- Devosia rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., novel plant growth promoting members of the genus Devosia, isolated from the rhizosphere of rice plants
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Geeta Chhetri , Inhyup Kim , Minchung Kang , Jiyoun Kim , Yoonseop So , Taegun Seo
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J. Microbiol. 2022;60(1):1-10. Published online November 26, 2021
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DOI: https://doi.org/10.1007/s12275-022-1474-8
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 Abstract
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Two novel Gram-negative, aerobic, asporogenous, motile, rodshaped,
orange and white pigmented, designated as LEGU1T
and G19T, were isolated from the roots of rice plants, collected
from Goyang, South Korea. Phylogenetic analysis based on
their 16S rRNA gene sequences revealed that they belonged to
the genus Devosia and formed a different lineage and clusters
with different members of the genus Devosia. These strains
shared common chemotaxonomic features. In particular, they
had Q-10 as the sole quinone, phosphatidylglycerol, diphosphatidylglycerol
as the principal polar lipids and C16:0, C18:1
ω7c 11-methyl and summed feature 8 (comprising C18:1 ω7c/
C18:1 ω6c) as the main fatty acids. The draft genome sequences
of strains LEGU1T and G19T were 3,524,978 and 3,495,520 bp
in size, respectively. Their average nucleotide identity (ANI)
and digital DNA-DNA hybridization (dDDH) values were
72.8–81.9% and 18.7–25.1%, respectively, with each other and
type strains of related species belonging to the genus Devosia,
suggesting that these two strains represent novel species. The
G + C content of strains LEGU1T and G19T were 62.1 and
63.8%, respectively. Of the two strains, only LEGU1T produced
carotenoid and flexirubin-type pigment. Both strains
produced siderophore and indole acetic acid (IAA) in the
presence of L-tryptophan. Siderophore biosynthesis genes,
auxin responsive genes and tryptophan biosynthesis genes
were present in their genomes. The present study aimed to
determine the detailed taxonomic positions of the strains
using the modern polyphasic approach. Based on the results
of polyphasic analysis, these strains are suggested to be two
novel bacterial species within the genus Devosia. The proposed
names are D. rhizoryzae sp. nov., and Devosia oryziradicis
sp. nov., respectively. The plant growth promoting effects
of these strains suggest that they can be exploited to improve
rice crop productivity. The type strain of D. rhizoryzae
is LEGU1T (KCTC 82712T = NBRC 114485T) and D. oryziradicis
is G19T (KCTC 82688T = NBRC 114842T).
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- Erratum]Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil
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Jiyoun Kim , Geeta Chhetri , Inhyup Kim , Hyungdong Kim , Myung Kyum Kim , Taegun Seo
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J. Microbiol. 2020;58(1):79-79.
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DOI: https://doi.org/10.1007/s12275-020-9722-2
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Abstract
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In the article by Kim et al. published in Journal of Microbiology 2019; 57, 959–966, The NBRC accession number NBRC 112879T
on 33th line of 2nd paragraph in the section of ‘Description of Methylobacterium terrae sp. nov.’ on page 964 should be corrected
in NBRC 112873T.
The sentence in abstract should have read: The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and genome
sequences of the type strain 17Sr1-28T (= KCTC 52904T = NBRC 112873T) are KY939566 and CP029553, respectively.
We apologize for any inconvenience that this may have caused.
