scholarly journals Methylotenera mobilis gen. nov., sp. nov., an obligately methylamine-utilizing bacterium within the family Methylophilaceae

2006 ◽  
Vol 56 (12) ◽  
pp. 2819-2823 ◽  
Author(s):  
Marina G. Kalyuzhnaya ◽  
Sarah Bowerman ◽  
Jimmie C. Lara ◽  
Mary E. Lidstrom ◽  
Ludmila Chistoserdova
Keyword(s):  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Methylamine Dehydrogenase ◽  
Carbon And Nitrogen ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Lake Washington ◽  
Ribulose Monophosphate Cycle ◽  
Ph Range ◽  
Single Flagellum

A novel obligate methylamine utilizer (strain JLW8T), isolated from Lake Washington sediment, was characterized taxonomically. The isolate was an aerobic, Gram-negative bacterium. Cells were rod-shaped and motile by means of a single flagellum. Reproduction was by binary fission and no resting bodies were formed. Growth was observed within a pH range of 5–8.5, with optimum growth at pH 7.5. It utilized methylamine as a single source of energy, carbon and nitrogen. Methylamine was oxidized via methylamine dehydrogenase and formaldehyde was assimilated via the ribulose monophosphate cycle. The cellular fatty acid profile was dominated by C16 : 0 ω7c and C16 : 0 and the major phospholipid was phosphatidylethanolamine. The DNA G+C content was 54 mol%. 16S rRNA gene sequence analysis indicated that the new isolate was closely related (97–98 % similarity) to a broad group of sequences from uncultured or uncharacterized Betaproteobacteria, but only distantly related (93–96 % similarity) to known methylotrophs of the family Methylophilaceae. Strain JLW8T (=ATCC BAA-1282T=DSM 17540T) is proposed as the type strain of a novel species in a new genus within the family Methylophilaceae, Methylotenera mobilis gen. nov., sp. nov.

scholarly journals Methylosarcina lacus sp. nov., a methanotroph from Lake Washington, Seattle, USA, and emended description of the genus Methylosarcina

2005 ◽  
Vol 55 (6) ◽  
pp. 2345-2350 ◽  
Author(s):  
Marina G. Kalyuzhnaya ◽  
Sergey M. Stolyar ◽  
Ann J. Auman ◽  
Jimmie C. Lara ◽  
Mary E. Lidstrom ◽  
...  
Keyword(s):  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Type I ◽  
Intracytoplasmic Membranes ◽  
Lake Washington ◽  
Ribulose Monophosphate Cycle ◽  
Ph Range ◽  
Genotypic Characteristics ◽  
Cellular Fatty Acid Profile ◽  
The 16S Rrna Gene

An obligately methanotrophic bacterial strain, LW14T, isolated from the sediment of Lake Washington, Seattle, USA, is described taxonomically. The isolate is an aerobic, Gram-negative, non-motile bacterium capable of growth on methane, and possesses type I intracytoplasmic membranes (i.e. it is a type I methanotroph). The strain possesses particulate methane monooxygenase (MMO) and has no soluble MMO. Formaldehyde is assimilated via the ribulose monophosphate cycle. The isolate grows within a pH range of 4–8, with the optimum between pH 5·5 and 6·5. The cellular fatty acid profile is dominated by C16 :  ω18c, C16 : 1 ω7c and C16 : 1 ω5t fatty acids. The DNA G+C content is 53·3±0·4 mol%. On the basis of sequence analysis of the 16S rRNA gene, isolate LW14T is related most closely to representatives of the genus Methylosarcina. However, DNA–DNA hybridization analysis reveals only a distant relationship between isolate LW14T and the previously described Methylosarcina species. On the basis of its phenotypic and genotypic characteristics, LW14T represents a novel species of the genus Methylosarcina, for which the name Methylosarcina lacus sp. nov. is proposed, with LW14T (=ATCC BAA-1047T=JCM 13284T) as the type strain.

scholarly journals Oceanipulchritudo coccoides gen. nov., sp. nov., isolated from marine sediment within the family Puniceicoccaceae

