scholarly journals Gordonia defluvii sp. nov., an actinomycete isolated from activated sludge foam

2006 ◽  
Vol 56 (10) ◽  
pp. 2265-2269 ◽  
Author(s):  
Jacques A. Soddell ◽  
Fiona M. Stainsby ◽  
Kathryn L. Eales ◽  
Robert J. Seviour ◽  
Michael Goodfellow
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Activated Sludge ◽  
Phylogenetic Trees ◽  
Gene Tree ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Spectrometric Data ◽  
Branching Patterns ◽  
Phyletic Line

Three strains of non-motile, Gram-positive, filamentous actinomycetes, isolates J4T, J5 and J59, initially recognized microscopically in activated sludge foam by their distinctive branching patterns, were isolated by micromanipulation. The taxonomic positions of the isolates were determined using a polyphasic approach. Almost-complete 16S rRNA gene sequences of the isolates were aligned with corresponding sequences of representatives of the suborder Corynebacterineae and phylogenetic trees were inferred using three tree-making algorithms. The organisms formed a distinct phyletic line in the Gordonia 16S rRNA gene tree. The three isolates showed 16S rRNA gene sequence similarities within the range 96.9–97.2 % with their nearest phylogenetic neighbours, namely Gordonia bronchialis DSM 43247T and Gordonia terrae DSM 43249T. Strain J4T was shown to have a chemotaxonomic profile typical of the genus Gordonia and was readily distinguished from representatives of the genus on the basis of Curie-point pyrolysis mass spectrometric data. The isolates shared nearly identical phenotypic profiles that distinguished them from representatives of the most closely related Gordonia species. It is evident from the genotypic and phenotypic data that the three isolates belong to a novel Gordonia species. The name proposed for this taxon is Gordonia defluvii sp. nov.; the type strain is J4T (=DSM 44981T=NCIMB 14149T).

scholarly journals Neutrotolerant acidophilic Streptomyces species isolated from acidic soils in China: Streptomyces guanduensis sp. nov., Streptomyces paucisporeus sp. nov., Streptomyces rubidus sp. nov. and Streptomyces yanglinensis sp. nov.

2006 ◽  
Vol 56 (5) ◽  
pp. 1109-1115 ◽  
Author(s):  
Chunguang Xu ◽  
Liming Wang ◽  
Qingfeng Cui ◽  
Ying Huang ◽  
Zhiheng Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Phylogenetic Trees ◽  
Gene Tree ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Acidic Soils ◽  
Phenotypic Data ◽  
Streptomyces Species

The taxonomic status of six neutrotolerant acidophilic streptomycetes isolated from acidic soils in Yunnan Province, China, was established using a polyphasic approach. The morphological and chemotaxonomic characteristics revealed that the isolates belong to the genus Streptomyces. Almost complete 16S rRNA gene sequences of the isolates were determined and aligned with available corresponding sequences of representatives of the family Streptomycetaceae; phylogenetic trees were inferred using four tree-making algorithms. The isolates formed a distinct, albeit heterogeneous, subclade in the Streptomyces 16S rRNA gene tree together with the type strain of Streptomyces yeochonensis, but were readily distinguishable from the latter using DNA–DNA hybridization and phenotypic data. It was evident from the genotypic and phenotypic data that the isolates belonged to four novel Streptomyces species, for which the following names are proposed: Streptomyces guanduensis sp. nov. (type strain 701T=CGMCC 4.2022T=JCM 13274T), Streptomyces paucisporeus sp. nov. (type strain 1413T=CGMCC 4.2025T=JCM 13276T), Streptomyces rubidus sp. nov. (type strain 13c15T=CGMCC 4.2026T=JCM 13277T) and Streptomyces yanglinensis sp. nov. (type strain 1307T=CGMCC 4.2023T=JCM 13275T); isolates 317 and 913 belong to this latter species.

scholarly journals Millisia brevis gen. nov., sp. nov., an actinomycete isolated from activated sludge foam

