The taxonomic positions of two environmental isolates from South Korea were established using a combination of genotypic and phenotypic data. The organisms, designated PB314(T) and Ho-08(T), were ...Gram-negative, rod-shaped and non-spore-forming and had chemotaxonomic properties consistent with their classification in the genus Deinococcus 16S rRNA gene tree, the highest sequence similarities being shown to the type strains of Deinococcus grandis (96.3-96.7 %) and Deinococcus indicus (96.3-96.4 %). The isolates shared relatively high 16S rRNA gene sequence similarity (98.1 %) but had a DNA-DNA relatedness value of only 22 %. Chemotaxonomic data revealed that both strains possess quinone system MK-8 as the predominant compound, C(16 : 1)omega7c and C(16 : 0) as major fatty acids and ornithine as a diamino acid in the peptidoglycan structure, corroborating our assignment of the strains to the genus Deinococcus. The results of phylogenetic analyses based on 16S rRNA gene sequences, DNA-DNA relatedness values and physiological and biochemical tests clearly demonstrated that the two strains represent distinct species. On the basis of these data, two novel species, Deinococcus aquaticus sp. nov. (type strain PB314(T) =KCTC 12552(T) =NBRC 101311(T)) and Deinococcus caeni sp. nov. (type strain Ho-08(T) =KCTC 12553(T) =NBRC 101312(T)), are proposed.
In biological particles such as Fusarium species, ice nucleation activity (INA) has been observed. Fusarium strains isolated from apple declined trees in Korea were identified with a multilocus ...sequence analysis using the tef1 and rpb1 genes. Droplet-freezing and tube-freezing assays were used to determine the INA of the strains, using Pseudomonas syringae pv. syringae KACC 21200 as a positive control and resulting in seven INA+ fungal strains that were identified as F. tricinctum (KNUF-21-F17, KNUF-21-F18, KNUF-21-F29, KNUF-21-F32, KNUF-21-F38, KNUF-21-F43, and KNUF-21-F44). The effect of Fusarium INA+ KNUF-21-F29 was compared to that of INA- strains on Chrysanthemum morifolium cv. Shinma explants. A higher callus formation and no-shoot formation were observed, suggesting that fungal INA could play a role in cold injuries and be a factor to consider in rapid apple decline. To the best of our knowledge, this is the first report of INA fungal strains isolated in Korea.
A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, aerobic bacterial strain, designated 16F3PT, was isolated from the Han River, South Korea, and characterized taxonomically using a ...polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed 16F3PT to be within the genus Hymenobacter, and most closely related to Hymenobacterchitinivorans Txc1T (98.62 %) and Hymenobacterelongatus VUG-A112T (98.46 %). The phylogenetic distance from other species of the genus Hymenobacter with validly published names was greater than 4 % (i.e. sequence similarity was less than 96.0 %). Chemotaxonomic data also supported the classification of strain 16F3PT within the genus Hymenobacter. C16 : 0 (19.8 %), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 15.4 %) and iso-C15 : 0 (13.0 %) were the major fatty acids, MK-7 was the predominant respiratory quinone, and phosphatidylethanolamine was the major polar lipid. The G+C content of the genomic DNA of strain 16F3PT was 61.9 mol%. DNA-DNA hybridization experiments showed that the values for DNA-DNA relatedness between strain 16F3PT and the phylogenetically closest neighbours were below 19 %. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain 16F3PT represents a novel species of the genus Hymenobacter, for which the name Hymenobacter aquaticus sp. nov. is proposed. The type strain is 16F3PT (=KCTC 52194T=JCM 31653T).
A bacterial strain, BT25
T
, was isolated from soil in Korea. The bacterial cells were Gram-negative and rod-shaped. Phylogenetic analysis using 16S rRNA gene sequences showed that the BT25
T
strain ...was related to the genus
Phyllobacterium
. BT25
T
was 96.6 and 96.5% similar to
Phyllobacterium brassicacearum
STM 196
T
and
Phyllobacterium myrsinacearum
DSM 5892
T
, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between BT25
T
and the two closest phylogenetic neighbors were calculated to be 78.5 and 77.7, 21.1 and 21.2%, respectively. The major cellular fatty acids were summed feature 8 (C
18:1
ω
7
c
/C
18:1
ω
6
c
) (29.3%), cyclo-C
19:0
ω
8
c
(27.5%), and C
16:0
(16.5%). The BT25
T
strain had menaquinone Q-10 as the predominant quinone, as well as phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, and phosphatidylcholine as the major polar lipids. Based on the phenotypic, phylogenetic, and chemotaxonomic data, the BT25
T
strain was classified as a novel
Phyllobacterium
species. The name
Phyllobacterium pellucidum
sp. nov. was proposed. The type strain is BT25
T
(= KCTC 62765
T
= NBRC 114381
T
).
