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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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2
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Tahon G, Gök D, Lebbe L, Willems A. Description and functional testing of four species of the novel phototrophic genus Chioneia gen. nov., isolated from different East Antarctic environments. Syst Appl Microbiol 2021; 44:126250. [PMID: 34592543 DOI: 10.1016/j.syapm.2021.126250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
Seven Gram-negative, aerobic, non-sporulating, motile strains were isolated from terrestrial (R-67880T, R-67883, R-36501 and R-36677T) and aquatic (R-39604, R-39161T and R-39594T) East Antarctic environments (i.e. soil and aquatic microbial mats), between 2007 and 2014. Analysis of near-complete 16S rRNA gene sequences revealed that the strains potentially form a novel genus in the family Sphingomonadaceae (Alphaproteobacteria). DNA-DNA reassociation and average nucleotide identity values indicated distinction from close neighbors in the family Sphingomonadaceae and showed that the seven isolates form four different species. The main central pathways present in the strains are the glycolysis, tricarboxylic acid cycle and pentose phosphate pathway. The strains can use only a limited number of carbon sources and mainly depend on ammonia and sulfate as a nitrogen and sulfur source, respectively. The novel strains showed the potential of aerobic anoxygenic phototrophy, based on the presence of bacteriochlorophyll a pigments, which was corroborated by the presence of genes for all building blocks for a type 2 photosynthetic reaction center in the annotated genomes. Based on the results of phenotypic, genomic, phylogenetic and chemotaxonomic analyses, the strains could be assigned four new species in the novel genus Chioneia gen. nov. in the family Sphingomonadaceae, for which the names C. frigida sp. nov. (R-67880T, R-67883 and R-36501), C. hiemis sp. nov. (R-36677T), C. brumae sp. nov. (R-39161T and R-39604) and C. algoris sp. nov. (R-39594T) are proposed.
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Affiliation(s)
- Guillaume Tahon
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| | - Duygu Gök
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| | - Liesbeth Lebbe
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
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Aguirre-von-Wobeser E, Alonso-Sánchez A, Méndez-Bravo A, Villanueva Espino LA, Reverchon F. Barks from avocado trees of different geographic locations have consistent microbial communities. Arch Microbiol 2021; 203:4593-4607. [PMID: 34160629 DOI: 10.1007/s00203-021-02449-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/22/2021] [Accepted: 06/16/2021] [Indexed: 01/07/2023]
Abstract
Bark is a permanent surface for microbial colonization at the interface of trees and the surrounding air, but little is known about its microbial communities. We used shotgun metagenomic sequencing to analyze the bark microbiomes of avocado trees from two orchards, and compared one of them to rhizospheric soil. It was shown that the microbial communities of avocado bark have a well-defined taxonomic structure, with consistent patterns of abundance of bacteria, fungi, and archaea, even in trees from two different locations. Bark microbial communities were distinct from rhizospheric soil, although they showed overlap in some taxa. Thus, avocado bark is a well-defined environment, providing niches for specific taxonomic groups, many of which are also found in other aerial plant tissues. The present in-depth characterization of bark microbial communities can form a basis for their future manipulation for agronomical purposes.
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Affiliation(s)
- Eneas Aguirre-von-Wobeser
- Unidad Regional Hidalgo, CONACYT, Centro de Investigación y Desarrollo, A.C., Blvd. Sta. Catarina s/n, Col. Santiago Tlapacoya, 42110, San Agustin Tlaxiaca, Hidalgo, Mexico.
| | - Alexandro Alonso-Sánchez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Col. El Haya, 91070, Xalapa, Veracruz, Mexico
| | - Alfonso Méndez-Bravo
- Laboratorio Nacional de Análisis y Síntesis Ecológica, CONACYT, Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Col. Ex-Hacienda de San José de La Huerta, 58190, Morelia, Michoacan, Mexico
| | - Luis Alberto Villanueva Espino
- Laboratorio Nacional de Análisis y Síntesis Ecológica, CONACYT, Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Col. Ex-Hacienda de San José de La Huerta, 58190, Morelia, Michoacan, Mexico
| | - Frédérique Reverchon
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Col. El Haya, 91070, Xalapa, Veracruz, Mexico
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4
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Sphingomonas hominis sp. nov., isolated from hair of a 21-year-old girl. Antonie Van Leeuwenhoek 2020; 113:1523-1530. [DOI: 10.1007/s10482-020-01460-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/04/2020] [Indexed: 11/25/2022]
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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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Menon RR, Kumari S, Kumar P, Verma A, Krishnamurthi S, Rameshkumar N. Sphingomonas pokkalii sp. nov., a novel plant associated rhizobacterium isolated from a saline tolerant pokkali rice and its draft genome analysis. Syst Appl Microbiol 2019; 42:334-342. [PMID: 30808585 DOI: 10.1016/j.syapm.2019.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/29/2019] [Accepted: 02/08/2019] [Indexed: 02/03/2023]
Abstract
Three strains L3B27T, 3CNBAF, L1A4 isolated from a brackish cultivated pokkali rice rhizosphere were characterised using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA and recA gene sequences revealed that these strains were highly similar among each other and formed a separate monophyletic cluster within the genus Sphingomonas with Sphingomonas pituitosa DSM 13101T, Sphingomonas azotifigens DSM 18530T and Sphingomonas trueperi DSM 7225T as their closest relatives sharing 97.9-98.3% 16S rRNA similarity and 91.3-94.0% recA similarity values, respectively. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridisation (dDDH) values between L3B27T (representative of the novel strains) and its phylogenetically closest Sphingomonas species were well below the established cut-off <94% (ANI/AAI) and <70% (dDDH) for species delineation. Further, the novel strains can be distinguished from its closest relatives based on several phenotypic traits. Thus, based on the polyphasic approach, we describe a novel Sphingomonas species for which the name Sphingomonas pokkalii sp. nov (type strain L3B27T=KCTC 42098T=MCC 3001T) is proposed. In addition, the novel strains were characterised for their plant associated properties and found to possess several phenotypic traits which probably explain its plant associated lifestyle. This was further confirmed by the presence of several plant associated gene features in the genome of L3B27T. Also, we could identify gene features which may likely involve in brackish water adaptation. Thus, this study provides first insights into the plant associated lifestyle, genome and taxonomy of a novel brackish adapted plant associated Sphingomonas.
