Microbiome Analysis and Agriculture
Harnessing the beneficial microbes found in soil and on plants, presents a promising strategy to optimize plant growth and agricultural sustainability. But until recently, the value of knowing the community of microorganisms (the microbiome) of plants and soil has been largely inaccessible.
This has changed over the last decade. Due to recent technological developments, analyzing the microbiome of a sample, for example from soil, plants or animals, has become possible.
BiomCare offer analyzing the microbiome in your agricultural sample. We use next generation sequencing (NGS) of the microbial DNA in a sample, which allow us to obtain an increasingly detailed picture of the range and diversity of microorganisms in a microbiome community. The high accuracy and low cost of this method makes it feasible to detect the microbial diversity at a much greater scale than previously possible.
At BiomCare we offer to analyze the microbiome in your samples and to actively support in the interpretation of results. Incorporating microbiome analysis in your activities can provide insight and guide developments. Microbiome analysis can provide valuable insights in many fields, such as:
- Development and evaluation of fertilizers.
- Smart farming – e.g. by providing insight into soil quality
- Sustainable agriculture. The soil microbiome is essential for many functions related to CO2 balance and optimal usage of fertilizers.
The microbiome of plants and soil is essential for both function and health
The microbiome is therefore often actively modified to improve agriculture incl. plant biomass, soil health and water retention. 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 microbiota 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 adaption measure to climate change.
A first step towards utilizing the microbiome to improve agriculture, is to gain insight and understand how the microbiome respond to inputs, such as fertilizers, and in turn influence plant growth, behavior and value.
Here are a few short stories that describe how microbiome profiling has been used to gain insight ↓
Microbiome profiling can help identify the microbes and enzymes associated with plant phenotypes
Microorganisms found in the soil around roots impact plant growth and development, but to fully harness the potential benefits it is necessary to use methods that reflect the sheer abundance and diversity of the microbes that influence plant traits.
The importance of root-associated microbes was highlighted in a study by Kevin Panke-Buisse and collegues (2018). They could, reproducibly, change the flowering times of plants by changing the soil microbiome.
And, by analysis of the soil microbiome profiles, using 16S rRNA gene sequencing, they could show distinct profiles associated with flowering time. They further found that changing the microbiome affected biomass of the plants. By analyzing the microbiome-related enzymes they could further identify a two- to five-fold increase in nitrogen mineralization activities in the soil associated with increased biomass.
Perspective: Microbiome profiling of soil samples can help identify the microbes and enzymes that facilitate a desired change in plant phenotype.
Microbiome profiling reveal how a fertilizer affect the soil ecosystem
The application of biofertilizer is known to effectively increase grassland nutrient availability. But how does it affect the soil microbiota?
A two-year experiment compared the effect of organic or Trichoderma biofertilizer on grassland biomass and soil properties. DNA sequencing was used to evaluate the effect of the fertilizers on the soil microbial ecosystem. The study, by Fengge Zhang and collegues (2018), found that the Trichoderma biofertilizer treatment increased soil antifungal compounds. The antifungal compounds can suppress pathogenic fungi and may therefore be partially responsible for the improved grassland biomass obtained by using the Trichoderma biofertilizer.
Perspective: Analyzing the soil microbiota profiles associated with specific fertilizers can help understand the effect on the soil ecosystem and identify the specific microbial factors involved in treatment effects.
Microbiome profiling identifies microbes important for silage quality
Ensilage is widely used to conserve grass for winter feed. Fermentation is key to the ensilage process and relies on lactic acid bacteria (LAB).
In a project by Javad Gharechahi and colleagues (2017), microbiome profiling was used to follow the dynamic behavior of the LAB community during the ensilage of maize biomass. The aim was to identify the key species involved in the process.
The study found that the composition of the microbiome that developed during the ensilage process differed markedly from the microbiota observed at baseline (when the ensilage process started).
The study found that both the abundance of specific bacteria (e.g. heterofermentative Leuconostocaceae sp) at baseline and the extent of the change during the ensilage period are important factors in determining silage quality.
Perspective: Detailed profiling of the microbial ecology of silages can lead to improved ensiling practices and selection of silage inoculants that work together with the natural feed microbiome to improve quality.
Microbiome profiling provide insight into regional differences in wine taste and quality
The unique flavor in wine is mainly generated from the microbial metabolic process during the wine making process. Therefore, selecting specific microbes for wine fermentation is important for the taste and quality of wine.
In a study from China by Yu-Jie Wei and colleagues (2018), microbiome profiling was used to study microbial community diversity of soil, grape, grapes leaves, grape juice and wine. The results enhanced their understanding of the microbiome in the vineyard from the Xinjiang region, and helped to establish correlation between wine quality and regional differences in microbiome profiles.
Perspective: Further identification and evaluation of the microbiome of soil and plants from vineyards can help to understand the beneficial nature of specific microbes. This can in-turn help the winery improve quality and local characteristics of their wine product.
At BiomCare our expertise is studying the microbiome. We are ready to support you in your next project on agricultural microbiome, from early sample collection to interpretation of results and everything in between. Independent of your field or the stage of your project, we are happy to discuss how our microbiome-expertise can help your work.
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 result 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 with the further analysis and interpretations of results. The statistical analysis we perform depend on what questions you 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, to identify the microorganisms in the samples.
(6) The statistical analysis we perform depend on what questions you like to have answered. When results are ready BiomCare will help you convey the results and the findings.
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.
The NGS-based microbiome field is in early stages and new organisms are constantly identified and/or known organisms are regrouped.
As a consequence, it can often be meaningful to re-analyse data at later time points. In exchange for the free re-runs, you allow us to make internal use of this (anonymized) data as a way to improve our service for other clients.