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Lee H, Chaudhary DK, Kim DU. Sphingomonas flavescens sp. nov., isolated from soil. Arch Microbiol 2024; 206:119. [PMID: 38396312 DOI: 10.1007/s00203-024-03851-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 02/25/2024]
Abstract
An aerobic bacterium, designated as PT-12T, was isolated from soil collected from agriculture field, and its taxonomic position was validated through a comprehensive polyphasic methodology. The strain was identified as Gram-stain-negative, non-motile, rod-shaped, and catalase- and oxidase-positive. The yellow-colored colonies showed growth ability at temperature range of 18-37 °C, NaCl content of 0-1.0% (w/v), and at a pH of 6.0-8.0. The 16S rRNA gene and phylogenetic analysis showed that strain PT-12T affiliated with the genus Sphingomonas in the family Sphingomonadaceae, and displayed the highest 16S rRNA nucleotide sequence similarity with Sphingomonas limnosediminicola 03SUJ6T (98.4%). The genome size of strain PT-12T was 2,656,862 bp and the DNA G + C content estimated from genome was 63.5%. The highest values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were observed between strain PT-12T and Sphingomonas segetis YJ09T, accounting to 76.2% and 20.2%, respectively. In addition, both ANI and dDDH values between strain PT-12T and other phylogenetically related neighbors ranged between 69.6% and 76.2% and 18.4% and 20.2%, respectively. Chemotaxonomic features exhibited Q-10 as the only ubiquinone; homospermidine as the major polyamine; summed feature 8 (C18:1ω7c and/or C18:1ω6c), C16:0, and 10-methyl C18:0 as the notable fatty acids; and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, and sphingoglycolipid as dominating polar lipids. Overall, the comprehensive polyphasic data supported that strain PT-12T represents a novel bacterial species within the genus Sphingomonas. Accordingly, we propose the name Sphingomonas flavescens sp. nov. The type strain is PT-12T (= KCTC 92114T = NBRC 115717T).
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Affiliation(s)
- Hyosun Lee
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Biomaterials, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600077, India
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea.
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2
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Araujo ASF, Pertile M, Costa RM, Costa MKL, de Aviz RO, Mendes LW, de Medeiros EV, da Costa DP, Melo VMM, Pereira APDA. Short-term responses of plant growth-promoting bacterial community to the herbicides imazethapyr and flumioxazin. CHEMOSPHERE 2023; 328:138581. [PMID: 37019406 DOI: 10.1016/j.chemosphere.2023.138581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/15/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
Imazethapyr and flumioxazin are widely recommended herbicides for soybean fields due to their broad-spectrum effects. However, although both herbicides present low persistence, their potential impact on the community of plant growth-promoting bacteria (PGPB) is unclear. To address this gap, this study assessed the short-term effect of imazethapyr, flumioxazin, and their mixture on the PGPB community. Soil samples from soybean fields were treated with these herbicides and incubated for 60 days. We extracted soil DNA at 0, 15, 30, and 60 days and sequenced the 16S rRNA gene. In general, the herbicides presented temporary and short-term effects on PGPB. The relative abundance of Bradyrhizobium increased, while Sphingomonas decreased on the 30th day with the application of all herbicides. Both herbicides increased the potential function of nitrogen fixation at 15th days and decreased at 30th and 60th days of incubation. The proportions of generalists were similar (∼42%) comparing each herbicide and the control, while the proportion of specialists increased (varying from 24.9% to 27.6%) with the application of herbicides. Imazethapyr, flumioxazin and their mixture did not change the complexity and interactions of the PGPB network. In conclusion, this study showed that, in the short term, the application of imazethapyr, flumioxazin, and their mixture, at the recommended field rates, does not negatively affect the community of plant growth-promoting bacteria.
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Affiliation(s)
| | - Mariane Pertile
- Soil Quality Lab., Agricultural Science Center, Federal University of Piauí, Teresina, PI Brazil
| | - Romário Martins Costa
- Soil Quality Lab., Agricultural Science Center, Federal University of Piauí, Teresina, PI Brazil
| | | | - Rhaiana Oliveira de Aviz
- Soil Quality Lab., Agricultural Science Center, Federal University of Piauí, Teresina, PI Brazil
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo CENA-USP, Piracicaba, SP Brazil
| | - Erika Valente de Medeiros
- Laboratory of Microbiology and Enzymology-LEMA, Federal University of Agreste Pernambuco, Garanhuns 55292-270, Brazil
| | - Diogo Paes da Costa
- Laboratory of Microbiology and Enzymology-LEMA, Federal University of Agreste Pernambuco, Garanhuns 55292-270, Brazil
| | - Vania Maria Maciel Melo
- Laboratório de Ecologia Microbiana e Biotecnologia, Federal University of Ceara, Fortaleza, CE Brazil
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Siddiqi MZ, Rajivgandhi G, Lee SY, Im WT. Characterization of four novel bacterial species of the genus Sphingomonas, Sphingomonas anseongensis, Sphingomonas alba, Sphingomonas brevis and Sphingomonas hankyongi sp.nov., isolated from wet land. Int J Syst Evol Microbiol 2023; 73. [PMID: 37216283 DOI: 10.1099/ijsem.0.005884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
Four novel bacterial strains, designated as RG327T, SE158T, RB56-2T and SE220T, were isolated from wet soil in the Republic of Korea. To determine their taxonomic positions, the strains were fully characterized. On the basis of genomic information (16S rRNA gene and draft genome sequences), all four isolates represent members of the genus Sphingomonas. The draft genomes of RG327T, SE158T, RB56-2T and SE220T consisted of circular chromosomes of 2 226 119, 2 507 338, 2 593 639 and 2 548 888 base pairs with DNA G+C contents of 64.6, 63.6, 63.0 and 63.1 %, respectively. All the isolates contained ubiquinone Q-10 as the predominant quinone compound and a fatty acid profile with C16 : 0, C17 : 1ω6c, C18 : 1 2-OH, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) as the major fatty acids, supporting the affiliation of strains RG327T, SE158T, RB56-2T and SE220T to the genus Sphingomonas. The major identified polar lipids in all four novel isolates were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. Moreover, the physiological, biochemical results and low level of DNA-DNA relatedness and average nucleotide identity values allowed the phenotypic and genotypic differentiation of RG327T, SE158T, RB56-2T and SE220T from other species of the genus Sphingomonas with validly published names and indicated that they represented novel species of the genus Sphingomonas, for which the names Sphingomonas anseongensis sp. nov. (RG327T = KACC 22409T = LMG 32497T), Sphingomonas alba sp. nov. (SE158T = KACC 224408T = LMG 324498T), Sphingomonas brevis (RB56-2T = KACC 22410T = LMG 32496T) and Sphingomonas hankyongi sp. nov., (SE220T = KACC 22406T = LMG 32499T) are proposed.
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Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro Anseong-si, Gyeonggi-do 17579, Republic of Korea
- HK Ginseng Research Center, Hankyong National University, 327 Jungang-ro Anseong-si, Gyonggi-do, 13449, Republic of Korea
- AceEMzyme Co., Ltd., Room 733, 815 Daewangpangyo-ro, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13449, Republic of Korea
| | - Govindan Rajivgandhi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun YatSen University, Guangzhou 510275, PR China
| | - Soon-Youl Lee
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro Anseong-si, Gyeonggi-do 17579, Republic of Korea
- HK Ginseng Research Center, Hankyong National University, 327 Jungang-ro Anseong-si, Gyonggi-do, 13449, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro Anseong-si, Gyeonggi-do 17579, Republic of Korea
- HK Ginseng Research Center, Hankyong National University, 327 Jungang-ro Anseong-si, Gyonggi-do, 13449, Republic of Korea
- AceEMzyme Co., Ltd., Room 733, 815 Daewangpangyo-ro, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13449, Republic of Korea
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Kim I, Chhetri G, So Y, Jung Y, Park S, Seo T. Sphingomonas liriopis sp. nov., Sphingomonas donggukensis sp. nov., and Sphingomonas tagetis sp. nov., isolated from Liriope platyphylla fruit, soil, and Tagetes patula roots. Arch Microbiol 2022; 205:16. [PMID: 36477930 DOI: 10.1007/s00203-022-03360-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Three bacterial strains, designated RP10T, RMG20T, and MG17T, were isolated from Liriope platyphylla fruit (strain RP10T), soil (RMG20T), and Tagetes patula roots (MG17T) collected in Goyang, Republic of Korea. The 16S rRNA gene sequences revealed that strains RP10T, RMG20T, and MG17T were closely related to Sphingomonas melonis DSM 14444 T (highest similarity of the strain RP10T), Sphingomonas asaccharolytica DSM 10564 T (strain RMG20T), and Sphingomonas suaedae JCM 33850 T (strain MG17T) with 98.0-99.0% highest sequence similarity. The 16S rRNA gene sequences similarity between strains RP10T, RMG20T, and MG17T was 96.6-97.4%. Strains RP10T, RMG20T, MG17T, and the closely related type strains have digital DNA-DNA hybridization and average nucleotide identity values of 19.4-65.3% and 74.0-95.7%, respectively. Based on phylogenetic, biochemical, chemotaxonomic, and phenotypic data, strains RP10T, RMG20T, and MG17T are considered to represent novel species of the genus Sphingomonas, for which the name Sphingomonas liriopis sp. nov. (type strain RP10T = KACC 22357 T = TBRC 15161 T), Sphingomonas donggukensis sp. nov. (type strain RMG20T = KACC 22358 T = TBRC 15162 T), and Sphingomonas tagetis sp. nov. (type strain MG17T = KACC 22355 T = TBRC 15160 T), are proposed.
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Affiliation(s)
- Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
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Wei DW, Yang Y, Zeng Y, Wang C, Feng J. Sphingomonas baiyangensis sp. nov., isolated from water in Baiyang Lake. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, short-rod-shaped, orange-pigmented bacterial strain, designated L-1–4 w-11T, was isolated from Baiyang Lake in China. The strain grew at 15–35 °C (optimum 30 °C) and pH 7–8 (optimum pH 7) in TSA medium. The predominant polar lipids of strain L-1–4 w-11T were sphingoglycolipid, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid and three unidentified lipids; the major cellular fatty acids were C17 : 1ω6c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c); and the major respiratory quinone was ubiquinone 10 (Q-10). Strain L-1–4 w-11T showed the highest 16S rRNA gene sequence similarity to
Sphingomonas japonica
JCM 15438T (98.3 %) and
S. spermidinifaciens
GDMCC 1.657T (98.0 %). The draft genome size of strain L-1–4 w-11T was 3.3 Mbp, and the G+C content was 67.8 mol%. Digital DNA–DNA hydridization and average nucleotide identity values between the genome sequences of strain L-1–4 w-11T and
S. spermidinifaciens
GDMCC 1.657T (76.9 and 21.0 %),
S. japonica
JCM 15438T (76.0 and 19.9 %) and
S. paucimobilis
CGMCC 1.12825T (72.8 and 19.6 %) were far below the thresholds for prokaryotic conspecific assignment. With the evidence from the phylogenetic, chemotaxonomic and genotypic analyses, we propose that strain L-1–4 w-11T represents a novel
Sphingomonas
species with the name S. baiyangensis sp. nov. The type strain is L-1–4 w-11T (=CGMCC 1.13572T=JCM 33962T).
