scholarly journals Desulfopila inferna sp. nov., a sulfate-reducing bacterium isolated from the subsurface of a tidal sand-flat

2010 ◽  
Vol 60 (7) ◽  
pp. 1626-1630 ◽  
Author(s):  
Antje Gittel ◽  
Michael Seidel ◽  
Jan Kuever ◽  
Alexander S. Galushko ◽  
Heribert Cypionka ◽  
...  
Keyword(s):  
Cellular Fatty Acid ◽  
Fatty Acid Analysis ◽  
Rrna Gene ◽  
Sand Flat ◽  
Sulfate Reducing ◽  
Branched Chain Fatty Acids ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Tidal Sand ◽  
Branched Chain

A Gram-negative, rod-shaped, sulfate-reducing bacterium (strain JS_SRB250LacT) was isolated from a tidal sand-flat in the German Wadden Sea. 16S rRNA gene sequence analysis showed that strain JS_SRB250LacT belonged to the Desulfobulbaceae (Deltaproteobacteria), with Desulfopila aestuarii MSL86T being the closest recognized relative (94.2 % similarity). Higher similarity (96.6 %) was shared with ‘Desulfobacterium corrodens’ IS4, but this name has not been validly published. The affiliation of strain JS_SRB250LacT to the genus Desulfopila was further supported by analysis of aprBA gene sequences and shared physiological characteristics, in particular the broad range of organic electron donors used for sulfate reduction. Compared with Desulfopila aestuarii MSL86T, strain JS_SRB250LacT additionally utilized butyrate and succinate and grew chemolithoautotrophically with hydrogen as an electron donor. CO dehydrogenase activity was demonstrated, indicating that the reductive acetyl-CoA pathway (Wood–Ljungdahl pathway) was used for CO2 fixation. Results of cellular fatty acid analysis allowed chemotaxonomic differentiation of strain JS_SRB250LacT from Desulfopila aestuarii MSL86T by the presence of C17 : 0 cyclo and the absence of hydroxy and unsaturated branched-chain fatty acids. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain JS_SRB250LacT represents a novel species of the genus Desulfopila, for which the name Desulfopila inferna sp. nov. is proposed. The type strain is JS_SRB250LacT (=DSM 19738T =NBRC 103921T).

scholarly journals Paenibacillus chungangensis sp. nov., isolated from a tidal-flat sediment

2011 ◽  
Vol 61 (2) ◽  
pp. 281-285 ◽  
Author(s):  
Mi-Hak Park ◽  
Jitsopin Traiwan ◽  
Min Young Jung ◽  
Yun Sung Nam ◽  
Ji Hoon Jeong ◽  
...  
Keyword(s):  
Tidal Flat ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Tidal Flat Sediment ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Type Strains

A Gram-stain-positive, rod-shaped, endospore-forming bacterium, strain CAU 9038T, was isolated from a tidal-flat sediment of DaeYiJac Island, Republic of Korea, and its taxonomic position was investigated using a polyphasic approach. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol, the major isoprenoid quinone was MK-7 and the dominant cellular fatty acid was anteiso-C15 : 0. The DNA G+C content was 51.6 mol%. 16S rRNA gene sequence analysis showed that the strain belonged to the genus Paenibacillus, with <96.1 % sequence similarity to type strains of Paenibacillus species with validly published names. The most closely related type strains to CAU 9038T were Paenibacillus thailandensis S3-4AT (96.1 % similarity) and Paenibacillus agaridevorans DSM 1355T (95.3 %). The phenotypic, chemotaxonomic and genotypic data clearly indicated that strain CAU 9038T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus chungangensis sp. nov. is proposed. The type strain is CAU 9038T (=KCTC 13717T =CCUG 59129T).

Indibacter alkaliphilus gen. nov., sp. nov., an alkaliphilic bacterium isolated from a haloalkaline lake

2010 ◽  
Vol 60 (4) ◽  
pp. 721-726 ◽  
Author(s):  
P. Anil Kumar ◽  
T. N. R. Srinivas ◽  
S. Madhu ◽  
R. Manorama ◽  
S. Shivaji
Keyword(s):  
Fatty Acids ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Branched Chain Fatty Acids ◽  
Lonar Lake ◽  
Bacterium Strain ◽  
Branched Chain ◽  
Alkaliphilic Bacterium

