Reclassification of Koreibacter algae as a later heterotypic synonym of Paraoerskovia marina and emended descriptions of the genus Paraoerskovia Khan et al. 2009 and of Paraoerskovia marina Khan et al. 2009

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 219-223 ◽  
Author(s):  
P. Schumann ◽  
R. Pukall ◽  
C. Spröer ◽  
E. Stackebrandt
Keyword(s):  
Type Species ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Maldi Tof Mass Spectra ◽  
Peptidoglycan Structure ◽  
Lipid Pattern ◽  
Type Strains ◽  
Produce Acid

16S rRNA gene sequences deposited for the type strains of Paraoerskovia marina (CTT-37T; GenBank accession no. AB445007) and Koreibacter algae (DSW-2T; FM995611) show a similarity of 100 %. Consequently, the type strains were subjected to a polyphasic recharacterization under direct comparison in order to clarify their taxonomic position. PvuII RiboPrint patterns and quantitative ratios of cellular fatty acids revealed strain-specific differences between P. marina DSM 21750T ( = CTT-37T) and K. algae DSM 22126T ( = DSW-2T). The percentage of DNA–DNA binding of 94 % indicated that the two type strains belong to the same genomospecies. Agreement in the peptidoglycan structure and polar lipid pattern, highly similar fatty acid profiles and MALDI-TOF mass spectra, the ability to produce acid from the same carbon sources, corresponding enzymic activities and DNA G+C contents of 70.8±0.3 mol%, in addition to the consistent characteristics reported in the original descriptions, support the view that the two strains should be affiliated to the same species. According to Rules 38 and 42 of the Bacteriological Code, Koreibacter algae should be reclassified as later heterotypic synonym of Paraoerskovia marina , and the descriptions of the genus Paraoerskovia Khan et al. 2009 and of Paraoerskovia marina Khan et al. 2009 are emended accordingly.

Flavobacterium hydrocarbonoxydans sp. nov., isolated from polluted soil

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Da Min Jung ◽  
Yeong Seok Kim ◽  
Jeong Hwan Bang ◽  
Seung Bum Kim
Keyword(s):  
Related Species ◽  
Type Species ◽  
Carbon Sources ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Soil Isolate ◽  
Type Strains ◽  
The 16S Rrna Gene

This paper presents a polyphasic taxonomic study of a Gram-stain-negative bacterium designated GA093T, a soil isolate capable of benzo(α)pyrene degradation. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain GA093T is a member of the genus Flavobacterium , and formed an independent phylogenetic line while clustering with the type strains of Flavobacterium hibernum , Flavobacterium branchiarum and Flavobacterium hydatis . Strain GA093T was facultatively anaerobic, and could grow at 4–33 °C (optimum, 30 °C), at pH 6–11 (optimum, pH 7) and in the presence of 0–2 % (w/v) NaCl (optimum, 0 %). Strain GA093T was capable of producing acid from various carbon sources, which was comparable to other related species of Flavobacterium . The strain contained MK-6 as the only isoprenoid quinone, iso-C15 : 0 as the major cellular fatty acid, phosphatidylethanolamine and phosphatidylinositol as diagnostic polar lipids, and sym-homospermidine as the major polyamine. The chemotaxonomic properties of strain GA093T were consistent with the general properties of Flavobacterium except the presence of phosphatidylinositol, which distinguished it from other related species. The total stretch of the obtained genome of GA093T was 5.05 Mbp, and the DNA G+C content was 34.79 mol%. The genome contained genes potentially related to the degradation of aromatic hydrocarbons. On the basis of the present polyphasic analysis, strain GA093T was found to have properties that distunguished it as representing a novel species of the genus Flavobacterium , for which the name Flavobacterium hydrocarbonoxydans sp. nov. is proposed. The type strain is GA093T (=KCTC 72594T=LMG 31760T).

