The Experts below are selected from a list of 6201 Experts worldwide ranked by ideXlab platform
Dirk Springael - One of the best experts on this subject based on the ideXlab platform.
-
draft genome sequence of the carbofuran mineralizing novosphingobium sp strain kn65 2
Genome Announcements, 2015Co-Authors: Thi Phi Oanh Nguyen, Rene De Mot, Dirk SpringaelAbstract:Complete mineralization of the N-methylcarbamate insecticide carbofuran, including mineralization of the aromatic moiety, appears to be confined to sphingomonad isolates. Here, we report the first draft genome sequence of such a sphingomonad strain, i.e., Novosphingobium sp. KN65.2, isolated from carbofuran-exposed agricultural soil in Vietnam.
-
influence of the carbon nitrogen phosphorus ratio on polycyclic aromatic hydrocarbon degradation by mycobacterium and Sphingomonas in soil
Applied Microbiology and Biotechnology, 2005Co-Authors: Natalie Leys, Willy Verstraete, Leen Bastiaens, Dirk SpringaelAbstract:Biodegradation of polycyclic aromatic hydrocarbons (PAHs) in the environment is often limited due to unfavorable nutrient conditions for the bacteria that use these PAHs as sole source of carbon and energy. Mycobacterium and Sphingomonas are 2 PAH-degrading specialists commonly present in PAH-polluted soil, but not much is known about their specific nutrient requirements. By adding different inorganic supplements of nitrogen (N) and phosphorus (P), affecting the overall carbon/nitrogen/phosphorus ratio of soil in soil slurry degradation tests, we investigated the impact of soil inorganic N and P nutrient conditions on PAH degradation by PAH-degrading Sphingomonas and Mycobacterium strains. The general theoretically calculated C/N/P ratio of 100/10/1 (expressed in moles) allowed rapid PAH metabolization by Sphingomonas and Mycobacterium strains without limitation. In addition, PAH-degradation rate and extent was not affected when ca. ten times lower concentrations of N and P were provided, indicating that Sphingomonas and Mycobacterium strains are capable of metabolizing PAHs under low nutrient conditions. Nor does PAH-degradation seem to be affected by excesses of N and P creating an imbalanced C/N/P ratio. However, supplements of N and P salts increased the salinity of soil slurry solutions and seriously limited or even completely blocked biodegradation.
-
streptomycin as a selective agent to facilitate recovery and isolation of introduced and indigenous Sphingomonas from environmental samples
Environmental Microbiology, 2004Co-Authors: Dirk Springael, Rene De Mot, Annemie Ryngaert, Leen Bastiaens, Karolien Vanbroekhoven, Pierre Wattiau, Marc Vancanneyt, Jean SwingsAbstract:Sphingomonas is an organism of major interest for the degradation of organic contaminants in soils and other environments. A medium based on the aminoglycoside antibiotic streptomycin (Sm) was developed, which, together with the yellow pigmentation of Sphingomonas, facilitated the detection, recovery and quantification of culturable Sphingomonas from soils. All 29 previously described bacterial strains belonging to 17 different Sphingomonas species were able to grow on mineral media containing 200 mug ml(-1) streptomycin, showing that the capacity to resist high concentrations of Sm is a common characteristic within Sphingomonas. Incorporation of Sm into the mineral medium led to a significant reduction in the background microbial population and a concomitant 100 times more sensitive detection of Sphingomonas inoculated in non-sterile soil matrices. The Sm-containing medium was used to examine a variety of hydrocarbon-contaminated soils for the presence and biodiversity of Sphingomonas. Incorporation of Sm in the medium led to a significant increase in the number of yellow-pigmented colonies. Comparison of contaminated and non-contaminated soils derived from the same site revealed colonization by culturable yellow-pigmented Sm-resistant bacteria of the polluted location solely. Both yellow and non-yellow-pigmented colonies were purified from plates containing glucose and Sm, and BOX-polymerase chain reaction (PCR) was used to sort out clonally related strains. Representative strains from the major BOX-PCR clusters were identified using FAME and partial 16S rRNA gene sequencing. Forty-eight of 58 Sm-resistant isolates were identified as Sphingomonas sp. Streptomycin-resistant Sphingomonas isolates generated BOX-PCR diversity patterns that were site dependent and represented different species mainly belonging to Sphingomonas subgroups containing species formerly designated as Sphingopyxis and Sphingobium. The ability to degrade phenanthrene was only found in a minority of the Sphingomonas isolates, which all originated from soils containing high phenanthrene concentrations.
