• Microbiology and Biotechnology Letters
• /
• v.49 no.3
• /
• pp.384-390
• /
• 2021

A Gram-negative, aerobic, motile by gliding, and rod-shaped marine bacterium, designated CE67^T was isolated from the marine sponge Callyspongia elegans on Biyang-do in Jeju Island. The CE67^T strain grew optimally at 25℃, pH 7.5, and in the presence of 2-3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain CE67^T was related to the genus Aureivirga and had the highest 16S rRNA gene sequence similarity to the Aureivirga marina VIII.04^T type strain (96.3%). The primary fatty acids (>10%) of strain CE67^T were iso-C_15:0 (35.3%) and iso-C_17:0 3OH (21.8%). The polar lipid profile of strain CE67^T contained phosphatidylethanolamine, unidentified aminolipids, and unidentified lipids. The predominant menaquinone was MK-6. The DNA G+C content was 29.1 mol%. Based on the polyphasic taxonomic analysis, strain CE67^T was determined to be a representative novel species of the genus Aureivirga for which we propose the name Aureivirga callyspongiae sp. nov., whose strain type is CE67^T (=KCTC 42847^T=JCM 34566^T).

• Journal of Microbiology and Biotechnology
• /
• v.23 no.4
• /
• pp.444-450
• /
• 2013

A Gram-negative, strictly aerobic, non-motile, non-spore-forming, and rod-shaped bacterial strain designated FW-$6^T$ was isolated from a freshwater sample and its taxonomic position was investigated by using a polyphasic approach. Strain FW-$6^T$ grew optimally at $10-42^{\circ}C$ and at pH 7.0 on nutrient and R2A agar. Strain FW-$6^T$ displayed ${\beta}$-glucosidase activity that was responsible for its ability to transform ginsenoside $Rb_1$ (one of the dominant active components of ginseng) to Rd. On the basis of 16S rRNA gene sequence similarity, strain FW-$6^T$ was shown to belong to the family Sphingomonadaceae and was related to Novosphingobium aromaticivorans DSM $12444^T$ (98.1% sequence similarity) and N. subterraneum IFO $16086^T$ (98.0%). The G+C content of the genomic DNA was 64.4%. The major menaquinone was Q-10 and the major fatty acids were summed feature 7 (comprising $C_{18:1}{\omega}9c/{\omega}12t/{\omega}7c$), summed feature 4 (comprising $C_{16:1}{\omega}7c/iso-C_{15:0}2OH$), $C_{16:0}$, and $C_{14:0}$ 2OH. DNA and chemotaxonomic data supported the affiliation of strain FW-$6^T$ to the genus Novosphingobium. Strain FW-$6^T$ could be differentiated genotypically and phenotypically from the recognized species of the genus Novosphingobium. The isolate that has ginsenoside converting ability therefore represents a novel species, for which the name Novosphingobium ginsenosidimutans sp. nov. is proposed, with the type strain FW-$6^T$ (= KACC $16615^T$ = JCM $18202^T$).

• Journal of Microbiology and Biotechnology
• /
• v.16 no.10
• /
• pp.1554-1560
• /
• 2006

A Gram-positive, aerobic or facultative anaerobic, non motile, endospore-forming bacterial strain, designated Gsoil $114^T$, was isolated from a soil sample of a ginseng field in Pocheon Province (South Korea), and was characterized taxonomically by using a polyphasic approach. It grew well on nutrient agar medium and utilized a limited number of organic substrates as sole carbon sources, including D-xylose and some other carbohydrates, but did not utilize L-amino acids and organic acids. The isolate was positive for oxidase test but negative for catalase, and negative for degradation of macromolecules such as starch, cellulose, xylan, casein, chitin, and DNA. The G+C content of the genomic DNA was 41.8 mol%. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The major fatty acids were $anteiso-C_{15:0}$ (32.1%), $iso-C_{15:0}$ (30.5%), and $anteiso-C_{17:0}$ (30.2%). Comparative 16S rRNA gene sequence analysis showed that strain Gsoil $114^T$ fell within the radiation of the cluster comprising Bacillus species and joined Bacillus shackletonii LMG $18435^T$ with a bootstrap value of 95%. The highest 16S rRNA gene sequence similarities were found with Bacillus shackletonii LMG $18435^T$ (97.6%), Bacillus acidicola DSM $14745^T$ (96.9%), Bacillus sporothermodurans DSM $10599^T$ (96.5%), and Bacillus oleronius DSM $9356^T$ (96.5%). The phylogenetic distance from any other validly described species within the genus Bacillus was less than 96%. DNA-DNA hybridization experiments showed that the DNA-similarities between strain Gsoil $114^T$ and closest phylogenetic neighbors were less than 39%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil $114^T$ (=KCTC $13944^T$=DSMZ $18134^T$) was classified in the genus Bacillus as the type strain of a novel species, for which the name Bacillus ginsengihumi sp. nov. is proposed.