A Gram-negative, motile by gliding, rod-shaped, aerobic bacterium, designated SD-b
T
, was isolated from a soil sample collected on Dokdo Island, South Korea. A polyphasic approach based on ...phenotypic, phylogenetic, and genomic analyses was used to characterize the new isolate. Phylogenetic analysis of 16S rRNA gene sequence showed that strain SD-b
T
belonged to the family
Sphingobacteriaceae
and most closely related to
Pedobacter psychrophilus
P4487A
T
(95.9% similarity). The isolate contained MK-7 as the predominant respiratory quinone; its main polar lipid was phosphatidylethanolamine; and the major fatty acids were summed feature 3 (C
16:1
ω
7
c
/C
16:1
ω
6
c
; 32.0%), C
15:0
iso (19.1%), C
17:0
iso 3-OH (8.3%), and C
16:0
(8.2%). The draft genome had a length of 3,842,102 bp with a G+C content of 36.0 mol%, predicting 3282 coding sequences, 3 rRNA genes, 3 ncRNAs, and 36 tRNAs genes. The digital DNA–DNA hybridization and average nucleotide identity values between strain SD-b
T
and
P. psychrophilus
LMG 29436
T
were 22.0% and 78.9%, respectively. The results of phenotypic properties, genotypic distinctiveness, and chemotaxonomic features support the discrimination of SD-b
T
from its phylogenetic relatives.
Pedobacter segetis
sp. nov. is therefore proposed with SD-b
T
(= KCTC 82351
T
= JCM 34283
T
) as the type strain.
A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, aerobic bacterium, designated 15J8-12T, was isolated from a water sample after exposure to 3 kGy of gamma radiation. The strain ...showed resistance to gamma radiation with a dose required to reduce the bacterial population 10 fold (D10) value of 4.7 kGy. The results of comparative 16S rRNA gene sequence analysis indicated that strain 15J8-12T represented a member of the family Cytophagaceae, phylum Bacteroidetes, and was most closely related to 'Spirosomafluminis' 15J17 (97.92 %) and Spirosoma arcticum R2-35T (92.22 %). The G+C content of the genomic DNA of 15J8-12T was 51.3 mol%. The detection of menaquinone MK-7 as the predominant respiratory quinone, a fatty acid profile with summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 40.5 %), C16 : 1ω5c (35.3 %), C15 : 0 iso (6.9 %) and C16 : 0 (6.8 %) as the major components and phosphatidylethanolamine as the major polar lipid also supported the affiliation of 15J8-12T with the genus Spirosoma. The DNA-DNA relatedness between 15J8-12T and 'Spirosoma fluminis' 15J17 was 27.8 %. On the basis of its phenotypic and genotypic properties, together with its phylogenetic distinctiveness, 15J8-12T should be considered to be a representative of a novel species of the genus Spirosoma, for which the name Spirosoma knui sp. nov. is proposed. The type strain is 15J8-12T (=KCTC 52510T=JCM 31407T).
A bacterial strain, 17J42-1
T
, was isolated from a soil sample collected on Jeju Island, Republic of Korea. Colonies grown on R2A agar were pink in color, and cells were Gram-stain negative, short ...and rod-shaped. Analysis of 16S rRNA gene sequences identified this strain as a member of the genus
Methylobacterium
in the family
Methylobacteriaceae
, with high levels of 16S rRNA sequence similarity shared with
Methylobacterium oxalidis
35a
T
(98.6%),
Methylobacterium jeotgali
S2R03-9
T
(97.5%), and
Methylobacterium soli
YIM 48816
T
(97.3%). Cells grew at 15–35 °C, pH 5–9, and in the presence of 0–1.0% NaCl. The genomic G + C content was 70.2 mol% based on the whole genome analysis. The predominant respiratory quinone was ubiquinone Q-10, the major fatty acid was C
18:1
ω
7
c
(85.3%), and the major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The phenotypic and chemotaxonomic data support the affiliation of strain 17J42-1
T
with the genus
Methylobacterium
. However, the DNA–DNA relatedness between the isolate and its closest phylogenetic neighbors was lower than 38%. The OrthoANI and dDDH values between strain 17J42-1
T
and the closest type strain
Methylobacterium oxalidis
NBRC 107715
T
were calculated to be 85.9% and 30.6%, respectively. The results of 16S rRNA gene sequence similarity analysis, DNA–DNA hybridization analysis, and the observed differentiating phenotypic properties from other closely related taxa clearly indicate that strain 17J42-1
T
represents a novel species in the genus
Methylobacterium,
for which the name
Methylobacterium segetis
sp. nov. is proposed. The type strain is 17J42-1
T
(= KCTC 62267
T
= JCM 33059
T
).