-
occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons
Applied and Environmental Microbiology, 2004Co-Authors: Dirk Springael, N Leys, Annemie Ryngaert, Leen Bastiaens, Willy Verstraete, Eva M TopAbstract:Bacterial strains of the genus Sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (PAH) as the sole source of carbon and energy. The direct detection of Sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes. In this study, a culture-independent PCR-based detection method using specific primers targeting the Sphingomonas 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) was developed to assess Sphingomonas diversity in PAH-contaminated soils. PCR using the new primer pair on a set of template DNAs of different bacterial genera showed that the method was selective for bacteria belonging to the family Sphingomonadaceae. Single-band DGGE profiles were obtained for most Sphingomonas strains tested. Strains belonging to the same species had identical DGGE fingerprints, and in most cases, these fingerprints were typical for one species. Inoculated strains could be detected at a cell concentration of 104 CFU g of soil−1. The analysis of Sphingomonas population structures of several PAH-contaminated soils by the new PCR-DGGE method revealed that soils containing the highest phenanthrene concentrations showed the lowest Sphingomonas diversity. Sequence analysis of cloned PCR products amplified from soil DNA revealed new 16S rRNA gene Sphingomonas sequences significantly different from sequences from known cultivated isolates (i.e., sequences from environmental clones grouped phylogenetically with other environmental clone sequences available on the web and that possibly originated from several potential new species). In conclusion, the newly designed Sphingomonas-specific PCR-DGGE detection technique successfully analyzed the Sphingomonas communities from polluted soils at the species level and revealed different Sphingomonas members not previously detected by culture-dependent detection techniques.
Ho Dong Park - One of the best experts on this subject based on the ideXlab platform.
-
detection and sequencing of the microcystin lr degrading gene mlra from new bacteria isolated from japanese lakes
Fems Microbiology Letters, 2003Co-Authors: Takeshi Saito, Kunihiro Okano, Ho Dong Park, Tomoaki Itayama, Yuhei Inamori, Brett A Neilan, Brendan P Burns, Norio SugiuraAbstract:mlrA is the only microcystin-degrading gene detected in Sphingomonas sp. MJ-PV. The gene has an extremely rare nucleotide sequence and homologous genes have not yet been discovered in the DNA database. We discovered the existence of a gene homologous to mlrA in new microcystin-degrading bacteria, MD-1 and Y2. These strains possessed mlrA homologues, and the identities of the genes of MD-1 and Y2 with the corresponding MJ-PV exceeded 98% and 84%, respectively. On the other hand, the mlrA gene was not detected in laboratory strains of the closely related Sphingomonas spp. strains employing hemi-nested polymerase chain reaction detection using two primer sets. Although the microcystin-degrading bacteria were closely related strains, they did not cluster together as the same species. We can conclude that the mlrA gene is conserved in three different bacterial species, and it is unique to microcystin degraders but not to the genus Sphingomonas. : 2003 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.
-
detection and sequencing of the microcystin lr degrading gene mlra from new bacteria isolated from japanese lakes
Fems Microbiology Letters, 2003Co-Authors: Takeshi Saito, Kunihiro Okano, Ho Dong Park, Tomoaki Itayama, Yuhei Inamori, Brett A Neilan, Brendan P Burns, Norio SugiuraAbstract:mlrA is the only microcystin-degrading gene detected in Sphingomonas sp. MJ-PV. The gene has an extremely rare nucleotide sequence and homologous genes have not yet been discovered in the DNA database. We discovered the existence of a gene homologous to mlrA in new microcystin-degrading bacteria, MD-1 and Y2. These strains possessed mlrA homologues, and the identities of the genes of MD-1 and Y2 with the corresponding MJ-PV exceeded 98% and 84%, respectively. On the other hand, the mlrA gene was not detected in laboratory strains of the closely related Sphingomonas spp. strains employing hemi-nested polymerase chain reaction detection using two primer sets. Although the microcystin-degrading bacteria were closely related strains, they did not cluster together as the same species. We can conclude that the mlrA gene is conserved in three different bacterial species, and it is unique to microcystin degraders but not to the genus Sphingomonas.