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Oso S, Walters M, Schlechter RO, Remus-Emsermann MNP. Utilisation of hydrocarbons and production of surfactants by bacteria isolated from plant leaf surfaces. FEMS Microbiol Lett 2019; 366:5420820. [DOI: 10.1093/femsle/fnz061] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/20/2019] [Indexed: 01/25/2023] Open
Affiliation(s)
- Simisola Oso
- School of Biological Sciences, University of Canterbury, 20 Kirkwood Avenue, Upper Riccarton, 8140 Christchurch, New Zealand
| | - Matthew Walters
- School of Biological Sciences, University of Canterbury, 20 Kirkwood Avenue, Upper Riccarton, 8140 Christchurch, New Zealand
| | - Rudolf O Schlechter
- School of Biological Sciences, University of Canterbury, 20 Kirkwood Avenue, Upper Riccarton, 8140 Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, 20 Kirkwood Avenue, Upper Riccarton, 8140 Christchurch, New Zealand
| | - Mitja N P Remus-Emsermann
- School of Biological Sciences, University of Canterbury, 20 Kirkwood Avenue, Upper Riccarton, 8140 Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, 20 Kirkwood Avenue, Upper Riccarton, 8140 Christchurch, New Zealand
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8
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Suleiman MK, Dixon K, Commander L, Nevill P, Quoreshi AM, Bhat NR, Manuvel AJ, Sivadasan MT. Evaluating the diversity and composition of bacterial communities associated with Vachellia pachyceras - the only existing native tree species in the Kuwait desert. Can J Microbiol 2018; 65:235-251. [PMID: 30495976 DOI: 10.1139/cjm-2018-0421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We investigated the diversity and composition of bacterial communities in rhizospheric and non-rhizospheric bulk soils as well as root nodule bacterial communities of Vachellia pachyceras - the only native tree species existing in the Kuwait desert. Community fingerprinting comparisons and 16S rDNA sequence identifications were used for characterization of the bacterial population using specific primers. The bacterial characterization of soil samples revealed four major phyla: Acidobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. In situ (desert) samples of both rhizospheric and non-rhizospheric bulk soil were dominated by the bacterial phyla Firmicutes and Bacteroidetes, whereas the phylum Betaproteobacteria was present only in non-rhizospheric bulk soil. Ex situ (nursery growing condition) V. pachyceras resulted in restricted bacterial communities dominated by members of a single phylum, Bacteroidetes. Results indicated that the soil organic matter and rhizospheric environments might drive the bacterial community. Despite harsh climatic conditions, data demonstrated that V. pachyceras roots harbor endophytic bacterial populations. Our findings on bacterial community composition and structure have major significance for evaluating how Kuwait's extreme climatic conditions affect bacterial communities. The baseline data obtained in this study will be useful and assist in formulating strategies in ecological restoration programs, including the application of inoculation technologies.
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Affiliation(s)
- Majda K Suleiman
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Kingsley Dixon
- b Department of Environment and Agriculture, ARC Centre for Mine Site Restoration Curtin University, Bentley, WA 6102, Australia
| | - Lucy Commander
- c School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Paul Nevill
- d Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Ali M Quoreshi
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Narayana R Bhat
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Anitha J Manuvel
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Mini T Sivadasan
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
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Madhaiyan M, Alex THH, Cho H, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L. Sphingomonas jatrophae sp. nov. and Sphingomonas carotinifaciens sp. nov., two yellow-pigmented endophytes isolated from stem tissues of Jatropha curcas L. Int J Syst Evol Microbiol 2017; 67:5150-5158. [PMID: 29087271 DOI: 10.1099/ijsem.0.002434] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two yellow-pigmented isolates, S5-249T and L9-754T, originating from surface-sterilized plant tissues of Jatropha curcas L. (Jatropha) cultivars were characterized using a polyphasic taxonomic approach. Strains S5-249T and L9-754T had 16S rRNA genes sharing 94.2 % sequence similarity with each other and 91.6-97.2 % sequence similarity with those of other species in the genus Sphingomonas, suggesting that they represent two potentially novel species. The 16S rRNA gene sequences of strains S5-249T and L9-754T shared the highest similarity to that of Sphingomonas sanguinis NBRC 13937T (96.1 and 97.2 %, respectively). The genomic DNA G+C contents of strains S5-249T and L9-754T were 66.9 and 68.5 mol%, respectively. The respiratory quinone was determined to be Q-10, and the major polyamine was homospermidine. Strains S5-249T and L9-754T contained summed feature 7 (comprising C18 : 1ω7c, C18 : 1ω9t and/or C18 : 1ω12t), C16 : 1, C14 : 0 2-OH and summed feature 4 (C16 : 1ω7t, iso-C15 : 0 2-OH and C16 : 1ω7c) as the major cellular fatty acids. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid. The average nucleotide identity (ANI) values between S. sanguinis NBRC 13937T and the two type strains (S5-249T and L9-754T) were 72.31 and 77.73 %, respectively. Digital DNA-DNA hybridization (dDDH) studies between the novel strains (S5-249T and L9-754T) and other species of the genus Sphingomonas were well below the thresholds used to discriminate between bacterial species. The results of dDDH and physiological tests allowed genotypic and phenotypic differentiation of the strains from each other as well as from the species of the genus Sphingomonas with validly published names. These data strongly support the classification of the strains as representatives of novel species, for which we propose the names Sphingomonas jatrophae sp. nov. (type strain S5-249T=DSM 27345T=KACC 17593T) and Sphingomonas carotinifaciens sp. nov. (type strain L9-754T=DSM 27347T=KACC 17595T).
