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1.
Arch Microbiol ; 202(2): 269-273, 2020 Mar.
Article in English | MEDLINE | ID: mdl-31605155

ABSTRACT

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterium, designated HYT19T, was isolated from soil of Mountain Danxia in southern China. It showed the highest similarity of 16S rRNA gene sequence (97.0%) and formed a monophyletic clade with Fibrisoma limi BUZ 3T. Strain HYT19T grew at 16-37 °C (optimum 28-30 °C) and at pH 6-7. The draft genome size of strain HYT19T was 7.8 Mb with a DNA G+C content of 54.0 mol%. The digital DDH and average nucleotide identity values between strain HYT19T and F. limi BUZ 3T were 28.8% and 85.1%, respectively. MK-7 was the sole respiratory quinone. The major polar lipids were phosphatidylethanolamine, unidentified aminophospholipid, two unidentified aminolipids, unidentified phospholipid and unidentified lipid. The strain contained C16:1ω5c, iso-C15:0, summed feature 3 (C16:1ω6c and/or C16:1ω7c), C16:0, iso-C17:0 3-OH and anteiso-C15:0 as the major fatty acids. On the basis of phylogenetic, genomic, phenotypic and chemotaxonomic analysis, we propose a new species Fibrisoma montanum sp. nov. of genus Fibrisoma. The type strain is HYT19T (= CCTCC AB 2018342T = JCM 33105T).


Subject(s)
Cytophagaceae/genetics , Cytophagaceae/isolation & purification , Soil Microbiology , Bacterial Typing Techniques , Base Composition/genetics , China , Cytophagaceae/growth & development , Cytophagaceae/metabolism , DNA, Bacterial/genetics , Fatty Acids/metabolism , Genome, Bacterial/genetics , Phospholipids/metabolism , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Soil
2.
FEMS Microbiol Lett ; 366(14)2019 07 01.
Article in English | MEDLINE | ID: mdl-31397847

ABSTRACT

We present experimental data that complement and validate some biochemical features at the genome level in the UVC-resistant Antarctic bacterium Hymenobacter sp. UV11 strain. The genome was sequenced, assembled and annotated. It has 6 096 246 bp, a GC content of 60.6% and 5155 predicted genes. The secretome analysis, by combining in silico predictions with shotgun proteomics data, showed that UV11 strain produces extracellular proteases and carbohydrases with potential biotechnological uses. We observed the formation of outer membrane vesicles, mesosomes and carbon-storage compounds by using transmission electron microscopy. The in silico analysis of the genome revealed the presence of genes involved in the metabolism of glycogen-like molecules and starch. By HPLC-UV-Vis analysis and 1H-NMR spectra, we verified that strain UV11 produces xanthophyll-like carotenoids such as 2'-hydroxyflexixanthin, and the in silico analysis showed that this bacterium has genes involved in the biosynthesis of cathaxanthin, zeaxanthin and astaxanthin. We also found genes involved in the repair of UV-damaged DNA such as a photolyase, the nucleotide excision repair system and the production of ATP-dependent proteases that are important cellular components involved in the endurance to physiological stresses. This information will help us to better understand the ecological role played by Hymenobacter strains in the extreme Antarctic environment.


Subject(s)
Cytophagaceae/genetics , Cytophagaceae/metabolism , Genome, Bacterial , Genomics , Antarctic Regions , Chromatography, High Pressure Liquid , Computational Biology/methods , Cytophagaceae/classification , Cytophagaceae/isolation & purification , Genomics/methods , Metabolic Networks and Pathways , Pigments, Biological/chemistry , Pigments, Biological/metabolism , Radiation Tolerance
3.
Antonie Van Leeuwenhoek ; 112(11): 1705-1713, 2019 Nov.
Article in English | MEDLINE | ID: mdl-31273482

ABSTRACT

A taxonomic study using a polyphasic approach was performed on a Gram-stain negative, red-pink, aerobic, non-motile, asporogenous, rod-shaped bacterium, designated strain KIRANT, isolated from soil collected from a rice paddy field. The 16S rRNA gene sequence analysis showed that strain KIRANT is phylogenetically related to Pontibacter actiniarum KMM 6156T, Pontibacter korlensis X14-1T, Pontibacter odishensis JC130T, Pontibacter litorisediminis YKTF-7T and Pontibacter aurantiacus NP1T (97.6, 97.5, 97.3, 97.3 and 96.7% sequence similarity, respectively). The major fatty acids of strain KIRANT were identified as iso-C15:0, iso-C15:0 3-OH and summed feature 4. The predominant menaquinone was identified as MK-7. The polar lipid profile was found to consist of phosphatidylethanolamine, four unidentified phospholipids, an unidentified glycolipid, an unidentified aminolipid and four unidentified lipids. The genome of strain KIRANT has a G + C content of 48.3 mol%. The in silico DNA-DNA hybridization and average nucleotide identity values between strain KIRANT and the closely related strains P. actiniarum KMM 6156T and P. korlensis X14-1T were 21.2%/21.8% and 76.4%/75.1%, respectively. On the basis of the data from phenotypic tests and genotypic differences between strain KIRANT and its close phylogenetic relatives, strain KIRANT is concluded to represent a new species belonging to the genus Pontibacter, for which the name Pontibacter oryzae sp. nov. is proposed. The type strain is KIRANT (= KACC 19815T = JCM 32880T).


