scholarly journals Actinospica robiniae gen. nov., sp. nov. and Actinospica acidiphila sp. nov.: proposal for Actinospicaceae fam. nov. and Catenulisporinae subord. nov. in the order Actinomycetales

2006 ◽  
Vol 56 (8) ◽  
pp. 1747-1753 ◽  
Author(s):  
Linda Cavaletti ◽  
Paolo Monciardini ◽  
Peter Schumann ◽  
Manfred Rohde ◽  
Ruggiero Bamonte ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Whole Cell ◽  
Distinct Cluster

Two novel Gram-positive, acidophilic bacterial strains were isolated from forest soil. According to their 16S rRNA gene sequences, these strains are related closely to each other and form a distinct cluster within the order Actinomycetales. They show the typical features of filamentous actinomycetes, with branched vegetative hyphae and production of aerial hyphae. The distinct phylogenetic positions and the combination of chemotaxonomic characteristics of these strains justify the proposal of Actinospica gen. nov. Both strains display 3-hydroxydiaminopimelic acid plus traces of meso-diaminopimelic acid, the phospholipids diphosphatidylglycerol, phosphatidylethanolamine, methylphosphatidylethanolamine and phosphatidylinositol, the predominant cellular fatty acids i-C15 : 0, i-C16 : 0 and ai-C15 : 0 and the whole-cell sugars mannose and rhamnose. They differ in the fatty acid profiles, in the quantitative ratios of the major menaquinones MK-9(H4), MK-9(H6) and MK-9(H8) and in the occurrence of additional whole-cell sugars (arabinose and xylose in strain GE134766T and galactose in strain GE134769T). Differences in the phenotypic characteristics and in the 16S rRNA gene sequences suggest the description of two species, Actinospica robiniae gen. nov., sp. nov. (the type species) and Actinospica acidiphila sp. nov., with the type strains GE134769T (=DSM 44927T=NRRL B-24432T) and GE134766T (=DSM 44926T=NRRL B-24431T), respectively. The DNA G+C contents of strains GE134769T and GE134766T are 70.8 and 69.2 mol%, respectively. Due to the large phylogenetic distance from known actinomycete genera, it is proposed to accommodate Actinospica gen. nov. in Actinospicaceae fam. nov. In addition, Catenulisporineae subord. nov. is proposed to harbour Actinospicaceae fam. nov. and the newly proposed family Catenulisporaceae, described in the accompanying paper.

scholarly journals Bacillus galliciensis sp. nov., isolated from faeces of wild seahorses (Hippocampus guttulatus)

2010 ◽  
Vol 60 (4) ◽  
pp. 892-895 ◽  
Author(s):  
José Luis Balcázar ◽  
José Pintado ◽  
Miquel Planas
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Positive Staining ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
North West ◽  
Hippocampus Guttulatus

A Gram-positive-staining, motile, rod-shaped, endospore-forming bacterium (BFLP-1T) was isolated from faeces of wild long-snouted seahorses (Hippocampus guttulatus) captured in north-west Spain (Toralla, Galicia). Strain BFLP-1T grew at 10–30 °C and pH 5.5–9 (optimally at 20 °C and pH 7.2) and with 0–7 % (w/v) NaCl (optimally with 2 % NaCl). The G+C content of the DNA was 48.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BFLP-1T was a member of the genus Bacillus and was most closely related to Bacillus herbersteinensis D-1,5aT (96.6 %), B. shackletonii LMG 18435T (96.0 %) and B. isabeliae CVS-8T (95.9 %). Chemotaxonomic data (peptidoglycan type, meso-diaminopimelic acid; major menaquinone, MK-7; predominant fatty acids, anteiso-C15 : 0, anteiso-C17 : 0 and C16 : 1 ω11c; major polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown aminoglycophospholipid) supported the affiliation of strain BFLP-1T to the genus Bacillus. Comparative analysis of 16S rRNA gene sequences and chemotaxonomic and phenotypic features indicated that strain BFLP-1T represents a novel species within the genus Bacillus, for which the name Bacillus galliciensis sp. nov. is proposed. The type strain is BFLP-1T (=DSM 21539T =LMG 24668T).

