scholarly journals Desulfopila aestuarii gen. nov., sp. nov., a Gram-negative, rod-like, sulfate-reducing bacterium isolated from an estuarine sediment in Japan

2007 ◽  
Vol 57 (3) ◽  
pp. 520-526 ◽  
Author(s):  
Daisuke Suzuki ◽  
Atsuko Ueki ◽  
Aya Amaishi ◽  
Katsuji Ueki

A strictly anaerobic, mesophilic, sulfate-reducing bacterial strain (MSL86T) isolated from an estuarine sediment in the Sea of Japan (around the Japanese islands) was characterized phenotypically and phylogenetically. The cells were found to be Gram-negative, motile, non-spore-forming rods. Catalase was not detected. The optimum NaCl concentration for growth was 1.0 % (w/v) and the optimum temperature was 35 °C. Strain MSL86T was slightly alkaliphilic, with optimum growth at pH 7.5–7.6. Organic electron donors were incompletely oxidized to (mainly) acetate. Strain MSL86T utilized formate, pyruvate, lactate, fumarate, ethanol, propanol, butanol and glycerol as electron donors for sulfate reduction and did not use acetate, propionate, butyrate, succinate, malate, methanol, glycine, alanine, serine, aspartate, glutamate or H2. Sulfite, thiosulfate and fumarate were used as electron acceptors with lactate as an electron donor. Without electron acceptors, the strain fermented pyruvate and fumarate. The genomic DNA G+C content was 54.4 mol%. Menaquinone MK-8(H4) was the major respiratory quinone. The major cellular fatty acids were C16 : 0, C16 : 1 ω7, C16 : 1 ω5 and C17 : 1 ω6. A phylogenetic analysis based on the 16S rRNA gene sequence placed the strain in the class Deltaproteobacteria. The recognized bacterium most closely related to strain MSL86T was [Desulfobacterium] catecholicum DSM 3882T (sequence similarity 94.4 %), and the next most closely related recognized species were Desulfotalea psychrophila (94.2 % sequence similarity with the type strain) and Desulfotalea arctica (93.7 %). As the physiological and chemotaxonomic characteristics of MSL86T were distinctly different from those of any related species, a novel genus and species Desulfopila aestuarii gen. nov., sp. nov. are proposed to accommodate the strain. The type strain of Desulfopila aestuarii is MSL86T (=JCM 14042T=DSM 18488T).

2007 ◽  
Vol 57 (4) ◽  
pp. 849-855 ◽  
Author(s):  
Daisuke Suzuki ◽  
Atsuko Ueki ◽  
Aya Amaishi ◽  
Katsuji Ueki

Two strictly anaerobic, mesophilic, sulfate-reducing bacterial strains, Pro1T and Pro16, were isolated from an estuarine sediment in the Sea of Japan of the Japanese islands and were characterized by phenotypic and phylogenetic methods. Strains Pro1T and Pro16 had almost the same physiological and chemotaxonomic characteristics. Cells of both strains were Gram-negative, motile, non-spore-forming rods. Catalase activity was not detected. The optimum NaCl concentration for growth was 3.0 % (w/v). The optimum temperature for growth was 35 °C and the optimum pH was 6.7. Both strains used formate, propionate, pyruvate, lactate, fumarate, malate, ethanol, propanol, butanol, glycerol, alanine, glucose, fructose and H2 as electron donors for sulfate reduction and did not use acetate, butyrate, succinate, methanol, glycine, serine, aspartate, glutamate, cellobiose or sucrose. Organic electron donors were incompletely oxidized mainly to acetate. Both strains also used thiosulfate as an electron acceptor. Without electron acceptors, both strains fermented pyruvate and lactate. The genomic DNA G+C contents of strains Pro1T and Pro16 were 48.6 and 46.0 mol%, respectively. The major respiratory quinone of both strains was menaquinone MK-5(H2). Major cellular fatty acids of both strains were C15 : 0, C16 : 0, C17 : 1 ω6 and C18 : 1 ω7. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the class Deltaproteobacteria. The closest recognized relative of strains Pro1T and Pro16 was Desulfobulbus mediterraneus with sequence similarities of 95.2 and 94.8 %, respectively. Based on phylogenetic, physiological and chemotaxonomic characteristics, strains Pro1T and Pro16 represent a novel species of the genus Desulfobulbus, for which the name Desulfobulbus japonicus is proposed. The type strain is Pro1T(=JCM 14043T=DSM 18378T) and strain Pro16 (=JCM 14044=DSM 18379) is a reference strain.


