A single
Pectobacterium
-like strain named 13-115
T
was isolated from a specimen of diseased cucumber stem tissue collected on Jeju Island, South Korea. The strain presented a rod-like shape and was ...negative for Gram staining. When grown on R2A medium at 25 °C, strain 13-115
T
formed round, convex and white colonies. This strain showed growth at temperatures ranging from 10 to 30 °C and tolerated a pH range of 6–9. The strain could also tolerate NaCl concentrations up to 5%. Analysis of the 16S rRNA gene sequence revealed that strain 13-115
T
exhibited similarity of over 99% with
Pectobacterium brasiliense
,
P. carotovorum
,
P. polaris
, and
P. parvum
. By conducting multilocus sequence analyses using
dnaX
,
leuS
, and
recA
genes, a separate phylogenetic lineage was discovered between strain 13-115
T
and other members of the genus
Pectobacterium
. Moreover, the strain showed relatively low in silico DNA–DNA hybridization (<60.6%) and average nucleotide identity (ANI) (<94.9%) values with recognized
Pectobacterium
species. The isolate has a genome size of 5,069,478 bp and a genomic G + C content of 52.04 mol%. Major fatty acids identified in the strain included C
16:0
(28.99%), summed feature 3 (C
16:1
ω
7
c
and/or C
16:1
ω
6
c
; 28.85%), and C
18:1
ω
7
c
(19.01%). Pathogenicity assay confirmed that the novel strain induced soft rot symptoms in cucumber plants and Koch’s postulates were fulfilled. Molecular analysis and phenotypic data indicated that strain 13-115
T
could be classified as a new species within the
Pectobacterium
genus, which has been named
Pectobacterium jejuense
. The type strain is 13-115
T
(= KCTC 92800
T
= JCM 35940
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 β-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.
To detect
pv
, a loop-mediated isothermal amplification (LAMP) detection method were developed. The LAMP assay was designed to test crude plant tissue without pre-extraction, or heating incubation, ...and without advanced analysis equipment. The LAMP primers were designed by targeting an ABC transporter ATP-binding protein, this primer set was tested using the genomic DNA of
and non-
strains, and a ladder product was generated from the genomic DNA of
pv
strain but not from 12 other
species strains and 6 strains of other genera. The LAMP conditions were checked with the healthy leaves of 31 peach varieties, and no reaction was detected using either the peach leaves or the peach DNA as a template. Furthermore, the high diagnostic accuracy of the LAMP method was confirmed with 13
pv
strains isolated from various regions in Korea, with all samples exhibiting a positive reaction in LAMP assays. In particular, the LAMP method successfully detected the pathogen in diseased peach leaves and fruit in the field, and the LAMP conditions were proven to be a reliable diagnostic method for the specific detection and identification of
pv
in peach orchards.
To exploit insect-derived fungi, insects were collected from seven different regions in Korea, including Gyeongbuk, Goryeong, and several fungi were isolated from them. A fungal strain designated ...21-64-D was isolated from riparian tiger beetle (Cicindela transbaicalica) and morphologically identified as a species belonging to the genus Oidiodendron. Phylogenetic analysis using the nucleotide sequences of internal transcribed spacer (ITS) regions and the partial sequence of the large subunit of the nuclear ribosomal RNA (LSU) gene revealed the distinct phylogenetic position of the isolate among recognized Oidiodendron species including its closest neighbors O. chlamydosporicum, O. citrinum, O. maius, and O. pilicola. The hyphal and conidial morphology of the strain, particularly club-shaped hyphae, clearly differentiated it from its close relatives. Results indicated that 21-64-D is a novel species in the genus Oidiodendron, for which the name Oidiodendron clavatum sp. nov. is proposed.
A plate assay based on the visible solubilization of small substrate particles and the formation of haloes on Petri dishes, containing a mixture of different dye-labelled polysaccharides as ...substrates, provides a specific, reliable and rapid simultaneous detection of corresponding polysaccharide-degrading microorganisms. It has potential for increasing the efficacy of screening of microorganisms, utilizing different polysaccharides, in large numbers of natural samples. Diversely colored insoluble forms of amylose, xylan and hydroxyethyl-cellulose (HE-cellulose) were prepared as chromogenic substrates by using the cross-linking reagent 1,4-butanediol diglycidyl ether and the dyes Brilliant Red 3B-A, Cibacron Blue 3GA and Reactive Orange 14. Using the method, the bacteria with amylase or xylanase or cellulase or a combination of these activities were screened from soil and sludge samples, selected and identified according to 16S rDNA sequencing.