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Citations
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Philippe de Lajudie, Seyed Abdollah Mousavi, J. Peter W. Young
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International Journal of Systematic and Evolutionary Microbiology
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- Flavobacterium humi sp. nov., a flexirubin-type pigment producing bacterium, isolated from soil
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Inhyup Kim , Jiyoun Kim , Geeta Chhetri , Taegun Seo
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J. Microbiol. 2019;57(12):1079-1085. Published online November 22, 2019
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DOI: https://doi.org/10.1007/s12275-019-9350-x
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Abstract
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A yellow pigmented, Gram-stain-negative, strictly aerobic,
rod-shaped, motile by means of gliding, catalase and oxidase
positive bacterium, designated strain DS2-AT, was isolated
from soil. Growth was observed at 4–32°C (optimum, 28°C),
pH 6–9 (optimum, 7.0), and with 0–0.25% (w/v) NaCl (optimum,
0%). Phylogenetic analysis of 16S rRNA gene sequence
revealed that strain DS2-AT belonged to the genus Flavobacterium
and was most closely related to Flavobacterium
aquatile LMG 4008T (96.4%), Flavobacterium terrae DSM
18829T (95.6%), Flavobacterium vireti THG-SM1T (95.5%),
Flavobacterium inkyongense IMCC27201T (95.4%), Flavobacterium
brevivitae TTM-43T (95.2%), and Flavobacterium
cucumis DSM 18830T (95.2%). Strain DS2-AT produces flexirubin-
type pigments. The major fatty acids were iso-C15:0,
iso-C17:0 3-OH, and iso-C15:0 3-OH. The major respiratory
quinone was identified as menaquinone-6. The major polar
lipid was found to be phosphatidylethanolamine. The average
nucleotide identity values between strain DS2-AT and selected
taxa, F. aquatile LMG 4008T, F. terrae DSM 18829T,
and F. cucumis DSM 18830T, were 72, 72.7, and 71.6%, respectively.
The draft genome of strain DS2-AT has a number
of 14 contigs, scaffold N50 of 476,310 bp and a total size of
3,563,867 bp. Additionally, strain DS2-AT contains 3,127 of
gene, 41 of tRNA, 6 of rRNA, and 3 of ncRNA. The DNA G
+ C content of stain DS2-AT was 40.7 mol%. Based on phylogenetic
and phenotypic analyses, strain DS2-AT is considered
as a novel species of the genus Flavobacterium, for which
the name Flavobacterium humi sp. nov., (type strain DS2-AT
= KACC 19715T = JCM 32786T) has been proposed.
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Geeta Chhetri, Jiyoun Kim, Inhyup Kim, Minchung Kang, Byungjo Lee, Wonhee Jang, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology
.2019;[Epub] CrossRef
- Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil
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Jiyoun Kim , Geeta Chhetri , Inhyup Kim , Hyungdong Kim , Myung Kyum Kim , Taegun Seo
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J. Microbiol. 2019;57(11):959-966. Published online August 28, 2019
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DOI: https://doi.org/10.1007/s12275-019-9007-9
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Abstract
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A Gram-stain-negative, asporogenous, aerobic rods, motile by
means of a single polar flagellum, catalase- and oxidase-positive,
methylotrophic bacterium, designated 17Sr1-28T, was
isolated from gamma ray-irradiated soil. The 16S rRNA gene
sequence analysis showed that strain 17Sr1-28T was phylogenetically
related to Methylobacterium currus PR1016AT (96.8%),
Methylobacterium platani PMB02T (96.2%), Methylobacterium
aquaticum DSM 16371T (96.3%), Methylobacterium tarhaniae
N4211T (96.4%), Methylobacterium frigidaeris IER25-16T
(95.8%), and Methylobacterium organophilum JCM 2833T
(92.7%). The G+C content calculated based on genome sequence
was 71.6%. The average nucleotide identity and in
silico DNA-DNA hybridization values between strain 17Sr1-
28T and M. currus, M. platani, M. aquaticum, M. tarhaniae,
M. frigidaeris, and M. organophilum were 77.7–90.4% and
22–39.6%, respectively. The major fatty acids of strain 17Sr1-
28T were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), and
summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The predominant
quinone was ubiquinone 10 and the major polar lipids
were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine,
and phosphatidylglycerol. On the basis
of the data from phenotypic tests and genotypic differences
between strain 17Sr1-28T and its close phylogenetic relatives,
strain 17Sr1-28T represents a new species belonging to the
genus Methylobacterium, for which the name Methylobacterium
terrae sp. nov. (= KCTC 52904T = NBRC 112873T) is
proposed.
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Citations
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