Proposal of a type strain for Frankia alni (Woronin 1866) Von Tubeuf 1895, emended description of Frankia alni, and recognition of Frankia casuarinae sp. nov. and Frankia elaeagni sp. nov.

Seven strains of the genus Sphaerotilus were obtained from natural thermal sulfide (strains D-501T, D-502, D-504, D-505 and D-507) and low-temperature ferrous (strain HST) springs and from an activated sludge system (strain D-380). These Sphaerotilus isolates and strains of Sphaerotilus natans obtained from the DSMZ (S. natans DSM 6575T, DSM 565 and DSM 566) were studied using a polyphasic taxonomic approach. All strains had Q-8 as the major quinone and C16 : 1ω7, C16 : 0 and C18 : 1ω7 as the major fatty acids. The DNA–DNA hybridization results and 16S rRNA, hsp60 and gyrB gene sequencing experiments showed that isolates D-501T, D-502, D-504, D-505, D-507 and D-380 were closely related to the type strain of S. natans DSM 6575T. However, strains D-501T, D-502, D-504, D-505 and D-507 significantly differed from the heterotrophic strain S. natans DSM 6575T by their capability for lithotrophic growth with reduced sulfur compounds as an electron donor for energy conservation and some other phenotypic features. For this reason, strains D-501T, D-502, D-504, D-505 and D-507 merit a separate taxonomic classification at the subspecies level. The name Sphaerotilus natans subsp. sulfidivorans subsp. nov. (type strain D-501T = DSM 22545T = VKM B-2573T) is proposed. The subspecies Sphaerotilus natans subsp. natans subsp. nov. is automatically created as a result of this proposal. Strain D-380 was phenotypically closely related to S. natans DSM 6575T. Strains D-380 and S. natans DSM 6575T were assigned to the subspecies Sphaerotilus natans subsp. natans subsp. nov. (type strain DSM 6575T = ATCC 13338T). The 16S rRNA, hsp60 and gyrB gene sequences obtained for strains HST and DSM 565 showed very low sequence similarity values of 97.3 %, 89.7 % and 88.4 %, respectively, with S. natans DSM 6575T. Strain HST shared 99 % DNA–DNA relatedness with strain

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Bacillus thermolactis sp. nov., isolated from dairy farms, and emended description of Bacillus thermoamylovorans

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.024240-0 ◽

2011 ◽

Vol 61 (8) ◽

pp. 1954-1961 ◽

Cited By ~ 36

Author(s):

An Coorevits ◽

Niall A. Logan ◽

Anna E. Dinsdale ◽

Gillian Halket ◽

Patsy Scheldeman ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Strain ◽

Gene Sequence ◽

Sequence Similarity ◽

Diaminopimelic Acid ◽

16S Rrna Gene Sequence ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Emended Description

A polyphasic taxonomic study was performed on 22 thermotolerant, aerobic, endospore-forming bacteria from dairy environments. Seventeen isolates were retrieved from raw milk, one from a filter cloth and four from grass, straw or milking equipment. These latter four isolates (R-6546, R-7499, R-7764 and R-7440) were identified as Bacillus thermoamylovorans based on DNA–DNA hybridizations (values above 70 % with Bacillus thermoamylovorans LMG 18084T) but showed discrepancies in characteristics with the original species description, so an emended description of this species is given. According to 16S rRNA gene sequence analysis and DNA–DNA hybridization experiments, the remaining 18 isolates (R-6488T, R-28193, R-6491, R-6492, R-7336, R-33367, R-6486, R-6770, R-31288, R-28160, R-26358, R-7632, R-26955, R-26950, R-33520, R-6484, R-26954 and R-7165) represented one single species, most closely related to Bacillus thermoamylovorans (93.9 % 16S rRNA gene sequence similarity), for which the name Bacillus thermolactis is proposed. Cells were Gram-stain-positive, facultatively anaerobic, endospore-forming rods that grew optimally at 40–50 °C. The cell wall peptidoglycan type of strain R-6488T, the proposed type strain, was A1γ based on meso-diaminopimelic acid. Major fatty acids of the strains were C16 : 0 (28.0 %), iso-C16 : 0 (12.1 %) and iso-C15 : 0 (12.0 %). MK-7 was the predominant menaquinone, and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and some unidentified phospholipids. DNA G+C content was 35.0 mol%. Phenotypic properties allowed discrimination from other thermotolerant species of the genus Bacillus and supported the description of the novel species Bacillus thermolactis, with strain R-6488T ( = LMG 25569T = DSM 23332T) as the proposed type strain.

