Description and Genome Analysis of Microvirga Antarctica Sp. Nov., A Novel Pink-Pigmented Psychrotolerant Bacterium Isolated From Antarctic Soil

2021 ◽  
Author(s):  
Lin Zhu ◽  
Weiwei Ping ◽  
Siyue Zhang ◽  
Ya Chen ◽  
Ying Zhang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Rrna Gene ◽  
Isolated Cells ◽  
Species Determination ◽  
Closely Related Species ◽  
Genomic Analyses ◽  
Genes Encoding ◽  
Psychrotolerant Bacterium ◽  
Ubiquinone 10 ◽  
Threshold Range

Abstract During the investigation of exploring potential psychrotolerant species from Antarctica soil, a novel pink-pigmented bacterium designated strain 3D7T was isolated. Cells of the isolate were observed to be rod-shaped (0.7–0.9×1.0–2.2 µm), Gram-stain negative and non-motile. It was able to grow at 4–32 ℃, pH 7.0–10.0 and in the presence of 0–3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 3D7T belongs to the genus Microvirga and was most closely related to ‘Microvirga brassicacearum’ CDVBN77T (98.3 %), Microvirga subterranea DSM 14364T (96.8 %), Microvirga guangxiensis 25BT (96.5 %) and Microvirga aerophila DSM 21344T (96.5 %). The predominant quinone was ubiquinone 10 (Q-10), and the major fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C19:0 cyclo ω8c. The predominant polar lipids were phosphatidylcholine and phosphatidylethanolamine. The genomic DNA G + C content of strain 3D7T was 63.5 mol%. Its genome sequence showed genes encoding phosphatases and lipases. Genetic machinery related to carbohydrate-active enzymes and secondary metabolites were also observed. The average nucleotide identity and digital DNA–DNA hybridization values based on whole genome sequences of strain 3D7T and its closely related species were below the threshold range for species determination. Phenotypic, chemotaxonomic, phylogenetic and genomic analyses suggested that strain 3D7T represents a novel species of the genus Microvirga, for which the name Microvirga antarctica sp. nov. is proposed. The type strain is 3D7T (= CGMCC 1.13821T = KCTC 72465T).

Sphingobium czechense sp. nov., isolated from a hexachlorocyclohexane dump site

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 723-728 ◽  
Author(s):  
Neha Niharika ◽  
Hana Moskalikova ◽  
Jasvinder Kaur ◽  
Fazlurrahman Khan ◽  
Miroslava Sedlackova ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
Closely Related Species ◽  
Dump Site ◽  
Content Type ◽  
Link Type ◽  
Physiological Tests

A yellow-pigmented bacterial strain, designated LL01T, was isolated from hexachlorocyclohexane (HCH)-contaminated soil at Spolana Neratovice, a former Czech producer of lindane. A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LL01T occupied a distinct phylogenetic position in the Sphingobium cluster, showing highest similarity to Sphingobium rhizovicinum CC-FH12-1T (98.5 %). The DNA G+C content of strain LL01T was 66.1 mol%. The predominant respiratory pigment was ubiquinone Q-10. The polar lipid profile of strain LL01T also corresponded to those reported for other Sphingobium species (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipids), supporting its identification as a member of the genus Sphingobium . Spermidine was the major polyamine observed. The results obtained from DNA–DNA hybridization and biochemical and physiological tests clearly distinguished strain LL01T from closely related species of the genus Sphingobium . Therefore, strain LL01T represents a novel species of the genus Sphingobium , for which the name Sphingobium czechense sp. nov. is proposed (type strain LL01T = CCM 7979T = DSM 25410T).

scholarly journals Pseudomonas guineae sp. nov., a novel psychrotolerant bacterium from an Antarctic environment

2007 ◽  
Vol 57 (11) ◽  
pp. 2609-2612 ◽  
Author(s):  
Núria Bozal ◽  
M. Jesús Montes ◽  
Elena Mercadé
Keyword(s):  
Dna Hybridization ◽  
Cellular Fatty Acid ◽  
South Shetland Islands ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Shetland Islands ◽  
Gene Sequence Analysis ◽  
Psychrotolerant Bacterium ◽  
The Antarctic ◽  
Type Strains