A novel Gram-stain-negative, rod-shaped, non-motile bacterium, strain LW1T, was isolated from a water sample collected at a depth of 3.5 m from Lonar Lake, Buldhana district, Maharashtra, India. The cell suspension was reddish-orange due to the presence of carotenoids. Strain LW1T was positive for catalase, oxidase, ornithine decarboxylase and lysine decarboxylase and negative for gelatinase, urease and lipase. Fatty acids were dominated by branched-chain fatty acids (>76 %), with a high abundance of iso-C15 : 0 (48 %), anteiso-C15 : 0 (7 %) and iso-C17 : 0 3-OH (11 %). Strain LW1T contained MK-4 and MK-7 as the major respiratory quinones and phosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine as the major phospholipids. A blast sequence similarity search based on 16S rRNA gene sequences indicated that members of the genera Belliella and Aquiflexum were the nearest phylogenetic neighbours with similarities of 91.8–92.3 %. Phylogenetic analyses indicated that strain LW1T formed a deep-rooted lineage distinct from the clades represented by the genera Belliella, Aquiflexum, Cyclobacterium, Echinicola and Algoriphagus. Based on the above-mentioned phenotypic and phylogenetic characteristics, it is proposed that strain LW1T represents a novel species in a new genus, Indibacter alkaliphilus gen. nov., sp. nov. (type strain LW1T=KCTC 22604T=CCUG 57479T). The genomic DNA G+C content of strain LW1T is 42.7±1 mol%.

scholarly journals Proposal of Effusibacillus lacus gen. nov., sp. nov., and reclassification of Alicyclobacillus pohliae as Effusibacillus pohliae comb. nov. and Alicyclobacillus consociatus as Effusibacillus consociatus comb. nov.

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2770-2774 ◽  
Author(s):  
Miho Watanabe ◽  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
Fatty Acids ◽  
Type Species ◽  
Cellular Fatty Acid ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Branched Chain Fatty Acids ◽  
Branched Chain

A novel thermophilic, facultatively anaerobic bacterium, strain skLN1T, was isolated from the sediment of a freshwater lake in Japan. Cells of strain skLN1T were rod-shaped and Gram-stain-variable. A KOH lysis test suggested that the cell wall of the isolate has a Gram-positive structure. For aerobic growth, the optimum pH was pH 7.25–7.50 and the optimum temperature was 50–52 °C. The G+C content of the genomic DNA was 50.8 mol%. Nitrate was reduced to nitrite. Alicyclic fatty acids were not detected, and branched-chain fatty acids were major components in the cellular fatty acid profile. MK-7 was the predominant respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolated strain was related most closely to Alicyclobacillus consociatus CCUG 53762T (95 % similarity). This analysis also showed that the monophyly of the genus Alicyclobacillus had been lost. On the basis of phylogenetic and phenotypic characterization, Effusibacillus lacus gen. nov., sp. nov. is proposed. The type strain of Effusibacillus lacus is skLN1T ( = NBRC 109614T = DSM 27172T). It is also proposed that Alicyclobacillus pohliae and Alicyclobacillus consociatus should be reclassified to the genus Effusibacillus as Effusibacillus pohliae comb. nov. and Effusibacillus consociatus comb. nov., respectively.

scholarly journals Aminiphilus circumscriptus gen. nov., sp. nov., an anaerobic amino-acid-degrading bacterium from an upflow anaerobic sludge reactor

2007 ◽  
Vol 57 (8) ◽  
pp. 1914-1918 ◽  
Author(s):  
C. Díaz ◽  
S. Baena ◽  
M.-L. Fardeau ◽  
B. K. C. Patel
Keyword(s):  
Anaerobic Sludge ◽  
Rrna Gene ◽  
Brewery Wastewater ◽  
Polyphasic Analysis ◽  
Degrading Bacterium ◽  
Branched Chain Fatty Acids ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Casamino Acids ◽  
Branched Chain

Strain ILE-2T was isolated from an upflow anaerobic sludge bed reactor treating brewery wastewater. The motile, non-sporulating, slightly curved cells (2–4×0.1 μm) stained Gram-negative and grew optimally at 42 °C and pH 7.1 with 0.5 % NaCl. The strain required yeast extract for growth and fermented Casamino acids, peptone, isoleucine, arginine, lysine, alanine, valine, glutamate, histidine, glutamine, methionine, malate, fumarate, glycerol and pyruvate to acetate, propionate and minor amounts of branched-chain fatty acids. Carbohydrates, formate, acetate, propionate, butyrate, isovalerate, methanol, ethanol, 1-propanol, butanol, lactate, succinate, starch, casein, gelatin, xylan and a number of other amino acids were not utilized. The DNA G+C content of strain ILE-2T was 52.7 mol%. 16S rRNA gene sequence analysis revealed that ILE-2T was distantly related to members of the genera Aminobacterium (83 % similarity) and Aminomonas (85 % similarity) in the family Syntrophomonadaceae, order Clostridiales, phylum Firmicutes. On the basis of the results of our polyphasic analysis, strain ILE-2T represents a novel species and genus within the family Syntrophomonadaceae, for which the name Aminiphilus circumscriptus gen. nov., sp. nov. is proposed. The type strain of Aminiphilus circumscriptus is ILE-2T (=DSM 16581T =JCM 14039T).

