scholarly journals Bacillus acidicola sp. nov., a novel mesophilic, acidophilic species isolated from acidic Sphagnum peat bogs in Wisconsin

2005 ◽  
Vol 55 (5) ◽  
pp. 2125-2130 ◽  
Author(s):  
Richard A. Albert ◽  
Julieta Archambault ◽  
Ramón Rosselló-Mora ◽  
Brian J. Tindall ◽  
Mike Matheny
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Peat Bogs ◽  
Peat Bog ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Molecular Analyses ◽  
Sphagnum Peat Bogs ◽  
Bacterium Strain

A mesophilic, acidophilic, spore-forming bacterium, strain 105-2T, was isolated from an acidic Sphagnum peat bog in Wisconsin, USA. Strain 105-2T has 16S rRNA gene sequence similarity to Bacillus sporothermodurans DSM 10599T and Bacillus oleronius DSM 9356T of 97·4 and 97·8 %, respectively. The primary lipoquinone is MK-7 and the major fatty acids are 15 : 0 iso, 15 : 0 anteiso and 17 : 0 anteiso. The predominant polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and a glycolipid. The DNA G+C content was found to be 43·2 mol%. The phenotypic, chemotaxonomic and molecular analyses identified strain 105-2T as a novel Bacillus species, for which the name Bacillus acidicola is proposed. The type strain is 105-2T (=DSM 14745T=ATCC BAA-366T=NRRL B-23453T).

scholarly journals Granulicella paludicola gen. nov., sp. nov., Granulicella pectinivorans sp. nov., Granulicella aggregans sp. nov. and Granulicella rosea sp. nov., acidophilic, polymer-degrading acidobacteria from Sphagnum peat bogs

2010 ◽  
Vol 60 (12) ◽  
pp. 2951-2959 ◽  
Author(s):  
Timofey A. Pankratov ◽  
Svetlana N. Dedysh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Peat Bogs ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence

Five strains of strictly aerobic, heterotrophic bacteria that form pink–red colonies and are capable of hydrolysing pectin, xylan, laminarin, lichenan and starch were isolated from acidic Sphagnum peat bogs and were designated OB1010T, LCBR1, TPB6011T, TPB6028T and TPO1014T. Cells of these isolates were Gram-negative, non-motile rods that produced an amorphous extracellular polysaccharide-like substance. Old cultures contained spherical bodies of varying sizes, which represent starvation forms. Cells of all five strains were acidophilic and psychrotolerant, capable of growth at pH 3.0–7.5 (optimum pH 3.8–4.5) and at 2–33 °C (optimum 15–22 °C). The major fatty acids were iso-C15 : 0, C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). The major menaquinone detected was MK-8. The pigments were carotenoids. The genomic DNA G+C contents were 57.3–59.3 mol%. The five isolates were found to be members of subdivision 1 of the phylum Acidobacteria and displayed 95.3–98.9 % 16S rRNA gene sequence similarity to each other. The closest described relatives to strains OB1010T, LCBR1, TPB6011T, TPB6028T, and TPO1014T were members of the genera Terriglobus (94.6–95.8 % 16S rRNA gene sequence similarity) and Edaphobacter (94.2–95.4 %). Based on differences in cell morphology, phenotypic characteristics and hydrolytic capabilities, we propose a novel genus, Granulicella gen. nov., containing four novel species, Granulicella paludicola sp. nov. with type strain OB1010T (=DSM 22464T =LMG 25275T) and strain LCBR1, Granulicella pectinivorans sp. nov. with type strain TPB6011T (=VKM B-2509T =DSM 21001T), Granulicella rosea sp. nov. with type strain TPO1014T (=DSM 18704T =ATCC BAA-1396T) and Granulicella aggregans sp. nov. with type strain TPB6028T (=LMG 25274T =VKM B-2571T).

scholarly journals Rubritalea marina gen. nov., sp. nov., a marine representative of the phylum ‘Verrucomicrobia’, isolated from a sponge (Porifera)

2006 ◽  
Vol 56 (9) ◽  
pp. 2119-2124 ◽  
Author(s):  
Matthias Scheuermayer ◽  
Tobias A. M. Gulder ◽  
Gerhard Bringmann ◽  
Ute Hentschel
Keyword(s):  
Genomic Dna ◽  
Type Strain ◽  
Marine Bacterium ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Ph Values ◽  
Novel Genus And Species ◽  
Bacterium Strain