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Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Tan Hian Hwee Alex
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Hayoung Cho
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - William B Whitman
- Department of Microbiology, University of Georgia, 527 Biological Sciences Building, Athens, GA 30602-2605, USA
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
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Coda R, Kianjam M, Pontonio E, Verni M, Di Cagno R, Katina K, Rizzello CG, Gobbetti M. Sourdough-type propagation of faba bean flour: Dynamics of microbial consortia and biochemical implications. Int J Food Microbiol 2017; 248:10-21. [PMID: 28242419 DOI: 10.1016/j.ijfoodmicro.2017.02.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/28/2016] [Accepted: 02/18/2017] [Indexed: 10/20/2022]
Abstract
The microbial ecology of faba bean sourdoughs obtained from an Italian (Ita) and a Finnish (Fi) cultivar, belonging respectively to Vicia faba major and V. faba minor groups, was described by 16S rRNA gene pyrosequencing and culture-dependent analysis. The sourdoughs were propagated with traditional backslopping procedure throughout 14days. Higher microbial diversity was found in the sourdough deriving from V. faba minor (Fi), still containing residual hulls after the milling procedure. After 2days of propagation, the microbial profile of Ita sourdough was characterized by the dominance of the genera Pediococcus, Leuconostoc and Weissella, while the genera Lactococcus, Lactobacillus and Escherichia, as well as Enterobacteriaceae were present in Fi sourdoughs. Yeasts were in very low cell density until the second backslopping and were not anymore found after this time by plate count or pyrosequencing analysis. Among the lactic acid bacteria isolates, Pediococcus pentosaceus, Leuconostoc mesenteroides and Weissella koreensis had the highest frequency of occurrence in both the sourdoughs. Lactobacillus sakei was the only lactobacillus isolated from the first to the last propagation day in Fi sourdough. According to microbiological and acidification properties, the maturity of the sourdoughs was reached after 5days. The presence of hulls and the different microbial composition reflected on biochemical characteristics of Fi sourdoughs, including acidification and phenolic compounds. Moreover, proteolysis in Fi sourdough was more intense compared to Ita. The microbial dynamic of the faba bean sourdoughs showed some differences with the most studied cereal sourdoughs.
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Affiliation(s)
- Rossana Coda
- University of Helsinki, Department of Food and Environmental Sciences, Agnes Sjioberginkatu 2, Helsinki, Finland
| | - Maryam Kianjam
- University of Helsinki, Department of Food and Environmental Sciences, Agnes Sjioberginkatu 2, Helsinki, Finland
| | - Erica Pontonio
- University of Bari "Aldo Moro", Department of Soil, Plant, and Food Science, Via Amendola 165/a, 70125 Bari, Italy
| | - Michela Verni
- University of Bari "Aldo Moro", Department of Soil, Plant, and Food Science, Via Amendola 165/a, 70125 Bari, Italy
| | - Raffaella Di Cagno
- Faculty of Food Science and Technology, University of Bozen, 39100 Bolzano, Italy
| | - Kati Katina
- University of Helsinki, Department of Food and Environmental Sciences, Agnes Sjioberginkatu 2, Helsinki, Finland
| | - Carlo Giuseppe Rizzello
- University of Bari "Aldo Moro", Department of Soil, Plant, and Food Science, Via Amendola 165/a, 70125 Bari, Italy.
| | - Marco Gobbetti
- Faculty of Food Science and Technology, University of Bozen, 39100 Bolzano, Italy
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Using a Control to Better Understand Phyllosphere Microbiota. PLoS One 2016; 11:e0163482. [PMID: 27669159 PMCID: PMC5036865 DOI: 10.1371/journal.pone.0163482] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/10/2016] [Indexed: 11/26/2022] Open
Abstract
An important data gap in our understanding of the phyllosphere surrounds the origin of the many microbes described as phyllosphere communities. Most sampling in phyllosphere research has focused on the collection of microbiota without the use of a control, so the opportunity to determine which taxa are actually driven by the biology and physiology of plants as opposed to introduced by environmental forces has yet to be fully realized. To address this data gap, we used plastic plants as inanimate controls adjacent to live tomato plants (phyllosphere) in the field with the hope of distinguishing between bacterial microbiota that may be endemic to plants as opposed to introduced by environmental forces. Using 16S rRNA gene amplicons to study bacterial membership at four time points, we found that the vast majority of all species-level operational taxonomic units were shared at all time-points. Very few taxa were unique to phyllosphere samples. A higher taxonomic diversity was consistently observed in the control samples. The high level of shared taxonomy suggests that environmental forces likely play a very important role in the introduction of microbes to plant surfaces. The observation that very few taxa were unique to the plants compared to the number that were unique to controls was surprising and further suggests that a subset of environmentally introduced taxa thrive on plants. This finding has important implications for improving our approach to the description of core phytobiomes as well as potentially helping us better understand how foodborne pathogens may become associated with plant surfaces.
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12
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Singh P, Singh SM, Roy U. Taxonomic characterization and the bio-potential of bacteria isolated from glacier ice cores in the High Arctic. J Basic Microbiol 2015; 56:275-85. [PMID: 26567474 DOI: 10.1002/jobm.201500298] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 10/18/2015] [Indexed: 11/05/2022]
Abstract
Glacier ice and firn cores have ecological and biotechnological importance. The present study is aimed at characterizing bacteria in crustal ice cores from Svalbard, the Arctic. Counts of viable isolates ranged from 10 to 7000 CFU/ml (mean 803 CFU/ml) while the total bacterial numbers ranged from 7.20 × 10(4) to 2.59 × 10(7) cells ml(-1) (mean 3.12 × 10(6) cells ml(-1) ). Based on 16S rDNA sequence data, the identified species belonged to seven species, namely Bacillus barbaricus, Pseudomonas orientalis, Pseudomonas oryzihabitans, Pseudomonas fluorescens, Pseudomonas syncyanea, Sphingomonas dokdonensis, and Sphingomonas phyllosphaerae, with a sequence similarity ranging between 93.5 and 99.9% with taxa present in the database. The isolates exhibited unique phenotypic properties, and three isolates (MLB-2, MLB-5, and MLB-9) are novel species, yet to be described. To the best of our knowledge, this is the first report on characterization of cultured bacterial communities from Svalbard ice cores. We conclude that high lipase, protease, cellulase, amylase, and urease activities expressed by most of the isolates provide a clue to the potential industrial applications of these organisms. These microbes, producing cold-adapted enzymes may provide an opportunity for biotechnological research.
