and SDS-PAGE of whole-cell proteins, fatty acid profiles and several phenotypic characteristics. DNA–DNA hybridization yielded relatedness of 19 and 14–43 %, respectively, with R. etli CFN 42T and strains representing different biovars of R. leguminosarum. All data obtained in this study showed that these V. faba isolates belong to a novel species, for which the name Rhizobium fabae sp. nov. is proposed. The type strain, CCBAU 33202T (=LMG 23997T =JCM 14381T), was isolated from Nanchang.
-
-
-
Marinobacter mobilis sp. nov. and Marinobacter zhejiangensis sp. nov., halophilic bacteria isolated from the East China Sea
More LessThree Gram-negative, aerobic, motile, halophilic, rod-shaped strains (CN46T, CN71 and CN74T) were isolated from sediment of the East China Sea and subjected to a polyphasic taxonomic study. Strains CN46T and CN71 had identical 16S rRNA gene sequences and phenotypic characteristics. Strain CN46T was moderately halophilic. Growth of strain CN46T was observed between 0.5 and 10.0 % (w/v) NaCl (optimal growth at 3.0–5.0 %) and between pH 6.5 and 9.0. Strain CN74T grew over a wider range of pH (pH 6.0–9.5); the optimum NaCl concentration for growth was 1.0–3.0 %. The major fatty acids of strain CN46T were C16 : 1 ω9c, C16 : 0 and C12 : 0, whereas strain CN74T contained C16 : 0, C16 : 1 ω9c, C18 : 1 ω9c and C12 : 0. The DNA G+C contents of the three isolates were between 58.0 and 58.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains CN46T, CN71 and CN74T grouped together within the cluster of Marinobacter species. 16S rRNA gene sequence similarities of the three strains with the type strains of Marinobacter species ranged from 94.0 to 97.1 %. The DNA–DNA hybridization values of strain CN74T with strains CN46T and CN71 were 35.0 and 36.0 %, respectively. Levels of DNA–DNA relatedness between strains CN46T and CN74T and Marinobacter pelagius CGMCC 1.6775T, Marinobacter gudaonensis CGMCC 1.6294T and Marinobacter koreensis DSM 17924T were 15.3–45.2 %. The results of DNA–DNA hybridizations, fatty acid analysis, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the isolates from closely related species. Two novel species are proposed, named Marinobacter mobilis sp. nov. (type strain CN46T =CGMCC 1.7059T =JCM 15154T) and Marinobacter zhejiangensis sp. nov. (type strain CN74T =CGMCC 1.7061T =JCM 15156T).
-
-
-
Thiohalorhabdus denitrificans gen. nov., sp. nov., an extremely halophilic, sulfur-oxidizing, deep-lineage gammaproteobacterium from hypersaline habitats
More LessSeven strains of extremely halophilic and obligately chemolithoautotrophic sulfur-oxidizing bacteria (SOB) were enriched and isolated at 4 M NaCl from sediments of hypersaline inland lakes in south-eastern Siberia and a Mediterranean sea solar saltern. Cells of the novel isolates were spindle-like, long and non-motile rods with a Gram-negative type of cell wall. They were obligately chemolithoautotrophic SOB using thiosulfate and tetrathionate as electron donors and represent the first example of extremely halophilic chemolithoautotrophs that are able to grow anaerobically with nitrate as electron acceptor. The characteristic feature of the group was the production of large amounts of tetrathionate as an intermediate during the oxidation of thiosulfate to sulfate. With thiosulfate, the novel strains grew within the pH range from 6.5 to 8.2 (optimum at pH 7.5–7.8) and at NaCl concentrations from 1.5 to 4.0 M (optimum at 3.0 M). Cells grown at 4 M NaCl accumulated extremely high concentrations of glycine betaine as a compatible solute. The dominant cellular fatty acids were 10MeC16 : 0 and C16 : 0. Based on the DNA–DNA relatedness values, the isolates consisted of a single genomic species and had a similar phenotype. Phylogenetic analysis placed the novel bacteria in the class Gammaproteobacteria as an independent lineage with no significant relationship to any other genera in this class. On the basis of phenotypic and genotypic analysis, the group is proposed to represent a new genus, Thiohalorhabdus gen. nov., with Thiohalorhabdus denitrificans gen. nov., sp. nov. as the type species (type strain HL 19T=DSM 15699T=UNIQEM U223T).