A marine bacterium, strain Pol012T, was isolated from the Mediterranean sponge Axinella polypoides and subsequently characterized as belonging to subphylum 1 of the phylum ‘Verrucomicrobia’. Strain Pol012T was non-motile, Gram-negative, coccoid or rod-shaped and red in colour. The menaquinones MK-8 and MK-9 were detected. The G+C content of the genomic DNA was 50.9 mol%. Growth was possible at temperatures between 8 and 30 °C and at pH values between 6.8 and 8.2. The closest cultured relative of strain Pol012T was Akkermansia muciniphila (83 % sequence similarity), while the closest environmental 16S rRNA gene sequence was the marine clone Arctic96BD-2 (95 % sequence similarity). Strain Pol012T is the first marine pure-culture representative of ‘Verrucomicrobia’ subphylum 1 and represents a novel genus and species, for which the name Rubritalea marina gen. nov., sp. nov. is proposed. The type strain is Pol012T (=DSM 177716T=CIP 108984T).

scholarly journals Dechloromonas hortensis sp. nov. and strain ASK-1, two novel (per)chlorate-reducing bacteria, and taxonomic description of strain GR-1

2005 ◽  
Vol 55 (5) ◽  
pp. 2063-2068 ◽  
Author(s):  
Arthur Wolterink ◽  
Sungyoun Kim ◽  
Margje Muusse ◽  
In S. Kim ◽  
Paul J. M. Roholl ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterium Strain ◽  
Reducing Bacteria

Recent studies on the occurrence of (per)chlorate-reducing bacteria have resulted in the characterization of strains capable of dissimilatory (per)chlorate reduction. Phylogenetic analysis has shown that these bacteria are members of the Proteobacteria. Strains have been isolated from polluted and pristine sites, but only strains from polluted sites have been characterized in detail and deposited in culture collections. Herein we describe the isolation and characterization of perchlorate-reducing bacterium strain MA-1T and chlorate-reducing bacterium strain ASK-1, respectively isolated from a pristine and a chlorate-polluted site. Both isolates are members of the Proteobacteria. The 16S rRNA gene sequence similarity of MA-1T to Dechloromonas agitata DSM 13637T is 97·6 %, but the relatedness in DNA–DNA reassociation is only 37 %. Therefore, we propose to classify strain MA-1T (=DSM 15637T=ATCC BAA-776T) as the type strain of a novel species, Dechloromonas hortensis sp. nov. Strain ASK-1 and a previously described strain GR-1 show 100 and 99 % 16S rRNA gene sequence similarity to Pseudomonas chloritidismutans DSM 13592T and Dechlorosoma suillum DSM 13638T, respectively. DNA–DNA hybridization studies indicated that strains ASK-1 and GR-1 are related at the species level to P. chloritidismutans DSM 13592T (79 %) and Dechlorosoma suillum DSM 13638T (85 %), respectively. As suggested previously, Dechlorosoma suillum appears to be a later heterotypic synonym of Azospira oryzae. Although strain ASK-1 is identified as P. chloritidismutans, its morphology and growth requirements are different from those of the type strain.

scholarly journals Exiguobacterium aestuarii sp. nov. and Exiguobacterium marinum sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

2005 ◽  
Vol 55 (2) ◽  
pp. 885-889 ◽  
Author(s):  
In-Gi Kim ◽  
Mi-Hwa Lee ◽  
Seo-Youn Jung ◽  
Jae Jun Song ◽  
Tae-Kwang Oh ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Yellow Sea ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Three Gram-variable, rod-shaped bacterial strains, TF-16T, TF-19 and TF-80T, were isolated from a tidal flat of Daepo Beach (Yellow Sea) near Mokpo City, Korea, and their taxonomic positions were investigated by a polyphasic approach. These isolates grew optimally in the presence of 2 % NaCl and at 30 °C. Their peptidoglycan types were based on l-Lys–Gly. The predominant menaquinone detected in the three strains was MK-7. The three strains contained large amounts of the branched fatty acids iso-C17 : 0, anteiso-C13 : 0, iso-C13 : 0 and iso-C15 : 0. The DNA G+C contents of strains TF-16T, TF-19 and TF-80T were 48·6, 48·4 and 48·0 mol%, respectively. The three strains formed a coherent cluster with Exiguobacterium species in a phylogenetic tree based on 16S rRNA gene sequences. They showed closest phylogenetic affiliation to Exiguobacterium aurantiacum, with 16S rRNA gene sequence similarity values of 98·1–98·3 %. The three strains exhibited 16S rRNA gene sequence similarity values of 94·0–94·6 % to the type strains of other Exiguobacterium species. Levels of DNA–DNA relatedness indicated that strains TF-16T and TF-19 and strain TF-80T are members of two species that are separate from E. aurantiacum. On the basis of phenotypic, phylogenetic and genetic data, strains TF-16T and TF-19 and strain TF-80T represent two novel species in the genus Exiguobacterium; the names Exiguobacterium aestuarii sp. nov. (type strain TF-16T=KCTC 19035T=DSM 16306T; reference strain TF-19) and Exiguobacterium marinum sp. nov. (type strain TF-80T=KCTC 19036T=DSM 16307T) are proposed.

