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ABSTRACT: To characterize the denitrifying phosphorus (P) uptake properties of Accumulibacter, a sequencing batch reactor (SBR) was operated with acetate. The SBR operation was gradually acclimated from anaerobic-oxic (AO) to anaerobic-anoxic-oxic (A2O) conditions by stepwise increases of nitrate concentration and the anoxic time. The communities of Accumulibacter and associated bacteria at the initial (AO) and final (A2O) stages were compared using 16S rRNA and polyphosphate kinase genes and using fluorescence in situ hybridization (FISH). The acclimation process led to a clear shift in the relative abundances of recognized Accumulibacter subpopulations from clades IIA > IA > IIF to clades IIC > IA > IIF, as well as to increases in the abundance of other associated bacteria [Dechloromonas (from 1.2% to 19.2%) and Competibacter (from 16.4% to 20.0%)], while overall Accumulibacter decreased (from 55.1% to 29.2%). A series of batch experiments combined with FISH/microautoradiography (MAR) analyses were performed to characterize the denitrifying P-uptake properties of the Accumulibacter clades. In FISH/MAR experiments using slightly diluted sludge (∼0.5 g/L), all Accumulibacter clades successfully took up phosphorus in the presence of nitrate. However, the Accumulibacter clades showed no P-uptake in the presence of nitrate when the sludge was highly diluted (∼0.005 g/L); under these conditions, reduction of nitrate to nitrite did not occur, whereas P-uptake by Accumulibacter clades occurred when nitrite was added. These results suggest that the Accumulibacter cells lack nitrate reduction capabilities and that P-uptake by Accumulibacter is dependent upon nitrite generated by associated nitrate-reducing bacteria such as Dechloromonas and Competibacter.
Applied and environmental microbiology 01/2013; · 3.69 Impact Factor
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ABSTRACT: A novel Gram-negative, heterotrophic, moderate halophilic and strictly aerobic bacterium, strain 105T, was isolated from a tidal flat of Taean in Korea. Cells were catalase- and oxidase-positive long rods that showed gliding motility. Optimum temperature, pH and salinity for the growth of strain 105T were observed at 30-37 °C, at pH 7.0-7.5, and in presence of 2-4% (w/v) NaCl, respectively. The major cellular fatty acids were iso-C15:1 G, iso-C15:0 and iso-C17:0 3-OH. Phosphatidylethanolamine and five unidentified lipids were identified as the major polar lipids. The genomic DNA G+C content of strain 105T was 42.4 mol % and MK-6 was detected as the predominant isoprenoid quinone. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 105T formed a phyletic lineage with members of the genus Muricauda. Strain 105T was most closely related to Muricauda aquimarina SW-63T (97.6%), Muricauda beolgyonensis BB-My12T (97.5%), Muricauda lutimaris SMK-108T (97.5%), Muricauda ruestringensis B1T (97.3%), Muricauda flavescens CL-SS4T (97.2%) and Muricauda olearia (96.2 %). The DNA-DNA relatedness values of strain 105T with M. aquimarina JCM 11811T, M. beolgyonensis KCTC 23501T, M. lutimaris KCTC 22173T, M. ruestringensis DSM 13258T and M. flavescens JCM 11812T were 17.2±6.0, 8.7±2.2, 3.7±0.5, 11.0±1.9 and 7.1±1.3 %, respectively. On the basis of phenotypic and molecular features, strain 105T represents a novel species of the genus Muricauda, for which the names Muricauda taeanensis sp. nov. is proposed. The type strain is 105T (=KACC 16195T = JCM 17757T).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 01/2013; · 2.11 Impact Factor
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ABSTRACT: A Gram-staining positive, facultative aerobic bacterium, designated strain RH-N24(T), was isolated from naked barley in South Korea. Cells of the isolate were observed to be motile rods by means of peritrichous flagella and showed catalase-positive and oxidase-negative reactions. Growth of strain RH-N24(T) was observed at 4-40 °C (optimum: 35-37 °C) and at pH 5.0-9.0 (optimum: pH 6.0-7.0). Chemotaxonomic data (major isoprenoid quinone: MK-7; DNA G + C content: 53.5 mol %; cell wall type: A1γ-meso-diaminopimelic acid; major fatty acids: anteiso-CB(15:0) and CB(16:0B)) supported the affiliation of the isolate to the genus Paenibacillus. The major cellular polar lipids were identified as phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and two unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences also supported the conclusion that strain RH-N24(T) belonged to the genus Paenibacillus. Comparative 16S rRNA gene sequence analysis showed that strain RH-N24(T) was most closely related to Paenibacillus hunanensis FeL05(T) and Paenibacillus illinoisensis NRRL NRS-1356(T) with similarities of 94.64 and 94.54 %, respectively. On the basis of phenotypic and molecular properties, strain RH-N24(T) represents a novel species within the genus Paenibacillus for which the name Paenibacillus hordei sp. nov. is proposed. The type strain is RH-N24(T) (=KACC 15511(T) = JCM 17570(T)).