2006 ◽  
Vol 56 (4) ◽  
pp. 739-744 ◽  
Author(s):  
Jacques A. Soddell ◽  
Fiona M. Stainsby ◽  
Kathryn L. Eales ◽  
Reiner M. Kroppenstedt ◽  
Robert J. Seviour ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Activated Sludge ◽  
Gene Tree ◽  
Mycolic Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Mycolic Acids ◽  
Distinct Lineage

The taxonomic position of two mycolic-acid-producing actinomycetes, isolates J81T and J82, which were recovered from activated sludge foam, was clarified. Comparative 16S rRNA gene sequence studies indicated that the organisms formed a distinct lineage within the Corynebacterineae 16S rRNA gene tree. The taxonomic integrity of this group was underpinned by a wealth of phenotypic data, notably characteristic rudimentary right-angled branching. In addition, isolate J81T contained the following: meso-diaminopimelic acid, arabinose and galactose; N-glycolated muramic acid residues; a dihydrogenated menaquinone with eight isoprene units as the predominant isoprenologue; a fatty acid profile rich in oleic and palmitoleic acids and with relatively small proportions of myristic, stearic and tuberculostearic acids; mycolic acids with 44–52 carbons; and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides as major polar lipids. Strain J81T was found to have a chemotaxonomic profile that serves to distinguish it from representatives of all of the other taxa classified as belonging to the suborder Corynebacterineae. In the light of these data, it is proposed that the two isolates be classified in a novel monospecific genus. The name proposed for this taxon is Millisia brevis gen. nov., sp. nov.; strain J81T (=DSM 44463T=NRRL B-24424T) is the type strain of Millisia brevis.

scholarly journals Amycolatopsis rhabdoformis sp. nov., an actinomycete isolated from a tropical forest soil

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1786-1793 ◽  
Author(s):  
Wallace Rafael Souza ◽  
Rafael Eduardo Silva ◽  
Michael Goodfellow ◽  
Kanungnid Busarakam ◽  
Fernanda Sales Figueiro ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Gene Tree ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

Strain SB026T was isolated from Brazilian rainforest soil and its taxonomic position established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological features consistent with its classification in the genus Amycolatopsis and formed a branch in the Amycolatopsis 16S rRNA gene tree together with Amycolatopsis bullii NRRL B-24847T, Amycolatopsis plumensis NRRL B-24324T, Amycolatopsis tolypomycina DSM 44544T and Amycolatopsis vancoresmycina NRRL B-24208T. It was related most closely to A. bullii NRRL B-24847T (99.0 % 16S rRNA gene sequence similarity), but was distinguished from this strain by a low level of DNA–DNA relatedness (~46 %) and discriminatory phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the isolate should be classified in the genus Amycolatopsis as representing a novel species, Amycolatopsis rhabdoformis sp. nov. The type strain is SB026T ( = CBMAI 1694T = CMAA 1285T = NCIMB 14900T).

scholarly journals Gluconobacter nephelii sp. nov., an acetic acid bacterium in the class Alphaproteobacteria

2011 ◽  
Vol 61 (9) ◽  
pp. 2117-2122 ◽  
Author(s):  
Jintana Kommanee ◽  
Somboon Tanasupawat ◽  
Pattaraporn Yukphan ◽  
Taweesak Malimas ◽  
Yuki Muramatsu ◽  
...  
Keyword(s):  
Acetic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
23S Rrna ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Dna Relatedness ◽  
23S Rrna Gene ◽  
Type Strains

