Woojun Park

Acinetobacter oleivorans sp. nov. is capable of adhering to and growing on diesel-oil.

A diesel-oil and n-hexadecane-degrading novel bacterial strain, designated DR1T, was isolated from a rice paddy in Deok-So, South Korea. The strain DR1T cells were Gram-negative, aerobic coccobacilli, and grew at 20–37°C with the optimal temperature of 30°C, and an optimal pH of 6–8. Interestingly, strain DR1T was highly motile (swimming and swarming motility) using its fimbriae, and generated N-acyl homoserine lactones as quorum-sensing signals. The predominant respiratory quinone as identified as ubiquinone-9 (Q-9) and DNA G+C content was 41.4 mol%. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a clade with the species A. calcoaceticus, A. haemolyticus, A. baumannii, A. baylyi, and A. beijerinckii, with which it evidenced sequence similarities of 98.2%, 97.4%, 97.2%, 97.1%, and 97.0%, respectively. DNA-DNA hybridization values between strain DR1T and other Acinetobacter spp. were all less than 20%. The physiological and taxonomic characteristics with the DNA-DNA hybridization data supported the identification of strain DR1T in the genus Acinetobacter as a novel species, for which the name Acinetobacter oleivorans sp. nov. is proposed. The type strain is DR1T (=KCTC 23045T =JCM 16667T).

Zoogloea caeni sp. nov., a floc-forming bacterium isolated from activated sludge.

Two floc-forming, nitrogen-fixing bacteria, strains EMB43(T) and EMB61, obtained from activated sludge of a domestic wastewater treatment plant in Korea, were characterized. The two strains were very closely related, sharing 99.7 % 16S rRNA gene sequence similarity and showing a level of DNA-DNA relatedness of 93 %, which suggests that they represent members of a single species. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two novel isolates formed a distinct phyletic lineage within the genus Zoogloea and were related most closely to Zoogloea resiniphila DhA-35(T) and Zoogloea oryzae A-7(T), with sequence similarities of 97.2 %. Levels of DNA-DNA relatedness between strain EMB43(T) and Z. resiniphila DhA-35(T) and Z. oryzae A-7(T) were 12.8 and 7.4 %, respectively. Cells of strains EMB43(T) and EMB61 were facultatively aerobic, rod-shaped, Gram-negative and motile by means of a polar flagellum. The strains grew at temperatures of 15-40 degrees C (optimum: 25-30 degrees C) and at pH 6.0-9.0 (optimum: pH 6.5-7.5). The predominant fatty acids were C(16 : 0), C(10 : 0) 3-OH and summed feature 3 (C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH), and the predominant polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 64.9-65.0 mol% and the major isoprenoid quinone was ubiquinone-8 (Q-8). On the basis of phenotypic, chemotaxonomic and molecular data, the isolates are considered to represent a novel species of the genus Zoogloea, for which the name Zoogloea caeni sp. nov. is proposed. The type strain is EMB43(T) (=KCTC 22084(T)=DSM 19389(T)).

Litorimonas taeanensis gen. nov., sp. nov., isolated from a sandy beach

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)).

New antioxidant with dual functions as a peroxidase and chaperone in Pseudomonas aeruginosa

Thiol-based peroxiredoxins (Prxs) are conserved throughout all kingdoms. We have found that a conserved typical 2-Cys Prx-like protein (PaPrx) from Pseudomonas aeruginosa bacteria displays diversity in its structure and apparent molecular weight (MW), and can act alternatively as a peroxidase and molecular chaperone. We have also identified a regulatory factor involved in this structural and functional switching. Exposure of P. aeruginosa to hydrogen peroxide (H2O2) causes PaPrx to convert from a high MW (HMW) complex to a low MW (LMW) form, which triggers a chaperone to peroxidase functional switch. This structural switching is primarily guided by either the thioredoxin (Trx) or glutathione (GSH) systems. Furthermore, comparison of our structural data [native and non-reducing polyacrylamide gel electrophoresis (PAGE) analysis, size exclusion chromatography (SEC) analysis, and electron microscopy (EM) observations] and enzymatic analyses (peroxidase and chaperone assay) revealed that the formation of oligomeric HMW complex structures increased chaperone activity of PaPrx. These results suggest that multimerization of PaPrx complexes promotes chaperone activity, and dissociation of the complexes into LMW species enhances peroxidase activity. Thus, the dual functions of PaPrx are clearly associated with their ability to form distinct protein structures.