Antonie van Leeuwenhoek 07/2012; · 2.09 Impact Factor
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ABSTRACT: Two novel Gram-negative, chemoheterotrophic and strictly aerobic bacteria, strains GY2T and SPO729T, were isolated from a tidal flat of Gwangyang bay in Korea and a marine sponge sample in the Pacific Ocean, respectively. The two strains were halotolerant, catalase- and oxidase-positive and non-motile rods. Optimum temperature and pH for growth of both strains were observed at 35°C and at pH 7.0-7.5, but optimum salinity of strain SPO729T (2-3 % (w/v)) was slightly higher than that of strain GY2T (1-2 %). The major cellular fatty acids of both strains were C16:0, iso-C15:0, iso-C17:0, iso-C17:1 ω9c, C18:1 ω7c, iso-C17:1 ω9c and iso-C11:0 3-OH. The genomic DNA G+C contents of strains GY2T and SPO729T were 55.1 and 57.9 mol %, respectively and ubiquinone 8 (Q-8) was detected as the sole respiratory quinone from the two strains. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains GY2T and SPO729T formed tight phyletic lineages with members of the genus Microbulbifer. Strain GY2T was closely related to Microbulbifer okinawensis ABABA23T (98.2 %), strain SPO729T (98.0 %) and Microbulbifer donghaiensis CN85T (97.0 %), whereas strain SPO729T was closely related to M. okinawensis ABABA23T (98.3 %) and M. donghaiensis CN85T (98.2 %). The DNA-DNA relatedness values of strain GY2T with M. okinawensis ABABA23T, strain SPO729T and M. donghaiensis CN85T were 40.0±2.1 %, 13.1±3.9 % and 16.2±5.8 %, respectively, whereas those of strain SPO729T with M. okinawensis ABABA23T and M. donghaiensis CN85T were 48.0±4.0 % and 34.6±9.3 %, respectively. On the basis of phenotypic and molecular features, two strains GY2T and SPO729T represent two novel species of the genus Microbulbifer, for which the names Microbulbifer gwangyangensis sp. nov. and Microbulbifer pacificus are proposed; the type strains are GY2T (=KACC 16189T = JCM 17800T) and SPO729T (=KCCM 42667T = JCM 14507T), respectively.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 07/2012; · 2.11 Impact Factor
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ABSTRACT: Following the 2007 oil spill in South Korean tidal flats, we sought to identify microbial players influencing the environmental fate of released polycyclic aromatic hydrocarbons (PAHs). Two years of monitoring showed that PAH concentrations in sediments declined substantially. Enrichment cultures were established using seawater and modified minimal media containing naphthalene as sole carbon source. The enriched microbial community was characterized by 16S rRNA-based DGGE profiling; sequencing selected bands indicated Alteromonas (among others) were active. Alteromonas sp. SN2 was isolated and was able to degrade naphthalene, phenanthrene, anthracene, and pyrene in laboratory-incubated microcosm assays. PCR-based analysis of DNA extracted from the sediments revealed naphthalene dioxygenase (NDO) genes of only two bacterial groups: Alteromonas and Cycloclasticus, having gentisate and catechol metabolic pathways, respectively. However, reverse transcriptase PCR-based analysis of field-fixed mRNA revealed in situ expression of only the Alteromonas-associated NDO genes; in laboratory microcosms these NDO genes were markedly induced by naphthalene addition. Analysis by GC/MS showed that naphthalene in tidal-flat samples was metabolized predominantly via the gentisate pathway; this signature metabolite was detected (0.04 μM) in contaminated field sediment. A quantitative PCR-based two-year data set monitoring Alteromonas-specific 16S rRNA genes and NDO transcripts in sea-tidal flat field samples showed that the abundance of bacteria related to strain SN2 during the winter season was 20-fold higher than in the summer season. Based on the above data, we conclude that strain SN2 and its relatives are site natives--key players in PAH degradation and adapted to winter conditions in these contaminated sea-tidal-flat sediments.