2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3081-3086 ◽  
Author(s):  
Daisuke Suzuki ◽  
Zhiling Li ◽  
Xinxin Cui ◽  
Chunfung Zhang ◽  
Arata Katayama

A strictly anaerobic, mesophilic, sulfate-reducing bacterial strain (DST), isolated from river sediment contaminated with volatile organic compounds, was characterized phenotypically and phylogenetically. Cells were Gram-reaction-negative, non-motile short rods. For growth, optimum NaCl concentration was 0.9 g l−1, optimum temperature was 30 °C and optimum pH was 7.2. Strain DST utilized phenol, benzoate, 4-hydroxybenzoate, 4-methylphenol, 4-chlorophenol, acetate, butyrate and pyruvate as electron donors for sulfate reduction. Electron donors were completely oxidized. Strain DST did not utilize sulfite, thiosulfate or nitrate as electron acceptors. The genomic DNA G+C content of strain DST was 58.9 mol%. Major cellular fatty acids were iso-C14 : 0, anteiso-C15 : 0 and C18 : 1ω7c. Phylogenetic analyses based on the 16S rRNA gene indicated its closest relatives were strains of Desulfobacterium anilini (about 98–99 % sequence similarity) but the DNA–DNA hybridization value with Desulfobacterium anilini Ani1T was around 40 %. Although strain DST and its relatives shared most phenotypic and chemotaxonomic characteristics, the utilization of 4-chlorophenol, the range of electron acceptors and the optimum growth conditions differed. Strain DST is closely related to strains of Desulfobacterium anilini , but constitutes a different species within the genus. Based on phylogeny, phenotypic characteristics and chemotaxonomic characteristics, strain DST and Desulfobacterium anilini were clearly different from strains of other species of the genus Desulfobacterium . We thus propose the reclassification of Desulfobacterium anilini within a new genus, Desulfatiglans gen. nov., as Desulfatiglans anilini comb. nov. We also propose Desulfatiglans parachlorophenolica sp. nov. to accommodate strain DST. The type strain is DST ( = JCM 19179T = DSM 27197T).


2005 ◽  
Vol 55 (4) ◽  
pp. 1667-1674 ◽  
Author(s):  
Kelly P. Nevin ◽  
Dawn E. Holmes ◽  
Trevor L. Woodard ◽  
Erich S. Hinlein ◽  
David W. Ostendorf ◽  
...  

Fe(III)-reducing isolates were recovered from two aquifers in which Fe(III) reduction is known to be important. Strain BemT was enriched from subsurface sediments collected in Bemidji, MN, USA, near a site where Fe(III) reduction is important in aromatic hydrocarbon degradation. Strains P11, P35T and P39 were isolated from the groundwater of an aquifer in Plymouth, MA, USA, in which Fe(III) reduction is important because of long-term inputs of acetate as a highway de-icing agent to the subsurface. All four isolates were Gram-negative, slightly curved rods that grew best in freshwater media. Strains P11, P35T and P39 exhibited motility via means of monotrichous flagella. Analysis of the 16S rRNA and nifD genes indicated that all four strains are δ-proteobacteria and members of the Geobacter cluster of the Geobacteraceae. Differences in phenotypic and phylogenetic characteristics indicated that the four isolates represent two novel species within the genus Geobacter. All of the isolates coupled the oxidation of acetate to the reduction of Fe(III) [iron(III) citrate, amorphous iron(III) oxide, iron(III) pyrophosphate and iron(III) nitrilotriacetate]. All four strains utilized ethanol, lactate, malate, pyruvate and succinate as electron donors and malate and fumarate as electron acceptors. Strain BemT grew fastest at 30 °C, whereas strains P11, P35T and P39 grew equally well at 17, 22 and 30 °C. In addition, strains P11, P35T and P39 were capable of growth at 4 °C. The names Geobacter bemidjiensis sp. nov. (type strain BemT=ATCC BAA-1014T=DSM 16622T=JCM 12645T) and Geobacter psychrophilus sp. nov. (strains P11, P35T and P39; type strain P35T=ATCC BAA-1013T=DSM 16674T=JCM 12644T) are proposed.