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Affiliation(s)
- Da-Wei Wei
- College of Life Science, University of Chinese Academy of Sciences, Beijing, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Yunzhen Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Yuan Zeng
- College of Life Science, University of Chinese Academy of Sciences, Beijing, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Chao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
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6
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Sphingomonas folii sp. nov., Sphingomonas citri sp. nov. and Sphingomonas citricola sp. nov., isolated from citrus phyllosphere. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three novel Gram-stain-negative, aerobic and rod-shaped bacterial strains, designated RHCKR7T, RRHST34T and RHCKR47T, were isolated from phyllosphere of healthy citrus collected in Renhua County, Guangdong Province, PR China. Phylogenetic analyses showed that they belonged to the genus
Sphingomonas
, among which both strains RHCKR7T and RRHST34T showed a close relationship with
Sphingomonas yunnanensis
YIM 003T with 16S rRNA gene similarity of 99.0 and 99.1%, respectively, and the similarity between the two novel strains was 99.2%, meanwhile strain RHCKR47T was most closely related to
Sphingomonas palmae
KACC 17591T (99.5%). Genome-derived average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between closely related novel strains RHCKR7T and RRHST34T were 90.43 and 40.80 %, respectively, and their most closely related type strain,
S. yunnanensis
YIM 003T, showed 90.43 % ANI and 40.7 % dDDH with RHCKR7T and 90.21 % and 42.9 % with RRHST34T, respectively, and the corresponding values between strain RHCKR47T and
S. palmae
KACC 17591T were 85.53 % and 29.30%, respectively. They all took C14 : 0 2-OH and summed feature 8 (C18 : 1
ω6c and/or C18 : 1
ω7c) as the major fatty acids, and ubiquinone 10 as the predominant respiratory quinone. The major polar lipids contained sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and unidentified phospholipids. sym-Homospermidine was the major polyamine. Based on phenotypic, genotypic and chemotaxonomic analyses, the new isolates should be considered as representing three novel species of the genus
Sphingomonas
, for which the names Sphingomonas folli sp. nov., Sphingomonas citri sp. nov. and Sphingomonas citricola sp. nov. are proposed with RHCKR7T (=GDMCC 1.2663T=JCM 34794T), RRHST34T (=GDMCC 1.2665T=JCM 34796T) and RHCKR47T (=GDMCC 1.2664T=JCM 34795T) as the type strains, respectively.
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Cho GY, Whang KS. Sandarakinorhabdus rubra sp. nov., and Sandarakinorhabdus oryzae sp. nov., isolated from oxidized rice paddy soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 33629948 DOI: 10.1099/ijsem.0.004722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-stain-negative, motile or non-motile, rod-shaped, facultatively aerobic strains, designated MO-4T, NP-34 and NM-18T, were isolated from oxidized rice paddy soil in Chungbuk, Republic of Korea. Colonies were circular and convex with entire margins, red in colour on R2A after 3 days at 30 °C. The three strains grew at pH 5.0-10.0 (optimum, pH 8.0), at 15-45 °C (optimum, 30 °C) and at salinities of 0-1.5 % (w/v) NaCl (optimum, 0.4 % NaCl). The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the three isolates represent members of the genus Sandarakinorhabdus and strains MO-4T and NP-34 were most closely related to Sandarakinorhabdus cyanobacteriorum TH057T (97.7 %) and Sandarakinorhabdus limnophila DSM 17366T (97.1 %). NM-18T showed highest 16S rRNA gene sequence similarities to Sandarakinorhabdus limnophila DSM 17366T (98.7 %) and Sandarakinorhabdus cyanobacteriorum TH057T (96.7 %). Genomic similarities between strains MO-4T and NM-18T and the two type strains of species of the genus Sandarakinorhabdus based on average nucleotide identity and digital DNA-DNA hybridization values were lower than the species delineation thresholds. The major fatty acids were iso-C18 : 1 ω7c and summed feature 3. The DNA G+C contents of strains MO-4T and NM-18T, obtained from genome sequencing data, were 67.6 and 66.6 mol%, respectively. On the basis of these genotypic and phenotypic characteristics, the three strains are assigned to two novel species of the genus Sandarakinorhabdus, for which the names Sandarakinorhabdus rubra sp. nov. (type strain MO-4T =KACC 21378=NBRC 114106) and Sandarakinorhabdus oryzae sp. nov. (type strain NM-18T=KACC 21379=NBRC 113957) are proposed.
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Affiliation(s)
- Geon-Yeong Cho
- Department of Microbiology & Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
| | - Kyung-Sook Whang
- Department of Microbiology & Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
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Lee JC, Whang KS. Altererythrobacter segetis sp. nov., Isolated from Farmland Soil. Curr Microbiol 2020; 78:389-396. [PMID: 33252774 DOI: 10.1007/s00284-020-02294-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/11/2020] [Indexed: 10/22/2022]
Abstract
A Gram-stain-negative bacterium, designated YJ20T, was isolated from rhizosphere soil of a spinach farmland at Shinan in Korea. Strain YJ20T was found to be aerobic, non-motile rods which can grow at 10-33 °C (optimum, 28 °C), at pH 6.5-8.5 (optimum, pH 6.5-7.5) and in the absence of NaCl. The 16S rRNA gene sequence analysis showed that strain YJ20T belongs to the genus Altererythrobacter with moderate sequence similarities to Altererythrobacter dongtanensis KCTC 22672T (96.8%), Altererythrobacter soli MN-1T (96.6%) and Altererythrobacter xinjiangensis S3-63T (96.5%). The phylogenomic analysis based on the whole-genome sequence demonstrated that strain YJ20T formed a distinct phyletic line with Altererythrobacter soli MN-1T and Altererythrobacter salegens XY-R17T showing average nucleotide identity (ANI) values of 79.4 and 77.5%, respectively. The predominant ubiquinone was identified as Q-10, and the major fatty acids were C17:1 ω6c, C18:1 ω7c and C15:0 2-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidycholin, sphingoglycolipid, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. The G+C content of the genome was determined to be 66.3 mol%. On the basis of phenotypic, chemotaxonomic properties and phylogenetic and phylogenomic analyses in this study, strain YJ20T is considered to represent a novel species in the genus Altererythrobacter, for which the name Altererythrobacter segetis sp. nov. is proposed. The type strain is YJ20T (= KACC 19554T = NBRC 113199T).
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Affiliation(s)
- Jae-Chan Lee
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea.,Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea. .,Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea.
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Lee JC, Whang KS. Lysobacter telluris sp. nov., isolated from Korean rhizosphere soil. Arch Microbiol 2020; 203:287-293. [PMID: 32920671 DOI: 10.1007/s00203-020-02032-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/04/2020] [Accepted: 09/02/2020] [Indexed: 11/28/2022]
Abstract
A Gram-stain-negative, aerobic, non-motile, non-spore-forming light-yellow-coloured rod-shaped bacterial strain, designated YJ15T, was isolated from soil at Bigeum island in Korea. Growth was observed at 10-37 °C (optimum, 28 °C), at pH 6.0-7.5 (optimum, pH 7.0) and in the absence of NaCl. Based on 16S rRNA gene sequence analysis, strain YJ15T was closely related to 'Lysobacter tongrenensis' YS037T (97.8%), Lysobacter pocheonensis Gsoil193T (96.5%) and Lysobacter daecheongensis Dae08T (95.8%) and phylogenetically grouped together with 'Lysobacter tongrenensis' YS037T, Lysobacter dokdonensis DS-58T and Lysobacter pocheonensis Gsoil 193T. The DNA-DNA relatedness between strain YJ15T and 'Lysobacter tongrenensis' KCTC 52206T was 12% and the phylogenomic analysis based on the whole genome sequence demonstrated that strain YJ20T formed a distinct phyletic line with Lysobacterlter dokdonensis DS-58T showing average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of 76.3 and 21.3%, respectively. The predominant ubiquinone was identified as Q-8, and polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified aminolipids. The major fatty acids were iso-C17:1 ω9c, iso-C15:0, iso-C16:0 and iso-C17:0. The genomic DNA G + C content was 68.2 mol %. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ15T is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter telluris sp. nov. is proposed. The type strain is YJ15T (= KACC 19552T = NBRC 113197T).
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Affiliation(s)
- Jae-Chan Lee
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea.,Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea. .,Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea.
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10
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Lee JC, Whang KS. Agriterribacter humi gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae isolated from soil of a farming field. Int J Syst Evol Microbiol 2020; 70:5123-5130. [PMID: 32812858 DOI: 10.1099/ijsem.0.004397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative bacterium, designated strain YJ03T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ03T was found to be an aerobic, non-motile and non-spore-forming bacterium which can grow at 10-33 °C (optimum, 25-28 °C), at pH 6.6-9.5 (optimum, pH 7.0-7.5) and at salinities of 0-1.0 % (w/v) NaCl (optimum, 0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ03T with the closely related relatives were in the range 93.9-92.2 %, and the results of phylogenomic analysis indicated that strain YJ03T was clearly separated from species of the genera in the family Chitinophagaceae, showing average nucleotide identity values of 68.8-64.3 %. The predominant isoprenoid quinone was identified as MK-7 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and an unidentified fatty acid with an equivalent chain-length of 13.565. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids and six unidentified lipids. The G+C content of the genome was determined to be 41.8 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences in this study, strain YJ03T is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Agriterribacter humi gen. nov., sp. nov., is proposed. The type strain of Agriterribacter humi is YJ03T (=KACC 19548T=NBRC 113195T).
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Affiliation(s)
- Jae-Chan Lee
- Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
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11
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Lee JC, Whang KS. Agromyces humi sp. nov., actinobacterium isolated from farm soil. Int J Syst Evol Microbiol 2020; 70:5032-5039. [PMID: 32790601 DOI: 10.1099/ijsem.0.004376] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive actinobacterial strain, designated ANK073T, was isolated from rhizosphere soil sampled at a spinach farming field in Shinan, Republic of Korea. Cells of strain ANK073T were found to be aerobic, non-motile, non-spore-forming rods which could grow at 20-40 °C (optimum, 30 °C), at pH 6.0-10.0 (optimum, pH 6.5-7.5) and at salinities of 0-4 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain ANK073T belongs to the genus Agromyces with high sequence similarities to Agromyces humatus CD5T (98.8 %), Agromyces tardus SJ-23T (98.5 %) and Agromyces iriomotensis IY07-20T (98.4 %). The phylogenetic analysis indicated that strain ANK073T formed a distinct phyletic line in the genus Agromyces and the results of DNA-DNA relatedness and phylogenomic analysis based on whole genome sequences demonstrated that strain ANK073T could be separated from its closest relatives in the genus Agromyces. The strain contained 2,4-diaminobutylic acid, glycine, d-glutamic acid and d-alanine in the peptidoglycan. The predominant menaquinones were identified as MK-12 and MK-11, and the major fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C15:0. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genome was determined to be 70.2 mol%. On the basis of its phenotypic and chemotaxonomic properties and the results of phylogenetic and phylogenomic analyses, strain ANK073T is considered to represent a novel species in the genus Agromyces, for which the name Agromyces humi sp. nov. is proposed. The type strain is ANK073T (=KACC 18683T=NBRC 111825T).