Environmental Science & Technology 06/2012; 46(14):7731-40. · 4.80 Impact Factor
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ABSTRACT: A Gram-staining-negative, dark orange-pigmented, strictly aerobic bacterium, designated strain HP12T, was isolated from a tidal flat of Hampyeong in Korea. Cells were moderately halotolerant, catalase- and oxidase-positive and non-motile rods. Growth was observed at 5-35°C (optimum, 25°C), at pH 6.0-8.5 (optimum, pH 7.0-7.5) and in the presence of 1-6 % (w/v) NaCl (optimum: 1-2 %). The major cellular fatty acids were summed feature 3 (comprising C16:1ω7c and/or iso-C15:0 2-OH), iso-C17:0 3-OH, C15:0, iso-C15:1 G and iso-C15:0. The polar lipid pattern indicated the presence of phosphatidylethanolamine and two unidentified lipids. The G+C content of the genomic DNA was 37.1 mol% and the predominant respiratory quinone was menaquinone 6. Phylogenetic inference based on 16S rRNA gene sequences showed that the strain formed a tight phyletic lineage with members of the genus Arenibacter. Strain HP12T was most closely related to Arenibacter palladensis LMG 21972T, Arenibacter troitsensis KMM 3674T and Arenibacter echinorum KMM 6032T with similarities of 98.1 %, 98.0 % and 97.8 %, respectively. However, the DNA-DNA relatedness values between strain HP12T and A. palladensis JCM 13509T, A. troitsensis KCTC 12362T and A. echinorum KCTC 22013T were 20.2±0.3 %, 22.6±0.6 % and 9.1±2.6 %, respectively. On the basis of phenotypic and molecular features, strain HP12T represents a novel species of the genus Arenibacter, for which the name Arenibacter hampyeongensis sp. nov. is proposed. The type strain is HP12T (=KACC 16193T = JCM 17788T).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 04/2012; · 2.11 Impact Factor
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ABSTRACT: A Gram-staining negative, strictly aerobic bacterium, designated 101-1T, was isolated from a sea tidal flat of Taean in Korea. The strain formed small light-yellow, smooth, and circular colonies on marine agar. Cells were weakly halophilic, motile rods showing catalase- and oxidase-positive reactions. Growth of strain 101-1T was observed at 15-40 °C (optimum: 30 °C), pH 5.0-8.0 (optimum: pH 6.5-7.0) and 1.0-9.0 % (w/v) of NaCl (optimum: 2.0-3.5 %). The G+C content of the genomic DNA was 53.3 mol%. Strain 101-1T contained ubiquinone-10 (Q-10) as the respiratory quinone and iso-C17:1 ω9c, iso-C15:0 and iso-C17:0 as major fatty acids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 101-1T formed a tight phylogenetic lineage with the members of the genus Kordiimonas and was most closely related to Kordiimonas gwangyangensis GW14-5T and Kordiimonas lacus S3-22T with 97.3 % and 96.3 % of 16S rRNA gene sequence similarities, respectively. The DNA-DNA relatedness between strain 101-1T and K. gwangyangensis GW14-5T K. lacus S3-22T was 24.8±4.4 % and 32.2±3.6 %, respectively. Based on the phenotypic and genotypic studies, strain 101-1T represents a novel species of the genus Kordiimonas, for which the name Kordiimonas aestuarii sp. nov. is proposed. The type strain is 101-1T (=KACC 16184T = JCM 17742T).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 02/2012; · 2.11 Impact Factor