Subject(s)
Carotenoids/metabolism , Cytophagaceae/classification , Cytophagaceae/metabolism , Oryza/microbiology , Plant Diseases/microbiology , Cytophagaceae/genetics , Genomics/methods , Phenotype , Phylogeny
4.
Appl Environ Microbiol ; 85(18)2019 09 15.
Article in English | MEDLINE | ID: mdl-31253686

ABSTRACT

As classified by the Carbohydrate-Active Enzymes (CAZy) database, enzymes in glycoside hydrolase (GH) family 10 (GH10) are all monospecific or bifunctional xylanases (except a tomatinase), and no endo-ß-1,4-glucanase has been reported in the family. Here, we identified Arcticibacterium luteifluviistationis carboxymethyl cellulase (AlCMCase) as a GH10 endo-ß-1,4-glucanase. AlCMCase originated from an Arctic marine bacterium, Arcticibacterium luteifluviistationis SM1504T It shows low identity (<35%) with other GH10 xylanases. The gene encoding AlCMCase was overexpressed in Escherichia coli Biochemical characterization showed that recombinant AlCMCase is a cold-adapted and salt-tolerant enzyme. AlCMCase hydrolyzes cello- and xylo-configured substrates via an endoaction mode. However, in comparison to its significant cellulase activity, the xylanase activity of AlCMCase is negligible. Correspondingly, AlCMCase has remarkable binding capacity for cello-oligosaccharides but no obvious binding capacity for xylo-oligosaccharides. AlCMCase and its homologs are grouped into a branch separate from other GH10 xylanases in a phylogenetic tree, and two homologs also displayed the same substrate specificity as AlCMCase. These results suggest that AlCMCase and its homologs form a novel subfamily of GH10 enzymes that have robust endo-ß-1,4-glucanase activity. In addition, given the cold-adapted and salt-tolerant characters of AlCMCase, it may be a candidate biocatalyst under certain industrial conditions, such as low temperature or high salinity.IMPORTANCE Cellulase and xylanase have been widely used in the textile, pulp and paper, animal feed, and food-processing industries. Exploring novel cellulases and xylanases for biocatalysts continues to be a hot issue. Enzymes derived from the polar seas might have novel hydrolysis patterns, substrate specificities, or extremophilic properties that have great potential for both fundamental research and industrial applications. Here, we identified a novel cold-adapted and salt-tolerant endo-ß-1,4-glucanase, AlCMCase, from an Arctic marine bacterium. It may be useful in certain industrial processes, such as under low temperature or high salinity. Moreover, AlCMCase is a bifunctional representative of glycoside hydrolase (GH) family 10 that preferentially hydrolyzes ß-1,4-glucans. With its homologs, it represents a new subfamily in this family. Thus, this study sheds new light on the substrate specificity of GH10.


Subject(s)
Bacterial Proteins/genetics , Cellulase/genetics , Cytophagaceae/genetics , Gene Expression Regulation, Bacterial , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Cellulase/chemistry , Cellulase/metabolism , Cytophagaceae/metabolism , Escherichia coli/genetics , Phylogeny , Sequence Alignment
5.
Antonie Van Leeuwenhoek ; 112(7): 1047-1054, 2019 Jul.
Article in English | MEDLINE | ID: mdl-30725326

ABSTRACT

Strain U15T, rod-shaped, catalase and oxidase positive, non-motile, hot pink pigmented, Gram-negative bacterium, was isolated from soil of Udo port, Udo Island, South Korea. Growth was observed at 10-48 °C, pH 6-11, and 0% (w/v) NaCl. Optimum growth conditions are 30-40 °C, pH 7-10, and 0% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA sequences showed that strain U15T forms a distinct clade with type strains of the family Cytophagaceae, with similarities below 89%. The major polar lipids are phosphatidylethanolamine and phosphatidylserine. Strain U15T was found to contain MK-7 as the only menaquinone, and iso-C15:0, C16:1ω5c, iso-C17:0 3-OH and summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c) as the major fatty acids (> 10%). The DNA G + C content of strain U15T was determined to be 54.3 mol%. Based on the phylogenetic, phenotypic characteristics and chemotaxonomic analysis data, strain U15T (= KCTC 62116T = JCM 32361T) should be classified as representing a novel species of a novel genus within the family Cytophagaceae for which the name Tellurirhabdus rosea gen. nov., sp. nov., is proposed.


