EGU General Assembly 2020
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.

Revealing how nitrogen fertilisation regulates the fluxes of COS and CO2 between soil communities and the atmosphere using a functional metagenomic and metatranscriptomic approach

Evert van Schaik1,2, Samuel Mondy1, Melanie Lelievre1, Marine Martin1, Solene Perrin1, Laura Meredith3, Aurore Kaisermann2, Samuel Jones2, Olivier Rue4, Valentin Loux4, and Lisa Wingate2
Evert van Schaik et al.
  • 1INRAE Genosol Platform, Agroécologie UMR1347, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
  • 2INRAE, ISPA UMR1391 Villenave d'Ornon, France
  • 3School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, USA
  • 4INRAE, MaIAGE UR1404, Université Paris-Saclay, Jouy-en-Josas, France

Recent interest in the seasonal and spatial variability of atmospheric COS has intensified as its use as an atmospheric tracer of biosphere productivity in the carbon cycle has recently been demonstrated. The key link between the COS and CO2 cycles in the biosphere is a family of enzymes called the carbonic anhydrases (CA) that catalyse both the hydration of CO2 and the hydrolysis of COS in both plants and soil microbes. Recently studies have demonstrated that the variability in soil COS and CO2 fluxes are modified significantly by fertilisation with inorganic N, indicating a strong coupling between soil carbon (C), nitrogen (N) and sulphur (S) cycling (Kaisermann et al., 2018). However, it is currently not clear whether the observed changes in COS and CO2 gas exchange were principally driven by important shifts in the microbial community size, structure or function or some combination of the three.

To elucidate the underlying mechanism(s) we used a functional metagenomic and metatranscriptomic approach coupled with climate controlled gas exchange measurements on soils. A set of 6 soils collected from boreal and temperate sites were sieved and re-packed in microcosms and incubated in the lab for 2 weeks at 23oC and 30% water holding capacity in the dark. For each site half the microcosms were fertilised with 5 mg N in the form of NH4NO3 at the start of the incubation period. At the end of the incubation period soil COS, CO2 fluxes were measured, and soil samples transported at -80oC to the Genosol platform for DNA and RNA extraction.  For each soil microcosm we quantified the abundance of bacterial, fungal and algal genes in each community using 16S, 18S and 23S amplicon sequencing. After assembling and cross-mapping the metagenomes and metatranscriptomes we used a HMM model (Meredith et al. 2018) to estimate and comparatively assess the abundance of CA genes between the different sites and treatments.

Our results indicate that the N treatment caused a relative increase in the abundance of fungi in N treated soils compared to those in the control. Generally, we also found that the total number of CAs in soils shifted when treated with N compared to the controls and that the β-D CA sub-family were the most prevalent CAs in all of the soils. In our presentation we will demonstrate how both the community structure and the abundance of CAs were modified upon N fertilisation and provide vital clues on the most likely mechanism(s) controlling COS and CO2 fluxes in soil communities and the significance of these results for interpreting atmospheric signals.

Kaisermann, Aurore, Sam P. Jones, Steven Wohl, Jérôme Ogée, and Lisa Wingate. 2018 Nitrogen Fertilization Reduces the Capacity of Soils to take up Atmospheric Carbonyl Sulphide. Soil Systems 2 (4), 62

Meredith, Laura K, Jérôme Ogée, Kristin Boye, Esther Singer, Lisa Wingate, Christian von Sperber, Aditi Sengupta, et al. 2018. “Soil Exchange Rates of COS and CO18O Differ with the Diversity of Microbial Communities and Their Carbonic Anhydrase Enzymes.” ISME Journal, 2018.

How to cite: van Schaik, E., Mondy, S., Lelievre, M., Martin, M., Perrin, S., Meredith, L., Kaisermann, A., Jones, S., Rue, O., Loux, V., and Wingate, L.: Revealing how nitrogen fertilisation regulates the fluxes of COS and CO2 between soil communities and the atmosphere using a functional metagenomic and metatranscriptomic approach, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-21605,, 2020

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Presentation version 1 – uploaded on 07 May 2020
  • CC1: Comment on EGU2020-21605, Yunyun Zheng, 08 May 2020

    Hi Evert,

    How about the N level (mg kg-1?)? Has N fertilizer affected microbial activity or growth as a whole? 

    • AC1: Reply to CC1, Evert van Schaik, 08 May 2020

      Hi Zheng,

      We added 5mg NH4NO3 per microcosm. That equals to ~15mg/kg of soil (you can find more detail here: In general the overal biomass seems to remain stable or decrease (depending on the soil) when the nitrogen is added. The soil is producing more COS and carbonic anhydrase transcription is up. This is of course only one aspect of activity.

      • CC2: Reply to AC1, Yunyun Zheng, 08 May 2020

        If N has caused negative impact on microbial activity or growth, fungi might have gained advantage over bacteria? The application rate is not high, very curious why fungi rise happened. Look forward to reading your paper.