• Journal of Microbiology and Biotechnology
• /
• v.18 no.6
• /
• pp.1011-1015
• /
• 2008

A Gram-negative, strictly aerobic, motile bacterial strain, designated Gsoil $124^T$, was isolated from a soil sample taken from a ginseng field in Pocheon Province (South Korea). The isolate contained Q-10 as the predominant lipoquinone, plus $C_{18:1}\;{\omega}7c$ and summed feature 4 ($C_{16:1}\;{\omega}6c$ and/or iso-$C_{15:0}$ 2-OH) as the major fatty acids. The G+C content of the genomic DNA was 68.1 mol%, and the major polar lipids consisted of sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, and phosphatidylethanolamine. A comparative 16S rRNA gene sequence analysis showed that strain Gsoil $124^T$ was most closely related to Sphingopyxis chilensis (98.7%), Sphingopyxis alaskensis (98.2%), Sphingopyxis witflariensis (98.2%), Sphingopyxis taejonensis (98.0%), and Sphingopyxis macrogoltabida (97.6%). However, the DNA-DNA relatedness between strain Gsoil $124^T$ and its phylogenetically closest neighbors was less than 22%. Thus, on the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil $124^T$ should be classified as representing a novel species in the genus Sphingopyxis, for which the name Sphingopyxis panaciterrae sp. nov. is proposed. The type strain is Gsoil $124^T$ (=KCTC $12580^T$=LMG $24003^T$).

• Journal of Microbiology and Biotechnology
• /
• v.19 no.3
• /
• pp.250-256
• /
• 2009

Acinetobacter strain $KNF2022^T$ was isolated from tobacco plant roots during the screening of antiviral substances having inhibitory effects on Tobacco mosaic virus (TMV) and examined by phenotypic, chemotaxonomic, and genetic characterization. It was a nonmotile, Gram-negative bacterium. This strain contained Q-9 as the main respiratory quinone. The major cellular fatty acids of the isolate were 16:0, 18:1 w9c, and 16:1 w7c/15 iso 2OH. The DNA base composition was 44 mol%. Phylogenetic analysis based on the 16S rRNA sequence revealed that the isolate formed an evolutionary lineage distinct from other Acinetobacter species. Based on the evaluation of morphologic, physiologic, and chemotaxonomic characteristics, DNA-DNA hybridization values, and 16S rRNA sequence comparison, we propose the new species Acinetobacter antiviralis sp. nov., the type strain of which is $KNF2022^T$ (=KCTC $0699BP^T$).

• Journal of Microbiology and Biotechnology
• /
• v.18 no.2
• /
• pp.189-193
• /
• 2008

A Gram-positive and endospore-forming strain, $JH8^T$, was isolated from deep-sea sediment and identified as a member of the genus Paenibacillus on the basis of 16S rRNA gene sequence and phenotypic analyses. According to a phylogenetic analysis, the most closely related species was Paenibacillus wynnii LMG $22176^T$ (96.9%). Strain $JH8^T$ was also facultatively anaerobic and grew optimally at $20-25^{\circ}C$. The major cellular fatty acid was anteiso-$C_{15:0}$, and the DNA G+C content was 53.1mol%. The DNA-DNA relatedness between the isolate and Paenibacillus wynnii LMG $22176^T$ was 7.6%, indicating that strain $JH8^T$ and P. wynnii belong to different species. Based on the phylogenetic, phenotypic, and chemotaxonomic characteristics, strain $JH8^T$ would appear to belong to a novel species, for which the name Paenibacillus donghaensis sp. novo is proposed (type strain=KCTC $13049^T=LMG\;237S0^T$).

• Journal of Microbiology and Biotechnology
• /
• v.17 no.11
• /
• pp.1743-1750
• /
• 2007

Two Gram-negative, nonmotile, coccobacilli, SW-$3^T$ and SW-$100^T$, were isolated from sea water of the Yellow Sea in Korea. Strains SW-$3^T$ and SW-$100^T$ contained ubiquinone-9 (Q-9) as the predominant respiratory lipoquinone and $C_{18:1}\;{\omega}9c$ and $C_{16:0}$ as the major fatty acids. The DNA G+C contents of strains SW-$3^T$ and SW- $100^T$ were 44.1 mol% and 41.9 mol%, respectively. A neighbor-joining tree based on l6S rRNA gene sequences showed that the two isolates fell within the evolutionary radiation enclosed by the genus Acinetobacter. Strains SW-$3^T$ and SW-$100^T$ exhibited a l6S rRNA gene similarity value of 95.7% and a mean DNA-DNA relatedness level of 9.2%. Strain SW-$3^T$ exhibited l6S rRNA gene sequence similarity levels of 93.5-96.9% to the validly described Acinetobacter species and fifteen Acinetobacter genomic species. Strain SW-$100^T$ exhibited l6S rRNA gene sequence similarity levels of less than 97.0% to the other Acinetobacter species except Acinetobacter towneri DSM $14962^T$ (98.0% similarity). Strains SW-$3^T$ and SW-$100^T$ exhibited mean levels of DNA-DNA relatedness of 7.3-l6.7% to the type strains of some phylogenetically related Acinetobacter species. On the basis of phenotypic, phylogenetic, and genetic data, strains SW-$3^T$ and SW-$100^T$ were classified in the genus Acinetobacter as two distinct novel species, for which the names Acinetobacter marinus sp. novo (type strain SW-$3^T$=KCTC $12259^T$=DSM $16312^T$) and Acinetobacter seohaensis sp. novo (type strain SW-$100^T$=KCTC $12260^T$=DSM $16313^T$) are proposed, respectively.