Subject(s)
Cytophagaceae/isolation & purification , Soil Microbiology , Bacterial Typing Techniques , Base Composition , Cytophagaceae/classification , Cytophagaceae/genetics , Cytophagaceae/metabolism , DNA, Bacterial/genetics , Fatty Acids/chemistry , Fatty Acids/metabolism , Phylogeny , RNA, Ribosomal, 16S/genetics , Republic of Korea
6.
Antonie Van Leeuwenhoek ; 112(7): 1019-1028, 2019 Jul.
Article in English | MEDLINE | ID: mdl-30689150

ABSTRACT

A bacterial strain, 1-3-3-3T, was isolated from a soil sample collected in Jeollabuk-do province, South Korea. Cells were observed to be Gram-stain negative, short rod-shaped and colonies to be red-pink in colour. Analysis of 16S rRNA gene sequences identified this strain as a member of the genus Hymenobacter in the family Hymenobacteraceae, with high levels of 16S rRNA sequence similarity with Hymenobacter algoricola VUG-A23aT (98.0%), Hymenobacter knuensis 16F7C-2 (97.9%), Hymenobacter fastidiosus VUG-A124T (97.1%), Hymenobacter elongatus VUG-A112T (97.0%), Hymenobacter chitinivorans Txc1T (97.0%) and Hymenobacter aquaticus 16F3PT (96.7%). Growth of strain 1-3-3-3T was observed at 10-30 °C, pH 6-8 and in the presence of 0-1.0% NaCl. The genomic G + C content was determined to be 61.6 mol %. The predominant respiratory quinone of the isolate was found to be MK-7; the major fatty acids were identified as iso-C15:0 (19.9%), summed feature 3 (C16:1ω7c/C16:1ω6c, 19.7%), summed feature 4 (iso-C17:1 I/anteiso-C17:1 B, 17.8%), C16:1ω5c (12.5%) and anteiso-C15:0 (11.2%), and the major polar lipid was found to be phosphatidylethanolamine. The phenotypic and chemotaxonomic data support the affiliation of strain 1-3-3-3T with the genus Hymenobacter. However, the DNA-DNA relatedness between the isolate and its closest phylogenetic neighbours was lower than 34%. The DNA-DNA hybridization result and the differentiating phenotypic properties clearly indicate that strain 1-3-3-3T represents a novel species in the genus Hymenobacter, for which the name Hymenobacter persicinus sp. nov. is proposed. The type strain is 1-3-3-3T (= KCTC 52742T = JCM 32191T).


Subject(s)
Cytophagaceae/isolation & purification , Bacteroidetes/classification , Bacteroidetes/genetics , Bacteroidetes/isolation & purification , Base Composition , Cytophagaceae/classification , Cytophagaceae/genetics , Cytophagaceae/metabolism , DNA, Bacterial/genetics , Fatty Acids/chemistry , Fatty Acids/metabolism , Phylogeny , RNA, Ribosomal, 16S/genetics , Republic of Korea
7.
Antonie Van Leeuwenhoek ; 111(12): 2283-2292, 2018 Dec.
Article in English | MEDLINE | ID: mdl-29934694

ABSTRACT

A polyphasic taxonomic study was carried out on strains PB105T and PB108 isolated from a grass soil in Korea. The cells of the strains were Gram-stain negative, non-spore-forming, non-motile, and rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of these strains with Bacteroidetes, which showed high pairwise sequence similarities with Hymenobacter algoricola VUG-A23aT (99.2%), Hymenobacter fastidiosus VUG-A124aT (97.4%), and Hymenobacter daecheongensis Dae14T (96.9%). The phylogenetic analysis based on 16S rRNA gene sequences showed that the strains formed a clear phylogenetic lineage with the genus Hymenobacter. The major fatty acids were identified as C15:0 iso, C15:0 anteiso, C16:1 ω5c, C15:0 iso 3-OH, C17:0 iso 3-OH, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c/t), and summed feature 4 (C17:1 anteiso B and/or C17:1 iso I). The major cellular polar lipids were identified as phosphatidylethanolamine, an unidentified aminolipid, and two unidentified lipids. The respiratory quinone was identified as MK-7 and the genomic DNA G+C content was determined to be 64.5 mol% for strain PB105T and 64.1 mol% for strain PB108. DNA-DNA hybridization value of type strain PB105T with H. algoricola VUG-A23aT was 32.3% (reciprocal 39.2). Based on the combined genotypic and phenotypic data, we propose that strains PB105T and PB108 represent a novel species of the genus Hymenobacter, for which the name Hymenobacter daejeonensis sp. nov. is proposed. The type strain is PB105T (= KCTC 52579T = JCM 31885T).


