scholarly journals Salinicoccus luteus sp. nov., isolated from a desert soil

2007 ◽  
Vol 57 (8) ◽  
pp. 1901-1905 ◽  
Author(s):  
Yu-Qin Zhang ◽  
Li-Yan Yu ◽  
Hong-Yu Liu ◽  
Yue-Qin Zhang ◽  
Li-Hua Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Desert Soil ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Moderately Halophilic Bacterium

A moderately halophilic bacterium, strain YIM 70202T, was isolated from a desert soil sample collected from Egypt and was subjected to a taxonomic investigation. In a phylogenetic dendrogram based on 16S rRNA gene sequence analysis, strain YIM 70202T was affiliated to the Salinicoccus clade, showing 94.5–96.8 % 16S rRNA gene sequence similarity to the recognized species of the genus Salinicoccus, in which Salinicoccus roseus CCM 3516T was the nearest neighbour. The DNA–DNA relatedness value of the novel isolate with S. roseus CCM 3516T was 12.7 %. The novel isolate grew at temperatures between 4 and 45 °C and at pH values ranging from 7.0 to 11.0, with an optimum of 30 °C and pH 8.0–9.0, respectively. Strain YIM 70202T grew optimally in the presence of 10 % NaCl (w/v) and growth was observed at NaCl concentrations in the range 1–25 % (w/v). Chemotaxonomic data revealed that strain YIM 70202T contained MK-6 as the predominant respiratory quinone, possessed l-Lys–Gly5 as the cell-wall peptidoglycan, had phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid as the polar lipids and contained i-C15 : 0 and ai-C15 : 0 as the predominant fatty acids. The DNA G+C content was 49.7 mol%. The biochemical and chemotaxonomic properties demonstrate that strain YIM 70202T represents a novel species of the genus Salinicoccus. The name Salinicoccus luteus sp. nov. is proposed with strain YIM 70202T (=CGMCC 1.6511T=KCTC 3941T) as the type strain.

scholarly journals Aggregicoccus edonensis gen. nov., sp. nov., an unusually aggregating myxobacterium isolated from a soil sample

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 745-753 ◽  
Author(s):  
Sakshi Sood ◽  
Ram Prasad Awal ◽  
Joachim Wink ◽  
Kathrin I. Mohr ◽  
Manfred Rohde ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Soil Sample ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Content Type

A novel myxobacterium, MCy1366T (Ar1733), was isolated in 1981 from a soil sample collected from a region near Tokyo, Japan. It displayed general myxobacterial features like Gram-negative-staining, rod-shaped vegetative cells, gliding on solid surfaces, microbial lytic activity, fruiting-body-like aggregates and myxospore-like structures. The strain was mesophilic, aerobic and showed a chemoheterotrophic mode of nutrition. It was resistant to many antibiotics such as cephalosporin C, kanamycin, gentamicin, hygromycin B, polymyxin and bacitracin, and the key fatty acids of whole cell hydrolysates were iso-C15 : 0, iso-C17 : 0 and iso-C17 : 0 2-OH. The genomic DNA G+C content of the novel strain was 65.6 mol%. The 16S rRNA gene sequence showed highest similarity (97.60 %) to ‘Stigmatella koreensis’ strain KYC-1019 (GenBank accession no. EF112185). Phylogenetic analysis based on 16S rRNA gene sequences and MALDI-TOF MS data revealed a novel branch in the family Myxococcaceae . DNA–DNA hybridization showed only 28 % relatedness between the novel strain and the closest recognized species, Corallococcus exiguus DSM 14696T (97 % 16S rRNA gene sequence similarity). A recent isolate from a soil sample collected in Switzerland, MCy10622, displayed 99.9 % 16S rRNA gene sequence similarity with strain MCy1366T and showed almost the same characteristics. Since some morphological features like fruiting-body-like aggregates were barely reproducible in the type strain, the newly isolated strain, MCy10622, was also intensively studied. On the basis of a comprehensive taxonomic study, we propose a novel genus and species, Aggregicoccus edonensis gen. nov., sp. nov., for strains MCy1366T and MCy10622. The type strain of the type species is MCy1366T ( = DSM 27872T = NCCB 100468T).

