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Saroj DB, Ahire JJ, Shukla R. Genetic and phenotypic assessments for the safety of probiotic Bacillus clausii 088AE. 3 Biotech 2023; 13:238. [PMID: 37333714 PMCID: PMC10275836 DOI: 10.1007/s13205-023-03662-4] [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: 12/29/2022] [Accepted: 06/05/2023] [Indexed: 06/20/2023] Open
Abstract
In this study, we report on whole genome sequence analysis of clinically documented, commercial probiotic Bacillus clausii 088AE and genome features contributing to probiotic properties. The whole genome sequence of B. clausii 088AE generated a single scaffold of 4,598,457 bp with 44.74 mol% G + C. This assembled genome sequence annotated by the RAST resulted in 4371 coding genes, 75 tRNAs, and 22 rRNAs. Gene ontology classification indicated 39.5% proteins with molecular function, 44.24% cellular component, and 16.25% proteins involved in biological processes. In taxonomic analysis, B. clausii 088AE shared 99% identity with B. clausii DSM 8716. The gene sequences related to safety and genome stability such as antibiotic resistance (840), virulence factors (706), biogenic amines (1), enterotoxin (0), emetic toxin (0), lanthipeptides (4), prophage (4) and clustered regularly interspaced short palindromic repeats (CRISPR) sequences (11), were identified and evaluated for safety and functions. The absence of functional prophage sequences and the presence of CRISPR indicated an advantage in genome stability. Moreover, the presence of genome features contributing to probiotic characteristics such as acid, and bile salt tolerance, adhesion to the gut mucosa, and environmental resistance ensure the strains survivability when consumed as a probiotic. In conclusion, the absence of risks associated with sequences/genes in the B. clausii 088AE genome and the presence of essential probiotic traits confirm the strain to be safe for use as a probiotic.
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Affiliation(s)
- Dina B. Saroj
- Advanced Enzyme Technologies Limited, Sun Magnetica, Louiswadi, Thane-West, Maharashtra 400 604 India
| | - Jayesh J. Ahire
- Advanced Enzyme Technologies Limited, Sun Magnetica, Louiswadi, Thane-West, Maharashtra 400 604 India
| | - Rohit Shukla
- Advanced Enzyme Technologies Limited, Sun Magnetica, Louiswadi, Thane-West, Maharashtra 400 604 India
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Singh A, Maity A, Singh N. Structure and Dynamics of dsDNA in Cell-like Environments. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1587. [PMID: 36359677 PMCID: PMC9689892 DOI: 10.3390/e24111587] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 06/01/2023]
Abstract
Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA's structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures.
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Khalilova EA, Kotenko ST, Islammagomedova EA, Abakarova AA, Chernyh NА, Aliverdiyeva DA. Halophilic bacteria of salt lakes and saline soils of the Peri-Caspian lowland (Republic of Daghestan) and their biotechnological potential. Vavilovskii Zhurnal Genet Selektsii 2021; 25:224-233. [PMID: 34901720 PMCID: PMC8627887 DOI: 10.18699/vj21.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 12/02/2022] Open
Abstract
The article presents the results of studying the biodiversity and biotechnological potential of halophilic
microorganisms from the thermal highly mineralized Berikey Lake, the salty Lake Tarumovskoye and saline soils of
the Peri-Caspian Lowland (Republic of Daghestan). Denitrifying halophilic bacteria of the genus Halomonas and
Virgibacillus were identified using microbiological methods and 16S rRNA gene analysis. A new species Halomonas sp. G2 (MW386470) with a similarity of the nucleotide sequences of the 16S rRNA genes is 95 %. Strain G2 is
an extreme halophile capable of growing in the range of 5–25 % NaCl (optimum 25 %) and forming a carotenoid
pigment. Mesophil, 30–37 °С (optimum 30 °С); neutrophil, pH 6–8 (optimum 7.2–7.4). Strain G2 chemolithotroph;
reduces nitrate or nitrite as electron donors; catalase-, amylase-, protease- and β-galactosidase-positive; lipase-,
oxidase- and urease-negative. Not able to hydrolyze inositol, indole; produces lysine, gelatin, ectoine; uses citrate
and sodium malate as a source of carbon and energy; does not produce ornitin, H2S or acid from d-mannose, sucrose, glycerol, cellobiose, except for lactose and d-glucose. Susceptible to trimethoprim, ciprofloxacin, ofloxacin,
kanamycin, vancomycin, rifampicin, cefuroxime, ampicillin, ceftazidime, fosfomycin, clarithromycin, cefepime, cefaclor. The G+C content in DNA is 67.3 %. A distinctive characteristic of the isolate was the production of industrially significant hydrolytic enzymes such as amylase, protease, β-galactosidase, and oxidoreductase (catalase) at a
NaCl concentration of 25 % in the medium. Habitat: saline soils on the territory of the Tersko-Kumskaya lowland
(Republic of Daghestan, Russia). The rest of the halophilic isolates of H. ventosae G1 (MW386469), H. elongata G3
(MW386471), V. salinarius B2 (MW386472), and V. salinarius B3 (MW386473) had a high degree of similarity (100 %)
with the type strains of H. elongata DSM 2581Т
and V. salarius DSM 18441Т
; the content of G+C in DNA was 65.8,
66.5, 42.8 and 37.3 %, respectively. The strains had a high biotechnological potential at NaCl concentrations of 5 and
25 % in the medium. The data obtained expanded the understanding of the diversity and ecological significance
of denitrifying bacteria in the functioning of arid ecosystems and make it possible to identify strains producing
enzymes of industrial importance.
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Affiliation(s)
- E A Khalilova
- Precaspian Institute of Biological Resources of the Daghestan Federal Research Center of the Russian Academy of Sciences, Makhachkala, Daghestan, Russia
| | - S T Kotenko
- Precaspian Institute of Biological Resources of the Daghestan Federal Research Center of the Russian Academy of Sciences, Makhachkala, Daghestan, Russia
| | - E A Islammagomedova
- Precaspian Institute of Biological Resources of the Daghestan Federal Research Center of the Russian Academy of Sciences, Makhachkala, Daghestan, Russia
| | - A A Abakarova
- Precaspian Institute of Biological Resources of the Daghestan Federal Research Center of the Russian Academy of Sciences, Makhachkala, Daghestan, Russia
| | - N А Chernyh
- Winogradsky Institute of Microbiology, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - D A Aliverdiyeva
- Precaspian Institute of Biological Resources of the Daghestan Federal Research Center of the Russian Academy of Sciences, Makhachkala, Daghestan, Russia
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Hugenholtz P, Chuvochina M, Oren A, Parks DH, Soo RM. Prokaryotic taxonomy and nomenclature in the age of big sequence data. THE ISME JOURNAL 2021; 15:1879-1892. [PMID: 33824426 PMCID: PMC8245423 DOI: 10.1038/s41396-021-00941-x] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 02/01/2023]
Abstract
The classification of life forms into a hierarchical system (taxonomy) and the application of names to this hierarchy (nomenclature) is at a turning point in microbiology. The unprecedented availability of genome sequences means that a taxonomy can be built upon a comprehensive evolutionary framework, a longstanding goal of taxonomists. However, there is resistance to adopting a single framework to preserve taxonomic freedom, and ever increasing numbers of genomes derived from uncultured prokaryotes threaten to overwhelm current nomenclatural practices, which are based on characterised isolates. The challenge ahead then is to reach a consensus on the taxonomic framework and to adapt and scale the existing nomenclatural code, or create a new code, to systematically incorporate uncultured taxa into the chosen framework.
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Affiliation(s)
- Philip Hugenholtz
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Maria Chuvochina
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Aharon Oren
- grid.9619.70000 0004 1937 0538Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Edmond J. Safra campus, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Donovan H. Parks
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Rochelle M. Soo
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
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Pankratov TA, Grouzdev DS, Patutina EO, Kolganova TV, Berestovskaya JJ, Ashikhmin AA. Lichenicoccus roseus gen. nov., sp. nov., the first bacteriochlorophyll a-containing, psychrophilic and acidophilic Acetobacteraceae bacteriobiont of lichen Cladonia species. Int J Syst Evol Microbiol 2020; 70:4591-4601. [PMID: 32658637 DOI: 10.1099/ijsem.0.004318] [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
Gram-negative, aerobic, chemo-organotrophic and bacteriochlorophyll a-containing bacterial strains, KEBCLARHB70RT, KAMCLST3051 and KAMCLST3152, were isolated from the thalli of Cladonia arbuscula and Cladonia stellaris lichens. Cells from the strains were coccoid and reproduced by binary division. They were motile at the early stages of growth and utilized sugars and alcohols. All strains were psychrophilic and acidophilic, capable of growth between pH 3.5 and 7.5 (optimum, pH 5.5), and at 4-30 °C (optimum, 10-15 °C). The major fatty acids were C18 : 1 ω7c and C18 : 0; the lipids were phosphatidylcholines, phosphatidylethanolamines, phosphatidic acids, phosphatidylglycerol, glycolipids, diphosphatidylglycerol and polar lipids with an unknown structure. The quinone was Q-10. The DNA G+C content was 67.8 mol%. Comparative 16S rRNA gene analysis together with other data, supported that the strains, KEBCLARHB70RT, KAMCLST3051 and KAMCLST3152 belonged to the same species. Whole genome analysis of the strain KEBCLARHB70RT and average amino acid identity values confirmed its distinctive phylogenetic position within the family Acetobacteraceae. Phenotypic, ecological and genomic characteristics distinguished strains KEBCLARHB70RT, KAMCLST3051 and KAMCLST3152 from all genera in the family Acetobacteraceae. Therefore, we propose a novel genus and a novel species, Lichenicoccus roseus gen. nov., sp. nov., for these novel Acetobacteraceae members. Strain KEBCLARHB70RT (=KCTC 72321T=VKM B-3305T) has been designated as the type strain.