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Affiliation(s)
- Jae-Chan Lee
- Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
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12
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Lee JC, Whang KS. Sphingomonas segetis sp. nov., isolated from spinach farming field soil. Int J Syst Evol Microbiol 2020; 70:3905-3911. [PMID: 32501785 DOI: 10.1099/ijsem.0.004257] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative bacterium, designated strain YJ09T, was isolated from spinach farming field soil at Shinan in the Republic of Korea. Cells of strain YJ09T were found to be strictly aerobic, non-motile, non-spore-forming creamy-yellow rods which can grow at 20-37 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and at salinities of 0-0.5 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain YJ09T belongs to the genus Sphingomonas with high sequence similarities to Sphingomonas parvus GP20-2 T (98.0 %), Sphingomonas agri HKS-06T (97.7 %) and Sphingomonas lutea JS5T (97.4 %). The results of phylogenetic analysis indicated that strain YJ09T formed a distinct phyletic line in the genus Sphingomonas and the results of DNA-DNA relatedness studies demonstrated that strain YJ09T could be separated from its closest relatives in the genus Sphingomonas. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified glycolipids, an unidentified phospholipid and sphingoglycolipid. The predominant ubiquinone and polyamine components were Q-10 and spermidine, respectively. The major fatty acids were C18:1 ω7c, C16 : 0 and C16:1 ω7c and/or iso-C15 : 0 2-OH. The DNA G+C content of this novel isolate was 65.9 mol%. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ09T is considered to represent a novel species in the genus Sphingomonas, for which the name Sphingomonas segetis sp. nov. is proposed. The type strain is YJ09T (=KACC 19551T=NBRC 113247T).
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Affiliation(s)
- Jae-Chan Lee
- Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
| | - Kyung-Sook Whang
- Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
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13
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Xu Z, Zhang Y, Muhammad Y, Wang G. Sphingomonas montanisoli sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 2020; 70:3606-3613. [DOI: 10.1099/ijsem.0.004187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A soil bacterium, designated ZX9611T, was isolated from Taihang Mountain in Henan province, PR China. The strain was Gram-stain-negative and strictly aerobic. The cells were motile, rod-shaped and formed light pink-colored colonies. The 16S rRNA gene sequence of ZX9611T shared the highest similarities with those of
Sphingomonas crocodyli
CCP-7T (97.0%),
Sphingomonas jatrophae
S5-249T (96.6%) and
Sphingomonas starnbergensis
382T (95.9%). Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that ZX9611T clustered with
S. crocodyli
CCP-7T,
S. jatrophae
S5-249T and
S. starnbergensis
382T. The average nucleotide identity (ANI) values between ZX9611T and two type strains (
S. crocodyli
BCRC 81096T and
S. jatrophae
DSM 27345T) were 88.3 and 68.6% respectively. ZX9611T exhibited genome-sequence-based digital DNA–DNA hybridization (dDDH) values of 53.3 % and 15.3 %, compared with
S. crocodyli
BCRC 81096T and
S
.
jatrophae
DSM 27345T, respectively. ZX9611T had a genome size of 4.12 Mb and an average DNA G+C content of 64.8 %. ZX9611T had major fatty acids (>5 %) including summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c), C14 : 0 2-OH, C16 : 0 and summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c), and the major polyamine was sym-homospermidine. The only respiratory quinone was ubiquinone-10. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, strain ZX9611T represents a novel species of genus Sphingomonas, for which the name Sphingomonas montanisoli sp. nov. is proposed. The type strain is ZX9611T (=KCTC 72622T=CCTCC AB 2019350T).
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Affiliation(s)
- Zixiao Xu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuxiao Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yasir Muhammad
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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14
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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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15
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Segeticoccus rhizosphaerae gen. nov., sp. nov., an actinobacterium isolated from soil of a farming field. Int J Syst Evol Microbiol 2020; 70:1785-1792. [DOI: 10.1099/ijsem.0.003973] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive actinobacterial strain, designated YJ01T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ01T was aerobic, non-motile, non-spore-forming cocci with diameters of 1.5–1.9 µm, and was able to grow at 10–37 °C (optimum, 28–30 °C), at pH 4.5–9.0 (optimum, pH 7.0–8.0) and at salinities of 0–7.5 % (w/v) NaCl (optimum, 1.0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ01T with closely related relatives were in the range 96.2–92.8 %, and the results of phylogenomic analysis indicated that strain YJ01T was clearly separated from species of genera in the family
Intrasporangiaceae
showing average nucleotide identity values of 84.2–83.4 %. The predominant isoprenoid quinone was identified as MK-8(H4) and the major fatty acids were iso-C15 : 0, iso-C16:1 h, iso-C16 : 0 and anteiso-C17 : 1ω9c. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn–Gly2–d-Glu. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, an unidentified phosphatidylglycolipid, two unidentified phosphoaminolipids and an unidentified phosphoglycoaminolipid. The G+C content of the genome was 70.1 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences, strain YJ01T is considered to represent a novel species of a new genus in the family
Intrasporangiaceae
, for which the name Segeticoccus rhizosphaerae gen. nov. sp. nov. is proposed. The type strain of Segeticoccus rhizosphaerae is YJ01T (=KACC 19547T=NBRC 113173T).
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16
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Cho GY, Whang KS. Aliifodinibius saliphilus sp. nov., a moderately halophilic bacterium isolated from sediment of a crystallizing pond of a saltern. Int J Syst Evol Microbiol 2019; 70:358-363. [PMID: 31622236 DOI: 10.1099/ijsem.0.003765] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, moderately halophilic bacteria, designated strains ECH52T and KHM46, were isolated from the sediment of a grey saltern located in Sinui island at Shinan, Korea. The isolates were aerobic, non-motile, short rods and grew at 15-45 °C (optimum, 37 °C), at pH 6.0-10.0 (optimum, pH 8.0) and with 3-25 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains ECH52T and KHM46 belonged to the genus Aliifodinibius in the family Balneolaceae with sequence similarities of 94.3-98.6 % and showed the highest sequence similarity to Aliifodinibius halophilus 2W32T (98.6 %), A. sediminis YIM J21T (94.7%), A. salicampi KHM44T (94.6 %) and A. roseus YIM D15T (94.3 %). The DNA G+C content of the genomic DNA of strain ECH52T was 40.8 mol%. The predominant isoprenoid quinone was menaquinone-7 (MK-7) and the major cellular fatty acids were iso-C17 : 1ω9c, iso-C15 : 0, and C16 : 1ω7c and/or iso-C15 : 0 2-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified glycolipids and four unidentified lipids. Based on the phylogenetic, phenotypic and chemotaxonomic data, strains ECH52T and KHM46 are considered to represent a novel species of the genus Aliifodinibius , for which the name Aliifodinibius saliphilus sp. nov. is proposed. The type strain is ECH52T (=KACC 19126T=NBRC 112664T).
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Affiliation(s)
- Geon-Yeong Cho
- Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
| | - Kyung-Sook Whang
- Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
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17
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Dada N, Lol JC, Benedict AC, López F, Sheth M, Dzuris N, Padilla N, Lenhart A. Pyrethroid exposure alters internal and cuticle surface bacterial communities in Anopheles albimanus. THE ISME JOURNAL 2019; 13:2447-2464. [PMID: 31171859 PMCID: PMC6776023 DOI: 10.1038/s41396-019-0445-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/02/2019] [Accepted: 05/09/2019] [Indexed: 01/19/2023]
Abstract
A deeper understanding of the mechanisms underlying insecticide resistance is needed to mitigate its threat to malaria vector control. Following previously identified associations between mosquito microbiota and insecticide resistance, we demonstrate for the first time, the effects of pyrethroid exposure on the microbiota of F1 progeny of field-collected Anopheles albimanus. Larval and adult mosquitoes were exposed to the pyrethroids alphacypermethrin (only adults), permethrin, and deltamethrin. While there were no significant differences in bacterial composition between insecticide-resistant and insecticide-susceptible mosquitoes, bacterial composition between insecticide-exposed and non-exposed mosquitoes was significantly different for alphacypermethrin and permethrin exposure. Along with other bacterial taxa not identified to species, Pantoea agglomerans (a known insecticide-degrading bacterial species) and Pseudomonas fragi were more abundant in insecticide-exposed compared to non-exposed adults, demonstrating that insecticide exposure can alter mosquito bacterial communities. We also show for the first time that the cuticle surfaces of both larval and adult An. albimanus harbor more diverse bacterial communities than their internal microbial niches. Together, these findings demonstrate how insecticide pressure could be selecting for certain bacteria within mosquitoes, especially insecticide-metabolizing bacteria, thus potentially contributing to insecticide resistance.
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Affiliation(s)
- Nsa Dada
- Entomology Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, United States Centers for Disease Control and Prevention, Atlanta, GA, USA.
- American Society for Microbiology, Washington, DC, USA.
| | - Juan C Lol
- Grupo de Biología y Control de Vectores, Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala, Guatemala
| | - Ana Cristina Benedict
- Grupo de Biología y Control de Vectores, Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala, Guatemala
| | - Francisco López
- Grupo de Biología y Control de Vectores, Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala, Guatemala
| | - Mili Sheth
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging & Zoonotic Infectious Diseases, United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nicole Dzuris
- Entomology Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Norma Padilla
- Grupo de Biología y Control de Vectores, Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala, Guatemala
| | - Audrey Lenhart
- Entomology Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, United States Centers for Disease Control and Prevention, Atlanta, GA, USA
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18
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Feng GD, Wang YH, Zhang XJ, Chen WD, Zhang J, Xiong X, Zhu HH. Sphingomonas lenta sp. nov., a slowly growing bacterium isolated from an abandoned lead–zinc mine. Int J Syst Evol Microbiol 2019; 69:2214-2219. [DOI: 10.1099/ijsem.0.003427] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Guang-Da Feng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Yong-Hong Wang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Xian-Jiao Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Wen-Di Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Jun Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Xiong Xiong
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Hong-Hui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
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19
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Lee JC, Whang KS. Aquibacillus sediminis sp. nov., a moderately halophilic bacterium isolated from saltern soil. Int J Syst Evol Microbiol 2019; 69:3121-3127. [PMID: 31339480 DOI: 10.1099/ijsem.0.003599] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, moderately halophilic bacterium, designated strain BH258T, was isolated from solar saltern sediment sampled at Shinan in the Republic of Korea. Cells of strain BH258T were found to be strictly aerobic, motile, endospore-forming rods which could grow at 15-45 °C (optimum, 35 °C), at pH 5.5-9.0 (pH 7.0) and at salinities of 0.5-20 % (w/v) NaCl (7-10%). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH258T belongs to the genus Aquibacillus, showing highest sequence similarity to Aquibacillus koreensis BH30097T (96.1 %), Aquibacillus albus YIM 93624T (95.9 %), Aquibacillus halophilus B6BT (95.6 %) and Aquibacillus salifodinae WSY08-1T (95.1 %). The predominant isoprenoid quinone was identified as menaquinone-7, and the cell-wall peptidoglycan was found to contain meso-diaminopimelic acid as the diagnostic diamino acid. The major fatty acids were identified as anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C15 : 0. The major polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol and three unidentified phospholipids. The DNA G+C content of this novel isolate was determined to be 37.35 mol%. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic analyses in this study, strain BH258T is considered to represent a novel species of the genus Aquibacillus, for which the name Aquibacillus sediminis sp. nov. is proposed. The type strain is BH258T (=KACC 18680T=NBRC 111875T).
