In recent years, Inholland's Green Biotechnology professorship has worked hard to master the sequencing and subsequent identification and classification of the microorganisms present. Nanopore sequencing is done with the MinION, the well-known system from Oxford NanoPore Technologies. This technique is not the standard for carrying out this type of microbiome analyses, but it is much easier and cheaper to apply. It remains important to compare old and new techniques and that research is done in the soil microbiome project.
This article is an initiative of the Hbo Key Technologies Theme Table. The aim of this national partnership is to make the impact of practice-oriented research by universities of applied sciences in the field of key technologies more visible.
The challenge: DNA sequencing of the soil microbiome
Green Biotechnology lecturer Nelleke Kreike from Inholland University of Applied Sciences conducts research into the design and application of the latest DNA key technologies. The aim is to develop sustainable and healthy food and ornamental crops.
The soil project conducts research into the composition of the micro-organisms present in the soil, in particular bacteria, fungi and protozoa. These are examined with special PCR (Polymerase Chain Reaction) enrichment methods, called Metabarcoding. This means performing three different PCR methods each time – a lot of work for one soil sample. That is why Inholland is working on setting up one comprehensive method, also called Metagenomics, to speed up soil analyzes and make them cheaper. The results of both methods are then compared.
Nelleke Kreike, lecturer in Green Biotechnology at Inholland: “I think it is fantastic that we have set up the important Nanopore DNA sequencing technique in our research laboratory and that we are further studying and developing the usability of this new state-of-the-art DNA key technology. already apply in our research. In addition, I am extremely proud of the team of researchers and students who are participating in this project: Sonia Jillings, Merijn de Boer, Peter Hoitinga, Frank van der Helm and Christiaan van der Heijden.”
Results
With the development and implementation of the Nanopore DNA sequencing technique, great leaps forward have been made and the bacteria present can be identified and classified. Now a step further is being taken to classify the bacteria present into ecological function groups, focusing on two questions:
- What is the function of these bacteria in the soil?
This looks at bacteria involved in the carbon, nitrogen and sulfur cycle. - Which bacteria promote plant growth and make the plant more resistant to diseases and pests?
The research partners, growers and soil researchers, are particularly interested in the composition of a good soil microbiome. Which microorganisms are crucial for plants to grow better and become more resilient during cultivation, so that they are less affected by diseases and pests? The effect of biostimulants to improve the composition of the soil microbiome is also an important research topic.
Peter Hoitinga, lecturer-researcher Green Biotechnology at Inholland: “The bioinformatics required after DNA sequencing to identify the micro-organisms is quite challenging and has cost a lot of headaches. This research has given an enormous boost to bioinformatics education. It is a good example of how research and education reinforce each other.”
The DNA sequencing analyzes of the bacterial microbiome of the sandy soil of the first year have now been carried out. Several replicates of soil samples were examined in the same field and soil samples were taken four times a year in different bulb and soil treatments. A total of about sixty soil samples have now been analyzed. No differences were observed in the bacterial composition between the replicates in a field and only minor differences in the composition throughout the year. Clearer differences have been found in soils that have had a different soil and crop treatment. The significance of this for the composition of a good soil microbiome and the further effects on plant growth are now being investigated.
Next steps
Until now, the focus has mainly been on the bacterial microbiome. Now attention is being paid to the composition of other micro-organisms in the soil, such as fungi and protozoa. The DNA sequences of the soil samples are ready for these analyses.
Inholland also collaborates with other colleges of CoE Groen in a larger research project. This is about increasing the carbon content in the soil in order to store more CO2. This cultivation of the soil will probably also have an impact on the composition of the soil microbiome. Inholland will investigate this further with the Nanopore DNA sequencing technique.
Projectpartners
- Inholland University of Applied Sciences
- E.J. Hogervorst & zonen from Noordwijkerhout, grower of the Hyacinth Multiflora in pots
- Agrifirm, cooperative of livestock farmers and plant growers
- Centre of Expertise Groen - CoE Groen: a collaboration of Inholland, HAS Green Academy, Aeres Hogeschool and Hogeschool Van Hall-Larenstein