scholarly journals Methylohalomonas lacus gen. nov., sp. nov. and Methylonatrum kenyense gen. nov., sp. nov., methylotrophic gammaproteobacteria from hypersaline lakes

2007 ◽  
Vol 57 (12) ◽  
pp. 2762-2769 ◽  
Author(s):  
Dimitry Yu. Sorokin ◽  
Yuri A. Trotsenko ◽  
Nina V. Doronina ◽  
Tatjana P. Tourova ◽  
Erwin A. Galinski ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Type Strain ◽  
Gene Sequence ◽  
Soda Lake ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The Family ◽  
Novel Genus And Species ◽  
Kulunda Steppe ◽  
Ph Range

Aerobic enrichment at 4 M NaCl, pH 7.5, with methanol as carbon and energy source from sediments of hypersaline chloride–sulfate lakes in Kulunda Steppe (Altai, Russia) resulted in the isolation of a moderately halophilic and obligately methylotrophic bacterium, strain HMT 1T. The bacterium grew with methanol and methylamine within a pH range of 6.8–8.2 with an optimum at pH 7.5 and at NaCl concentrations of 0.5–4 M with an optimum at 2 M. In addition to methanol and methylamine, it can oxidize ethanol, formate, formaldehyde and dimethylamine. Carbon is assimilated via the serine pathway. The main compatible solute is glycine betaine. 16S rRNA gene sequence analysis placed the isolate as a new lineage in the family Ectothiorhodospiraceae (Gammaproteobacteria). It is proposed, therefore, to accommodate this bacterium within a novel genus and species, Methylohalomonas lacus gen. nov., sp. nov., with HMT 1T (=DSM 15733T =NCCB 100208T =UNIQEM U237T) as the type strain. Two strains were obtained in pure culture from sediments of soda lake Magadi in Kenya and the Kulunda Steppe (Russia) on a mineral medium at pH 10 containing 0.6 M total Na+ using methanol as a substrate. Strain AMT 1T was enriched with methanol, while strain AMT 3 originated from an enrichment culture with CO. The isolates are restricted facultative methylotrophs, capable of growth with methanol, formate and acetate as carbon and energy sources. With methanol, the strains grew within a broad salinity range from 0.3 to 3.5–4 M total Na+, with an optimum at 0.5–1 M. The pH range for growth was between 8.3 and 10.5, with an optimum at pH 9.5, which characterized the soda lake isolates as obligate haloalkaliphiles. Carbon is assimilated autotrophically via the Calvin–Benson cycle. Sequence analysis of the gene coding for the key enzyme RuBisCO demonstrated that strain AMT 1T possessed a single cbbL gene of the ‘green’ form I, clustering with members of the family Ectothiorhodospiraceae. Analysis of the 16S rRNA gene sequence showed that strains AMT 1T and AMT 3 belong to a single species that forms a separate lineage within the family Ectothiorhodospiraceae. On the basis of phenotypic and genetic data, the novel haloalkaliphilic methylotrophs are described as representing a novel genus and species, Methylonatrum kenyense gen. nov., sp. nov. (type strain AMT 1T =DSM 15732T =NCCB 100209T =UNIQEM U238T).

scholarly journals Description of Ruminococcus catenae SW178 sp. nov., a new anaerobic species isolated from feral chicken

2019 ◽  
Author(s):  
Supapit Wongkuna ◽  
Sudeep Ghimire ◽  
Surang Chankhamhaengdecha ◽  
Tavan Janvilisri ◽  
Joy Scaria
Keyword(s):  
Sequence Analysis ◽  
South Dakota ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family ◽  
The 16S Rrna Gene

AbstractA Gram-positive, obligately anaerobic coccobacillus, with the white raised circular colony was isolated from the cecum of feral chickens in Brookings, South Dakota, USA. The 16S rRNA gene sequence analysis suggested that the closest species to strain SW178 was Ruminococcus torques ATCC 27756T (96.94% similarity) that belongs to the family Lachnospiraceae. The genome of strain SW178 is 3.18 Mbp with G+C content of 46.9 mol%. Based on the phylogenetic and phenotypic comparison, we propose that strain SW178 be assigned to the genus Ruminococcus as a novel species, for which the name Ruminococcus catenae is proposed. The type strain is SW178 (= CCOS 1886 T, =DSM 109242T).