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ABSTRACT: Alteromonas species are globally distributed copiotrophic bacteria in marine habitats. Among these, sea-tidal flats are distinctive: undergoing seasonal temperature and oxygen-tension changes, plus periodic exposure to petroleum hydrocarbons. Strain SN2 of the genus Alteromonas was isolated from hydrocarbon-contaminated sea-tidal flat sediment and has been shown to metabolize aromatic hydrocarbons there. Strain SN2's genomic features were analyzed bioinformatically and compared to those of Alteromonas macleodii ecotypes: AltDE and ATCC 27126. Strain SN2's genome differs from that of the other two strains in: size, average nucleotide identity value, tRNA genes, noncoding RNAs, dioxygenase gene content, signal transduction genes, and the degree to which genes collected during the Global Ocean Sampling project are represented. Patterns in genetic characteristics (e.g., GC content, GC skew, Karlin signature, CRISPR gene homology) indicate that strain SN2's genome architecture has been altered via horizontal gene transfer (HGT). Experiments proved that strain SN2 was far more cold tolerant, especially at 5°C, than the other two strains. Consistent with the HGT hypothesis, a total of 15 genomic islands in strain SN2 likely confer ecological fitness traits (especially membrane transport, aromatic hydrocarbon metabolism, and fatty acid biosynthesis) specific to the adaptation of strain SN2 to its seasonally cold sea-tidal flat habitat.
PLoS ONE 01/2012; 7(4):e35784. · 4.09 Impact Factor
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ABSTRACT: Pseudoxanthomonas spadix BD-a59, able to metabolize all six BTEX (benzene, toluene, ethylbenzene, and o-, m-, and p-xylene) compounds, was isolated from gasoline-contaminated sediment. Here, we report the complete 3.45-Mb genome sequence and annotation of strain BD-a59. These advance the understanding of strain BD-a59's genomic properties and pollutant metabolic versatility.
Journal of bacteriology 01/2012; 194(2):544. · 3.94 Impact Factor
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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 08/2011; 61(Pt 8):2023. · 2.11 Impact Factor
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ABSTRACT: Polaromonas naphthalenivorans strain CJ2 metabolizes naphthalene via the gentisate pathway and has recently been shown to carry a third copy of gentisate 1,2-dioxygenase (GDO), encoded by nagI3, within a previously uncharacterized naphthalene catabolic gene cluster. The role of this cluster (especially nagI3) in naphthalene metabolism of strain CJ2 was investigated by documenting patterns in regulation, transcription and enzyme activity. Transcriptional analysis of wild-type cells showed the third cluster to be polycistronic and that nagI3 was expressed at a relatively high level. Individual knockout mutants of all three nagI genes were constructed and their influence on both GDO activity and cell growth was evaluated. Of the three knockout strains, CJ2ΔnagI3 showed severely diminished GDO activity and grew slowest on aromatic substrates. These observations are consistent with the hypothesis that nagI3 may prevent toxic intracellular levels of gentisate from accumulating in CJ2 cells. All three nagI genes from strain CJ2 were cloned into Escherichia coli: the nagI2 and nagI3 genes were successfully overexpressed. The subunit mass of the GDOs were ~36-39 kDa, and their structures were deduced to be dimeric. The K(m) values of NagI2 and NagI3 were 31 and 10 µM, respectively, indicating that the higher affinity of NagI3 for gentisate may protect the wild-type cells from gentisate toxicity. These results provide clues for explaining why the third gene cluster, particularly the nagI3 gene, is important in strain CJ2. The organization of genes in the third gene cluster matched that of clusters in Polaromonas sp. JS666 and Leptothrix cholodnii SP-6. While horizontal gene transfer (HGT) is one hypothesis for explaining this genetic motif, gene duplication within the ancestral lineage is equally valid. The HGT hypothesis was discounted by noting that the nagI3 allele of strain CJ2 did not share high sequence identity with its homologues in Polaromonas sp. JS666 and L. cholodnii SP-6.