-
degradation of the cyanobacterial hepatotoxin microcystin by a new bacterium isolated from a hypertrophic lake
Environmental Toxicology, 2001Co-Authors: Ho Dong Park, Akira Hiraishi, Youhei Sasaki, Tomoko Maruyama, Eiji Yanagisawa, Kenji KatoAbstract:A bacterium capable of degrading microcystins-RR, -YR, and -LR was isolated from a hypertrophic lake. The bacterium, designated Y2 and classified phenotypically as a member of the genus Sphingomonas, was shown to be distinct phylogenetically from any established species of Sphingomonas on the basis of 16S rDNA sequencing. The bacterium was tentatively identified as Sphingomonas by manual chemotaxonomy, but 16S rRNA sequencing analysis suggests that it is in fact a new species or even a new genus. When the Y2 bacterium was added to microcystins present in culture medium, the microcystins were degraded thoroughly in 4 days. The highest degradation rates of microcystins-RR and -LR were 13 and 5.4 mg L-1 day-1, respectively. The degradation rates were strongly dependent on temperature and the maximum rate was at 30 degrees C.
-
degradation of the cyanobacterial hepatotoxin microcystin by a new bacterium isolated from a hypertrophic lake
Environmental Toxicology, 2001Co-Authors: Ho Dong Park, Akira Hiraishi, Youhei Sasaki, Tomoko Maruyama, Eiji Yanagisawa, Kenji KatoAbstract:A bacterium capable of degrading microcystins-RR, -YR, and -LR was isolated from a hypertrophic lake. The bacterium, designated Y2 and classified phenotypically as a member of the genus Sphingomonas, was shown to be distinct phylogenetically from any established species of Sphingomonas on the basis of 16S rDNA sequencing. The bacterium was tentatively identified as Sphingomonas by manual chemotaxonomy, but 16S rRNA sequencing analysis suggests that it is in fact a new species or even a new genus. When the Y2 bacterium was added to microcystins present in culture medium, the microcystins were degraded thoroughly in 4 days. The highest degradation rates of microcystins-RR and -LR were 13 and 5.4 mg L 1 day 1 , respectively. The degradation rates were strongly dependent on temperature and the maximum rate was at 30C. 2001 by John Wiley & Sons, Inc. Environ Toxicol 16: 337343, 2001
Kenji Kato - One of the best experts on this subject based on the ideXlab platform.
-
complementary cooperation between two syntrophic bacteria in pesticide degradation
Journal of Theoretical Biology, 2009Co-Authors: Chie Katsuyama, Shinji Nakaoka, Masahito Hayatsu, Yasuhiro Takeuchi, Kenji KatoAbstract:Interactions between microbial species, including competition and mutualism, influence the abundance and distribution of the related species. For example, metabolic cooperation among multiple bacteria plays a major role in the maintenance of consortia. This study aims to clarify how two bacterial species coexist in a syntrophic association involving the degradation of the pesticide fenitrothion. To elucidate essential mechanisms for maintaining a syntrophic association, we employed a mathematical model based on an experimental study, because experiment cannot elucidate various conditions for two bacterial coexistence. We isolated fenitrothion-degrading Sphingomonas sp. TFEE and its metabolite of 3-methyl-4-nitrophenol (3M4N)-degrading Burkholderia sp. MN1 from a fenitrothion-treated soil microcosm. Neither bacterium can completely degrade fenitrothion alone, but they can utilize the second intermediate, methylhydroquinone (MHQ). Burkholderia sp. MN1 excretes a portion of MHQ during the degradation of 3M4N, from which Sphingomonas sp. TFEE carries out degradation to obtain carbon and energy. Based on experimental findings, we developed mathematical models that represent the syntrophic association involving the two bacteria. We found that the two bacteria are characterized by the mutualistic degradation of fenitrothion. Dynamics of two bacteria are determined by the degree of cooperation between two bacteria (i.e., supply of 3M4N by Sphingomonas sp. TFEE and excretion of MHQ by Burkholderia sp. MN1) and the initial population sizes. The syntrophic association mediates the coexistence of the two bacteria under the possibility of resource competition for MHQ, and robustly facilitates the maintenance of ecosystem function in terms of degrading xenobiotics. Thus, the mathematical analysis and numerical computations based on the experiment indicate the key mechanisms for coexistence of Sphingomonas sp. TFEE and Burkholderia sp. MN1 in syntrophic association involving fenitrothion degradation.