Polylactic acid (PLA) and polycaprolactone (PCL) are commercially available bioplastics that are exploited worldwide, and both are biodegradable. The PLA and PCL polymer-degrading activity of 30 ...fungal strains that were isolated from terrestrial environments were screened based on the formation of a clear zone around fungal colonies on agar plates containing emulsified PLA or PCL. Among them, five strains yielded positive results of biodegradation. Strains Korean Agricultural Culture Collection (KACC) 83034BP and KNUF-20-PPH03 exhibited PCL degradation; two other strains, KACC 83035BP and KNUF-20-PDG05, degraded PLA; and the fifth strain, KACC 83036BP, biodegraded both tested plastics. Based on phylogenetic analyses using various combinations of the sequences of internal transcribed spacer (ITS) regions, RPB2, LSU, CAL, and b-TUB genes, the above-mentioned strains were identified as Apiotrichum porosum, Penicillium samsonianum, Talaromyces pinophilus, Purpureocillium lilacinum, and Fusicolla acetilerea, respectively. Based on our knowledge, this is the first report on (i) plastic biodegraders among Apiotrichum and Fusicolla species, (ii) the capability of T. pinophilus to degrade biodegradable plastics, (iii) the biodegradative activity of P. samsonianum against PCL, and (iv) the accurate identification of P. lilacinum as a PLA biodegrader. Further studies should be conducted to determine how the fungal species can be utilized in Korea.
A Gram-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated TR6-04(T), was isolated from compost and characterized taxonomically by using a polyphasic ...approach. The organism grew optimally at 30 degrees Celsius and at pH 6.5-7.0. The isolate was positive for catalase and oxidase tests but negative for gelatinase, indole and H(2)S production. Comparative 16S rRNA gene sequence analysis showed that strain TR6-04(T) fell within the radiation of the cluster comprising Sphingobacterium species and clustered with Sphingobacterium mizutaii ATCC 33299(T) (96.7 % sequence similarity); the similarity to sequences of other species within the family Sphingobacteriaceae was less than 92.0 %. The G+C content of the genomic DNA was 38.7 mol%. The predominant respiratory quinone was MK-7. The major fatty acids were iso-C(15 : 0), iso-C(17 : 0) 3-OH and summed feature 4 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c). These chemotaxonomic data supported the affiliation of strain TR6-04(T) to the genus Sphingobacterium. However, on the basis of its phenotypic properties and phylogenetic distinctiveness, strain TR6-04(T) (=KCTC 12579(T)=LMG 23402(T)=CCUG 52468(T)) should be classified as the type strain of a novel species, for which the name Sphingobacterium daejeonense sp. nov. is proposed.
A Gram-negative, motile by gliding, rod-shaped, aerobic bacterium, designated S7-3-19
, was isolated from apple orchard soil in Gyeongsangnam-do Province, Republic of Korea, and characterized ...taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain S7-3-19
belonged to the family Cytophagaceae and was most closely related to Spirosoma linguale DSM 74
(96.38 %), Spirosoma fluviale MSd3
(96.38 %), Spirosoma pulveris JSH5-14
(96.35 %) and Spirosoma radiotolerans DG5A
(96.24 %). Chemotaxonomic characteristics supported the classification of strain S7-3-19
within the genus Spirosoma. Summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 46.7 %) and C16 : 1ω5c (23.8 %) were the major fatty acids. Phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified phospholipid and two unidentified lipids were the major polar lipids. Menaquinone with seven isoprene units was the predominant respiratory quinone. The G+C content of the genomic DNA of strain S7-3-19
was 48.6 mol%. On the basis of its phenotypic properties, genotypic distinctiveness and chemotaxonomic features, strain S7-3-19
represents a novel species of the genus Spirosoma, for which the name Spirosomahorti sp. nov. is proposed. The type strain is S7-3-19
(=KCTC 52728
=JCM 32131
).
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