scholarly journals Agromyces kandeliae sp. nov., isolated from rhizosphere soil of Kandelia candel in a mangrove

2020 ◽  
Vol 70 (11) ◽  
pp. 5861-5867 ◽  
Author(s):  
Ruijun Wang ◽  
Yanghui Ye ◽  
Yanfen Huang ◽  
Yanfang Nie ◽  
ShuaiBo Han ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Rhizosphere Soil ◽  
Novel Species ◽  
Kandelia Candel ◽  
Gram Stain ◽  
Mangrove Plant ◽  
Content Type ◽  
Reference Strains

A novel, Gram-stain-positive, aerobic, non-spore-forming, non-motile and irregular rod-shaped bacterium designated Q22T was isolated from the rhizosphere soil of mangrove plant, Kandelia candel collected in Zhangzhou, Fujian province, China. Strain Q22T was able to grow at 10–40 °C (optimum 30 °C), pH 5.5–9.0 (optimum 7.0–8.0) and with 0–5.0% (w/v) NaCl (optimum 1.0 %). The genomic DNA G+C content was 71.9%. The average nucleotide identity, and in silico DNA–DNA hybridization values between strain Q22T and the reference strains were 79.7–88.9% and 22.6–37.4%, respectively. The predominant isoprenoid quinone was MK-12 and the major fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The major polar lipids of strain Q22T were diphosphatidylglycerol, phosphatidylglycerol, one glycolipid and three unidentified lipids. The strain Q22T contained 2,4-diaminobutyric acid, alanine acid, glutamic acid and glycine in the peptidoglycans. The phylogenetic analysis and genotypic features, along with the phenotypic and chemotaxonomic characteristics, indicate that strain Q22T represents a novel species of the genus Agromyces , for which the name Agromyces kandeliae sp. nov. is proposed. The type strain is Q22T (=MCCC 1K03340T= KCTC 39961T).

scholarly journals Barrientosiimonas endolithica sp. nov., isolated from pebbles, reclassification of the only species of the genus Tamlicoccus, Tamlicoccus marinus Lee 2013, as Barrientosiimonas marina comb. nov. and emended description of the genus Barrientosiimonas

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3031-3036 ◽  
Author(s):  
B. Parag ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Novel Species ◽  
Uttar Pradesh ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Gene Sequences ◽  
The Family ◽  
Emended Description

Strain JC268T was isolated from pebbles collected from a dam located in Lalitpur, Uttar Pradesh, India. Cells of strain JC268T were coccoid, appeared in pairs/triads/tetrads or short chains and were Gram-stain-positive, non-spore-forming, non-motile and obligately aerobic. Strain JC268T was catalase- and oxidase-positive and utilized citrate for growth. The genomic DNA G+C content of strain JC268T was 65.3 mol%. The cell-wall peptidoglycan contained l-lysine–l-serine–d-aspartic acid as interpeptide bridge with the type A4α. The major menaquinone was MK-8(H4). Major (>10 %) fatty acids were iso-C16 : 0, iso-C16 : 1H and anteiso-C17 : 1ω9c. Diphosphatidylglycerol, phosphoglycolipid, phosphatidylinositol, glycolipid, four unidentified lipids, an amino lipid and phospholipid were the polar lipids of strain JC268T. EzTaxon-e blast search of 16S rRNA gene sequences showed that strain JC268T has highest similarity to Barrientosiimonas humi 39T (98.65 %) and Tamlicoccus marinus MSW-24T (97.8 %) of the family Dermacoccaceae. Genome reassociation (based on DNA–DNA hybridization) of strain JC268T with Barrientosiimonas humi CGMCC 4.6864T ( = 39T) and T. marinus KCTC 19485T ( = MSW-24T) yielded values of 32.5 ± 2 % and 27.3 ± 2 %, respectively. Based on the data from phylogenetic and polyphasic taxonomic analyses, strain JC268T represents a novel species of the genus Barrientosiimonas for which the name Barrientosiimonas endolithica sp. nov., is proposed. The type strain of Barrientosiimonas endolithica is JC268T ( = KCTC 29672T = NBRC 110608T). Our data suggest that T. marinus should be reclassified within the genus Barrientosiimonas. Thus, a reclassification is proposed for T. marinus, the type and only species of the genus Tamlicoccus, as Barrientosiimonas marina comb. nov., which implies the emendation of the description of the genus Barrientosiimonas.