Three strains, RBY-1T, PHD-1 and PHD-2, were isolated from fruits in Thailand. The strains were Gram-negative, aerobic rods with polar flagella, produced acetic acid from ethanol and did not oxidize acetate or lactate. In phylogenetic trees based on 16S rRNA gene sequences and 16S–23S rRNA gene internal transcribed spacer (ITS) sequences, the strains formed a cluster separate from the type strains of recognized species of the genus Gluconobacter. The calculated 16S rRNA gene sequence and 16S–23S rRNA gene ITS sequence similarities were respectively 97.7–99.7 % and 77.3–98.1 %. DNA G+C contents ranged from 57.2 to 57.6 mol%. The strains showed high DNA–DNA relatedness of 100 % to one another, but low DNA–DNA relatedness of 11–34 % to the tested type strains of recognized Gluconobacter species. Q-10 was the major quinone. On the basis of the genotypic and phenotypic data obtained, the three strains clearly represent a novel species, for which the name Gluconobacter nephelii sp. nov. is proposed. The type strain is RBY-1T ( = BCC 36733T = NBRC 106061T = PCU 318T), whose DNA G+C content is 57.2 mol%.

scholarly journals Streptacidiphilus oryzae sp. nov., an actinomycete isolated from rice-field soil in Thailand

2006 ◽  
Vol 56 (6) ◽  
pp. 1257-1261 ◽  
Author(s):  
Liming Wang ◽  
Ying Huang ◽  
Zhiheng Liu ◽  
Michael Goodfellow ◽  
Carlos Rodríguez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Rice Field ◽  
Gene Tree ◽  
Morphological Properties ◽  
Rrna Gene ◽  
New Taxon ◽  
Field Soil ◽  
Rice Field Soil

The taxonomic position of ten acidophilic actinomycetes isolated from an acidic rice-field soil was established using a polyphasic approach. 16S rRNA gene sequences determined for the isolates were aligned with corresponding sequences of representatives of the genera Kitasatospora, Streptacidiphilus and Streptomyces and phylogenetic trees were inferred using four tree-making algorithms. The isolates had identical sequences and formed a distinct branch at the periphery of the Streptacidiphilus 16S rRNA gene tree. The chemotaxonomic and morphological properties of representative isolates were consistent with their assignment to the genus Streptacidiphilus. The isolates shared nearly identical phenotypic profiles that readily distinguished them from representatives of the established species of Streptacidiphilus. It is evident from the genotypic and phenotypic data that the isolates form a homogeneous group that corresponds to a novel species in the genus Streptacidiphilus. The name proposed for this new taxon is Streptacidiphilus oryzae sp. nov.; the type strain is strain TH49T (=CGMCC 4.2012T=JCM 13271T).

scholarly journals Rhodococcus gordoniae sp. nov., an actinomycete isolated from clinical material and phenol-contaminated soil

2004 ◽  
Vol 54 (2) ◽  
pp. 407-411 ◽  
Author(s):  
Amanda L. Jones ◽  
June M. Brown ◽  
Vachaspati Mishra ◽  
John D. Perry ◽  
Arnold G. Steigerwalt ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Tree ◽  
Growth Cycle ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Gene Similarity

The taxonomic relationships of two actinomycetes provisionally assigned to the genus Rhodococcus were determined using a polyphasic taxonomic approach. The generic assignment was confirmed by 16S rRNA gene similarity data, as the organisms, strains MTCC 1534 and W 4937T, were shown to belong to the Rhodococcus rhodochrous subclade. These organisms had phenotypic properties typical of rhodococci; they were aerobic, Gram-positive, weakly acid-fast actinomycetes that showed an elementary branching-rod–coccus growth cycle and contained meso-diaminopimelic acid, arabinose and galactose in whole-organism hydrolysates, N-glycolated muramic acid residues, dehydrogenated menaquinones with eight isoprene units as the predominant isoprenologue and mycolic acids that co-migrated with those extracted from the type strain of R. rhodochrous. The strains had identical phenotypic profiles and belong to the same genomic species, albeit one distinguished from Rhodococcus pyridinivorans, with which they formed a distinct phyletic line. They were also distinguished from representatives of all of the species classified in the R. rhodochrous 16S rRNA gene tree using a set of phenotypic features. The genotypic and phenotypic data show that the strains merit recognition as a novel species of Rhodococcus. The name proposed is Rhodococcus gordoniae sp. nov., with the type strain W 4937T (=DSM 44689T=NCTC 13296T).

