Reclassification of Herbaspirillum putei as a later heterotypic synonym of Herbaspirillum huttiense, with the description of H. huttiense subsp. huttiense subsp. nov. and H. huttiense subsp. putei subsp. nov., comb. nov., and description of Herbaspirillum aquaticum sp. nov.

2010 ◽  
Vol 60 (6) ◽  
pp. 1418-1426 ◽  
Author(s):  
Anatoly P. Dobritsa ◽  
M. C. S. Reddy ◽  
Mansour Samadpour
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Phenotypic Characteristics ◽  
Phylogenetic Relatedness ◽  
The 16S Rrna Gene

Resequencing of the 16S rRNA gene of the type strain of Herbaspirillum putei Ding and Yokota 2004 revealed 99.9 % sequence similarity to that of the type strain of Herbaspirillum huttiense (Leifson 1962) Ding and Yokota 2004. This high phylogenetic relatedness of H. putei and H. huttiense was confirmed by the results of DNA–DNA hybridization between H. huttiense DSM 10281T and H. putei ATCC BAA-806T (reassociation value 96 %). Therefore, it is proposed to reclassify the type strain of H. putei as a strain of H. huttiense. However, the genome of the type strain of H. putei is about 0.9 Mb larger than that of the H. huttiense type strain. This results in a decrease in the reassociation value in the reciprocal DNA–DNA hybridization to 72 %, a level slightly above the threshold for delineating bacterial species. These data and distinctive phenotypic characteristics indicate that the name Herbaspirillum putei is a later heterotypic synonym of Herbaspirillum huttiense and permit the description of two novel subspecies, Herbaspirillum huttiense subsp. huttiense subsp. nov. (type strain ATCC 14670T =JCM 21423T =DSM 10281T) and Herbaspirillum huttiense subsp. putei subsp. nov., comb. nov. (type strain 7-2T =JCM 21495T =ATCC BAA-806T). Three bacterial strains, IEH 4430T, IEH 4515 and IEH 8757, isolated from water were found to be the closest relatives of these strains. Strain IEH 8757 was classified as a strain of H. huttiense subsp. putei. Studies of genotypic and phenotypic features of strains IEH 4430T and IEH 4515 showed that the strains represent a novel species, which is most closely related to H. huttiense and for which the name Herbaspirillum aquaticum sp. nov. is proposed (type strain IEH 4430T =DSM 21191T =ATCC BAA-1628T).

scholarly journals Rhodococcus kyotonensis sp. nov., a novel actinomycete isolated from soil

2007 ◽  
Vol 57 (9) ◽  
pp. 1956-1959 ◽  
Author(s):  
Bing Li ◽  
Keiko Furihata ◽  
Lin-Xian Ding ◽  
Akira Yokota
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Mycolic Acids ◽  
Rhodococcus Fascians ◽  
The 16S Rrna Gene ◽  
Is Strain

A polyphasic study was undertaken to establish the taxonomic position of an isolate, strain DS472T, from soil in Kyoto, Japan. Phylogenetic analysis, based on the 16S rRNA gene sequences, revealed that this strain constitutes a new subline within the genus Rhodococcus, with Rhodococcus yunnanensis YIM 70056T and Rhodococcus fascians DSM 20669T as its nearest phylogenetic neighbours (98.2 and 97.8 % sequence similarity, respectively). DNA–DNA hybridization experiments revealed 36 and 29 % relatedness between the isolate and its phylogenetic relatives, R. yunnanensis and R. fascians, respectively. Chemotaxonomic characteristics, including the major quinone MK-8(H2), predominant fatty acids C16 : 0, C18 : 1 ω9c and 10-methyl C18 : 0, the presence of cell-wall chemotype IV and mycolic acids, were consistent with the properties of members of the genus Rhodococcus. The DNA G+C content was 64.5 mol%. On the basis of both phenotypic and genotypic evidence, strain DS472T represents a novel species of the genus Rhodococcus, for which the name Rhodococcus kyotonensis sp. nov. is proposed. The type strain is strain DS472T (=IAM 15415T=CCTCC AB206088T).

scholarly journals Paenibacillus rhizosphaerae sp. nov., isolated from the rhizosphere of Cicer arietinum

2005 ◽  
Vol 55 (3) ◽  
pp. 1305-1309 ◽  
Author(s):  
Raúl Rivas ◽  
Carmen Gutiérrez ◽  
Adriana Abril ◽  
Pedro F. Mateos ◽  
Eustoquio Martínez-Molina ◽  
...  
Keyword(s):  
Cicer Arietinum ◽  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Gas Production ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences

Two sporulating bacterial strains designated CECAP06T and CECAP16 were isolated from the rhizosphere of the legume Cicer arietinum in Argentina. Almost-complete 16S rRNA gene sequences identified the isolates as a Paenibacillus species. It was most closely related to Paenibacillus cineris LMG 18439T (99·6 % sequence similarity), Paenibacillus favisporus LMG 20987T (99·4 % sequence similarity) and Paenibacillus azoreducens DSM 13822T (97·7 % sequence similarity). The cells of this novel species were motile, sporulating, rod-shaped, Gram-positive and strictly aerobic. The predominant fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. The DNA G+C content of strains CECAP06T and CECAP16 was 51·3 and 50·9 mol%, respectively. Growth was observed from many carbohydrates, but gas production was not observed from glucose. Catalase and oxidase activities were present. The isolates produced β-galactosidase and hydrolysed aesculin. Gelatinase, caseinase and urease were not produced. The results of DNA–DNA hybridization showed that the strains from this study constitute a novel species of the genus Paenibacillus, for which the name Paenibacillus rhizosphaerae sp. nov. is proposed. The type strain is CECAP06T (=LMG 21955T=CECT 5831T).

scholarly journals Luteipulveratus halotolerans sp. nov., an actinobacterium (Dermacoccaceae) from forest soil

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4113-4120 ◽  
Author(s):  
Holed Juboi ◽  
Ann Anni Basik ◽  
Sunita Sara Gill Shamsul ◽  
Phil Arnold ◽  
Esther K. Schmitt ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Monophyletic Clade ◽  
Phenotypic Characteristics ◽  
Pacbio Rs Ii ◽  
The Family ◽  
The 16S Rrna Gene

The taxonomic position of an actinobacterium strain, C296001T, isolated from a soil sample collected in Sarawak, Malaysia, was established using a polyphasic approach. Phylogenetically, strain C296001T was closely associated with the genus Luteipulveratus and formed a distinct monophyletic clade with the only described species, Luteipulveratus mongoliensis NBRC 105296T. The 16S rRNA gene sequence similarity between strain C296001T and L. mongoliensis was 98.7 %. DNA–DNA hybridization results showed that the relatedness of strain C296001T to L. mongoliensis was only 21.5 %. The DNA G+C content of strain C296001T was 71.7 mol%. Using a PacBio RS II system, whole genome sequences for strains C296001T and NBRC 105296T were obtained. The genome sizes of 4.5 Mbp and 5.4 Mbp determined were similar to those of other members of the family Dermacoccaceae. The cell-wall peptidoglycan contained lysine, alanine, aspartic acid, glutamic acid and serine, representing the peptidoglycan type A4α l-Lys-l-Ser-d-Asp. The major menaquinones were MK-8(H4), MK-8 and MK-8(H2). Phosphatidylglycerol, phosphatidylinositol, diphosphatidylglycerol and phosphoglycolipid were the polar lipids, while the whole-cell sugars were glucose, fucose and lesser amounts of ribose and galactose. The major fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C16 : 1 H, anteiso-C17 : 1ω9c, iso-C18 : 0 and 10-methyl C17 : 0. Chemotaxonomic analyses showed that C296001T had typical characteristics of members of the genus Luteipulveratus, with the main differences occurring in phenotypic characteristics. On the basis of the phenotypic and chemotaxonomic evidence, it is proposed that strain C296001T be classified as a representative of a novel species in the genus Luteipulveratus, for which the name Luteipulveratus halotolerans sp. nov. is recommended. The type strain is C296001T ( = ATCC TSD-4T = JCM 30660T).

scholarly journals Virgibacillus olivae sp. nov., isolated from waste wash-water from processing of Spanish-style green olives

2007 ◽  
Vol 57 (5) ◽  
pp. 906-910 ◽  
Author(s):  
Teresa Quesada ◽  
Margarita Aguilera ◽  
José Antonio Morillo ◽  
Alberto Ramos-Cormenzana ◽  
Mercedes Monteoliva-Sánchez
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Wash Water ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Phenotypic Differences ◽  
The 16S Rrna Gene