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Affiliation(s)
- Purnima Singh
- Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, Zuarinagar, Goa-403726, India
| | - Shiv Mohan Singh
- National Centre for Antarctic and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, Goa-403804, India
| | - Utpal Roy
- Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, Zuarinagar, Goa-403726, India
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13
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Kämpfer P, Busse HJ, McInroy JA, Glaeser SP. Sphingomonas zeae sp. nov., isolated from the stem of Zea mays. Int J Syst Evol Microbiol 2015; 65:2542-2548. [PMID: 25944808 DOI: 10.1099/ijs.0.000298] [Citation(s) in RCA: 13] [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 yellow-pigmented bacterial isolate (strain JM-791T) obtained from the healthy internal stem tissue of 1-month-old corn (Zea mays, cultivar 'Sweet Belle') grown at the Plant Breeding Unit of the E.V. Smith Research Center in Tallassee (Elmore county), Alabama, USA, was taxonomically characterized. The study employing a polyphasic approach, including 16S RNA gene sequence analysis, physiological characterization, estimation of the ubiquinone and polar lipid patterns, and fatty acid composition, revealed that strain JM-791T shared 16S rRNA gene sequence similarities with type strains of Sphingomonas paucimobilis (98.3%), Sphingomonas pseudosanguinis (97.5%) and Sphingomonas yabuuchiae (97.4%), but also showed pronounced differences, both genotypically and phenotypically. On the basis of these results, a novel species of the genus Sphingomonas is described, for which we propose the name Sphingomonas zeae sp. nov. with the type strain JM-791T ( = LMG 28739T = CCM 8596T).
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
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14
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Schada von Borzyskowski L, Remus-Emsermann M, Weishaupt R, Vorholt JA, Erb TJ. A set of versatile brick vectors and promoters for the assembly, expression, and integration of synthetic operons in Methylobacterium extorquens AM1 and other alphaproteobacteria. ACS Synth Biol 2015; 4:430-43. [PMID: 25105793 DOI: 10.1021/sb500221v] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The discipline of synthetic biology requires standardized tools and genetic elements to construct novel functionalities in microorganisms; yet, many model systems still lack such tools. Here, we describe a novel set of vectors that allows the convenient construction of synthetic operons in Methylobacterium extorquens AM1, an important alphaproteobacterial model organism for methylotrophy and a promising platform organism for methanol-based biotechnology. In addition, we provide a set of constitutive alphaproteobacterial promoters of different strengths that were characterized in detail by two approaches: on the single-cell scale and on the cell population level. Finally, we describe a straightforward strategy to deliver synthetic constructs to the genome of M. extorquens AM1 and other Alphaproteobacteria. This study defines a new standard to systematically characterize genetic parts for their use in M. extorquens AM1 by using single-cell fluorescence microscopy and opens the toolbox for synthetic biological applications in M. extorquens AM1 and other alphaproteobacterial model systems.
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Affiliation(s)
- Lennart Schada von Borzyskowski
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg
4, 8093 Zurich, Switzerland
| | - Mitja Remus-Emsermann
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg
4, 8093 Zurich, Switzerland
| | - Ramon Weishaupt
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg
4, 8093 Zurich, Switzerland
| | - Julia A. Vorholt
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg
4, 8093 Zurich, Switzerland
| | - Tobias J. Erb
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg
4, 8093 Zurich, Switzerland
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15
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Remus-Emsermann MNP, Lücker S, Müller DB, Potthoff E, Daims H, Vorholt JA. Spatial distribution analyses of natural phyllosphere-colonizing bacteria onArabidopsis thalianarevealed by fluorescencein situhybridization. Environ Microbiol 2014; 16:2329-40. [DOI: 10.1111/1462-2920.12482] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/05/2014] [Indexed: 01/05/2023]
Affiliation(s)
| | - Sebastian Lücker
- Division of Microbial Ecology; Department of Microbiology and Ecosystem Science; University of Vienna; Altanstrasse 14 Vienna 1090 Austria
| | - Daniel B. Müller
- Institute of Microbiology; ETH Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Eva Potthoff
- Institute of Microbiology; ETH Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Holger Daims
- Division of Microbial Ecology; Department of Microbiology and Ecosystem Science; University of Vienna; Altanstrasse 14 Vienna 1090 Austria
| | - Julia A. Vorholt
- Institute of Microbiology; ETH Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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16
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Bodenhausen N, Bortfeld-Miller M, Ackermann M, Vorholt JA. A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota. PLoS Genet 2014; 10:e1004283. [PMID: 24743269 PMCID: PMC3990490 DOI: 10.1371/journal.pgen.1004283] [Citation(s) in RCA: 238] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 02/18/2014] [Indexed: 12/12/2022] Open
Abstract
The identity of plant host genetic factors controlling the composition of the plant microbiota and the extent to which plant genes affect associated microbial populations is currently unknown. Here, we use a candidate gene approach to investigate host effects on the phyllosphere community composition and abundance. To reduce the environmental factors that might mask genetic factors, the model plant Arabidopsis thaliana was used in a gnotobiotic system and inoculated with a reduced complexity synthetic bacterial community composed of seven strains representing the most abundant phyla in the phyllosphere. From a panel of 55 plant mutants with alterations in the surface structure, cell wall, defense signaling, secondary metabolism, and pathogen recognition, a small number of single host mutations displayed an altered microbiota composition and/or abundance. Host alleles that resulted in the strongest perturbation of the microbiota relative to the wild-type were lacs2 and pec1. These mutants affect cuticle formation and led to changes in community composition and an increased bacterial abundance relative to the wild-type plants, suggesting that different bacteria can benefit from a modified cuticle to different extents. Moreover, we identified ein2, which is involved in ethylene signaling, as a host factor modulating the community's composition. Finally, we found that different Arabidopsis accessions exhibited different communities, indicating that plant host genetic factors shape the associated microbiota, thus harboring significant potential for the identification of novel plant factors affecting the microbiota of the communities. The leaves of plants are inhabited by a diverse community of microorganisms. These leaf inhabitants influence their hosts with respect to growth and resistance to abiotic and biotic stresses. Recent studies revealed that the bacterial communities associated with leaves undergo selection, resulting in conserved microbial communities. However, the factors that are involved in structuring of bacterial communities are not well understood. In order to uncover host genetic factors that determine the community composition and to exclude confounding environmental effects, we inoculated Arabidopsis thaliana with a synthetic bacterial community under controlled conditions We screened a panel of Arabidopsis mutants defective in various traits for alterations in community structure and abundance and were able to show that cuticle synthesis and ethylene perception affect the bacterial community. In addition, we identified plant ecotypes with drastic differences in the community composition. Our system can thus be used to identify additional host genes and to broaden insights into plant microbe interactions, potentially providing a basis for applied plant protection through the identification of traits that enhance growth of plant probiotic bacteria.
