Structural and physiological adaptations of soil microorganisms to freezing revealed by position-specific labeling and compound-specific 13C analysis

  • Ezekiel K. BoreEmail author
  • Sara Halicki
  • Yakov Kuzyakov
  • Michaela A. Dippold


Psychrotolerant microbes are crucial for carbon cycling and biotechnological applications. Nonetheless, the mechanisms enabling their survival and functioning in frozen environments remain unclear. To elucidate adaptations of microbial cell membranes to freezing, we incubated soils with position-specific 13C labeled glucose at + 5 (control), − 5 and − 20 °C and quantified 13C in CO2 and phospholipid fatty acids. High oxidation of glucose C-1 at + 5 °C revealed a transformation via the pentose phosphate pathway. At subzero temperatures, however, the preferential oxidation of C-4 position suggested a switch to glycolysis. The threefold increase of Gram-negative phospholipid fatty acids in soil incubated at − 5 °C was accompanied by a twofold increase in 13C incorporation. This unequal increase of phospholipid fatty acids and incorporated 13C can be explained by simultaneous desaturation of existing fatty acid chains and the de novo synthesis of monounsaturated fatty acids, which indicates microbial growth. In contrast, Gram-positive bacteria incorporated 2 times higher 13C into their phospholipid fatty acids at − 20 °C than at − 5 and + 5 °C without a significant increase in their fatty acid contents. This reflects intensive repair of membranes damaged at − 20 °C without microbial growth. The fungal/bacterial ratio was 1.5 times lower at subzero temperatures than at + 5 °C, reflecting a shift in microbial community structure towards bacteria. Accordingly, soil microorganisms adapted to freezing by (1) switching their metabolic pathway from the pentose phosphate pathway to glycolysis, (2) modifying phospholipid fatty acids by desaturation and, (3) shifting microbial community structure towards Gram-negative bacteria by reducing the fungal population.


Community structure Metabolic tracing Phospholipid adaptations Psychrotolerant microbes Subzero temperatures 



We thank Paul Dijkstra for helpful discussions, DAAD for facilitating the discussions by providing the travel Grant PPP USA (ID-57211766) and for jointly funding Ezekiel K. Bore with the Kenyan government, and the DFG for funding the work under Grant Numbers DI-2136/1-1 and NTS 186/1006-1/P. We also thank the technical staff of the Department of Agricultural Soil Science and the Department of Soil Science of Temperate Ecosystems of the University Goettingen for sample preparation, the entire team at KOSI (Centre for Stable Isotopes Analysis) for δ13C analysis and Joshua Bostic for English editing. Two anonymous reviewers and the handling editor are also acknowledged for their insightful comments that greatly improved this manuscript.

Supplementary material

10533_2019_558_MOESM1_ESM.docx (60 kb)
Supplementary material 1 (DOCX 60 kb)


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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Department of Agricultural Soil ScienceUniversity of GoettingenGöttingenGermany
  2. 2.Department of Soil Science of Temperate EcosystemsUniversity of GoettingenGöttingenGermany
  3. 3.Institute of Environmental SciencesKazan Federal UniversityKazanRussia
  4. 4.Department of Biogeochemistry of AgroecosystemsUniversity of GoettingenGöttingenGermany

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