scholarly journals Paenibacillus algorifonticola sp. nov., isolated from a cold spring

2011 ◽  
Vol 61 (9) ◽  
pp. 2167-2172 ◽  
Author(s):  
Qi-Yong Tang ◽  
Na Yang ◽  
Jian Wang ◽  
Yu-Qing Xie ◽  
Biao Ren ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Cold Spring ◽  
Xinjiang Uyghur Autonomous Region ◽  
The 16S Rrna Gene

A Gram-stain-positive, endospore-forming, rod-shaped bacterium, designated XJ259T, was isolated from a cold spring sample from Xinjiang Uyghur Autonomous Region, China. The isolate grew optimally at 20–30 °C and pH 7.3–7.8. Comparative analysis of the 16S rRNA gene sequence showed that isolate XJ259T belonged phylogenetically to the genus Paenibacillus, and was most closely related to Paenibacillus xinjiangensis B538T (with 96.6 % sequence similarity), Paenibacillus glycanilyticus DS-1T (96.3 %) and Paenibacillus castaneae Ch-32T (96.1 %), sharing less than 96.0 % sequence similarity with all other members of the genus Paenibacillus. Chemotaxonomic analysis revealing menaquinone-7 (MK-7) as the major isoprenoid quinone, diphosphatidylglycerol, phosphatidylethanolamine and two unknown phosphoglycolipids as the major cellular polar lipids, a DNA G+C content of 47.0 mol%, and anteiso-C15 : 0 and C16 : 0 as the major fatty acids supported affiliation of the new isolate to the genus Paenibacillus. Based on these data, isolate XJ259T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus algorifonticola sp. nov. is proposed. The type strain is XJ259T ( = CGMCC 1.10223T  = JCM 16598T).

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

2011 ◽  
Vol 61 (8) ◽  
pp. 1954-1961 ◽  
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.

scholarly journals Effusibacillus dendaii sp. nov. isolated from farm soil

2021 ◽  
Author(s):  
Tomoyuki Konishi ◽  
Tomohiko Tamura ◽  
Toru Tobita ◽  
Saori Sakai ◽  
Namio Matsuda ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Genome Analyses

Abstract Gram-positive, rod-shaped, spore-forming, thermophilic, acidophilic bacterium, designated strain skT53T, was isolated from farm soil in Tokyo, Japan. The strain grew aerobically at 37–55°C (optimum 50°C) and pH 4.0–6.0 (optimum 5.0). Phylogenetic analysis of the 16S rRNA gene sequence showed that the isolate was most closely related to the type strain of Effusibacillus consociatus (94.3% similarity). The G + C content of the genomic DNA was 48.22 mol%. MK-7 was the predominant respiratory quinone. The major fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0 and C18:3ω6c. The results of phenotypic and chemotaxonomic, 16S rRNA gene sequence similarity, and whole genome analyses support strain skT53T as representing a novel species of Effusibacillus dendaii sp. nov. is proposed. The type strain is strain skT53T (= NBRC 114101T = TBRC 11241T).

scholarly journals Rarimicrobium hominis gen. nov., sp. nov., representing the fifth genus in the phylum Synergistetes that includes human clinical isolates

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3965-3970 ◽  
Author(s):  
Estelle Jumas-Bilak ◽  
Philippe Bouvet ◽  
Emma Allen-Vercoe ◽  
Fabien Aujoulat ◽  
Paul A. Lawson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Clinical Isolates ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence

