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

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Abstract

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.

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Acknowledgements

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.

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  1. Ezekiel K. Bore and Sara Halicki contributed equally.

Authors and Affiliations

  1. Department of Agricultural Soil Science, University of Goettingen, 37077, Göttingen, Germany

    Ezekiel K. Bore, Sara Halicki, Yakov Kuzyakov & Michaela A. Dippold

  2. Department of Soil Science of Temperate Ecosystems, University of Goettingen, 37077, Göttingen, Germany

    Yakov Kuzyakov

  3. Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia, 420049

    Yakov Kuzyakov

  4. Department of Biogeochemistry of Agroecosystems, University of Goettingen, 37077, Göttingen, Germany

    Ezekiel K. Bore, Sara Halicki & Michaela A. Dippold

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  1. Ezekiel K. Bore
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Correspondence to Ezekiel K. Bore.

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Bore, E.K., Halicki, S., Kuzyakov, Y. et al. Structural and physiological adaptations of soil microorganisms to freezing revealed by position-specific labeling and compound-specific 13C analysis. Biogeochemistry 143, 207–219 (2019). https://doi.org/10.1007/s10533-019-00558-5

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