-
-
-
Luteimonas marina sp. nov., isolated from seawater
More LessA marine bacterial strain, designated FR1330T, was isolated from a seawater sample collected near Ganghwa Island, the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FR1330T belonged to the Gammaproteobacteria and was related to the genus Luteimonas; its closest neighbours were the type strains of Luteimonas composti (97.9 % sequence similarity) and Luteimonas mephitis (95.0 %). DNA–DNA relatedness values for strain FR1330T with Luteimonas composti CC-YY255T and Luteimonas mephitis KACC 11391T were 33 and 10 %, respectively. Cells of strain FR1330T were Gram-negative, aerobic, rod-shaped and oxidase- and catalase-positive. The predominant respiratory lipoquinone was ubiquinone-8. The major fatty acids were branched-chain saturated iso-C15 : 0 (26.2 %) and unsaturated iso-C17 : 1 ω9c (26.0 %). The DNA G+C content was 67.6 mol%. On the basis of several phenotypic characteristics, strain FR1330T could be differentiated from Luteimonas composti and Luteimonas mephitis. The data obtained from the polyphasic study demonstrated clearly that strain FR1330T represents a novel species of the genus Luteimonas. The name Luteimonas marina sp. nov. is proposed, with strain FR1330T (=KCTC 12327T=JCM 12488T=IMSNU 60306T) as the type strain.
-
-
-
Rhodospirillum sulfurexigens sp. nov., a phototrophic alphaproteobacterium requiring a reduced sulfur source for growth
More LessA Gram-negative, spiral-shaped, phototrophic, purple non-sulfur bacterial strain, JA143T, was isolated from a freshwater habitat. Strain JA143T was motile by means of bipolar tufts of flagella. Intracellular photosynthetic membranes are of the lamellar stacked type. Bacteriochlorophyll a and carotenoids of the spirilloxanthin series with rhodovibrin are present as photosynthetic pigments. Thiamine and a reduced sulfur source are required for growth. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA143T clusters with species of the genus Rhodospirillum, belonging to the class Alphaproteobacteria. The highest sequence similarities of strain JA143T were found with the type strains of Rhodospirillum rubrum (95.6 %) and Rhodospirillum photometricum (95.7 %). Based on 16S rRNA gene sequence analysis and morphological and physiological characteristics, strain JA143T was significantly different from the other two recognized species of the genus Rhodospirillum and represents a novel species, for which the name Rhodospirillum sulfurexigens sp. nov. is proposed. The type strain is JA143T (=DSM 19785T =NBRC 104433T).
-
- Eukaryotic Micro-Organisms
-
-
Metschnikowia cubensis sp. nov., a yeast species isolated from flowers in Cuba
More LessA novel yeast species is described from 19 strains isolated from flowers and insects in three provinces of Cuba. The species is so far known only from Cuba. Characteristic asci and ascospores as well as phylogenetic analysis of the rDNA sequence place the novel species in the genus Metschnikowia. The novel species belongs to the New World subclade of large-spored species of Metschnikowia. Mating tests with other members of the subclade resulted in the formation of sterile asci without ascospores, showing that the Cuban strains represent a distinct biological species. Intraspecies matings lead to the production of fertile asci containing large needle-shaped ascospores. The novel species was further distinguished from its close relatives by rDNA sequences and PCR fingerprinting using primers derived from mini- and microsatellites. We propose the name Metschnikowia cubensis sp. nov. and designate MUCL 45753T (=CRGF 279T =CBS 10832T, h+) as the type strain and MUCL 45751 (=CRGF 278 =CBS 10833, h−) as the allotype.
-
-
-
Cryptococcus keelungensis sp. nov., an anamorphic basidiomycetous yeast isolated from the sea-surface microlayer of the north-east coast of Taiwan
More LessStrain SN-82T was isolated from the sea-surface microlayer at Keelung on the north-east coast of Taiwan. Sequence analysis of the D1/D2 domain of the 26S rDNA of strain SN-82T suggested that this strain is related to the aerius clade in the Filobasidiales. Phenotypic characteristics such as the absence of sexual structures and ballistoconidia, the assimilation of myo-inositol and d-glucuronate, the inability to ferment glucose, the possession of coenzyme Q-10 and positive Diazonium blue B and urease reactions also indicated that this strain belongs to the genus Cryptococcus. However, divergences of more than 3.6 % were observed in the D1/D2 domain when compared with other described Cryptococcus species, which indicated that the isolated yeast represents a previously unrecognized member of this genus. Therefore, the novel yeast species Cryptococcus keelungensis sp. nov. is proposed, with strain SN-82T (=CBS 10876T =BCRC 23107T =JCM 14893T) as the type strain.