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Affiliation(s)
- Timofey A Pankratov
- S.N. Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Denis S Grouzdev
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Ekaterina O Patutina
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Tatiana V Kolganova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Julia J Berestovskaya
- S.N. Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Aleksandr A Ashikhmin
- Institute of Basic Biological Problems of Russian Academy of Sciences, Federal Research Center, Pushchino Scientific Center for Biological Research of Russian Academy of Sciences, Pushchino 142290, Russia
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Kevbrin V, Boltyanskaya Y, Grouzdev D, Koziaeva V, Park M, Cho JC. Natronospirillum operosum gen. nov., sp. nov., a haloalkaliphilic satellite isolated from decaying biomass of a laboratory culture of cyanobacterium Geitlerinema sp. and proposal of Natronospirillaceae fam. nov., Saccharospirillaceae fam. nov. and Gynuellaceae fam. nov. Int J Syst Evol Microbiol 2020; 70:511-521. [DOI: 10.1099/ijsem.0.003781] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Vadim Kevbrin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Yulia Boltyanskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Denis Grouzdev
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Veronika Koziaeva
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Miri Park
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
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7
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Niu R, Du CX, Esposito E, Ng J, Brenner MP, McEuen PL, Cohen I. Magnetic handshake materials as a scale-invariant platform for programmed self-assembly. Proc Natl Acad Sci U S A 2019; 116:24402-24407. [PMID: 31754038 PMCID: PMC6900514 DOI: 10.1073/pnas.1910332116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Programmable self-assembly of smart, digital, and structurally complex materials from simple components at size scales from the macro to the nano remains a long-standing goal of material science. Here, we introduce a platform based on magnetic encoding of information to drive programmable self-assembly that works across length scales. Our building blocks consist of panels with different patterns of magnetic dipoles that are capable of specific binding. Because the ratios of the different panel-binding energies are scale-invariant, this approach can, in principle, be applied down to the nanometer scale. Using a centimeter-sized version of these panels, we demonstrate 3 canonical hallmarks of assembly: controlled polymerization of individual building blocks; assembly of 1-dimensional strands made of panels connected by elastic backbones into secondary structures; and hierarchical assembly of 2-dimensional nets into 3-dimensional objects. We envision that magnetic encoding of assembly instructions into primary structures of panels, strands, and nets will lead to the formation of secondary and even tertiary structures that transmit information, act as mechanical elements, or function as machines on scales ranging from the nano to the macro.
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Affiliation(s)
- Ran Niu
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853;
| | - Chrisy Xiyu Du
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02139
| | - Edward Esposito
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853
| | - Jakin Ng
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853
| | - Michael P Brenner
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02139
| | - Paul L McEuen
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853
| | - Itai Cohen
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853;
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853
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Kurilenko VV, Romanenko LA, Isaeva MP, Svetashev VI, Mikhailov VV. Winogradskyella algae sp. nov., a marine bacterium isolated from the brown alga. Antonie Van Leeuwenhoek 2019; 112:731-739. [PMID: 30519785 DOI: 10.1007/s10482-018-1207-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
Abstract
An aerobic, Gram-negative, yellow-pigmented non-motile rod-shaped bacterium Kr9-9T was isolated from a brown alga specimen collected near the Kuril Islands. Based on the 16S rRNA gene sequence analysis strain Kr9-9T was assigned to the genus Winogradskyella, and its close phylogenetic neighbors were found to be Winogradskyella damuponensis KCTC 23552T, Winogradskyella sediminis LMG 28075T, and Winogradskyella rapida CCUG 59098T showing high similarities of 98.1%, 97.5%, and 97.1%, respectively. It contained MK-6 as the predominant menaquinone and iso-C15:0, anteiso-C15:0, iso-C16:0 3-OH followed by iso-C15:1 as the major fatty acids. Polar lipids included phosphatidylethanolamine, three unidentified aminolipids and an unidentified lipid. The DNA C+C content was 32.3 mol%. Based on the phylogenetic analysis and distinctive phenotypic characteristics, strain Kr9-9T is concluded to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella algae sp. nov. is proposed. The type strain of the species is strain Kr9-9T (= KMM 8180T = KACC 19709T).
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Affiliation(s)
- Valeriya V Kurilenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok, Russia, 690022
| | - Lyudmila A Romanenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok, Russia, 690022.
| | - Marina P Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok, Russia, 690022
| | - Vassilii I Svetashev
- Zhirmunsky Institute of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia, 690041
| | - Valery V Mikhailov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok, Russia, 690022
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Romanenko LA, Kurilenko VV, Guzev KV, Svetashev VI. Characterization of Labrenzia polysiphoniae sp. nov. isolated from red alga Polysiphonia sp. Arch Microbiol 2019; 201:705-712. [DOI: 10.1007/s00203-019-01640-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/21/2019] [Accepted: 02/20/2019] [Indexed: 10/27/2022]
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Winogradskyella profunda sp. nov. isolated from the Chukchi Sea bottom sediments. Arch Microbiol 2018; 201:45-50. [DOI: 10.1007/s00203-018-1567-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 10/28/2022]
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Belova SE, Suzina NE, Rijpstra WIC, Sinninghe Damsté JS, Dedysh SN. Edaphobacter lichenicola sp. nov., a member of the family Acidobacteriaceae from lichen-dominated forested tundra. Int J Syst Evol Microbiol 2018; 68:1265-1270. [PMID: 29465339 DOI: 10.1099/ijsem.0.002663] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An isolate of aerobic, Gram-stain-negative, rod-shaped, non-motile and light-pink pigmented bacteria, designated SBC68T, was obtained from slightly decomposed thalli of the lichen Cladonia sp. collected from the forested tundra of north-western Siberia. Cells of this isolate occurred singly, in pairs or in rosettes. These bacteria were acidophilic (optimum growth at pH 4.3-5.6) and mesophilic (optimum growth at 20-30 °C) but were also capable of growth at low temperatures, down to 7 °C. The preferred growth substrates were sugars, some organic acids and lichenan. The major fatty acids were iso-C15 : 0, C16 : 1ω7c, C16 : 0, C16 : 1ω7t, and 13,16-dimethyl octacosanedioic acid. The only quinone was MK-8, and the G+C content of the DNA was 54.7 mol%. SBC68T represented a member of the family Acidobactericeae; the closest taxonomically described relatives were Edaphobacter dinghuensis DHF9T and Granulicella aggregans TPB6028T (97.2 and 97.1 % 16S rRNA gene sequence similarity, respectively). In 16S rRNA gene-based trees, SBC68T clustered together with species of the genus Edaphobacter. However, this isolate differed from all previously described species of the genus Edaphobacter with respect to the pink pigmentation, formation of cell rosettes and substrate utilization pattern. On the basis of these data, strain SBC68T should be considered to represent a novel species of acidobacteria, for which the name Edaphobacter lichenicola sp. nov. is proposed. The type strain is SBC68T (=DSM 104462T=VKM B-3208T).
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Affiliation(s)
- Svetlana E Belova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Natalia E Suzina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Russia
| | - W Irene C Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands.,Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht University, Utrecht, The Netherlands
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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Vologodskii A, Frank-Kamenetskii MD. DNA melting and energetics of the double helix. Phys Life Rev 2017; 25:1-21. [PMID: 29170011 DOI: 10.1016/j.plrev.2017.11.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 10/23/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
Abstract
Studying melting and energetics of the DNA double helix has been one of the major topics of molecular biophysics over the past six decades. The main objective of this article is to overview the current state of the field and to emphasize that there are still serious gaps in our understanding of the issue. We start with a concise description of the commonly accepted theoretical model of the DNA melting. We then concentrate on studies devoted to the comparison with experiment of theoretically predicted melting profiles of DNAs with known sequences. For long DNA molecules, such comparison is significant from the basic-science viewpoint while an accurate theoretical description of melting of short duplexes is necessary for various very important applications in biotechnology. Several sets of DNA melting parameters, proposed within the framework of the nearest neighbor model, are compared and analyzed. The analysis leads to a conclusion that in case of long DNA molecules the consensus set of nearest neighbor parameters describes well the experimental melting profiles. Unexpectedly, for short DNA duplexes the same set of parameters hardly yields any improvement as compared to the simplest model, which completely ignores the effect of heterogeneous stacking. Possible causes of this striking observation are discussed. We then overview the issue of separation of base-pairing and base-stacking contributions into the double helix stability. The recent experimental attempts to solve the problem are extensively analyzed. It is concluded that the double helix is essentially stabilized by stacking interaction between adjacent base pairs. Base pairing between complementary pairs does not appreciably contribute into the duplex stability. In the final section of the article, kinetic aspects of the DNA melting phenomenon are discussed. The main emphasis is made on the hysteresis effects often observed in melting of long DNA molecules. It is argued that the phenomenon can be well described via an accurate theoretical treatment of the random-walk model of melting kinetics of an isolated helical segment in DNA.
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Proteinivorax hydrogeniformans sp. nov., an anaerobic, haloalkaliphilic bacterium fermenting proteinaceous compounds with high hydrogen production. Antonie van Leeuwenhoek 2017; 111:275-284. [DOI: 10.1007/s10482-017-0949-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/20/2017] [Indexed: 10/18/2022]
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14
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Kulichevskaya IS, Ivanova AA, Detkova EN, Rijpstra WIC, Sinninghe Damsté JS, Dedysh SN. Tundrisphaera lichenicola gen. nov., sp. nov., a psychrotolerant representative of the family Isosphaeraceae from lichen-dominated tundra soils. Int J Syst Evol Microbiol 2017; 67:3583-3589. [PMID: 28829024 DOI: 10.1099/ijsem.0.002172] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of aerobic, budding, pink-pigmented bacteria, P12T and P515, were isolated from a lichen-dominated peatland and a forested tundra soil of north-western Siberia, respectively. Cells of these isolates were represented by non-motile spheres that occurred singly or were arranged in short chains and aggregates. While growing on solid media, cells of strains P12T and P515 attached to the surface by means of holdfast-like appendages. These isolates were mildly acidophilic (optimum growth at pH 5.5-6.0), psychrotolerant bacteria, which displayed tolerance of low temperatures (4-15 °C), grew optimally at 15-22 °C and did not grow at temperatures above 28 °C. The preferred growth substrates were sugars and some heteropolysaccharides. The major fatty acids were C18 : 1ω9c, C16 : 0 and C14 : 0. Trimethylornithine lipid was the major polar lipid. The only quinone was MK-6, and the G+C content of the DNA was 61.2-62.2 mol%. Strains P12T and P515 possessed identical 16S rRNA gene sequences, which affiliated them with the family Isosphaeraceae, order Planctomycetales, and these displayed the highest similarity (93-94 %) to 16S rRNA gene sequences from members of the genus Singulisphaera. However, the signature fatty acid of species of the genus Singulisphaera, i.e. C18 : 2ω6c,12c, was absent in cells of strains P12T and P515. They also differed from members of the genus Singulisphaera by substrate utilization pattern and a number of physiological characteristics. Based on these data, the novel isolates should be considered as representing a novel genus and species of planctomycetes, for which the name Tundrisphaera lichenicola gen. nov., sp. nov, is proposed. The type strain is P12T (=LMG 29571T=VKM B-3044T).
