Details
| Original language | English |
|---|---|
| Pages (from-to) | 156-167 |
| Number of pages | 12 |
| Journal | Soil biology & biochemistry |
| Volume | 127 |
| Early online date | 28 Sept 2018 |
| Publication status | Published - Dec 2018 |
| Externally published | Yes |
Abstract
Soil membrane zymography enables 2D mapping of enzyme activities on the surface of soil samples. The method is based on diffusion of components of enzymatically-mediated reactions to/from membrane, and, thus, 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.
Keywords
- In situ 2D zymography, Soil enzyme activity, Microbial hotspot's localization, Diffusion processes
ASJC Scopus subject areas
- Immunology and Microbiology(all)
- Microbiology
- Agricultural and Biological Sciences(all)
- Soil Science
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In: Soil biology & biochemistry, Vol. 127, 12.2018, p. 156-167.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - Quantitative soil zymography
T2 - Mechanisms, processes of substrate and enzyme diffusion in porous media
AU - Guber, Andrey
AU - Kraychenko, Alexandra
AU - Razavi, Bahar S.
AU - Uteau, Daniel
AU - Peth, Stephan
AU - Blagodatskaya, Evgenia
AU - Kuzyakov, Yakov
N1 - Funding Information: This research was partly funded by the National Science Foundation's Long-Term Ecological Research Program (DEB 1027253), by the National Science Foundation's Geobiology and Low Temperature Geochemistry Program (Award no. 1630399), by the Department of Energy Great Lakes Bioenergy Research Center (DOE O_ce of Science BER DE-FC02-07ER64494), by Michigan State University's AgBioResearch (Project GREEEN), and by Michigan State University's Discretionary Funding Initiative. The work was supported by DAAD- German Academic Exchange Service’ program “Research Stays for University Academics and Scientists, 2017” (57314018) and by the Research Award from Alexander von Humboldt Foundation. Contributions of BSR and EB were motivated and supported within the framework of the priority program 2089, funded by the DFG- Projects Nr. 403670038 and Nr. 403664478, respectively. This work has also been conducted in part as a preparatory study for the recently launched DFG priority program 2089 Rhizosphere spatiotemporal organization—a key to rhizosphere functions PE 1523/10–1.
PY - 2018/12
Y1 - 2018/12
N2 - Soil membrane zymography enables 2D mapping of enzyme activities on the surface of soil samples. The method is based on diffusion of components of enzymatically-mediated reactions to/from membrane, and, thus, 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.
AB - Soil membrane zymography enables 2D mapping of enzyme activities on the surface of soil samples. The method is based on diffusion of components of enzymatically-mediated reactions to/from membrane, and, thus, 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.
KW - In situ 2D zymography
KW - Soil enzyme activity
KW - Microbial hotspot's localization
KW - Diffusion processes
UR - http://www.scopus.com/inward/record.url?scp=85054737854&partnerID=8YFLogxK
U2 - 10.1016/j.soilbio.2018.09.030
DO - 10.1016/j.soilbio.2018.09.030
M3 - Article
VL - 127
SP - 156
EP - 167
JO - Soil biology & biochemistry
JF - Soil biology & biochemistry
SN - 0038-0717
ER -