-
-
-
Mrakiella cryoconiti gen. nov., sp. nov., a psychrophilic, anamorphic, basidiomycetous yeast from alpine and arctic habitats
More LessA novel psychrophilic basidiomycetous species is described in a new anamorphic genus as Mrakiella cryoconiti gen. nov., sp. nov.; the type strain of Mrakiella cryoconiti is strain A15T (=CBS 10834T =DSM 21094T). Two representatives were isolated from alpine glacier cryoconite and from northern Siberian sediment. Physiological and biochemical properties are similar to characteristics shared by members of the genus Mrakia, although sexual reproduction is absent. Mrakiella cryoconiti strains are psychrophilic and produce cold-active pectate lyase. Sequence analyses of the ITS and 26S rRNA D1/D2 regions indicated that these strains represent a distinct taxon within the Mrakia clade of the order Cystofilobasidiales, class Tremellomycetes and phylum Basidiomycota. On the basis of phenotypic and genotypic characteristics, Cryptococcus aquaticus (a member of the Mrakia clade) is transferred to the newly described genus as Mrakiella aquatica comb. nov.
-
-
-
Sporobolomyces koalae sp. nov., a basidiomycetous yeast isolated from nasal smears of Queensland koalas kept in a Japanese zoological park
More LessThree strains (JCM 15063T, JCM 15098 and JCM 15099) of a novel basidiomycetous yeast species belonging to the genus Sporobolomyces were isolated from nasal smears of Queensland koalas kept in a Japanese zoological park. Analyses of sequences of the nuclear rDNA internal transcribed spacer region and the 26S rDNA D1/D2 domain and morphological studies indicated that these strains represent a novel species with a close phylogenetic relationship to Sporobolomyces carnicolor and Sporobolomyces japonicus in the Sporidiobolus lineage, for which the name Sporobolomyces koalae sp. nov. is proposed (type strain JCM 15063T =CBS 10914T =DSM 19992T).
-
- Other Gram-Positive Bacteria
-
-
Sharpea azabuensis gen. nov., sp. nov., a Gram-positive, strictly anaerobic bacterium isolated from the faeces of thoroughbred horses
Four bacterial strains, designated ST18T, HM244, HM250 and DI49, were isolated from the fresh faeces of four thoroughbred horses in Japan. Cells were Gram-positive, strictly anaerobic, catalase-negative, non-spore-forming, non-motile rods that occurred in chains. They were placed in the same subcluster based on 16S rRNA gene sequence analysis, phenotypic characteristics and levels of DNA–DNA relatedness. Their DNA G+C content ranged from 36 to 38 mol%. Lactobacillus catenaformis, Lactobacillus vitulinus and Catenibacterium mitsuokai belong to cluster XVII of the Clostridium subphylum. Strain ST18T was most closely related to L. catenaformis ATCC 25536T in the phylogenetic tree, but these strains shared only 89.9 % (1336/1486 bp) 16S rRNA gene sequence similarity. L. catenaformis, L. vitulinus and C. mitsuokai are homofermentative bacteria, whereas ST18T produced CO2 from glucose. Whereas the cell-wall peptidoglycan type of L. catenaformis and L. vitulinus was l-Lys–l-Ala3, that of C. mitsuokai and the subgroup represented by ST18T was A1γ (l-Ala–d-Glu–meso-diaminopimelic acid). On the basis of 16S rRNA gene sequence divergence of more than 10 % from L. catenaformis as well as phenotypic characteristics, strains ST18T, HM244, HM250 and DI49 are considered to represent a novel species of a new genus belonging to the Clostridium subphylum cluster XVII, for which the name Sharpea azabuensis gen. nov., sp. nov. is proposed. The type strain of Sharpea azabuensis is ST18T (=JCM 14210T =DSM 18934T).
-
-
-
Lactobacillus bobalius sp. nov., a lactic acid bacterium isolated from Spanish Bobal grape must
More LessA Lactobacillus strain, designated 203T, previously isolated from Bobal grape must was characterized phylogenetically, genotypically and phenotypically in order to establish whether it represents a novel species. On the basis of the 16S rRNA gene sequence, strain 203T was shown to belong to the genus Lactobacillus, falling within the Lactobacillus alimentarius–Lactobacillus farciminis group and being closely related to the type strains of L. alimentarius, Lactobacillus kimchii and Lactobacillus paralimentarius. DNA–DNA hybridization results confirmed the separate status of strain 203T at the species level. To establish the similarities and differences between 203T and the three aforementioned closest species, the following methods were used: amplified rDNA restriction analysis, analysis of the 16S–23S rDNA intergenic spacer region, random amplification of polymorphic DNA (RAPD) profiling, ribotyping, carbohydrate fermentation and physiological tests. Strain 203T could be differentiated genetically using RAPD analysis and ribotyping. Phenotypically, it can be distinguished from its closest relatives by its ability to grow at pH 3.3, by gas production from gluconate and by certain carbohydrate fermentations. On the basis of these data, strain 203T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus bobalius sp. nov. is proposed. The type strain is 203T (=CECT 7310T =DSM 19674T).