Subject(s)
Cytophagaceae/isolation & purification , Soil Microbiology , Base Composition , Cytophagaceae/classification , Cytophagaceae/genetics , Cytophagaceae/metabolism , DNA, Bacterial/genetics , Fatty Acids/chemistry , Fatty Acids/metabolism , Multilocus Sequence Typing , Phylogeny , Poaceae/growth & development , RNA, Ribosomal, 16S/genetics
8.
Curr Microbiol ; 75(6): 694-700, 2018 Jun.
Article in English | MEDLINE | ID: mdl-29362880

ABSTRACT

A Gram-negative, non-motile, rod-shaped, aerobic bacterial strain, designated S7-3-3T, was isolated from apple orchard soil in Gyeongsangnam-do province, South Korea, and was characterized taxonomically using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain S7-3-3T belonged to the family Cytophagaceae in the phylum Bacteroidetes was most closely related to Spirosoma rigui WPCB118T (94.3%), Spirosoma pulveris JSH5-14T (93.9%), and Spirosoma linguale DSM 74T (93.7%). The strain showed typical chemotaxonomic characteristics of the genus Spirosoma with a predominant respiratory quinone of menaquinone MK-7 and the major fatty acids of summed feature 3 (C16:1 ω7c/C16:1 ω6c; 43.9%) and C16:1 ω5c (25.6%). The G+C content of genomic DNA was 49.6 mol%. The polar lipid profile contained major amounts of phosphatidylethanolamine, an unidentified aminophospholipid, and an unidentified polar lipid. Phenotypic and chemotaxonomic data supported the affiliation of strain S7-3-3T with the genus Spirosoma. The results of physiological and biochemical tests showed the genotypic and phenotypic differentiation of the isolate from recognized Spirosoma species. On the basis of its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain S7-3-3T represents a novel species of the genus Spirosoma, for which the name Spirosoma agri sp. nov. is proposed. The type strain is S7-3-3T (= KCTC 52727T = JCM 32199T).


Subject(s)
Cytophagaceae/genetics , Cytophagaceae/isolation & purification , Malus , Soil Microbiology , Base Composition/genetics , Cytophagaceae/classification , Cytophagaceae/metabolism , DNA, Bacterial/genetics , Phenotype , Phospholipids/metabolism , Phylogeny , RNA, Ribosomal, 16S/genetics
9.
J Microbiol ; 56(1): 30-35, 2018 Jan.
Article in English | MEDLINE | ID: mdl-29299846

ABSTRACT

The taxonomic position of bacterial strain, designated 15J16-1T3AT, recovered from a soil sample was established using a polyphasic approach. Phylogenic analysis based on the 16S rRNA gene sequence showed that strain 15J16-1T3AT belonged to the family Cytophagaceae, phylum Bacteroidetes, and was most closely related to 'Larkinella harenae' 15J9-9 (95.9% similarity), Larkinella ripae 15J11-11T (95.6%), Larkinella bovis M2TB15T (94.7%), Larkinella arboricola Z0532T (93.9%), and Larkinella insperata LMG 22510T (93.5%). Cells were rod-shaped, Gram-stain-negative, aerobic, and nonmotile. The isolate grew on NA, R2A, TSA, but not on LB agar. The strain was able to grow at temperature range from 10°C to 30°C with an optimum at 25°C and pH 6-8. Menaquinone MK-7 was the predominant respiratory quinone. The major cellular fatty acids comprised C16:1ω5c (48.6%) and C15:0 iso (24.1%). Phosphatidylethanolamine, phosphatidylserine, and an unidentified lipid were the major polar lipids. The G + C content of the genomic DNA was 49.5 mol%. Strain 15J16-1T3AT could be distinguished from its closest phylogenetic neighbors based on its phenotypic, genotypic, and chemotaxonomic features. Therefore, the isolate is considered to represent a novel species in the genus Larkinella, for which the name Larkinella roseus sp. nov. is proposed. The type strain is 15J16-1T3AT (= KCTC 52004T = JCM 31991T).


Subject(s)
Cytophagaceae/isolation & purification , Soil Microbiology , Base Composition , Cytophagaceae/classification , Cytophagaceae/genetics , Cytophagaceae/metabolism , DNA, Bacterial/genetics , Fatty Acids/chemistry , Fatty Acids/metabolism , Phosphatidylethanolamines/metabolism , Phylogeny , RNA, Ribosomal, 16S/genetics
10.
FEMS Microbiol Ecol ; 94(2)2018 02 01.
Article in English | MEDLINE | ID: mdl-29272384