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Affiliation(s)
| | | | - Martin Ackermann
- Department of Environmental Sciences, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland
| | - Julia A. Vorholt
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
- * E-mail:
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17
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Kim SJ, Moon JY, Lim JM, Ahn JH, Weon HY, Ahn TY, Kwon SW. Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively. Int J Syst Evol Microbiol 2014; 64:926-932. [DOI: 10.1099/ijs.0.055269-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains, designated 5413J-26T and KIS18-15T, were isolated from the air and forest soil, respectively, in South Korea. Cells of the two strains were Gram-stain-negative, aerobic, polar-flagellated and rod-shaped. According to the phylogenetic tree, strains 5413J-26T and KIS18-15T fell into the cluster of
Sphingomonas
sensu stricto. Strain 5413J-26T showed the highest sequence similarities with
Sphingomonas trueperi
LMG 2142T (96.6 %),
Sphingomonas molluscorum
KMM 3882T (96.5 %),
Sphingomonas azotifigens
NBRC 15497T (96.3 %) and
Sphingomonas pituitosa
EDIVT (96.1 %), while strain KIS18-15T had the highest sequence similarity with
Sphingomonas soli
T5-04T (96.8 %),
Sphingomonas pituitosa
EDIVT (96.6 %),
Sphingomonas leidyi
ATCC 15260T (96.6 %),
Sphingomonas asaccharolytica
NBRC 15499T (96.6 %) and
Sphingomonas koreensis
JSS26T (96.6 %). The 16S rRNA gene sequence similarity between strains 5413J-26T and KIS18-15T was 95.4 %. Ubiquinone 10 was the predominant respiratory quinone and homospermidine was the major polyamine. The major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and several unidentified phospholipids and lipids. The main cellular fatty acids (>10 % of the total fatty acids) of strain 5413J-26T were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C14 : 0 2-OH, and those of strain KIS18-15T were summed feature 8 and C16 : 0. Based on the results of 16S rRNA gene sequence analysis, and physiological and biochemical characterization, two novel species with the suggested names Sphingomonas aerophila sp. nov. (type strain 5413J-26T = KACC 16533T = NBRC 108942T) and Sphingomonas naasensis sp. nov. (type strain KIS18-15T = KACC 16534T = NBRC 108943T) are proposed.
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Affiliation(s)
- Soo-Jin Kim
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Ji-Young Moon
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Jun-Muk Lim
- Department of Microbiology, Dankook University, Anseo-dong, Cheonan 330-714, Republic of Korea
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Jae-Hyung Ahn
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Tae-Young Ahn
- Department of Microbiology, Dankook University, Anseo-dong, Cheonan 330-714, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
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18
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Huang HY, Li J, Zhao GZ, Zhu WY, Yang LL, Tang HY, Xu LH, Li WJ. Sphingomonas endophytica sp. nov., isolated from Artemisia annua L. Int J Syst Evol Microbiol 2012; 62:1576-1580. [DOI: 10.1099/ijs.0.031484-0] [Citation(s) in RCA: 25] [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 novel bacterium (strain YIM 65583T) belonging to the genus
Sphingomonas
was isolated from surface-sterilized tissue of Artemisia annua L., which was collected from Yunnan province, south-west China. Its morphology, physiology and biochemical features were consistent with those of members of the genus
Sphingomonas
. Analysis of the 16S rRNA gene sequence of strain YIM 65583T further confirmed that it should be classified as a member of the genus
Sphingomonas
and was most closely related to
Sphingomonas phyllosphaerae
FA2T (99.7 %) and
Sphingomonas yunnanensis
YIM 003T (98.3 %). The isolate was Gram-negative and formed yellow-pigmented colonies on ISP 2 medium. It grew optimally at pH 6.0–8.0, at 20–37 °C and in the presence of 0–1 % (w/v) NaCl. The major respiratory lipoquinone was ubiquinone-10; C18 : 1ω7c, anteiso-C16 : 1, C14 : 0-2OH, C17 : 1ω6c, C16 : 0 and C15 : 0 were the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid. The G+C content of the genomic DNA was 63.3 mol%. The DNA–DNA relatedness values of the isolate YIM 65583T with
S. phyllosphaerae
FA2T and
S. yunnanensis
YIM 003T were 43.1 % and 37.9 %, respectively. Based on these features, it is concluded that the strain represents a novel species of the genus Sphingomonas, for which the name
Sphingomonas
endophytica sp. nov. is proposed, with YIM 65583T ( = CCTCC AA 209035T = JCM 17394T) as the type strain.
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Affiliation(s)
- Hai-Yu Huang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Jie Li
- Key Laboratory of Marine Bio-resources Sustainable Utilization CAS, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Guo-Zhen Zhao
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Wen-Yong Zhu
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Ling-Ling Yang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Hai-Yun Tang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Li-Hua Xu
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Wen-Jun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, PR China
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
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19
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Thawornwiriyanun P, Tanasupawat S, Dechsakulwatana C, Techkarnjanaruk S, Suntornsuk W. Identification of newly zeaxanthin-producing bacteria isolated from sponges in the Gulf of Thailand and their zeaxanthin production. Appl Biochem Biotechnol 2012; 167:2357-68. [PMID: 22715027 DOI: 10.1007/s12010-012-9760-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 05/29/2012] [Indexed: 11/24/2022]
Abstract
Sponge-associated bacteria have been found to produce a variety of bioactive compounds including natural pigments. Here, we report the molecular identification of zeaxanthin-producing sponge-associated bacteria isolated from sponges in the Gulf of Thailand and the effect of environmental factors on zeaxanthin production from a bacterium. Three colorful sponge-associated bacteria (CHOB06-6, KODA19-6, and MAKB08-4) were identified based on the 16S rDNA profile. The 16S rDNA sequence-based analyses revealed that CHOB 06-6 and MAKB 08-4 were the closest relatives to Sphingomonas phyllosphaerae FA2(T), and KODA19-6 was a relative of Shingomonas (Blastomonas) natatoria DSM 3183(T). After all bacteria were cultivated in a modified Zobell medium, S. natatoria KODA19-6 was found to produce the highest zeaxanthin at 0.62 mg/l. pH and temperature considerably affected its zeaxanthin production. Its optimal condition for zeaxanthin production was found at a pH of 7 and 30 °C. The bacterium had a maximum specific growth rate (μ(max)) of 0.06 1/h with zeaxanthin productivity (Q(p)) of 6.27 μg/l·h. Therefore, this newly zeaxanthin-producing bacterium has a potential to produce natural zeaxanthin for the food, feed, pharmaceutical, and cosmetic industries.