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Affiliation(s)
- Jae-Chan Lee
- Department of Microbial and Nano Materials, College of Science and Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Department of Microbial and Nano Materials, College of Science and Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
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20
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Li YQ, Narsing Rao MP, Zhang H, Guo YM, Dong ZY, Alkhalifah DHM, Hozzein WN, Xiao M, Li WJ. Description of Sphingomonas mesophila sp. nov., isolated from Gastrodia elata Blume. Int J Syst Evol Microbiol 2019; 69:1030-1034. [PMID: 30735115 DOI: 10.1099/ijsem.0.003263] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, strictly aerobic, non-motile strain, SYSUP0001T, was isolated from tubers of Gastrodia elata Blume. The 16S rRNA gene sequence result indicated that SYSUP0001T represents a member of the genus Sphingomonas, with the highest sequence similarity (97.7 %) to the type strain of Sphingomonasginsengisoli. SYSUP0001T grew at 14-37 °C and pH 6-8, with optimum growth at 28 °C and pH 7. Tolerance to NaCl was up to 3 % (w/v) with optimum growth in the absence of NaCl. The respiratory quinone was Q-10. The major fatty acids were C18 : 1ω7c, Summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), and C16 : 0. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), sphingoglycolipid (SGL), phosphatidylcholine (PC) and four unidentified polar lipids (L). The DNA G+C content was 67.5 %. The average nucleotide identity (ANI) values between SYSUP0001T and closely related members of the genus Sphingomonas were below the cut-off level (95-96 %) for species delineation. On the basis of the phenotypic, phylogenetic and chemotaxonomic characterizations, SYSUP0001T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasmesophila sp. nov. is proposed. The type strain is SYSUP0001T (=KCTC 62179 T=CGMCC 1.16462T).
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Affiliation(s)
- Yan-Qiong Li
- Kunming Medical University Haiyuan College, Kunming, 650106, PR China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China
| | - Hui Zhang
- Kunming Medical University Haiyuan College, Kunming, 650106, PR China
| | - Yan-Mei Guo
- Kunming Medical University Haiyuan College, Kunming, 650106, PR China
| | - Zhou-Yan Dong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China
| | - Dalal Hussien M Alkhalifah
- Biology Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh 11564, Kingdom of Saudi Arabia
| | - Wael N Hozzein
- Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia.,Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China
| | - Wen-Jun Li
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China
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Lee JC, Song JS, Whang KS. Sphingobium pinisoli sp. nov., isolated from the rhizosphere soil of a Korean native pine tree. Antonie van Leeuwenhoek 2018; 112:815-825. [PMID: 30565024 DOI: 10.1007/s10482-018-01215-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/10/2018] [Indexed: 10/27/2022]
Abstract
A Gram-stain negative, aromatic compound degrading bacterium, designated strain ASA28T, was isolated from the rhizosphere soil of a pine tree at Anmyon island, Taean in Korea. Strain ASA28T was found to be strictly aerobic, non-motile, short rods which can grow at 15-28 °C (optimum, 25-28 °C), at pH 5.0-11.0 (optimum, pH 7.0) and at salinities of 0-1.0% (w/v) NaCl (optimum, 0% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain ASA28T belongs to the genus Sphingobium, showing high sequence similarity to Sphingobium scionense WP01T (97.8%), Sphingobium vermicocomposti VC-230T (96.8%), Sphingobium yanoikuyae ATCC 51230T (96.5%) and Sphingobium herbicidovorans MHT (95.6%). The predominant ubiquinone and polyamine components were identified as Q-10 and spermidine, respectively. The major fatty acids were identified as C18:1ω7c, C16:0, C14:0 2-OH and C16:1ω7c and/or C15:0 iso 2-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, sphingoglycolipid, phosphoglycolipid, four unidentified aminophospholipids, an unidentified aminolipid, two unidentified phospholipids and six unidentified lipids. The DNA G+C content of this novel isolate was determined to be 63.0 mol%. DNA-DNA relatedness between strain ASA28T and S. herbicidovorans KCTC 2939T, S. vermicocomposti DSM 21299T and S. scionense DSM 19371T was determined to be 32 ± 5%, 30 ± 4% and 25 ± 5%, respectively. On the basis of the phylogenetic, phenotypic and chemotaxonomic analyses in this study, strain ASA28T is considered to represent a novel species of the genus Sphingobium, for which the name Sphingobium pinisoli sp. nov. is proposed. The type strain is ASA28T (= KACC 18700T = NBRC 112246T).
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Affiliation(s)
- Jae-Chan Lee
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea.,Department of Microbial and Nano Materials, College of Science and Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea
| | - Jun-Soo Song
- Department of Microbial and Nano Materials, College of Science and Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea. .,Department of Microbial and Nano Materials, College of Science and Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea.
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22
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Xue H, Piao CG, Wang XZ, Lin CL, Guo MW, Li Y. Sphingomonas aeria sp. nov., isolated from air. Int J Syst Evol Microbiol 2018; 68:2866-2871. [PMID: 30010528 DOI: 10.1099/ijsem.0.002910] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
A Gram-negative, aerobic, non-spore-forming, non-motile, yellow-pigmented and rod-shaped bacterial strain, designated B093034T, was isolated from air at the foot of Xiangshan mountain, located in Beijing, China. Cells of strain B093034T were oxidase-negative and catalase-positive. Growth was observed at 4-41 °C, at pH 4.5-10.0 and at 0-7 % (w/v) NaCl. The isolate contained Q-10 as the predominant isoprenoid quinone, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C14 : 02-OH as the major fatty acids, sym-homospermidine as the major polyamine, and sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol, aminolipid, two unidentified phospholipids and three unidentified polar lipids as the polar lipids. The DNA G+C content was 67.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain B093034T grouped with members of the genus Sphingomonas and was closely related to Sphingomonas sanguinis IFO 13937T (96.49 % similarity), Sphingomonas pseudosanguinis G1-2T (96.37 %), Sphingomonas ginsenosidimutansGsoil 1429T (95.99 %) and Sphingomonas endophytica YIM 65583T (95.78 %). On the basis of the polyphasic evidence presented here, strain B093034T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasaeria sp. nov. is proposed. The type strain is B093034T (=CFCC 13949T=LMG 30133T).
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Affiliation(s)
- Han Xue
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Dong xiao-fu No. 1, Haidian District, Beijing 100091, PR China
| | - Chun-Gen Piao
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Dong xiao-fu No. 1, Haidian District, Beijing 100091, PR China
| | - Xi-Zhuo Wang
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Dong xiao-fu No. 1, Haidian District, Beijing 100091, PR China
| | - Cai-Li Lin
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Dong xiao-fu No. 1, Haidian District, Beijing 100091, PR China
| | - Min-Wei Guo
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Dong xiao-fu No. 1, Haidian District, Beijing 100091, PR China
| | - Yong Li
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Dong xiao-fu No. 1, Haidian District, Beijing 100091, PR China
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Lee JC, Whang KS. Salirhabdus salicampi sp. nov., a halotolerant bacterium isolated from a saltern. Int J Syst Evol Microbiol 2017; 67:4578-4583. [PMID: 28945542 DOI: 10.1099/ijsem.0.002334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, halotolerant bacterium, designated strain BH128T, was isolated from soil of a saltern located at Bigeum Island in south-west Korea. Cells were aerobic, motile, spore-forming rods and grew at 15-53 °C (optimum, 35 °C), at pH 5.5-9.0 (optimum, pH 7.0) and at salinities of 0-16 % (w/v) NaCl (optimum, 8 % NaCl). The predominant isoprenoid quinone was menaquinone-7 (MK-7), and the cell-wall peptidoglycan type was A1γ, with meso-diaminopimelic acid as the diagnostic diamino acid. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 and anteiso-C17 : 0. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and four unknown phospholipids. The DNA G+C content was 36.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH128T belonged to the genus Salirhabdus and showed highest similarity to Salirhabduseuzebyi CVS-14T (95.8 %). On the basis of the phylogenetic, phenotypic and chemotaxonomic analyses in this study, strain BH128T is considered to represent a novel species of the genus Salirhabdus, for which the name Salirhabdussalicampi sp. nov. is proposed. The type strain is BH128T (=KACC 18690T=NBRC 111874T).
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Affiliation(s)
- Jae-Chan Lee
- Department of Microbial and Nano Materials, College of Science and Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
| | - Kyung-Sook Whang
- Department of Microbial and Nano Materials, College of Science and Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
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Lee H, Kim DU, Lee S, Yun J, Park S, Yoon JH, Park SY, Ka JO. Sphingomonas carri sp. nov., isolated from a car air-conditioning system. Int J Syst Evol Microbiol 2017; 67:4069-4074. [PMID: 28905694 DOI: 10.1099/ijsem.0.002250] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, yellow-pigmented bacterial strain, designated PR0302T, was isolated from a car evaporator core collected in Korea. The cells were strictly aerobic, non-spore-forming and rod-shaped. The strain grew at 15-37 °C (optimum, 25 °C), at pH 6.0-8.0 (optimum, 7.0) and in the presence of 0-1 % (w/v) NaCl. Phylogenetically, the strain was closely related to members of the genus Sphingomonas(97.04-91.22 % 16S rRNA gene sequence similarities) and showed the highest sequence similarity of 97.04 % to Sphingomonas kyeonggiensis THG-DT81T. It contained C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C14 : 0 2-OH as the predominant fatty acids and Q-10 as the major ubiquinone. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid. The major polyamine was sym-homospermidine. The serine palmitoyl transferase gene (spt) was detected and sphingolipid synthesis was confirmed. The mean DNA G+C content of the strain was 67.8±0.5 mol%. DNA-DNA relatedness between strain PR0302T and closely related type strains of Sphingomonas species was less than 30 %. The low levels of DNA-DNA relatedness identified strain PR0302T as a member of a novel species in the genus Sphingomonas. Based on phenotypic, genotypic and chemotaxonomic data, strain PR0302T represents a novel species in the genus Sphingomonas, for which the name Sphingomonas carri sp. nov. is proposed. The type strain is PR0302T (=KACC 18487T=NBRC 111532T).
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Affiliation(s)
- Hyosun Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Dong-Uk Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Suyeon Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jungpyo Yun
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - So Yoon Park
- Research & Development Division, Hyundai Motor Group, Uiwang, 437-815, Republic of Korea
| | - Jong-Ok Ka
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea
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Gatheru Waigi M, Sun K, Gao Y. Sphingomonads in Microbe-Assisted Phytoremediation: Tackling Soil Pollution. Trends Biotechnol 2017; 35:883-899. [DOI: 10.1016/j.tibtech.2017.06.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/18/2017] [Accepted: 06/22/2017] [Indexed: 12/24/2022]
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Cho GY, Lee JC, Whang KS. Aliifodinibius salicampi sp. nov., a moderately halophilic bacterium isolated from a grey saltern. Int J Syst Evol Microbiol 2017; 67:2598-2603. [PMID: 28758626 DOI: 10.1099/ijsem.0.001981] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains of a Gram-stain-negative, moderately halophilic bacterium, designated strain KHM44T, KHM29 and HHM4, were isolated from the sediment of a grey saltern located on Sinui island at Shinan, Korea. The isolates were aerobic, non-motile rods and grew at 15-50 °C (optimum, 37 °C), at pH 6.0-9.0 (optimum, pH 8.0) and at salinities of 3-25 % (w/v) NaCl (optimum, 10 % NaCl). The predominant isoprenoid quinone was menaquinone-7 (MK-7), and the major fatty acids were iso-C15 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH, iso-C17 : 1ω9c and anteiso-C15 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and glycolipid. The DNA G+C contents were 48.5-48.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains KHM44T, KHM29 and HHM4 belonged to the genus Aliifodinibius in the family Balneolaceae, with sequence similarities of 95.1-97.2 % to members of this genus. Levels of DNA-DNA relatedness between strain KHM44T and the type strains of the other species of the genus Aliifodinibius ranged from 35.4 to 48.0 %. On the basis of polyphasic analysis from this study, strains KHM44T, KHM29 and HHM4 are considered to represent a novel species of the genus Aliifodinibius, for which the name Aliifodinibius salicampi sp. nov. is proposed. The type strain is KHM44T (=KACC 19060T=NBRC 112531T).