Microbiology 07/2011; 157(Pt 10):2891-903. · 3.06 Impact Factor
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ABSTRACT: A heterotrophic, gram-negative, prosthecate bacterium, designated strain G5(T), was isolated from a sandy beach of Taean in South Korea. Cells of strain G5(T) were aerobic, catalase- and oxidase-positive, straight to slightly curved motile rods with a single flagellum and formed yellow-orange colonies on agar. Growth occurred at 15-40 °C (optimum 25-30 °C) and pH 6-9 (optimum pH 7-8). The major cellular fatty acids were C(18 : 1)ω7c, C(17 : 0), C(16 : 0), 11-methyl C(18 : 1)ω7c, C(17 : 1)ω8c and C(17 : 1)ω6c. The polar lipid pattern indicated the presence of phosphatidylglycerol, monoglycosyldiglyceride, glucuronopyranosyldiglyceride and two unidentified glycolipids. The G+C content of the genomic DNA was 63.6 mol% and the major quinone was Q-10. Comparative 16S rRNA gene sequence analysis showed that strain G5(T) belonged to the branch containing the genera Hellea, Robiginitomaculum and Hypomonas within the family Hyphomonadaceae. Within this group, strain G5(T) was most closely related to Hellea balneolensis 26III/A02/215(T) with 95.8 % 16S rRNA gene sequence similarity. Based on its phylogenetic position and its phenotypic, chemotaxonomic and molecular properties, strain G5(T) represents a novel species of a novel genus of the family Hyphomonadaceae, for which the name Litorimonas taeanensis gen. nov., sp. nov. is proposed. The type strain is G5(T) ( = KACC 13701(T) = DSM 22008(T)).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 07/2011; 61(Pt 7):1534-8. · 2.11 Impact Factor
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ABSTRACT: A Gram-reaction-negative, strictly aerobic, non-motile bacterium, designated strain G4(T), was isolated from a sandy beach of Taean in South Korea. Cells were ovoid rods and were catalase- and oxidase-positive. Growth of strain G4(T) was determined at 15-35 °C (optimum 25-30 °C) and pH 6-8 (optimum pH 6.5-7.5). Strain G4(T) contained Q-10 as the predominant isoprenoid quinone and C(18 : 1)ω7c (59.0 %), C(18 : 1)ω7c 11-methyl (11.3 %) and C(12 : 1) 3-OH (9.8 %) as the major fatty acids. The major cellular polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified amino lipid, an unidentified phospholipid and an unidentified lipid. The DNA G+C content was 62.4 mol%. Phylogenetic and comparative analysis based on 16S rRNA gene sequences indicated that strain G4(T) fell within the family Rhodobacteraceae of Alphaproteobacteria and was most closely related to members of the genera Marinovum, Leisingera and Phaeobacter with 95.5-96.4 % sequence similarities. On the basis of phenotypic, chemotaxonomic and molecular properties, strain G4(T) represents a novel species of a novel genus within the family Rhodobacteraceae, for which the name Litorimicrobium taeanense gen. nov., sp. nov. is proposed. The type strain is G4(T) ( = KACC 13706(T) = DSM 22007(T)).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 06/2011; 61(Pt 6):1392-6. · 2.11 Impact Factor