Devosia geojensis sp. nov., isolated from diesel-contaminated soil in Korea.

A Gram-negative, strictly aerobic, non-spore-forming bacterium, designated strain BD-c194(T), was isolated from diesel-contaminated soil in Geoje, Korea. The cells were short, motile rods with single polar flagella. Growth of strain BD-c194(T) was observed between 15 and 45 degrees C (optimally at 30-35 degrees C) and between pH 6.0 and 9.5 (optimally at pH 7.5-9.0). The predominant fatty acids were 11-methyl C(18 : 1)omega7c, C(16 : 0), C(18 : 1)omega7c, C(18 : 0) and an unknown fatty acid (equivalent chain-length 18.814); a large amount of phosphatidylglycerol and a small amount of diphosphatidylglycerol were present as polar lipids. The G+C content of the genomic DNA was 60.8 mol% and the major isoprenoid quinone was Q-10. A comparative 16S rRNA gene sequence analysis showed that strain BD-c194(T) formed a well-defined phyletic lineage within the genus Devosia (with 100 % bootstrap support). The levels of 16S rRNA gene sequence similarity with respect to the type strains of other Devosia species ranged from 95.0 to 96.1 %. On the basis of chemotaxonomic data and molecular properties, strain BD-c194(T) represents a novel species within the genus Devosia, for which the name Devosia geojensis sp. nov. is proposed. The type strain is BD-c194(T) (=KCTC 22082(T) =DSM 19414(T)).

Luteimonas lutimaris sp. nov., isolated from a tidal flat

A Gram-staining-negative, strictly aerobic bacterium, designated strain G3(T), was isolated from a tidal flat of the Taean coast in South Korea. Cells were moderately halotolerant and non-motile rods showing catalase- and oxidase-positive reactions. Growth of strain G3(T) was observed between 15 and 40 °C (optimum 30 °C) and between pH 5.5 and 9.0 (optimum pH 6.5-7.5). Strain G3(T) contained Q-8 as the predominant lipoquinone and iso-C(15 : 0), iso-C(17 : 1)ω9c, iso-C(16 : 0) and iso-C(11 : 0) as the major fatty acids. The G+C content of the genomic DNA was 69.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain G3(T) formed a tight phylogenetic lineage with Luteimonas mephitis B1953/27.1(T) within the genus Luteimonas and was most closely related to L. mephitis B1953/27.1(T) with 98.0 % 16S rRNA gene sequence similarity. The DNA-DNA relatedness between strain G3(T) and L. mephitis B1953/27.1(T) was 35.2 ± 3.3 %. On the basis of chemotaxonomic data and molecular properties, strain G3(T) represents a novel species of the genus Luteimonas, for which the name Luteimonas lutimaris sp. nov. is proposed. The type strain is G3(T) (= KACC 14929(T) = JCM 16916(T)).