Herbaspirillum psychrotolerans sp. nov., a member of the family Oxalobacteraceae from a glacier forefield

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3197-3203 ◽  
Author(s):  
Felizitas Bajerski ◽  
Lars Ganzert ◽  
Kai Mangelsdorf ◽  
André Lipski ◽  
Hans-Jürgen Busse ◽  
...  
Keyword(s):  
Type Species ◽  
Carbon Sources ◽  
Dry Weight ◽  
Rrna Gene ◽  
Content Type ◽  
Glacier Forefield ◽  
Link Type ◽  
The Family ◽  
Curved Rod ◽  
Type Strains

A novel psychrotolerant, Gram-negative, shiny white, curved-rod-shaped, facultatively anaerobic bacterium PB1T was isolated from a soil sample collected from a glacier forefield of the Larsemann Hills, East Antarctica. Isolate PB1T has catalase and low urease activity and hydrolyses gelatin and starch. Strain PB1T is able to grow between −5 °C and 30 °C with optimum growth at 14–20 °C. Glycerol, dl-arabinose, d-xylose, d-galactose, d-fructose, d-lyxose, d-fucose and potassium gluconate are used as sole carbon sources. The major quinone is ubiquinone Q-8. The major fatty acids (>10 %) for PB1T are C16 : 0 (19.1 %), C16 : 1ω7cis (44.6 %) and C18 : 1ω7cis (16.2 %). The major polyamines are putrescine [54.9 µmol (g dry weight)−1] and 2-hydroxy putrescine [18.5 µmol (g dry weight)−1]. DNA G+C content is 62.5 mol%. Strain PB1T is phylogenetically related to species of the genus Herbaspirillum , with highest 16S rRNA gene sequence similarities to Herbaspirillum canariense (97.3 %), Herbaspirillum aurantiacum (97.2 %), Herbaspirillum soli (97.2 %) and Herbaspirillum frisingense (97.0 %). The DNA–DNA relatedness values were below 30 % between PB1T and the type strains of Herbaspirillum canariense , Herbaspirillum aurantiacum and Herbaspirillum soli . The different geographical origin of strain PB1T from its closest phylogenetic relatives resulted in different phenotypic and genotypic specifications, whereby strain PBT represents a novel species of the genus Herbaspirillum , for which the name Herbaspirillum psychrotolerans is proposed. The type strain is PB1T (DSM 26001T = LMG 27282T).

scholarly journals Gluconobacter cerevisiae sp. nov., isolated from the brewery environment

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1134-1141 ◽  
Author(s):  
Freek Spitaels ◽  
Anneleen Wieme ◽  
Tom Balzarini ◽  
Ilse Cleenwerck ◽  
Anita Van Landschoot ◽  
...  
Keyword(s):  
Gluconic Acid ◽  
Type Species ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Environment Analysis ◽  
Content Type ◽  
Link Type ◽  
Yeast Extract Medium ◽  
Type Strains

Three strains, LMG 27748T, LMG 27749 and LMG 27882 with identical MALDI-TOF mass spectra were isolated from samples taken from the brewery environment. Analysis of the 16S rRNA gene sequence of strain LMG 27748T revealed that the taxon it represents was closely related to type strains of the species Gluconobacter albidus (100 % sequence similarity), Gluconobacter kondonii (99.9 %), Gluconobacter sphaericus (99.9 %) and Gluconobacter kanchanaburiensis (99.5 %). DNA–DNA hybridization experiments on the type strains of these species revealed moderate DNA relatedness values (39–65 %). The three strains used d-fructose, d-sorbitol, meso-erythritol, glycerol, l-sorbose, ethanol (weakly), sucrose and raffinose as a sole carbon source for growth (weak growth on the latter two carbon sources was obtained for strains LMG 27748T and LMG 27882). The strains were unable to grow on glucose-yeast extract medium at 37 °C. They produced acid from meso-erythritol and sucrose, but not from raffinose. d-Gluconic acid, 2-keto-d-gluconic acid and 5-keto-d-gluconic acid were produced from d-glucose, but not 2,5-diketo-d-gluconic acid. These genotypic and phenotypic characteristics distinguish strains LMG 27748T, LMG 27749 and LMG 27882 from species of the genus Gluconobacter with validly published names and, therefore, we propose classifying them formally as representatives of a novel species, Gluconobacter cerevisiae sp. nov., with LMG 27748T ( = DSM 27644T) as the type strain.

scholarly journals Description of Xenorhabdus khoisanae sp. nov., the symbiont of the entomopathogenic nematode Steinernema khoisanae

