Laboratory of Wetland Microbiology

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, 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 wetlands.

Main research directions are:

  • Molecular analysis of microbial diversity in terrestrial ecosystems;
  • Biology, diversity, and ecology of methanotrophic bacteria;
  • Molecular identification of filterable microbial forms in freshwater;
  • Research on microbial agents of biopolymer degradation in northern wetlands;
  • Cultivation and 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 wetlands, one of the most extensive ecosystems in the Northern Hemisphere. These ecosystems are recognized as a major global carbon store, a source of atmospheric methane (CH4), and one of the largest reservoirs of freshwater. Methodology of these studies includes high-throughput sequencing of phylogenetic and functional genes (Serkebaeva et al., PLoS ONE 2013; Oshkin et al., AEM 2014), fluorescent in situ hybridization (Dedysh et al., AEM 2006; Pankratov et al., ISME J. 2008; Pankratov et al., Environ. Microbiol. 2011), and metatranscriptomics.

One of the major research directions is biology and ecology of methanotrophic bacteria responsible for methane oxidation in acidic northern wetlands. 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) and obligately microaerobic methanotrophs (Danilova et al., ISME J. 2016).

The laboratory is one of the internationally recognized leaders in cultivation and characterization of bacteria from northern peatlands (Dedysh, Front. Microbiol. 2011). Two novel families, 20 novel genera and 35 novel bacterial species have been validly described. Head of the laboratory, Svetlana N. Dedysh, is a trustee of Bergey’s Manual Trust (http://www.bergeys.org/trust.html).

One of the major current projects is focused on 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., 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.
  2. 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.
  3. 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.
  4. 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.
  5. Dedysh S.N., Ivanova A.A. Planctomycetes in boreal and subarctic wetlands: diversity patterns and potential ecological functions. FEMS Microbiology Ecology, 2019, 94, fly227
  6. 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.
  7. 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
  8. 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.
  9. 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.
  10. 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
  11. 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
  12. 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.
  13. 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
  14. 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
  15. 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
  16. 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
  17. Dedysh S.N. Cultivating uncultured bacteria from Northern wetlands: knowledge gained and remaining gaps. Frontiers in Microbiology, 2011, v. 2: 184
  18. 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
  19. 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