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 Tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3′-dithiodipropionic acid

2006 ◽  
Vol 56 (6) ◽  
pp. 1305-1310 ◽  
Author(s):  
Jan Hendrik Wübbeler ◽  
Tina Lütke-Eversloh ◽  
Stefanie Van Trappen ◽  
Peter Vandamme ◽  
Alexander Steinbüchel
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Alcaligenes Faecalis ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Rrna Gene Sequence ◽  
Nearest Neighbours ◽  
The 16S Rrna Gene

In this study, a novel betaproteobacterium, strain DPN7T, was isolated under mesophilic conditions from compost because of its capacity to utilize the organic disulfide 3,3′-dithiodipropionic acid. Analysis of the 16S rRNA gene sequence of strain DPN7T revealed 98.5 % similarity to that of Tetrathiobacter kashmirensis LMG 22695T. Values for sequence similarity to members of the genera Alcaligenes, Castellaniella and Taylorella, the nearest neighbours of the genus Tetrathiobacter, were about 95 % or less. The DNA G+C content of strain DPN7T was 55.1 mol%. The level of DNA–DNA hybridization between strain DPN7T and T. kashmirensis LMG 22695T was 41 %, whereas it was much lower between strain DPN7T and Alcaligenes faecalis LMG 1229T (7 %) or Castellaniella defragrans LMG 18538T (5 %). This genotypic divergence was supported by differences in biochemical and chemotaxonomic characteristics. For this reason, and because of the differences in the protein and fatty acid profiles, strain DPN7T should be classified within a novel species of Tetrathiobacter, for which the name Tetrathiobacter mimigardefordensis sp. nov. is proposed. The type strain is strain DPN7T (=DSM 17166T=LMG 22922T).

scholarly journals Agromyces arachidissp. nov. Isolated from a Peanut (Arachis hypogaea) Crop Field

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Chandandeep Kaur ◽  
Anil Kumar Pinnaka ◽  
Nitin Kumar Singh ◽  
Monu Bala ◽  
Shanmugam Mayilraj
Keyword(s):  
Arachis Hypogaea ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Crop Field ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

A Gram-positive, yellowish bacterium strain AK-1Twas isolated from soil sample collected from peanut (Arachis hypogaea) crop field and studied by using a polyphasic approach. The organism had morphological and chemotaxonomic properties consistent with its classification in the genusAgromyces. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain AK-1Twas closely related toAgromyces aurantiacus(98.6%) followed byAgromyces soli(98.3%),Agromyces tropicus(97.6%),Agromyces ulmi(97.3%),Agromyces flavus(97.2%), andAgromyces italicus(97.0%), whereas the sequence similarity values with respect to the otherAgromycesspecies with validly published names were between 95.3 and 96.7 %. However, the DNA-DNA hybridization values obtained between strain AK-1Tand other related strains were well below the threshold that is required for the proposal of a novel species. The DNAG+Ccontent of the strain is 71.8 mol%. The above data in combination with the phenotypic distinctiveness of AK-1Tclearly indicate that the strain represents a novel species, for which the nameAgromyces arachidissp. nov. is proposed. The type strain is AK-1T(=MTCC 10524T= JCM 19251T).

scholarly journals Plantactinospora sonchi sp. nov., an actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.)

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4895-4901 ◽  
Author(s):  
Zhaoxu Ma ◽  
Chongxi Liu ◽  
Jianlong Fan ◽  
Hairong He ◽  
Chuang Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Sonchus Oleraceus

A novel actinobacterium, designated strain NEAU-QY2T, was isolated from the leaves of Sonchus oleraceus L. specimen, collected from Wuchang, Heilongjiang Province, China. A polyphasic study was carried out to establish the taxonomic position of this strain. The organism formed single spores with rough surfaces on substrate mycelia. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-QY2T belonged to the genus Plantactinospora and formed a monophyletic clade with its closest related strains Plantactinospora endophytica YIM 68255T (99.2 % 16S rRNA gene sequence similarity), Plantactinospora veratri NEAU-FHS4T (98.8 %) and Plantactinospora mayteni YIM 61359T (98.7 %), an association that was supported by a bootstrap value of 90 % in the neighbour-joining tree and also recovered with the maximum-likelihood algorithm. However, DNA–DNA hybridization values between strain NEAU-QY2T and the three closely related strains were below 70 %. With reference to phenotypic characteristics, phylogenetic data and DNA–DNA hybridization results, strain NEAU-QY2T was distinguished from closely related strains and is classified as representing a novel species of the genus Plantactinospora, for which the name Plantactinospora sonchi sp. nov. is proposed. The type strain is NEAU-QY2T ( = CGMCC 4.7216T = JCM 30345T).