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3220-3224 ◽  
Author(s):  
Tiarin Ferreira ◽  
Carol A. van Reenen ◽  
Akihito Endo ◽  
Cathrin Spröer ◽  
Antoinette P. Malan ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Data ◽  
Entomopathogenic Nematode ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Carbohydrate Fermentation ◽  
Type Strains ◽  
Produce Acid

Bacterial strain SF87T, and additional strains SF80, SF362 and 106-C, isolated from the nematode Steinernema khoisanae, are non-bioluminescent Gram-reaction-negative bacteria that share many of the carbohydrate fermentation reactions recorded for the type strains of recognized Xenorhabdus species. Based on 16S rRNA gene sequence data, strain SF87T is shown to be closely related (98 % similarity) to Xenorhabdus hominickii DSM 17903T. Nucleotide sequences of strain SF87 obtained from the recA, dnaN, gltX, gyrB and infB genes showed 96–97 % similarity with Xenorhabdus miraniensis DSM 17902T . However, strain SF87 shares only 52.7 % DNA–DNA relatedness with the type strain of X. miraniensis , confirming that it belongs to a different species. Strains SF87T, SF80, SF362 and 106-C are phenotypically similar to X. miraniensis and X. beddingii , except that they do not produce acid from aesculin. These strains are thus considered to represent a novel species of the genus Xenorhabdus , for which the name Xenorhabdus khoisanae sp. nov. is proposed. The type strain is SF87T ( = DSM 25463T = ATCC BAA-2406T).

scholarly journals Jeotgalibaca dankookensis gen. nov., sp. nov., a member of the family Carnobacteriaceae, isolated from seujeot (Korean traditional food)

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1729-1735 ◽  
Author(s):  
Dong-Geol Lee ◽  
Martha E. Trujillo ◽  
Heecheol Kang ◽  
Tae-Young Ahn
Keyword(s):  
Type Species ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Traditional Food ◽  
The Novel ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Type Strains

A novel, Gram-stain-positive bacterium, designated strain EX-07T, was isolated from seujeot (Korean traditional food). The strain was aerobic, halotolerant and non-motile; it formed cocci that grouped into tetrads and sarcinae or formed irregular conglomerates. Growth occurred at pH 7–9, at 10–37 °C and with up to 9 % NaCl. Isolate EX-07T was catalase- and oxidase-negative and used sugars and organic acids as carbon sources. The 16S rRNA gene sequence of the novel strain showed 94.2–94.5 % similarity with the type strains of Trichococcus pasteurii , Trichococcus patagoniensis , Trichococcus collinsii , Trichococcus flocculiformis and Trichococcus palustris and only 92.2 % with representatives of the genera Bavariicoccus , Carnobacterium and Granulicatella . Sequence similarities based on the groEL gene ranged from 81.3 to 82.8 % between the novel isolate and the type strains of all species of the genus Trichococcus , and only 74.2 and 75.3 % with type strains of members of the genera Bavariicoccus and Granulicatella , respectively. The G+C content of the genomic DNA was 39.6 mol%. The predominant fatty acids were C16 : 1ω9c, C18 : 1ω9c, C16 : 0 and C14 : 0. The polar lipid profile was very complex and included phosphatidylethanolamine and several unidentified aminolipids, glycolipids and phospholipids. Based on the genotypic and phenotypic results obtained in this study, it is proposed that isolate EX-07T represents a novel species of a new genus in the family Carnobacteriaceae for which the name Jeotgalibaca dankookensis gen. nov., sp. nov. is proposed. The type strain of Jeotgalibaca dankookensis is EX-07T ( = KCCM 90229T = JCM 19215T).

Shewanella aestuarii sp. nov., a marine bacterium isolated from a tidal flat

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4683-4690 ◽  
Author(s):  
Hye Yoon Park ◽  
Che Ok Jeon
Keyword(s):  
16S Rrna ◽  
Tidal Flat ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Molecular Features ◽  
Lipid Pattern ◽  
Type Strains