-
-
-
Dialister succinatiphilus sp. nov. and Barnesiella intestinihominis sp. nov., isolated from human faeces
More LessTwo anaerobic, non-spore-forming, bacteria (YIT 11850T and YIT 11860T) that stained Gram-negative, were isolated from human faeces. Cells of strain YIT 11850T were coccobacilli, asaccharolytic and largely unreactive, with only traces of lactate and propionate as metabolic end products; however, strain YIT 11850T was able to decarboxylate succinate to propionate. The DNA G+C content of strain YIT 11850T was 51.9 mol%. Following 16S rRNA gene sequence analysis, this strain was found to be most closely related to Dialister propionicifaciens, with 95.1 % sequence similarity between the two taxa. Biochemical data supported the affiliation of strain YIT 11850T to the genus Dialister. Strain YIT 11850T therefore represents a novel species for which the name Dialister succinatiphilus sp. nov. is proposed; the type strain is YIT 11850T (=DSM 21274T=JCM 15077T). Cells of the other isolate, strain YIT 11860T, were non-motile, rod-shaped, positive for aesculin hydrolysis, negative for indole production, produced succinic and acetic acids as end products of glucose metabolism and possessed a DNA G+C content of 45.5 mol%. On the basis of 16S rRNA gene sequence similarity values, this strain was shown to belong to the family ‘Porphyromonadaceae’ related to Barnesiella viscericola (96.0 %); similarity values with species within the family ‘Porphyromonadaceae’ with validly published names were less than 86 %. Biochemical data supported the affiliation of strain YIT 11860T to the genus Barnesiella. Strain YIT 11860T therefore represents a novel species for which the name Barnesiella intestinihominis sp. nov. is proposed; the type strain is YIT 11860T (=DSM 21032T=JCM 15079T).
-
-
-
Weissella ghanensis sp. nov., isolated from a Ghanaian cocoa fermentation
More LessDuring a study on lactic acid bacteria (and their species diversity) in spontaneous heap fermentations of Ghanaian cocoa beans, two strains, designated 215T and 194B, were isolated. A phylogenetic analysis based on 16S rRNA gene sequences demonstrated that these strains represented a distinct lineage close to the genus Weissella and showing only 92.1 % 16S rRNA gene sequence similarity with respect to their closest neighbour, Weissella soli LMG 20113T. Whole-cell protein electrophoresis, fluorescent amplified fragment length polymorphism fingerprinting of whole genomes and physiological and biochemical tests confirmed the unique taxonomic position of the two novel isolates. On the basis of the results of the morphological and biochemical tests and 16S rRNA gene sequence analysis, strains 215T and 194B represent the most peripheral lineage of the genus Weissella, for which we propose the name Weissella ghanensis sp. nov. The type strain is 215T (=LMG 24286T=DSM 19935T).
-
-
-
Veillonella magna sp. nov., isolated from the jejunal mucosa of a healthy pig, and emended description of Veillonella ratti
More LessA bacterium, designated strain lac18T, was isolated in pure culture from the mucosal jejunum of a healthy pig, using a medium selective for anaerobic lactic acid bacteria and containing porcine gastric mucin as the main carbon and nitrogen source. Cells of this strain were coccus-shaped, arranged singly or in pairs and were Gram-stain-negative, oxidase-negative, non-spore-forming, anaerobic and microaerotolerant. An analysis based on 16S rRNA gene sequences indicated that strain lac18T should be assigned to the genus Veillonella, class Clostridia, phylum Firmicutes. 16S rRNA and dnaK gene sequence-based phylogenetic analyses both indicated that the most closely related species were Veillonella ratti ATCC 17746T (similarities of 96.6 and 84.5 %, respectively) and Veillonella criceti ATCC 17747T (similarities of 96.6 and 83.4 %, respectively). The results of DNA–DNA hybridizations between strain lac18T and these Veillonella species and the type species of the genus, Veillonella parvula DSM 2008T, confirmed the genotypic distinctness of the novel isolate. Data from phenotypic studies also served to differentiate strain lac18T from related strains. Therefore strain lac18T represents a novel species of the genus Veillonella, for which the name Veillonella magna sp. nov. is proposed. The type strain is lac18T (=CCUG 55454T=CIP 109767T=DSM 19857T=JCM 15053T).
