The soil microbiome includes bacteria, fungi, archaea, and other microorganisms that play a key role in organic matter decomposition, nutrient cycling, and improving soil structure. This complex ecosystem helps plants better absorb nutrients, strengthens their resistance to pathogens and overall contributes to the sustainability of agricultural systems. Knowledge of the composition of the soil microbiome can be essential for optimizing agricultural practices and improving crop quality.
For whom is the soil microbiome analysis in our laboratory intended?
- Farmers - Knowing the composition of the soil microbiome can help you improve crop quality, increase yields and optimize the use of fertilizers and pesticides. Awareness of the presence of beneficial microorganisms can promote more sustainable agricultural practices and reduce the cost of chemical inputs.
- Winemakers and gardeners - Microbial communities have a direct effect on the quality and health of plants. Analysis of the soil microbiome can provide you with important information about how microorganisms affect your plants and help you adjust growing conditions.
- Ecologists and scientists - For the research of ecological processes, the restoration of degraded soils or the monitoring of environmental changes, the analysis of the soil microbiome provides invaluable data on the state of soil ecosystems.
- And others
We are collaborating with a regenerative agriculture farm in the Czech Republic on a systematic analysis of the soil microbiome
In cooperation with the leading Czech farm of regenerative agriculture, we are currently (2024) collaborating on the analysis of an extensive set of soil samples collected across the Czech Republic.
The goal of this collaboration is a better understanding of the connections between the composition of the soil microbiome and its influence on the results of plant production on both cultivated and currently unused plots from which soil samples were taken. The analysis also includes an extensive set of metadata, which allows us to search and find connections.
This is a study based on the interest of the client and the offer of the SEQme company, which is financed exclusively from internal sources and no governmental or European support is provided for it.
If you are interested in this kind of cooperation, we will be very happy if you contact us!
Technology
The analysis of the microbiome can be performed in basically two ways. One of them is the analysis of selected informative markers such as the 16S rRNA gene and other standard or specifically selected markers suitable for evaluating the diversity of microbial populations. Any such appropriately chosen marker is capable of capturing changes in the diversity of the bacterial community, however this analysis is typically limited purely to the detection of the microorganisms present.
If we want to analyze the microbiome in more detail, an alternative technique called deep or shot-gun sequencing comes into play. With this method, we not only reveal the identity of the organisms present, but we are also able to perform functional profiling. In functional profiling, the present biosynthetic pathways of the microorganisms represented in the microbiome are reconstructed - the analysis thus at least partly tells about what is "going on" in the microbiome.
Both methodological approaches have their pros and cons, and their choice is a matter of assignment and discussion.
How does a custom microbiome analysis work?
- Study design - Based on your specification, we will jointly determine the objectives of the analysis of the microbiome in your samples, including the broader context, typically the collection of metadata in connection with the collection of samples. We will explain to you the possibilities of analyzing the microbiome using sequencing techniques, taking into account the nature of the study and what questions you can and cannot expect to be answered.
- Sampling - We will provide you with instructions for collection, storage and transport and recommend suitable sampling kits. In case of interest and if it is technically possible, we will carry out or assist in the collection of samples.
- DNA Extraction - After receiving the samples, we extract the microbial DNA in such a way that the overall integrity of the sample is preserved and all microorganisms present are included.
- Sequencing - We analyze the microbial composition of the sample using DNA sequencing techniques.
- Bioinformatics analysis - We process sequencing data using tools and databases that enable accurate identification of microorganisms, their functional capabilities and their representation in the sample.
- Report and interpretation of results - We will provide you with a clear report on the composition of the microbiome in the analyzed samples. In cooperation with you and based on all the data obtained, we will try to interpret the results to the maximum extent possible so that you can draw conclusions from them with regard to the set goals of the project.
If you are interested in our services in soil microbiome analysis, contact us.