Five human clinical isolates of an unknown, strictly anaerobic, slow-growing, Gram-stain-negative, rod-shaped micro-organism were subjected to a polyphasic taxonomic study. Comparative 16S rRNA gene sequence-based phylogeny showed that the isolates grouped in a clade that included members of the genera Pyramidobacter, Jonquetella, and Dethiosulfovibrio; the type strain of Pyramidobacter piscolens was the closest relative with 91.5–91.7 % 16S rRNA gene sequence similarity. The novel strains were mainly asaccharolytic and unreactive in most conventional biochemical tests. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic acid and propionic acid and the major cellular fatty acids were C13 : 0 and C16 : 0, each of which could be used to differentiate the strains from P. piscolens. The DNA G+C content based on whole genome sequencing for the reference strain 22-5-S 12D6FAA was 57 mol%. Based on these data, a new genus, Rarimicrobium gen. nov., is proposed with one novel species, Rarimicrobium hominis sp. nov., named after the exclusive and rare finding of the taxon in human samples. Rarimicrobium is the fifth genus of the 14 currently characterized in the phylum Synergistetes and the third one in subdivision B that includes human isolates. The type strain of Rarimicrobium hominis is ADV70T ( = LMG 28163T = CCUG 65426T).

scholarly journals Corynebacterium tapiri sp. nov. and Corynebacterium nasicanis sp. nov., isolated from a tapir and a dog, respectively

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3885-3893 ◽  
Author(s):  
Sandra Baumgardt ◽  
Igor Loncaric ◽  
Peter Kämpfer ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Established Species

Two Gram-stain-positive bacterial isolates, strain 2385/12T and strain 2673/12T were isolated from a tapir and a dog's nose, respectively. The two strains were rod to coccoid-shaped, catalase-positive and oxidase-negative. The highest 16S rRNA gene sequence similarity identified Corynebacterium singulare CCUG 37330T (96.3 % similarity) as the nearest relative of strain 2385/12T and suggested the isolate represented a novel species. Corynebacterium humireducens DSM 45392T (98.7 % 16S rRNA gene sequence similarity) was identified as the nearest relative of strain 2673/12T. Results from DNA–DNA hybridization with the type strain of C. humireducens demonstrated that strain 2673/12T also represented a novel species. Strain 2385/12T showed a quinone system consisting predominantly of menaquinones MK-8(H2) and MK-9(H2) whereas strain 2673/12T contained only MK-8(H2) as predominant quinone. The polar lipid profiles of the two strains showed the major compounds phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. Phosphatidylinositol was identified as another major lipid in 2673/12T whereas it was only found in moderate amounts in strain 2385/12T. Furthermore, moderate to minor amounts of phosphatidylinositol-mannoside, β-gentiobiosyl diacylglycerol and variable counts of several unidentified lipids were detected in the two strains. Both strains contained corynemycolic acids. The polyamine patterns were characterized by the major compound putrescine in strain 2385/12T and spermidine in strain 2673/12T. In the fatty acid profiles, predominantly C18 : 1ω9c and C16 : 0 were detected. The two strains are distinguishable from each other and the nearest related established species of the genus Corynebacterium phylogenetically and phenotypically. In conclusion, two novel species of the genus Corynebacterium are proposed, namely Corynebacterium tapiri sp. nov. (type strain, 2385/12T = CCUG 65456T = LMG 28165T) and Corynebacterium nasicanis sp. nov. (type strain, 2673/12T = CCUG 65455T = LMG 28166T).

Paenibacillus allorhizosphaerae sp. nov., from soil of the rhizosphere of Zea mays

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Dominique Clermont ◽  
Alexis Criscuolo ◽  
...  
Keyword(s):  
Zea Mays ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A Gram-stain-positive, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays, was studied for its detailed taxonomic allocation. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-447T was shown to be a member of the genus Paenibacillus , most closely related to the type strain of Paenibacillus solanacearum (97.8 %). The 16S rRNA gene sequence similarity values to all other Paenibacillus species were below 97.0 %. DNA–DNA hybridization (DDH) values with the type strain of P. solanacearum were 35.9 % (reciprocal 27%), respectively. The average nucleotide identity and in silico DDH values with the type strain of P. solanacearum were 84.86 and 28.9 %, respectively. The quinone system of strain JJ-447T consisted exclusively of menaquinones and the major component was MK-7 (96.4 %) but minor amounts of MK–6 (3.6 %) were detected as well. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. Major fatty acids were iso- and anteiso-branched with the major compounds anteiso-C15 : 0 and iso-C15 : 0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-447T from the most closely related species on the basis of d-glucose, l-arabinose and d-mannose assimilation and other physiological tests. Thus, JJ-447T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus allorhizosphaerae sp. nov. is proposed, with JJ-447T (=LMG 31601T=CCM 9021T=CIP 111802T) as the type strain.

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