Two Gram-negative, cold-adapted, aerobic bacteria, designated strains M8T and M6, were isolated from soil collected from the South Shetland Islands. The organisms were rod-shaped, catalase- and oxidase-positive and motile by means of polar flagella. These two psychrotolerant strains grew between −4 and 30 °C. 16S rRNA gene sequence analysis placed strains M8T and M6 within the genus Pseudomonas. DNA–DNA hybridization experiments between the Antarctic isolate M8T and type strains of phylogenetically related species, namely Pseudomonas peli and Pseudomonas anguilliseptica, revealed levels of relatedness of 33 and 37 %, respectively. Strain M6 showed 99 % DNA similarity to strain M8T. Several phenotypic characteristics, together with data on cellular fatty acid composition, served to differentiate strains M8T and M6 from related pseudomonads. On the basis of the polyphasic taxonomic evidence presented in this study, it can be concluded that strains M8T and M6 belong to the same genospecies, representing a novel species of the genus Pseudomonas, for which the name Pseudomonas guineae sp. nov. is proposed. The type strain is M8T (=LMG 24016T=CECT 7231T).

Vibrio hemicentroti sp. nov., an alginate lyase-producing bacterium, isolated from the gut microflora of sea urchin (Hemicentrotus pulcherrimus)

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3697-3703 ◽  
Author(s):  
Duwoon Kim ◽  
Keun Sik Baik ◽  
Ye Seul Hwang ◽  
Jong-Soon Choi ◽  
Joseph Kwon ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Dna Hybridization ◽  
Alginate Lyase ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
South Sea ◽  
Hemicentrotus Pulcherrimus

An alginate lyase-producing bacterium, designated AlyHP32T, was isolated from the gut of sea urchin (Hemicentrotus pulcherrimus) obtained from the South Sea, Republic of Korea. Cells of strain AlyHP32T were Gram-reaction-negative and motile with a single polar flagellum. The strain grew with 1–6 % (w/v) NaCl (optimum 2–4 %) and at 4–30 °C (optimum 15–25 °C). Phylogenetic analysis based on sequences of the 16S rRNA gene and five housekeeping genes (atpA, pyrH, recA, rpoA and rpoD) revealed that strain AlyHP32T belonged to the genus Vibrio and formed a compact clade with the Vibrio splendidus group. However, DNA–DNA hybridization and fingerprints using the repetitive primers BOX and REP indicated that strain AlyHP32T was distinct from closely related species of the genus Vibrio . The major fatty acids were summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16:0. The DNA G+C content was 44.1 mol%. The predominant quinone was ubiquinone Q-8. Based on genotypic, phenotypic and DNA–DNA hybridization analysis, strain AlyHP32T represents a novel species of the genus Vibrio ; the name Vibrio hemicentroti sp. nov. (type strain AlyHP32T = KCTC 32085T = DSM 26178T) is proposed for this novel taxon.

Streptomyces graminilatus sp. nov., isolated from bamboo litter

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 528-532 ◽  
Author(s):  
Hyo-Jin Lee ◽  
Kyung-Sook Whang
Keyword(s):  
Dna Hybridization ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Sequence Similarities

A Gram-stain-positive, novel actinobacterium, designated strain JL-6T, was isolated from the litter of a bamboo (Sasa borealis) forest in Damyang, Korea. Strain JL-6T had white‐grey, smooth, cylindrical spores that were borne in straight, long spore-chains. The novel strain grew aerobically at 15–28 °C (optimum, 28 °C), pH 4.0–8.0 (optimum, pH 5.5) and with 0–1.5 % (w/v) NaCl. The cell-wall peptidoglycan contained ll-diaminopimelic acid, glutamic acid, alanine and glycine. The predominant menaquinones were MK-9(H6) and MK-9(H8). Whole-cell hydrolysates mainly contained glucose and ribose. Phosphatidylinositol and phosphatidylcholine were the diagnostic phospholipids. The G+C content of the genomic DNA was 72.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JL-6T belonged to the genus Streptomyces with sequence similarities ranging from 97.3 % to 98.3 %. However, DNA–DNA hybridization between JL-6T and the closest related strain, Streptomyces turgidiscabies , ATCC 700248T and other closely related species in the genus Streptomyces showed <50 % relatedness. Based on these observations, strain JL-6T is proposed to represent a novel species of the genus Streptomyces , for which the name Streptomyces graminilatus sp. nov. is proposed. The type strain is JL-6T ( = KACC 16470T = NBRC 108882T).