scholarly journals Limibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium in the family Rhodospirillaceae isolated from reclaimed land

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3155-3161 ◽  
Author(s):  
Jong-Hwa Kim ◽  
Maytiya Konkit ◽  
Jung-Hoon Yoon ◽  
Wonyong Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Reclaimed Land ◽  
Moderately Halophilic Bacterium ◽  
The Family

A Gram-stain-negative, aerobic, non-motile, non-spore-forming and short rod-shaped bacterial strain, designated CAU 1121T, was isolated from reclaimed land in the Republic of Korea and its taxonomic position was investigated using a polyphasic approach. The bacterium grew optimally at 37 °C, at pH 6.5 and in the presence of 2 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity, the novel isolate belonged to the family Rhodospirillaceae within the class Alphaproteobacteria and formed an independent lineage within the evolutionary radiation encompassed by the phylum Proteobacteria. Strain CAU 1121T exhibited very low levels of 16S rRNA gene sequence similarity with its phylogenetic neighbours Pelagibius litoralis (similarity, 92.5 %), Fodinicurvata fenggangensis (similarity, 91.4 %), Fodinicurvata sediminis (similarity, 90.7 %) and Tistlia consotensis (similarity, 91.0 %). Strain CAU 1121T contained ubiquinone-10 as the only respiratory quinone and C18 : 1ω7c as the major cellular fatty acid. The DNA G+C content of the strain was 65 mol%. On the basis of phylogenetic inference, and physiological and chemotaxonomic data, it is proposed that strain CAU 1121T represents a novel genus and novel species in the family Rhodospirillaceae, for which the name Limibacillus halophilus gen. nov., sp. nov. is suggested. The type strain is CAU 1121T ( = KCTC 42420T = CECT 8803T = NBRC 110928T).

scholarly journals Terriglobus albidus sp. nov., a member of the family Acidobacteriaceae isolated from Namibian semiarid savannah soil

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3297-3304 ◽  
Author(s):  
Javier Pascual ◽  
Pia K. Wüst ◽  
Alicia Geppert ◽  
Bärbel U. Foesel ◽  
Katharina J. Huber ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Bacterium Strain ◽  
Higher Temperature

A novel aerobic, chemo-organoheterotrophic bacterium, strain Ac_26_B10T, was isolated from a semiarid savannah soil collected in northern Namibia (Mashare, Kavango region). Based on analysis of its nearly full-length 16S rRNA gene sequence, the isolate belongs to the genus Terriglobus (family Acidobacteriaceae, order Acidobacteriales, class Acidobacteria) and shares 98.3 and 96.9 % 16S rRNA gene sequence similarity with its closest relatives, Terriglobus tenax DRP 35T and T. aquaticus O3SUJ4T. Cells were Gram-negative, coccoid to rod-shaped, non-motile and divided by binary fission. Strain Ac_26_B10T showed weak catalase activity and, in contrast to the other described species of the genus Terriglobus, was oxidase-positive. Compared with the already established species of the genus Terriglobus, the novel strain used a larger range of sugars and sugar alcohols for growth, lacked α-mannosidase activity and exhibited a higher temperature optimum of growth. DNA–DNA hybridization studies with its closest phylogenetic relative, T. tenax DSM 28898T, confirmed that strain Ac_26_B10T represents a distinct genomospecies. Its most abundant fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. Dominant polar lipids were phosphatidylethanolamine and diphosphatidylglycerol. The predominant menaquinone was MK-8; minor amounts of MK-7 and MK-8(H2) were also recorded. The G+C content of the genomic DNA was 58.5 mol%. On the basis of our polyphasic analysis, Ac_26_B10T represents a novel species of the genus Terriglobus, for which the name Terriglobus albidus sp. nov. is proposed. The type strain is Ac_26_B10T ( = DSM 26559T = LMG 27984T).