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Affiliation(s)
- Patcharee Thawornwiriyanun
- Department of Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi, Thung-Kru, Bangkok 10140, Thailand
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20
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Chung EJ, Jo EJ, Yoon HS, Song GC, Jeon CO, Chung YR. Sphingomonas oryziterrae sp. nov. and Sphingomonas jinjuensis sp. nov. isolated from rhizosphere soil of rice (Oryza sativa L.). Int J Syst Evol Microbiol 2011; 61:2389-2394. [DOI: 10.1099/ijs.0.023846-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-reaction-negative, yellow–orange-pigmented, rod-shaped bacterial strains, designated YC6722T and YC6723T, were isolated from rhizosphere soil samples collected from rice fields in Jinju, Korea. Strains YC6722T and YC6723T grew optimally at 25–30 °C and at pH 7.0–8.5. Phylogenetic analyses of 16S rRNA gene sequences showed that strain YC6722T was most closely related to Sphingomonas jaspsi TDMA-16T (96.6 % sequence similarity) and strain YC6723T was related most closely to Sphingomonas aquatilis JSS7T (96.9 %). The two strains contained ubiquinone-10 (Q-10) as the major respiratory quinone system and sym-homospermidine as the major polyamine. The G+C contents of the genomic DNA of strains YC6722T and YC6723T were 63.3 and 61.0 mol%, respectively. The major fatty acid was C18 : 1ω7c. The polar lipids detected in the two strains were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, sphingoglycolipid, phosphatidyldimethylethanolamine and other unknown lipids. On the basis of their phylogenetic positions, and their biochemical and phenotypic characteristics, strains YC6722T and YC6723T represent two novel species of the genus Sphingomonas, for which the names Sphingomonas oryziterrae sp. nov. ( = KCTC 22476T = DSM 21455T) and Sphingomonas jinjuensis sp. nov. (KCTC 22477T = DSM 21457T) are proposed.
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Affiliation(s)
- Eu Jin Chung
- Department of Research and Development, JGreen Inc., Changnyeong 635-806, Republic of Korea
| | - Eun Ju Jo
- Division of Applied Life Science (BK 21), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Hwan Sik Yoon
- Division of Applied Life Science (BK 21), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Geun Cheol Song
- Division of Applied Life Science (BK 21), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Che Ok Jeon
- Department of Life Sciences, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Young Ryun Chung
- Division of Applied Life Science (BK 21), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
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21
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Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. Appl Environ Microbiol 2011; 77:3202-10. [PMID: 21421777 DOI: 10.1128/aem.00133-11] [Citation(s) in RCA: 290] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Diverse bacterial taxa live in association with plants without causing deleterious effects. Previous analyses of phyllosphere communities revealed the predominance of few bacterial genera on healthy dicotyl plants, provoking the question of whether these commensals play a particular role in plant protection. Here, we tested two of them, Methylobacterium and Sphingomonas, with respect to their ability to diminish disease symptom formation and the proliferation of the foliar plant pathogen Pseudomonas syringae pv. tomato DC3000 on Arabidopsis thaliana. Plants were grown under gnotobiotic conditions in the absence or presence of the potential antagonists and then challenged with the pathogen. No effect of Methylobacterium strains on disease development was observed. However, members of the genus Sphingomonas showed a striking plant-protective effect by suppressing disease symptoms and diminishing pathogen growth. A survey of different Sphingomonas strains revealed that most plant isolates protected A. thaliana plants from developing severe disease symptoms. This was not true for Sphingomonas strains isolated from air, dust, or water, even when they reached cell densities in the phyllosphere comparable to those of the plant isolates. This suggests that plant protection is common among plant-colonizing Sphingomonas spp. but is not a general trait conserved within the genus Sphingomonas. The carbon source profiling of representative isolates revealed differences between protecting and nonprotecting strains, suggesting that substrate competition plays a role in plant protection by Sphingomonas. However, other mechanisms cannot be excluded at this time. In conclusion, the ability to protect plants as shown here in a model system may be an unexplored, common trait of indigenous Sphingomonas spp. and may be of relevance under natural conditions.