scholarly journals Croceifilum oryzae gen. nov., sp. nov., isolated from rice paddy soil

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4061-4065 ◽  
Author(s):  
Kouta Hatayama ◽  
Teruaki Kuno
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Paddy Soil ◽  
Rice Paddy ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Rice Paddy Soil

A mesophilic, aerobic, Gram-stain-positive, filamentous bacterial strain, designated ZYf1a3T, was isolated from rice paddy soil in Japan. This strain grew on a solid medium with formation of substrate mycelium; endospores were produced singly along the mycelium. Formation of aerial mycelium was not observed on any of the media tested. This strain produced a characteristic saffron yellow soluble pigment. Cloned 16S rRNA gene sequences of strain ZYf1a3T yielded three different copies (similarity between the three sequences: 99.8–99.9 %). One of these sequences had one base deletion. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain ZYf1a3T belongs to an independent phylogenetic lineage of the family Thermoactinomycetaceae. The cell wall of strain ZYf1a3T contained meso-diaminopimelic acid, alanine and glutamic acid, but no characteristic sugars. It contained menaquinone 7 as the sole menaquinone. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0.The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl-N-methylethanolamine and unidentified aminophospholipids. The DNA G+C content was 42.5 mol%. From phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics, this strain is considered to represent a novel species in a new genus, for which the name Croceifilum oryzae gen. nov., sp. nov. is proposed. The type strain of Croceifilum oryzae is ZYf1a3T ( = JCM 30426T = CCUG 66446T = DSM 46876T).

scholarly journals Caenispirillum bisanense gen. nov., sp. nov., isolated from sludge of a dye works

2007 ◽  
Vol 57 (6) ◽  
pp. 1217-1221 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Sooyeon Park ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
The 16S Rrna Gene

Two Gram-negative, non-spore-forming, motile and helical-shaped bacterial strains, K92T and K93, were isolated from sludge from a dye works in Korea, and their taxonomic positions were investigated by means of a polyphasic approach. Strains K92T and K93 grew optimally at 37 °C and pH 7.0–8.0 in the presence of 0.5 % (w/v) NaCl. They contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified amino-group-containing lipids that were ninhydrin-positive. Their DNA G+C contents were 70.0 mol%. The 16S rRNA gene sequences of K92T and K93 showed no differences, and the two strains had a mean DNA–DNA relatedness of 93 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains K92T and K93 formed a distinct evolutionary lineage within the Alphaproteobacteria. The 16S rRNA gene sequences of strains K92T and K93 exhibited similarity values of less than 91.5 % with respect to the 16S rRNA gene sequences of other members of the Alphaproteobacteria. The two strains were distinguishable from phylogenetically related genera through differences in several phenotypic properties. On the basis of the phenotypic, phylogenetic and genetic data, strains K92T and K93 represent a novel genus and species, for which the name Caenispirillum bisanense gen. nov., sp. nov. is proposed. The type strain of Caenispirillum bisanense is K92T (=KCTC 12839T=JCM 14346T).

Novel mycolic acid-containing bacteria in the family Segniliparaceae fam. nov., including the genus Segniliparus gen. nov., with descriptions of Segniliparus rotundus sp. nov. and Segniliparus rugosus sp. nov.

2005 ◽  
Vol 55 (4) ◽  
pp. 1615-1624 ◽  
Author(s):  
W. Ray Butler ◽  
Margaret M. Floyd ◽  
June M. Brown ◽  
Sean R. Toney ◽  
Maryam I. Daneshvar ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Health Department ◽  
Mycolic Acid ◽  
Diaminopimelic Acid ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Mycolic Acids

