Microbiome in soil

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Soil contain a diverse community of microorganisms, and these organisms are essential for both function and health. Different types of soil are characterized by their own unique composition of microbes, and even within soil types the composition differ dependent on factors such as pH, water content and usage such as 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 agricultural sustainability.

How does microbiome insight play an active role in farming?

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

  • Microbes improve plants ability to utilize nutrients such as phosphorus and nitrogen. 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 can fix nitrogen (N) from the air and help plants to access nutrients such as phosphorus (P) and N from organic fertilizers. Furthermore, certain microbes can improve drought tolerance, improve plant health or increase salt tolerance.
  • Improving crop yield, while reducing cost of fertilizers. Crop yields can be increased by up to 40 percent if beneficial soil microorganisms – so-called biofertilisers – are added to the soil during sowing. The use of beneficial microbes to improve the plant’s use of phosphorus and nitrogen can save costs by reducing the need for mineral fertilizers. In turn, this reduces the environmental impact of over-fertilisation. This is shown in a global study summarizing results from 171 systematically selected publications worldwide by the Research Institute of Organic Agriculture FiBL and the University of Basel, which was recently published in the journal “Frontiers in Plant Science”.
  • Improving 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 (please see references below).

How it all works

At BIOMCARE we use the genetic material (DNA) in a sample to evaluate what microorganisms it contains. Depending on what sequencing method is selected, we can evaluate both the specific organisms in the sample and what the microbes are doing. DNA sequencing results in large amounts of data that need processing before interesting information can be gained from the data.

Therefore, at BIOMCARE we first 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).

Depending on your wish, we can provide you with the microbiome profiles for your own further statistical analysis, or we can help you with the analysis and interpretation of results. The statistical analysis we perform depend on what questions you would like to have answered. We will often relate the microbiome data to other information (called metadata) such as used fertilizers, plant yield, plant infections etc.

This will allow us to identify interesting differences e.g. between soil from high yield vs low yield areas. We can identify broad differences such as microbe diversity, or specific differences such as single bacteria that associate with the metadata.


  1. It all starts with a question or a hypothesis; why are the plants not doing as well on the southern facing fields? Might the soil microbiome differ between sites and explain yield differences? Are my biofertilizers affecting the soil ecosystem?
  2. When faced with such questions, give us a call at BiomCare. We will discuss the possibilities and together we plan the necessary steps towards answering your questions.
  3. We deliver sampling equipment with the necessary instructions.
  4. You follow the provided instructions on how to collect samples and send the collected samples to BiomCare.
  5. At BiomCare we use the genetic material (DNA) in the samples to evaluate what microorganisms it contains. First the samples are subjected to next generation sequencing. Then we do extensive data processing and analysis in order to identify the microorganisms in the samples.
  6. The statistical analysis we perform depend on what questions you would like to have answered. When results are ready BiomCare will help you convey the results and the findings.

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

 

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.

We used Biomcare to analyse 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