Sequencing soil microorganisms

A wheat field in Italy

An apple orchard near Maidstone in Kent where soil was sampled for the project. The National Institute of Agricultural Botany (NIAB) East Malling experimental site, image by Flavia Pinzari

Investigating the microbial community response to the introduction of non-endemic fungal bioinoculant in soil

Fungal bioinoculants have a huge potential in agriculture because they can help to increase crop yields and quality and allow a reduction in the application of chemicals.

While the effectiveness of bio-inoculants as bio-fertilisers or biopesticides is widely tested for crop yield and pathogens control, little is known about the effect of bioinoculants on microbial assemblages in the bulk soil of agroecosystems. 

What happens to soil microbes when you introduce fungus to the soil?

ALIENinSoil will assess the impact of a fungal inoculum, the globally-used biofertiliser Trichoderma afroharzianum T22, on microbial assemblages of a model soil system.

A sudden artificial introduction of a fungal species in soil could create a substantial impact on the biodiversity of endemic microbial species and local community functions, as well as lead to changes in the food webs and nutrients availability.

Sequencing the DNA of soil microbes

This project will apply an innovative rapid metagenomic approach based on long-read Oxford Nanopore Technology to assess the effects of the fungal inoculum on soil microbial communities and functions in a laboratory-based microcosms experiment.

Oxford Nanopore sequencing has great potential to be used for real-time diagnostics in agricultural surveys and the development of indicators for monitoring soil biodiversity and functionality.

This project will use innovative and cutting-edge techniques to understand:

  • to what extent the native microbial community richness and relative abundance is influenced by a fungal strain introduced to soil
  • whether or not the keystone microbial taxa are resilient to the disturbance by the introduced fungus
  • how far the bioinoculant impacts the functions of soil microorganisms.

This study will gain new in-depth knowledge and help to stimulate innovation in the field of soil bioinoculants and agriculture by way of competitive technology transfer.

A field of a gran crop surrounded by trees

A field planted with cereals near Milton Keynes

Research in the field

Soil sampling at the East Malling experimental site (Kent, UK). Image © Flavia Pinzari.

The soil microcosms used in the experiment sit in sterile, ventilated tubes. Image © Flavia Pinzari.

Research in the lab

The fungus used in the experiments, Trichoderma afroharzianum   n.20847TM. Image © Flavia Pinzari.

Fungi naturally populating 100 mg of the National Institute of Agricultural Botany (NIAB) apple orchard soil​. Image © Flavia Pinzari.

Observing bacterial filaments from soil through a scanning electron microscope. Image © Flavia Pinzari.

Extracted fungal DNA visualised as bands in a gel after UV imaging. Image © Flavia Pinzari.

European Union flag with the words, 'funded by the European Union

The project

The EU-funded ALIENinSoil project is investigating the effects of a fungus, widely used as biofertiliser, on microbial communities in soil.

Utilising Oxford Nanopore Technologies sequencing, which enables the direct, real-time analysis of long DNA fragments, the team will evaluate if the presence of this foreign fungus affects the growth and functioning of the native microorganisms.

Read more about the project (PDF) 

Museum staff

  • Flavia Pinzari: Principal investigator
  • Dr Anne D. Jungblut: Researcher at the Natural History Museum
  • Dr Matt Clark: Research Leader at the Natural History Museum
  • Dr Raju Misra: Head of the Natural History Museum Molecular Biology Laboratories
  • Piotr Cubert (Research Assistant, Core Research Laboratories)
  • Silvia Salatino (Computational Biologist, Core Research Laboratories)

External staff

Prof Xiangming Xu: Head of Science at NIAB East Malling Research Station (EMR)

Project timeframe

January 2021 - January 2023


This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 892048.

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