Laboratory of Molecular ecology and phylogenomics of bacteria

Dedysh Svetlana N. Dedysh
Dr.Sci. (Biology)
Head of Laboratory
INMI, room 401
Телефон +7 (499) 135-03-89
E-Mail dedysh@mail.ru

Keywords: molecular microbial ecology, microbial diversity, phylogenomics, bacterial taxonomy and systematics, microbiology of wetlands, methanotrophic bacteria, molecular identification, filterable forms of microbes, planctomycetes, acidobacteria, functional role of microorganisms.

Main field of research is microbiology of northern terrestrial ecosystems.

Main research directions are:

  • Molecular analysis of microbial diversity in terrestrial ecosystems;
  • Cultivation, genome analysis and taxonomic description of novel bacteria;
  • Biology, diversity, and ecology of methanotrophic bacteria;
  • Biotechnological applications of methanotrophs;
  • Characterization of bacteria from poorly studied phyla – Acidobacteria and Planctomycetes;
  • Metatranscriptomics of microbial communities in northern wetlands;
  • Analysis of shifts in a microbial community composition of peatlands after wildfire.

 

The research is focused on assessing the phylogenetic diversity and functional structure of microbial communities in northern terrestrial ecosystems, such as wetlands, soils and freshwater habitats. Methodology of these studies includes high-throughput sequencing of phylogenetic and functional genes (Serkebaeva et al., PLoS ONE 2013; Oshkin et al., AEM 2014; Ivanova et al., Microorganisms 2020), fluorescent in situ hybridization (Dedysh et al., AEM 2006; Pankratov et al., ISME J. 2008; Pankratov et al., Environ. Microbiol. 2011), metagenomics (Dedysh et al., Environ. Microbiol. 2020) and metatranscriptomics (Ivanova et al., Molecular Ecology 2016).

One of the major research directions is biology, diversity, ecology and biotechnological applications of methanotrophic bacteria. Key contributions have been made in discoveries of acidophilic methanotrophs (Dedysh et al., Science 1998), facultative methanotrophy (Dedysh et al., J. Bacteriol. 2005; Dunfield & Dedysh, Trends Microbiol. 2014), obligately microaerobic methanotrophs (Danilova et al., ISME J. 2016) and high-affinity methane oxidizers from USCalpha group (Tveit et al., PNAS 2019). One of the major current research projects is focused on various aspects of microbial protein production from methane.

The laboratory is one of the internationally recognized leaders in cultivation and characterization of bacteria from northern peatlands (Dedysh, Front. Microbiol. 2011) and other terrestrial ecosystems. The list of newly described taxa includes two classes, seven orders, eight families, 40 novel genera and over 50 novel bacterial species. Head of the laboratory, Svetlana N. Dedysh, is a trustee of Bergey’s Manual Trust (http://www.bergeys.org/trust.html) and one of the editors of Bergey’s Manual of Systematics of Archaea and Bacteria.

One of the key research directions is exploring the uncultured diversity, genomic potential and the range of potentially valuable metabolites (enzymes, antibiotics and other bioactive molecules) of bacteria from two poorly studied phyla – Acidobacteria and Planctomycetes.

 

 

Selected publications:

  1. Dedysh S.N., Beletsky A.V., Ivanova A.A., Kulichevskaya I.S., Suzina N.E., Philippov D.A., Rakitin A.L., Mardanov A.V., Ravin N.V. Wide distribution of Phycisphaera-like planctomycetes from WD2101 soil group in peatlands and genome analysis of the first cultivated representative. Environmental Microbiology, 2021, 23(5): 1510-1526.
  2. Dedysh S.N., Henke P., Ivanova A.A., Kulichevskaya I.S., Philippov D.A., Meier-Kolthoff J.P., Göker, Huang S., Overmann J. 100-year-old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii. Environmental Microbiology, 2020, 22(1): 198-211.
  3. Dedysh S.N., Kulichevskaya I.S., Beletsky A.V., Ivanova A.A., Rijpstra W.I.C., Damste J.S.S., Mardanov A.V., Ravin N.V. Lacipirellula parvula nov., sp. nov., representing a lineage of planctomycetes widespread in low-oxygen habitats, description of the family Lacipirellulaceae fam. nov. and proposal of the orders Pirellulales ord. nov., Gemmatales ord. nov. and Isosphaerales ord. nov. Systematic and Applied Microbiology, 2020, 43(1):126050.
  4. Ivanova A.A., Zhelezova A.D., Chernov T.I., Dedysh S.N. Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils. PLoS ONE, 2020, 15(3): e0230157.
  5. Tveit A.T., Hestnes A.G., Robinson S., Schintlmeiser A., Dedysh S.N., Jehmlich N., von Bergen M., Herbold C., Wagner M., Richter A., Svenning M.M. Widespread soil bacterium that oxidizes atmospheric methane. PNAS, 2019, doi: 10.1073/pnas.1817812116.
  6. Dedysh S.N., Ivanova A.A. Planctomycetes in boreal and subarctic wetlands: diversity patterns and potential ecological functions. FEMS Microbiology Ecology, 2019, 94, fly227
  7. Oshkin I.Y., Miroshnikov K.K., Danilova O.V., Hakobyan A., Liesack W., Dedysh S.N. Thriving in wetlands: Ecophysiology of the spiral-shaped methanotroph Methylospira mobilis as revealed by the complete genome sequence. Microorganisms, 2019, 7(12), pii: E683.
  8. Belova S.E., Ravin N.V., Pankratov T.A., Rakitin A.L., Ivanova A.A., Beletsky A.V., Mardanov A.V., Sinninghe Damsté J.S., Dedysh S.N. Hydrolytic capabilities as a key to environmental success: chitinolytic and cellulolytic Acidobacteriafrom acidic Sub-arctic soils and boreal peatlands. Frontiers in Microbiology, 2018, 9:2775. doi: 10.3389/fmicb.2018.02775
  9. Dedysh S.N., Yilmaz P. Refining the taxonomic structure of the phylum Acidobacteria. International Journal of Systematic and Evolutionary Microbiology, 2018, v. 68, p. 3796-3806.
  10. Ravin N.V., Rakitin A.L., Ivanova A.A., Beletsky A.V., Kulichevskaya I.S., Mardanov A.V., Dedysh S.N. 2018. Genome analysis of Fimbriiglobus ruber SP5T, a planctomycete with confirmed chitinolytic capability. Applied and Environmental Microbiology, 2018, 84: e02645-17.
  11. Ivanova A.A., Naumoff D.G., Miroshnikov K.K., Liesack W., Dedysh S.N. Comparative genomics of four Isosphaeraceae planctomycetes: a common pool of plasmids and glycoside hydrolase genes shared by Paludisphaera borealis PX4T, Isosphaera pallida IS1BT, Singulisphaera acidiphila DSM 18658T, and strain SH-PL62. Frontiers in Microbiology; 2017, 8:412
  12. Ivanova A.A., Kim Y., Wegner C.E., Liesack W., Dedysh S.N. Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis. Molecular Ecology, 2016, v. 25, p. 4818-4835
  13. Danilova O.V., Suzina N.E., Van De Kamp J., Svenning M.M., Bodrossy L., Dedysh S.N. A new morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments. ISME Journal, 2016, v. 10(11), p. 2734-2743.
  14. Oshkin I.Y., Wegner C.-E., Lüke C., Glagolev M.V., Filippov I.F., Pimenov N.V., Liesack W., Dedysh S.N. Gammaproteobacterial methanotrophs dominate cold methane seeps in floodplains of West Siberian rivers. Applied and Environmental Microbiology, 2014, v. 80(19), p. 5944-5954
  15. Serkebaeva Y.M., Kim Y., Liesack W., Dedysh S.N. Pyrosequencing-based assessment of the Bacteria diversity in surface and subsurface peat layers of a northern wetland, with focus on poorly studied phyla and candidate divisions. PLOS ONE, 2013, v, 8(5): e63994
  16. Sinninghe Damsté J.S., Rijpstra I.C., Hopmans E.C., Weijers J.W.H., Foesel B.U., Overmann J., Dedysh S.N. 13,16-Dimethyl octacosanedioic acid (iso-diabolic acid), a common membrane-spanning lipid of Acidobacteria subdivisions 1 and 3. Applied and Environmental Microbiology, 2011, v, 77(12), p, 4147-4154
  17. Pankratov T,A., Ivanova A.O., Dedysh S.N., Liesack W. Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat. Environmental Microbiology, 2011, v, 13 (7), p, 1800-1814
  18. Dedysh S.N. Cultivating uncultured bacteria from Northern wetlands: knowledge gained and remaining gaps. Frontiers in Microbiology, 2011, v. 2: 184
  19. Dedysh S.N., Pankratov T.A., Belova S.E., Kulichevskaya I.S., Liesack W. Phylogenetic analysis and in situ identification of Bacteria community composition in an acidic Sphagnum peat bog. Applied and Environmental Microbiology, 2006, v, 72 (3), p, 2110-2117
  20. Dedysh S.N., Panikov N.S., Liesack W., Großkopf R., Zhou J., Tiedje J.M. Isolation of acidophilic methane-oxidizing bacteria from northern peat wetlands. Science, 1998, v, 282, p, 281-284