scholarly journals Nesterenkonia muleiensis sp. nov., a novel actinobacterium isolated from sap of Populus euphratica

2020 ◽  
Vol 70 (3) ◽  
pp. 1888-1894 ◽  
Author(s):  
Ruijun Wang ◽  
Nusratgul Anwar ◽  
Jinglin Ding ◽  
Yanghui Ye ◽  
Yanhu Ren ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Phylogenetic Analysis ◽  
Genomic Dna ◽  
Type Strain ◽  
Novel Species ◽  
Populus Euphratica ◽  
Gram Stain ◽  
Content Type ◽  
Pr China ◽  
Isoprenoid Quinones

A novel, Gram-stain-positive, aerobic, non-endospore-forming, non-motile and rod-shaped bacterium designated RB2T was isolated from sap of Populus euphratica collected in Mulei county, Xinjiang province, PR China. RB2T was able to grow at 10–45 °C (optimum 35 °C), pH 6.0–12.0 (optimum 8.0) and with 0–12 % (w/v) NaCl (optimum 1 %). The genomic DNA G+C content was 63.5 % (from the genome sequence). The results of the chemotaxonomic analysis indicated that the predominant isoprenoid quinones were MK-8 and MK-9. The major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The major polar lipids of RB2T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two glycolipids. The peptidoglycan type of RB2T was A4α, l-Lys–Gly–l-Glu. The results of the phylogenetic analysis, along with the phenotypic and chemotaxonomic characteristics, indicate that strain RB2T represents a novel species of the genus Nesterenkonia , for which the name Nesterenkonia muleiensis sp. nov. is proposed. The type strain is RB2T (=MCCC 1K03528T=KCTC 49017T).

scholarly journals Leptospira mayottensis sp. nov., a pathogenic species of the genus Leptospira isolated from humans

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4061-4067 ◽  
Author(s):  
Pascale Bourhy ◽  
Louis Collet ◽  
Sylvain Brisse ◽  
Mathieu Picardeau
Keyword(s):  
Sequence Analysis ◽  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Leptospira Borgpetersenii

A group of strains representing species of the genus Leptospira, isolated from patients with leptospirosis in Mayotte (Indian Ocean), were previously found to be considerably divergent from other known species of the genus Leptospira . This was inferred from sequence analysis of rrs (16S rRNA) and other genetic loci and suggests that they belong to a novel species. Two strains from each serogroup currently identified within this novel species were studied. Spirochaete, aerobic, motile, helix-shaped strains grew well at 30–37 °C, but not at 13 °C or in the presence of 8-azaguanine. Draft genomes of the strains were also analysed to study the DNA relatedness with other species of the genus Leptospira . The new isolates formed a distinct clade, which was most closely related to Leptospira borgpetersenii , in multilocus sequence analysis using concatenated sequences of the genes rpoB, recA, fusA, gyrB, leuS and sucA. Analysis of average nucleotide identity and genome-to-genome distances, which have recently been proposed as reliable substitutes for classical DNA–DNA hybridization, further confirmed that these isolates should be classified as representatives of a novel species. The G+C content of the genomic DNA was 39.5 mol%. These isolates are considered to represent a novel species, for which the name Leptospira mayottensis sp. nov. is proposed, with 200901116T ( = CIP 110703T = DSM 28999T) as the type strain.