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Description of Sulfitobacter donghicola sp. nov., isolated from seawater of the East Sea in Korea, transfer of Staleya guttiformis Labrenz et al. 2000 to the genus Sulfitobacter as Sulfitobacter guttiformis comb. nov. and emended description of the genus Sulfitobacter

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.65071-0 ◽

2007 ◽

Vol 57 (8) ◽

pp. 1788-1792 ◽

Cited By ~ 33

Author(s):

Jung-Hoon Yoon ◽

So-Jung Kang ◽

Mi-Hwa Lee ◽

Tae-Kwang Oh

Keyword(s):

Type Strain ◽

Gene Sequence ◽

Novel Species ◽

Sequence Similarity ◽

Major Fatty Acid ◽

East Sea ◽

Rrna Gene ◽

Phenotypic Properties ◽

Unidentified Phospholipid ◽

Emended Description

A Gram-negative, non-motile and rod-, oval- or coccoid-shaped bacterial strain, DSW-25T, which is phylogenetically closely related to the genera Staleya and Sulfitobacter, was isolated from seawater of the East Sea, Korea, and subjected to a polyphasic taxonomic study. Strain DSW-25T grew optimally at pH 7.0–8.0 and at 25 °C. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. Major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The DNA G+C content was 56.9 mol%. Strain DSW-25T exhibited 16S rRNA gene sequence similarity values of 98.4 % to the type strain of Staleya guttiformis and of 96.6–97.6 % to Sulfitobacter species. There were no distinct phenotypic, particularly chemotaxonomic, properties to differentiate Staleya guttiformis and strain DSW-25T from the genus Sulfitobacter. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain DSW-25T differs from recognized Sulfitobacter species and Staleya guttiformis. On the basis of phenotypic, chemotaxonomic, phylogenetic and genetic data, strain DSW-25T was classified in the genus Sulfitobacter as a member of a novel species, for which the name Sulfitobacter donghicola sp. nov. is proposed. The type strain is strain DSW-25T (=KCTC 12864T =JCM 14565T). It is also proposed that Staleya guttiformis be transferred to the genus Sulfitobacter as Sulfitobacter guttiformis comb. nov.

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Henriciella litoralis sp. nov., isolated from a tidal flat, transfer of Maribaculum marinum Lai et al. 2009 to the genus Henriciella as Henriciella aquimarina nom. nov. and emended description of the genus Henriciella

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.020396-0 ◽

2011 ◽

Vol 61 (4) ◽

pp. 722-727 ◽

Cited By ~ 54

Author(s):

Se Hee Lee ◽

Jae Kuk Shim ◽

Jeong Myeong Kim ◽

Hyung-Kyoon Choi ◽

Che Ok Jeon

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Tidal Flat ◽

Type Strain ◽

Gene Sequence ◽

The Yellow Sea ◽

16S Rrna Gene Sequence ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Emended Description

A Gram-staining-negative, strictly aerobic bacterium, designated strain SD10T, was isolated from a tidal flat of the Yellow Sea, South Korea. Cells were non-spore-forming rods that showed catalase- and oxidase-positive reactions. Growth of strain SD10T was observed at 15–40 °C (optimum, 25–30 °C), at pH 6.0–9.0 (optimum, pH 6.5–8.5) and in the presence of 1–10 % (w/v) NaCl. Strain SD10T contained ubiquinone-10 (Q-10) as a major isoprenoid quinone and C18 : 1ω7c (39.3 %), C16 : 0 (20.2 %), C17 : 0 (8.9 %) and C17 : 1ω6c (8.1 %) as major fatty acids. The cellular polar lipids were identified as phosphatidylglycerol, monoglycosyldiglyceride, glucuronopyranosyldiglyceride and two unidentified glycolipids. The G+C content of the genomic DNA was 55.2 mol%. Based on 16S rRNA gene sequence similarities, the strain was most closely related to Henriciella marina Iso4T and Maribaculum marinum P38T, with similarities of 97.8 and 97.0 %, respectively. The DNA–DNA relatedness between strain SD10T and H. marina Iso4T was 12.0±3.2 %. A phylogenetic analysis based on 16S rRNA gene sequences showed that M. marinum P38T and H. marina Iso4T formed a monophyletic cluster and that their 16S rRNA gene sequence similarity was 98.1 %. DNA–DNA hybridization between H. marina Iso4T and M. marinum LMG 24711T was 22.9±2.7 %, indicating that the two strains belong to separate species. On the basis of chemotaxonomic data and molecular properties, we propose that strain SD10T represents a novel species of the genus Henriciella, for which the name Henriciella litoralis sp. nov. is proposed. The type strain is SD10T ( = KACC 13700T = DSM 22014T). In addition, we propose to transfer Maribaculum marinum Lai et al. 2009 to the genus Henriciella as Henriciella aquimarina nom. nov. (type strain P38T = CCTCC AB 208227T = LMG 24711T = MCCC 1A01086T), and we present an emended description of the genus Henriciella.

