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Sung-taik Lee - One of the best experts on this subject based on the ideXlab platform.
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novosphingobium sediminicola sp nov isolated from Freshwater Sediment
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Sanghoon Baek, Ju Hyoung Lim, Long Jin, Hyunggwan Lee, Sung-taik LeeAbstract:A yellow-pigmented, Gram-negative, short rod-shaped, non-motile and non-spore-forming bacterial strain, designated HU1-AH51T, was isolated from Freshwater Sediment and was characterized using a polyphasic approach, in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain HU1-AH51T was shown to belong to the genus Novosphingobium, showing the highest level of sequence similarity with respect to Novosphingobium resinovorum NCIMB 8767T (96.0 %), Novosphingobium naphthalenivorans TUT562T (96.0 %) and Novosphingobium panipatense SM16T (96.0 %). Strain HU1-AH51T had a genomic DNA G+C content of 62.6 mol% and Q-10 as the predominant respiratory quinone. Furthermore, the major polyamine component (spermidine) in the cytoplasm and the presence of sphingoglycolipids suggested that strain HU1-AH51T belongs to the family Sphingomonadaceae. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain HU1-AH51T represents a novel species of the genus Novosphingobium, for which the name Novosphingobium sediminicola sp. nov. is proposed. The type strain is HU1-AH51T ( = LMG 24320T = KCTC 22311T).
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Sphingobium vulgare sp. nov., isolated from Freshwater Sediment.
International Journal of Systematic and Evolutionary Microbiology, 2010Co-Authors: Sanghoon Baek, Ju Hyoung Lim, Sung-taik LeeAbstract:A Gram-negative, motile, non-spore-forming bacterial strain, designated HU1-GD12T, was isolated from Freshwater Sediment. The strain was characterized by using a polyphasic approach in order to determine its taxonomic position. Comparative analysis of the 16S rRNA gene sequence showed that the isolate constituted a distinct branch within the genus Sphingobium, showing the highest level of sequence similarity with respect to Sphingobium ummariense RL-3T (96.2 %). Strain HU1-GD12T had a genomic DNA G+C content of 66.8 mol% and Q-10 as the predominant respiratory quinone. Furthermore, the major polyamine component (spermidine) in the cytoplasm and the presence of sphingoglycolipids suggested that strain HU1-GD12T belonged to the family Sphingomonadaceae. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain HU1-GD12T represents a novel species of the genus Sphingobium, for which the name Sphingobium vulgare sp. nov. is proposed. The type strain is HU1-GD12T (=LMG 24321T=KCTC 22289T).
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ferruginibacter alkalilentus gen nov sp nov and ferruginibacter lapsinanis sp nov novel members of the family chitinophagaceae in the phylum bacteroidetes isolated from Freshwater Sediment
International Journal of Systematic and Evolutionary Microbiology, 2009Co-Authors: Ju Hyoung Lim, Sanghoon Baek, Sung-taik LeeAbstract:Six Gram-negative, non-gliding, rod-shaped bacterial strains isolated from Freshwater Sediment were subjected to polyphasic analyses to determine their taxonomic positions. Analysis of the 16S rRNA gene sequences of the six strains revealed that they represent two separate genomic species in a new lineage within the phylum Bacteroidetes, related to members of the family 'Chitinophagaceae', in which they were most closely related to members of the genus Terrimonas (93.4-90.5 %). Two of the isolates, HU1-GD23(T) and HU1-HG42(T), had a sequence similarity of 96.2 %, with DNA G+C contents of 39.4 and 38.5 mol%, respectively. They possessed MK-7 as the predominant respiratory quinone and contained high amounts of iso-pentadecanoic acid and 3-hydroxy-iso-heptadecanoic acid in their cell envelopes, properties shared by members of the family 'Chitinophagaceae'. They were well differentiated from other members of the family 'Chitinophagaceae' by additional physiological and biochemical characteristics. In conclusion, strains HU1-GD23(T) (=KCTC 22306(T)=LMG 24312(T)) and HU1-HG42(T) (=KCTC 22305(T)=LMG 24324(T)) are considered to represent two novel species of a novel genus, Ferruginibacter gen. nov., for which the names Ferruginibacter alkalilentus sp. nov. and Ferruginibacter lapsinanis sp. nov., are proposed, respectively.