Undibacterium baiyunense sp. nov., Undibacterium curvum sp. nov., Undibacterium fentianense sp. nov., Undibacterium flavidum sp. nov., Undibacterium griseum sp. nov., Undibacterium hunanense sp. nov., Undibacterium luofuense sp. nov., Undibacterium nitidum sp. nov., Undibacterium rivi sp. nov., Undibacterium rugosum sp. nov. and Undibacterium umbellatum sp. nov., isolated from streams in China

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Huibin Lu ◽  
Fei Liu ◽  
Tongchu Deng ◽  
Meiying Xu
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Gene Sequences ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

Twelve Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (CY7WT, CY18WT, CY22WT, FT31WT, FT137WT, FT147WT, BYS50W, BYS107WT, LFS511WT, LX15WT, LX22WT and NL8WT) were isolated from streams in China. Comparisons based on 16S rRNA gene sequences indicated that these strains take species of genus Undibacterium as close neighbours. The reconstructed phylogenetic and phylogenomic trees also showed that these strains cluster with species of genus Undibacterium together. The genome G+C contents of these strains were in the range of 45.3 to 53.3 mol%. The calculated pairwise OrthoANIu values and digital DNA–DNA hybridization values among these strains and related strains were in the range of 70.4 to 94.1% and 19.3 to 55.3% except that the values between strains CY7WT and BYS50W were 99.0 and 91.8 %, respectively. Q-8 was their predominant respiratory quinone. C16 : 1  ω7c and C16 : 0 were their major fatty acids. Their polar lipids profiles were similar, including phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and two kinds of unidentified aminolipids. Combining polyphasic taxonomic characteristics and phylogenetic relationships, twelve strains should represent eleven independent novel species of genus Undibacterium , for which the names Undibacterium baiyunense sp. nov. (type strain BYS107WT=GDMCC 1.2453T=KCTC 82653T), Undibacterium curvum sp. nov. (type strain CY22WT=GDMCC 1.1906T=KACC 21951T), Undibacterium fentianense sp. nov. (type strain FT137WT=GDMCC 1.2456T=KCTC 82656T), Undibacterium flavidum sp. nov. (type strain LX15WT=GDMCC 1.1910T=JCM 34286T), Undibacterium griseum sp. nov. (type strain FT31WT=GDMCC 1.1908T=KACC 21953T), Undibacterium hunanense sp. nov. (type strain CY18WT=GDMCC 1.1904T=KACC 21949T), Undibacterium luofuense sp. nov. (type strain LFS511WT=GDMCC 1.2458T=KCTC 82658T), Undibacterium nitidum sp. nov. (type strain LX22WT=GDMCC 1.1912T=KACC 21957T), Undibacterium rivi sp. nov. (type strain FT147WT=GDMCC 1.2457T=KCTC 82657T), Undibacterium rugosum sp. nov. (type strain CY7WT=GDMCC 1.1903T=KACC 21961T) and Undibacterium umbellatum sp. nov. (type strain NL8WT=GDMCC 1.1915T=KACC 21960T) are proposed.

Undibacterium jejuense sp. nov. and Undibacterium seohonense sp. nov., isolated from soil and freshwater, respectively

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 236-241 ◽  
Author(s):  
Soo-Jin Kim ◽  
Ji-Young Moon ◽  
Hang-Yeon Weon ◽  
Seung-Beom Hong ◽  
Soon-Ja Seok ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Gram Stain ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Sequence Similarities