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 Phaeobacterium nitratireducens gen. nov., sp. nov., a phototrophic gammaproteobacterium isolated from a mangrove forest sediment sample

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2357-2364 ◽  
Author(s):  
Nupur ◽  
Naga Radha Srinivas Tanuku ◽  
Takaichi Shinichi ◽  
Anil Kumar Pinnaka
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sediment Sample ◽  
Type Strain ◽  
Mangrove Forest ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The Family

A novel brown-coloured, Gram-negative-staining, rod-shaped, motile, phototrophic, purple sulfur bacterium, designated strain AK40T, was isolated in pure culture from a sediment sample collected from Coringa mangrove forest, India. Strain AK40T contained bacteriochlorophyll a and carotenoids of the rhodopin series as major photosynthetic pigments. Strain AK40T was able to grow photoheterotrophically and could utilize a number of organic substrates. It was unable to grow photoautotrophically and did not utilize sulfide or thiosulfate as electron donors. Thiamine and riboflavin were required for growth. The dominant fatty acids were C12 : 0, C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The polar lipid profile of strain AK40T was found to contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and eight unidentified lipids. Q-10 was the predominant respiratory quinone. The DNA G+C content of strain AK40T was 65.5 mol%. 16S rRNA gene sequence comparisons indicated that the isolate represented a member of the family Chromatiaceae within the class Gammaproteobacteria. 16S rRNA gene sequence analysis indicated that strain AK40T was closely related to Phaeochromatium fluminis, with 95.2 % pairwise sequence similarity to the type strain; sequence similarity to strains of other species of the family was 90.8–94.8 %. Based on the sequence comparison data, strain AK40T was positioned distinctly outside the group formed by the genera Phaeochromatium, Marichromatium, Halochromatium, Thiohalocapsa, Rhabdochromatium and Thiorhodovibrio. Distinct morphological, physiological and genotypic differences from previously described taxa supported the classification of this isolate as a representative of a novel species in a new genus, for which the name Phaeobacterium nitratireducens gen. nov., sp. nov. is proposed. The type strain of Phaeobacterium nitratireducens is AK40T ( = JCM 19219T = MTCC 11824T).

scholarly journals Candidimonas nitroreducens gen. nov., sp. nov. and Candidimonas humi sp. nov., isolated from sewage sludge compost

2011 ◽  
Vol 61 (9) ◽  
pp. 2238-2246 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
Vânia Figueira ◽  
Ana R. Lopes ◽  
Evie De Brandt ◽  
Peter Vandamme ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sludge Compost ◽  
The Family

Two bacterial strains (SC-089T and SC-092T) isolated from sewage sludge compost were characterized by using a polyphasic approach. The isolates were Gram-negative short rods, catalase- and oxidase-positive, and showed good growth at 30 °C, at pH 7 and with 1 % (w/v) NaCl. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, the strains were observed to be members of the family Alcaligenaceae, but could not be identified as members of any validly described genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa, together with comparative analysis of phenotypic traits and chemotaxonomic markers, supported the proposal of a new genus within the family Alcaligenaceae, for which the name Candidimonas gen. nov. is proposed. Strains SC-089T and SC-092T, which shared 99.1 % 16S rRNA gene sequence similarity, could be differentiated at the phenotypic level, and DNA–DNA hybridization results supported their identification as representing distinct species. The names proposed for these novel species are Candidimonas nitroreducens sp. nov. (type strain, SC-089T = LMG 24812T = CCUG 55806T) and Candidimonas humi sp. nov. (type strain, SC-092T = LMG 24813T = CCUG 55807T).

scholarly journals Pseudosphingobacterium domesticum gen. nov., sp. nov., isolated from home-made compost

2007 ◽  
Vol 57 (7) ◽  
pp. 1535-1538 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
M. Fernanda Nobre ◽  
Olga C. Nunes ◽  
Célia M. Manaia
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family

A bacterial strain, DC-186T, isolated from home-made compost, was characterized for its phenotypic and phylogenetic properties. The isolate was a Gram-negative rod that was able to grow at 15–36 °C and pH 5.5–8.0. Strain DC-186T was positive in tests for catalase, oxidase and β-galactosidase activities and aesculin hydrolysis. The predominant fatty acids were the summed feature C16 : 1/iso-C15 : 0 2-OH (42 %) and iso-C15 : 0 (26 %), the major respiratory quinone was menaquinone-7 and the genomic DNA G+C content was 42 mol%. 16S rRNA gene sequence analysis and phenetic characterization indicated that this organism belongs to the phylum Bacteroidetes and revealed its affiliation to the family Sphingobacteriaceae. Of recognized taxa, strain DC-186T was most closely related to Sphingobacterium daejeonense (90 % sequence similarity) based on 16S rRNA gene sequence analysis. The low 16S rRNA gene sequence similarity with other recognized taxa and the identification of distinctive phenetic features for this isolate support the definition of a new genus within the family Sphingobacteriaceae. The name Pseudosphingobacterium domesticum gen. nov., sp. nov. is proposed, with strain DC-186T (=CCUG 54353T=LMG 23837T) as the type strain.

Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil

2010 ◽  
Vol 60 (11) ◽  
pp. 2577-2582 ◽  
Author(s):  
Myungjin Lee ◽  
Sung-Geun Woo ◽  
Joonhong Park ◽  
Soon-Ae Yoo
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels

A Gram-negative, non-motile, aerobic bacterial strain, designated MJ20T, was isolated from farm soil near Daejeon (South Korea) and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ20T belongs to the family Cytophagaceae, class Sphingobacteria, and was related most closely to Dyadobacter fermentans DSM 18053T (98.9 % sequence similarity), Dyadobacter beijingensis JCM 14200T (98.0 %) and Dyadobacter ginsengisoli KCTC 12589T (96.4 %). The G+C content of the genomic DNA of strain MJ20T was 48.5 mol%. The detection of MK-7 as the predominant menaquinone and a fatty acid profile with summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 0 and C16 : 1 ω5c as major components supported the affiliation of strain MJ20T to the genus Dyadobacter. The new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to D. fermentans DSM 18053T (mean±sd of three determinations, 47±7 %) and D. beijingensis JCM 14200T (38±8 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain MJ20T (=KCTC 22481T =JCM 16232T) should be classified in the genus Dyadobacter as the type strain of a novel species, for which the name Dyadobacter soli sp. nov. is proposed.

scholarly journals Proposal of Giesbergeria voronezhensis gen. nov., sp. nov. and G. kuznetsovii sp. nov. and reclassification of [Aquaspirillum] anulus, [A.] sinuosum and [A.] giesbergeri as Giesbergeria anulus comb. nov., G. sinuosa comb. nov. and G. giesbergeri comb. nov., and [Aquaspirillum] metamorphum and [A.] psychrophilum as Simplicispira metamorpha gen. nov., comb. nov. and S. psychrophila comb. nov.

2006 ◽  
Vol 56 (3) ◽  
pp. 569-576 ◽  
Author(s):  
Margarita Grabovich ◽  
Ekaterina Gavrish ◽  
Jan Kuever ◽  
Anatoly M. Lysenko ◽  
Daria Podkopaeva ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
New Genus ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Distinct Cluster ◽  
The Family

Five Gram-negative, motile, spiral-shaped strains were isolated from a sulfide spring (D-412T), active sludge of wastewater (D-419T, D-420, D-424) and industrial wastewater (D-416). Comparative 16S rRNA gene sequence analysis showed that the isolates belong to the family Comamonadaceae, within the class Betaproteobacteria, but fall into a distinct cluster. On the basis of phenotypic, chemotaxonomic and phylogenetic data, a new genus, Giesbergeria gen. nov., is proposed, including five species. The type species of the genus is Giesbergeria voronezhensis sp. nov. (type strain D-419T=DSM 12825T=CIP 107340T=VKM B-2350T) and other novel members of the genus are Giesbergeria kuznetsovii sp. nov. (type strain D-412T=DSM 12827T=VKM B-2352T), Giesbergeria giesbergeri comb. nov. (basonym Aquaspirillum giesbergeri), Giesbergeria sinuosa comb. nov. (basonym Aquaspirillum sinuosum) and Giesbergeria anulus comb. nov. (basonym Aquaspirillum anulus). Using the same criteria, isolate D-416 (=DSM 12826) was identified as a strain of [Aquaspirillum] metamorphum. Strain D-416, the type strain of [A.] metamorphum and the type strain of [Aquaspirillum] psychrophilum form a distinct cluster within the family Comamonadaceae (97–97·2 % 16S rRNA gene sequence similarity) and share phenotypic and chemotaxonomic properties. Therefore, it is proposed that these strains are reclassified as members of a new genus, Simplicispira gen. nov., as Simplicispira metamorpha comb. nov. (the type species) and Simplicispira psychrophila comb. nov., respectively.

scholarly journals Reclassification of Nonomuraea flexuosa (Meyer 1989) Zhang et al. 1998 as Thermopolyspora flexuosa gen. nov., comb. nov., nom. rev.