Ju Hyoung Lim - One of the best experts on this subject based on the ideXlab platform.
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novosphingobium sediminicola sp nov isolated from Freshwater Sediment
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Sanghoon Baek, Ju Hyoung Lim, Long Jin, Hyunggwan Lee, Sung-taik LeeAbstract:A yellow-pigmented, Gram-negative, short rod-shaped, non-motile and non-spore-forming bacterial strain, designated HU1-AH51T, was isolated from Freshwater Sediment and was characterized using a polyphasic approach, in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain HU1-AH51T was shown to belong to the genus Novosphingobium, showing the highest level of sequence similarity with respect to Novosphingobium resinovorum NCIMB 8767T (96.0 %), Novosphingobium naphthalenivorans TUT562T (96.0 %) and Novosphingobium panipatense SM16T (96.0 %). Strain HU1-AH51T had a genomic DNA G+C content of 62.6 mol% and Q-10 as the predominant respiratory quinone. Furthermore, the major polyamine component (spermidine) in the cytoplasm and the presence of sphingoglycolipids suggested that strain HU1-AH51T belongs to the family Sphingomonadaceae. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain HU1-AH51T represents a novel species of the genus Novosphingobium, for which the name Novosphingobium sediminicola sp. nov. is proposed. The type strain is HU1-AH51T ( = LMG 24320T = KCTC 22311T).
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Sphingobium vulgare sp. nov., isolated from Freshwater Sediment.
International Journal of Systematic and Evolutionary Microbiology, 2010Co-Authors: Sanghoon Baek, Ju Hyoung Lim, Sung-taik LeeAbstract:A Gram-negative, motile, non-spore-forming bacterial strain, designated HU1-GD12T, was isolated from Freshwater Sediment. The strain was characterized by using a polyphasic approach in order to determine its taxonomic position. Comparative analysis of the 16S rRNA gene sequence showed that the isolate constituted a distinct branch within the genus Sphingobium, showing the highest level of sequence similarity with respect to Sphingobium ummariense RL-3T (96.2 %). Strain HU1-GD12T had a genomic DNA G+C content of 66.8 mol% and Q-10 as the predominant respiratory quinone. Furthermore, the major polyamine component (spermidine) in the cytoplasm and the presence of sphingoglycolipids suggested that strain HU1-GD12T belonged to the family Sphingomonadaceae. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain HU1-GD12T represents a novel species of the genus Sphingobium, for which the name Sphingobium vulgare sp. nov. is proposed. The type strain is HU1-GD12T (=LMG 24321T=KCTC 22289T).
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ferruginibacter alkalilentus gen nov sp nov and ferruginibacter lapsinanis sp nov novel members of the family chitinophagaceae in the phylum bacteroidetes isolated from Freshwater Sediment
International Journal of Systematic and Evolutionary Microbiology, 2009Co-Authors: Ju Hyoung Lim, Sanghoon Baek, Sung-taik LeeAbstract:Six Gram-negative, non-gliding, rod-shaped bacterial strains isolated from Freshwater Sediment were subjected to polyphasic analyses to determine their taxonomic positions. Analysis of the 16S rRNA gene sequences of the six strains revealed that they represent two separate genomic species in a new lineage within the phylum Bacteroidetes, related to members of the family 'Chitinophagaceae', in which they were most closely related to members of the genus Terrimonas (93.4-90.5 %). Two of the isolates, HU1-GD23(T) and HU1-HG42(T), had a sequence similarity of 96.2 %, with DNA G+C contents of 39.4 and 38.5 mol%, respectively. They possessed MK-7 as the predominant respiratory quinone and contained high amounts of iso-pentadecanoic acid and 3-hydroxy-iso-heptadecanoic acid in their cell envelopes, properties shared by members of the family 'Chitinophagaceae'. They were well differentiated from other members of the family 'Chitinophagaceae' by additional physiological and biochemical characteristics. In conclusion, strains HU1-GD23(T) (=KCTC 22306(T)=LMG 24312(T)) and HU1-HG42(T) (=KCTC 22305(T)=LMG 24324(T)) are considered to represent two novel species of a novel genus, Ferruginibacter gen. nov., for which the names Ferruginibacter alkalilentus sp. nov. and Ferruginibacter lapsinanis sp. nov., are proposed, respectively.