-
degradation of the cyanobacterial hepatotoxin microcystin by a new bacterium isolated from a hypertrophic lake
Environmental Toxicology, 2001Co-Authors: Ho Dong Park, Akira Hiraishi, Youhei Sasaki, Tomoko Maruyama, Eiji Yanagisawa, Kenji KatoAbstract:A bacterium capable of degrading microcystins-RR, -YR, and -LR was isolated from a hypertrophic lake. The bacterium, designated Y2 and classified phenotypically as a member of the genus Sphingomonas, was shown to be distinct phylogenetically from any established species of Sphingomonas on the basis of 16S rDNA sequencing. The bacterium was tentatively identified as Sphingomonas by manual chemotaxonomy, but 16S rRNA sequencing analysis suggests that it is in fact a new species or even a new genus. When the Y2 bacterium was added to microcystins present in culture medium, the microcystins were degraded thoroughly in 4 days. The highest degradation rates of microcystins-RR and -LR were 13 and 5.4 mg L-1 day-1, respectively. The degradation rates were strongly dependent on temperature and the maximum rate was at 30 degrees C.
-
degradation of the cyanobacterial hepatotoxin microcystin by a new bacterium isolated from a hypertrophic lake
Environmental Toxicology, 2001Co-Authors: Ho Dong Park, Akira Hiraishi, Youhei Sasaki, Tomoko Maruyama, Eiji Yanagisawa, Kenji KatoAbstract:A bacterium capable of degrading microcystins-RR, -YR, and -LR was isolated from a hypertrophic lake. The bacterium, designated Y2 and classified phenotypically as a member of the genus Sphingomonas, was shown to be distinct phylogenetically from any established species of Sphingomonas on the basis of 16S rDNA sequencing. The bacterium was tentatively identified as Sphingomonas by manual chemotaxonomy, but 16S rRNA sequencing analysis suggests that it is in fact a new species or even a new genus. When the Y2 bacterium was added to microcystins present in culture medium, the microcystins were degraded thoroughly in 4 days. The highest degradation rates of microcystins-RR and -LR were 13 and 5.4 mg L 1 day 1 , respectively. The degradation rates were strongly dependent on temperature and the maximum rate was at 30C. 2001 by John Wiley & Sons, Inc. Environ Toxicol 16: 337343, 2001
Norio Sugiura - One of the best experts on this subject based on the ideXlab platform.
-
detection and sequencing of the microcystin lr degrading gene mlra from new bacteria isolated from japanese lakes
Fems Microbiology Letters, 2003Co-Authors: Takeshi Saito, Kunihiro Okano, Ho Dong Park, Tomoaki Itayama, Yuhei Inamori, Brett A Neilan, Brendan P Burns, Norio SugiuraAbstract:mlrA is the only microcystin-degrading gene detected in Sphingomonas sp. MJ-PV. The gene has an extremely rare nucleotide sequence and homologous genes have not yet been discovered in the DNA database. We discovered the existence of a gene homologous to mlrA in new microcystin-degrading bacteria, MD-1 and Y2. These strains possessed mlrA homologues, and the identities of the genes of MD-1 and Y2 with the corresponding MJ-PV exceeded 98% and 84%, respectively. On the other hand, the mlrA gene was not detected in laboratory strains of the closely related Sphingomonas spp. strains employing hemi-nested polymerase chain reaction detection using two primer sets. Although the microcystin-degrading bacteria were closely related strains, they did not cluster together as the same species. We can conclude that the mlrA gene is conserved in three different bacterial species, and it is unique to microcystin degraders but not to the genus Sphingomonas. : 2003 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.
-
detection and sequencing of the microcystin lr degrading gene mlra from new bacteria isolated from japanese lakes
Fems Microbiology Letters, 2003Co-Authors: Takeshi Saito, Kunihiro Okano, Ho Dong Park, Tomoaki Itayama, Yuhei Inamori, Brett A Neilan, Brendan P Burns, Norio SugiuraAbstract:mlrA is the only microcystin-degrading gene detected in Sphingomonas sp. MJ-PV. The gene has an extremely rare nucleotide sequence and homologous genes have not yet been discovered in the DNA database. We discovered the existence of a gene homologous to mlrA in new microcystin-degrading bacteria, MD-1 and Y2. These strains possessed mlrA homologues, and the identities of the genes of MD-1 and Y2 with the corresponding MJ-PV exceeded 98% and 84%, respectively. On the other hand, the mlrA gene was not detected in laboratory strains of the closely related Sphingomonas spp. strains employing hemi-nested polymerase chain reaction detection using two primer sets. Although the microcystin-degrading bacteria were closely related strains, they did not cluster together as the same species. We can conclude that the mlrA gene is conserved in three different bacterial species, and it is unique to microcystin degraders but not to the genus Sphingomonas.