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Affiliation(s)
- Geon-Yeong Cho
- Department of Microbial and Nano Materials, College of Science and Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
| | - Jae-Chan Lee
- Department of Microbial and Nano Materials, College of Science and Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
| | - Kyung-Sook Whang
- Department of Microbial and Nano Materials, College of Science and Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
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Lee JH, Kim DI, Choe HN, Lee SD, Seong CN. Sphingomonas limnosediminicola sp. nov. and Sphingomonas palustris sp. nov., isolated from freshwater environments. Int J Syst Evol Microbiol 2017; 67:2834-2841. [DOI: 10.1099/ijsem.0.002029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Dae In Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Han Na Choe
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Soon Dong Lee
- Faculty of Science Education, Jeju National University, Jeju63243, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
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Cho GY, Lee JC, Whang KS. Rhodanobacter rhizosphaerae sp. nov., isolated from soil of ginseng rhizosphere. Int J Syst Evol Microbiol 2017; 67:1387-1392. [DOI: 10.1099/ijsem.0.001825] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Geon-Yeong Cho
- Department of Microbial and Nano Materials, College of Science and Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
| | - Jae-Chan Lee
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
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Lee JH, Kim DI, Kang JW, Seong CN. Sphingomonas lutea sp. nov., isolated from freshwater of an artificial reservoir. Int J Syst Evol Microbiol 2016; 66:5493-5499. [DOI: 10.1099/ijsem.0.001546] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Dae In Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Joo Won Kang
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
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Lee JC, Kim SJ, Whang KS. Halomonas sediminicola sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment. Int J Syst Evol Microbiol 2016; 66:3865-3872. [DOI: 10.1099/ijsem.0.001278] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jae-Chan Lee
- Department of Microbial & Nano Materials, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
| | - Su-Jin Kim
- Department of Microbial & Nano Materials, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
- Department of Microbial & Nano Materials, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
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Kim SJ, Lee JC, Han SI, Whang KS. Halobacillus salicampi sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment. Antonie van Leeuwenhoek 2016; 109:713-20. [PMID: 26942918 DOI: 10.1007/s10482-016-0672-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/27/2016] [Indexed: 11/25/2022]
Abstract
A Gram-positive, moderately halophilic bacterium, designated strain TGS-15(T), was isolated from the sediment of a solar saltern pond located in Shinan, Korea. Strain TGS-15(T) was found to be a strictly aerobic, non-motile rod which can grow at pH 6.0-10.0 (optimum, pH 9.0), at 20-35 °C (optimum, 28 °C) and at salinities of 1-20 % (w/v) NaCl (optimum, 9 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain TGS-15(T) belongs to the genus Halobacillus, with sequence similarity of 98.5-96.0 % to known type strains, showing high sequence similarity to Halobacillus locisalis MSS-155(T) (98.5 %), Halobacillus faecis IGA7-4(T) (98.2 %) and Halobacillus alkaliphilus FP5(T) (98.0 %), and less than 98.0 % sequence similarity to other currently recognised type strains of the genus. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid and an unidentified lipid. The cell wall peptidoglycan was found to be based on L-Orn-D-Asp, the predominant isoprenoid quinone was identified as menaquinone-7 (MK-7) and the major fatty acids were identified as anteiso-C15:0, iso-C15:0, anteiso-C17:0 and C16:1 ω7c alcohol. The DNA G+C content of this novel isolate was determined to be 45.3 mol %. Levels of DNA:DNA relatedness between strain TGS-15(T) and the type strains of 13 other species of the genus ranged from 52 to 9 %. On the basis of the polyphasic analysis conducted in this study, strain TGS-15(T) is concluded to represent a novel species of the genus Halobacillus, for which the name Halobacillus salicampi sp. nov. is proposed. The type strain is TGS-15(T) (=KACC 18264(T) = NBRC 110640(T)).
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Affiliation(s)
- Su-Jin Kim
- Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 302-318, Republic of Korea
| | - Jae-Chan Lee
- Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 302-318, Republic of Korea.,Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 302-318, Republic of Korea
| | - Song-Ih Han
- Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 302-318, Republic of Korea
| | - Kyung-Sook Whang
- Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 302-318, Republic of Korea. .,Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 302-318, Republic of Korea.
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Lee JC, Kim YS, Yun BS, Whang KS. Halomonas salicampi sp. nov., a halotolerant and alkalitolerant bacterium isolated from a saltern soil. Int J Syst Evol Microbiol 2015; 65:4792-4799. [PMID: 26431725 DOI: 10.1099/ijsem.0.000650] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, halotolerant and alkalitolerant bacterium, designated strain BH103T, was isolated from saltern soil in Gomso, Korea. Cells of strain BH103T were strictly aerobic, motile, straight rods and grew at pH 7.0-10.8 (optimum, pH 8.5), at 10-55 °C (optimum, 28 °C) and at salinities of 0-23 % (w/v) NaCl (optimum, 14 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH103T belongs to the genus Halomonas, showing highest sequence similarity to Halomonas boliviensis LC1T (97.7 %), Halomonas neptunia Eplume1T (97.7 %), Halomonas variabilis IIIT (97.7 %), Halomonas alkaliantarctica CRSST (97.7 %), Halomonas olivaria TYRC17T (97.5 %), Halomonas titanicae BH1T (97.2 %) and Halomonas sulfidaeris Esulfide1T (96.2 %). The predominant ubiquinone was Q-9. The major fatty acids were C18 : 1ω7c, C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C12 : 0 3-OH. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and an unknown phospholipid. The DNA G+C content of this novel isolate was 54.7 mol%. DNA-DNA relatedness between strain BH103T and H. boliviensis KACC 16615T, H. neptunia KCTC 2888T, H. variabilis KCTC 2889T, H. alkaliantarctica KCTC 22844T, H. olivaria DSM 19074T, H. titanicae JCM 16411T and H. sulfidaeris DSM 15722T was 45, 41, 39, 32, 38, 45 and 35 %, respectively. On the basis of polyphasic analysis from this study, strain BH103T represents a novel species of the genus Halomonas, for which the name Halomonas salicampi sp. nov. is proposed. The type strain is BH103T ( = KACC 17609T = NBRC 109914T = NCAIM B 02528T).
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Affiliation(s)
- Jae-Chan Lee
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
| | - Young-Sook Kim
- Division of Biotechnology and Advanced Institute of Environment and Bioscience, College of Environmental and Bioresource Sciences, Chonbuk National University, 79 Gobong-ro, Iksan-si 570-752, Republic of Korea.,Research Center for Biobased Chemistry, Eco-friendly New Materials Research Group, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon 305-600, Republic of Korea
| | - Bong-Sik Yun
- Division of Biotechnology and Advanced Institute of Environment and Bioscience, College of Environmental and Bioresource Sciences, Chonbuk National University, 79 Gobong-ro, Iksan-si 570-752, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea.,Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
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Wei S, Wang T, Liu H, Zhang C, Guo J, Wang Q, Liang K, Zhang Z. Sphingomonas hengshuiensis sp. nov., isolated from lake wetland. Int J Syst Evol Microbiol 2015; 65:4644-4649. [PMID: 26410379 DOI: 10.1099/ijsem.0.000626] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic study was undertaken to establish the status of a novel bacterium, designated strain WHSC-8T, which was isolated from soil of Hengshui Lake Wetland Reserve in Hebei province, northern China. Colonies of this strain were yellow and cells were rod-shaped, polar-flagellated and obligately aerobic, exhibiting negative Gram reaction. The strain was able to grow at 0-1 % (w/v) NaCl, pH 5-10 and 20-35 °C, with optimal growth occurring at pH 7.0 and 28 °C without NaCl. Chemotaxonomic data revealed that strain WHSC-8T possesses ubiquinone Q-10 as the predominant respiratory quinone, C18 : 1ω7c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids, and sym-homospermidine as the major polyamine. Sphingomonadaceae-specific sphingoglycolipid was detected in the polar lipid patterns. The G+C content of the genomic DNA was 68.7 mol%. All of the above characters corroborated the assignment of the novel strain to the genus Sphingomonas. Strain WHSC-8T shared less than 97.0 % 16S rRNA gene sequence similarity with the type strains of other species of the genus Sphingomonas, except for Sphingomonas asaccharolytica DSM 10564T (97.5 %). The low DNA-DNA relatedness value and distinct phenotypic and chemotaxonomic characteristics distinguished strain WHSC-8T from closely related species of the genus Sphingomonas. Therefore, strain WHSC-8T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas hengshuiensis sp. nov. is proposed. The type strain is WHSC-8T ( = KCTC 42455T = CCTCC AB 2015265T).
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Affiliation(s)
- Shuzhen Wei
- College of Life Sciences, Hengshui University, Heping West Road 1088, Taocheng District, Hengshui 053000, Hebei, PR China
| | - Tingting Wang
- College of Life Sciences, Hengshui University, Heping West Road 1088, Taocheng District, Hengshui 053000, Hebei, PR China
| | - Hongliang Liu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo 255049, Shandong, PR China
| | - Caifeng Zhang
- College of Life Sciences, Hengshui University, Heping West Road 1088, Taocheng District, Hengshui 053000, Hebei, PR China
| | - Jiping Guo
- College of Life Sciences, Hengshui University, Heping West Road 1088, Taocheng District, Hengshui 053000, Hebei, PR China
| | - Qian Wang
- College of Life Sciences, Hengshui University, Heping West Road 1088, Taocheng District, Hengshui 053000, Hebei, PR China
| | - Kuijing Liang
- College of Life Sciences, Hengshui University, Heping West Road 1088, Taocheng District, Hengshui 053000, Hebei, PR China
| | - Zhiqiang Zhang
- College of Life Sciences, Hengshui University, Heping West Road 1088, Taocheng District, Hengshui 053000, Hebei, PR China
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Lee JC, Whang KS. Burkholderia humisilvae sp. nov., Burkholderia solisilvae sp. nov. and Burkholderia rhizosphaerae sp. nov., isolated from forest soil and rhizosphere soil. Int J Syst Evol Microbiol 2015; 65:2986-2992. [DOI: 10.1099/ijs.0.000368] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains Y-12T and Y-47T were isolated from mountain forest soil and strain WR43T was isolated from rhizosphere soil, at Daejeon, Korea. The three strains grew at 10–55 °C (optimal growth at 28–30 °C), at pH 3.0–8.0 (optimal growth at pH 6.0) and in the presence of 0–4.0 % (w/v) NaCl, growing optimally in the absence of added NaCl. On the basis of 16S rRNA gene sequence analysis, the three strains were found to belong to the genus Burkholderia, showing the closest phylogenetic similarity to Burkholderia diazotrophica JPY461T (97.2–97.7 %); the similarity between the three sequences ranged from 98.3 to 98.7 %. Additionally, the three strains formed a distinct group in phylogenetic trees based on the housekeeping genes recA and gyrB. The predominant ubiquinone was Q-8, the major fatty acids were C16 : 0 and C17 : 0 cyclo and the DNA G+C content of the novel isolates was 61.6–64.4 mol%. DNA–DNA relatedness among the three strains and the type strains of the closest species of the genus Burkholderia was less than 50 %. On the basis of 16S rRNA, recA and gyrB gene sequence similarities, chemotaxonomic and phenotypic data, the three strains represent three novel species within the genus Burkholderia, for which the names Burkholderia humisilvae sp. nov. (type strain Y-12T = KACC 17601T = NBRC 109933T = NCAIM B 02543T), Burkholderia solisilvae sp. nov. (type strain Y-47T = KACC 17602T = NBRC 109934T = NCAIM B 02539T) and Burkholderia rhizosphaerae sp. nov. (type strain WR43T = KACC 17603T = NBRC 109935T = NCAIM B 02541T) are proposed.