Christopher G. Ingersoll - One of the best experts on this subject based on the ideXlab platform.
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development and application of Freshwater Sediment toxicity benchmarks for currently used pesticides
Science of The Total Environment, 2016Co-Authors: Lisa H Nowell, Christopher G. Ingersoll, Julia E Norman, Patrick W MoranAbstract:Abstract Sediment-toxicity benchmarks are needed to interpret the biological significance of currently used pesticides detected in whole Sediments. Two types of Freshwater Sediment benchmarks for pesticides were developed using spiked-Sediment bioassay (SSB) data from the literature. These benchmarks can be used to interpret Sediment-toxicity data or to assess the potential toxicity of pesticides in whole Sediment. The Likely Effect Benchmark (LEB) defines a pesticide concentration in whole Sediment above which there is a high probability of adverse effects on benthic invertebrates, and the Threshold Effect Benchmark (TEB) defines a concentration below which adverse effects are unlikely. For compounds without available SSBs, benchmarks were estimated using equilibrium partitioning (EqP). When a Sediment sample contains a pesticide mixture, benchmark quotients can be summed for all detected pesticides to produce an indicator of potential toxicity for that mixture. Benchmarks were developed for 48 pesticide compounds using SSB data and 81 compounds using the EqP approach. In an example application, data for pesticides measured in Sediment from 197 streams across the United States were evaluated using these benchmarks, and compared to measured toxicity from whole-Sediment toxicity tests conducted with the amphipod Hyalella azteca (28-d exposures) and the midge Chironomus dilutus (10-d exposures). Amphipod survival, weight, and biomass were significantly and inversely related to summed benchmark quotients, whereas midge survival, weight, and biomass showed no relationship to benchmarks. Samples with LEB exceedances were rare (n = 3), but all were toxic to amphipods (i.e., significantly different from control). Significant toxicity to amphipods was observed for 72% of samples exceeding one or more TEBs, compared to 18% of samples below all TEBs. Factors affecting toxicity below TEBs may include the presence of contaminants other than pesticides, physical/chemical characteristics of Sediment, and uncertainty in TEB values. Additional evaluations of benchmarks in relation to Sediment chemistry and toxicity are ongoing.
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predictions of Sediment toxicity using consensus based Freshwater Sediment quality guidelines
Archives of Environmental Contamination and Toxicology, 2001Co-Authors: Christopher G. Ingersoll, Donald D Macdonald, N Wang, Judy L Crane, L J Field, Pamela S Haverland, Nile E Kemble, R A Lindskoog, Corinne G Severn, D E SmorongAbstract:The objectives of this study were to compare approaches for evaluating the combined effects of chemical mixtures on the toxicity in field-collected Sediments and to evaluate the ability of consensus-based probable effect concentrations (PECs) to predict toxicity in a Freshwater database on both a national and regional geographic basis. A database was developed from 92 published reports, which included a total of 1,657 samples with high-quality matching Sediment toxicity and chemistry data from across North America. The database was comprised primarily of 10- to 14-day or 28- to 42-day toxicity tests with the amphipod Hyalella azteca (designated as the HA10 or HA28 tests) and 10- to 14-day toxicity tests with the midges Chironomus tentans or C. riparius (designated as the CS10 test). Mean PEC quotients were calculated to provide an overall measure of chemical contamination and to support an evaluation of the combined effects of multiple contaminants in Sediments. There was an overall increase in the incidence of toxicity with an increase in the mean quotients in all three tests. A consistent increase in the toxicity in all three tests occurred at a mean quotient > 0.5, however, the overall incidence of toxicity was greater in the HA28 test compared to the short-term tests. The longer-term tests, in which survival and growth are measured, tend to be more sensitive than the shorter-term tests, with acute to chronic ratios on the order of six indicated for H. azteca. Different patterns were observed among the various procedures used to calculate mean quotients. For example, in the HA28 test, a relatively abrupt increase in toxicity was associated with elevated polychlorinated biphenyls (PCBs) alone or with elevated polycyclic aromatic hydrocarbons (PAHs) alone, compared to the pattern of a gradual increase in toxicity observed with quotients calculated using a combination of metals, PAHs, and PCBs. These analyses indicate that the different patterns in toxicity may be the result of unique chemical signals associated with individual contaminants in samples. Though mean quotients can be used to classify samples as toxic or nontoxic, individual quotients might be useful in helping identify substances that may be causing or substantially contributing to the observed toxicity. An increase in the incidence of toxicity was observed with increasing mean quotients within most of the regions, basins, and areas in North America for all three toxicity tests. The results of these analyses indicate that the consensus-based PECs can be used to reliably predict toxicity of Sediments on both a regional and national basis.