Akira Hiraishi - One of the best experts on this subject based on the ideXlab platform.
-
proposal of the genus Sphingomonas sensu stricto and three new genera sphingobium novosphingobium and sphingopyxis on the basis of phylogenetic and chemotaxonomic analyses
International Journal of Systematic and Evolutionary Microbiology, 2001Co-Authors: Mariko Takeuchi, Koei Hamana, Akira HiraishiAbstract:Phylogenetic analyses of 16S rRNA gene sequences by distance matrix and parsimony methods indicated that the currently known species of the genus Sphingomonas can be divided into four clusters. Some chemotaxonomic and phenotypic differences were noted among these clusters. Three new genera, Sphingobium, Novosphingobium and Sphingopyxis, are proposed in addition to the genus Sphingomonas sensu stricto. The genus Sphingobium is proposed to accommodate Sphingomonas chlorophenolica, Sphingomonas herbicidovorans and Sphingomonas yanoikuyae. The genus Novosphingobium is proposed for Sphingomonas aromaticivorans, Sphingomonas capsulata, Sphingomonas rosa, Sphingomonas stygia, Sphingomonas subarctica and Sphingomonas subterranea. Sphingomonas macrogoltabidus and Sphingomonas terrae are reclassified in the genus Sphingopyxis. The type species of Sphingobium, Novosphingobium and Sphingopyxis are Sphingobium yanoikuyae, Novosphingobium capsulatum and Sphingopyxis macrogoltabida, respectively.
-
degradation of the cyanobacterial hepatotoxin microcystin by a new bacterium isolated from a hypertrophic lake
Environmental Toxicology, 2001Co-Authors: Ho Dong Park, Akira Hiraishi, Youhei Sasaki, Tomoko Maruyama, Eiji Yanagisawa, Kenji KatoAbstract:A bacterium capable of degrading microcystins-RR, -YR, and -LR was isolated from a hypertrophic lake. The bacterium, designated Y2 and classified phenotypically as a member of the genus Sphingomonas, was shown to be distinct phylogenetically from any established species of Sphingomonas on the basis of 16S rDNA sequencing. The bacterium was tentatively identified as Sphingomonas by manual chemotaxonomy, but 16S rRNA sequencing analysis suggests that it is in fact a new species or even a new genus. When the Y2 bacterium was added to microcystins present in culture medium, the microcystins were degraded thoroughly in 4 days. The highest degradation rates of microcystins-RR and -LR were 13 and 5.4 mg L-1 day-1, respectively. The degradation rates were strongly dependent on temperature and the maximum rate was at 30 degrees C.
-
degradation of the cyanobacterial hepatotoxin microcystin by a new bacterium isolated from a hypertrophic lake
Environmental Toxicology, 2001Co-Authors: Ho Dong Park, Akira Hiraishi, Youhei Sasaki, Tomoko Maruyama, Eiji Yanagisawa, Kenji KatoAbstract:A bacterium capable of degrading microcystins-RR, -YR, and -LR was isolated from a hypertrophic lake. The bacterium, designated Y2 and classified phenotypically as a member of the genus Sphingomonas, was shown to be distinct phylogenetically from any established species of Sphingomonas on the basis of 16S rDNA sequencing. The bacterium was tentatively identified as Sphingomonas by manual chemotaxonomy, but 16S rRNA sequencing analysis suggests that it is in fact a new species or even a new genus. When the Y2 bacterium was added to microcystins present in culture medium, the microcystins were degraded thoroughly in 4 days. The highest degradation rates of microcystins-RR and -LR were 13 and 5.4 mg L 1 day 1 , respectively. The degradation rates were strongly dependent on temperature and the maximum rate was at 30C. 2001 by John Wiley & Sons, Inc. Environ Toxicol 16: 337343, 2001
