Soil Microbiome Analysis

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The importance of microorganisms in soil

Soil contains diverse communities of microorganisms that perform numerous functions, allowing the soil to support plant growth and health by fixation of nutrients, fighting diseases, creating resistance to drought, expanding root reach, and decomposing organic material.
Therefore, knowledge about the presence of specific microorganisms and their functional capacity is of great importance when working with soil. 
Different types of soil are characterized by their unique composition of microbes, and even within soil types, the composition differs depending on factors such as pH, water content, fertilization, and crop type.

Characterizing and modifying the beneficial microbes found in soil and on plants presents a promising strategy to optimize plant growth and health, and greater knowledge of the diverse communities of microorganisms in the soil, therefore, paves way for creating more robust crops that can be produced more sustainably.


Til soil side website

Why is profiling of the soil microbiome important?

At Biomcare we offer soil microorganism profiling services, which help you detect the microorganisms in your soil and the functional capacity of these microorganisms. Statistical analysis is performed to detect associations between the microbiome and specific soil measures such as crop yield or crop diseases. Unfavorable microbial compositions in soil affect the supply of nitrogen, phosphorus, and other nutrients to plants, altering nutrient availability and plant growth.
Soil microbiome profiling thus gives an insight into, and control over, these factors in your agricultural work.

Through the knowledge of the composition of microorganisms in your soil you can:

  • Predict what biofertilizers to use.
  • Detect and take precautions against harmful fungi and pathogens.
  • Understand interactions between plants and microorganisms.
  • Optimize crops and cultivation methods so the crops attract beneficial microorganisms present in the soil.
  • Provide documentation for new farming solutions and products.


How do soil microbiome analysis and microbiome insight play an active role in farming?

The microbiome is often actively modified to improve agriculture. A few examples include:

Improvement of plants’ ability to utilize nutrients, such as phosphorus and nitrogen, through microbes. Microbial inoculants, or biofertilizers, show promising results and may be implemented in agriculture to reduce the use of inorganic fertilizers. Many microbes can serve as biofertilizers as they are able to fix nitrogen from the air and thus help plants to access nutrients from organic fertilizers. Furthermore, certain microbes can improve drought tolerance, improve plant health or increase salt tolerance.

Improvement of crop yield, while reducing the cost of fertilizers. Crop yields can be increased by up to 40 percent if beneficial soil microorganisms, or biofertilizers, are added to the soil during sowing. The use of beneficial microbes to improve the plant’s utilization of phosphorus and nitrogen can save costs by reducing the need for mineral fertilizers. In turn, this reduces the environmental impact of overfertilization (1).

Improvement of the soil microbiome improves water retention.Biofertilizers show the greatest effect on crop yield in dry areas (yield response: dry climate +20.0 ± 1.7%, tropical climate +14.9 ± 1.2%, oceanic climate +10.0 ± 3.7%, continental climate +8.5 ± 2.4%). This is important with the increase in dry farmland and promotes biofertilizers as an adaptation to climate change (2-5).

How we work with soil microbiome analysis at Biomcare

At Biomcare we ue sequencing solutions to assess the composition of microorganisms. Sequencing offers several advantages, as it:

  • Allows for 100-1000s of microbes to be detected at once.
  • Is untargeted. There is no need to know what specific microbe we are looking for.
  • Is sensitive and specific, permitting thorough investigation without the need for culturing or microscopy.
  • Is quantitative, whereas many other methods only provide detection/no detection results.
  • Allows for investigations of functional capacities.

Different methods are available for the sequencing of DNA in samples. At Biomcare we are specialists in sequencing methods, including:

  • 16s sequencing involve sequencing of the 16s rRNA gene. With this sequencing method, we can identify which bacteria are present in a sample and calculate their relative abundance. This is possible with a resolution down to the species level.
  • ITS sequencing involves sequencing of the Internal Transcribed Spacer (ITS), located in the rRNA gene transcription region. This method is used for fungi phylogenetic profiling and is used to identify fungi and their relative abundance in a sample.
  • Shotgun sequencing is a method used for non-targeted sequencing of DNA. This method involves breaking up the microbial genomes into small DNA fragments, which are then sequenced individually. Shotgun sequencing provides information on biodiversity (both fungi and bacteria), the abundance of detected microorganisms, and their function.

As DNA sequencing results in large amounts of data, this data needs processing before relevant information can be gained from the data. Therefore, a key step at Biomcare, when data is generated, is to perform all necessary data cleaning and processing. This results in a so-called microbiome profile for each sample (tables of relative abundance for the individual microbes). When profiles are ready, we proceed to the biostatistical analysis where we integrate meta-data, such as used fertilizers, plant yield, plant infections, etc., to answer your defined project questions.

We provide support for all steps of a project, ranging from planning to the interpretation of results. The key steps of a new soil microbiome project are:

  • Project planning
  • Collection of samples and supportive meta-data
  • Shipment of samples for sequencing
  • Data processing and generation of microbiome profiles
  • Biostatistical analysis
  • Evaluation of results

Depending on your wish, we can support you through all steps of the project, or step in where you need our support.

Please see the page “Microbiome profiling at Biomcare” for a step-by-step introduction to a microbiome project in collaboration with Biomcare.


"We used Biomcare to analyze the occurrence and composition of bacteria and fungi in soil samples, in a project evaluating soil fertility and the effect of tilling.
...The results were presented in easily understandable and illustrative reports, and by personal communication, and all communication went swiftly. I can highly recommend Biomcare for their expertise." 

Annette Vibeke Vestergaard

Senior specialist, Soil and Soil Management. Crop Innovation and Environment, SEGES

Illustration - plant and soil microbiome

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Reference and suggested reading

Gharechahi, J. et al. (2017) ‘The dynamics of the bacterial communities developed in maize silage’, Microbial Biotechnology. doi: 10.1111/1751-7915.12751.

Panke-Buisse, K. et al. (2015) ‘Selection on soil microbiomes reveals reproducible impacts on plant function’, ISME Journal. doi: 10.1038/ismej.2014.196.

Schütz, L. et al. (2018) ‘Improving Crop Yield and Nutrient Use Efficiency via Biofertilization—A Global Meta-analysis’, Frontiers in Plant Science. doi: 10.3389/fpls.2017.02204.

Wei, Y. J. et al. (2018) ‘High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China’, PLoS ONE. doi: 10.1371/journal.pone.0193097.

Zhang, F. et al. (2018) ‘Trichoderma biofertilizer links to altered soil chemistry, altered microbial communities, and improved grassland biomass’, Frontiers in Microbiology. doi: 10.3389/fmicb.2018.00848.