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ABSTRACT: The presence of glycogen-accumulating organisms (GAO) has been hypothesized to be a cause of deterioration in enhanced biological phosphorus removal (EBPR) processes due to their abilities to out-compete polyphosphate-accumulating organisms (PAO). Based on 16S rRNA gene sequences, new members of uncultured gammaproteobacterial GAO (GB) were identified from sludge samples of a lab-scale sequencing batch reactor used for EBPR. The new GB formed a phylogenetic lineage (GB8) clearly distinct from the previously reported seven GB subgroups. Because the new GB8 members were not targeted by the known fluorescence in situ hybridization (FISH) oligonucleotide probes, a GB8-specific FISH probe (GB429) and a new FISH probe (GB742) targeting all eight GB subgroups were designed, and the phenotypic properties of the new GB8 members were investigated. FISH and microautoradiography approaches showed that GB429-targeted cells (GB8) were large coccobacilli (2-4 µm in size) with the ability to take up acetate under anaerobic conditions, but unable to accumulate polyphosphate under the subsequent aerobic conditions, consistent with in situ phenotypes of GB. FISH analyses on several sludge samples showed that members of GB8 were commonly detected as the majority of GB in lab- and full-scale EBPR processes. In conclusion, this study showed that members of GB8 could be a subgroup of GB with an important role in EBPR deterioration. Designs of FISH probes which hybridize with broader GB subgroups at different hierarchical levels will contribute to studies of the distributions and ecophysiologies of GB in lab- or full-scale EBPR plants.
Microbiology 05/2011; 157(Pt 8):2287-96. · 3.06 Impact Factor
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ABSTRACT: We constructed a facilitative and efficient promoter-trap vector, pCM-EGFP, for capturing and analyzing functional promoters from environmental DNA. The pCM-EGFP vector showed good chloramphenicol sensitivity and no enhanced green fluorescent protein (EGFP) gene expression. Promoter libraries were constructed for screening promoters responding to naringenin, a key molecule released from plant roots. After electroporation, E. coli transformants were incubated in LB broth containing chloramphenicol (10 μg/ml) to select against transformants with no cloned promoter. E. coli cells were sorted using flow cytometry without naringenin, and then sorted again with high fluorescence after incubation in LB broth with naringenin (1 mM) at 28 °C for 12 h. The inducible properties of approximately 400 sorted cells were evaluated, with most cells showing only strong EGFP gene expression without inducible properties. Two clones (5-4E and 15-3D) displayed naringenin inducibility, and both contained a promoter bounded by a TetR-family regulator. The regulator knock-out mutant of the 5-4E clone lost its ability to be induced by naringenin. In conclusion, the pCM-EGFP vector may be used as an efficient promoter-trap vector and a combination of the vector with flow cytometric cell sorting was demonstrated to be an useful method for screening promoters responding to specific conditions or inducers.
Journal of Basic Microbiology 02/2011; 51(1):52-60. · 1.27 Impact Factor
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ABSTRACT: Kimchi, a traditional food in the Korean culture, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process. Metagenomic DNA was extracted from kimchi samples obtained periodically and was sequenced using a 454 GS FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera: Leuconostoc, Lactobacillus, and Weissella. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, the Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 and Lactobacillus sakei subsp. sakei 23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity to Leuconostoc mesenteroides and Lactobacillus genes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophages during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.