Four strains of novel, rapidly growing, acid–alcohol-fast-staining bacteria were characterized with a polyphasic approach. Isolates were received by the Centers for Disease Control and Prevention from domestic health department laboratories for reference testing as unidentifiable, clinical mycobacteria. Bacteria were rod-shaped and produced non-pigmented (white to beige), non-photochromogenic, smooth or wrinkled-rough colonies on Middlebrook 7H10 and 7H11 media at 33 °C. The smooth and wrinkled colony forms were representative of two species with 68·0 and 72·0 mol% DNA G+C content. The cell wall contained meso-diaminopimelic acid and mycolic acids. Species were characterized by cellular fatty acids of C10 : 0, C14 : 0, C16 : 1ω9t, C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0 (tuberculostearic acid). HPLC analysis of mycolic acids produced a novel late-emerging, genus-specific mycolate pattern. TLC analysis demonstrated a novel α +-mycolate. Species were 98·9 % similar by comparison of 16S rRNA gene sequences; however, the DNA–DNA association was <28 %. Phylogenetic analysis of 16S rRNA gene sequences demonstrated an association with Rhodococcus equi, although a DNA–DNA relatedness value of 2 % did not support a close relationship. PCR analysis of a proposed, selected actinomycete-specific 439 bp fragment of the 65 kDa heat-shock protein was negative for three of the four isolates. The creation of Segniliparaceae fam. nov. is proposed to encompass the genus Segniliparus gen. nov., including two novel species, the type species Segniliparus rotundus sp. nov. and Segniliparus rugosus sp. nov., with the respective type strains CDC 1076T (=ATCC BAA-972T=CIP 108378T) and CDC 945T (=ATCC BAA-974T=CIP 108380T).

scholarly journals Limnohabitans planktonicus sp. nov. and Limnohabitans parvus sp. nov., planktonic betaproteobacteria isolated from a freshwater reservoir, and emended description of the genus Limnohabitans

2010 ◽  
Vol 60 (12) ◽  
pp. 2710-2714 ◽  
Author(s):  
Vojtěch Kasalický ◽  
Jan Jezbera ◽  
Karel Šimek ◽  
Martin W. Hahn
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Phylogenetic Cluster ◽  
The 16S Rrna Gene

Two bacterial strains, II-B4T and II-D5T, isolated from the meso-eutrophic freshwater Římov reservoir (Czech Republic), were characterized phenotypically, phylogenetically and chemotaxonomically. Both strains were chemo-organotrophic, facultatively anaerobic, non-motile rods, with identical DNA G+C contents of 59.9 mol%. Their major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and their major fatty acids were C16 : 1 ω7c/C16 : 1 ω6c, C16 : 0, C18 : 1 ω7c/C18 : 1 ω6c and C12 : 0. Both strains contained Q-8 as the only respiratory quinone component. The 16S rRNA gene sequences of the two strains possessed 99.1 % similarity; however, the level of DNA–DNA reassociation was only 26.7 %. The strains can also be discriminated from each other by several chemotaxonomic and biochemical traits. Phylogenetic analysis of the 16S rRNA gene sequences revealed the affiliation of both strains with the genus Limnohabitans within the family Comamonadaceae. The two investigated strains represent the first isolated members of a narrow phylogenetic cluster (the so-called R-BT065 cluster) formed by a large number of environmental sequences and abundant populations detected in the pelagic zones of various freshwater habitats. We propose to place the two strains in separate novel species within the genus Limnohabitans, Limnohabitans planktonicus sp. nov., with the type strain II-D5T (=DSM 21594T =CIP 109844T), and Limnohabitans parvus sp. nov., with the type strain II-B4T (=DSM 21592T =CIP 109845T). The description of the genus Limnohabitans is emended accordingly.

scholarly journals Maribacter dokdonensis sp. nov., isolated from sea water off a Korean island, Dokdo

2005 ◽  
Vol 55 (5) ◽  
pp. 2051-2055 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Choong-Hwan Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sea Water ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness