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Affiliation(s)
- Irina S Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Anastasia A Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Ekaterina N Detkova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - W Irene C Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands.,Department of Earth Sciences, Geochemistry, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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15
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Singh AR, Granek R. Sufficient minimal model for DNA denaturation: Integration of harmonic scalar elasticity and bond energies. J Chem Phys 2017; 145:144101. [PMID: 27782499 DOI: 10.1063/1.4964285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We study DNA denaturation by integrating elasticity - as described by the Gaussian network model - with bond binding energies, distinguishing between different base pairs and stacking energies. We use exact calculation, within the model, of the Helmholtz free-energy of any partial denaturation state, which implies that the entropy of all formed "bubbles" ("loops") is accounted for. Considering base pair bond removal single events, the bond designated for opening is chosen by minimizing the free-energy difference for the process, over all remaining base pair bonds. Despite of its great simplicity, for several known DNA sequences our results are in accord with available theoretical and experimental studies. Moreover, we report free-energy profiles along the denaturation pathway, which allow to detect stable or meta-stable partial denaturation states, composed of bubble, as local free-energy minima separated by barriers. Our approach allows to study very long DNA strands with commonly available computational power, as we demonstrate for a few random sequences in the range 200-800 base-pairs. For the latter, we also elucidate the self-averaging property of the system. Implications for the well known breathing dynamics of DNA are elucidated.
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Affiliation(s)
- Amit Raj Singh
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
| | - Rony Granek
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
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16
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Kulichevskaya IS, Ivanova AA, Baulina OI, Rijpstra WIC, Sinninghe Damsté JS, Dedysh SN. Fimbriiglobus ruber gen. nov., sp. nov., a Gemmata-like planctomycete from Sphagnum peat bog and the proposal of Gemmataceae fam. nov. Int J Syst Evol Microbiol 2017; 67:218-224. [PMID: 27902209 DOI: 10.1099/ijsem.0.001598] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, budding, dark pink to red-pigmented bacterium was isolated from an acidic boreal Sphagnum peat bog and designated strain SP5T. Cells of this strain were non-motile spheres that were uniformly covered with crateriform pits and fimbria, and tended to form aggregates during growth in liquid media. Strain SP5T was capable of growth between pH 4.0 and pH 6.8 (optimum at pH 5.5-6.0) and at temperatures between 10 and 30 °C (optimum at 20-25 °C). The preferred growth substrates were sugars and some heteropolysaccharides. The major fatty acids were C20 : 1ω9c, C16 : 1ω9c and C16 : 0, and the major polar lipid was trimethylornithine. Cells contained also significant amounts of bound (ω-1)OH-C30 : 1 fatty acid. The quinone was menaquinone-6, and the G+C content of the DNA was 60.7 mol%. Strain SP5T was a member of the order Planctomycetales and belonged to the phylogenetic lineage defined by the genus Gemmata. It displayed 88 and 89 % 16S rRNA gene sequence similarity to Gemmata obscuriglobusUQM 2246T and 'Gemmata massiliana' IIL30, 89 % to Zavarzinella formosa A10T and 86 % to Telmatocola sphagniphila SP2T. However, strain SP5T differed from members of these genera by cell morphology, substrate utilization pattern and fatty acid composition. Based on these data, the novel isolate should be considered as representing a novel species of a new genus of planctomycetes, for which the name Fimbriiglobus ruber gen. nov., sp. nov, is proposed. The type strain is SP5T (=LMG 29572T=VKM B-3045T). We also suggest the establishment of a novel family, Gemmataceaefam. nov., which includes the phylogenetically related genera Gemmata, Zavarzinella, Telmatocola and Fimbriiglobus.
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Affiliation(s)
- Irina S Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Anastasia A Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Olga I Baulina
- Department of Bioengineering, Faculty of Biology, M.V. Lomonosov Moscow State University, GSP-1, Moscow 119234, Russia
| | - W Irene C Rijpstra
- Department of Marine Microbiology and Biogeochemistry and Utrecht University, NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S Sinninghe Damsté
- Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht University, Utrecht, The Netherlands.,Department of Marine Microbiology and Biogeochemistry and Utrecht University, NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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17
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Arango Isaza RE, Diaz-Trujillo C, Dhillon B, Aerts A, Carlier J, Crane CF, V. de Jong T, de Vries I, Dietrich R, Farmer AD, Fortes Fereira C, Garcia S, Guzman M, Hamelin RC, Lindquist EA, Mehrabi R, Quiros O, Schmutz J, Shapiro H, Reynolds E, Scalliet G, Souza M, Stergiopoulos I, Van der Lee TAJ, De Wit PJGM, Zapater MF, Zwiers LH, Grigoriev IV, Goodwin SB, Kema GHJ. Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control. PLoS Genet 2016; 12:e1005876. [PMID: 27512984 PMCID: PMC4981457 DOI: 10.1371/journal.pgen.1005876] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 01/27/2016] [Indexed: 12/03/2022] Open
Abstract
Black Sigatoka or black leaf streak disease, caused by the Dothideomycete fungus Pseudocercospora fijiensis (previously: Mycosphaerella fijiensis), is the most significant foliar disease of banana worldwide. Due to the lack of effective host resistance, management of this disease requires frequent fungicide applications, which greatly increase the economic and environmental costs to produce banana. Weekly applications in most banana plantations lead to rapid evolution of fungicide-resistant strains within populations causing disease-control failures throughout the world. Given its extremely high economic importance, two strains of P. fijiensis were sequenced and assembled with the aid of a new genetic linkage map. The 74-Mb genome of P. fijiensis is massively expanded by LTR retrotransposons, making it the largest genome within the Dothideomycetes. Melting-curve assays suggest that the genomes of two closely related members of the Sigatoka disease complex, P. eumusae and P. musae, also are expanded. Electrophoretic karyotyping and analyses of molecular markers in P. fijiensis field populations showed chromosome-length polymorphisms and high genetic diversity. Genetic differentiation was also detected using neutral markers, suggesting strong selection with limited gene flow at the studied geographic scale. Frequencies of fungicide resistance in fungicide-treated plantations were much higher than those in untreated wild-type P. fijiensis populations. A homologue of the Cladosporium fulvum Avr4 effector, PfAvr4, was identified in the P. fijiensis genome. Infiltration of the purified PfAVR4 protein into leaves of the resistant banana variety Calcutta 4 resulted in a hypersensitive-like response. This result suggests that Calcutta 4 could carry an unknown resistance gene recognizing PfAVR4. Besides adding to our understanding of the overall Dothideomycete genome structures, the P. fijiensis genome will aid in developing fungicide treatment schedules to combat this pathogen and in improving the efficiency of banana breeding programs.