-
-
-
Butyricicoccus pullicaecorum gen. nov., sp. nov., an anaerobic, butyrate-producing bacterium isolated from the caecal content of a broiler chicken
Five isolates that produced large amounts of butyrate were obtained in the course of a study on the butyrate-producing microbiota from the caecal content of a 4-week-old broiler chicken. The five isolates were virtually indistinguishable in biochemical and genetic terms, suggesting that they were derived from a single bacterial clone colonizing this habitat. A phylogenetic analysis based on 16S rRNA gene sequences demonstrated that the five isolates represented a unique lineage within the Clostridium leptum subgroup of the clostridia, with Eubacterium desmolans as the closest phylogenetic neighbour (about 93 % similarity). These data indicate that the five novel isolates represent a single novel species within a novel genus, for which we propose the name Butyricicoccus pullicaecorum gen. nov., sp. nov. The type strain of Butyricicoccus pullicaecorum is 25-3T (=LMG 24109T =CCUG 55265T). The DNA G+C content of strain 25-3T was 54.5 mol% .
-
-
-
Bacillus aidingensis sp. nov., a moderately halophilic bacterium isolated from Ai-Ding salt lake in China
More LessA Gram-positive, halophilic bacterium was isolated from a sediment sample from Ai-Ding salt lake in China. The isolate, designated strain 17-5T, grew at salinities of 8–33 % (w/v) NaCl (optimally at 12 %, w/v). The genomic DNA G+C content of strain 17-5T was 48.1 mol%. The predominant isoprenoid quinone was MK-7(H2) and the cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and an unidentified glycolipid. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 17-5T was a member of the genus Bacillus, being most closely related to Bacillus qingdaonensis JCM 14087T (96.0 % sequence similarity) and Bacillus salarius DSM 16461T (95.6 %). The levels of 16S rRNA gene sequence similarity with respect to other Bacillus species were less than 91.7 %. Comparative analysis of the 16S rRNA gene sequence data, chemotaxonomy and phenotypic features of the novel isolate and related species of Bacillus indicated that strain 17-5T represents a novel species within the genus Bacillus, for which the name Bacillus aidingensis sp. nov. is proposed. The type strain is 17-5T (=CGMCC 1.3227T=DSM 18341T).
-
-
-
Bacillus pallidus sp. nov., isolated from forest soil
Yu Zhou, Wei Wei, Qiaolin Che, Yuxin Xu, Xu Wang, Xing Huang and Ren LaiA Gram-positive bacterium, designated strain CW 7T, was isolated from forest soil in Anhui Province, south-east China. Cells were strictly aerobic, motile with peritrichous flagella and rod-shaped. The strain grew optimally at 30–37 °C and pH 7.0–8.0. The major fatty acids of strain CW 7T were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The G+C content of the genomic DNA was 42.3 mol%. Phylogenetic analysis indicated that strain CW 7T belonged to a monophyletic cluster within the genus Bacillus and showed 16S rRNA gene sequence similarities of less than 96.5 % to recognized species of the genus Bacillus. The results of the polyphasic taxonomic study, including phenotypic, chemotaxonomic and phylogenetic analyses, showed that strain CW 7T represents a novel species of the genus Bacillus, for which the name Bacillus pallidus sp. nov. is proposed. The type strain is CW 7T (=KCTC 13200T=CCTCC AB 207188T=LMG 24451T).
-
-
-
Alicyclobacillus ferrooxydans sp. nov., a ferrous-oxidizing bacterium from solfataric soil
More LessA novel mesophilic and acidophilic Gram-positive bacterium, designated strain TC-34T, was isolated from solfataric soil. Strain TC-34T grew aerobically at 17–40 °C and pH 2.0–6.0, and optimally at 28 °C and pH 3.0. Analysis based on 16S rRNA gene sequences showed that strain TC-34T was phylogenetically related to members of the genus Alicyclobacillus, with the highest similarity (94.8 %) to Alicyclobacillus pomorum. Strain TC-34T showed a range of phenotypic characteristics that differentiated it from recognized Alicyclobacillus species, including growth temperature, assimilation of carbon sources and production of acids from a range of compounds. Strain TC-34T was able to oxidize ferrous iron and its growth was correlated with the oxidation of Fe2+ in culture medium. ω-Alicyclic fatty acids were not detected. On the basis of these results, it was concluded that strain TC-34T represents a novel species of the genus Alicyclobacillus, for which the name Alicyclobacillus ferrooxydans (type strain TC-34T=JCM 15090T=CGMCC 1.6357T) is proposed.
-
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)