scholarly journals Burkholderia phytofirmans sp. nov., a novel plant-associated bacterium with plant-beneficial properties

2005 ◽  
Vol 55 (3) ◽  
pp. 1187-1192 ◽  
Author(s):  
A. Sessitsch ◽  
T. Coenye ◽  
A. V. Sturz ◽  
P. Vandamme ◽  
E. Ait Barka ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Related Species ◽  
Sequence Data ◽  
Single Species ◽  
Homoserine Lactone ◽  
Plant Production ◽  
Cell Protein ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Beneficial Bacterium

A Gram-negative, non-sporulating, rod-shaped, motile bacterium, with a single polar flagellum, designated strain PsJNT, was isolated from surface-sterilized onion roots. This isolate proved to be a highly effective plant-beneficial bacterium, and was able to establish rhizosphere and endophytic populations associated with various plants. Seven related strains were recovered from Dutch soils. Based on 16S rRNA gene sequence data, strain PsJNT and the Dutch strains were identified as representing a member of the genus Burkholderia, as they were closely related to Burkholderia fungorum (98·7 %) and Burkholderia phenazinium (98·5 %). Analysis of whole-cell protein profiles and DNA–DNA hybridization experiments confirmed that all eight strains belonged to a single species. Strain PsJNT had a DNA G+C content of 61·0 mol%. Only low levels of DNA–DNA hybridization to closely related species were found. Qualitative and quantitative differences in fatty acid composition between strain PsJNT and closely related species were identified. The predominant fatty acids in strain PsJNT were 16 : 0, 18 : 1ω7c and summed feature 3 (comprising 16 : 1ω7c and/or iso-15 : 0 2-OH). Isolate PsJNT showed high 1-aminocyclopropane-1-carboxylate deaminase activity and is therefore able to lower the ethylene level in a developing or stressed plant. Production of the quorum-sensing signal compound 3-hydroxy-C8-homoserine lactone was detected. Based on the results of this polyphasic taxonomic study, strain PsJNT and the seven Dutch isolates are considered to represent a single, novel species, for which the name Burkholderia phytofirmans sp. nov. is proposed. The type strain is strain PsJNT (=LMG 22146T=CCUG 49060T).

scholarly journals Shewanella canadensis sp. nov. and Shewanella atlantica sp. nov., manganese dioxide- and hexahydro-1,3,5-trinitro-1,3,5-triazine-reducing, psychrophilic marine bacteria

2007 ◽  
Vol 57 (9) ◽  
pp. 2155-2162 ◽  
Author(s):  
Jian-Shen Zhao ◽  
Dominic Manno ◽  
Sonia Thiboutot ◽  
Guy Ampleman ◽  
Jalal Hawari
Keyword(s):  
Dna Hybridization ◽  
Genomic Dna ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Closely Related Species ◽  
Organic Acids And Sugars

Two strains belonging to the genus Shewanella, HAW-EB2T and HAW-EB5T, were isolated previously from marine sediment sampled from the Atlantic Ocean, near Halifax harbour in Canada, for their potential to degrade explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). In the present study, strains HAW-EB2T and HAW-EB5T were found to display high 16S rRNA gene sequence similarity (90–99.5 %) to species of Shewanella, but their gyrB sequences were significantly different from each other and from species of Shewanella (79–87.6 %). Furthermore, DNA–DNA hybridization showed that the genomic DNA of the two strains was only 22 % related and showed less than 41 % relatedness to closely related species of Shewanella. In comparison to other species of Shewanella, strains HAW-EB2T and HAW-EB5T were also unique in some phenotypic properties such as activities of β-galactosidase and tyrosine arylamidase and the ability to metabolize certain organic acids and sugars. Both strains HAW-EB2T and HAW-EB5T utilize malate, valerate, peptone and yeast extract as sole carbon and energy sources. The major membrane fatty acids of the two strains were C14 : 0, iso-C15 : 0, C16 : 0, C16 : 1 ω7, C18 : 1 ω7 and C20 : 5 ω3 and their major quinones were Q-7, Q-8 and MK-7. On the basis of these results, strain HAW-EB2T (=NCIMB 14238T =CCUG 54553T) is proposed as the type strain of Shewanella canadensis sp. nov. and strain HAW-EB5T (=NCIMB 14239T =CCUG 54554T) is proposed as the type strain of Shewanella atlantica sp. nov.

