EGU General Assembly 2020
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.

Unraveling the Molecular Mechanisms Underlying the Microbiome Response to Soil Rewetting

Mary Lipton, Montana Smith, Karl Weitz, Sneha Couvillion, Vanessa Paurus, Thomas Metz, Janet Jansson, and Kirsten Hofmockel
Mary Lipton et al.
  • Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, Richland, United States of America (

Soil microbes are highly sensitive to changes in their environment, and rapidly measuring their responses is necessary to fully understand the biological processes. Drought is one of the most common environmental stresses that soil microbiomes experience, and it is important to understand the mechanisms by which the soil microbiome respond to soil dehydration. We used 13C as a tracer of nutrient fluxes in desiccated soil microbiomes after rewetting to simultaneously measure aerobic respiration and track the metabolic state of the community. Here, we describe a Real Time Mass Spectrometry (RTMS) approach for rapid gas monitoring combined with omics approaches to track 13C flow through a soil system.

The mechanism(s) behind the burst of rapid mineralization of soil organic matter and increased rate of COrelease upon rewetting dry soil (termed the ‘Birch Effect’) are yet to be fully defined. One known mechanism used by microbes to protect against dehydration is the production of intracellular compounds known as osmolytes. We evaluated metabolic mechanisms produced upon rewetting a marginal soil testing the hypothesis that the rapid release of COarises from the microbial processing of putative intracellular osmolytes that build up during desiccation. RTMS allows for the simultaneous, rapid and fine scale (every 2 sec) evaluation and deconvolution of the production and consumption of a number of gasses including 12CO2,13CO2, O2, Nand H2O.  We compared the hydration response (production of COin real time) between the addition of water and 13C labeled glucose dissolved in water. The initial burst of 12COfollowed by a leveling off was identical in both treatments with an additional larger increase in 13COabout 20 minutes later in the 13C labeled glucose experiment. Examination of the two minutes after the water addition revealed a rapid rate of 12CO2 (38 sec) and H2O (47 sec) production and slow rate of 13CO2 (56 sec) production followed by the consumption of O(67 sec) and N2 (73 sec).  Evaluation of the soil metabolomes at specified time points within 3 hours after wetting revealed the immediate release of sugars from the cells into the extracellular matrix. These results provide evidence for respiration of putative intracellular osmolytes as one driving mechanism of the Birch Effect. 

How to cite: Lipton, M., Smith, M., Weitz, K., Couvillion, S., Paurus, V., Metz, T., Jansson, J., and Hofmockel, K.: Unraveling the Molecular Mechanisms Underlying the Microbiome Response to Soil Rewetting, EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-11994,, 2020


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displays version 1 – uploaded on 03 May 2020
  • CC3: Comment on EGU2020-11994, Martin Maier, 07 May 2020

    Dear Mary Lipton, 

    thank you very much for your intersting presentation.  You could show that the  reaction after rewetting is very fast. Do you think the observed CO2 emissions are of biological origin, ie. respiration emissions, or are they of physico-chemical origin? Are there ways to find out about this?


    Best wiishes



  • AC1: Comment on EGU2020-11994, Mary Lipton, 07 May 2020

    Martin,  Thanks for the question.  We have looked into the orgin of the carbon at such short time scales and have found that there is a component of abiotic CO2 release, but it accounts for only about 10% of the total carbon release seen (as evidenced by the experiment being done on sterile soil).  We are in the process of defining the origin of the biotically derived carbon using soil amendments and stable isotope labeling.  Our preliminary results point to a biotic respiration of intracellular carbon at a time scale similar to that of the abiotic release.  This increase in carbon output is then followed by a second release that corresponds to the respiration of extracellular carbon.  We are in the process of getting statistically significant data that we are hoping appears in publication later this year.