ABSTRACT

Verminephrobacter, the most common specific symbionts in the nephridia (excretory organs) of lumbricid earthworms, have been shown to improve reproduction of the garden earthworm Aporrectodea tuberculata under nutrient limitation. It is unknown how general this beneficial trait is in the Verminephrobacter-earthworm symbiosis, whether other nephridial symbionts also affect host fitness and what the mechanism of the fitness increase is. Here we report beneficial effects of Verminephrobacter and Candidatus Nephrothrix on life history traits of the compost worm Eisenia andrei, which in addition to these two symbionts also hosts Agromyces-like bacteria in its mixed nephridial community: while growth was identical between control, Verminephrobacter-free and aposymbiotic worms, control worms produced significantly more cocoons and offspring than both Verminephrobacter-free and aposymbiotic worms, confirming the reproductive benefit of Verminephrobacter in a second host with different ecology and feeding behavior. Furthermore, worms with Verminephrobacter and Ca. Nephrothrix, or with only Ca. Nephrothrix present, reached sexual maturity significantly earlier than aposymbiotic worms; this is the first evidence for a beneficial role of Ca. Nephrothrix in earthworms. Riboflavin content in cocoons and whole earthworms was unaffected by the presence or absence of nephridial symbionts, suggesting that nutritional supplementation with this vitamin does not play a major role in this symbiosis.


Subject(s)
Comamonadaceae/metabolism , Cytophagaceae/metabolism , Host Microbial Interactions/physiology , Oligochaeta/growth & development , Oligochaeta/microbiology , Animals , Comamonadaceae/genetics , Cytophagaceae/genetics , DNA, Bacterial/genetics , Pupa/physiology , Reproduction , Riboflavin/pharmacology , Symbiosis
11.
Curr Microbiol ; 75(4): 492-498, 2018 Apr.
Article in English | MEDLINE | ID: mdl-29209820

ABSTRACT

The taxonomic position of bacterial strain, designated 15J9-4T, recovered from a beach soil sample on Jeju Island, South Korea, was established using a polyphasic approach. Strain 15J9-4T was assigned to phylum Bacteroidetes within the family Cytophagaceae based on 16S rRNA gene similarities. The closest phylogenetic relatives with validly published names were Spirosoma panaciterrae Gsoil 1519T (94.2% similarity) and Spirosoma luteolum 16F6ET (94.1%). Cells were rod-shaped, Gram-stain-negative, and non-motile. The isolate grew on NA, R2A, TSA, and LB agar. The temperature limits for growth were 10 and 30 °C with an optimum at 25 °C and the pH range was 7-8. Menaquinone MK-7 was the predominant respiratory quinone. The major cellular fatty acids comprised summed feature 3 (C16:1 ω6c/C16:1 ω7c, 30.2%), C16:1 ω5c (22.2%), iso C15:0 (12.9%), and C16:0 (8.8%). Phosphatidylethanolamine was identified as the major polar lipid. The G+C content of the genomic DNA was 48.4 mol%. The results obtained from the polyphasic analyses allowed for the genotypic and phenotypic differentiation of strain 15J9-4T from recognized Spirosoma species. Therefore, the isolate is considered to represent a novel species in the genus Spirosoma, for which the name Spirosoma terrae sp. nov. is proposed. The type strain is 15J9-4T (= KCTC 52035T = JCM 31994T).


Subject(s)
Cytophagaceae/isolation & purification , Soil Microbiology , Bacterial Typing Techniques , Base Composition , Cytophagaceae/classification , Cytophagaceae/genetics , Cytophagaceae/metabolism , DNA, Bacterial/genetics , Fatty Acids/chemistry , Fatty Acids/metabolism , Phylogeny , RNA, Ribosomal, 16S/genetics , Republic of Korea , Soil/chemistry
12.
Arch Microbiol ; 200(1): 91-96, 2018 Jan.
Article in English | MEDLINE | ID: mdl-28799031

ABSTRACT

A Gram-stain-negative and yellow-pigmented bacterial strain, designated TX0653T, was isolated from an automobile evaporator core collected in Korea. The cells were aerobic and rod-shaped. The strain grew at 10-28 °C (optimum, 25 °C), at pH 6.0-7.5 (optimum, 6.5), and in the presence of 0-1% (w/v) NaCl (optimum, 0%). Phylogenetically, the strain was related to members of the genus Spirosoma (95.1-90.8% 16S rRNA sequence similarity) and distantly related to Spirosoma pulveris JSH5-14T (95.1%), Spirosoma fluviale MSd3T (95.0%), Spirosoma endophyticum DSM 26130T (94.8%), and Spirosoma linguale DSM 74T (94.6%). The major fatty acids of the strain were summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), C16:1 ω5c, iso-C15:0, iso-C17:0 3-OH, and C16:0. MK-7 was identified as the predominant menaquinone. The polar lipids profile indicated the presence of one phosphatidylethanolamine, one unidentified aminolipid, one unidentified aminophospholipid, two unidentified phospholipids, and three unidentified lipids. On the basis of the phenotypic, genotypic, and chemotaxonomic characteristics, strain TX0653T represents a novel species in the genus Spirosoma, for which the name Spirosoma metallum sp. nov. (= KACC 19278T = NBRC 112495T) is proposed.