A Gram-stain-negative, non-spore-forming, facultatively anaerobic bacterium, designated strain SC18T, was isolated from a tidal flat of Suncheon bay in South Korea. Cells were rod-shaped and motile by means of a polar flagellum. Cells were catalase-, oxidase- and β-haemolysis-positive. Growth was observed at 4–37 °C (optimum, 25–30 °C), at pH 5.0–9.0 (optimum, pH 7.0) and in the presence of 0–5.0 % (w/v) NaCl (optimum, 0–2 %). The major cellular fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and C16 : 0. The polar lipid pattern indicated the presence of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanolamine, an unidentified aminolipid and three unidentified lipids. Strain SC18T contained Q-7, Q-8, MK-7 and MMK-7 as the dominant respiratory quinones and the G+C content of the genomic DNA was 41.3 mol%. Phylogenetic analysis based on 16S rRNA and gyrase B (gyrB) gene sequences showed that strain SC18T formed a tight phyletic lineage with members of the genus Shewanella . Strain SC18T was related most closely to Shewanella denitrificans OS217T (97.3 % 16S rRNA gene sequence similarity) and Shewanella gaetbuli TF-27T (97.1 %), but the DNA–DNA relatedness levels between strain SC18T and the type strains of S. denitrificans and S. gaetbuli were 18.3±2.8 and 22.5±1.6 % (mean±sd), respectively. On the basis of phenotypic, chemotaxonomic and molecular features, strain SC18T represents a novel species of the genus Shewanella , for which the name Shewanella aestuarii sp. nov. is proposed. The type strain is SC18T ( = KACC 16187T = JCM 17801T).

Catenulispora graminis sp. nov., a rhizobacterium from bamboo (Phyllostachys nigro var. henonis) rhizosphere soil

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2589-2592 ◽  
Author(s):  
Hyo-Jin Lee ◽  
Song-Ih Han ◽  
Kyung-Sook Whang
Keyword(s):  
Type Species ◽  
Rhizosphere Soil ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Isoprenoid Quinones ◽  
Type Strains

A novel actinobacterium, designated strain BR-34T, was isolated from rhizosphere soil of bamboo (Phyllostachys nigro var. henonis) sampled in Damyang, Korea. The strain was found to have morphological and chemotaxonomic characteristics typical of the genus Catenulispora . The strain contained iso-C16 : 0 as the major fatty acid and MK-9(H4), MK-9(H6) and MK-9(H8) as major isoprenoid quinones. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BR-34T formed a cluster separate from members of the genus Catenulispora and was related most closely to Catenulispora acidiphila ID139908T (97.4 % similarity), Catenulispora rubra Aac-30T (97.3 %), Catenulispora yoronensis TT N02-20T (97.3 %) and Catenulispora subtropica TT 99-48T (97 %). However, the level of DNA–DNA relatedness between strain BR-34T and C. acidiphila ID139908T was only 45.32 %. Based on DNA–DNA relatedness, morphological and phenotypic data, strain BR-34T could be distinguished from the type strains of phylogenetically related species. It is therefore considered to represent a novel species of the genus Catenulispora , for which the name Catenulispora graminis sp. nov. is proposed. The type strain is BR-34T ( = KACC 15070T = NBRC 107755T).

Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai‘i, and emended description of the genus Flavobacterium

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3280-3286 ◽  
Author(s):  
Iris Kuo ◽  
Jimmy Saw ◽  
Durrell D. Kapan ◽  
Stephanie Christensen ◽  
Kenneth Y. Kaneshiro ◽  
...  
Keyword(s):  
Type Species ◽  
Original Description ◽  
Gliding Motility ◽  
Rrna Gene ◽  
Content Type ◽  
Phenotypic Differences ◽  
Whole Cells ◽  
Link Type ◽  
Decaying Wood ◽  
Type Strains

Strain IK-1T was isolated from decaying tissues of the shrub Wikstroemia oahuensis collected on O‘ahu, Hawai‘i. Cells were rods that stained Gram-negative. Gliding motility was not observed. The strain was oxidase-negative and catalase-positive. Zeaxanthin was the major carotenoid. Flexirubin-type pigments were not detected. The most abundant fatty acids in whole cells of IK-1T grown on R2A were iso-C15 : 0 and one or both of C16 : 1ω7c and C16 : 1ω6c. Based on comparisons of the nucleotide sequence of the 16S rRNA gene, the closest neighbouring type strains were Flavobacterium rivuli WB 3.3-2T and Flavobacterium subsaxonicum WB 4.1-42T, with which IK-1T shares 93.84 and 93.67 % identity, respectively. The G+C content of the genomic DNA was 44.2 mol%. On the basis of distance from its nearest phylogenetic neighbours and phenotypic differences, the species Flavobacterium akiainvivens sp. nov. is proposed to accommodate strain IK-1T ( = ATCC BAA-2412T = CIP 110358T) as the type strain. The description of the genus Flavobacterium is emended to reflect the DNA G+C contents of Flavobacterium akiainvivens IK-1T and other species of the genus Flavobacterium described since the original description of the genus.