2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3965-3970 ◽  
Author(s):  
Estelle Jumas-Bilak ◽  
Philippe Bouvet ◽  
Emma Allen-Vercoe ◽  
Fabien Aujoulat ◽  
Paul A. Lawson ◽  
...  

Five human clinical isolates of an unknown, strictly anaerobic, slow-growing, Gram-stain-negative, rod-shaped micro-organism were subjected to a polyphasic taxonomic study. Comparative 16S rRNA gene sequence-based phylogeny showed that the isolates grouped in a clade that included members of the genera Pyramidobacter, Jonquetella, and Dethiosulfovibrio; the type strain of Pyramidobacter piscolens was the closest relative with 91.5–91.7 % 16S rRNA gene sequence similarity. The novel strains were mainly asaccharolytic and unreactive in most conventional biochemical tests. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic acid and propionic acid and the major cellular fatty acids were C13 : 0 and C16 : 0, each of which could be used to differentiate the strains from P. piscolens. The DNA G+C content based on whole genome sequencing for the reference strain 22-5-S 12D6FAA was 57 mol%. Based on these data, a new genus, Rarimicrobium gen. nov., is proposed with one novel species, Rarimicrobium hominis sp. nov., named after the exclusive and rare finding of the taxon in human samples. Rarimicrobium is the fifth genus of the 14 currently characterized in the phylum Synergistetes and the third one in subdivision B that includes human isolates. The type strain of Rarimicrobium hominis is ADV70T ( = LMG 28163T = CCUG 65426T).


2007 ◽  
Vol 57 (10) ◽  
pp. 2376-2380 ◽  
Author(s):  
Mubina M. Merchant ◽  
Allana K. Welsh ◽  
Robert J. C. McLean

A Gram-negative, rod-shaped, motile, non-spore-forming bacterium, designated strain A62-14BT, was isolated from a constant-temperature, spring-fed, freshwater lake. On the basis of the complete 16S rRNA gene sequence, strain A62-14BT was shown to belong to the class Gammaproteobacteria, being most closely related to Rheinheimera sp. HTB082 (96.2 % sequence similarity), Rheinheimera baltica (95.01 %), Rheinheimera pacifica (96.35 %), Rheinheimera perlucida and Alishewanella fetalis (95.9 %). The major fatty acids (C16 : 1 ω7c, 38.56 %; C16 : 0, 19.04 %; C12 : 0 3-OH, 12.83 %; C18 : 1 ω7c, 7.70 %) and the motility of strain A62-14BT support its affiliation to the genus Rheinheimera. The salt intolerance of strain A62-14BT, together with the results of other physiological and biochemical tests, allowed the differentiation of this strain from the three species of the genus Rheinheimera with validly published names. Therefore strain A62-14BT represents a novel species of the genus Rheinheimera, for which the name Rheinheimera texasensis sp. nov. is proposed. The type strain is A62-14BT (=ATCC BAA-1235T=DSM 17496T). The description of the genus Rheinheimera is emended to reflect the halointolerance and freshwater origin of strain A62-14BT.


Author(s):  
Inna A. Panova ◽  
Olga Ikkert ◽  
Marat R. Avakyan ◽  
Dmitry S. Kopitsyn ◽  
Andrey V. Mardanov ◽  
...  