2020 ◽  
Vol 70 (11) ◽  
pp. 5654-5664 ◽  
Author(s):  
Xi Feng ◽  
Qi-Hang Zou ◽  
Xiao-Yu Zhang ◽  
Meng-Qi Ye ◽  
Zong-Jun Du
Keyword(s):  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Marine Isolate ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Pr China ◽  
Ph Range

A Gram-stain-negative, aerobic coccus, designated CK1056T, was isolated from coastal sediment of Xiaoshi Island, Weihai, PR China. Strain CK1056T was found to grow at 15–37 °C (optimum, 30 °C), with 0.5–6.5 % (w/v) NaCl (optimum, 3.5 %) and displayed alkaliphilic growth within the pH range of pH 6.5–10.0 (optimum, pH 8.0). The major fatty acids identified were iso-C15 : 0 and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c). The main polar lipids consisted of aminophosphoglycolipid and phosphatidylethanolamine. The predominant respiratory quinone was MK-7. The G+C content of the genomic DNA was 54.0 mol%. The result of the 16S rRNA gene sequence analysis confirmed the affiliation of this micro-organism to the family Puniceicoccaceae , with Coraliomargarita akajimensis KCTC 12865T as its closest relative with only 88.0 % sequence similarity. From the taxonomic data obtained in this study, we propose that the new marine isolate be placed into a novel species within a novel genus in the family Puniceicoccaceae , phylum Verrucomicrobia , for which the name Oceanipulchritudo coccoides gen. nov., sp. nov. is proposed. The type strain is CK1056T (=KCTC 72798T=MCCC 1H00425T).

scholarly journals Frondicola australicus gen. nov., sp. nov., isolated from decaying leaf litter from a pine forest

2007 ◽  
Vol 57 (6) ◽  
pp. 1177-1182 ◽  
Author(s):  
Li Zhang ◽  
Zhihong Xu ◽  
Bharat K. C. Patel
Keyword(s):  
Cell Wall ◽  
Fatty Acid ◽  
Leaf Litter ◽  
Cellular Fatty Acid ◽  
Pine Forest ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Gene Sequence Analysis ◽  
The Family ◽  
A Cell

An aerobic bacterium, designated strain E1HC-02T, was isolated from the decaying leaf litter of a slash pine forest located in southeast Queensland, Australia. Cells of strain E1HC-02T were short irregular rods (0.5–1.0×0.2–0.4 μm) which stained Gram-positive and possessed a cell-wall ultrastructure which appeared to be made of protein subunits. The novel strain grew optimally in 1 % trypticase soy broth (TSB) at 25 °C and at a pH of 9.1. Strain E1HC-02T metabolized a range of carbohydrates, organic acids and amino acids. The G+C content of the DNA was 71±1 mol% as determined by the thermal denaturation method. 16S rRNA gene sequence analysis of strain E1HC-02T showed that it was a member of the family Microbacteriaceae, phylum Actinobacteria. The cell wall contained a type B2β peptidoglycan, the dominant cellular fatty acid was 18 : 1ω7c and the major hydroxy fatty acid was 2-OH 14 : 0. The major menaquinones were MK-8 (76 %) and MK-7 (24 %) and the glycolipids present were disphosphatidylglycerol, phosphatidylglycerol and three unidentified phospholipids. The chemotaxonomic properties of strain E1HC-02T were distinctly different to all of the 17 genera of the family Microbacteriaceae and hence strain E1HC-02T is designated as representing a novel species of a new genus, Frondicola australicus gen. nov., sp. nov. The type strain of the type species is E1HC-02T (=JCM 13598T=DSM 17894T).

Thermovum composti gen. nov., sp. nov., an alphaproteobacterium from compost

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2991-2996 ◽  
Author(s):  
Shuhei Yabe ◽  
Yoshifumi Aiba ◽  
Yasuteru Sakai ◽  
Masaru Hazaka ◽  
Akira Yokota
Keyword(s):  
New Genus ◽  
Sequence Similarity ◽  
Thermophilic Bacterium ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Ph Range