scholarly journals Shewanella irciniae sp. nov., a novel member of the family Shewanellaceae, isolated from the marine sponge Ircinia dendroides in the Bay of Villefranche, Mediterranean Sea

2006 ◽  
Vol 56 (12) ◽  
pp. 2871-2877 ◽  
Author(s):  
On On Lee ◽  
Stanley C. K. Lau ◽  
Mandy M. Y. Tsoi ◽  
Xiancui Li ◽  
Ioulia Plakhotnikova ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Marine Sponge ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Phenotypic Data ◽  
Shewanella Algae ◽  
The Family

Strain UST040317-058T, comprising non-pigmented, rod-shaped, facultatively anaerobic, Gram-negative cells that are motile by means of single polar flagella, was isolated from the surface of a marine sponge (Ircinia dendroides) collected from the Mediterranean Sea. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a separate cluster with the recognized bacterium Shewanella algae IAM 14159T, with which it showed a sequence similarity of 95.0 %. The sequence similarity between strain UST040317-058T and its other (six) closest relatives ranged from 91.6 to 93.8 %. Strain UST040317-058T showed oxidase, catalase and gelatinase activities. The typical respiratory quinones for shewanellas, menaquinone MK-7 and ubiquinones Q-7 and Q-8, were also detected. The predominant fatty acids in strain UST040317-058T were i15 : 0, 16 : 0, 17 : 1ω8c and summed feature 3 (comprising i15 : 0 2-OH and/or 16 : 1ω7c), altogether representing 56.9 % of the total. The DNA G+C content was 39.9 mol%. The strain could be differentiated from other Shewanella species by its inability to reduce nitrate or produce H2S and by 10–22 additional phenotypic characteristics. On the basis of the phylogenetic and phenotypic data presented in this study, strain UST040317-058T represents a novel species in the genus Shewanella, for which the name Shewanella irciniae sp. nov. is proposed. The type strain is UST040317-058T (=JCM 13528T=NRRL B-41466T).

scholarly journals Streptomyces sparsus sp. nov., isolated from a saline and alkaline soil

2011 ◽  
Vol 61 (7) ◽  
pp. 1601-1605 ◽  
Author(s):  
Yi Jiang ◽  
Yan-Ru Cao ◽  
Jutta Wiese ◽  
Shu-Kun Tang ◽  
Li-Hua Xu ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Aerial Hyphae ◽  
Actinomycete Strain ◽  
The 16S Rrna Gene

A salt- and alkali-tolerant actinomycete strain, YIM 90018T, was isolated from a saline and alkaline soil sample collected from Qinghai, China. Aerial hyphae of strain YIM 90018T were only produced on YIM 82 agar. Vegetative hyphae were well developed and did not fragment. Straight or flexuous (rectiflexibiles) spore chains were produced. The isolate grew well with 25 % (w/v) MgCl2 . 6H2O and at pH 10. All of these characters indicated that strain YIM 90018T belonged to the genus Streptomyces. On the basis of phylogenetic analysis of the 16S rRNA gene sequence, DNA–DNA hybridization and phenotypic characteristics, strain YIM 90018T could be differentiated from all recognized species of the genus Streptomyces. A novel species, Streptomyces sparsus sp. nov., is proposed, with strain YIM 90018T ( = CCTCC AA204019T = DSM 41858T) as the type strain.

scholarly journals Paenibacillus mendelii sp. nov., from surface-sterilized seeds of Pisum sativum L.