scholarly journals Burkholderia insulsa sp. nov., a facultatively chemolithotrophic bacterium isolated from an arsenic-rich shallow marine hydrothermal system

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 189-194 ◽  
Author(s):  
Antje Rusch ◽  
Shaer Islam ◽  
Pratixa Savalia ◽  
Jan P. Amend
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Shallow Marine Hydrothermal System ◽  
Type Strains

Enrichment cultures inoculated with hydrothermally influenced nearshore sediment from Papua New Guinea led to the isolation of an arsenic-tolerant, acidophilic, facultatively aerobic bacterial strain designated PNG-AprilT. Cells of this strain were Gram-stain-negative, rod-shaped, motile and did not form spores. Strain PNG-AprilT grew at temperatures between 4 °C and 40 °C (optimum 30–37 °C), at pH 3.5 to 8.3 (optimum pH 5–6) and in the presence of up to 2.7 % NaCl (optimum 0–1.0 %). Both arsenate and arsenite were tolerated up to concentrations of at least 0.5 mM. Metabolism in strain PNG-AprilT was strictly respiratory. Heterotrophic growth occurred with O2 or nitrate as electron acceptors, and aerobic lithoautotrophic growth was observed with thiosulfate or nitrite as electron donors. The novel isolate was capable of N2-fixation. The respiratory quinones were Q-8 and Q-7. Phylogenetically, strain PNG-AprilT belongs to the genus Burkholderia and shares the highest 16S rRNA gene sequence similarity with the type strains of Burkholderia fungorum (99.8 %), Burkholderia phytofirmans (98.8 %), Burkholderia caledonica (98.4 %) and Burkholderia sediminicola (98.4 %). Differences from these related species in several physiological characteristics (lipid composition, carbohydrate utilization, enzyme profiles) and DNA–DNA hybridization suggested the isolate represents a novel species of the genus Burkholderia , for which we propose the name Burkholderia insulsa sp. nov. The type strain is PNG-AprilT ( = DSM 28142T = LMG 28183T).

Reclassification of Parvularcula flava as Aquisalinus luteolus nom. nov. and emended description of the genus Aquisalinus

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Jun-Jie Ying ◽  
Zhi-Cheng Wu ◽  
Yuan-Chun Fang ◽  
Lin Xu ◽  
Cong Sun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Parvularcula flava was proposed as a novel member of genus Parvularcula in 2016. Some time earlier, Aquisalinus flavus has been proposed as a novel species of a novel genus named Aquisalinus . When comparing the 16S rRNA gene sequences of type strains P. flava NH6-79T and A. flavus D11M-2T, they showed 97.9 % sequence identity, much higher than the sequence identities 92.7–94.3 % between P. flava NH6-79T and type strains in the genus Parvularcula , indicating that the later proposed novel taxon Parvularcula flava need reclassification. The phylogenetic trees based on 16S rRNA gene sequences and genome sequences both showed that P. flava NH6-79T and A. flavus D11M-2T formed a separated branch away from strains in the genera Parvularcula , Marinicaulis and Amphiplicatus . The average amino acid identity and average nucleotide identity values of P. flava NH6-79T and A. flavus D11M-2T were 87.9 and 85.0 %, respectively, much higher than the values between P. flava NH6-79T and other closely related type strains (54.3 %–58.1 % and 68.6–70.4 %, respectively). P. flava NH6-79T and A. flavus D11M-2T also contained summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c) and C16 : 0 as major fatty acids, distinguishing them from other closely related taxa. Based on the results of the phylogenetic, comparative genomic and phenotypic analyses, Parvularcula flava should be reclassified as Aquisalinus luteolus nom. nov. and the description of genus Aquisalinus is emended.

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