A Gram-stain-positive thermophilic bacterium, designated strain Nis3T, was isolated from compost. The strain grew at 23–57 °C (optimum, 50 °C); no growth was observed below 15 or above 60 °C. The pH range for growth was 5.9–8.8 (optimum, 7.0); no growth was observed below pH 5.4 or above pH 9.3. The DNA G+C content of strain Nis3T was 63.4 mol%. The dominant quinone type was ubiquinone Q-10. The major fatty acids were C18 : 1ω7c, C19 : 0ω8c cyclo and C18 : 0. The polar lipids comprised phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol, phosphatidylmonomethylethanolamine, an unknown glycolipid and a ninhydrin-positive phospholipid. 16S rRNA gene sequence analysis assigned this bacterium to the family Phyllobacteriaceae in the Alphaproteobacteria but it shared less than 95.2 % sequence similarity with other members of the family. The chemotaxonomic and phenotypic characteristics of strain Nis3T differed in some respects from those of members of the family Phyllobacteriaceae . Therefore, strain Nis3T is considered to represent a novel species of a new genus in the family Phyllobacteriaceae , for which the name Thermovum composti gen. nov., sp. nov. is proposed. The type strain is Nis3T ( = JCM 17863T = KCTC 23707T).

scholarly journals Pseudonocardia Pini Sp. Nov., An Endophytic Actinobacterium Isolated From Roots of the Pine Tree Callitris Preissii

2021 ◽  
Author(s):  
Onuma Kaewkla ◽  
Christopher Milton Mathew Franco
Keyword(s):  
Genome Mining ◽  
South Australia ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Pine Tree ◽  
Gene Sequence Analysis ◽  
Endophytic Actinobacterium ◽  
The Family ◽  
Genes Encoding ◽  
Diamino Acid

Abstract A Gram positive, aerobic, actinobacterial strain with rod-shaped spores, CAP47RT, which was isolated from the surface-sterilized root of a native pine tree (Callitris preissii), South Australia is described. The major cellular fatty acid of this strain was iso-H-C16:1 and major menaquinone was MK-8(H4). The diagnostic diamino acid in the cell-wall peptidoglycan was identified as meso-diaminopimelic acid. These chemotaxonomic data confirmed the affiliation of strain CAP47RT to the genus Pseudonocardia. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this strain in the familyPseudonocardiaceae, being most closely related to Pseudonocardia xishanensis JCM 17906T (98.8%), Pseudonocardia oroxyli DSM 44984T (98.7%),Pseudonocardia thailandensis CMU-NKS-70T (98.7%), and Pseudonocardia ailaonensis DSM 44979T (97.9%). The results of the polyphasic study which contain genome comparisons of ANIb, ANIm and digital DNA-DNA hybridization revealed the differentiation of strain CAP47RT from the closest species with validated names. This strain represents a novel species and the name proposed for this microorganism is Pseudonocardia pini sp. nov., indicating the source of actinobacteria from a pine tree. The type strain is CAP47RT (= DSM 108967T = NRRL B-65534T). Genome mining revealed that this strain contained a variety of genes encoding enzymes to degrade hazard chemicals.

scholarly journals Microbispora clausenae sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of a Thai medicinal plant, Clausena excavala Burm. f.

2020 ◽  
Vol 70 (12) ◽  
pp. 6213-6219
Author(s):  
Onuma Kaewkla ◽  
Wilaiwan Koomsiri ◽  
Arinthip Thamchaipenet ◽  
Christopher Milton Mathew Franco
Keyword(s):  
Medicinal Plant ◽  
Type Species ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Endophytic Actinobacterium ◽  
The Family

An endophytic actinobacterium, strain CLES2T, was discovered from the surface-sterilized stem of a Thai medicinal plant, Clausena excavala Burm. f., collected from the Phujong-Nayoa National Park, Ubon Ratchathani Province, Thailand. The results of a polyphasic taxonomic study identified this strain as a member of the genus Microbispora and a Gram-stain-positive, aerobic actinobacterium. It had well-developed substrate mycelia, which were non-motile and possessed paired spores. A phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this strain in the family Streptosporangiaceae , being most closely related to Microbispora bryophytorum NEAU-TX2-2T (99.4 %), Microbispora camponoti 2C-HV3T (99.2 %), Microbispora catharanthi CR1-09T (99.2 %) and Microbispora amethystogenes JCM 3021T and Microbispora fusca NEAU-HEGS1-5T (both at 99.1 %). The major cellular fatty acid of this strain was iso-C16 : 0 and major menaquinone was MK-9(H4). The polar lipid profile of strain CLES2T contained diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol and phosphatidylinositol dimannosides. These chemotaxonomic data confirmed the affiliation of strain CLES2T to the genus Microbispora . The DNA G+C content of this strain was 70 mol%. Digital DNA–DNA hybridization and average nucleotide identity blast values between strain CLES2T and M. catharanthi CR1-09T were 62.4 and 94.0 %, respectively. The results of the polyphasic study allowed the genotypic and phenotypic differentiation of strain CLES2T from its closest species with valid names. The name proposed for the new species is Microbispora clausenae sp. nov. The type strain is CLES2T (=DSM 101759T=NRRL B-65340T).