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Affiliation(s)
- Rafael E. Arango Isaza
- Escuela de Biociencias, Universidad Nacional de Colombia, Medellín, Colombia
- Plant Biotechnology Unit, Corporación Para Investigaciones Biológicas, Medellín, Colombia
| | | | - Braham Dhillon
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Andrea Aerts
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | | | - Charles F. Crane
- USDA-Agricultural Research Service, West Lafayette, Indiana, United States of America
| | - Tristan V. de Jong
- Plant Research International, Wageningen University and Research, Wageningen, The Netherlands
| | - Ineke de Vries
- Plant Research International, Wageningen University and Research, Wageningen, The Netherlands
| | - Robert Dietrich
- Syngenta Biotechnology Inc., Research Triangle Park, United States of America
| | - Andrew D. Farmer
- National Center for Genome Resources, Santa Fe, United States of America
| | | | | | - Mauricio Guzman
- National Banana Corporation of Costa Rica (CORBANA), La Rita de Pococí, Limón, Costa Rica
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada
| | - Erika A. Lindquist
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Rahim Mehrabi
- Department of Genetics, Seed and Plant Improvement Institute, Karaj, Iran
| | - Olman Quiros
- National Banana Corporation of Costa Rica (CORBANA), La Rita de Pococí, Limón, Costa Rica
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Harris Shapiro
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Elizabeth Reynolds
- General Bioinformatics at Syngenta Crop protection Jeallots Hill International Research Centre, Bracknell Berkshire, United Kingdom
| | | | - Manoel Souza
- Embrapa-LABEX Europe, Wageningen, The Netherlands
| | | | - Theo A. J. Van der Lee
- Plant Research International, Wageningen University and Research, Wageningen, The Netherlands
| | | | | | | | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Stephen B. Goodwin
- USDA-Agricultural Research Service, West Lafayette, Indiana, United States of America
| | - Gert H. J. Kema
- Plant Research International, Wageningen University and Research, Wageningen, The Netherlands
- Wageningen University, Laboratory of Phytopathology, Wageningen, The Netherlands
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Rafikova GF, Korshunova TY, Minnebaev LF, Chetverikov SP, Loginov ON. A new bacterial strain, Pseudomonas koreensis IB-4, as a promising agent for plant pathogen biological control. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716030115] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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19
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Oshkin IY, Belova SE, Danilova OV, Miroshnikov KK, Rijpstra WIC, Sinninghe Damsté JS, Liesack W, Dedysh SN. Methylovulum psychrotolerans sp. nov., a cold-adapted methanotroph from low-temperature terrestrial environments, and emended description of the genus Methylovulum. Int J Syst Evol Microbiol 2016; 66:2417-2423. [DOI: 10.1099/ijsem.0.001046] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Igor Y. Oshkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Svetlana E. Belova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Olga V. Danilova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | | | - W. Irene C. Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S. Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, PO Box 59, 1790 AB Den Burg, The Netherlands
- Utrecht University, Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht, The Netherlands
| | - Werner Liesack
- Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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20
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Dziuba M, Koziaeva V, Grouzdev D, Burganskaya E, Baslerov R, Kolganova T, Chernyadyev A, Osipov G, Andrianova E, Gorlenko V, Kuznetsov B. Magnetospirillum caucaseum sp. nov., Magnetospirillum marisnigri sp. nov. and Magnetospirillum moscoviense sp. nov., freshwater magnetotactic bacteria isolated from three distinct geographical locations in European Russia. Int J Syst Evol Microbiol 2016; 66:2069-2077. [PMID: 26921147 DOI: 10.1099/ijsem.0.000994] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Three strains of helical, magnetotactic bacteria, SO-1T, SP-1T and BB-1T, were isolated from freshwater sediments collected from three distinct locations in European Russia. Phylogenetic analysis showed that the strains belong to the genus Magnetospirillum. Strains SO-1T and SP-1T showed the highest 16S rRNA gene sequence similarity to Magnetospirillum magnetotacticum MS-1T (99.3 and 98.1 %, respectively), and strain BB-1T with Magnetospirillum gryphiswaldense MSR-1T (97.3 %). The tree based on concatenated deduced amino acid sequences of the MamA, B, K, M, O, P, Q and T proteins, which are involved in magnetosome formation, was congruent with the tree based on 16S rRNA gene sequences. The genomic DNA G+C contents of strains SO-1T, SP-1T and BB-1T were 65.9, 63.0 and 65.2 mol%, respectively. As major fatty acids, C18 : 1ω9, C16 : 1ω7c, C16 : 0 and C18 : 0 were detected. DNA-DNA hybridization values between the novel strains and their closest relatives in the genus Magnetospirillum were less than 51.7 ± 2.3 %. In contrast to M. magnetotacticum MS-1T, the strains could utilize butyrate and propionate; strains SO-1T and BB-1T could also utilize glycerol. Strain SP-1T showed strictly microaerophilic growth, whereas strains SO-1T and BB-1T were more tolerant of oxygen. The results of DNA-DNA hybridization and physiological tests allowed genotypic and phenotypic differentiation of the strains from each other as well as from the two species of Magnetospirillum with validly published names. Therefore, the strains represent novel species, for which we propose the names Magnetospirillum caucaseum sp. nov. (type strain SO-1T = DSM 28995T = VKM B-2936T), Magnetospirillum marisnigri sp. nov. (type strain SP-1T = DSM 29006T = VKM B-2938T) and Magnetospirillum moscoviense sp. nov. (type strain BB-1T = DSM 29455T = VKM B-2939T).
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Affiliation(s)
- Marina Dziuba
- Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences,Leninsky Ave 33, bld. 2, Moscow 119071,Russia
| | - Veronika Koziaeva
- Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences,Leninsky Ave 33, bld. 2, Moscow 119071,Russia
| | - Denis Grouzdev
- Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences,Leninsky Ave 33, bld. 2, Moscow 119071,Russia
| | - Ekaterina Burganskaya
- Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences,Leninsky Ave 33, bld. 2, Moscow 119071,Russia
| | - Roman Baslerov
- Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences,Leninsky Ave 33, bld. 2, Moscow 119071,Russia
| | - Tatjana Kolganova
- Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences,Leninsky Ave 33, bld. 2, Moscow 119071,Russia
| | - Alexander Chernyadyev
- Education and Research Center Nanotechnology, Vyatka State University,Moscovskaya str. 36, Kirov 610000,Russia
| | - Georgy Osipov
- Bakulev Center of Cardiovascular Surgery, Russian Academy of Medical Sciences,Rublevskoe shosse 135, Moscow 121552,Russia
| | - Ekaterina Andrianova
- Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences,Leninsky Ave 33, bld. 2, Moscow 119071,Russia
| | - Vladimir Gorlenko
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences,Leninsky Ave 33, bld. 2, Moscow 119071,Russia
| | - Boris Kuznetsov
- Institute of Bioengineering, Federal Research Center of Biotechnology of the Russian Academy of Sciences,Leninsky Ave 33, bld. 2, Moscow 119071,Russia
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Nuyanzina-Boldareva EN, Akimov VN, Takaichi S, Gorlenko VM. New strains of an aerobic anoxygenic phototrophic bacterium Porphyrobacter donghaensis isolated from a Siberian thermal spring and a weakly mineralized lake. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716010070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Bravo-Anaya LM, Rinaudo M, Martínez FAS. Conformation and Rheological Properties of Calf-Thymus DNA in Solution. Polymers (Basel) 2016; 8:polym8020051. [PMID: 30979142 PMCID: PMC6432584 DOI: 10.3390/polym8020051] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/03/2016] [Accepted: 02/05/2016] [Indexed: 11/30/2022] Open
Abstract
Studies of DNA molecule behavior in aqueous solutions performed through different approaches allow assessment of the solute-solvent interactions and examination of the strong influence of conformation on its physicochemical properties, in the presence of different ionic species and ionic concentrations. Firstly, the conformational behavior of calf-thymus DNA molecules in TE buffer solution is presented as a function of temperature. Secondly, their rheological behavior is discussed, as well as the evidence of the critical concentrations, i.e., the overlap and the entanglement concentrations (C* and Ce, respectively) from steady state flow and oscillatory dynamic shear experiments. The determination of the viscosity in the Newtonian plateau obtained from flow curves η (γ˙) allows estimation of the intrinsic viscosity and the specific viscosities at zero shear when C[η] < 40. At end, a generalized master curve is obtained from the variation of the specific viscosity as a function of the overlap parameter C[η]. The variation of the exponent s obtained from the power law η~γ˙−s for both flow and dynamic results is discussed in terms of Graessley’s analysis. In the semi-dilute regime with entanglements, a dynamic master curve is obtained as a function of DNA concentration (CDNA > 2.0 mg/mL) and temperature (10 °C < T < 40 °C).
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Affiliation(s)
- Lourdes Mónica Bravo-Anaya
- Grenoble Alpes University, Laboratoire Rhéologie et Procédés (LRP), F-38000, Grenoble 38000, France.
- Departamento de Ingeniería Química, Universidad de Guadalajara, Blvd. M. García Barragán, Guadalajara C.P. 44430, Jalisco, Mexico.
| | | | - Félix Armando Soltero Martínez
- Departamento de Ingeniería Química, Universidad de Guadalajara, Blvd. M. García Barragán, Guadalajara C.P. 44430, Jalisco, Mexico.
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Dedysh SN, Didriksen A, Danilova OV, Belova SE, Liebner S, Svenning MM. Methylocapsa palsarum sp. nov., a methanotroph isolated from a subArctic discontinuous permafrost ecosystem. Int J Syst Evol Microbiol 2015; 65:3618-3624. [DOI: 10.1099/ijsem.0.000465] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic methanotrophic bacterium was isolated from a collapsed palsa soil in northern Norway and designated strain NE2T. Cells of this strain were Gram-stain-negative, non-motile, non-pigmented, slightly curved thick rods that multiplied by normal cell division. The cells possessed a particulate methane monooxygenase enzyme (pMMO) and utilized methane and methanol. Strain NE2T grew in a wide pH range of 4.1–8.0 (optimum pH 5.2–6.5) at temperatures between 6 and 32 °C (optimum 18–25 °C), and was capable of atmospheric nitrogen fixation under reduced oxygen tension. The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and C16 : 1ω7c, and the DNA G+C content was 61.7 mol%. The isolate belonged to the family Beijerinckiaceae of the class Alphaproteobacteria and was most closely related to the facultative methanotroph Methylocapsa aurea KYGT (98.3 % 16S rRNA gene sequence similarity and 84 % PmoA sequence identity). However, strain NE2T differed from Methylocapsa aurea KYGT by cell morphology, the absence of pigmentation, inability to grow on acetate, broader pH growth range, and higher tolerance to NaCl. Therefore, strain NE2T represents a novel species of the genus Methylocapsa, for which we propose the name Methylocapsa palsarum sp. nov. The type strain is NE2T ( = LMG 28715T = VKM B-2945T).