Sejongia marina sp. nov., isolated from Antarctic seawater

2007 ◽  
Vol 57 (12) ◽  
pp. 2917-2921 ◽  
Author(s):  
Kiyoung Lee ◽  
Hong Kum Lee ◽  
Tae-Hwan Choi ◽  
Jang-Cheon Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Respiratory Quinone ◽  
Marine Isolate ◽  
Phyletic Line ◽  
Major Respiratory Quinone ◽  
The Antarctic

A Gram-negative, psychrotolerant, chemoheterotrophic, aerobic, non-gliding, non-motile, yellow-pigmented bacterium, designated IMCC3228T, was isolated from coastal seawater of the Antarctic. On the basis of 16S rRNA gene sequence comparisons, the strain was most closely related to the genera Sejongia (95.3–96.1 %) and Chryseobacterium (94.2–95.9 %) in the family Flavobacteriaceae. Phylogenetic trees generated using several treeing algorithms based on 16S rRNA gene sequences showed that this Antarctic marine isolate formed a distinct phyletic line within the genus Sejongia. The DNA G+C content of the strain was 35.0 mol% and the major respiratory quinone was MK-6. Several phenotypic and chemotaxonomic characteristics, including temperature and NaCl optima for growth, oxidase activity and the proportions of major cellular fatty acids, served to differentiate the strain from the recognized species of the genus Sejongia. Therefore strain IMCC3228T represents a novel species of the genus Sejongia, for which the name Sejongia marina sp. nov. is proposed. The type strain is IMCC3228T (=KCCM 42689T=NBRC 103143T).

scholarly journals ‘Candidatus Phytoplasma stylosanthis’, a novel taxon with a diverse host range in Australia, characterised using multilocus sequence analysis of 16S rRNA, secA, tuf, and rp genes

2020 ◽  
Author(s):  
Bianca Rodrigues Jardim ◽  
Wycliff M. Kinoti ◽  
Lucy T. T. Tran-Nguyen ◽  
Cherie Gambley ◽  
Brendan Rodoni ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
In Silico ◽  
Phylogenetic Trees ◽  
Gene Tree ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Pattern Similarity ◽  
The 16S Rrna Gene

In Australia, Stylosanthes little leaf (StLL) phytoplasma has been detected in Stylosanthes scabra Vogel, Arachis pintoi Krapov, Saccharum officinarum L., Carica papaya L., Medicago sativa L., and Solanum tuberosum L. The 16S rRNA gene sequence of StLL phytoplasma strains from S. scabra, C. papaya, S. officinarum and S. tuberosum were compared and share 99.93–100 % nucleotide sequence identity. Phylogenetic comparisons between the 16S rRNA genes of StLL phytoplasma and other ‘Candidatus Phytoplasma’ species indicate that StLL represents a distinct phytoplasma lineage. It shares its most recent known ancestry with ‘Ca. Phytoplasma luffae’ (16SrVIII-A), with which it has 97.17–97.25 % nucleotide identity. In silico RFLP analysis of the 16S rRNA amplicon using iPhyClassifier indicate that StLL phytoplasmas have a unique pattern (similarity coefficient below 0.85) that is most similar to that of ‘Ca. Phytoplasma luffae’. The unique in silico RFLP patterns were confirmed in vitro. Nucleotide sequences of genes that are more variable than the 16S rRNA gene, namely tuf (tu-elongation factor), secA (partial translocation gene), and the partial ribosomal protein (rp) gene operon (rps19-rpl22-rps3), produced phylogenetic trees with similar branching patterns to the 16S rRNA gene tree. Sequence comparisons between the StLL 16S rRNA spacer region confirmed previous reports of rrn interoperon sequence heterogeneity for StLL, where the spacer region of rrnB encodes a complete tRNA-Isoleucine gene and the rrnA spacer region does not. Together these results suggest that the Australian phytoplasma, StLL, is unique according to the International Organization for Mycoplasmology (IRPCM) recommendations. The novel taxon ‘Ca. Phytoplasma stylosanthis’ is proposed, with the most recent strain from a potato crop in Victoria, Australia, serving as the reference strain (deposited in the Victorian Plant Pathology Herbarium as VPRI 43683).