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predictions of Sediment toxicity using consensus based Freshwater Sediment quality guidelines
Archives of Environmental Contamination and Toxicology, 2001Co-Authors: Christopher G. Ingersoll, Donald D Macdonald, N Wang, Judy L Crane, L J Field, Pamela S Haverland, Nile E Kemble, R A Lindskoog, Corinne G Severn, D E SmorongAbstract:The objectives of this study were to compare approaches for evaluating the combined effects of chemical mixtures on the toxicity in field-collected Sediments and to evaluate the ability of consensus-based probable effect concentrations (PECs) to predict toxicity in a Freshwater database on both a national and regional geographic basis. A database was developed from 92 published reports, which included a total of 1,657 samples with high-quality matching Sediment toxicity and chemistry data from across North America. The database was comprised primarily of 10- to 14-day or 28- to 42-day toxicity tests with the amphipod Hyalella azteca (designated as the HA10 or HA28 tests) and 10- to 14-day toxicity tests with the midges Chironomus tentans or C. riparius (designated as the CS10 test). Mean PEC quotients were calculated to provide an overall measure of chemical contamination and to support an evaluation of the combined effects of multiple contaminants in Sediments. There was an overall increase in the incidence of toxicity with an increase in the mean quotients in all three tests. A consistent increase in the toxicity in all three tests occurred at a mean quotient > 0.5, however, the overall incidence of toxicity was greater in the HA28 test compared to the short-term tests. The longer-term tests, in which survival and growth are measured, tend to be more sensitive than the shorter-term tests, with acute to chronic ratios on the order of six indicated for H. azteca. Different patterns were observed among the various procedures used to calculate mean quotients. For example, in the HA28 test, a relatively abrupt increase in toxicity was associated with elevated polychlorinated biphenyls (PCBs) alone or with elevated polycyclic aromatic hydrocarbons (PAHs) alone, compared to the pattern of a gradual increase in toxicity observed with quotients calculated using a combination of metals, PAHs, and PCBs. These analyses indicate that the different patterns in toxicity may be the result of unique chemical signals associated with individual contaminants in samples. Though mean quotients can be used to classify samples as toxic or nontoxic, individual quotients might be useful in helping identify substances that may be causing or substantially contributing to the observed toxicity. An increase in the incidence of toxicity was observed with increasing mean quotients within most of the regions, basins, and areas in North America for all three toxicity tests. The results of these analyses indicate that the consensus-based PECs can be used to reliably predict toxicity of Sediments on both a regional and national basis.