Two bacterial strains, designated JS4-4T and SHS5-24T, were isolated from forest soil of Jeju Island and fresh water of Seoho lake in Suwon city, respectively, South Korea. Both strains were Gram-stain-negative, aerobic, motile rods. Strains JS4-4T and SHS5-24T showed high sequence similarities (97.6–95.8 %) and (96.5–95.6 %), respectively, to the members of the genus Undibacterium . The sequence similarity between strains JS4-4T and SHS5-24T was 97.0 %. A phylogenetic tree showed that these strains fell within the radius of the genus Undibacterium . The main fatty acids of strains JS4-4T and SHS5-24T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (50.1 and 58.7 %, respectively) and C16 : 0 (28.3 and 24.5 %, respectively). Both strains had ubiquinone 8 as the only respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids. Strain JS4-4T showed <70 % DNA–DNA hybridization with members of the genus Undibacterium . Thus, based on the evidence of a polyphasic study, it is proposed that strains JS4-4T and SHS5-24T represent two novel species, for which the names Undibacterium jejuense sp. nov. (type strain JS4-4T = KACC 12607T = NBRC 108922T) and Undibacterium seohonense sp. nov. (type strain SHS5-24T = KACC 16656T = NBRC 108929T) are proposed.

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 Pantoea coffeiphila sp. nov., cause of the ‘potato taste’ of Arabica coffee from the African Great Lakes region

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 23-29 ◽  
Author(s):  
Dominique Gueule ◽  
Gérard Fourny ◽  
Elisabeth Ageron ◽  
Anne Le Flèche-Matéos ◽  
Mathias Vandenbogaert ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Gene Sequencing ◽  
Great Lakes Region ◽  
The Novel ◽  
Content Type ◽  
African Great Lakes ◽  
Link Type

Six isolates recovered from coffee seeds giving off a potato-like flavour were studied. Gene sequencing (rrs and rpoB) showed they belong to the genus Pantoea . By DNA–DNA hybridization, the isolates constituted a genomic species with less than 17 % relatedness to 96 strains representing enterobacterial species. Multilocus sequence analysis (gyrB, rpoB, atpD and infB genes) showed the isolates to represent a discrete species of the genus Pantoea . Nutritional versatility of the novel species was poor. The novel species is proposed as Pantoea coffeiphila sp.nov. and its type strain is Ca04T ( = CIP 110718T = DSM 28482T).

scholarly journals Kocuria koreensis sp. nov., isolated from fermented seafood

2010 ◽  
Vol 60 (1) ◽  
pp. 140-143 ◽  
Author(s):  
Eun-Jin Park ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
Mi-Ja Jung ◽  
Kee-Sun Shin ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Phylogenetic Trees ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
The 16S Rrna Gene

A Gram-positive, aerobic, non-motile and coccoid actinobacterium, designated P31T, was isolated from a traditional, fermented seafood. The strain was catalase-positive and oxidase-negative. Cells grew in the presence of 0–15.0 % (w/v) NaCl, and at pH 5–10 and 15–37 °C. Major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. Strain P31T contained MK-7 as the predominant menaquinone. The DNA G+C content of the genomic DNA of strain P31T was 65.2 mol%. A phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain P31T was most closely related to Kocuria kristinae DSM 20032T, with 96.9 % similarity, and these two strains clustered together in constructed phylogenetic trees. The DNA–DNA hybridization value between strain P31T and K. kristinae DSM 20032T was 21.1 %. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, it is suggested that strain P31T represents a novel species of the genus Kocuria, for which the name Kocuria koreensis sp. nov. is proposed. The type strain is P31T (=KCTC 19595T=JCM 15915T).

scholarly journals Xanthomonas hydrangeae sp. nov., a novel plant pathogen isolated from Hydrangea arborescens

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Nay C. Dia ◽  
Johan Van Vaerenbergh ◽  
Cinzia Van Malderghem ◽  
Jochen Blom ◽  
Theo H. M. Smits ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Close Relation ◽  
Genome Sequences ◽  
Content Type ◽  
Phylogenetic Characterization ◽  
Link Type ◽  
Amplification Assay