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Pseudomonas moraviensis sp. nov. and Pseudomonas vranovensis sp. nov., soil bacteria isolated on nitroaromatic compounds, and emended description of Pseudomonas asplenii

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63988-0 ◽

2006 ◽

Vol 56 (11) ◽

pp. 2657-2663 ◽

Cited By ~ 47

Author(s):

Ludmila Tvrzová ◽

Peter Schumann ◽

Cathrin Spröer ◽

Ivo Sedláček ◽

Zdena Páčová ◽

...

Keyword(s):

Dna Hybridization ◽

Type Strain ◽

Additional Data ◽

Sequence Similarity ◽

Rrna Gene ◽

Gram Negative Bacteria ◽

Selective Enrichment ◽

Gene Sequence Analysis ◽

Emended Description ◽

Pseudomonas Jessenii

Two strains of Gram-negative bacteria isolated from soil by selective enrichment with nitroaromatics were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA gene sequence analysis, the two strains were found to belong to the genus Pseudomonas, within the Gammaproteobacteria. Strain 1B4T shared the highest sequence similarity with Pseudomonas koreensis DSM 16610T (99.5 %) and Pseudomonas jessenii CCM 4840T (99.3 %), and strain 2B2T with Pseudomonas asplenii DSM 17133T (98.9 %), Pseudomonas fuscovaginae DSM 7231T (98.9 %) and Pseudomonas putida DSM 291T (98.7 %). On the basis of phylogenetic analysis, DNA–DNA hybridization and phenotype, including chemotaxonomic characteristics, two novel species, Pseudomonas moraviensis sp. nov. with the type strain 1B4T (=CCM 7280T=DSM 16007T) and Pseudomonas vranovensis sp. nov. with the type strain 2B2T (=CCM 7279T=DSM 16006T), are proposed. The description of P. asplenii was emended on the basis of additional data obtained in this study.

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Microcella alkaliphila sp. nov., a novel member of the family Microbacteriaceae isolated from a non-saline alkaline groundwater, and emended description of the genus Microcella

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64320-0 ◽

2006 ◽

Vol 56 (10) ◽

pp. 2313-2316 ◽

Cited By ~ 28

Author(s):

Igor Tiago ◽

Paula V. Morais ◽

Milton S. da Costa ◽

António Veríssimo

Keyword(s):

Type Strain ◽

Rrna Gene ◽

Saline Groundwater ◽

Optimum Growth Temperature ◽

Groundwater Environment ◽

Dna Reassociation ◽

Gene Sequence Analysis ◽

The Family ◽

Emended Description ◽

Diamino Acid

A high-G+C-content Gram-positive bacterium, designated as strain AC4rT, was isolated from a highly alkaline, non-saline groundwater environment (pH 11.4). This organism formed small rod-shaped cells, was aerobic, heterotrophic, catalase-positive and oxidase-negative and had an optimum growth temperature of 35 °C and an optimum pH of 9.5. The strain possessed a B2β-type cell-wall peptidoglycan, with d-Orn as the diagnostic diamino acid. The major respiratory quinones were unsaturated menaquinones with 13 and 14 isoprene units. The predominant fatty acids were anteiso-15 : 0, iso-16 : 0, iso-14 : 0 and iso-15 : 0. The G+C content of the DNA was 67.1 mol%. In a 16S rRNA gene sequence analysis, strain AC4rT showed the highest level of similarity (99.2 %) to the type strain of Microcella putealis; however, the DNA–DNA reassociation value between these two organisms was low (38.3 %). On the basis of phylogenetic analysis, the DNA–DNA reassociation value and distinct phenotypic characteristics, strain AC4rT represents a novel species within the genus Microcella, for which the name Microcella alkaliphila sp. nov. is proposed. The type strain is AC4rT (=LMG 22690T=CIP 108473T).