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Interlaboratory study of precision: Hyalella azteca and Chironomus tentans Freshwater Sediment toxicity assays
Environmental Toxicology and Chemistry, 1996Co-Authors: G. Allen Burton, Gerald T. Ankley, Teresa J. Norberg-king, Duane A. Benoit, Parley V. Winger, Jody A. Kubitz, James M. Lazorchak, Mark E. Smith, Daniel J. Call, Christopher G. IngersollAbstract:Standard 10-d whole-Sediment toxicity test methods have recently been developed by the U.S. Environmental Protection Agency (EPA) for the amphipod Hyalella azteca and the midge Chironomus tentans. An interlaboratory evaluation of method precision was performed using a group of seven to 10 laboratories, representing government, academia, and environmental consulting firms. The test methods followed the EPA protocols for 4-d water-only reference toxicant (KCl) testing (static exposure) and for 10-d whole-Sediment testing. Test Sediments included control Sediment, two copper-containing Sediments, and a Sediment contaminated primarily with polycyclic aromatic hydrocarbons. Reference toxicant tests resulted in H. azteca and C. tentans median lethal concentration (LC50) values with coefficents of variation (CVs) of 15.8 and 19.6%, respectively. Whole Sediments which were moderately contaminated provided the best estimates of precision using CVs. Hyalella azteca and C. tentans tests in moderately contaminated Sediments exhibited LC50 CVs of 38.9 and 13.5%, respectively. The CV for C. tentans growth was 31.9%. Only 3% (1 of 28) of samples exceeded acceptable interlaboratory precision limits for the H. azteca survival tests. No samples exceeded the intralaboratory precision limit for H. azteca or C. tentans survival tests. However, intralaboratory variability limits for C. tentans growth were exceeded by 80 and 100% of the laboratories for a moderately toxic and control sample, respectively. Interlaboratory variability limits for C. tentans survival were not exceeded by any laboratory. The results showed these test methods to have relatively low variance and acceptable levels of precision in interlaboratory comparisons.
J. Alary - One of the best experts on this subject based on the ideXlab platform.
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Liquid chromatography study of pyrene degradation by two micromycetes in a Freshwater Sediment
Chemosphere, 2001Co-Authors: C. Ravelet, Bernard Montuelle, C. Grosset, J.l. Benoit Guyot, J. AlaryAbstract:Pyrene biodegradation in a Freshwater Sediment without fungi supply, or inoculated with two Sediment Micromycetes, Mucor racemosus var. sphaerosporus and Phialophora alba was studied after 0, 5, 13, 28, 60 and 90 days. The influence of glucose addition was estimated, and a liquid chromatographic method for simultaneous quantitative determination of residual anthracene, fluoranthene and pyrene in the Sediment was developed. Samples with PAHs were extracted in Soxhlet with ethyl acetate, and LC analysis was performed on a 5µm Supelcosil(TM) column (150×4.6mmI.D.) with gradient elution (2 ml min1) of acetonitrile-water and UV detection at 254 nm. Recoveries of anthracene, fluoranthene and pyrene were 90.3%±1.1%,93.2%±0.9% and 90.42%±1.9%, respectively, without interference. The native Sediment microorganisms (with or without glucose added) have shown35% pyrene degradation and Sediment with glucose inoculated by the strains revealed 40%.
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Pyrene degradation by two fungi in a Freshwater Sediment and evaluation of fungal biomass by ergosterol content
Applied Microbiology and Biotechnology, 2001Co-Authors: C. Ravelet, Bernard Montuelle, C. Grosset, S. Krivobok, J. AlaryAbstract:Mucor racemosus var. sphaerosporus and Phialophora alba were investigated for their abilities to degrade pyrene in a Freshwater Sediment, with or without glucose supply as nutrient or carbon source, during 90 days. The ergosterol contents in Sediment were quantified to estimate fungal biomass and to assess the correlation between fungal activity and biodegradation of pyrene. Results showed that, in an heterogeneous environment, these fungi presented different abilities to degrade pyrene. P. alba increased the degree of pyrene degradation by 9%, compared to the native micro-organisms, but a supply of glucose acted as an inhibitor to pyrene disappearance. M. racemosus var. sphaerosporus was not efficient at Sediment bioremediation (with or without glucose added), because it reduced the rate of pyrene degradation by the native microflora. In any case, there was no increase of ergosterol in boxes during bioremediation experiments.In our experimental conditions, ergosterol content could not be correlated to pyrene degradation.
Sanghoon Baek - One of the best experts on this subject based on the ideXlab platform.