scholarly journals Pseudoalteromonas marina sp. nov., a marine bacterium isolated from tidal flats of the Yellow Sea, and reclassification of Pseudoalteromonas sagamiensis as Algicola sagamiensis comb. nov.

2007 ◽  
Vol 57 (1) ◽  
pp. 12-18 ◽  
Author(s):  
Young-Do Nam ◽  
Ho-Won Chang ◽  
Ja Ryeong Park ◽  
Hyuk-Yong Kwon ◽  
Zhe-Xue Quan ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Closely Related Species ◽  
Gene Sequence Analysis ◽  
Pseudoalteromonas Marina ◽  
Type Strains

Two Gram-negative, motile and strictly aerobic marine bacteria were isolated from a tidal flat sediment sample obtained from Dae-Chun, Chung-Nam, Korea. They were preliminarily identified as Pseudoalteromonas-like bacteria, based on 16S rRNA gene sequence analysis showing nearly identical sequences (>99.7 % sequence similarity) and the highest similarity (98.4 %) to the species Pseudoalteromonas undina. Some phenotypic features of the newly isolated strains were similar to those of members of the genus Pseudoalteromonas, but several physiological and chemo-taxonomical properties readily distinguished the new isolates from previously described species. DNA–DNA hybridization with type strains of phylogenetically closely related species demonstrated that the isolates represent a novel Pseudoalteromonas species, for which the name Pseudoalteromonas marina sp. nov. is proposed, with the type strain mano4T (=KCTC 12242T=DSM 17587T). In addition, on the basis of this study and polyphasic data obtained from previous work, it is proposed that the species Pseudoalteromonas sagamiensis should be reclassified as Algicola sagamiensis comb. nov. and that strain B-10-31T (=DSM 14643T=JCM 11461T) be designated the type strain.

Mycetocola miduiensis sp. nov., a psychrotolerant bacterium isolated from Midui glacier

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2661-2665 ◽  
Author(s):  
Lang Zhu ◽  
Qing Liu ◽  
Hongcan Liu ◽  
Yuguang Zhou ◽  
Yuhua Xin ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Psychrotolerant Bacterium ◽  
Sequence Similarities

An aerobic, asporous, flagellated, Gram-stain-positive, rod-shaped bacterium MD-T1-10-2T was isolated from the topsoil of Midui Glacier, Tibet Province, China. Phylogenetic analysis based on 16S rRNA gene sequence analysis placed the strain in a clade containing Mycetocola manganoxydans CCTCC AB 209002T, Mycetocola reblochoni DSM 18580T, Mycetocola tolaasinivorans JCM 11656T, Mycetocola lacteus JCM 11654T and Mycetocola saprophilus JCM 11655T, with the sequence similarities of 99.2, 98.1, 96.7, 96.6 and 96.4 %, respectively. DNA–DNA hybridization analysis indicated that strain MD-T1-10-2T represented a new member of this genus. The optimal ranges of temperature and pH for growth were 20–25 °C and 7.0–9.0, respectively; the strain could even grow at 0 °C. The major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinones were MK-10 and MK-11. The cell wall amino acids were lysine, alanine, glycine and glutamic acids. The DNA G+C content was 65.9 mol%. Based on the genotypic and phenotypic data, strain MD-T1-10-2T for which the name Mycetocola miduiensis sp. nov. is proposed; the type strain is MD-T1-10-2T ( = CGMCC 1.11101T = NBRC 107877T).

scholarly journals Pseudomonas yamanorum sp. nov., a psychrotolerant bacterium isolated from a subantarctic environment