scholarly journals Dyadobacter ginsengisoli sp. nov., isolated from soil of a ginseng field

2006 ◽  
Vol 56 (8) ◽  
pp. 1939-1944 ◽  
Author(s):  
Qing-Mei Liu ◽  
Wan-Taek Im ◽  
Myungjin Lee ◽  
Deok-Chun Yang ◽  
Sung-Taik Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
The Family

A Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterium, strain Gsoil 043T, was isolated from soil from a ginseng field in Pocheon province, South Korea. The novel isolate was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 043T was shown to belong to the family ‘Flexibacteraceae’ and was related to Dyadobacter fermentans (96.7 %), Dyadobacter crusticola (96.3 %) and Dyadobacter hamtensis (95.8 %). The 16S rRNA gene sequence similarity of the novel strain to other recognized species within the family ‘Flexibacteraceae’ was less than 87.0 %. The G+C content of genomic DNA was 48 mol%. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, C16 : 1 ω7c, iso-C15 : 0 and C16 : 0) supported the affiliation of strain Gsoil 043T to the genus Dyadobacter. The results of physiological and biochemical tests enabled strain Gsoil 043T to be differentiated genotypically and phenotypically from the three Dyadobacter species with validly published names. The novel isolate therefore represents a novel species for which the name Dyadobacter ginsengisoli sp. nov. is proposed, with the type strain Gsoil 043T (=KCTC 12589T=LMG 23409T).

scholarly journals Halomonas kribbensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea

2007 ◽  
Vol 57 (10) ◽  
pp. 2194-2198 ◽  
Author(s):  
Che Ok Jeon ◽  
Jee-Min Lim ◽  
Jung Ro Lee ◽  
Gye Suk Lee ◽  
Dong-Jin Park ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Rrna Gene Sequence ◽  
Moderately Halophilic ◽  
Moderately Halophilic Bacterium

A moderately halophilic, Gram-negative bacterium, designated strain BH843T, was isolated from a solar saltern in Korea and subjected to a taxonomic analysis. Strain BH843T grew at salinities of 1–14 % (w/v) NaCl and at temperatures of 10–40 °C. The cells were motile cocci or short rods with single flagella and contained C16 : 0, C19 : 0 cyclo ω8c and C17 : 0 cyclo as the major fatty acids. The G+C content of the genomic DNA was 66 mol% and the predominant ubiquinone was Q-9. Comparative 16S rRNA gene sequence analyses showed that strain BH843T formed a distinct phyletic line within the genus Halomonas, and the levels of 16S rRNA gene sequence similarity with respect to recognized Halomonas species were below 95.1 %. The levels of DNA–DNA relatedness between strain BH843T and the type strains of phylogenetically closely related Halomonas species were below 25 %. On the basis of phenotypic, chemotaxonomic and molecular data, strain BH843T represents a novel species within the genus Halomonas, for which the name Halomonas kribbensis is proposed. The type strain is BH843T (=KCTC 12584T=DSM 17892T).

scholarly journals Shimia sagamensis sp. nov., a marine bacterium isolated from cold-seep sediment

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2786-2790 ◽  
Author(s):  
Yuichi Nogi ◽  
Kozue Mori ◽  
Hiromi Uchida ◽  
Yuji Hatada
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Cold Seep ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence

A novel marine bacterial strain designated JAMH 011T was isolated from the cold-seep sediment in Sagami Bay, Japan. Cells were Gram-stain-negative, rod-shaped, non-spore-forming, aerobic chemo-organotrophs and motile by means of a single polar flagellum. Growth occurred at temperatures below 31 °C, with the optimum at 25 °C. The major respiratory quinone was Q-10. The predominant fatty acid was C18 : 1ω7c. On the basis of 16S rRNA gene sequence analysis, the isolated strain was closely affiliated with members of the genus Shimia in the class Alphaproteobacteria, and the 16S rRNA gene sequence similarity of the novel isolate with the type strain of the closest related species, Shimia haliotis WM35T, was 98.1  %. The DNA G+C content of the novel strain was 57.3 mol%. The hybridization values for DNA–DNA relatedness between strain JAMH 011T and reference strains belonging to the genus Shimia were less than 9.4 ± 0.7  %. Based on differences in taxonomic characteristics, the isolated strain represents a novel species of the genus Shimia, for which the name Shimia sagamensis sp. nov. is proposed. The type strain is JAMH 011T ( = JCM 30583T = DSM 29734T)

scholarly journals Vibrio casei sp. nov., isolated from the surfaces of two French red smear soft cheeses

2010 ◽  
Vol 60 (8) ◽  
pp. 1745-1749 ◽  
Author(s):  
Anne Bleicher ◽  
Klaus Neuhaus ◽  
Siegfried Scherer
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Separate Species

Three Gram-negative, rod-shaped, catalase- and oxidase-positive, facultatively anaerobic and motile bacteria, strains WS 4538, WS 4539T and WS 4540, were isolated from the surfaces of two fully ripened French red smear soft cheeses. Based on 16S rRNA gene sequence similarity, all three strains were shown to belong to the genus Vibrio. They are most closely related to Vibrio rumoiensis S-1T (96.3 % similarity) and Vibrio litoralis MANO22DT (95.9 %). DNA–DNA hybridization confirmed that all three isolates belong to the same species and clearly separated strain WS 4539T from V. rumoiensis DSM 19141T (38–42 % relatedness) and V. litoralis DSM 17657T (28–37 %). In contrast to their nearest relatives, the strains exhibited β-galactosidase and aesculin hydrolase activities. A 14 bp insertion in the 16S rRNA gene sequence forms an elongated structure at helix 10 in the rRNA molecule and provides a tool for PCR-based identification of the novel species. Partial sequences of the housekeeping genes atpA, recA, rpoA and pyrH supported the conclusion that the three isolates constitute a separate species within the genus Vibrio. The name Vibrio casei sp. nov. is proposed for the novel taxon. Strain WS 4539T (=DSM 22364T =LMG 25240T; DNA G+C content 41.8 mol%) is the type strain and WS 4540 (=DSM 22378 =LMG 25241) is a reference strain.

scholarly journals Marinobacter oulmenensis sp. nov., a moderately halophilic bacterium isolated from brine of a salt concentrator

2011 ◽  
Vol 61 (9) ◽  
pp. 2210-2214 ◽  
Author(s):  
Karima Kharroub ◽  
Margarita Aguilera ◽  
María Luján Jiménez-Pranteda ◽  
Ana González-Paredes ◽  
Alberto Ramos-Cormenzana ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Halophilic Bacterium ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Moderately Halophilic ◽  
Moderately Halophilic Bacterium

A Gram-negative, aerobic, moderately halophilic bacterium, designated Set74T, was isolated from brine of a salt concentrator at Ain Oulmene, Algeria. The strain grew optimally at 37–40 °C, at pH 6.5–7.0 and with 5–7.5 % (w/v) NaCl and used various organic compounds as sole carbon, nitrogen and energy sources. Ubiquinone 9 (Q-9) was the major lipoquinone. The main cellular fatty acids were C16 : 0, C18 : 1ω9c, summed feature 7 (ECL 18.846; C19 : 0 cyclo ω10c and/or C19 : 1ω6c), C12 : 0 3-OH, C16 : 1ω9c, C18 : 0 and C12 : 0. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was 57.4 mol%. The 16S rRNA gene sequence analysis indicated that strain Set74T was a member of the genus Marinobacter. The closest relatives of strain Set74T were Marinobacter santoriniensis NKSG1T (97.5 % 16S rRNA gene sequence similarity) and Marinobacter koreensis DD-M3T (97.4 %). DNA–DNA relatedness between strain Set74T and M. santoriniensis DSM 21262T and M. koreensis DSM 17924T was 45 and 37 %, respectively. On the basis of the phenotypic, chemotaxonomic and phylogenetic features, a novel species, Marinobacter oulmenensis sp. nov., is proposed. The type strain is Set74T ( = CECT 7499T  = DSM 22359T).

