Laboratory of Soil Organic Matter

We focus on organic matter decomposition, soil carbon sequestration, and nutrient fluxes in ecosystems. In addition, we focus on factors that influence all these processes.

We investigate mostly forest ecosystems, but also agricultural soils or extreme environments such as caves or arctic soils.


We provide these analyses:

  • physical - texture, water holding capacity
  • chemical - organic matter content, soil carbon sequestration, contents of available and total nutrients (C, N, P), pH, conductivity
  • microbial - soil respiration, microbial biomass C and N content, phospholipid fatty acids (PLFA)


We take part in top research in the public interest in the frame of Strategy AV21 Foods for the Future.

We cooperate with students from high schools (Open Science, Středoškolská odborná činnost) and universities (bachelor and master theses).


Research projects

Pyroseq: Pyrogenic organic matter sequestration in forest soils affected by climate change

Czech Science Foundation (CSF), principal investigator, 2024-2026

Forest wildfires lead to the production of chemically altered biomass residues known as pyrogenic organic matter (pyOM), which has been thought to be highly resistant and contribute to soil organic carbon (SOC) sequestration. A significant portion of pyOM may, however, be utilized by soil biota and as such may be fragmented, digested, and released as carbon dioxide into the atmosphere or stabilized in the soil. In addition, soil succession after the fire event and climate change may have a significant effect on all of the biotic processes. Here, we observe successional changes in the soil properties on a 100-year post-fire chronosequence in pine forests in the Mediterranean, temperate, and boreal zones and along the soil profile. The focus is on the effect of increased temperature on the transformation and stabilization of pyOM by soil faunal and microbial communities. The proposed project consists of field samplings and observations, 13C-labelled pine litter and pyOM production, as well as a slightly manipulated field experiment and a heavily manipulated laboratory experiment.

HYDROLYZE: Innovative utilization of hydrolysate from animal waste for improvement of agricultural soil quality

Technology Agency of the Czech Republic (TA ČR), principal investigator, 2023-2025

The project aim is to test a new type of bioadditive, hydrolysate from animal waste, in order to protect physical, chemical, and biological properties of agricultural soils and decrease greenhouse gases emissions. The main aim is to test the efficiency and longevity of hydrolysate phase and dose in improving the soil quality and health. The secondary aim is to verify the efficiency of hydrolysate in the stabilization of plant biomass from harvesting remnants in the soil and in decreasing greenhouse gases emissions from the soil. All this will be tested considering the type of soil and crop ensuring their sustainability, maximum water retention, plenty of nutrients and microbial communities.

SOMForClim: Soil organic matter fractions and soil carbon storage as affected by forest type and climate change

Czech Science Foundation (CSF), principal investigator, 2022-2024

Temperate forests hold a great potential for storing soil organic C (SOC). The bulk SOC, however, is partitioned into fractions of soil organic matter (SOM) that differ in terms of formation, persistence, and function. As a result, the fractions might be differently affected by carbon (C) input chemistry (quality) and climate change. Here, we compare the amounts of C in SOM fractions among deciduous, coniferous, and mixed forest soils along the soil profile. We also determine how the formation and persistence of SOM fractions are affected by C input quality (i.e., litter leachates vs. root exudates), increased temperature, and soil fauna and microorganisms. The proposed project consists of field samplings and observations, a slightly manipulated field experiment that explains a part of the process, and two heavily manipulated laboratory experiments that explain the process in detail. Finally, the acquired data will be compiled and used to improve and validate selected soil C models.

The effect of soil fauna on carbon sequestration in extreme environments

European Cooperation in Science and Technology (COST), team member, 2017-2019

We aimed to determine the relative importance of respective groups of soil fauna in soil carbon sequestration not only in extreme environments, which, however, served as models for such processes. We were interested in estimation of relative proportions of soil organic matter fractions, which resulted from litter decomposition as affected by various functional groups of soil fauna. In situ enclosure experiments as well as lab manipulative experiments under controlled conditions were used.

Linking functional traits of three organism levels as driving mechanisms of ecosystem functions in the Arctic

Czech Science Foundation (CSF), team member, 2017-2019

There is an increasing evidence that functional traits of biota may serve as important indicators of ecosystem services. Although it is known that different organism levels interact in providing ecosystem services, there are so far only few studies linking functional traits of several trophic levels together. Here we proposed to interconnect functional traits of three organism levels plants, soil fauna and soil microorganisms - to ecosystem functions underlying ecosystem services in the Arctic terrestrial ecosystem, representing a less complex, model system. Several ecosystem functions were approached (C sequestration potential and soil stability, fertility and water retention) in a set of manipulative experiments. We expected that joining relevant functional traits across organism levels into "multitrophic" trait clusters will allow us to identify key traits underlying the ecosystem functions.

Organic matter decomposition and carbon sequestration on a natural gradient of labile carbon sources in coniferous temperate forest soils

Czech Science Foundation (CSF), principal investigator, 2017-2019 

This project dealt with the effect of labile carbon (C) from various sources (litter, rhizodeposition, honeydew) on soil organic matter (SOM) decomposition and C sequestration in temperate coniferous forest soils, which are of global importance in terms of organic C storage. The proposed project mainly dealt with: (i) the rate of SOM decomposition and C sequestration on a natural gradient of labile C sources; (ii) potential increase in SOM decomposition and C sequestration with increased labile C input; (iii) effect of microbial and faunal community on labile C flux; and (iv) the role of respective labile C sources in C fluxes through soil. Field samplings and observations were combined with field and laboratory manipulation experiments, both followed by laboratory analyses.


Biology Centre CAS
Institute of Soil Biology and Biogeochemistry
Na Sádkách 702/7
370 05 České Budějovice

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