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Combined Methylome, Transcriptome and Proteome Analyses Document Rapid Acclimatization of a Bacterium to Environmental Changes

Authors
  • Srivastava, Abhishek1, 2
  • Murugaiyan, Jayaseelan3, 4
  • Garcia, Juan A. L.2
  • De Corte, Daniele5
  • Hoetzinger, Matthias6
  • Eravci, Murat7
  • Weise, Christoph7
  • Kumar, Yadhu8
  • Roesler, Uwe3
  • Hahn, Martin W.9
  • Grossart, Hans-Peter1, 10
  • 1 Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin , (Germany)
  • 2 Department of Functional and Evolutionary Ecology, University of Vienna, Vienna , (Austria)
  • 3 Centre for Infectious Medicine, Institute for Animal Health and Environmental Hygiene, Freie Universität Berlin, Berlin , (Germany)
  • 4 Department of Biotechnology, SRM University-AP, Guntur , (India)
  • 5 Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka , (Japan)
  • 6 Department of Biology and Environmental Science, Linnaeus University, Kalmar , (Sweden)
  • 7 Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin , (Germany)
  • 8 Eurofins Genomics Europe Sequencing GmbH, Konstanz , (Germany)
  • 9 Research Department for Limnology, University of Innsbruck, Mondsee , (Austria)
  • 10 Institute for Biochemistry and Biology, Potsdam University, Potsdam , (Germany)
Type
Published Article
Journal
Frontiers in Microbiology
Publisher
Frontiers Media SA
Publication Date
Sep 15, 2020
Volume
11
Identifiers
DOI: 10.3389/fmicb.2020.544785
PMID: 33042055
PMCID: PMC7522526
Source
PubMed Central
Keywords
License
Unknown

Abstract

Polynucleobacter asymbioticus strain QLW-P1DMWA-1T represents a group of highly successful heterotrophic ultramicrobacteria that is frequently very abundant (up to 70% of total bacterioplankton) in freshwater habitats across all seven continents. This strain was originally isolated from a shallow Alpine pond characterized by rapid changes in water temperature and elevated UV radiation due to its location at an altitude of 1300 m. To elucidate the strain’s adjustment to fluctuating environmental conditions, we recorded changes occurring in its transcriptomic and proteomic profiles under contrasting experimental conditions by simulating thermal conditions in winter and summer as well as high UV irradiation. To analyze the potential connection between gene expression and regulation via methyl group modification of the genome, we also analyzed its methylome. The methylation pattern differed between the three treatments, pointing to its potential role in differential gene expression. An adaptive process due to evolutionary pressure in the genus was deduced by calculating the ratios of non-synonymous to synonymous substitution rates for 20 Polynucleobacter spp. genomes obtained from geographically diverse isolates. The results indicate purifying selection.

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