Desulfothermus okinawensis sp. nov., a thermophilic and heterotrophic sulfate-reducing bacterium isolated from a deep-sea hydrothermal field

2007 ◽  
Vol 57 (10) ◽  
pp. 2360-2364 ◽  
Author(s):  
Takuro Nunoura ◽  
Hanako Oida ◽  
Masayuki Miyazaki ◽  
Yohey Suzuki ◽  
Ken Takai ◽  
...  
Keyword(s):  
Deep Sea ◽  
Gene Sequence ◽  
Okinawa Trough ◽  
Hydrothermal Field ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

A novel thermophilic and heterotrophic sulfate-reducing bacterium, strain TFISO9T, was isolated from a deep-sea hydrothermal field at the Yonaguni Knoll IV in the Southern Okinawa Trough. The cells were motile rods 2.5–5.0 μm in length and 0.6–0.9 μm in width. Strain TFISO9T was an obligate heterotroph and reduced sulfate. It grew between 35 and 60 °C (optimum 50 °C), at pH 5.4–7.9 (optimum pH 5.9–6.4) and with 1.5–4.5 % NaCl (optimum 2.5 %). The fatty acid composition was C16 : 0 (61.5 %) and 12Me16 : 0 (38.5 %). The DNA G+C content was 34.9 mol%. The 16S rRNA gene sequence analysis indicated that strain TFISO9T belonged to the genus Desulfothermus. Based on physiological and phylogenetic characteristics, strain TFISO9T represents a novel species for which the name Desulfothermus okinawensis sp. nov. is proposed. The type strain is TFISO9T (=JCM 13304T=DSM 17375T).

scholarly journals Promicromonospora iranensis sp. nov., an actinobacterium isolated from rhizospheric soil

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3314-3319 ◽  
Author(s):  
Fatemeh Mohammadipanah ◽  
Javad Hamedi ◽  
Cathrin Spröer ◽  
María del Carmen Montero-Calasanz ◽  
Peter Schumann ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Fatty Acid Pattern ◽  
Molecular Characteristics ◽  
Rrna Gene ◽  
Fars Province ◽  
Pairwise Sequence Identity ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Branched Chain

A novel strain of the genus Promicromonospora , designated HM 792T, was isolated from soil in Fars Province, Iran. On ISP 2 medium, the yellow-pigmented isolate produced long and branched hyphae that developed into a large number of irregularly shaped spores. It showed growth at 25–30 °C and pH 6.0–9.0 with 0–8 % (w/v) NaCl. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Promicromonospora . Whole-cell hydrolysates of strain HM 792T contained the amino acids d-glutamic acid, l-alanine and l-lysine along with the sugars glucose and ribose. The main polar lipids were diphosphatidylglycerol, two unknown phospholipids, two unknown glycolipids and two unknown phosphoglycolipids, complemented by minor concentrations of phosphatidylinositol and phosphatidylglycerol. MK-9(H4) was the predominant menaquinone. The fatty-acid pattern was composed mainly of the saturated branched-chain acids anteiso-C15 : 0 and iso-C15 : 0. 16S rRNA gene sequence analysis showed the highest pairwise sequence identity (96.6–99.0 %) with the members of the genus Promicromonospora . Based on phenotypic and genotypic features, strain HM 792T is considered to represent a novel species of the genus Promicromonospora , for which the name Promicromonospora iranensis sp. nov. is proposed. Strain HM 792T ( = DSM 45554T = UTMC00792T = CCUG 63022T) is the type strain.

scholarly journals Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2831-2837 ◽  
Author(s):  
Peter Kämpfer ◽  
Karin Martin ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
High Sequence Similarity ◽  
Polar Lipid Profile ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Type Strains ◽  
Sequence Similarities

A Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain JM-1396T) producing a yellow pigment, was isolated from the healthy internal stem tissue of post-harvest cotton (Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit at the E. V. Smith Research Center in Tallassee (Macon county), AL, USA. 16S rRNA gene sequence analysis of strain JM-1396T showed high sequence similarity values to the type strains of Novosphingobium mathurense, Novosphingobium panipatense (both 98.6 %) and Novosphingobium barchaimii (98.5 %); sequence similarities to all other type strains of species of the genus Novosphingobium were below 98.3 %. DNA–DNA pairing experiments of the DNA of strain JM-1396T and N. mathurense SM117T, N. panipatense SM16T and N. barchaimii DSM 25411T showed low relatedness values of 8 % (reciprocal 7 %), 24 % (reciprocal 26 %) and 19 % (reciprocal 25 %), respectively. Ubiquinone Q-10 was detected as the dominant quinone; the fatty acids C18 : 1ω7c (71.0 %) and the typical 2-hydroxy fatty acid, C14 : 0 2-OH (11.7 %), were detected as typical components. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. The polyamine pattern contained the major compound spermidine and only minor amounts of other polyamines. All these data revealed that strain JM-1396T represents a novel species of the genus Novosphingobium. For this reason we propose the name Novosphingobium gossypii sp. nov. with the type strain JM-1396T ( = LMG 28605T = CCM 8569T = CIP 110884T).

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.

scholarly journals Halomonas daqiaonensis sp. nov., a moderately halophilic, denitrifying bacterium isolated from a littoral saltern

2011 ◽  
Vol 61 (7) ◽  
pp. 1612-1616 ◽  
Author(s):  
Lingyun Qu ◽  
Qiliang Lai ◽  
Fengling Zhu ◽  
Xuguang Hong ◽  
Jinxing Zhang ◽  
...  
Keyword(s):  
Gene Sequence ◽  
East Coast ◽  
Novel Species ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Cellular Fatty Acids ◽  
Gene Sequence Analysis

Two novel Gram-negative, oxidase- and catalase-positive, rod-shaped bacterial strains, designated YCSA28T and YCSA39, were isolated from sediment of Daqiao saltern, Jimo, Qingdao, on the east coast of China. The two strains grew optimally at 28–30 °C, at pH 7.5 and in the presence of 7–8 % (w/v) NaCl. They were assigned to the genus Halomonas, class Gammaproteobacteria, based on 16S rRNA gene sequence analysis. The major cellular fatty acids of the two strains were C18 : 1ω7c (42.9 %), C16 : 0 (23.1 %) and C16 : 1ω7c/ω6c (18.0 %), and Q-9 was the major ubiquinone. The G+C content of the DNA of strains YCSA28T and YCSA39 was 63.7 and 63.9 mol%, respectively. The predominant respiratory lipoquinone, cellular fatty acid profiles and DNA G+C content of strains YCSA28T and YCSA39 were consistent with those of recognized species of the genus Halomonas. Levels of DNA–DNA relatedness between strains YCSA28T and YCSA39, between YCSA28T and Halomonas ventosae Al12T, and between YCSA39 and H. ventosae Al12T were 95, 45 and 50 %, respectively. Together, these data indicated that strains YCSA28T and YCSA39 represent a single novel species of the genus Halomonas, for which the name Halomonas daqiaonensis sp. nov. is proposed. The type strain is YCSA28T ( = CGMCC 1.9150T  = NCCB 100305T  = MCCC 1B00920T).

scholarly journals Serinicoccus chungangensis sp. nov., isolated from tidal flat sediment, and emended description of the genus Serinicoccus

2011 ◽  
Vol 61 (6) ◽  
pp. 1299-1303 ◽  
Author(s):  
Jitsopin Traiwan ◽  
Mi-Hak Park ◽  
Wonyong Kim
Keyword(s):  
Tidal Flat ◽  
Sequence Similarity ◽  
Halophilic Bacterium ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Tidal Flat Sediment ◽  
Bacterium Strain ◽  
Type Strains

A Gram-positive, halophilic bacterium, strain CAU 9536T, was isolated from a tidal flat sediment in the Yellow Sea, Republic of Korea. Strain CAU 9536T grew optimally at 30 °C, at pH 9.0 and in the presence of 13.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 9536T belonged to the genus Serinicoccus, and showed sequence similarity levels of 99.0 % to Serinicoccus profundi MCCC 1A05965T and 98.0 % to Serinicoccus marinus JC1078T. DNA–DNA relatedness values between strain CAU 9536T and the above two type strains were below 45.0 %. The cell-wall peptidoglycan of strain CAU 9536T was based on meso-diaminopimelic acid, in contrast to those of S. profundi and S. marinus. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol. Whole-cell hydrolysates contained mainly glucose and ribose. The major isoprenoid quinone was menaquinone MK-8 (H4), and the predominant cellular fatty acid was iso-C15 : 0. The DNA G+C content of strain CAU 9536T was 73.5 mol%. Based on phenotypic, chemotaxonomic and genotypic data, strain CAU 9536T is considered to represent a novel species of the genus Serinicoccus, for which the name Serinicoccus chungangensis sp. nov. is proposed. The type strain is CAU 9536T ( = KCTC 19774T = CCUG 59777T).

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