Four bacterial strains (E308T, E5549, I3077 and N30129) were isolated from the residual wash-water produced during the processing of Spanish-style green table olives. The isolates were subjected to a polyphasic taxonomic study using phenotypic, phylogenetic and genotypic methods. The bacteria were Gram-positive, spore-forming rods. Moreover, they were heterotrophs that were able to utilize cellobiose, glucose, mannose and rhamnose as carbon sources. The G+C content of their genomic DNA ranged from 30.7 to 33.4 mol%. The major cellular fatty acids found in strain E308T were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 and anteiso-C17 : 0. DNA–DNA hybridization shows 76.2–88.3 % relatedness among the four strains. The 16S rRNA gene sequence of isolate E308T shows that it belongs to the genus Virgibacillus, with the highest sequence similarity (99 %) to Virgibacillus marismortui 123T. However, phenotypic differences and DNA–DNA relatedness between strain E308T and V. marismortui ATCC 700626T of less than 47 % suggest the placement of these strains within a novel species of the genus Virgibacillus. The name Virgibacillus olivae sp. nov. is proposed, with strain E308T (=LMG 23503T=DSM 18098T) as the type strain.

Dyadobacter koreensis sp. nov., isolated from fresh water

2007 ◽  
Vol 57 (6) ◽  
pp. 1227-1231 ◽  
Author(s):  
Keun Sik Baik ◽  
Mi Sun Kim ◽  
Eun Mi Kim ◽  
Hyung Rak Kim ◽  
Chi Nam Seong
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Gram Negative ◽  
Light Yellow ◽  
Relatedness Data

A non-motile, rod-shaped, light-yellow-pigmented bacterium, designated strain WPCB159T, was isolated from freshwater samples collected from the Woopo wetland in Korea. The cells were Gram-negative, aerobic and catalase- and oxidase-positive. The major fatty acids were C16 : 1 ω7c (34.8 %), iso-C15 : 0 (24.2 %) and C16 : 0 (9.4 %). The DNA G+C content was 44 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain WPCB159T forms a lineage within the genus Dyadobacter (family ‘Flexibacteraceae’) and is closely related to Dyadobacter hamtensis HHS 11T (97.8 % sequence similarity) and to other members of the genus Dyadobacter (95.2–96.8 % sequence similarity). The phenotypic characteristics and DNA–DNA hybridization relatedness data indicate that strain WPCB159T should be distinguished from D. hamtensis HHS 11T. On the basis of the evidence presented in this study, strain WPCB159T represents a novel species of the genus Dyadobacter, for which the name Dyadobacter koreensis sp. nov. is proposed. The type strain is WPCB159T (=KCTC 12537T=NBRC 101116T).

scholarly journals Pseudomonas reinekei sp. nov., Pseudomonas moorei sp. nov. and Pseudomonas mohnii sp. nov., novel species capable of degrading chlorosalicylates or isopimaric acid

2007 ◽  
Vol 57 (5) ◽  
pp. 923-931 ◽  
Author(s):  
Beatriz Cámara ◽  
Carsten Strömpl ◽  
Susanne Verbarg ◽  
Cathrin Spröer ◽  
Dietmar H. Pieper ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Phenotypic Characteristics ◽  
Isopimaric Acid ◽  
Gene Sequence Analysis

Three bacterial strains, designated MT1T, RW10T and IpA-2T, had been isolated previously for their ability to degrade chlorosalicylates or isopimaric acid. 16S rRNA gene sequence analysis demonstrated that these bacteria are related to species of the genus Pseudomonas. Analysis of the results of DNA–DNA hybridization with several close phylogenetic neighbours revealed a low level of hybridization (less than 57 %). On the basis of phenotypic characteristics, phylogenetic analysis, DNA–DNA relatedness data and chemotaxonomic analysis, it is concluded that these isolates represent separate novel species, for which the names Pseudomonas reinekei sp. nov. (type strain MT1T =DSM 18361T=CCUG 53116T), Pseudomonas moorei sp. nov. (type strain RW10T =DSM 12647T=CCUG 53114T) and Pseudomonas mohnii sp. nov. (type strain IpA-2T =DSM 18327T=CCUG 53115T) 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 Psychroserpens Luteus Sp. Nov., Isolated fFrom Red Algae

2021 ◽  
Author(s):  
Xiu-Ya Ping ◽  
Kai Wang ◽  
Jin-Yu Zhang ◽  
Shu-Xin Wang ◽  
Zong-Jun Du ◽  
...  
Keyword(s):  
Red Algae ◽  
Genomic Dna ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
Optimum Ph ◽  
The 16S Rrna Gene