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Affiliation(s)
- Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Alena Didriksen
- UiT The Arctic University of Norway, Department of Arctic and Marine Biology, 9037 Tromsø, Norway
| | - Olga V. Danilova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Svetlana E. Belova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Section 4.5 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Mette M. Svenning
- UiT The Arctic University of Norway, Department of Arctic and Marine Biology, 9037 Tromsø, Norway
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Tarasov AL, Osipov GA, Borzenkov IA. Desulfovibrios from marine biofoulings at the South Vietnam coastal area and description of Desulfovibrio hontreensis sp. nov. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715050161] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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25
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Reiter-Schad M, Werner E, Tegenfeldt JO, Mehlig B, Ambjörnsson T. How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model. J Chem Phys 2015; 143:115101. [DOI: 10.1063/1.4930220] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Michaela Reiter-Schad
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - Erik Werner
- Department of Physics, University of Gothenburg, Origovägen 6B, SE-412 96 Göteborg, Sweden
| | - Jonas O. Tegenfeldt
- Division of Solid State Physics, Department of Physics and NanoLund, Lund University, Box 118, SE-221 00 Lund, Sweden
| | - Bernhard Mehlig
- Department of Physics, University of Gothenburg, Origovägen 6B, SE-412 96 Göteborg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
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26
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Tarasov AL, Borzenkov IA. Sulfate-reducing bacteria of the genus Desulfovibrio from south vietnam seacoast. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715040165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Romanenko LA, Tanaka N, Svetashev VI, Kurilenko VV, Mikhailov VV. Flavobacterium maris sp. nov. isolated from shallow sediments of the Sea of Japan. Arch Microbiol 2015; 197:941-7. [DOI: 10.1007/s00203-015-1128-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 06/03/2015] [Accepted: 06/18/2015] [Indexed: 11/30/2022]
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Beleneva IA, Shamshurina EV, Eliseikina MG. Assessment of the toxic effect exerted by fluorescent pseudomonads on embryos and larvae of the sea urchin Strongylocentrotus nudus. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2015; 115:263-271. [PMID: 25728358 DOI: 10.1016/j.ecoenv.2015.02.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 01/23/2015] [Accepted: 02/18/2015] [Indexed: 06/04/2023]
Abstract
Strains of bacteria capable of growing on artificial culture media were isolated from the fouling of brass plates submerged in Nha Trang Bay, South China Sea, and from tissues of the seastar Distolasterias nipon, caught in Peter the Great Bay, Sea of Japan. According to the complex of data of genetic and physiological/biochemical analyzes, two strains of cultivated bacteria were identified by us as the species Pseudomonas aeruginosa, two strains as Pseudomonas fluorescens, and one strain as Ruegeria sp. It was shown that the cultivated strains of P. aeruginosa released exotoxins, particularly phenazine pigments, into the environment. Production of the toxins did not depend on presence of a target organism in the system and was aimed at regulation of interactions in the microbial community. The toxicity of the studied natural isolates of fluorescent pseudomonads was analyzed by using embryos and larvae of the sea urchin Strongylocentrotus nudus, which are the sensitive and dynamic toxicological sea-urchin embryo test (SET) system. As was established, exotoxins produced by the strains of P. aeruginosa inhibit activity of cilia in sea urchin larvae, as well as disturb processes of cell differentiation in embryos and larvae. Their toxic influence is accompanied by disturbances of protein synthesis and the disruptions of cytoskeleton in the course of zygote cleavage and larval development. Unlike P. aeruginosa, the strains of P. fluorescens and Ruegeria sp. did not exert the toxic effect on SET. The obtained data allow considering objects of the environment as the natural reservoir of opportunistic microorganisms posing a potential threat to human, whereas the use of SET for determination of toxicity of isolated bacteria provides an opportunity to study the mechanisms of their interactions with organisms in marine ecosystems.
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Affiliation(s)
- I A Beleneva
- A.V. Zhirmunsky Institute of Marine Biology FEB RAS, Palchevsky Str. 17, Vladivostok 690041, Russia
| | - E V Shamshurina
- A.V. Zhirmunsky Institute of Marine Biology FEB RAS, Palchevsky Str. 17, Vladivostok 690041, Russia; Far Eastern Federal University, Sukhanova Str. 8, 690950 Vladivostok, Russia
| | - M G Eliseikina
- A.V. Zhirmunsky Institute of Marine Biology FEB RAS, Palchevsky Str. 17, Vladivostok 690041, Russia; Far Eastern Federal University, Sukhanova Str. 8, 690950 Vladivostok, Russia.
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Kulichevskaya IS, Ivanova AA, Detkova EN, Rijpstra WIC, Sinninghe Damsté JS, Dedysh SN. Planctomicrobium piriforme gen. nov., sp. nov., a stalked planctomycete from a littoral wetland of a boreal lake. Int J Syst Evol Microbiol 2015; 65:1659-1665. [DOI: 10.1099/ijs.0.000154] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, budding, non-pigmented and rosette-forming bacterium was isolated from a littoral wetland of a boreal lake located in Valaam Island, northern Russia, and designated strain P3T. Ellipsoidal to pear-shaped cells of this bacterium were covered with crateriform pits and possessed stalks suggesting a planctomycete morphotype. 16S rRNA gene sequence analysis confirmed that strain P3T was a member of the order
Planctomycetales
and belonged to a phylogenetic lineage defined by the genus
Planctomyces
, with 89 and 86 % sequence similarity to
Planctomyces brasiliensis
and
Planctomyces maris
, respectively. Strain P3T was a mildly acidophilic, mesophilic organism capable of growth at pH values between pH 4.2 and 7.1 (with an optimum at pH 6.0–6.5) and at temperatures between 10 and 30 °C (optimum at 20–28 °C). Most sugars, a number of polysaccharides and several organic acids were the preferred growth substrates. Compared with
Planctomyces brasiliensis
and
Planctomyces maris
, which require NaCl for growth, strain P3T was salt-sensitive and did not develop at NaCl concentrations above 0.5 % (w/v). The major fatty acids were C16 : 0 and C16 : 1ω7c; the cells also contained significant amounts of C18 : 1ω7c and C18 : 0. The major intact polar lipids were diacylglycerol-O-(N,N,N-trimethyl)homoserine (DGTS) lipids; the major neutral lipids were long-chain 1,(ω-1)-diols and C31 : 9 hydrocarbon. The quinone was MK-6, and the G+C content of the DNA was 59.0 mol%. Strain P3T differed from
Planctomyces brasiliensis
and
Planctomyces maris
by cell morphology, substrate utilization pattern and a number of physiological characteristics. Based on these data, the novel isolate should be considered as representing a novel genus and species of planctomycetes, for which the name Planctomicrobium piriforme gen. nov., sp. nov., is proposed. The type strain is P3T ( = DSM 26348T = VKM B-2887T).
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Affiliation(s)
- Irina S. Kulichevskaya
- S. N. Winogradsky Institute of Microbiology, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | - Anastasia A. Ivanova
- S. N. Winogradsky Institute of Microbiology, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | - Ekaterina N. Detkova
- S. N. Winogradsky Institute of Microbiology, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | - W. Irene C. Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S. Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Svetlana N. Dedysh
- S. N. Winogradsky Institute of Microbiology, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
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Bryantseva IA, Gaisin VA, Gorlenko VM. Rhodobaculum claviforme gen. nov., sp. nov., a new alkaliphilic nonsulfur purple bacterium. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715020022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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31
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Gorlenko VM, Bryantseva IA, Lunina ON, Tourova TP. Phylogenetic position of the purple sulfur bacterium Lamprobacter modestohalophilus determined based on the data on new strains of the species. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714060071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Romanenko LA, Tanaka N, Svetashev VI, Mikhailov VV. Sphingorhabdus pacificus sp. nov., isolated from sandy sediments of the Sea of Japan seashore. Arch Microbiol 2014; 197:147-53. [DOI: 10.1007/s00203-014-1033-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 08/05/2014] [Accepted: 08/21/2014] [Indexed: 11/28/2022]
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33
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Nuyanzina-Boldareva EN, Gorlenko VM. Roseibacula alcaliphilum gen. nov. sp. nov., a new alkaliphilic aerobic anoxygenic phototrophic bacterium from a meromictic soda lake Doroninskoe (East Siberia, Russia). Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714040134] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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34
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Tanaka N, Romanenko LA, Svetashev VI, Mikhailov VV. Simiduia litorea sp. nov., isolated from seashore sediments of the Sea of Japan. Int J Syst Evol Microbiol 2014; 64:2688-2692. [DOI: 10.1099/ijs.0.061846-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-negative, agarolytic rod-shaped bacterium, designated KMM 9504T, was isolated from a sediment sample collected from the seashore of the Sea of Japan. Comparative 16S rRNA gene sequence analysis showed that strain KMM 9504T belonged to the genus
Simiduia
as it was most closely related to
Simiduia areninigrae
KCTC 23293T (97.3 % sequence similarity). Strain KMM 9504T was characterized by the major ubiquinone Q-8, and by the predominance of C16 : 1ω7c, C17 : 1ω8c, followed by C16 : 0, C15 : 0, C17 : 0 and C12 : 1 in its fatty acid profile. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid, an unknown aminolipid, unknown phospholipids, and unknown lipids. Based on the distinctive phenotypic characteristics, phylogenetic analysis and DNA–DNA hybridization results, it is concluded that strain KMM 9504T represents a novel species of the genus
Simiduia
, for which the name Simiduia
litorea sp. nov. is proposed. The type strain of the species is strain KMM 9504T ( = NRIC 0917T = JCM 19759T).
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Affiliation(s)
- Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Lyudmila A. Romanenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia
| | - Vassilii I. Svetashev
- Institute of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690041, Russia
| | - Valery V. Mikhailov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia
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Kulichevskaya IS, Suzina NE, Rijpstra WIC, Damsté JSS, Dedysh SN. Paludibaculum fermentans gen. nov., sp. nov., a facultative anaerobe capable of dissimilatory iron reduction from subdivision 3 of the Acidobacteria. Int J Syst Evol Microbiol 2014; 64:2857-2864. [DOI: 10.1099/ijs.0.066175-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively anaerobic, non-pigmented, non-spore-forming bacterium was isolated from a littoral wetland of a boreal lake located on Valaam Island, northern Russia, and designated strain P105T. Cells of this isolate were Gram-negative, non-motile rods coated by S-layers with p2 lattice symmetry. Sugars were the preferred growth substrates. Under anoxic conditions, strain P105T was capable of fermentation and dissimilatory Fe(III) reduction. End products of fermentation were acetate, propionate and H2. Strain P105T was a mildly acidophilic, mesophilic organism, capable of growth at pH 4.0–7.2 (optimum pH 5.5–6.0) and at 4–35 °C (optimum at 20–28 °C). The major fatty acids were iso-C15 : 0 and C16 : 1ω7c; the cells also contained significant amounts of 13,16-dimethyl octacosanedioic acid (isodiabolic acid). The major polar lipids were phosphocholine and phosphoethanolamine; the quinone was MK-8. The G+C content of the DNA was 60.5 mol%. 16S rRNA gene sequence analysis showed that strain P105T belongs to subdivision 3 of the
Acidobacteria
and is only distantly related (90 % sequence similarity) to the only currently characterized member of this subdivision,
Bryobacter aggregatus
. The novel isolate differs from
Bryobacter aggregatus
in its cell morphology and ability to grow under anoxic conditions and in the presence of iron- and nitrate-reducing capabilities as well as quinone and polar lipid compositions. These differences suggest that strain P105T represents a novel genus and species, for which the name Paludibaculum fermentans gen. nov., sp. nov., is proposed. The type strain of Paludibaculum fermentans is P105T ( = DSM 26340T = VKM B-2878T).