scholarly journals Paenibacillus zanthoxyli sp. nov., a novel nitrogen-fixing species isolated from the rhizosphere of Zanthoxylum simulans

2007 ◽  
Vol 57 (4) ◽  
pp. 873-877 ◽  
Author(s):  
Yuchao Ma ◽  
Jian Zhang ◽  
Sanfeng Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences

Five endospore-forming, nitrogen-fixing strains were isolated from rhizosphere soils of Zanthoxylum simulans planted in Beijing, China. Phylogenetic analysis based on full-length 16S rRNA gene sequences revealed that the five strains formed a distinct cluster within the genus Paenibacillus. High levels of 16S rRNA gene sequence similarity were found between these novel strains and Paenibacillus azotofixans ATCC 35681T (97.8–98.5 % similarity) and Paenibacillus stellifer DSM 14472T (95.4–96.3 %). Levels of 16S rRNA gene sequence similarity between the novel isolates and other species of the genus Paenibacillus were less than 95.0 %. Levels of 16S rRNA gene sequence similarity among the isolates were more than 98.0 %. DNA–DNA relatedness between the five novel isolates and P. azotofixans ATCC 35681T was 45.50–47.45 % and relatedness among the five novel strains was 95.8–99.6 %. A significant feature of the novel strains that differentiated them from P. azotofixans and other Paenibacillus species was that none of the novel strains could produce acid or gas from the following various carbohydrates: glucose, sucrose, lactose, fructose, glycerol, xylose, maltose, d-sorbitol, sodium succinate, sodium citrate, glycine or l-aspartate. Anteiso-branched C15 : 0 was the major fatty acid component (36.59 %) of novel strain JH29T. On the basis of phenotypic properties, 16S rRNA gene sequences, DNA G+C content, DNA–DNA hybridization, chemotaxonomic properties and the nifH gene sequence, the five novel strains form a very homogeneous group which is different from other related species within the genus Paenibacillus. Therefore, the five novel strains are considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus zanthoxyli sp. nov. is proposed. The type strain is JH29T (=CCBAU 10243T=DSM 18202T).

scholarly journals Koreibacter algae gen. nov., sp. nov., isolated from seaweed

2010 ◽  
Vol 60 (7) ◽  
pp. 1510-1515 ◽  
Author(s):  
Dong Wan Lee ◽  
Soon Dong Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Chemotaxonomic Markers

A Gram-positive, aerobic, non-motile, rod-shaped actinomycete, designated strain DSW-2T, was isolated from a seaweed sample collected around Mara Island, Jeju, Republic of Korea. Comparative 16S rRNA gene sequence analysis showed that strain DSW-2T belongs to the suborder Micrococcineae and forms a distinct clade separated from representatives of the several families of this order. Levels of 16S rRNA gene sequence similarity between the novel strain and members of this suborder were lower than 96.4 %. The peptidoglycan type is A3α with Lys–Ser as the interpeptide bridge. Whole-cell sugars are glucose and galactose. The major menaquinone is MK-9(H4). The predominant fatty acid is ai-C15 : 0. The polar lipids are phosphatidylglycerol and phosphatidylinositol. The DNA G+C content was 68.3 mol%. On the basis of the chemotaxonomic markers and phylogenetic distinctiveness presented here, it is evident that the isolate represents a novel taxon within the suborder Micrococcineae. The name Koreibacter algae gen. nov., sp. nov. is proposed, with the type strain DSW-2T (=KCTC 13436T =DSM 22126T).

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