2005 ◽  
Vol 55 (6) ◽  
pp. 2351-2354 ◽  
Author(s):  
Jakub Šmerda ◽  
Ivo Sedláček ◽  
Zdena Páčová ◽  
Eva Durnová ◽  
Alexandra Smíšková ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Garden Pea ◽  
Phenotypic Profile ◽  
Pisum Sativum L ◽  
The 16S Rrna Gene

A Gram-variable, facultatively anaerobic, endospore-forming bacterium was isolated from surface-sterilized seeds of the garden pea and characterized with phenotypic and molecular methods. A PCR with the Paenibacillus-specific primer PAEN515F and the 16S rRNA gene sequence indicated that strain C/2T belongs to the genus Paenibacillus and is closely related to Paenibacillus phyllosphaerae (94·0 % sequence similarity). Strain C/2T generated a unique phenotypic profile, in particular for the production of acid from substrates. The DNA G+C content (50·8 mol%) and the major fatty acid (anteiso-C15 : 0) are consistent with the genus Paenibacillus. DNA–DNA hybridization distinguished strain C/2T from other phylogenetically related Paenibacillus species and, therefore, strain C/2T (=CCM 4839T=LMG 23002T) is here described as the type strain of a novel species, for which the name Paenibacillus mendelii sp. nov. is proposed.

scholarly journals Sphingobium vulgare sp. nov., isolated from freshwater sediment

2010 ◽  
Vol 60 (10) ◽  
pp. 2473-2477 ◽  
Author(s):  
Sang-Hoon Baek ◽  
Ju Hyoung Lim ◽  
Sung-Taik Lee
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Freshwater Sediment ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
The Family ◽  
Distinct Branch ◽  
The 16S Rrna Gene

A Gram-negative, motile, non-spore-forming bacterial strain, designated HU1-GD12T, was isolated from freshwater sediment. The strain was characterized by using a polyphasic approach in order to determine its taxonomic position. Comparative analysis of the 16S rRNA gene sequence showed that the isolate constituted a distinct branch within the genus Sphingobium, showing the highest level of sequence similarity with respect to Sphingobium ummariense RL-3T (96.2 %). Strain HU1-GD12T had a genomic DNA G+C content of 66.8 mol% and Q-10 as the predominant respiratory quinone. Furthermore, the major polyamine component (spermidine) in the cytoplasm and the presence of sphingoglycolipids suggested that strain HU1-GD12T belonged to the family Sphingomonadaceae. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain HU1-GD12T represents a novel species of the genus Sphingobium, for which the name Sphingobium vulgare sp. nov. is proposed. The type strain is HU1-GD12T (=LMG 24321T=KCTC 22289T).

scholarly journals Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov., isolated from effective nodules of peanut

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4655-4661 ◽  
Author(s):  
Yong Hua Li ◽  
Rui Wang ◽  
Xiao Xia Zhang ◽  
J. Peter. W. Young ◽  
En Tao Wang ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Lablab Purpureus ◽  
Phenotypic Characteristics ◽  
Slow Growing ◽  
Type Strains

Seven slow-growing rhizobia isolated from effective nodules of Arachis hypogaea were assigned to the genus Bradyrhizobium based on sharing 96.3–99.9 % 16S rRNA gene sequence similarity with the type strains of recognized Bradyrhizobium species. Multilocus sequence analysis of glnII, recA, gyrB and dnaK genes indicated that the seven strains belonged to two novel species represented by CCBAU 51649T and CCBAU 53363T. Strain CCBAU 51649T shared 94, 93.4, 92.3 and 94.9 % and CCBAU 53363T shared 91.4, 94.5, 94.6 and 97.7 % sequence similarity for the glnII, recA, gyrB and dnaK genes, respectively, with respect to the closest related species Bradyrhizobium manausense BR 3351T and Bradyrhizobium yuanmingense CCBAU 10071T. Summed feature 8 and C16 : 0 were the predominant fatty acid components for strains CCBAU 51649T and CCBAU 53363T. DNA–DNA hybridization and analysis of phenotypic characteristics also distinguished these strains from the closest related Bradyrhizobium species. The strains formed effective nodules on Arachis hypogaea, Lablab purpureus and Aeschynomene indica, and they had identical nodA genes to Bradyrhizobium sp. PI237 but were phylogenetically divergent from other available nodA genes at less than 66 % similarity. Based in these results, strains CCBAU 51649T ( = CGMCC 1.15034T = LMG 28620T) and CCBAU 53363T ( = CGMCC 1.15035T = LMG 28621T) are designated the type strains of two novel species, for which the names Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov. are proposed, respectively.

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.

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).

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