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Affiliation(s)
- Jae-Chan Lee
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
| | - Kyung-Sook Whang
- Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
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van Bruggen AHC, Francis IM. Case Investigation and Forensic Evidence for a New Plant Disease: The Case of Lettuce Corky Root. PLANT DISEASE 2015; 99:300-309. [PMID: 30699699 DOI: 10.1094/pdis-09-14-0953-fe] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The process of disease diagnosis reminds of the process of solving a crime. This starts with a so-called 'crime scene investigation' (CSI) carried out in a highly systematic manner. The CSI is followed by 'forensic investigation' in specialized laboratories. The final step in solving a crime is the 'crime scene reconstruction' process, which involves systematic elimination of unlikely scenarios and comparison of results from the analysis of physical evidence with eye witness accounts. If more evidence becomes available, an 'old case may be reactivated'. In this review, the same sequence of activities is followed to solve a plant disease problem using a case study of a disease that was difficult to diagnose, namely the 'case' of corky root of lettuce.
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Affiliation(s)
- Ariena H C van Bruggen
- Emerging Pathogens Institute and Department of Plant Pathology, University of Florida, Gainesville
| | - Isolde M Francis
- Emerging Pathogens Institute and Department of Plant Pathology, University of Florida, Gainesville
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Lee JC, Kim SG, Whang KS. Sphingobium subterraneum sp. nov., isolated from ground water. Int J Syst Evol Microbiol 2015; 65:393-398. [DOI: 10.1099/ijs.0.069708-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, non-motile, non-spore-forming, yellow, rod-shaped bacterium, designated S-II-13T, was isolated from ground water at Daejeon in Korea. Strain S-II-13T grew between 15 and 30 °C (optimal growth at 28 °C), between pH 6.0 and 9.0 (optimal growth at pH 7.5) and at salinities of 0.3–1.5 % (w/v) NaCl, growing optimally with 0.5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain S-II-13T was found to belong to the genus
Sphingobium
, showing closest phylogenetic similarity to
Rhizorhapis suberifaciens
CA1T (97.0 % 16S rRNA gene sequence similarity),
Sphingobium sufflavum
HL-25T (96.9 %) and
Sphingobium vulgare
HU1-GD12T (96.6 %). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine and sphingoglycolipid. The predominant ubiquinone was Q-10. The major fatty acids were C18 : 1ω7c, C14 : 0 2-OH, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain S-II-13T was 63.5 mol%. DNA–DNA relatedness between strain S-II-13T and
Rhizorhapis suberifaciens
LMG 17323T,
Sphingobium sufflavum
KCTC 23953T and
Sphingobium vulgare
KCTC 22289T was 24, 52 and 55 %, respectively. On the basis of evidence from this taxonomic study using a polyphasic approach, strain S-II-13T represents a novel species of the genus
Sphingobium
for which the name Sphingobium subterraneum sp. nov. is proposed. The type strain is S-II-13T ( = KACC 17606T = NBRC 109814T).
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Affiliation(s)
- Jae-Chan Lee
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
| | - Song-Gun Kim
- University of Science and Technology, Daejeon 305-850, Republic of Korea
- Microbial Resource Center/KCTC, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea
| | - Kyung-Sook Whang
- Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
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Ren L, Chang X, Jiang F, Kan W, Qu Z, Qiu X, Fang C, Peng F. Parablastomonas arctica gen. nov., sp. nov., isolated from high Arctic glacial till. Int J Syst Evol Microbiol 2015; 65:260-266. [DOI: 10.1099/ijs.0.067231-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A pale yellow, aerobic bacterium, strain M0-2T, was isolated from a till sample. Its taxonomic position was investigated by using a polyphasic approach. Cells were Gram-stain-negative, rod-shaped and motile. Cells reproduced by budding or asymmetrical cell division. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M0-2T belonged to the family
Sphingomonadaceae
and was closely related to species of the genera
Novosphingobium
(96.4–92.0 %) and
Blastomonas
(94.6 %),
Sphingopyxis witflariensis
W-50T (94.0 %),
Sphingosinicella soli
KSL-125T (93.6 %) and
Sphingomonas astaxanthinifaciens
TDMA-17T (93.5 %). Ubiquinone-10 (Q-10) was the predominant respiratory quinone. The major fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c, 31.9 %), summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 19.8 %) and C14 : 0 2-OH (8.9 %). Sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine were the major polar lipids. Spermidine was the major polyamine observed in the cell. The genomic DNA G+C content was 47.5 mol%. On the basis of phylogenetic relationships and the low DNA G+C content compared with most other genera of the family
Sphingomonadaceae
, combined with phenotypic and chemotaxonomic data, strain M0-2T is considered to represent a novel species in a new genus in the family
Sphingomonadaceae
for which the name Parablastomonas arctica gen. nov., sp. nov. is proposed. The type strain of Parablastomonas arctica gen. nov., sp. nov. is M0-2T ( = CCTCC AB 2012968T = NRRL B-59110T).
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Affiliation(s)
- Lvzhi Ren
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xulu Chang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Fan Jiang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Wenjing Kan
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Zhihao Qu
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xia Qiu
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Chengxiang Fang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Fang Peng
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan 430072, PR China
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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Bull CT, Goldman PH, Martin KJ. Novel primers and PCR protocols for the specific detection and quantification of Sphingobium suberifaciens in situ. Mol Cell Probes 2014; 28:211-7. [PMID: 24647265 DOI: 10.1016/j.mcp.2014.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/06/2014] [Accepted: 03/09/2014] [Indexed: 11/22/2022]
Abstract
The pathogen causing corky root on lettuce, Sphingobium suberifaciens, is recalcitrant to standard epidemiological methods. Primers were developed from 16S rDNA sequences to be useful for the specific detection and quantification of S. suberifaciens. Quantitative PCR (qPCR) protocols specifically amplified DNA from the type strain of S. suberifaciens (LMG 17323) and other members of this species but not from other members of the Sphingomonadaceae. The detection limit was as little as 100 fg DNA (equivalent to 2 × 10(2) cells) in the qPCR. Detection was successful from soils inoculated with as little as 1 × 10(3) CFU/g soil. DNA isolated from naturally infested soils and diseased lettuce roots was amplified and sequenced fragments were identical or nearly identical to 16S rDNA sequences from S. suberifaciens. In growth chamber experiments, there was a positive correlation between disease severity and S. suberifaciens population levels in roots and soil, as detected by qPCR. Detection levels were below population levels of the pathogen necessary for disease development.
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Affiliation(s)
| | | | - Kendall J Martin
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
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Lee JC, Kim SG, Whang KS. Novosphingobium
aquiterrae sp. nov., isolated from ground water. Int J Syst Evol Microbiol 2014; 64:3282-3287. [DOI: 10.1099/ijs.0.060749-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, strictly aerobic, non-motile, non-spore-forming, yellow and rod-shaped bacterium, designated E-II-3T, was isolated from ground water at Daejeon in Korea. Strain E-II-3T grew between 4 and 45 °C (optimal growth at 28 °C), between pH 6.0 and 9.0 (optimal growth at pH 7.5) and at salinities of 0–2.0 % (w/v) NaCl, growing optimally with 0.5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain E-II-3T was shown to belong to the genus
Novosphingobium
and showed closest phylogenetic similarity to ‘Novosphingobium ginsenosidimutans’ FW-6 (97.7 %),
Novosphingobium aromaticivorans
F199T (96.9 %) and
Novosphingobium subterraneum
B0478T (96.5 %). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid. The predominant ubiquinone and polyamine components were Q-10 and spermidine, respectively. The major fatty acids were C18 : 1ω7c (34.0 %), C16 : 1ω7c and/or iso-C15 : 0 2-OH (23.8 %) and C17 : 1ω6c (19.3 %). The DNA G+C content of this novel isolate was 62.7 mol%. DNA–DNA relatedness between strain E-II-3T and ‘N. ginsenosidimutans’ KACC 16615,
N. aromaticivorans
KCTC 2888T and
N. capsulatum
KCTC 22844T was 38, 33 and 29 %, respectively. On the basis of polyphasic analysis from this study, strain E-II-3T represents a novel species of the genus
Novosphingobium
for which the name Novosphingobium aquiterrae sp. nov. is proposed. The type strain is E-II-3T ( = KACC 17599T = NBRC 109812T = NCAIM B 02537T).
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Affiliation(s)
- Jae-Chan Lee
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
| | - Song-Gun Kim
- University of Science and Technology, Daejeon 305-850, Republic of Korea
- Microbial Resource Center/KCTC, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea
| | - Kyung-Sook Whang
- Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
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Sphingomonas oligoaromativorans sp. nov., an oligotrophic bacterium isolated from a forest soil. Int J Syst Evol Microbiol 2014; 64:1679-1684. [DOI: 10.1099/ijs.0.052894-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A halo- and organo-sensitive oligotrophic bacterium, designated strain SY-6T, was isolated from humus forest soil at Gyeryong mountain in Korea. Cells of the strain were Gram-negative, strictly aerobic, non-motile rods and the strain formed yellow-pigmented colonies on 100-fold-diluted nutrient broth. Strain SY-6T grew at pH 6.0–7.0 (optimal growth at pH 7.0), at 10–37 °C (optimal growth at 28 °C) and at salinities of 0–0.5 % (w/v) NaCl, growing optimally at 0.01 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain SY-6T was shown to belong to the genus
Sphingomonas
and showed the closest phylogenetic similarity to
Sphingomonas polyaromaticivorans
B2-7T (96.7 %). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. The predominant ubiquinone and polyamine were Q-10 and sym-homospermidine, respectively. The major fatty acids were C18 : 1ω7c and C16 : 0. The DNA G+C content of the novel isolate was 65.3 mol%. On the basis of the evidence from this polyphasic study, strain SY-6T represents a novel species of the genus
Sphingomonas
, for which the name Sphingomonas oligoaromativorans sp. nov. is proposed. The type strain is SY-6T ( = KACC 12948T = NBRC 105508T).