Subject(s)
Air Microbiology , Cytophagaceae/isolation & purification , Air Conditioning , Automobiles , Bacterial Typing Techniques , Base Composition , Cytophagaceae/classification , Cytophagaceae/genetics , Cytophagaceae/metabolism , DNA, Bacterial/genetics , Fatty Acids/metabolism , Phosphatidylethanolamines/metabolism , Phospholipids/metabolism , Phylogeny , RNA, Ribosomal, 16S/genetics , Republic of Korea , Sequence Analysis, DNA
13.
Curr Microbiol ; 75(3): 328-335, 2018 Mar.
Article in English | MEDLINE | ID: mdl-29116346

ABSTRACT

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterial strain, designated S7-4-1T, was isolated from soil in Gyeongsangnam-do, South Korea and characterized using a polyphasic approach to determine its taxonomic position. Phylogenic analysis based on the 16S rRNA gene sequence showed that strain S7-4-1T belonged to the family Cytophagaceae and was most closely related to Spirosoma fluviale MSd3T (96.2%), 'Spirosoma radiotolerans' DG5A (96.0%), Spirosoma pulveris JSH5-14T (95.9%), and Spirosoma linguale DSM 74T (95.8%). The G+C content of the genomic DNA of the isolate was 49.0 mol%. The strain contained summed feature 3 (C16:1 ω7c/C16:1 ω6c; 41.0%), C16:1 ω5c (24.9%), and C15:0 iso (9.3%) as the major fatty acids, menaquinone MK-7 as the predominant respiratory quinone, and phosphatidylethanolamine and an unidentified aminophospholipid as the main polar lipids, which supported its affiliation with the genus Spirosoma. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of the isolate from recognized Spirosoma species. On the basis of its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain S7-4-1T represents a novel species of the genus Spirosoma, for which the name Spirosoma humi sp. nov. is proposed. The type strain is S7-4-1T (= KCTC 52729T = JCM 32132T).


Subject(s)
Cytophagaceae/isolation & purification , Soil Microbiology , Bacterial Typing Techniques , Base Composition , Cytophagaceae/classification , Cytophagaceae/genetics , Cytophagaceae/metabolism , DNA, Bacterial , Fatty Acids/chemistry , Fatty Acids/metabolism , Phylogeny , RNA, Ribosomal, 16S/genetics , Republic of Korea
14.
J Microbiol ; 55(12): 927-932, 2017 Dec.
Article in English | MEDLINE | ID: mdl-29214490

ABSTRACT

A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, aerobic bacterium, designated 15J9-8T, was isolated from soil on Jeju Island, Republic of Korea. The isolate was able to grow between 10 and 30°C, pH 6.5-8.5, and in presence of 0-1% (w/v) NaCl. The results of comparative 16S rRNA gene sequence analysis indicated that strain 15J9-8T represented a member of the family Cytophagaceae, phylum Bacteroidetes, and was most closely related to Spirosoma aerophilum 5516J-17T (96.1% similarity), Spirosoma pulveris JSH5-14T (95.6%), and Spirosoma linguale DSM 74T (95.2%). The G + C content of the genomic DNA of the isolate was 47.0 mol%. Strain 15J9-8T contained summed feature 3 (C16:1 ω7c/C16:1 ω6c), C16:1 ω5c, and iso-C15:0 as the major fatty acids, phosphatidylethanolamine and an unidentified aminophospholipid as the main polar lipids, and menaquinone MK-7 as the predominant respiratory quinone. On the basis of its phenotypic and genotypic properties, and phylogenetic distinctiveness, strain 15J9-8T should be classified as a representative of a novel species of the genus Spirosoma, for which the name Spirosoma migulaei sp. nov. is proposed. The type strain is 15J9-8T (=KCTC 52028T =JCM 31996T).


Subject(s)
Cytophagaceae/isolation & purification , Soil Microbiology , Bacterial Typing Techniques , Base Composition , Cytophagaceae/classification , Cytophagaceae/genetics , Cytophagaceae/metabolism , DNA, Bacterial/genetics , Fatty Acids/chemistry , Fatty Acids/metabolism , Phylogeny , RNA, Ribosomal, 16S/genetics , Republic of Korea
15.
J Microbiol ; 55(11): 850-855, 2017 Nov.
Article in English | MEDLINE | ID: mdl-29076067

