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Fungi, bacteria and soil pH: the oxalate–carbonate pathway as a model for metabolic interaction

Authors

  • Gaëtan Martin,

    1. Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
    2. Biogeosciences Laboratory, Institute of Geology and Palaeontology, , University of Lausanne, Lausanne, Switzerland
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    • These authors contributed equally to this study.
  • Matteo Guggiari,

    1. Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
    2. Biogeosciences Laboratory, Institute of Geology and Palaeontology, , University of Lausanne, Lausanne, Switzerland
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    • These authors contributed equally to this study.
  • Daniel Bravo,

    1. Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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  • Jakob Zopfi,

    1. Biogeosciences Laboratory, Institute of Geology and Palaeontology, , University of Lausanne, Lausanne, Switzerland
    2. Laboratory of Aquatic Biogeochemistry, Institute of Environmental Sciences, University of Basel, Basel, Switzerland
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  • Guillaume Cailleau,

    1. Biogeosciences Laboratory, Institute of Geology and Palaeontology, , University of Lausanne, Lausanne, Switzerland
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  • Michel Aragno,

    1. Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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  • Daniel Job,

    1. Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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  • Eric Verrecchia,

    1. Biogeosciences Laboratory, Institute of Geology and Palaeontology, , University of Lausanne, Lausanne, Switzerland
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  • Pilar Junier

    Corresponding author
    • Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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For correspondence. E-mail pilar.junier@unine.ch; Tel. (+41) 32 7182230; Fax (+41) 32 7182231.

Summary

The oxalate–carbonate pathway involves the oxidation of calcium oxalate to low-magnesium calcite and represents a potential long-term terrestrial sink for atmospheric CO 2. In this pathway, bacterial oxalate degradation is associated with a strong local alkalinization and subsequent carbonate precipitation. In order to test whether this process occurs in soil, the role of bacteria, fungi and calcium oxalate amendments was studied using microcosms. In a model system with sterile soil amended with laboratory cultures of oxalotrophic bacteria and fungi, the addition of calcium oxalate induced a distinct pH shift and led to the final precipitation of calcite. However, the simultaneous presence of bacteria and fungi was essential to drive this pH shift. Growth of both oxalotrophic bacteria and fungi was confirmed by qPCR on the frc (oxalotrophic bacteria) and 16S rRNA genes, and the quantification of ergosterol (active fungal biomass) respectively. The experiment was replicated in microcosms with non-sterilized soil. In this case, the bacterial and fungal contribution to oxalate degradation was evaluated by treatments with specific biocides (cycloheximide and bronopol). Results showed that the autochthonous microflora oxidized calcium oxalate and induced a significant soil alkalinization. Moreover, data confirmed the results from the model soil showing that bacteria are essentially responsible for the pH shift, but require the presence of fungi for their oxalotrophic activity. The combined results highlight that the interaction between bacteria and fungi is essential to drive metabolic processes in complex environments such as soil.

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