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Affiliation(s)
- Irina S. Kulichevskaya
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | - Natalia E. Suzina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region 142292, Russia
| | - W. Irene C. Rijpstra
- Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S. Sinninghe Damsté
- Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Svetlana N. Dedysh
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
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36
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Romanenko LA, Tanaka N, Kurilenko VV, Svetashev VI. Tamlana sedimentorum sp. nov., isolated from shallow sand sediments of the Sea of Japan. Int J Syst Evol Microbiol 2014; 64:2891-2896. [PMID: 24876238 DOI: 10.1099/ijs.0.061812-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
An aerobic, Gram-stain-negative, saffron-pigmented, non-motile bacterial strain KMM 9545(T), was isolated from a marine sand sediment sample obtained from the Sea of Japan seashore and characterized in a taxonomic study using a polyphasic approach. The 16S rRNA gene sequence of strain KMM 9545(T) showed a high level of similarity to species of the genus Gaetbulibacter (95.1-96.2%), the type strains of species of the genus Tamlana (94.9-96.1%) and members of the genus Algibacter (94.8-96.1%). Phylogenetic analysis based on the 16S rRNA gene sequences positioned strain KMM 9545(T) as a distinct lineage in the cluster comprising species of the genus Tamlana. Strain KMM 9545(T) grew at temperatures between 5-36 °C and in the presence of 2-4% (w/v) NaCl. It contained MK-6 as the predominant menaquinone and iso-C(15 : 0), iso-C(15 : 1), iso-C(17 : 1) 3-OH, iso-C(15 : 0) 3-OH and iso-C(15 : 0) 2-OH as the major fatty acids. The genomic DNA G+C content was 31.3 mol%. On the basis of the phenotypic characteristics and phylogenetic distance, it can be concluded that strain KMM 9545(T) represents a novel species of the genus Tamlana, for which the name Tamlana sedimentorum sp. nov. is proposed. The type strain is KMM 9545(T) ( = NRIC 0921(T) = JCM 19808(T)).
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Affiliation(s)
- Lyudmila A Romanenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Valeriya V Kurilenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia
| | - Vassilii I Svetashev
- Institute of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690041, Russia
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37
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Nuyanzina-Boldareva EN, Kalashnikov AM, Gaisin VA, Sukhacheva MV, Kuznetsov BB, Gorlenko VM. Characterization of a new strain of a purple nonsulfur bacterium from a thermal spring. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714020027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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38
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Kulichevskaya IS, Danilova OV, Tereshina VM, Kevbrin VV, Dedysh SN. Descriptions of Roseiarcus fermentans gen. nov., sp. nov., a bacteriochlorophyll a-containing fermentative bacterium related phylogenetically to alphaproteobacterial methanotrophs, and of the family Roseiarcaceae fam. nov. Int J Syst Evol Microbiol 2014; 64:2558-2565. [PMID: 24812364 DOI: 10.1099/ijs.0.064576-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A light-pink-pigmented, microaerophilic bacterium was obtained from a methanotrophic consortium enriched from acidic Sphagnum peat and designated strain Pf56(T). Cells of this bacterium were Gram-negative, non-motile, thick curved rods that contained a vesicular intracytoplasmic membrane system characteristic of some purple non-sulfur alphaproteobacteria. The absorption spectrum of acetone/methanol extracts of cells grown in the light showed maxima at 363, 475, 505, 601 and 770 nm; the peaks at 363 and 770 nm are characteristic of bacteriochlorophyll a. However, in contrast to purple non-sulfur bacteria, strain Pf56(T) was unable to grow phototrophically under anoxic conditions in the light. Best growth occurred on some sugars and organic acids under micro-oxic conditions by means of fermentation. The fermentation products were propionate, acetate and hydrogen. Slow chemo-organotrophic growth was also observed under fully oxic conditions. Light stimulated growth. C1 substrates were not utilized. Strain Pf56(T) grew at pH 4.0-7.0 (optimum pH 5.5-6.5) and at 15-30 °C (optimum 22-28 °C). The major cellular fatty acids were 19 : 0 cyclo ω8c and 18 : 1ω7c; quinones were represented by ubiquinone Q-10. The G+C content of the DNA was 70.0 mol%. Strain Pf56 displays 93.6-94.7 and 92.7-93.7% 16S rRNA gene sequence similarity to members of the families Methylocystaceae and Beijerinckiaceae, respectively, and belongs to a large cluster of environmental sequences retrieved from various wetlands and forest soils in cultivation-independent studies. Phenotypic, genotypic and chemotaxonomic characteristics of strain Pf56(T) suggest that it represents a novel genus and species of bacteriochlorophyll a-containing fermentative bacteria, for which the name Roseiarcus fermentans gen. nov., sp. nov. is proposed. Strain Pf56(T) ( = DSM 24875(T) = VKM B-2876(T)) is the type strain of Roseiarcus fermentans, and is also the first characterized member of a novel family within the class Alphaproteobacteria, Roseiarcaceae fam. nov.
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Affiliation(s)
- Irina S Kulichevskaya
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Olga V Danilova
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Vera M Tereshina
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Vadim V Kevbrin
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Svetlana N Dedysh
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
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39
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Schmatko T, Muller P, Maaloum M. Surface charge effects on the 2D conformation of supercoiled DNA. SOFT MATTER 2014; 10:2520-2529. [PMID: 24647451 DOI: 10.1039/c3sm53071j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We have adsorbed plasmid pUc19 DNA on a supported bilayer. By varying the fraction of cationic lipids in the membrane, we have tuned the surface charge. Plasmid conformations were imaged by Atomic Force Microscopy (AFM). We performed two sets of experiments: deposition from salt free solution on charged bilayers and deposition from salty solutions on neutral bilayers. Both sets show similar trends: at low surface charge density or low bulk salt concentration, the internal electrostatic repulsion forces plasmids to adopt completely opened structures, while at high surface charge density or higher bulk salt concentration, usual supercoiled plectonemes are observed. We experimentally demonstrate the equivalence of surface screening by mobile interfacial charges and bulk screening from salt ions. At low to medium screening, the electrostatic repulsion at plasmid crossings is predominant, leading to a number of crossovers decreasing linearly with the characteristic screening length. We compare our data with an analytical 2D-equilibrated model developed recently for the system and extract the DNA effective charge density when strands are adsorbed at the surface.
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Affiliation(s)
- Tatiana Schmatko
- Institut Charles Sadron, CNRS UPR 22 et Université de Strasbourg, 23 rue du loess, BP 84047 67034 Strasbourg Cedex2, France.
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40
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Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352-356. [PMID: 24505073 DOI: 10.1099/ijs.0.056994-0] [Citation(s) in RCA: 432] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The G+C content of a genome is frequently used in taxonomic descriptions of species and genera. In the past it has been determined using conventional, indirect methods, but it is nowadays reasonable to calculate the DNA G+C content directly from the increasingly available and affordable genome sequences. The expected increase in accuracy, however, might alter the way in which the G+C content is used for drawing taxonomic conclusions. We here re-estimate the literature assumption that the G+C content can vary up to 3-5 % within species using genomic datasets. The resulting G+C content differences are compared with DNA-DNA hybridization (DDH) similarities calculated in silico using the GGDC web server, with 70% similarity as the gold standard threshold for species boundaries. The results indicate that the G+C content, if computed from genome sequences, varies no more than 1% within species. Statistical models based on larger differences alone can reject the hypothesis that two strains belong to the same species. Because DDH similarities between two non-type strains occur in the genomic datasets, we also examine to what extent and under which conditions such a similarity could be <70% even though the similarity of either strain to a type strain was ≥ 70%. In theory, their similarity could be as low as 50%, whereas empirical data suggest a boundary closer (but not identical) to 70%. However, it is shown that using a 50% boundary would not affect the conclusions regarding the DNA G+C content. Hence, we suggest that discrepancies between G+C content data provided in species descriptions on the one hand and those recalculated after genome sequencing on the other hand ≥ 1% are due to significant inaccuracies of the applied conventional methods and accordingly call for emendations of species descriptions.
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Affiliation(s)
- Jan P Meier-Kolthoff
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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41
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Methanospirillum stamsii sp. nov., a psychrotolerant, hydrogenotrophic, methanogenic archaeon isolated from an anaerobic expanded granular sludge bed bioreactor operated at low temperature. Int J Syst Evol Microbiol 2014; 64:180-186. [DOI: 10.1099/ijs.0.056218-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A psychrotolerant hydrogenotrophic methanogen, strain Pt1, was isolated from a syntrophic propionate-oxidizing methanogenic consortium obtained from granulated biomass of a two-stage low-temperature (3–8 °C) anaerobic expanded granular sludge bed (EGSB) bioreactor, fed with a mixture of volatile fatty acids (VFAs) (acetate, propionate and butyrate). The strain was strictly anaerobic, and cells were curved rods, 0.4–0.5×7.5–25 µm, that sometimes formed wavy filaments from 25 to several hundred micrometres in length. Cells stained Gram-negative and were non-sporulating. They were gently motile by means of tufted flagella. The strain grew at 5–37 °C (optimum at 20–30 °C), at pH 6.0–10 (optimum 7.0–7.5) and with 0–0.3 M NaCl (optimum 0 M NaCl). Growth and methane production was found with H2/CO2 and very weak growth with formate. Acetate and yeast extract stimulated growth, but were not essential. The G+C content of the DNA of strain Pt1 was 40 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Pt1 was a member of the genus
Methanospirillum
and showed 97.5 % sequence similarity to
Methanospirillum hungatei
JF1T and 94 % sequence similarity to
Methanospirillum lacunae
Ki8-1T. DNA–DNA hybridization of strain Pt1 with
Methanospirillum hungatei
JF1T revealed 39 % relatedness. On the basis of its phenotypic characteristics and phylogenetic position, strain Pt1 is a representative of a novel species of the genus
Methanospirillum
, for which the name Methanospirillum stamsii sp. nov. is proposed. The type strain is Pt1T ( = DSM 26304T = VKM B-2808T).