ABSTRACT

A novel, Gram-staining negative, yellow pigmented bacterial strain, designated 15J11-2T, was isolated from soil sample on Jeju Island, Republic of Korea. The strain was subjected to a taxonomic study using a polyphasic approach. The strain was able to grow at temperature range from 10°C to 30°C, pH 7-8, and in presence of 0-1% (w/v) NaCl. Comparative 16S rRNA gene sequence analysis showed that strain 15J11-2T belongs to the genus Spirosoma and levels of 16S rRNA gene sequence similarity ranged from 91.5% to 89.8%. The genomic DNA G + C content of strain 15J11-2T was 46.0 mol%. The isolate contained phosphatidylethanolamine and an unidentified aminophospholipid as the main polar lipids, menaquinone MK-7 as the predominant respiratory quinone, and summed feature 3 (C16:1 ω6c/C16:1 ω7c; 39.4%), C16:1 ω5c (27.1%), and C16:0 (13.0%) as the major fatty acids, which supported the affiliation of strain 15J11-2T to the genus Spirosoma. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 15J11-2T from recognized Spirosoma species. On the basis of its phenotypic properties, genotypic distinctiveness, chemotaxonomic features, strain 15J11-2T represents a novel species of the genus Spirosoma, for which the name Spirosoma flavus sp. nov. is proposed. The type strain is 15J11-2T (= KCTC 52026T = JCM 31998T).


Subject(s)
Cytophagaceae/genetics , Cytophagaceae/isolation & purification , Soil Microbiology , Bacterial Typing Techniques , Base Composition , Cytophagaceae/classification , Cytophagaceae/metabolism , DNA, Bacterial/genetics , Fatty Acids/analysis , Phenotype , Phospholipids/analysis , Phylogeny , RNA, Ribosomal, 16S/genetics , Republic of Korea , Sequence Analysis, DNA
16.
Curr Microbiol ; 74(10): 1148-1152, 2017 Oct.
Article in English | MEDLINE | ID: mdl-28698912

ABSTRACT

A yellow-colored Gram-negative strain, Arct 1-12T, was isolated from a soil sample collected in Seoul Women's University, South Korea, and grown on R2A agar at 25 °C. Growth of strain Arct 1-12T was observed at a temperature range of 15-30 °C (optimal 25 °C), but not at 4 or 42 °C. The strain tolerated up to 1% NaCl (w/v) and displayed optimal growth in the absence of NaCl. Growth occurred at pH 6.0-9.0 (optimally at pH 7). According to the 16S rRNA gene sequence, the strain is moderately related to Spirosoma spitsbergense DSM 19989T (93.54%), S. endophyticum EX36T (93.25%), S. linguale LMG 10896T (92%), S. luteum DSM 19990T (93.16%), S. panaciterrae DSM 21099T (91.09%), S. oryzae RHs22T (90.37%), and S. rigui WPCB118T (91.54%). Chemotaxonomic analyses revealed that strain Arct 1-12T possesses MK-7 as the predominant menaquinone, a polar lipid profile consisting of phosphatidylethanolamine, an unknown aminolipid, an unknown aminophospholipid, and an unknown lipid, and iso-C15:0, C16:1 ω5c and Summed Feature 3 (C16:1 ω6c and/or C16:1 ω7c) as the major fatty acids. The DNA G+C content is 52.3 mol %. Based on polyphasic evidence, strain Arct 1-12T (=JCM 31025 T = KCTC 42814T) is classified as the type strain of a novel Spirosoma species for which the name Spirosoma areae sp. nov. is proposed.


Subject(s)
Cytophagaceae/classification , Soil Microbiology , Bacterial Typing Techniques , Base Composition , Cytophagaceae/genetics , Cytophagaceae/isolation & purification , Cytophagaceae/metabolism , DNA Barcoding, Taxonomic , Metabolomics/methods , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
17.
Curr Microbiol ; 74(7): 798-802, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28417190

ABSTRACT

A Gram-negative, short rod-shaped, gliding motile, and pale pink-pigmented bacterial strain, designated 15J9-9T, was isolated from the soil of Iho Tewoo Beach, Jeju Island, Korea, and characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 15J9-9T belonged to the family Cytophagaceae and was related to Larkinella bovis M2T2B15T (96.5% similarity), Larkinella arboricola Z0532T (95.3% similarity), and Larkinella insperata LMG 22510T (95.2% similarity). The DNA G+C content of strain 15J9-9T was 48 mol%. The detection of phosphatidylethanolamine, phosphatidylserine, two unknown aminophospholipids (APL1 and APL2), and two unknown polar lipids (L1 and L2) in polar lipid profile, menaquinone-7 as the predominant quinone, and a fatty acid profile of C16:1 ω5c, iso-C15:0, and iso-C17:0 3-OH as the major fatty acids supported the affiliation of strain 15J9-9T to the genus Larkinella. Based on its phenotypic properties and phylogenetic distinctiveness, strain 15J9-9T should be classified in the genus Larkinella as a representative of a novel species, for which the name Larkinella harenae sp. nov. is proposed. The type strain is 15J9-9T (=KCTC 42999T = JCM 31656T).