Applied and environmental microbiology 02/2011; 77(7):2264-74. · 3.69 Impact Factor
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ABSTRACT: A moderately halophilic Gram-staining-negative bacterium, designated strain Y26(T), was isolated from a tidal flat of Taean coast in South Korea. Cells were strictly aerobic, motile cocci with a single flagellum and showed catalase- and oxidase-positive reactions. Growth of strain Y26(T) was observed at 15-35 °C (optimum 25-30°C), pH 6.0-8.0 (optimum pH6.5-7.5) and with 1.5-6.0 % (w/v) NaCl (optimum 2.0-3.0 %). The predominant fatty acids were C(18 : 1)ω7c (66.2 %), C(16 : 0) (12.4 %) and C(10 : 0) 3-OH (5.0 %) and the G+C content of the genomic DNA was 61.0 mol%. Strain Y26(T) contained ubiquinone-10 (Q-10) as the major respiratory quinone. Comparative 16S rRNA gene sequence analysis showed that strain Y26(T) formed a distinct phyletic lineage from other genera within the Roseobacter clade of the class Alphaproteobacteria and was most closely related to members of the genera Maribius, Maritimibacter and Palleronia with 93.8-94.6 % sequence similarity. On the basis of chemotaxonomic data and molecular properties, strain Y26(T) represents a novel genus, Hwanghaeicola, within the family Rhodobacteraceae, for which the name Hwanghaeicola aestuarii gen. nov., sp. nov. is proposed. The type strain is Y26(T) (=KACC 13705(T) =DSM 22009(T)).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 12/2010; 60(Pt 12):2877-81. · 2.11 Impact Factor
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ABSTRACT: A Gram-staining-negative, strictly aerobic bacterium, designated strain SD10(T), was isolated from a tidal flat of the Yellow Sea, South Korea. Cells were non-spore-forming rods that showed catalase- and oxidase-positive reactions. Growth of strain SD10(T) was observed at 15-40 °C (optimum, 25-30 °C), at pH 6.0-9.0 (optimum, pH 6.5-8.5) and in the presence of 1-10 % (w/v) NaCl. Strain SD10(T) contained ubiquinone-10 (Q-10) as a major isoprenoid quinone and C(18 : 1)ω7c (39.3 %), C(16 : 0) (20.2 %), C(17 : 0) (8.9 %) and C(17 : 1)ω6c (8.1 %) as major fatty acids. The cellular polar lipids were identified as phosphatidylglycerol, monoglycosyldiglyceride, glucuronopyranosyldiglyceride and two unidentified glycolipids. The G+C content of the genomic DNA was 55.2 mol%. Based on 16S rRNA gene sequence similarities, the strain was most closely related to Henriciella marina Iso4(T) and Maribaculum marinum P38(T), with similarities of 97.8 and 97.0 %, respectively. The DNA-DNA relatedness between strain SD10(T) and H. marina Iso4(T) was 12.0±3.2 %. A phylogenetic analysis based on 16S rRNA gene sequences showed that M. marinum P38(T) and H. marina Iso4(T) formed a monophyletic cluster and that their 16S rRNA gene sequence similarity was 98.1 %. DNA-DNA hybridization between H. marina Iso4(T) and M. marinum LMG 24711(T) was 22.9±2.7 %, indicating that the two strains belong to separate species. On the basis of chemotaxonomic data and molecular properties, we propose that strain SD10(T) represents a novel species of the genus Henriciella, for which the name Henriciella litoralis sp. nov. is proposed. The type strain is SD10(T) ( = KACC 13700(T) = DSM 22014(T)). In addition, we propose to transfer Maribaculum marinum Lai et al. 2009 to the genus Henriciella as Henriciella aquimarina nom. nov. (type strain P38(T) = CCTCC AB 208227(T) = LMG 24711(T) = MCCC 1A01086(T)), and we present an emended description of the genus Henriciella.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 04/2010; 61(Pt 4):722-7. · 2.11 Impact Factor