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42
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Zavarzina DG, Zhilina TN, Kuznetsov BB, Kolganova TV, Osipov GA, Kotelev MS, Zavarzin GA. Natranaerobaculum magadiense gen. nov., sp. nov., an anaerobic, alkalithermophilic bacterium from soda lake sediment. Int J Syst Evol Microbiol 2013; 63:4456-4461. [PMID: 23859946 DOI: 10.1099/ijs.0.054536-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately alkaliphilic, anaerobic, thermo- and halotolerant, spore-forming bacterium was isolated from sediments of soda lake Magadi (Kenya) and designated strain Z-1001(T). Cells of strain Z-1001(T) were straight, Gram-positive rods, slowly motile. Strain Z-1001(T) was found to be an obligate anaerobe. It grew within a pH range from 7.5 to 10.7 with an optimum at 9.25-9.5 (at 40 °C), a temperature range from 20 to 57 °C with an optimum at 45-50 °C, and a NaCl concentration range from 0 to 1.55 M with an optimum at 1.2-1.4 M. Peptides, such as meat and yeast extracts, peptone and tryptone, were fermented by Z-1001(T). Carbohydrates did not support growth. With yeast extract as an electron donor, strain Z-1001(T) reduced S(2)O(3)(2-), NO(-)(3), AsO(3-)(4), Fe(III) citrate and anthraquinone-2,6-disulfonate (AQDS) as electron acceptors. The isolate was able to grow oligotrophically with a very small amount of yeast extract: 0.03 g l(-1). The main fatty acids were C16 : 0, C16 : 1ω7c, C18 : 0 and C18 : 1ω9. The DNA G+C content of the isolate was 35.6 mol%. 16S rRNA gene sequence analysis showed that strain Z-1001(T) is a member of family Natranaerobiaceae, clustering with the type strain of Natranaerobius thermophilus (95.8-96.0 % sequence similarity). On the basis of physiological and phylogenetic data it is proposed that strain Z-1001(T) ( = DSM 24923(T) = VKM B-2666(T)) represents a novel genus and species, Natranaerobaculum magadiense gen. nov., sp. nov.
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Affiliation(s)
- Daria G Zavarzina
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - Tatyana N Zhilina
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - Boris B Kuznetsov
- Center 'Bioengineering', Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/1, 117312 Moscow, Russia
| | - Tatyana V Kolganova
- Center 'Bioengineering', Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/1, 117312 Moscow, Russia
| | - Georgy A Osipov
- Bakulev Center of Cardiovascular Surgery, Russian Academy of Medical Sciences, Rublevskoe shosse, Moscow 135, Russia
| | - Mikhail S Kotelev
- Gubkin Russian State University of Oil and Gas, Leninskii Prospect 65, 119991 Moscow, Russia
| | - Georgy A Zavarzin
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
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Danilova OV, Kulichevskaya IS, Rozova ON, Detkova EN, Bodelier PLE, Trotsenko YA, Dedysh SN. Methylomonas paludis sp. nov., the first acid-tolerant member of the genus
Methylomonas
, from an acidic wetland. Int J Syst Evol Microbiol 2013; 63:2282-2289. [DOI: 10.1099/ijs.0.045658-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic methanotrophic bacterium was isolated from an acidic (pH 3.9) Sphagnum peat bog in north-eastern Russia and designated strain MG30T. Cells of this strain were Gram-negative, pale pink-pigmented, non-motile, thick rods that were covered by large polysaccharide capsules and contained an intracytoplasmic membrane system typical of type I methanotrophs. They possessed a particulate methane monooxygenase enzyme (pMMO) and utilized only methane and methanol. Carbon was assimilated via the ribulose-monophosphate pathway; nitrogen was fixed via an oxygen-sensitive nitrogenase. Strain MG30T was able to grow at a pH range of 3.8–7.3 (optimum pH 5.8–6.4) and at temperatures between 8 and 30 °C (optimum 20–25 °C). The major cellular fatty acids were C16 : 1ω5t, C16 : 1ω8c, C16 : 1ω7c and C14 : 0; the DNA G+C content was 48.5 mol%. The isolate belongs to the family
Methylococcaceae
of the class
Gammaproteobacteria
and displayed 94.7–96.9 % 16S rRNA gene sequence similarity to members of the genus
Methylomonas
. However, strain MG30T differed from all taxonomically characterized members of this genus by the absence of motility, the ability to grow in acidic conditions and low DNA G+C content. Therefore, we propose to classify this strain as representing a novel, acid-tolerant species of the genus
Methylomonas
, Methylomonas paludis sp. nov. Strain MG30T ( = DSM 24973T = VKM B-2745T) is the type strain.
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Affiliation(s)
- Olga V. Danilova
- S.N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Irina S. Kulichevskaya
- S.N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Olga N. Rozova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, 142292, Russia
| | - Ekaterina N. Detkova
- S.N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Paul L. E. Bodelier
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, PO Box 50 6700AB, The Netherlands
| | - Yuri A. Trotsenko
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, 142292, Russia
| | - Svetlana N. Dedysh
- S.N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
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44
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Zhilina TN, Zavarzina DG, Panteleeva AN, Osipov GA, Kostrikina NA, Tourova TP, Zavarzin GA. Fuchsiella alkaliacetigena gen. nov., sp. nov., an alkaliphilic, lithoautotrophic homoacetogen from a soda lake. Int J Syst Evol Microbiol 2012; 62:1666-1673. [DOI: 10.1099/ijs.0.034363-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The first alkaliphilic obligately anaerobic hydrogenotrophic homoacetogenic bacterium, strain Z-7100T, was isolated from sediments of the soda-depositing soda lake Tanatar III (Altay, Russia). Cells were thin, flexible rods, motile, Gram-negative and spore-forming. The organism was an obligate alkaliphile, growing at pH 8.5 to 10.5, with optimum growth at pH 8.8–9.3, and it grew in soda brines containing 1.9–4.7 M total Na+ (optimum at 2.8–3.3 M). It exhibited an obligate dependence upon sodium carbonate but not upon chloride ions with an NaCl range for growth of 0–14 % (w/v) and an optimum at 7.0–8.5 % (w/v). The isolate was mesophilic and grew at temperatures from 25 to 45 °C, with an optimum at 40 °C. An H2+CO2 mixture, ethanol, pyruvate and lactate were utilized with the formation of acetate as the sole metabolic product. Carbohydrates and amino acids did not support growth. The isolate had a respiratory type of metabolism, reducing
NO
3
–
, SeO4
2− or anthraquinone-2,6-disulfonate (as electron acceptors with ethanol as an electron donor). It was able to grow chemolithotrophically on H2+CO2 in medium supplemented with a vitamin solution only. The major cellular fatty acids were the saturated fatty acids anteiso-C15, C14 : 0 and C16 : 0 and the aldehydes C16, C14 and anteiso-C15. The DNA G+C content of the isolate was 32.0 mol%. 16S rRNA gene sequence analysis showed that strain Z-7100T is a member of the order
Halanaerobiales
and represents a new branch within the family
Halobacteroidaceae
, clustering with the type strain of
Selenihalanaerobacter shriftii
(92.9 % gene sequence similarity). On the basis of its physiological characteristics and phylogenetic position, the isolate is considered to represent a novel species in a new genus within the family
Halobacteroidaceae
. The name Fuchsiella alkaliacetigena gen. nov., sp. nov. is proposed. The type strain of the type species is Z-7100T ( = DSM 24880T = VKM B-2667T).
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Affiliation(s)
- Tatyana N. Zhilina
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - Daria G. Zavarzina
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - Angela N. Panteleeva
- Bioengineering Center, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/1, Moscow 117312, Russia
| | - Georgy A. Osipov
- Bakulev Center for Cardiovascular Surgery, Russian Academy of Medical Sciences, Rublevskoe shosse, Moscow 135, Russia
| | - Nadezhda A. Kostrikina
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - Tatyana P. Tourova
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - Georgy A. Zavarzin
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
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45
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Belova SE, Kulichevskaya IS, Bodelier PLE, Dedysh SN. Methylocystis bryophila sp. nov., a facultatively methanotrophic bacterium from acidic Sphagnum peat, and emended description of the genus Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993. Int J Syst Evol Microbiol 2012; 63:1096-1104. [PMID: 22707532 DOI: 10.1099/ijs.0.043505-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A novel species is proposed for two facultatively methanotrophic representatives of the genus Methylocystis, strains H2s(T) and S284, which were isolated from an acidic (pH 4.3) Sphagnum peat-bog lake (Teufelssee, Germany) and an acidic (pH 3.8) peat bog (European North Russia), respectively. Cells of strains H2s(T) and S284 are aerobic, Gram-negative, non-motile, curved coccoids or short rods that contain an intracytoplasmic membrane system typical of type-II methanotrophs. They possess both a soluble and a particulate methane monooxygenase (MMO); the latter is represented by two isozymes, pMMO1 and pMMO2. The preferred growth substrates are methane and methanol. In the absence of C1 substrates, however, these methanotrophs are capable of slow growth on acetate. Atmospheric nitrogen is fixed by means of an aerotolerant nitrogenase. Strains H2s(T) and S284 grow between pH 4.2 and 7.6 (optimum pH 6.0-6.5) and at 8-37 °C (optimum 25-30 °C). The major fatty acids are C18 : 1ω8c, C18 : 1ω7c and C16 : 1ω7c; the major quinone is Q-8. The DNA G+C content is 62.0-62.3 mol%. Strains H2s(T) and S284 share identical 16S rRNA gene sequences, which displayed 96.6-97.3 % similarity to sequences of other taxonomically characterized members of the genus Methylocystis. Therefore, strains H2s(T) and S284 are classified as members of a novel species, for which the name Methylocystis bryophila sp. nov. is proposed; strain H2s(T) ( = DSM 21852(T) = VKM B-2545(T)) is the type strain.