A novel, spore-forming, acidophilic and metal-resistant sulfate-reducing bacterium, strain OLT, was isolated from a microbial mat in a tailing dam at a gold ore mining site. Cells were slightly curved immotile rods, 0.5 µm in diameter and 2.0–3.0 µm long. Cells were stained Gram-negative, despite the Gram-positive cell structure revealed by electron microscopy of ultrathin layers. OLT grew at pH 4.0–7.0 with an optimum at 5.5. OLT utilised H2, lactate, pyruvate, malate, formate, propionate, ethanol, glycerol, glucose, fructose, sucrose, peptone and tryptone as electron donors for sulfate reduction. Sulfate, sulfite, thiosulfate, nitrate and fumarate were used as electron acceptors in the presence of lactate. Elemental sulfur, iron (III), and arsenate did not serve as electron acceptors. The major cellular fatty acids were C16:1ω7c (39.0 %) and C16 : 0 (12.1 %). The draft genome of OLT was 5.29 Mb in size and contained 4909 protein-coding genes. The 16S rRNA gene sequence placed OLT within the phylum Firmicutes , class Clostridia , family Peptococcaceae , genus Desulfosporosinus. Desulfosporosinus nitroreducens 59.4BT was the closest relative with 97.6 % sequence similarity. On the basis of phenotypic and phylogenetic characteristics, strain OLT represents a novel species within the genus Desulfosporosinus , for which we propose the name Desulfosporosinus metallidurans sp. nov. with the type strain OLT (=DSM 104464T=VKM В−3021T).


2006 ◽  
Vol 56 (10) ◽  
pp. 2437-2441 ◽  
Author(s):  
Sylvia H. Duncan ◽  
Rustam I. Aminov ◽  
Karen P. Scott ◽  
Petra Louis ◽  
Thaddeus B. Stanton ◽  
...  

Seven recently cultured bacterial isolates, although similar in their 16S rRNA gene sequences to Roseburia intestinalis L1-82T (DSM 14610T), were not sufficiently related for inclusion within existing species, forming three separate clusters in a 16S rRNA gene phylogenetic tree. The isolates, which were obtained from human stools, were Gram-variable or Gram-negative, strictly anaerobic, slightly curved rods; cells from all strains measured approximately 0.5×1.5–5.0 μm and were motile. Two strains belonging to one cluster (A2-181 and A2-183T) were the only strains that were able to grow on glycerol and that failed to grow on any of the complex substrates tested (inulin, xylan and amylopectin). Strains belonging to a second cluster (represented by M6/1 and M72/1T) differed from the other isolates in their ability to grow on sorbitol. Isolates belonging to a third cluster (L1-83 and A2-194T) were the only strains that failed to grow on xylose and that gave good growth on inulin (strains M6/1 and M72/1T gave weak growth). All strains were net acetate utilizers. The DNA G+C contents of representative Roseburia strains A2-183T, A2-194T, M72/1T and R. intestinalis L1-82T were 47.4, 41.4, 42.0 and 42.6 mol%, respectively. Based on 16S rRNA gene sequence similarity, three novel Roseburia species are proposed, with the names Roseburia hominis sp. nov. (type strain A2-183T=DSM 16839T=NCIMB 14029T), Roseburia inulinivorans sp. nov. (type strain A2-194T=DSM 16841T=NCIMB 14030T) and Roseburia faecis sp. nov. (type strain M72/1T=DSM 16840T=NCIMB 14031T).


2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2290-2295 ◽  
Author(s):  
Srinivasan Krishnamurthi ◽  
Stefan Spring ◽  
Pinnaka Anil Kumar ◽  
Shanmugam Mayilraj ◽  
Hans-Peter Klenk ◽  
...  

