1
Soil Scientists from RUDN University Have Determined the Optimal Size of Soil Pores for the Activity of Microorganisms

Soil Scientists from RUDN University Have Determined the Optimal Size of Soil Pores for the Activity of Microorganisms

Soil scientists from RUDN University found that the most favorable conditions for microorganisms are created in soil pores with a size of 60 to 180 micrometers. To visualize the relationship between the enzymes that produce soil microorganisms and pore size, the researchers created a three-dimensional map of soil structure. To do this, they used soil 2D zymography and X-ray computed tomography (3D). The article is published in the leading soil science journal Soil Biology and Biochemistry.

Soil types differ from each other not only in their chemical properties, but also in their location, shape, and pore size. Although any soil has both small and large pores, their ratio may be different. Larger pores (from 100 micrometers) are filled with air and are located between the soil lumps, small pores (10-100 micrometers) inside the lumps are filled with water. The pores are home to colonies of microbes that are responsible for biochemical reactions associated with the circulation of carbon, phosphorus, nitrogen and other chemical elements. Microorganisms improve soil fertility and carbon sequestration, so understanding what parameters (including pore sizes) determine the ‘well-being’ of microorganisms will help farmers increase yield.

Previously, the distribution of enzymes that secrete soil microorganisms was associated only with the chemical and biological properties of the soil. However, the physical structure of the soil also affects beneficial microbial communities and, consequently, enzymes. For the first time, soil scientists from RUDN University found optimal parameters of soil pores for microbial communities. To do this, they examined the pores using soil 2D-zymography — a biochemical method for studying the activity of enzymes, and X-ray computed tomography.

Soil samples from five land-use systems were taken from plots prepared for experiments by The Kellogg Biological Station in Michigan (USA): soil on which only corn was grown (1); white rye (2); millet (3); hybrid poplar with grassy undergrowth, (4) and soil on which plant communities successively changed as a result of natural factors or human activity (5). There were no live roots in the samples, meaning all the enzymes are produced by microorganisms.

To determine the distribution and size of pores in soils, samples measuring 5-10 centimeters were scanned with X-rays. Enzyme activity was mapped using zymography. Special membranes with substrates were placed on the surface of the samples, which emit fluorescent products upon contact. These products display the activity of enzymes in ultraviolet light. We studied the enzymes involved in the turnover of carbon, nitrogen and phosphorus in the soil: cellobiohydrolase, xylonase, acid phosphatase, β-glucosidase, leucinaminopeptidase and N-acetylglucosaminidase. Combining zymography and computer microtomography data allowed creating 3D maps that visualize the size of soil pores and enzyme activity in an intact soil sample.

In all the studied soil samples, regardless of the type, the most enzymes (and therefore the highest activity of microorganisms) were observed in pores with a diameter of 60-180 micrometers. Therefore, pores of this size are an ideal habitat for soil microbes. In smaller or larger pores, the activity of all six enzymes was less. Whole microbial colonies are located in the pores of this size (60-180 microns), and the access of water and oxygen is optimal. In the pores of this size (60-180 microns), more small roots grow, which provides greater saturation of the soil with readily available carbon. Thus, the size of soil pores does affect the distribution of enzymes.

The experiment confirmed for the first time that the combination of these two methods is effective for studying enzymes. In the future, soil scientists plan to improve the resolution of images and take into account additional factors such as fresh carbon intake, soil moisture and acidity. This will provide more accurate data and strengthen understanding of biochemical processes in situ — in the place where they occur, without any interference.

Article in Soil Biology and Biochemistry

Main Publications View all
15 Nov 2017
RUDN University scientists publish results of their scientific researches in highly-recognized in whole world and indexed in international databases journals (Web of Science, Scopus ect.). That, of course, corresponds to the high status of the University and its international recognition. Publications of June-September 2017 ( In Journals of categories Q1-Q3)
1307
Visiting Professors View all
03 Nov 2017
Michele Pagano is a graduate of the University of Pisa, a leading scientist, the author of more than 200 publications in international journals, and a participant in many international research projects
2025
Similar newsletter View all
15 Jul
RUDN physicians have identified genetic characteristics that may affect the predisposition to re-stenosis

RUDN University physicians have identified genetic characteristics that may affect the predisposition to re-stenosis — narrowing of the lumen of the vessel — after the installation of a stent. The results will help to determine the risk of restenosis and select personalized therapy more accurately.

26
15 Jul
RUDN Chemists Have Created a Reusable Switch Catalyst for The Synthesis of Two Different Compounds

RUDN chemists have created a reusable catalyst for the oxidation of sulfides for the synthesis of drugs, dyes, and other compounds. It can “switch” the final product and provides “green” reaction conditions.

40
15 Jul
Scientists Report New Hydrogel to Protect Wounds from Germs

RUDN University and Shahid Beheshti University (SBU) chemist together with colleagues from Iran created a hydrogel film for wound dressing. It protects the wound from germs and is harmless to healthy tissues. Moreover, its porous structure can hold antibiotic, which kills dangerous microorganisms and provide additional protection.

19
Similar newsletter View all