• The Plant Pathology Journal
• /
• v.34 no.4
• /
• pp.269-285
• /
• 2018

Bacterial leaf blight is a major disease of eucalypt, especially under nursery conditions. Different bacterial species have been associated with the disease in several countries, and despite its importance worldwide, it is not clear to date whether similar disease symptoms are caused by the same or by different etiological agents. In this study, 43 bacterial strains were isolated from blighted eucalypt leaves collected in different geographic areas of Brazil and inoculated onto a susceptible eucalypt clone. Polyphasic taxonomy, including morphological, physiological, biochemical, molecular, and pathogenicity tests showed that only certain strains of Xanthomonas axonopodis caused symptoms of the disease. Strains varied in their aggressiveness, but no correlation with geographic origin was observed. MLSA-based phylogenetic analysis using concatenated dnaK, fyuA, gyrB and rpoD gene sequences allocated the strains in a well-defined clade, corresponding to Rademarker's group RG 9.6. Inoculation of nineteen plant species belonging to seven botanical families with representative strain LPF 602 showed it to be pathogenic only on Eucalyptus spp, and Corymbia spp. Based on distinct biochemical and pathogenic characteristics that differentiate the eucalypt strains from other pathovars of the X. axonopodis species, here we propose their allocation into the new pathovar X. axonopodis pv. eucalyptorum pv. nov.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.5
• /
• pp.705-711
• /
• 2007

Two novel strains of the Cytophaga-Flexibacter-Bacteroides(CFB) group, designated Gsoil $219^T$ and Gsoil $238^T$, were isolated from soil of a ginseng field of Pocheon Province in Korea. Both strains were Gram-negative, aerobic, nonmotile, nonspore-forming, and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both isolates belong to the genus Chitinophaga but were clearly separated from established species of this genus. The sequence similarities between strain Gsoil $219^T$ and type strains of the established species and between strain Gsoil $238^T$ and type strains of the established species ranged from 91.4 to 94.7% and 91.6 to 94.2%, respectively. Phenotypic and chemotaxonomic data(major menaquinone, MK-7; major fatty acids, $iso-C_{15:0}\;and\;C_{16:1}\omega5c$; major hydroxy fatty acid, $iso-C_{17:0}3-OH$; major polyamine, homospermidine) supported the affiliation of both strains Gsoil $219^T$ and Gsoil $238^T$ to the genus Chitinophaga. Furthermore, the results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of both strains from the other validated Chitinophaga species. Therefore, the two isolates represent two novel species, for which the name Chitinophaga soli sp. nov.(type strain, Gsoil $219^T=KCTC\;12650^T=DSM\;18093^T$) and Chitinophaga terrae sp. nov.(type strain, Gsoil $238^T=KCTC\;12651^T=DSM\;18078^T$) are proposed.

• Journal of Microbiology and Biotechnology
• /
• v.33 no.6
• /
• pp.753-759
• /
• 2023

The genus Paenibacillus contains a variety of biologically active compounds that have potential applications in a range of fields, including medicine, agriculture, and livestock, playing an important role in the health and economy of society. Our study focused on the bacterium SS4^T (KCTC 43402^T = GDMCC 1.3498^T), which was characterized using a polyphasic taxonomic approach. This strain was analyzed using antiSMASH, BAGEL4, and PRISM to predict the secondary metabolites. Lassopeptide clusters were found using all three analysis methods, with the possibility of secretion. Additionally, PRISM found three biosynthetic gene clusters (BGC) and predicted the structure of the product. Genome analysis indicated that glucoamylase is present in SS4^T. 16S rRNA sequence analysis showed that strain SS4^T most closely resembled Paenibacillus marchantiophytorum DSM 29850^T (98.22%), Paenibacillus nebraskensis JJ-59^T (98.19%), and Paenibacillus aceris KCTC 13870^T (98.08%). Analysis of the 16S rRNA gene sequences and Type Strain Genome Server (TYGS) analysis revealed that SS4^T belongs to the genus Paenibacillus based on the results of the phylogenetic analysis. As a result of the matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) results, SS4^T was determined to belong to the genus Paenibacillus. Comparing P. marchantiophytorum DSM 29850^T with average nucleotide identity (ANI 78.97%) and digital DNA-DNA hybridization (dDDH 23%) revealed values that were all less than the threshold for bacterial species differentiation. The results of this study suggest that strain SS4^T can be classified as a Paenibacillus andongensis species and is a novel member of the genus Paenibacillus.