Two Gram-negative, non-spore-forming, slightly halophilic gliding bacterial strains, DSW-8T and DSW-9, were isolated from sea water off a Korean island, Dokdo, of the East Sea, Korea, and their taxonomic position was investigated by a polyphasic study. The two strains grew optimally at 30 °C and in the presence of 2–3 % (w/v) NaCl. Strains DSW-8T and DSW-9 were characterized chemotaxonomically as containing MK-6 as the predominant menaquinone and iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 1 as the major fatty acids. Major polar lipids were phosphatidylethanolamine, two unidentified phospholipids, an unidentified glycolipid and an amino group-containing lipid that was ninhydrin-positive. Their DNA G+C contents were 36·1 and 35·9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains DSW-8T and DSW-9 fell within the genus Maribacter of the family Flavobacteriaceae. Strains DSW-8T and DSW-9 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 89 %. Strains DSW-8T and DSW-9 exhibited 16S rRNA gene sequence similarity levels of 96·9–98·0 % to the type strains of the four recognized Maribacter species, but their low level of DNA–DNA relatedness with these species demonstrated that they constitute a distinct Maribacter species. On the basis of phenotypic and phylogenetic data and genetic distinctiveness, strains DSW-8T (=KCTC 12393T=DSM 17201T) and DSW-9 were classified in the genus Maribacter as members of a novel species, for which the name Maribacter dokdonensis sp. nov. is proposed.

scholarly journals Woodsholea maritima gen. nov., sp. nov., a marine bacterium with a low diversity of polar lipids

2004 ◽  
Vol 54 (4) ◽  
pp. 1227-1234 ◽  
Author(s):  
Wolf-Rainer Abraham ◽  
Carsten Strömpl ◽  
Marc Vancanneyt ◽  
Antonio Bennasar ◽  
Jean Swings ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Gene Sequencing ◽  
Single Strand Conformation Polymorphism ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Low Diversity

Two cauliform bacteria (CM243T and CM251) isolated by J. Poindexter from the Atlantic Ocean were characterized by 16S rRNA gene sequencing, TaqI restriction fragment length polymorphism and single-strand conformation polymorphism analyses of the internally transcribed 16S–23S rDNA spacer (ITS1) region, analysis of fatty acids from cellular lipids, mass spectrometry of polar lipids and physiological properties. The two strains showed very low diversity of polar lipids with diacyl-sulfoquinovosyl glycerols as the predominant lipids. The two bacterial strains were observed to have nearly identical 16S rRNA gene sequences and could not be differentiated by their ITS1 regions. The isolates differed from species of the genus Maricaulis by their 16S rRNA gene sequences, polar lipids and fatty acid patterns. On the basis of the genotypic analyses and estimations of phylogenetic similarities, physiological and chemotaxonomic characteristics, it is proposed that the isolates represent a new genus and species, for which the name Woodsholea maritima gen. nov., sp. nov. (type strain CM243T=VKM B-1512T=LMG 21817T) is proposed.

scholarly journals Brevundimonas kwangchunensis sp. nov., isolated from an alkaline soil in Korea

2006 ◽  
Vol 56 (3) ◽  
pp. 613-617 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Hyun Woo Oh ◽  
Jung-Sook Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness

Two Gram-negative, rod-shaped bacterial strains, KSL-102T and KSL-110, were isolated from an alkaline soil in Korea, and their taxonomic positions were investigated by use of a polyphasic study. The two strains grew optimally at pH 7·0–8·0 and 30 °C without NaCl. They contained Q-10 as the predominant ubiquinone. The major fatty acids were C18 : 1 ω7c and C16 : 0 on trypticase soy agar, but 11-methyl C18 : 1 ω7c was also a major component when the two strains were cultivated on LMG medium no. 221. Their DNA G+C contents were 68·4–68·7 mol%. Strains KSL-102T and KSL-110 exhibited three nucleotide differences in their 16S rRNA gene sequences and a mean DNA–DNA relatedness value of 85 %. Phylogenetic trees based on 16S rRNA gene sequences showed that the two strains fell within the evolutionary radiation encompassed by the genus Brevundimonas. Levels of 16S rRNA gene sequence similarity between the two strains and the type strains of recognized Brevundimonas species ranged from 96·3 to 98·4 %. DNA–DNA relatedness levels between the two strains and recognized Brevundimonas species were 8–21 %. On the basis of phenotypic, phylogenetic and genetic data, strains KSL-102T and KSL-110 were classified in the genus Brevundimonas as members of a novel species, for which the name Brevundimonas kwangchunensis sp. nov. is proposed. The type strain is KSL-102T (=KCTC 12380T=DSM 17033T).