scholarly journals Halotalea alkalilenta gen. nov., sp. nov., a novel osmotolerant and alkalitolerant bacterium from alkaline olive mill wastes, and emended description of the family Halomonadaceae Franzmann et al. 1989, emend. Dobson and Franzmann 1996

2007 ◽  
Vol 57 (9) ◽  
pp. 1975-1983 ◽  
Author(s):  
Spyridon Ntougias ◽  
Georgios I. Zervakis ◽  
Constantinos Fasseas
Keyword(s):  
16S Rrna ◽  
Rrna Gene ◽  
The Novel ◽  
Two Phase ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Emended Description ◽  
Obligate Aerobe ◽  
Ph Range ◽  
Olive Mill

A novel Gram-negative, motile, nonsporulating, rod-shaped bacterium isolated from alkaline sludge-like wastes (‘alpeorujo’ or ‘alperujo’) of two-phase olive oil extraction is described. The strain, designated AW-7T, is an obligate aerobe that is halotolerant (tolerating up to 15 % w/v NaCl), sugar-tolerant (tolerating up to 45 % and 60 % w/v (+)-d-glucose and maltose respectively; these are the highest concentrations tolerated by any known members of the Bacteria domain) and alkalitolerant (growing at a broad pH range of 5–11). Strain AW-7T is chemo-organotrophic. Ubiquinone-9 was detected in the respiratory chain of strain AW-7T. The major fatty acids present are C18 : 1 ω7c, C16 : 0, C19 : 0 cyclo ω8c, C12 : 0 3-OH and C16 : 1 ω7c/iso-C15 : 0 2-OH. Based on 16S rRNA gene sequence analysis, strain AW-7T showed almost equal phylogenetic distances from Zymobacter palmae (95.6 % similarity) and Carnimonas nigrificans (95.4 % similarity). In addition, low DNA–DNA relatedness values were found for strain AW-7T against Carnimonas nigrificans CECT 4437T (22.5–25.4 %) and Z. palmae DSM 10491T (11.9–14.4 %). The DNA G+C content of strain AW-7T is 64.4 mol%. Physiological and chemotaxonomic data further confirmed the differentiation of strain AW-7T from the genera Zymobacter and Carnimonas. Thus, strain AW-7T represents a novel bacterial genus within the family Halomonadaceae, for which the name Halotalea gen. nov. is proposed. Halotalea alkalilenta sp. nov. (type strain AW-7T=DSM 17697T=CECT 7134T) is proposed as the type species of the genus Halotalea gen. nov. A reassignment of the descriptive 16S rRNA signature characteristics of the family Halomonadaceae permitted the placement of the novel genus Halotalea into the family; in contrast, the genus Halovibrio possessed only 12 out of the 18 signature characteristics proposed, and hence it was excluded from the family Halomonadaceae.

scholarly journals Mariniflexile gromovii gen. nov., sp. nov., a gliding bacterium isolated from the sea urchin Strongylocentrotus intermedius

2006 ◽  
Vol 56 (7) ◽  
pp. 1635-1638 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Seung Bum Kim ◽  
Jangryul Kwak ◽  
Valery V. Mikhailov ◽  
Kyung Sook Bae
Keyword(s):  
Phylogenetic Analyses ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Novel Genus And Species ◽  
Respective Type ◽  
Gliding Bacterium ◽  
Type Strains ◽  
Sequence Similarities