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Francis IM, Jochimsen KN, De Vos P, van Bruggen AHC. Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. Int J Syst Evol Microbiol 2014; 64:1340-1350. [PMID: 24436067 DOI: 10.1099/ijs.0.058909-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
The genus Rhizorhapis gen. nov. (to replace the illegitimate genus name Rhizomonas) is proposed for strains of Gram-negative bacteria causing corky root of lettuce, a widespread and important lettuce disease worldwide. Only one species of the genus Rhizomonas was described, Rhizomonas suberifaciens, which was subsequently reclassified as Sphingomonas suberifaciens based on 16S rRNA gene sequences and the presence of sphingoglycolipid in the cell envelope. However, the genus Sphingomonas is so diverse that further reclassification was deemed necessary. Twenty new Rhizorhapis gen. nov.- and Sphingomonas-like isolates were obtained from lettuce or sow thistle roots, or from soil using lettuce seedlings as bait. These and previously reported isolates were characterized in a polyphasic study including 16S rRNA gene sequencing, DNA-DNA hybridization, DNA G+C content, whole-cell fatty acid composition, morphology, substrate oxidation, temperature and pH sensitivity, and pathogenicity to lettuce. The isolates causing lettuce corky root belonged to the genera Rhizorhapis gen. nov., Sphingobium, Sphingopyxis and Rhizorhabdus gen. nov. More specifically, we propose to reclassify Rhizomonas suberifaciens as Rhizorhapis suberifaciens gen. nov., comb. nov. (type strain, CA1(T) = LMG 17323(T) = ATCC 49355(T)), and also propose the novel species Sphingobium xanthum sp. nov., Sphingobium mellinum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. with the type strains NL9(T) ( = LMG 12560(T) = ATCC 51296(T)), WI4(T) ( = LMG 11032(T) = ATCC 51292(T)) and SP1(T) ( = LMG 12581(T) = ATCC 51289(T)), respectively. Several strains isolated from lettuce roots belonged to the genus Sphingomonas, but none of them were pathogenic.
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Affiliation(s)
- Isolde M Francis
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Kenneth N Jochimsen
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Paul De Vos
- Laboratory of Microbiology, Ghent University, 9000 Ghent, Belgium
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Huang J, Huang Z, Zhang ZD, He LY, Sheng XF. Sphingomonas yantingensis sp. nov., a mineral-weathering bacterium isolated from purplish paddy soil. Int J Syst Evol Microbiol 2014; 64:1030-1034. [DOI: 10.1099/ijs.0.055954-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel type of mineral-weathering bacterium was isolated from purplish soils collected from Yanting (Sichuan, south-western China). Cells of strain 1007T were Gram-stain-negative and rod-shaped, motile and yellow-pigmented. The isolate was strictly aerobic, catalase- and oxidase-positive, and grew optimally at 28-30 °C and pH 6.0-7.0. The genomic DNA G+C content of strain 1007T was 67±0.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1007T belonged to the genus
Sphingomonas
and was most closely related to
Sphingomonas pruni
IFO 15498T (97.3 %),
Sphingomonas mali
IFO 15500T (97.2 %),
Sphingomonas japonica
KC7T (97.2 %) and
Sphingomonas koreensis
JSS26T (97.0 %). This affiliation of strain 1007T to the genus
Sphingomonas
was confirmed by the presence of Q-10 as the major ubiquinone, sphingoglycolipid, C14 : 0 2-OH and by the absence of 3-hydroxy fatty acids. The major polyamine was homospermidine. The main cellular fatty acids included summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. Based on the low level of DNA–DNA relatedness (ranging from 26.1 % to 58.7 %) to these type strains of species of the genus
Sphingomonas
and unique phenotypic characteristics, strain 1007T represents a novel species of the genus
Sphingomonas
, for which the name Sphingomonas yantingensis sp. nov. is proposed. The type strain is 1007T ( = DSM 27244T = JCM 19201T = CCTCC AB 2013146T).
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Affiliation(s)
- Jing Huang
- Key Laboratory of Agricultural Environment Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhi Huang
- Key Laboratory of Agricultural Environment Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhen-Dong Zhang
- Key Laboratory of Agricultural Environment Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Lin-Yan He
- Key Laboratory of Agricultural Environment Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xia-Fang Sheng
- Key Laboratory of Agricultural Environment Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
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43
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Shahina M, Hameed A, Lin SY, Hsu YH, Liu YC, Cheng IC, Lee MR, Lai WA, Lee RJ, Young CC. Sphingomicrobium astaxanthinifaciens sp. nov., an astaxanthin-producing glycolipid-rich bacterium isolated from surface seawater and emended description of the genus
Sphingomicrobium. Int J Syst Evol Microbiol 2013; 63:3415-3422. [DOI: 10.1099/ijs.0.047704-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, strictly aerobic, flagellated and non-spore-forming marine bacterium designated strain CC-AMO-30BT was isolated from coastal surface seawater, Taiwan. Strain CC-AMO-30BT synthesized astaxanthin [40 µg (g dry weight)−1] and formed reddish-orange-coloured colonies on marine agar (Difco 2216). The strain showed highest pairwise 16S rRNA gene sequence similarity to
Sphingomicrobium lutaoense
CC-TBT-3T (96.4 %) followed by other members of the family
Sphingomonadaceae
(<94 %) and established a discrete phyletic lineage associated with the former. The polar lipid profile constituted a remarkable number of unidentified glycolipids (GL1–8), in addition to diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and two unidentified lipids (L1–2). The major fatty acids (>5 % of total fatty acids) were C18 : 1ω7c/C18 : 1ω6c (summed feature 8), C16 : 1ω7c/C16 : 1ω6c (summed feature 3), C18 : 1 2-OH, methyl C18 : 1ω7c, C17 : 1ω6c and C16 : 0. DNA G+C content was 70.6 %; major respiratory quinone was ubiquinone Q-10; predominant polyamine was the triamine sym-homospermidine. Chemotaxonomic evidence including characteristic glycolipid profile, presence of significant amounts of C18 : 1 2-OH and absence of typical hydroxylated fatty acids such as C14 : 0 2-OH, C15 : 0 2-OH and C16 : 0 2-OH in considerable amounts, accompanied by phylogenetic distinctiveness and several other phenotypic features support the classification of strain CC-AMO-30BT as a representative of a novel species within the genus
Sphingomicrobium
for which the name Sphingomicrobium astaxanthinifaciens sp. nov. is proposed; the type strain is CC-AMO-30BT ( = JCM 18551T = BCRC 80465T).
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Affiliation(s)
- Mariyam Shahina
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - Asif Hameed
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - Shih-Yao Lin
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - Yi-Han Hsu
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - You-Cheng Liu
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - I-Chen Cheng
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - Maw-Rong Lee
- Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan
| | - Wei-An Lai
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
| | - Ren-Jye Lee
- Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan
| | - Chiu-Chung Young
- Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan
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44
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Shahina M, Hameed A, Lin SY, Hsu YH, Liu YC, Huang YM, Lin JC, Young CC. Sphingomicrobium marinum sp. nov. and Sphingomicrobium flavum sp. nov., isolated from surface seawater, and emended description of the genus Sphingomicrobium. Int J Syst Evol Microbiol 2013; 63:4469-4476. [PMID: 23859943 DOI: 10.1099/ijs.0.052837-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-staining-negative, yellow-pigmented, rod-shaped, strictly aerobic, non-flagellated and non-spore-forming amylolytic marine bacterial strains, designated CC-AMZ-30M(T) and CC-AMZ-30N(T), were isolated from coastal surface seawater in Taiwan. Strain CC-AMZ-30M(T) shared pairwise 16S rRNA gene sequence similarities of 95.8, 95.0 and <94.0 % to Sphingomicrobium lutaoense CC-TBT-3(T), Sphingomicrobium astaxanthinifaciens CC-AMO-30B(T) and other sphingomonads, respectively. Strain CC-AMZ-30N(T) shared 97.0, 96.7, 95.0 and <95.1 % similarities to strain CC-AMZ-30M(T), Sphingomicrobium lutaoense CC-TBT-3(T), Sphingomicrobium astaxanthinifaciens CC-AMO-30B(T) and other sphingomonads, respectively. The common polar lipids of the two strains include a signature glycolipid (GL2), diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid in major amounts besides moderate-to-trace amounts of an unidentified aminolipid and several unidentified glycolipids. Both strains contained C18 : 1ω7c/C18 : 1ω6c, C16 : 1ω7c/C16 : 1ω6c, C16 : 0 and C18 : 1 2-OH as major (>5 % of the total) fatty acids. Strains CC-AMZ-30M(T) and CC-AMZ-30N(T) had DNA G+C contents of 64.2 and 65.2 mol%, respectively. The major polyamine was spermidine in strain CC-AMZ-30M(T) and triamine sym-homospermidine in strain CC-AMZ-30N(T). Both strains contained ubiquinone Q-10 as the predominant respiratory quinone. Differential phylogenetic and chemotaxonomic evidence including the presence of characteristic GL2, C18 : 1 2-OH and several other phenotypic features supported the classification of strains CC-AMZ-30M(T) and CC-AMZ-30N(T) as two novel species of the genus Sphingomicrobium, for which we propose the names Sphingomicrobium marinum sp. nov. and Sphingomicrobium flavum sp. nov., respectively; corresponding type strains are Sphingomicrobium marinum CC-AMZ-30M(T) ( = JCM 18554(T) = BCRC 80466(T)) and Sphingomicrobium flavum CC-AMZ-30N(T) ( = JCM 18555(T) = BCRC 80467(T)). An emended description of the genus Sphingomicrobium is also proposed.
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Affiliation(s)
- Mariyam Shahina
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Asif Hameed
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Shih-Yao Lin
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Yu-Ming Huang
- Bachelor program of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Jou-Chun Lin
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Chiu-Chung Young
- Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan, ROC.,Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
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45
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Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ, Tindall BJ, Spröer C, Overmann J. Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family
Sphingomonadaceae
, and reclassification of
Sphingomonas suberifaciens
as Sphingobium suberifaciens comb. nov. Int J Syst Evol Microbiol 2013; 63:735-743. [DOI: 10.1099/ijs.0.040105-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel chemo-organoheterotrophic members of the
Sphingomonadaceae
were isolated from alpine and pre-alpine lakes. Cells stained Gram-negative, were motile and rod-shaped, and formed yellow, circular, convex colonies on different agar media. Strains 301T and 469T were strictly aerobic, catalase- and oxidase-positive, and grew at temperatures between 10 and 40 °C (optimum, 28 °C), and at pH values between 5 and 10 (optimum, pH 7). Both strains contained Q-10 as the dominant quinone, sphingoglycolipids and 2-hydroxymyristic acid, whereas 3-hydroxy fatty acids were absent. Major fatty acids of strain 301T were C18 : 1ω7c (53.3 %) and C16 : 1ω7c (22.9 %), with C14 : 0 2-OH (10.8 %) as the major 2-hydroxy fatty acid. Fatty acids of strain 469T were dominated by C18 : 1ω7c (34.4 %), C16 : 1ω7c (32.0 %) and C14 : 0 2-OH (15.2 %) as the major 2-hydroxy fatty acid. The genomic DNA G+C contents of strains 301T and 469T were 63.4 and 64.6 mol%, respectively. 16S rRNA gene sequence comparison indicated that both strains belonged to the genus
Sphingobium
. This classification was supported by the presence of spermidine as the major polyamine. The phylogenetically closest relatives of strain 301T were
Sphingobium amiense
DSM 16289T,
Sphingobium vermicomposti
DSM 21299T,
Sphingobium yanoikuyae
DSM 7462T and
Sphingobium scionense
DSM 19371T (98.8, 98.0, 97.9 and 97.4 % sequence similarity, respectively). DNA–DNA hybridization of genomic DNA yielded similarities in the range 43.2–12.1 % between strain 301T and the type strains of these four
Sphingobium
species. Closest relatives of strain 469T were
Sphingomonas suberifaciens
DSM 7465T and
Sphingobium scionense
DSM 19371T (97.1 and 96.5 % 16S rRNA gene sequence similarity, respectively). The degree of DNA–DNA hybridization between strain 469T and
Sphingomonas suberifaciens
DSM 7465T was 17.9 %. Based on the results of the molecular analyses and their phenotypic characteristics, strains 301T and 469T represent two novel species of the genus
Sphingobium
. The name Sphingobium limneticum sp. nov. is proposed for strain 301T( = DSM25076T = LMG 26659T). The name Sphingobium boeckii sp. nov. is proposed for strain 469T ( = DSM 25079T = LMG 26901T). The polyphasic analysis also suggests that
Sphingomonas suberifaciens
should be reclassified as Sphingobium suberifaciens comb. nov. with Ca1T ( = EY 2404T = ATCC 49355T = CIP 105429T = DSM 7465T = ICMP 12535T = NBRC 15211T = JCM 8521T = LMG 17323T = NCPPB 3629T) as the type strain.