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novosphingobium sediminicola sp nov isolated from Freshwater Sediment
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Sanghoon Baek, Ju Hyoung Lim, Long Jin, Hyunggwan Lee, Sung-taik LeeAbstract:A yellow-pigmented, Gram-negative, short rod-shaped, non-motile and non-spore-forming bacterial strain, designated HU1-AH51T, was isolated from Freshwater Sediment and was characterized using a polyphasic approach, in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain HU1-AH51T was shown to belong to the genus Novosphingobium, showing the highest level of sequence similarity with respect to Novosphingobium resinovorum NCIMB 8767T (96.0 %), Novosphingobium naphthalenivorans TUT562T (96.0 %) and Novosphingobium panipatense SM16T (96.0 %). Strain HU1-AH51T had a genomic DNA G+C content of 62.6 mol% and Q-10 as the predominant respiratory quinone. Furthermore, the major polyamine component (spermidine) in the cytoplasm and the presence of sphingoglycolipids suggested that strain HU1-AH51T belongs to the family Sphingomonadaceae. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain HU1-AH51T represents a novel species of the genus Novosphingobium, for which the name Novosphingobium sediminicola sp. nov. is proposed. The type strain is HU1-AH51T ( = LMG 24320T = KCTC 22311T).
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Sphingobium vulgare sp. nov., isolated from Freshwater Sediment.
International Journal of Systematic and Evolutionary Microbiology, 2010Co-Authors: Sanghoon Baek, Ju Hyoung Lim, Sung-taik LeeAbstract:A Gram-negative, motile, non-spore-forming bacterial strain, designated HU1-GD12T, was isolated from Freshwater Sediment. The strain was characterized by using a polyphasic approach in order to determine its taxonomic position. Comparative analysis of the 16S rRNA gene sequence showed that the isolate constituted a distinct branch within the genus Sphingobium, showing the highest level of sequence similarity with respect to Sphingobium ummariense RL-3T (96.2 %). Strain HU1-GD12T had a genomic DNA G+C content of 66.8 mol% and Q-10 as the predominant respiratory quinone. Furthermore, the major polyamine component (spermidine) in the cytoplasm and the presence of sphingoglycolipids suggested that strain HU1-GD12T belonged to the family Sphingomonadaceae. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain HU1-GD12T represents a novel species of the genus Sphingobium, for which the name Sphingobium vulgare sp. nov. is proposed. The type strain is HU1-GD12T (=LMG 24321T=KCTC 22289T).
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ferruginibacter alkalilentus gen nov sp nov and ferruginibacter lapsinanis sp nov novel members of the family chitinophagaceae in the phylum bacteroidetes isolated from Freshwater Sediment
International Journal of Systematic and Evolutionary Microbiology, 2009Co-Authors: Ju Hyoung Lim, Sanghoon Baek, Sung-taik LeeAbstract:Six Gram-negative, non-gliding, rod-shaped bacterial strains isolated from Freshwater Sediment were subjected to polyphasic analyses to determine their taxonomic positions. Analysis of the 16S rRNA gene sequences of the six strains revealed that they represent two separate genomic species in a new lineage within the phylum Bacteroidetes, related to members of the family 'Chitinophagaceae', in which they were most closely related to members of the genus Terrimonas (93.4-90.5 %). Two of the isolates, HU1-GD23(T) and HU1-HG42(T), had a sequence similarity of 96.2 %, with DNA G+C contents of 39.4 and 38.5 mol%, respectively. They possessed MK-7 as the predominant respiratory quinone and contained high amounts of iso-pentadecanoic acid and 3-hydroxy-iso-heptadecanoic acid in their cell envelopes, properties shared by members of the family 'Chitinophagaceae'. They were well differentiated from other members of the family 'Chitinophagaceae' by additional physiological and biochemical characteristics. In conclusion, strains HU1-GD23(T) (=KCTC 22306(T)=LMG 24312(T)) and HU1-HG42(T) (=KCTC 22305(T)=LMG 24324(T)) are considered to represent two novel species of a novel genus, Ferruginibacter gen. nov., for which the names Ferruginibacter alkalilentus sp. nov. and Ferruginibacter lapsinanis sp. nov., are proposed, respectively.