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Affiliation(s)
- Svetlana E Belova
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Irina S Kulichevskaya
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Paul L E Bodelier
- Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, The Netherlands
| | - Svetlana N Dedysh
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
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46
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Kulichevskaya IS, Serkebaeva YM, Kim Y, Rijpstra WIC, Damsté JSS, Liesack W, Dedysh SN. Telmatocola sphagniphila gen. nov., sp. nov., a novel dendriform planctomycete from northern wetlands. Front Microbiol 2012; 3:146. [PMID: 22529844 PMCID: PMC3327967 DOI: 10.3389/fmicb.2012.00146] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 03/27/2012] [Indexed: 11/13/2022] Open
Abstract
Members of the phylum Planctomycetes are common inhabitants of northern wetlands. We used barcoded pyrosequencing to survey bacterial diversity in an acidic (pH 4.0) Sphagnum peat sampled from the peat bog Obukhovskoye, European North Russia. A total of 21189 bacterial 16S rRNA gene sequences were obtained, of which 1081 reads (5.1%) belonged to the Planctomycetes. Two-thirds of these sequences affiliated with planctomycete groups for which characterized representatives have not yet been available. Here, we describe two organisms from one of these previously uncultivated planctomycete groups. One isolate, strain OB3, was obtained from the peat sample used in our molecular study, while another strain, SP2(T) (=DSM 23888(T) = VKM B-2710(T)), was isolated from the peat bog Staroselsky moss. Both isolates are represented by aerobic, budding, pink-pigmented, non-motile, spherical cells that are arranged in unusual, dendriform-like structures during growth on solid media. These bacteria are moderately acidophilic and mesophilic, capable of growth at pH 4.0-7.0 (optimum pH 5.0-5.5) and at 6-30°C (optimum 20-26°C). The preferred growth substrates are various heteropolysaccharides and sugars, the latter being utilized only if provided in low concentrations (≤0.025%). In contrast to other described planctomycetes, strains SP2(T) and OB3 possess weak cellulolytic potential. The major fatty acids are C16:1ω5c, C18:1ω5c, C16:0, and C18:0. Characteristic lipids are the n-C31 polyunsaturated alkene (9-10 double bonds) and C30:1/C32:1 (ω-1) hydroxy fatty acids. The G + C content of the DNA is 58.5-59.0 mol%. Strains SP2(T) and OB3 share identical 16S rRNA gene sequences, which exhibit only 86 and 87% similarity to those of Gemmata obscuriglobus and Zavarzinella formosa. Based on the characteristics reported here, we propose to classify these novel planctomycetes as representatives of a novel genus and species, Telmatocola sphagniphila gen. nov., sp. nov.
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Affiliation(s)
| | - Yulia M. Serkebaeva
- S.N. Winogradsky Institute of Microbiology, Russian Academy of SciencesMoscow, Russia
- Max-Planck-Institut für Terrestrische MikrobiologieMarburg, Germany
| | - Yongkyu Kim
- Max-Planck-Institut für Terrestrische MikrobiologieMarburg, Germany
| | - W. Irene C. Rijpstra
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea ResearchAB Den Burg, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea ResearchAB Den Burg, Netherlands
| | - Werner Liesack
- Max-Planck-Institut für Terrestrische MikrobiologieMarburg, Germany
| | - Svetlana N. Dedysh
- S.N. Winogradsky Institute of Microbiology, Russian Academy of SciencesMoscow, Russia
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47
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Romanenko LA, Tanaka N, Svetashev VI, Falsen E. Description of Cobetia amphilecti sp. nov., Cobetia litoralis sp. nov. and Cobetia pacifica sp. nov., classification of Halomonas halodurans as a later heterotypic synonym of Cobetia marina and emended descriptions of the genus Cobetia and Cobetia marina. Int J Syst Evol Microbiol 2012; 63:288-297. [PMID: 22427450 DOI: 10.1099/ijs.0.036863-0] [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 group of five Gram-negative, aerobic, halotolerant, non-pigmented bacteria isolated from shallow sediment samples and invertebrate specimens collected from the Gulf of Alaska and the Sea of Japan was subjected to taxonomic study. On the basis of 16S rRNA gene sequence analysis, the novel isolates were affiliated to the genus Cobetia, sharing the highest sequence similarity of 99.3-99.9 % with Cobetia marina DSM 4741(T). DNA-DNA hybridization experiments between and among the novel strains and C. marina DSM 4741(T) and Cobetia crustatorum JCM 15644(T) revealed that the five strains represent three separate genospecies, which could be differentiated in their morphological, physiological and biochemical characteristics. Halomonas halodurans NBRC 15607(T) was included in this study as it has recently been reported to exhibit high 16S rRNA gene sequence similarity to C. marina DSM 4741(T), and it showed a high DNA relatedness value of 96 % with C. marina DSM 4741(T), indicating that they belong to the same species. On the basis of phylogenetic analysis, DNA-DNA hybridization and phenotypic characterization, three novel species are proposed, named Cobetia amphilecti sp. nov. (type strain KMM 1561(T) = NRIC 0815(T) = CCUG 49560(T)), Cobetia litoralis sp. nov. (type strain KMM 3880(T) =NRIC 0814(T) =CCUG 49563(T)) and Cobetia pacifica sp. nov. (type strain KMM 3879(T) = NRIC 0813(T) = CCUG 49562(T)). It is also proposed that Halomonas halodurans is a later heterotypic synonym of Cobetia marina, and emended descriptions of the genus Cobetia and the species Cobetia marina are provided.
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Affiliation(s)
- Lyudmila A Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, Vladivostoku 159 Prospect 100 Let, Vladivostok 690022, Russia
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Vassilii I Svetashev
- Institute of Marine Biology, Far-Eastern Branch, Russian Academy of Sciences, 6 17 Palchevsky Street, Vladivostok 690041, Russia
| | - Enevold Falsen
- Culture Collection, Department of Clinical Bacteriology, University of Göteborg, SE-405 30 Göteborg, Sweden
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48
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Bryocella elongata gen. nov., sp. nov., a member of subdivision 1 of the Acidobacteria isolated from a methanotrophic enrichment culture, and emended description of Edaphobacter aggregans Koch et al. 2008. Int J Syst Evol Microbiol 2012; 62:654-664. [DOI: 10.1099/ijs.0.031898-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, pink-pigmented, chemo-organotrophic bacterium, designated strain SN10T, was isolated from a methanotrophic enrichment culture obtained from an acidic Sphagnum peat. This isolate was represented by Gram-negative, non-motile rods that multiply by normal cell division and form rosettes. Strain SN10T is an obligately acidophilic, mesophilic bacterium capable of growth at pH 3.2–6.6 (with an optimum at pH 4.7–5.2) and at 6–32 °C (with an optimum at 20–24 °C). The preferred growth substrates are sugars and several heteropolysaccharides of plant and microbial origin, such as pectin, lichenan, fucoidan and gellan gum. While not being capable of growth on C1 compounds, strain SN10T can develop in co-culture with exopolysaccharide-producing methanotrophs by utilization of their capsular material. The major fatty acids determined in strain SN10T using the conventional lipid extraction procedure are iso-C15 : 0 and C16 : 1ω7c. Upon hydrolysis of total cell material, substantial amounts of the uncommon membrane-spanning lipid 13,16-dimethyl octacosanedioic acid (isodiabolic acid) were also detected. The polar lipids are two phosphohexoses, phosphatidylethanolamine, phosphatidylglycerol and several phospholipids of unknown structure. The major quinone is MK-8. Pigments are carotenoids. The G+C content of the DNA is 60.7 mol%. Strain SN10T forms a separate lineage within subdivision 1 of the phylum Acidobacteria and displays 94.0–95.4 % 16S rRNA gene sequence similarity to members of the genera Edaphobacter and Granulicella, 93.0–93.7 % similarity to members of the genus Terriglobus and 92.2–92.3 % similarity to the type strains of Telmatobacter bradus and Acidobacterium capsulatum. Therefore, strain SN10T is classified within a novel genus and species, for which the name Bryocella elongata gen. nov., sp. nov. is proposed. Strain SN10T ( = LMG 25276T = DSM 22489T) is the type strain of Bryocella elongata. An emended description of Edaphobacter aggregans Koch et al. 2008 is also given.
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49
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Sorokina AY, Chernousova EY, Dubinina GA. Hoeflea siderophila sp. nov., a new neutrophilic iron-oxidizing bacterium. Microbiology (Reading) 2012. [DOI: 10.1134/s0026261712010146] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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50
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Kulichevskaya IS, Detkova EN, Bodelier PLE, Rijpstra WIC, Sinninghe Damsté JS, Dedysh SN. Singulisphaera rosea sp. nov., a planctomycete from acidic Sphagnum peat, and emended description of the genus Singulisphaera. Int J Syst Evol Microbiol 2012; 62:118-123. [DOI: 10.1099/ijs.0.025924-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, pink-pigmented, budding bacterium, designated strain S26T, was isolated from an acidic Sphagnum peat bog of north-western Russia. Cells were non-motile and spherical, occurring singly, in pairs or in short chains, and were able to attach to surfaces by means of a holdfast material. Strain S26T was a moderately acidophilic, mesophilic organism capable of growth at pH 3.2–7.1 (optimum at pH 4.8–5.0) and at 4–33 °C (optimum at 20–26 °C). Most sugars, several organic acids and polyalcohols were the preferred growth substrates. The major fatty acids were C16 : 0, C18 : 1ω9c and C18 : 2ω6c,12c. The major neutral lipids were n-C31 : 9 hydrocarbon and squalene; the polar lipids were phosphatidylglycerol, phosphatidylcholine and components with an unknown structure. The DNA G+C content of strain S26T was 62.2 mol%. 16S rRNA gene sequence analysis showed that strain S26T is a member of the order Planctomycetales. Among taxonomically characterized representatives of this order, highest levels of 16S rRNA gene sequence similarity (95.1–95.2 %) were observed with strains of the non-filamentous, peat-inhabiting planctomycete Singulisphaera acidiphila. Strain S26T could be differentiated from Singulisphaera acidiphila based on pigmentation, significant differences in substrate utilization patterns, greater tolerance of acidic conditions and the presence of C16 : 1ω9c. Based on the data presented, strain S26T is considered to represent a novel species of the genus Singulisphaera, for which the name Singulisphaera rosea sp. nov. is proposed; the type strain is S26T ( = DSM 23044T = VKM B-2599T).
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Affiliation(s)
- Irina S. Kulichevskaya
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | - Ekaterina N. Detkova
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | | | - W. Irene C. Rijpstra
- Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S. Sinninghe Damsté
- Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Svetlana N. Dedysh
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
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