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Affiliation(s)
- Hong Chen
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 80539 Munich, Germany
| | - Mareike Jogler
- Leibniz-Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, 38124 Braunschweig, Germany
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 80539 Munich, Germany
| | - Manfred Rohde
- Helmholtz-Zentrum für Infektionsforschung, Medizinische Mikrobiologie, 38106 Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz-Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, 38124 Braunschweig, Germany
| | - Hans-Jürgen Busse
- Institute of Bacteriology, Mycology and Hygiene (IBMH), University of Veterinary Medicine Vienna, A-1210 Vienna, Austria
| | - Brian J. Tindall
- Leibniz-Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, 38124 Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, 38124 Braunschweig, Germany
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 80539 Munich, Germany
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46
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Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ, Tindall BJ, Spröer C, Overmann J. Reclassification and emended description of
Caulobacter leidyi
as Sphingomonas leidyi comb. nov., and emendation of the genus
Sphingomonas. Int J Syst Evol Microbiol 2012; 62:2835-2843. [DOI: 10.1099/ijs.0.039636-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
‘
Caulobacter leidyi
’ DSM 4733T has been shown to be affiliated with the family
Sphingomonadaceae
instead of the
Caulobacteraceae
, and due to its poor characterization has been omitted from the current edition of Bergey’s Manual of Systematic Bacteriology and removed to limbo. We isolated a novel sphingoglycolipid-containing dimorphic prosthecate bacterium, designated strain 247, from a pre-alpine freshwater lake. Strain 247 and ‘
Caulobacter leidyi
’ DSM 4733T were characterized in detail. The rod-shaped cells were Gram-stain-negative, aerobic, catalase- and oxidase-positive, and formed a stalk or polar flagellum. Both strains grew optimally at 28–30 °C, and pH 6.0–8.0. The major fatty acids were C18 : 1ω7c, C16 : 0 and 11-methyl C18 : 1ω7c. C14 : 0 2-OH represents the major 2-hydroxy fatty acid. Q-10 was the major respiratory quinone and the major polar lipids were diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, three glycolipids, two phosphoaminolipids and two unidentified sphingoglycolipids. The major polyamine was sym-homospermidine. The G+C content of genomic DNA of strains 247 and DSM 4733T was 67.6 mol% and 67.0 mol%, respectively. According to 16S rRNA gene sequence analysis and DNA–DNA hybridization, strains DSM 4733T and 247 were phylogenetically closely related (99.6 % 16S rRNA gene sequence similarity, 82.9 % DNA–DNA hybridization value) and affiliated to the genus
Sphingomonas
. The closest recognized species was
Sphingomonas aquatilis
DSM 15581T (98.1 % sequence similarity). In addition, the presence of cystine arylamidase, absence of β-galactosidase, and the inability to utilize l-arabinose, galactose and sucrose distinguished strains DSM 4733T and 247 from most other members of the family
Sphingomonadaceae
. So far, the dimorphic life cycle that involves a prosthecate and a flagellated stage is unique for strains DSM 4733T and 247 among all members of the family
Sphingomonadaceae
. Therefore,
Caulobacter leidyi
is reclassified as Sphingomonas leidyi, with the type strain DSM 4733T ( = ATCC 15260T = CIP 106443T = VKM B-1368T) and strain 247 (DSM 25078 = LMG 26658) as an additional strain of this species.
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Affiliation(s)
- Hong Chen
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen Braunschweig GmbH, Germany
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Mareike Jogler
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen Braunschweig GmbH, Germany
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Manfred Rohde
- Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen Braunschweig GmbH, Germany
| | - Hans-Jürgen Busse
- Institute of Bacteriology, Mycology and Hygiene (IBMH), University of Veterinary Medicine Vienna, Austria
| | - Brian J. Tindall
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen Braunschweig GmbH, Germany
| | - Cathrin Spröer
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen Braunschweig GmbH, Germany
| | - Jörg Overmann
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen Braunschweig GmbH, Germany
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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47
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Kämpfer P, Arun AB, Young CC, Busse HJ, Kassmannhuber J, Rosselló-Móra R, Geueke B, Rekha PD, Chen WM. Sphingomicrobium lutaoense gen. nov., sp. nov., isolated from a coastal hot spring. Int J Syst Evol Microbiol 2012; 62:1326-1330. [DOI: 10.1099/ijs.0.034413-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A yellowish pigmented, Gram-negative, rod-shaped, non-spore-forming bacterium (strain CC-TBT-3T), was isolated on marine agar 2216 from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan. 16S rRNA gene sequence analysis of strain CC-TBT-3T showed a relatively low similarity (<95.5 %) to representatives of the genera
Novosphingobium
,
Sphingosinicella
and
Sphingomonas
of the
Sphingomonadaceae
, with the most related strain being the type strain of
Novosphingobium soli
. In addition to the relatively low 16S rRNA gene sequence similarity to members of established species, the isolate also showed some unique chemotaxonomic features, including the presence of some glycolipids with unusual chromatographic behaviour. The major components of the polar lipid profile were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and three unidentified glycolipids. The major respiratory quinone was ubiquinone Q-10. The polyamine pattern was characterized by the triamine sym-homospermidine as a major component. Although the predominant fatty acids were C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), the isolate did not show the typical hydroxyl fatty acids, such as C14 : 0 2-OH, C15 : 0 2-OH and C16 : 0 2-OH, found in members of the genera
Novosphingobium
,
Sphingomonas
and
Sphingosinicella
, but showed instead high amounts of C18 : 1 2-OH (12.0 %). The DNA G+C content of strain CC-TBT-3T was 63.4 mol%. 16S rRNA gene sequence, chemotaxonomic and physiological analyses revealed that strain CC-TBT-3T represents a novel species in a new genus in the family
Sphingomonadaceae
for which the name Sphingomicrobium lutaoense gen. nov., sp. nov. is proposed; the type strain is of the type species S. lutoaense, CC-TBT-3T ( = DSM 24194T = CCM 7794T).
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - A. B. Arun
- Yenepoya Research Center, Yenepoya University, University Road, Deralakatee, Mangalore, Karnataka State, India
| | - Chiu-Chung Young
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Hans-Jürgen Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - Johannes Kassmannhuber
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Institut Mediterrani d’Estudis Avançats (CSIC-UIB), C/Miquel Marqués 21, 07190 Esporles, Spain
| | - Birgit Geueke
- Environmental Microbiology, Eawag, Ueberlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - P. D. Rekha
- Yenepoya Research Center, Yenepoya University, University Road, Deralakatee, Mangalore, Karnataka State, India
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung, Taiwan, ROC
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48
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Matsumoto M, Iwama D, Arakaki A, Tanaka A, Tanaka T, Miyashita H, Matsunaga T. Altererythrobacter ishigakiensis sp. nov., an astaxanthin-producing bacterium isolated from a marine sediment. Int J Syst Evol Microbiol 2011; 61:2956-2961. [DOI: 10.1099/ijs.0.024729-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-motile, non-spore-forming, halophilic rod, designated JPCCMB0017T, was isolated from a marine sediment of the coastal area of Okinawa, Japan. The isolate formed orange–red colonies on marine agar. Bacteriochlorophyll α was absent and sphingoglycolipid 1 and other carotenoids, including astaxanthin, adonixanthin and zeaxanthin, were present. Ubiquinone-10 (Q-10) was the main respiratory quinone and C18 : 1ω7c was the major cellular fatty acid. The G+C content of DNA was 59.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the genus Altererythrobacter in the family Erythrobacteraceae. Strain JPCCMB0017T exhibited 96.8 % 16S rRNA gene sequence similarity with Altererythrobacter marinus H32T. Unlike other members of the genus Altererythrobacter, strain JPCCMB0017T reduced nitrate. On the basis of genotypic and phenotypic data, a novel species is proposed to accommodate this isolate, with the name Altererythrobacter ishigakiensis sp. nov. The type strain is JPCCMB0017T ( = NITE-AP48T = ATCC BAA-2084T = NBRC 107699T).
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Affiliation(s)
- Mitsufumi Matsumoto
- Biotechnology Laboratory, Electric Power Development Co., 1, Yanagisaki-machi, Wakamatsu-ku, Kitakyusyu 808-0111, Japan
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Daisuke Iwama
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Atsushi Arakaki
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Akira Tanaka
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Tsuyoshi Tanaka
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Hideaki Miyashita
- Department of Technology and Ecology, Hall of Global Environmental Studies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tadashi Matsunaga
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
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49
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Sphingomonas rubra sp. nov., isolated from bioreactor wastewater. Int J Syst Evol Microbiol 2011; 61:1028-1032. [DOI: 10.1099/ijs.0.020958-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, rod-shaped, motile, neutrophilic bacterium, designated strain BH3T, was isolated from wastewater of a sequential batch reactor treating wastewater taken from a leather plant. The isolate grew in 0–8 % (w/v) NaCl, at pH 6–9 and at 4–45 °C. Chemotaxonomic analysis showed that strain BH3T had characteristics typical of members of the genus Sphingomonas, such as the presence of sphingolipids, Q-10 and 2-hydroxymyristic acid and the absence of 3-hydroxy fatty acids. The presence of C18 : 1ω7c (39.2 %) and C16 : 0 (11.2 %) as major fatty acids, C14 : 0 2-OH (20.6 %) as the major 2-hydroxy fatty acid and homospermidine as the major polyamine indicated that strain BH3T belonged to the genus Sphingomonas sensu stricto. The genomic DNA G+C content of strain BH3T was 65.6 mol%. 16S rRNA gene sequence similarities between the isolate and closely related members of the genus Sphingomonas sensu stricto ranged from 92.6 to 97.3 %, the highest sequence similarities being to Sphingomonas melonis DSM 14444T (97.3 %) and Sphingomonas aquatilis DSM 15581T (97.3 %). Based on its phenotypic characteristics and the results of DNA–DNA hybridization studies and 16S rRNA gene sequence comparisons, strain BH3T represents a novel species of the genus Sphingomonas sensu stricto, for which the name Sphingomonas rubra sp. nov. is proposed. The type strain is BH3T ( = CGMCC 1.9113T = JCM 16230T).
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Chen QH, Chen JH, Ruan Y, Zhang YQ, Tang SK, Liu ZX, Li WJ, Chen YG. Sphingomonas hunanensis sp. nov., isolated from forest soil. Antonie van Leeuwenhoek 2011; 99:753-60. [DOI: 10.1007/s10482-011-9549-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 01/03/2011] [Indexed: 10/18/2022]
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