Subject(s)
Cytophagaceae/isolation & purification , Soil Microbiology , Bacterial Typing Techniques , Base Composition , Cytophagaceae/classification , Cytophagaceae/genetics , Cytophagaceae/metabolism , Fatty Acids/chemistry , Fatty Acids/metabolism , Phylogeny , Republic of Korea
18.
Curr Microbiol ; 73(5): 633-638, 2016 Nov.
Article in English | MEDLINE | ID: mdl-27460580

ABSTRACT

A gram-negative bacterium, designated FJY1(T), was isolated from a soil sample obtained from a university campus in South Korea. Examination showed that FJY1(T) was red-pigmented, aerobic, motile, and composed of nonspore-forming rods. This strain grew in a temperature range of 15-37 °C and a pH range of 7-9. Based on 16S rRNA gene sequence similarity, strain FJY1(T) was most closely related to Rufibacter roseus H359(T) and Rufibacter tibetensis 1351(T), with sequence similarities of 95.98 and 95.46 %, respectively. Its major cellular fatty acids were iso-C15:0 (18.16 %) and summed feature 4 (C17:1 iso I and C17:1 anteiso B; 15.17 %). The DNA G+C content of FJY1(T) was 49.7 mol%; its predominant quinone was MK-7; and its major polar lipid was phosphatidylethanolamine. Phylogenetic analysis and analysis of its physiological and biochemical characteristics indicated that this isolate constituted a novel species, for which we propose the name Rufibacter soli sp. nov., with the type strain FJY1(T) (=KCTC 42815(T) = JCM 31024(T)).


Subject(s)
Cytophagaceae/isolation & purification , Soil Microbiology , Base Composition , Cytophagaceae/classification , Cytophagaceae/genetics , Cytophagaceae/metabolism , DNA, Bacterial/genetics , DNA, Ribosomal/genetics , Fatty Acids/chemistry , Fatty Acids/metabolism , Phylogeny , RNA, Ribosomal, 16S/genetics , Republic of Korea
19.
Int J Syst Evol Microbiol ; 66(1): 308-314, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26508300

ABSTRACT

An aerobic, Gram-stain-negative, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped, pink-pigmented bacterium, designated strain R49T, was isolated from soil. Flexirubin-type pigments were absent. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain R49T formed a lineage within the family Cytophagaceae of the phylum Bacteroidetes that was distinct from the most closely related genera Dyadobacter (91.98-93.85 % sequence similarity), Persicitalea (88.69 %) and Runella (84.79-85.81 %). The major isoprenoid quinone was menaquinone-7 (MK-7) and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0, C16 : 1ω5c, C16 : 0 and iso-C17 : 0 3-OH. The DNA G+C content of strain R49T was 53.9 mol%. On the basis of phenotypic, genotypic and phylogenetic analysis, strain R49T represents a novel species of a new genus in the family Cytophagaceae, for which the name Rhabdobacter roseus gen. nov., sp. nov. is proposed. The type strain of Rhabdobacter roseus is R49T ( = KEMB 9005-318T = KACC 18395T = JCM 30685T).


Subject(s)
Cytophagaceae/classification , Phylogeny , Soil Microbiology , Bacterial Typing Techniques , Base Composition , Cytophagaceae/genetics , Cytophagaceae/metabolism , DNA, Bacterial/genetics , Fatty Acids/chemistry , Molecular Sequence Data , Pigmentation , RNA, Ribosomal, 16S/genetics , Republic of Korea , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
20.
PLoS One ; 10(7): e0132766, 2015.
Article in English | MEDLINE | ID: mdl-26171779

ABSTRACT

A great challenge in wastewater bioremediation is the sustained activity of viable microorganisms, which can contribute to the breakdown of waste contaminants, especially in alkaline pH conditions. Identification of extremophiles with bioremediation capability can improve the efficiency of wastewater treatment. Here, we report the discovery of an electrochemically active alkaliphilic halotolerant bacterium, Anditalea andensis ANESC-ST (=CICC10485T=NCCB 100412T), which is capable of generating bioelectricity in alkaline-saline conditions. A. andensis ANESC-ST was shown to grow in alkaline conditions between pH 7.0-11.0 and also under high salt condition (up to 4 wt% NaCl). Electrical output was further demonstrated in microbial fuel cells (MFCs) with an average current density of ~0.5 µA/cm2, even under the harsh condition of 4 wt% NaCl and pH 9.0. Subsequent introduction of secreted extracellular metabolites into MFCs inoculated with Escherichia coli or Pseudomonas aeruginosa yielded enhanced electrical output. The ability of A. andensis ANESC-ST to generate energy under alkaline-saline conditions points towards a solution for bioelectricity recovery from alkaline-saline wastewater. This is the first report of A.andensis ANESC-ST producing bioelectricity at high salt concentration and pH.


Subject(s)
Bioelectric Energy Sources/microbiology , Cytophagaceae/drug effects , Cytophagaceae/metabolism , Sodium Chloride/pharmacology , Biodegradation, Environmental/drug effects , Cytophagaceae/cytology , Dose-Response Relationship, Drug , Electric Conductivity , Electron Transport/drug effects , Hydrogen-Ion Concentration , Wastewater/microbiology
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