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22
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Sphingomonas ginsenosidimutans sp. nov., with ginsenoside converting activity. J Microbiol 2011; 48:760-6. [DOI: 10.1007/s12275-010-0469-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 12/14/2010] [Indexed: 10/18/2022]
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23
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Yi TH, Han CK, Srinivasan S, Lee KJ, Kim MK. Sphingomonas humi sp. nov., isolated from soil. J Microbiol 2010; 48:165-9. [DOI: 10.1007/s12275-010-0011-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 04/12/2010] [Indexed: 10/19/2022]
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24
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Suda W, Oto M, Amachi S, Shinoyama H, Shishido M. A Direct Method to Isolate DNA from Phyllosphere Microbial Communities without Disrupting Leaf Tissues. Microbes Environ 2008; 23:248-52. [DOI: 10.1264/jsme2.23.248] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Wataru Suda
- Graduate School of Horticulture, Chiba University
| | - Michiei Oto
- Department of Biotechnology, Tokyo Technical College
| | - Seigo Amachi
- Graduate School of Horticulture, Chiba University
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25
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Zurdo-Piñeiro JL, Rivas R, Trujillo ME, Vizcaíno N, Carrasco JA, Chamber M, Palomares A, Mateos PF, Martínez-Molina E, Velázquez E. Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain. Int J Syst Evol Microbiol 2007; 57:784-788. [PMID: 17392207 DOI: 10.1099/ijs.0.64613-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains named ESC1(T) and ESC5 were isolated from nodules of Cytisus scoparius growing in a Spanish soil. Phylogenetic analysis of the 16S rRNA gene showed that these strains belong to the genus Ochrobactrum, their closest relatives being Ochrobactrum anthropi and Ochrobactrum lupini, with 100 and 99.9 % similarity to the respective type strains. Despite this high similarity, the results of DNA-DNA hybridization, phenotypic tests and fatty acid analyses showed that these strains represent a novel species of genus Ochrobactrum. The DNA-DNA hybridization values were respectively 70, 66 and 55 % with respect to O. lupini LUP21(T), O. anthropi DSM 6882(T) and Ochrobactrum tritici DSM 13340(T). The predominant fatty acids were C(18 : 1)omega7c and C(18 : 1) 2-OH. Strains ESC1(T) and ESC5 were strictly aerobic and were able to reduce nitrate and to hydrolyse aesculin. They produced beta-galactosidase and beta-glucosidase and did not produce urease after 48 h incubation. The G+C content of strain ESC1(T) was 56.4 mol%. Both strains ESC1(T) and ESC5 contained nodD and nifH genes on megaplasmids that were related phylogenetically to those of rhizobial strains nodulating Phaseolus, Leucaena, Trifolium and Lupinus. From the results of this work, we propose that the strains isolated in this study be included in a novel species named Ochrobactrum cytisi sp. nov. The type strain is ESC1(T) (=LMG 22713(T)=CECT 7172(T)).
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Affiliation(s)
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Nieves Vizcaíno
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | | | | | - Antonio Palomares
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
| | - Pedro F Mateos
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | | | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
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Rivas R, García-Fraile P, Peix A, Mateos PF, Martínez-Molina E, Velázquez E. Alcanivorax balearicus sp. nov., isolated from Lake Martel. Int J Syst Evol Microbiol 2007; 57:1331-1335. [PMID: 17551053 DOI: 10.1099/ijs.0.64912-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated MACL04(T) was isolated from Lake Martel, a subterraneous saline lake in Mallorca (Spain). The complete 16S rRNA gene sequence of this strain showed nearly 100 % similarity to that of Alcanivorax dieselolei B-5(T). Despite this high similarity, strain MACL04(T) showed phenotypic, chemotaxonomic and molecular differences with respect to A. dieselolei, indicating that strain MACL04(T) represents a separate species. Cells of strain MACL04(T) were motile by means of a single polar or subpolar flagellum and colonies formed on media containing 1 % (v/v) Tween 20 were opaque and mucoid, with blue-green iridescence. The generation time of strain MACL04(T) in this medium was approximately half that of A. dieselolei B-5(T) and strain MACL04(T) did not produce lipases after incubation for 5 days. Strain MACL04(T) did not require NaCl for growth and grew in the presence of up to 15 % (w/v) NaCl. The strain was able to use alkanes as a sole carbon source; however, glucose could also be used, albeit weakly, as a carbon source. Several amino acids and organic acids were used as carbon sources. Strain MACL04(T) produced acid in media containing pyruvate as the sole carbon source. The major fatty acids were C(19 : 0) cyclo omega8c and C(16 : 0). The fatty acid C(16 : 1)omega8c, present in strain MACL04(T), was not detected in the recognized Alcanivorax species. The sequences of the large and short 16S-23S intergenic spacer regions showed similarities of 97.2 and 98.8 % (ungapped) with respect to A. dieselolei B-5(T). Partial sequences of gyrB and alkb genes showed 94.0 % similarity between strain MACL04(T) and A. dieselolei B-5(T). The G+C content of strain MACL04(T) was 62.8 mol%. The data from this polyphasic study indicate that strain MACL04(T) represents a novel species of the genus Alcanivorax, for which the name Alcanivorax balearicus sp. nov. is proposed. The type strain is MACL04(T) (=LMG 22508(T)=CECT 5683(T)).
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MESH Headings
- Alcanivoraceae/classification
- Alcanivoraceae/drug effects
- Alcanivoraceae/isolation & purification
- Alcanivoraceae/physiology
- Alkanes/metabolism
- Amino Acids/metabolism
- Anti-Bacterial Agents/pharmacology
- Bacterial Proteins/genetics
- Bacterial Typing Techniques
- Base Composition
- Carboxylic Acids/metabolism
- DNA Gyrase/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Fatty Acids/analysis
- Flagella/physiology
- Genes, rRNA
- Lipase/analysis
- Locomotion
- Mixed Function Oxygenases/genetics
- Molecular Sequence Data
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Saline Solution, Hypertonic/pharmacology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Spain
- Water Microbiology
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Affiliation(s)
- Raúl Rivas
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie en Microbiologie, Universiteit Gent KL, Ledeganckstraat 35, B-9000 Gent, Belgium
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
| | | | - Alvaro Peix
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
| | - Pedro F Mateos
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
| | | | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
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Gich F, Overmann J. Sandarakinorhabdus limnophila gen. nov., sp. nov., a novel bacteriochlorophyll a-containing, obligately aerobic bacterium isolated from freshwater lakes. Int J Syst Evol Microbiol 2006; 56:847-854. [PMID: 16585705 DOI: 10.1099/ijs.0.63970-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains (so36, so42T and wo26) representing a novel Gram-negative, obligately aerobic, bacteriochlorophyll a-containing species of the alpha-4 subgroup of the Proteobacteria were isolated from freshwater lakes using a high-throughput cultivation technique. The non-motile and slender rod-shaped cells formed orange-red-pigmented colonies. The main carotenoids were nostoxanthin and keto-nostoxanthin. According to the absorption spectrum, two different photosynthetic light-harvesting complexes, an LHI complex and a B800-830-type peripheral LHII complex, were present in the cells. The predominant fatty acids of strain so42T were hexadecenoic acid (16 : 1omega7c) and octadecenoic acid (18 : 1omega7c), whereas 17 : 1omega6c and 14 : 0 iso 2-OH were present in smaller amounts. The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, glycolipid and sphingoglycolipids. The major respiratory lipoquinone was ubiquinone-10, whereas ubiquinone-9 was present in smaller amounts. The three strains were cytochrome oxidase-negative and catalase-positive and formed alkaline and acid phosphatases. The strains grew chemoorganoheterotrophically in mineral media supplemented with various organic acids, amino acids or complex substrates such as peptone and yeast extract. The G+C content of the genomic DNA of strain so42T was 64.3 mol%. The three novel isolates contained the same 16S rRNA gene sequence. The 16S rRNA gene sequence similarity to the closest phylogenetic relative Sandaracinobacter sibiricus was only 92.8 %. Accordingly, the three strains represent a new genus and species, for which the name Sandarakinorhabdus limnophila gen. nov., sp. nov., is proposed, with strain so42T (=DSM 17366T = CECT 7086T) as the designated type strain.