A marine bacterium, designated strain KMM 6038T, was subjected to taxonomic analysis via a polyphasic approach. Cells of the strain were heterotrophic, orange-pigmented, Gram-negative and motile by means of gliding. 16S rRNA gene sequence analysis indicated that strain KMM 6038T was closely related to the type species of the genera Algibacter and Yeosuana, members of the family Flavobacteriaceae, with sequence similarities of 93.8 and 93.6 % to the respective type strains. However, several chemotaxonomic and phenotypic characteristics, such as the cellular fatty acid profile (iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1, C15 : 0, C15 : 1 ω6c, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH) and the low G+C content of the DNA (35.7 mol%), indicated that the strain should be separated from these two genera. From the results of phenotypic, genotypic, chemotaxonomic and phylogenetic analyses, the bacterium should be classified as representing a novel genus and species, for which the name Mariniflexile gromovii gen. nov., sp. nov. is proposed. The type strain of Mariniflexile gromovii is KMM 6038T (=KCTC 12570T=LMG 22578T).

scholarly journals Winogradskyella thalassocola gen. nov., sp. nov., Winogradskyella epiphytica sp. nov. and Winogradskyella eximia sp. nov., marine bacteria of the family Flavobacteriaceae

2005 ◽  
Vol 55 (1) ◽  
pp. 49-55 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Seung Bum Kim ◽  
Suk Kyun Han ◽  
Cindy Snauwaert ◽  
Marc Vancanneyt ◽  
...  
Keyword(s):  
Type Strain ◽  
New Genus ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Peter The Great ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Major Respiratory Quinone

Three novel heterotrophic, Gram-negative, yellow-pigmented, aerobic, gliding, oxidase- and catalase-positive bacteria were isolated from algae collected in the Gulf of Peter the Great, Sea of Japan. 16S rRNA gene sequence analysis revealed that the strains studied represented members of the family Flavobacteriaceae and showed 93·5–93·8 % similarity with their closest relative, Psychroserpens burtonensis. The DNA G+C content of the strains was 34–37 mol%. The major respiratory quinone was MK-6. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1, iso-C16 : 0-3OH and iso-C17 : 0-3OH. On the basis of their phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the newly described bacteria have been assigned to the new genus Winogradskyella gen. nov., as Winogradskyella thalassocola sp. nov. (type strain, KMM 3907T=KCTC 12221T=LMG 22492T=DSM 15363T), Winogradskyella epiphytica sp. nov. (type strain, KMM 3906T=KCTC 12220T=LMG 22491T=CCUG 47091T) and Winogradskyella eximia sp. nov. (type strain, KMM 3944T (=KCTC 12219T=LMG 22474T).

scholarly journals Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces

2007 ◽  
Vol 57 (5) ◽  
pp. 941-946 ◽  
Author(s):  
Hidenori Hayashi ◽  
Kensaku Shibata ◽  
Mitsuo Sakamoto ◽  
Shinichi Tomita ◽  
Yoshimi Benno
Keyword(s):  
Fatty Acid ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Phenotypic Characteristics ◽  
Human Faeces ◽  
Gene Sequence Analysis ◽  
Type Strains ◽  
Fatty Acid Compositions

Six strains (CB7T, CB18, CB23, CB26, CB28 and CB35T) were isolated from human faeces. Based on phylogenetic analysis, phenotypic characteristics, cellular fatty acid profiles and menaquinone profiles, these strains could be included within the genus Prevotella and made up two clusters. 16S rRNA gene sequence analysis indicated that five strains were most closely related to Prevotella veroralis, sharing about 92 % sequence similarity; the remaining strain was most closely related to Prevotella shahii, sharing about 90 % sequence similarity. All six strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. The cellular fatty acid compositions of the six strains differed significantly from those of other Prevotella species. Five strains (CB7T, CB18, CB23, CB26 and CB28) contained dimethyl acetals and the major menaquinones of these strains were MK-11, MK-12 and MK-13. The major menaquinones of CB35T were MK-12 and MK-13. Based on phenotypic and phylogenetic findings, two novel species, Prevotella copri sp. nov. and Prevotella stercorea sp. nov., are proposed, representing the two different strain clusters. The DNA G+C contents of strains CB7T and CB35T were 45.3 and 48.2 mol%, respectively. The type strains of P. copri and P. stercorea are CB7T (=JCM 13464T=DSM 18205T) and CB35T (=JCM 13469T=DSM 18206T), respectively.

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