Functional switching of a novel prokaryotic 2-Cys peroxiredoxin (PpPrx) under oxidative stress

Many proteins have been isolated from eukaryotes as redox-sensitive proteins, but whether these proteins are present in prokaryotes is not clear. Redox-sensitive proteins contain disulfide bonds, and their enzymatic activity is modulated by redox in vivo. In the present study, we used thiol affinity purification and mass spectrometry to isolate and identify 19 disulfide-bond-containing proteins in Pseudomonas putida exposed to potential oxidative damages. Among these proteins, we found that a typical 2-Cys Prx-like protein (designated PpPrx) displays diversity in structure and apparent molecular weight (MW) and can act as both a peroxidase and a molecular chaperone. We also identified a regulatory factor involved in this structural and functional switching. Exposure of pseudomonads to hydrogen peroxide (H2O2) caused the protein structures of PpPrx to convert from high MW complexes to low MW forms, triggering a chaperone-to-peroxidase functional switch. This structural switching was primarily guided by the thioredoxin system. Thus, the peroxidase efficiency of PpPrx is clearly associated with its ability to form distinct protein structures in response to stress.

Hwanghaeicola aestuarii gen. nov., sp. nov., a moderately halophilic bacterium isolated from a tidal flat of the Yellow Sea.

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)).

Caenimonas koreensis gen. nov., sp. nov., isolated from activated sludge.

A Gram-negative, rod-shaped bacterium, designated strain EMB320T, was isolated from activated sludge performing enhanced biological phosphorus removal in a sequencing batch reactor. The isolate was strictly aerobic and non-motile. Growth was observed between 10 and 35 degrees C (optimum 30 degrees C) and between pH 6.0 and 9.0 (optimum pH 7.0-8.0). The predominant cellular fatty acids of strain EMB320T were C16 : 0, C18 : 1omega7c and summed feature 3 (C16 : 1omega7c and/or iso-C15 : 0 2-OH). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Strain EMB320T contained ubiquinone-8 (Q-8) as the major respiratory quinone system and 2-hydroxyputrescine and putrescine as the major polyamines, which suggests that it belongs to the Betaproteobacteria. The G+C content of the genomic DNA was 62.7 mol%. Comparative 16S rRNA gene sequence analysis showed that strain EMB320T formed a phyletic lineage distinct from other genera within the family Comamonadaceae. On the basis of chemotaxonomic data and molecular properties, strain EMB320T represents a novel genus and species within the family Comamonadaceae, for which the name Caenimonas koreensis sp. nov. is proposed. The type strain of Caenimonas koreensis is EMB320T (=KCTC 12616T =DSM 17982T).

Pusillimonas harenae sp. nov., isolated from a sandy beach, and emended description of the genus pusillimonas

A Gram-stain-negative, motile bacterium with two lateral flagella, designated strain B201(T), was isolated from beach sand from the Taean coast in South Korea. Cells were ovoid rods and positive for catalase and oxidase. Growth of strain B201(T) was observed between 15 and 45 °C (optimum, 30 °C) and between pH 5.0 and 9.0 (optimum, pH 6.0-7.5). Strain B201(T) contained ubiquinone Q-8 as the major isoprenoid quinone, but MK-6 was also present as a minor quinone. The major fatty acids of strain B201(T) were C(17:0) cyclo, C(16:0), summed feature 2 (iso-C(16:1) I/C(14:0) 3-OH and/or C(12:0) ALDE), C(12:0) and C(19:0) cyclo ω8c. The major cellular polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and three aminolipids. The genomic DNA G+C content was 53.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain formed a phyletic lineage with Pusillimonas ginsengisoli DCY25(T) within the genus Pusillimonas. Strain B201(T) was most closely related to P. ginsengisoli DCY25(T) and Pusillimonas soli MJ07(T) with similarities of 98.6 and 97.5%, respectively. However, DNA-DNA relatedness values of strain B201(T) with P. ginsengisoli DCY25(T) and P. soli MJ07(T) were 30.2±5.4 and 4.9±1.8%, respectively. On the basis of chemotaxonomic data and molecular properties, strain B201(T) represents a novel species of the genus Pusillimonas, for which the name Pusillimonas harenae sp. nov. is proposed; the type strain is B201(T) (=KACC 14927(T)=JCM 16917(T)). An emended description of the genus Pusillimonas is given.