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 noshoot 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-negative, motile, rod-shaped, aerobic bacterial strain, designated S7-2-11
T
, was isolated from apple orchard soil from Gyeongsangnam-do Province, Republic of Korea, and was characterized ...taxonomically using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain S7-2-11
T
belongs to the family
Cytophagaceae
in phylum
Bacteroidetes
, and is closely related to
Spirosoma luteolum
16F6E
T
(94.2% identity),
Spirosoma knui
15J8-12
T
(92.7%), and
Spirosoma linguale
DSM 74
T
(91.0%). The G + C content of the genomic DNA of strain S7-2-11
T
was 49.8 mol%. Strain S7-2-11
T
contained summed feature 3 (C
16:1
ω7c/C
16:1
ω6c; 35.1%), C
16:1
ω5c (22.4%), C
15:0
iso (13.9%), and C
17:0
iso 3-OH (10.6%) as major cellular fatty acids, and MK-7 as the predominant respiratory quinone. The main polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid, and two unidentified polar lipids. Phenotypic and chemotaxonomic data supported the affiliation of strain S7-2-11
T
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 S7-2-11
T
represents a novel species of the genus
Spirosoma
, for which the name
Spirosoma pomorum
sp. nov. is proposed. The type strain is S7-2-11
T
(= KCTC 52726
T
= JCM 32130
T
).
A novel Gram-negative and rod-shaped bacterial strain, designated as 16F6E
T
, was isolated from a water sample. Cells were yellowish in color and catalase- and oxidase-positive. The strain grew at ...10–37°C (optimum at 25°C) but not at 4 and 42°C, and pH 5–7 (optimum at pH 7). It showed moderate resistance to gamma-ray irradiation. Comparative phylogenetic analysis showed that strain 16F6E
T
belonged to the family
Cytophagaceae
of the class
Cytophagia
. Furthermore, this isolate showed relatively low 16S rRNA gene sequence similarities (90.7–93.1%) to the members of the genus
Spirosoma
. The major fatty acids were summed feature 3 (C
16:1
ω
7
c
/C
16:1
ω
6
c
), C
16:1
ω
5
c
, C
16:0
N alcohol, and C
16:0
. The polar lipid profile indicated presence of phosphatidylethanolamine, unknown aminophospholipids, an unknown amino lipid, unknown phospholipids, and unknown polar lipids. The predominant isoprenoid quinone was MK-7. The genomic DNA G+C content of strain 16F6E
T
was 56.5 mol%. Phenotypic, phylogenetic, and chemotaxonomic properties indicated that isolate 16F6E
T
represents a novel species within the genus
Spirosoma
, for which the name
Spirosoma luteolum
sp. nov. is proposed. The type strain is 16F6E
T
(=KCTC 52199
T
=JCM 31411
T
).
A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, aerobic bacterium, designated 15J9-8
T
, 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 15J9-8
T
represented a member of the family
Cytophagaceae
, phylum
Bacteroidetes
, and was most closely related to
Spirosoma aerophilum
5516J-17
T
(96.1% similarity),
Spirosoma pulveris
JSH5-14
T
(95.6%), and
Spirosoma linguale
DSM 74
T
(95.2%). The G + C content of the genomic DNA of the isolate was 47.0 mol%. Strain 15J9-8
T
contained summed feature 3 (C
16:1
ω
7
c
/C
16:1
ω
6
c
), C
16:1
ω
5
c
, and iso-C
15:0
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 15J9-8
T
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 15J9-8
T
(=KCTC 52028
T
=JCM 31996
T
).
A Gram-staining-negative, non-motile, curved rod-shaped, aerobic bacterium, designated S1-2-4
T
, was isolated from soil in Jeollabuk-do province, Republic of Korea, and was characterized ...taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain S1-2-4
T
was a member of the family
Cytophagaceae
and most closely related to ‘
Spirosoma radiotolerans
’ DG5A (97.2%),
Spirosoma fluviale
MSd3
T
(96.4%), and
Spirosoma linguale
DSM 74
T
(96.3%). The genomic DNA G + C content of strain S1-2-4
T
was 49.7 mol%. The major fatty acids were summed feature 3 (C
16:1
ω
7
c
/C
16:1
ω
6
c
), C
16:1
ω
5
c
, and C
16:0
, and the major polar lipid was phosphatidylethanolamine. MK-7 was the predominant respiratory quinone. Phenotypic and chemotaxonomic data supported the affiliation of strain S1-2-4
T
with the genus
Spirosoma
. DNA-DNA hybridization between strain S1-2-4
T
and ‘
Spirosoma radiotolerans
’ showed relatively low DNA-DNA relatedness (31%). Strain S1-2-4
T
could be distinguished from its closest phylogenetic neighbors based on its phenotypic, genotypic, and chemotaxonomic features. Therefore, strain S1-2-4
T
represents a novel member of the genus
Spirosoma
, for which the name
Spirosoma lituiforme
sp. nov. is proposed. The type strain is S1-2-4
T
(= KCTC 52724
T
= JCM 32128
T
).
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