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 424-431 ◽  
Author(s):  
Víctor Gonzalo Arnau ◽  
Leandro Arturo Sánchez ◽  
Osvaldo Daniel Delgado
Keyword(s):  
16S Rrna ◽  
Related Species ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Psychrotolerant Bacterium ◽  
Type Strains

A psychrotolerant strain, 8H1T, was isolated from soil samples collected in Isla de los Estados, Ushuaia, Argentina. Cells were Gram-negative, aerobic, straight rods, occurring singly or in pairs, non-spore-forming and motile by means of two polar flagella. The isolate was able to grow in the range 4–35 °C, with optimum growth at 28 °C. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid pattern of strain 8H1T comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. Ubiquinone 9 (Q-9) was the predominant lipoquinone. The DNA G+C content was 59.8 mol%. 16S rRNA gene sequence-based phylogeny suggested the affiliation of strain 8H1T to the ‘Pseudomonas fluorescens group’, displaying ≥98.5 % sequence similarity to 29 type strains. A multilocus sequence analysis (MLSA) study performed by concatenating 16S rRNA, gyrB, rpoD and rpoB gene sequences showed that isolate 8H1T could be discriminated from closely related species of the genus Pseudomonas and placed in the ‘Pseudomonas gessardii subgroup’, including the species with the highest MLSA sequence similarities: Pseudomonas brenneri (96.2 %), P. gessardii (96.1 %), P. proteolytica (96.0 %), P. meridiana (96.0 %) and P. mucidolens (95.4 %). DNA–DNA hybridization analysis between 8H1T and the type strains of these closely related species revealed relatedness values of 27.0, 8.8, 41.2, 39.7 and 46.1 %, respectively. These results, together with differences in several phenotypic features, support the classification of a novel species, for which the name Pseudomonas yamanorum sp. nov. is proposed. The type strain is 8H1T ( = DSM 26522T = CCUG 63249T = LMG 27247T).

Bacillus tequilensis sp. nov., isolated from a 2000-year-old Mexican shaft-tomb, is closely related to Bacillus subtilis

2006 ◽  
Vol 56 (7) ◽  
pp. 1475-1484 ◽  
Author(s):  
Joshua W. Gatson ◽  
Bruce F. Benz ◽  
Chitra Chandrasekaran ◽  
Masataka Satomi ◽  
Kasthuri Venkateswaran ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Related Species ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Whole Cell ◽  
Bacillus Tequilensis ◽  
The 16S Rrna Gene

A Gram-positive, spore-forming bacillus was isolated from a sample taken from an approximately 2000-year-old shaft-tomb located in the Mexican state of Jalisco, near the city of Tequila. Tentative identification using conventional biochemical analysis consistently identified the isolate as Bacillus subtilis. DNA isolated from the tomb isolate, strain 10bT, and closely related species was used to amplify a Bacillus-specific portion of the highly conserved 16S rRNA gene and an internal region of the superoxide dismutase gene (sodA int). Trees derived from maximum-likelihood methods applied to the sodA int sequences yielded non-zero branch lengths between strain 10bT and its closest relative, whereas a comparison of a Bacillus-specific 546 bp amplicon of the 16S rRNA gene demonstrated 99 % similarity with B. subtilis. Although the 16S rRNA gene sequences of strain 10bT and B. subtilis were 99 % similar, PFGE of NotI-digested DNA of strain 10bT revealed a restriction profile that was considerably different from those of B. subtilis and other closely related species. Whereas qualitative differences in whole-cell fatty acids were not observed, significant quantitative differences were found to exist between strain 10bT and each of the other closely related Bacillus species examined. In addition, DNA–DNA hybridization studies demonstrated that strain 10bT had a relatedness value of less than 70 % with B. subtilis and other closely related species. Evidence from the sodA int sequences, whole-cell fatty acid profiles and PFGE analysis, together with results from DNA–DNA hybridization studies, justify the classification of strain 10bT as representing a distinct species, for which the name Bacillus tequilensis sp. nov. is proposed. The type strain is 10bT (=ATCC BAA-819T=NCTC 13306T).

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