A novel sulfate-reducing, strictly anaerobic and endospore-forming bacterium, designated strain A5LFS102T, was isolated from a subsurface landfill sample. The strain was characterized using a polyphasic approach. Optimal growth was observed at 37 °C and pH 7.5 with sulfate as an electron acceptor. Sulfite and thiosulfate were utilized as electron acceptors. The respiratory isoprenoid quinone was menaquinone MK-7. 16S rRNA gene sequence analysis assigned strain A5LFS102T to the genus Desulfotomaculum . Both 16S rRNA and dissimilatory sulfate reductase (dsr) genes were compared with those of representative members of the genus Desulfotomaculum . Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A5LFS102T was closely related to Desulfotomaculum aeronauticum DSM 10349T (94.6 % sequence similarity). The G+C content of the DNA was 45.4 mol%. The total cellular fatty acid profile was dominated by C16 fatty acids. These phenotypic and genotypic data showed that strain A5LFS102T should be recognized as representative of a novel species of the genus Desulfotomaculum , for which the name Desulfotomaculum defluvii sp. nov. is proposed. The type strain is A5LFS102T ( = DSM 23699T = JCM 14036T = MTCC 7767T).


2007 ◽  
Vol 57 (6) ◽  
pp. 1227-1231 ◽  
Author(s):  
Keun Sik Baik ◽  
Mi Sun Kim ◽  
Eun Mi Kim ◽  
Hyung Rak Kim ◽  
Chi Nam Seong

A non-motile, rod-shaped, light-yellow-pigmented bacterium, designated strain WPCB159T, was isolated from freshwater samples collected from the Woopo wetland in Korea. The cells were Gram-negative, aerobic and catalase- and oxidase-positive. The major fatty acids were C16 : 1 ω7c (34.8 %), iso-C15 : 0 (24.2 %) and C16 : 0 (9.4 %). The DNA G+C content was 44 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain WPCB159T forms a lineage within the genus Dyadobacter (family ‘Flexibacteraceae’) and is closely related to Dyadobacter hamtensis HHS 11T (97.8 % sequence similarity) and to other members of the genus Dyadobacter (95.2–96.8 % sequence similarity). The phenotypic characteristics and DNA–DNA hybridization relatedness data indicate that strain WPCB159T should be distinguished from D. hamtensis HHS 11T. On the basis of the evidence presented in this study, strain WPCB159T represents a novel species of the genus Dyadobacter, for which the name Dyadobacter koreensis sp. nov. is proposed. The type strain is WPCB159T (=KCTC 12537T=NBRC 101116T).


Author(s):  
Karine Alain ◽  
Anne Postec ◽  
Elodie Grinsard ◽  
Françoise Lesongeur ◽  
Daniel Prieur ◽  
...  

A novel, strictly anaerobic, thermophilic, sulfate-reducing bacterium, designated strain AT1325T, was isolated from a deep-sea hydrothermal vent at the Rainbow site on the Mid-Atlantic Ridge. This strain was subjected to a polyphasic taxonomic analysis. Cells were Gram-negative motile rods (approximately 2.4×0.6 μm) with a single polar flagellum. Strain AT1325T grew at 55–75 °C (optimum, 65–70 °C), at pH 5.5–8.0 (optimum, 6.5–7.5) and in the presence of 1.5–4.5 % (w/v) NaCl (optimum, 2.5 %). Cells grew chemolithoautotrophically with H2 as an energy source and as an electron acceptor. Alternatively, the novel isolate was able to use methylamine, peptone or yeast extract as carbon sources. The dominant fatty acids (>5 % of the total) were C16 : 0, C18 : 1 ω7c, C18 : 0 and C19 : 0 cyclo ω8c. The G+C content of the genomic DNA of strain AT1325T was 45.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain AT1325T within the family Thermodesulfobacteriaceae, in the bacterial domain. Comparative 16S rRNA gene sequence analysis indicated that strain AT1325T belonged to the genus Thermodesulfatator, sharing 97.8 % similarity with the type strain of Thermodesulfatator indicus, the unique representative species of this genus. On the basis of the data presented, it is suggested that strain AT1325T represents a novel species of the genus Thermodesulfatator, for which the name Thermodesulfatator atlanticus sp. nov. is proposed. The type strain is AT1325T (=DSM 21156T=JCM 15391T).


Sign in / Sign up

Export Citation Format

Share Document