scholarly journals Lacisediminihabitans profunda gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from freshwater sediment

2019 ◽  
Vol 113 (3) ◽  
pp. 365-375 ◽  
Author(s):  
Ye Zhuo ◽  
Chun-Zhi Jin ◽  
Feng-Jie Jin ◽  
Taihua Li ◽  
Dong Hyo Kang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
The Family ◽  
Diamino Acid ◽  
Rrna Gene Sequencing ◽  
Sequence Similarities

Abstract A novel Gram-stain-positive bacterial strain, CHu50b-6-2T, was isolated from a 67-cm-long sediment core collected from the Daechung Reservoir at a water depth of 17 m, Daejeon, Republic of Korea. The cells of strain CHu50b-6-2T were aerobic non-motile and formed yellow colonies on R2A agar. The phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain formed a separate lineage within the family Microbacteriaceae, exhibiting 98.0%, 97.7% and 97.6% 16S rRNA gene sequence similarities to Glaciihabitans tibetensis KCTC 29148T, Frigoribacterium faeni KACC 20509T and Lysinibacter cavernae DSM 27960T, respectively. The phylogenetic trees revealed that strain CHu50b-6-2T did not show a clear affiliation to any genus within the family Microbacteriaceae. The chemotaxonomic results showed B1α type peptidoglacan containg 2, 4-diaminobutyric acid (DAB) as the diagnostic diamino acid, MK-10 as the predominant respiratory menaquinone, diphosphatidylglycerol, phosphatidylglycerol, and an unidentified glycolipid as the major polar lipids, anteiso-C15:0, iso-C16:0, and anteiso-C17:0 as the major fatty acids, and a DNA G + C content of 67.3 mol%. The combined genotypic and phenotypic data showed that strain CHu50b-6-2T could be distinguished from all genera within the family Microbacteriaceae and represents a novel genus, Lacisediminihabitans gen. nov., with the name Lacisediminihabitans profunda sp. nov., in the family Microbacteriaceae. The type strain is CHu50b-6-2T (= KCTC 49081T = JCM 32673T).

scholarly journals Paraperlucidibaca baekdonensis gen. nov., sp. nov., isolated from seawater

2011 ◽  
Vol 61 (6) ◽  
pp. 1382-1385 ◽  
Author(s):  
Ki-Hoon Oh ◽  
Soo-Young Lee ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data ◽  
Gene Sequence Analysis

A Gram-negative, non-spore-forming, rod-shaped bacterial strain, RL-2T, was isolated from seawater of the East Sea in Korea and was subjected to a polyphasic taxonomic study. Strain RL-2T grew optimally at pH 7.5–8.0, at 20 °C and in the absence of NaCl. Phylogenetic trees based on 16S rRNA gene sequence analysis showed that strain RL-2T forms a cluster with Perlucidibaca piscinae IMCC1704T and various uncultured and unidentified gammaproteobacteria. Strain RL-2T exhibited 16S rRNA gene sequence similarity values of 96.1 % to Perlucidibaca piscinae IMCC1704T and 93.7–99.7 % to the uncultured bacterial clones belonging to the cluster and an unidentified gammaproteobacterium. The fatty acid profile of strain RL-2T was similar to that of Perlucidibaca piscinae IMCC1704T, but the predominant ubiquinone type (Q-11) of strain RL-2T was different from that (Q-8) of Perlucidibaca piscinae IMCC1704T. The DNA G+C content of strain RL-2T was 61.3 mol%. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain RL-2T is considered to represent a novel species of a new genus in the family Moraxellaceae, for which the name Paraperlucidibaca baekdonensis gen. nov., sp. nov. is proposed. The type strain of Paraperlucidibaca baekdonensis is RL-2T ( = KCTC 23145T  = CCUG 59307T).

Sign in / Sign up

Export Citation Format

Share Document