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Affiliation(s)
- Frederic Gich
- Bereich Mikrobiologie, Ludwig-Maximilians-Universität München, Maria-Ward-Str. 1a, D-80638 München, Germany
| | - Jörg Overmann
- Bereich Mikrobiologie, Ludwig-Maximilians-Universität München, Maria-Ward-Str. 1a, D-80638 München, Germany
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Yang DC, Im WT, Kim MK, Ohta H, Lee ST. Sphingomonas soli sp. nov., a β-glucosidase-producing bacterium in the family Sphingomonadaceae in the α-4 subgroup of the Proteobacteria. Int J Syst Evol Microbiol 2006; 56:703-707. [PMID: 16585680 DOI: 10.1099/ijs.0.63839-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain T5-04T, a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from soil of a ginseng field in South Korea and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain T5-04T belongs to the α-4 subgroup of the Proteobacteria, and the highest degrees of sequence similarity determined were to Sphingomonas asaccharolytica IFO 10564T (97·5 %), Sphingomonas koreensis JSS26T (97·1 %), Sphingomonas mali IFO 15500T (96·7 %) and Sphingomonas pruni IFO 15498T (96·6 %). Chemotaxonomic data revealed that strain T5-04T possesses ubiquinone Q-10 predominantly, C18 : 1 as the predominant fatty acid and sphingoglycolipids, all of which corroborate its assignment to the genus Sphingomonas. The results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that strain T5-04T represents a distinct species. Based on polyphasic evidence, T5-04T (=KCTC 12210T=NBRC 100801T=IAM 15213T) should be classified as the type strain of a novel Sphingomonas species, for which the name Sphingomonas soli sp. nov. is proposed.
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Affiliation(s)
- Deok-Chun Yang
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University, 1 Seocheon, Kihung Yongin, Kyunggi 449-701, South Korea
| | - Wan-Taek Im
- Environmental and Molecular Microbiology Lab., Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Guseong-dong 373-1, Yuseong-gu, Daejeon 305-701, South Korea
| | - Myung Kyum Kim
- Environmental and Molecular Microbiology Lab., Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Guseong-dong 373-1, Yuseong-gu, Daejeon 305-701, South Korea
| | - Hiroyuki Ohta
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ami-machi, Ibaraki 300-0393, Japan
| | - Sung-Taik Lee
- Environmental and Molecular Microbiology Lab., Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Guseong-dong 373-1, Yuseong-gu, Daejeon 305-701, South Korea
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Zhang YQ, Chen YG, Li WJ, Tian XP, Xu LH, Jiang CL. Sphingomonas yunnanensis sp. nov., a novel Gram-negative bacterium from a contaminated plate. Int J Syst Evol Microbiol 2005; 55:2361-2364. [PMID: 16280497 DOI: 10.1099/ijs.0.63697-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative bacterium, YIM 003T, which was isolated from a contaminated plate in the laboratory, was subjected to a polyphasic taxonomic study. The organism had short-rod-shaped, motile cells, formed yellow-pigmented colonies on ISP2 medium and its optimum growth pH was 7·0–7·5. The major respiratory lipoquinone was ubiquinone Q-10. The phosphate-containing lipids detected in strain YIM 003T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and one unidentified phospholipid. The major fatty acids were C18 : 1
ω7c (59·8 %), C16 : 0 (9·9 %), ai-C17 : 0 (5·3 %), i-C17 : 0 (4·4 %) and C14 : 0 2-OH (15·8 %). The G+C content of the genomic DNA was 67·5 mol%. Strain YIM 003T exhibited levels of 16S rRNA gene sequence similarity of 98·2 % to Sphingomonas phyllosphaerae FA2T and 98·0 % to Sphingomonas adhaesiva DSM 7418T but showed less than 97·0 % similarity with respect to other species with validly published names. The DNA–DNA relatedness values of the isolate with S. phyllosphaerae FA2T and S. adhaesiva DSM 7418T were 59 and 26 %, respectively. The phenotypic characteristics and genotypic data indicate that strain YIM 003T should be distinguished from S. phyllosphaerae FA2T and S. adhaesiva DSM 7418T. Therefore, on the basis of the polyphasic taxonomic data presented, a novel species of the genus Sphingomonas, Sphingomonas yunnanensis sp. nov., is proposed, with the type strain YIM 003T (=CCTCC AB 204064T=KCTC 12346T).
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Affiliation(s)
- Yu-Qin Zhang
- The Key Laboratory for Microbial Resources of Ministry of Education, Yunnan Institute of Microbiology and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Yi-Guang Chen
- The Key Laboratory for Microbial Resources of Ministry of Education, Yunnan Institute of Microbiology and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Wen-Jun Li
- The Key Laboratory for Microbial Resources of Ministry of Education, Yunnan Institute of Microbiology and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Xin-Peng Tian
- The Key Laboratory for Microbial Resources of Ministry of Education, Yunnan Institute of Microbiology and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Li-Hua Xu
- The Key Laboratory for Microbial Resources of Ministry of Education, Yunnan Institute of Microbiology and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650091, PR China
| | - Cheng-Lin Jiang
- The Key Laboratory for Microbial Resources of Ministry of Education, Yunnan Institute of Microbiology and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan 650091, PR China
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