scholarly journals Salinibacterium hongtaonis sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai–Tibet Plateau

2019 ◽  
Vol 69 (4) ◽  
pp. 1093-1098 ◽  
Author(s):  
Junqin Li ◽  
Shan Lu ◽  
Dong Jin ◽  
Jing Yang ◽  
Xin-He Lai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tibet Plateau ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Qinghai Tibet Plateau

Two novel aerobic, Gram-staining-positive and non-spore-forming bacterial strains, 194T and S1194, were isolated from faeces of Tibetan antelopes sampled at the Qinghai–Tibet Plateau of China. The strains were able to grow in medium up to 10 % NaCl, similar to the NaCl-resistant property of the genus Salinibacterium members. The 16S rRNA gene sequences of the strains showed the highest similarity to Salinibacterium xinjiangense(98.1–98.2 %), and phylogenetic analysis based on 16S rRNA gene sequences indicated that strains 194T and S1194 represent a new lineage. The DNA G+C contents of strain 194T and S1194 are 64.1 and 64.2 mol%. Their genomes exhibit less than 96 % average nucleotide identity and 70 % DNA–DNA relatedness to known species of Salinibacterium . Strains 194T and S1194 are unable to utilize d-mannose or produce naphthol-AS-BI-phosphohydrolase. The two strains had anteiso-C15 : 0 and anteiso-C17 : 0 as major fatty acids, and their cell walls contained lysine, alanine, glycine and glutamic acid. The predominant menaquinones identified were MK-11 and MK-10, with diphosphatidylglycerol and phosphatidylglycerol as major polar lipids. Overall, the major cellular content profiles of 194T agreed with those of Salinibacterium xinjiangense and Salinibacterium amurskyense, though the proportions were distinct. Based on genotypic, phenotypic and biochemical analyses, the novel species Salinibacterium hongtaonis sp. nov. is proposed. The type strain is 194T (=CGMCC 1.16371T=DSM 106171T).

scholarly journals Nocardioides kribbensis sp. nov., isolated from an alkaline soil

2005 ◽  
Vol 55 (4) ◽  
pp. 1611-1614 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
In-Gi Kim ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness

Three Gram-positive, rod- or coccoid-shaped bacterial strains, KSL-2T, KSL-5 and KSL-6, were isolated from an alkaline soil in Korea and subjected to a polyphasic taxonomical analysis. These isolates grew optimally at pH 9·0 and 30 °C. They were characterized chemotaxonomically as having cell wall peptidoglycan based on ll-2,6-diaminopimelic acid, MK-8(H4) as the predominant menaquinone and iso-C16 : 0 as the major fatty acid. The DNA G+C content of the isolates was 73–74 mol%. Strains KSL-2T, KSL-5 and KSL-6 were identical in their 16S rRNA gene sequences and exhibited DNA–DNA relatedness values of 88–93 %. Phylogenetic trees based on 16S rRNA gene sequences showed that the three isolates fell within the evolutionary radiation encompassed by the genus Nocardioides. Levels of 16S rRNA gene sequence similarity between the three strains and the type strains of Nocardioides species ranged from 93·6 % (with Nocardioides albus) to 97·2 % (with Nocardioides aquiterrae). DNA–DNA relatedness levels between the three isolates and N. aquiterrae CJ-14T were 8–15 %. On the basis of phenotypic, phylogenetic and genetic data, strains KSL-2T, KSL-5 and KSL-6 were classified in the genus Nocardioides as members of a novel species for which the name Nocardioides kribbensis sp. nov. is proposed, with KSL-2T (=KCTC 19038T=DSM 16314T) as the type strain.

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