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ABSTRACT: To investigate the fine-scale diversity of the polyphosphate-accumulating organisms (PAO) "Candidatus Accumulibacter phosphatis" (henceforth referred to as "Ca. Accumulibacter"), two laboratory-scale sequencing batch reactors (SBRs) for enhanced biological phosphorus removal (EBPR) were operated with sodium acetate as the sole carbon source. During SBR operations, activated sludge always contained morphologically different "Ca. Accumulibacter" strains showing typical EBPR performances, as confirmed by the combined technique of fluorescence in situ hybridization (FISH) and microautoradiography (MAR). Fragments of "Ca. Accumulibacter" 16S rRNA genes were retrieved from the sludge. Phylogenetic analyses together with sequences from the GenBank database showed that "Ca. Accumulibacter" 16S rRNA genes of the EBPR sludge were clearly differentiated into four "Ca. Accumulibacter" clades, Acc-SG1, Acc-SG2, Acc-SG3, and Acc-SG4. The specific FISH probes Acc444, Acc184, Acc72, and Acc119 targeting these clades and some helpers and competitors were designed by using the ARB program. Microbial characterization by FISH analysis using specific FISH probes also clearly indicated the presence of different "Ca. Accumulibacter" cell morphotypes. Especially, members of Acc-SG3, targeted by probe Acc72, were coccobacillus-shaped cells with a size of approximately 2 to 3 mum, while members of Acc-SG1, Acc-SG2, and Acc-SG4, targeted by Acc444, Acc184, and Acc119, respectively, were coccus-shaped cells approximately 1 mum in size. Subsequently, cells targeted by each FISH probe were sorted by use of a flow cytometer, and their polyphosphate kinase 1 (ppk1) gene homologs were amplified by using a ppk1-specific PCR primer set for "Ca. Accumulibacter." The phylogenetic tree based on sequences of the ppk1 gene homologs was basically congruent with that of the 16S rRNA genes, but members of Acc-SG3 with a distinct morphology comprised two different ppk1 genes. These results suggest that "Ca. Accumulibacter" strains may be diverse physiologically and ecologically and represent distinct populations with genetically determined adaptations in EBPR systems.
Applied and environmental microbiology 04/2010; 76(12):3825-35. · 3.69 Impact Factor
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ABSTRACT: A strictly aerobic Gram-positive, moderately halophilic spore forming bacterium, designated strain SL6-1(T), was isolated from a salt lake in Xin-jiang province, China. Growth of strain SL6-1(T) was observed at NaCl concentrations of 0 approximately 20% (w/v) (the optimum being 5 approximately 7%, w/v). The peptidoglycan type of strain SL6-1(T) was Algamma-meso-diaminopimelic acid and its major cellular fatty acids were iso-C(14:0) and iso-C(16:0) and ante-iso-C(15:0). The major respiratory isoprenoid quinone was MK-7 and the G+C content of the genomic DNA was 44.5 mol%. The major cellular phospholipids were phosphatidylglycerol and diphosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SL6-1(T) formed a phylogenetic lineage within the genus Virgibacillus. Based on 16S rRNA gene sequence similarity, the strain was most closely related to Virgibacillus olivae E(30)8(T), Virgibacillus kekensis YIM kkny16(T), Virgibacillus marismortui DSM 12325(T) with 97.1%, 97.1%, and 97.0% gene sequence similarities, respectively and the sequence similarities to other related taxa were less than 96.7%. The DNA relatedness values between strain SL6-1(T) and V. olivae E(30)8(T), V. kekensis YIM kkny16(T), V. marismortui DSM 12325(T) were 16.7%, 51.0%, and 22.8%, respectively. On the basis of physiological, biochemical and phylogenetic properties, strain SL6-1(T) represents a novel species, for which the name Virgibacillus xinjiangensis sp. nov. is proposed. The type strain is SL6-1(T) (=KCTC 13128(T) =DSM 19031(T)).
The Journal of Microbiology 12/2009; 47(6):705-9. · 1.10 Impact Factor