Abstract A Gram-stain-negative, gliding-motile, positive for catalase, facultative anaerobic, designated strain XSD401T, was isolated from the red algae of Xiaoshi Island, Shandong Province, China. Growth occurred at 20–37 °C (optimum, 33 °C), pH 5.5–9.5 (optimum, pH 6.5–7.5), and with 0.5–5% (w/v) NaCl (optimum, 3%). The main fatty acids are iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, iso-C15:0 3-OH, C16:0. Phosphatidylethanolamine (PE), three unidentified aminolipids (AL1, AL2, AL3) and one unidentified lipid (L) were the major polar lipids. The G+C content of the genomic DNA was 33.9 mol%. Strain XSD401T had the highest sequence similarity (96.88%) to the 16S rRNA gene of Psychroserpens damuponensis KCTC 23539T. The similarities with Psychroserpens burtonensis DSM 12212T was 96.31%. The dDDH values between strain XSD401T and P. damuponensis KCTC 23539T, P. burtonensis DSM 12212T, were 20.40% and 20.30%, respectively. The average nucleotide identity (ANI) values between strain XSD401T and P. damuponensis KCTC 23539T, P. burtonensis DSM 12212T were 76.91%, 76.88%, respectively. The differences in morphology, physiology and genotype from the previously described taxa support the classification of strain XSD401T as a representative of a novel species of the genus Psychroserpens, for which the name Psychroserpens luteus sp. nov. is proposed. The type strain is XSD401T (= MCCC 1H00396T = KCTC 72684T = JCM 33931T).

scholarly journals Corticibacter populi gen. nov., sp. nov., a new member of the family Comamonadaceae, from the bark of Populus euramericana

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3333-3338 ◽  
Author(s):  
Wei Fang ◽  
Yong Li ◽  
Han Xue ◽  
Guozhong Tian ◽  
Laifa Wang ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Populus Euramericana ◽  
The Family ◽  
Distinct Branch ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Three novel endophytic strains, designated 17B10-2-12T, 26C10-4-4 and D13-10-4-9, were isolated from the bark of Populus euramericana in Heze, Shandong Province, China. They were Gram-reaction-negative, aerobic, non-motile, short-rod-shaped, oxidase-positive and catalase-negative. A phylogenetic analysis of the 16S rRNA gene showed that the three novel strains clustered with members of the family Comamonadaceae and formed a distinct branch. The isolates shared 100 % similarities among themselves and had the highest sequence similarity with Xenophilus azovorans DSM 13620T (95.2 %) and Xenophilus arseniciresistens YW8T (95.0 %), and less than 95.0 % sequence similarities with members of other species. Their major fatty acids were C16 : 0, C17 : 0 cyclo, C18 : 1ω7c and C16 : 1ω7c/C16 : 1ω6c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unknown aminophospholipids. The predominant quinone was ubiquinone-8 (Q-8). The DNA G+C content was 69.5–70.0 mol%. Based on data from a polyphasic taxonomy study, the three strains represent a novel species of a novel genus of the family Comamonadaceae, for which the name Corticibacter populi gen. nov., sp. nov. is proposed. The type strain is 17B10-2-12T ( = CFCC 12099T = KCTC 42091T).

scholarly journals Methylobacterium variabile sp. nov., a methylotrophic bacterium isolated from an aquatic environment

2005 ◽  
Vol 55 (4) ◽  
pp. 1429-1433 ◽  
Author(s):  
Virginia Gallego ◽  
Maria Teresa García ◽  
Antonio Ventosa
Keyword(s):  
Dna Hybridization ◽  
Distribution System ◽  
Bacterial Population ◽  
Sequence Similarity ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Natural Habitats ◽  
Hybridization Data ◽  
The 16S Rrna Gene

Strain GR3T was isolated from drinking water during a screening programme to monitor the bacterial population present in the distribution system of Seville (Spain), and it was studied phenotypically, genotypically and phylogenetically. This pink-pigmented bacterium was identified as a Methylobacterium sp. Members of this genus are distributed in a wide variety of natural habitats, including soil, dust, air, freshwater and aquatic sediments. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain GR3T was closely related to Methylobacterium aquaticum (97·4 % sequence similarity), whereas sequence similarity values with respect to the rest of the species belonging to this genus were lower than 96 %. Furthermore, the DNA–DNA hybridization data and its phenotypic characteristics clearly indicate that the isolate represents a novel Methylobacterium species, for which the name Methylobacterium variabile sp. nov. is proposed. GR3T (=DSM 16961T=CCM 7281T=CECT 7045T) is the type strain; the DNA G+C content of this strain is 69·2 mol%.

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