This paper describes a novel species isolated in 2011 and 2012 from nursery-grown Hydrangea arborescens cultivars in Flanders, Belgium. After 4 days at 28 °C, the strains yielded yellow, round, convex and mucoid colonies. Pathogenicity of the strains was confirmed on its isolation host, as well as on Hydrangea quercifolia. Analysis using MALDI-TOF MS identified the Hydrangea strains as belonging to the genus Xanthomonas but excluded them from the species Xanthomonas hortorum . A phylogenetic tree based on gyrB confirmed the close relation to X. hortorum . Three fatty acids were dominant in the Hydrangea isolates: anteiso-C15 : 0, iso-C15 : 0 and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c). Unlike X. hortorum pathovars, the Hydrangea strains were unable to grow in the presence of lithium chloride and could only weakly utilize d-fructose-6-PO4 and glucuronamide. Phylogenetic characterization based on multilocus sequence analysis and phylogenomic characterization revealed that the strains are close to, yet distinct from, X. hortorum . The genome sequences of the strains had average nucleotide identity values ranging from 94.35–95.19 % and in silico DNA–DNA hybridization values ranging from 55.70 to 59.40 % to genomes of the X. hortorum pathovars. A genomics-based loop-mediated isothermal amplification assay was developed which was specific to the Hydrangea strains for its early detection. A novel species, Xanthomonas hydrangeae sp. nov., is proposed with strain LMG 31884T (=CCOS 1956T) as the type strain.

scholarly journals Maricaulis alexandrii sp. nov., a novel dimorphic prosthecate and active bioflocculants-bearing bacterium isolated from phycosphere microbiota of laboratory cultured highly-toxic Alexandrium catenella LZT09

2021 ◽  
Author(s):  
Xiao-ling Zhang ◽  
Min Qi ◽  
Qiu-hong Li ◽  
Zhen-dong Cui ◽  
Qiao Yang
Keyword(s):  
Genomic Dna ◽  
Type Strain ◽  
Novel Species ◽  
Average Nucleotide Identity ◽  
Gram Stain ◽  
Unidentified Phospholipid ◽  
Alexandrium Catenella ◽  
Sulfoquinovosyl Diacylglycerol ◽  
Curved Rods ◽  
Prosthecate Bacterium

Abstract An aerobic, Gram-stain-negative, straight or curved rods, prosthecate bacterium designated as LZ-16-1T was isolated from phycosphere microbiota of highly-toxic and laboratory cultured dinoflagellate Alexandrium catenella LZT09. This new isolate produces active bioflocculanting exopolysaccharides (EPS). Cells were dimorphic with non-motile prostheca, or non-stalked and motile by a single polar flagellum. Growth occurred at 10-40 °C, pH 5–9 and 1–8 % (w/v) NaCl, with optimum growth at 25 °C, pH 7–8 and 2-4 % (w/v) NaCl, respectively. Phylogenetic analysis based on 16S rRNA indicated that strain LZ-16-1T was affiliated to the genus Maricaulis, and closely related to Maricaulis parjimensis MCS 25T (99.48%) and M. virginensis VC-5T (99.04%),. However, based on genome sequencing and phylogenomic calculations, the average nucleotide identity (ANI) and digtal DNA-DNA genome hybridization (dDDH) values between the two strains were only 85.0 and 20.9%, respectively. Strain LZ-16-1T owned Q-10 as predominant isoprenoid quinone; summed feature 8, C16:0, C17:0, C18:0, C18:1 ω9c and summed feature 9 as dominant fatty acids; and sulfoquinovosyl diacylglycerol, glycolipids and unidentified phospholipid as major polar lipids. The genomic DNA G+C content is 63.6 mol%. Physiological and chemotaxonomic characterization further confirmed the distinctiveness of strain LZ-16-1T from other Maricaulis members. Thus, strain LZ-16-1T represents a novel species of the genus Maricaulis, for which the name Maricaulis alexandrii sp. nov. (type strain LZ-16-1T=KCTC 72194T=CCTCC AB 2019006T) is proposed .

Sign in / Sign up

Export Citation Format

Share Document