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Title: Quantitative soil zymography: Mechanisms, processes of substrate and enzyme diffusion in porous media

Abstract

Soil membrane zymography enables 2D mapping of enzyme activities on the surface of soil samples. The method is according to diffusion of components of enzymatically-mediated reactions to/from membrane, and, hence, reflects the distribution of enzyme activities at the intact soil surface. Zymography has been already successfully implemented in numerous soil ecology applications. Here we identify two methodological aspects for further improvement and expansion of the method at micro and macro scales: first, accounting for the area of contact between the soil surface and the zymography membranes and, second, accounting for diffusion effects during the zymography procedure. We tested three methods, namely, laser-scanning, staining with a fluorescent product (e.g. MUF: 4-methylumbelliferone), and X-ray computed micro-tomography, for assessing the area of the soil surface in contact with the membranes. We quantified diffusion of MUF, enzymes and substrate between the substrate-saturated membrane and soil as well as diffusion processes during membrane zymography via HP2 software. Diffusion of the substrate from the membrane and of the MUF-product to the membrane was detected, while there were no clear evidence of enzyme diffusion to/in the membrane. According to the model simulations, the enzyme activities detected via 2D zymography probably represent only a small portion, about 20%,more » of the actual reactions within the soil volume that is in both direct contact and in hydrological contact with zymography membranes. This is a result of omnidirectional diffusion of reaction products. The membrane contact with the soil surface estimated by three methods ranged from 3.4 to 36.5% further signifying that only a fraction of enzymes activity is detectable in a course of 2D soil zymography.« less

Authors:
 [1];  [2];  [3];  [4]; ORCiD logo [4]; ORCiD logo [5];  [6]
  1. Michigan State Univ., East Lansing, MI (United States)
  2. Michigan State Univ., East Lansing, MI (United States); Gottingen Univ., Gottingen (Germany)
  3. Gottingen Univ., Gottingen (Germany); Univ. of Kiel, Kiel (Germany)
  4. Univ. of Kassel, Witzenhausen (Germany)
  5. Gottingen Univ., Gottingen (Germany); Inst. of Physicochemical and Biological Problems in Soil Science, Pushchino (Russia)
  6. RUDN Univ., Moscow (Russia)
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1506665
Grant/Contract Number:  
SC0018409
Resource Type:
Accepted Manuscript
Journal Name:
Soil Biology and Biochemistry
Additional Journal Information:
Journal Volume: 127; Journal Issue: C; Journal ID: ISSN 0038-0717
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; In situ 2D zymography; Soil enzyme activity; Microbial hotspot's localization; Diffusion processes

Citation Formats

Guber, Andrey, Kravchenko, Alexandra, Razavi, Bahar S., Uteau, Daniel, Peth, Stephan, Blagodatskaya, Evgenia, and Kuzyakov, Yakov. Quantitative soil zymography: Mechanisms, processes of substrate and enzyme diffusion in porous media. United States: N. p., 2018. Web. doi:10.1016/j.soilbio.2018.09.030.
Guber, Andrey, Kravchenko, Alexandra, Razavi, Bahar S., Uteau, Daniel, Peth, Stephan, Blagodatskaya, Evgenia, & Kuzyakov, Yakov. Quantitative soil zymography: Mechanisms, processes of substrate and enzyme diffusion in porous media. United States. doi:10.1016/j.soilbio.2018.09.030.
Guber, Andrey, Kravchenko, Alexandra, Razavi, Bahar S., Uteau, Daniel, Peth, Stephan, Blagodatskaya, Evgenia, and Kuzyakov, Yakov. Fri . "Quantitative soil zymography: Mechanisms, processes of substrate and enzyme diffusion in porous media". United States. doi:10.1016/j.soilbio.2018.09.030. https://www.osti.gov/servlets/purl/1506665.
@article{osti_1506665,
title = {Quantitative soil zymography: Mechanisms, processes of substrate and enzyme diffusion in porous media},
author = {Guber, Andrey and Kravchenko, Alexandra and Razavi, Bahar S. and Uteau, Daniel and Peth, Stephan and Blagodatskaya, Evgenia and Kuzyakov, Yakov},
abstractNote = {Soil membrane zymography enables 2D mapping of enzyme activities on the surface of soil samples. The method is according to diffusion of components of enzymatically-mediated reactions to/from membrane, and, hence, reflects the distribution of enzyme activities at the intact soil surface. Zymography has been already successfully implemented in numerous soil ecology applications. Here we identify two methodological aspects for further improvement and expansion of the method at micro and macro scales: first, accounting for the area of contact between the soil surface and the zymography membranes and, second, accounting for diffusion effects during the zymography procedure. We tested three methods, namely, laser-scanning, staining with a fluorescent product (e.g. MUF: 4-methylumbelliferone), and X-ray computed micro-tomography, for assessing the area of the soil surface in contact with the membranes. We quantified diffusion of MUF, enzymes and substrate between the substrate-saturated membrane and soil as well as diffusion processes during membrane zymography via HP2 software. Diffusion of the substrate from the membrane and of the MUF-product to the membrane was detected, while there were no clear evidence of enzyme diffusion to/in the membrane. According to the model simulations, the enzyme activities detected via 2D zymography probably represent only a small portion, about 20%, of the actual reactions within the soil volume that is in both direct contact and in hydrological contact with zymography membranes. This is a result of omnidirectional diffusion of reaction products. The membrane contact with the soil surface estimated by three methods ranged from 3.4 to 36.5% further signifying that only a fraction of enzymes activity is detectable in a course of 2D soil zymography.},
doi = {10.1016/j.soilbio.2018.09.030},
journal = {Soil Biology and Biochemistry},
number = C,
volume = 127,
place = {United States},
year = {2018},
month = {9}
}

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