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Anaerostipes butyraticus sp. nov., an anaerobic, butyrate-producing bacterium from Clostridium cluster XIVa isolated from broiler chicken caecal content, and emended description of the genus Anaerostipes

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.015289-0 ◽

2010 ◽

Vol 60 (5) ◽

pp. 1108-1112 ◽

Cited By ~ 31

Author(s):

Venessa Eeckhaut ◽

Filip Van Immerseel ◽

Frank Pasmans ◽

Evie De Brandt ◽

Freddy Haesebrouck ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Strain ◽

Broiler Chicken ◽

Rrna Gene ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

Caecal Content ◽

Emended Description ◽

Bacterial Clone

Four butyrate-producing isolates were obtained from the caecal content of a 4-week-old broiler chicken. The 16S rRNA gene sequences were determined and confirmed the close relatedness of the four isolates, which suggested that they were derived from a single bacterial clone. Phylogenetic analysis based on 16S rRNA gene sequences showed that its closest relatives were members of cluster XIVa of the Clostridium subphylum of Gram-positive bacteria and that the closest related type strain was Anaerostipes caccae L1-92T (94.5 % similarity). Similarity levels of 96–98 % with sequences from uncultured bacteria from human stool samples were observed. On the basis of morphological, biochemical and phylogenetic characteristics, this strain is assigned to a novel species in the genus Anaerostipes, for which the name Anaerostipes butyraticus sp. nov. is proposed. The type strain is 35-7T (=LMG 24724T =DSM 22094T). An emended description of the genus Anaerostipes is also provided.

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Sphingosinicella vermicomposti sp. nov., isolated from vermicompost, and emended description of the genus Sphingosinicella

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.010777-0 ◽

2010 ◽

Vol 60 (3) ◽

pp. 580-584 ◽

Cited By ~ 20

Author(s):

Muhammad Yasir ◽

Zubair Aslam ◽

Geun Cheol Song ◽

Che Ok Jeon ◽

Young Ryun Chung

Keyword(s):

Type Strain ◽

Novel Species ◽

Rrna Gene ◽

Gram Stain ◽

16S Rrna Gene Sequences ◽

Respiratory Quinone ◽

The Family ◽

Emended Description ◽

Major Respiratory Quinone ◽

Total Dna

A Gram-stain-negative, rod-shaped bacterium, designated strain YC7378T was isolated from vermicompost (VC) collected at Masan, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain YC7378T grew optimally at 30 °C and at pH 6.5–8.5. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YC7378T belongs to the genus Sphingosinicella in the family Sphingomonadaceae. The most closely related strains are Sphingosinicella soli KSL-125T (95.7 %), Sphingosinicella xenopeptidilytica 3-2W4T (95.6 %) and Sphingosinicella microcystinivorans Y2T (95.5 %). Strain YC7378T contained ubiquinone Q-10 as the major respiratory quinone system and sym-homospermidine as the major polyamine. The major fatty acids of strain YC7378T were C18 : 1 ω7c, C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C14 : 0 2-OH and C16 : 0. The major polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The total DNA G+C content was 59.4 mol%. The phenotypic, phylogenetic and chemotaxonomic data showed that strain YC7378T represents a novel species of the genus Sphingosinicella, for which the name Sphingosinicella vermicomposti sp. nov. is proposed. The type strain is YC7378T (=KCTC 22446T =DSM 21593T).

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Skermanella aerolata sp. nov., isolated from air, and emended description of the genus Skermanella

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64676-0 ◽

2007 ◽

Vol 57 (7) ◽

pp. 1539-1542 ◽

Cited By ~ 27

Author(s):

Hang-Yeon Weon ◽

Byung-Yong Kim ◽

Seung-Beom Hong ◽

Jae-Ho Joa ◽

Sang-Sik Nam ◽

...

Keyword(s):

Genomic Dna ◽

Type Strain ◽

Novel Species ◽

Optimal Growth ◽

Rrna Gene ◽

Strictly Aerobic ◽

16S Rrna Gene Sequences ◽

Emended Description ◽

Air Sample ◽

Sequence Similarities

A light-pink-coloured bacterium, designated strain 5416T-32T, was isolated from an air sample in Korea. Cells of the strain were strictly aerobic, Gram-negative, motile (single polar or subpolar flagellum) and rod-shaped. Optimal growth occurred at 25–30 °C and at pH 6.0–7.0. The major quinones were Q-10 and Q-8. The major fatty acids were C18 : 1 ω7c (53.8 %) and C16 : 0 (15.9 %). The G+C content of the genomic DNA was 65.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 5416T-32T was most closely related to Skermanella parooensis, with a similarity of 96.2 %, but relatively low sequence similarities (<92 %) were found with respect to other species with validly published names held in GenBank. Phenotypic and genotypic analyses indicated that strain 5416T-32T could not be assigned to any recognized species. Therefore strain 5416T-32T represents a novel species of the genus Skermanella, for which the name Skermanella aerolata sp. nov. is proposed. The type strain is 5416T-32T (=KACC 11604T=DSM 18479T).

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