2005 ◽  
Vol 55 (5) ◽  
pp. 1979-1983 ◽  
Author(s):  
Michael Goodfellow ◽  
Luis A. Maldonado ◽  
Erika T. Quintana
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Data ◽  
Physiological Properties ◽  
Pcr Product ◽  
The Family

A polyphasic study was undertaken to clarify the taxonomic position of Nonomuraea flexuosa DSM 41386T. The distinct 16S rRNA gene sequence phyletic branch formed by this strain was equated with nine related monophyletic clades composed of representatives of the genera classified in the family Streptosporangiaceae. The organism produced a PCR product characteristic of this taxon when examined using a set of oligonucleotide primers specific for members of the family Streptosporangiaceae. Strain DSM 41386T could also be distinguished from representatives of the nine genera assigned to this family using a combination of chemotaxonomic, morphological and physiological properties. It is evident from the genotypic and phenotypic data that strain DSM 41386T is misclassified in the genus Nonomuraea and merits recognition as a monospecific genus within the family Streptosporangiaceae. It is proposed that the name Thermopolyspora flexuosa gen. nov., comb. nov., nom. rev. be used for this purpose, with the type strain DSM 41386T (=NRRL B-24348T).

Lysinimonas soli gen. nov., sp. nov., isolated from soil, and reclassification of Leifsonia kribbensis Dastager et al. 2009 as Lysinimonas kribbensis sp. nov., comb. nov.

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1403-1410 ◽  
Author(s):  
Yun-Hee Jang ◽  
Soo-Jin Kim ◽  
Tomohiko Tamura ◽  
Moriyuki Hamada ◽  
Hang-Yeon Weon ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The Family

A Gram-stain-positive, non-motile rod, designated strain SGM3-12T, was isolated from paddy soil in Suwon, Republic of Korea. 16S rRNA gene sequence analysis revealed that the strain represented a novel member of the family Microbacteriaceae . The nearest phylogenetic neighbour was Leifsonia kribbensis MSL-13T (97.4 % 16S rRNA gene sequence similarity). Strain SGM3-12T and Leifsonia kribbensis MSL-13T formed a distinct cluster within the family Microbacteriaceae . Strain SGM3-12T contained MK-12(H2) and MK-11(H2) as the predominant menaquinones with moderate amounts of MK-12 and MK-11; anteiso-C15 : 0 and iso-C16 : 0 as the major cellular fatty acids (>10 % of total); and diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipids as the polar lipids. The peptidoglycan type of the isolate was B1δ with l-Lys as the diagnostic cell-wall diamino acid. On the basis of these results, strain SGM3-12T represents a novel species within a new genus, for which the name Lysinimonas soli gen. nov., sp. nov. is proposed (the type strain of the type species is SGM3-12T = KACC 13362T = NBRC 107106T). It is also proposed that Leifsonia kribbensis be transferred to this genus as Lysinimonas kribbensis comb. nov. (the type strain is MSL-13T = DSM 19272T = JCM 16015T = KACC 21108T = KCTC 19267T).

scholarly journals Parapedobacter koreensis gen. nov., sp. nov.

2007 ◽  
Vol 57 (6) ◽  
pp. 1336-1341 ◽  
Author(s):  
Myung Kyum Kim ◽  
Ju-Ryun Na ◽  
Dong Ha Cho ◽  
Nak-Kyun Soung ◽  
Deok-Chun Yang
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Distinct Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Novel Genus And Species ◽  
Physiological And Biochemical

Strain Jip14T, a Gram-negative, non-spore-forming, rod-shaped, non-motile bacterium, was isolated from dried rice straw and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Jip14T belongs to the family Sphingobacteriaceae, and the highest degree of sequence similarity was determined to be to Pedobacter saltans DSM 12145T (88.5 %), Pedobacter africanus DSM 12126T (87.6 %), Pedobacter heparinus DSM 2366T (87.1 %) and Pedobacter caeni LMG 22862T (86.9 %). Chemotaxonomic data revealed that strain Jip14T possesses menaquinone MK-7 and the predominant fatty acids C15 : 0 iso, C16 : 0, C16 : 0 10-methyl, C17 : 0 iso 3-OH and summed feature 3 (C15 : 0 iso 2-OH/C16 : 1 ω7c). The results of physiological and biochemical tests clearly demonstrated that strain Jip14T represents a distinct species. Based on these data, Jip14T should be classified within a novel genus and species, for which the name Parapedobacter koreensis gen. nov., sp. nov. is proposed. The type strain of Parapedobacter koreensis is Jip14T (=KCTC 12643T=LMG 23493T).

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