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Sensing soil processes for improved crop nitrogen bioavailability

Periodic Reporting for period 4 - SENSOILS (Sensing soil processes for improved crop nitrogen bioavailability)

Reporting period: 2020-01-01 to 2022-02-28

The crop yields that currently sustain the global population relies largely on agrochemicals (e.g. N/P/K fertilisers and pesticides) and modern crop varieties (e.g. dwarf wheat varieties) developed in the late 20th century at the expense of soil health. As part of the Farm to Fork strategy, the European Commission aims at reducing nutrient losses of at least 50% by 2030, a 20% reduction in fertiliser use while improving soil quality. To address this challenge, it is urgent to identify sustainable solutions to soil fertility and crop performance based on the understanding of soil microbial processes.
In the SENSOIL project, we have tested radical new ideas to study the dynamics of roots and soil microbes. The research showed that inventing artificial soils and imaging technologies, it is possible to track microbial interactions and association with crop roots, while also observing changes to chemical composition of the soil. Using these new technologies, the project revealed new forms of bacterial movement, indicating migrations in soil may be faster and further than previously estimated but equally revealing how such processes becomes sensitive to change in soil properties. Discoveries in the SENSOIL project could have wide-ranging impact in our understanding of soil ecosystem while helping the agritech industry develop more sustainable solutions
We developed a new generation of artificial soils able to report on the nature of chemical changes taking place in soil because of biological activity using a commonly available plastic of low refractive index and to introduce functions using a thin shell made of functional material. For the core of the particle, we used FEP (Fluorinated Ethylene Propylene), and the project has successfully identified and synthesized polymers with adequate functions for use in an artificial soil. We have developed a new microscopy platform and pipelines for the fabrication of microcosm chambers where microorganisms, nutrient and various other amendments can flexibly be introduced and imaged live and in situ. We have also made key progress with the development of computational techniques, proposing the first whole organ model to simulate morphogenesis as cellular resolution.
Using these new technologies, we were able to track the behaviour of soil microbes during colonisation of the rhizosphere. Using our new live imaging systems, we have revealed the stunning level of coordination employed by soil bacteria to move through the soil structure and colonise plant host. We showed that bacterial cells move as flocks, in ways that are normally observed in more complex higher organisms such as birds and fish. We also demonstrated that such movements are made possible because the bacteria is able to create localised, but steady laminar flows of water through soil, therefore moving as a group rather than as individuals.
The project has led to several high-profile publications in journals such as PNAS, New Phytologist, ISME Journal, with other publication still under considerations in high impact factor journals. The project has also been a formidable boost to further scientific development with numerous follow-on projects funded nationally and internationally. Other outcomes include publications in national newspapers, social media and early carrier scientists growing their careers in various research institutions around the world.
Four main areas of the project have significantly advanced the field and moved beyond the state.
First, the development of core shell structure technologies to make sensing soil particles or "Sensing soils”. These will have a broad range of application, for example in scientific research, breeding and development of fertiliser. It has required significant advancement in polymer sciences, and the techniques could be used in other areas of science and technology.
Our work is greatly contributing to the field of soil microscopy. We have developed a series of approaches that allow live observation of soil microbes. We fabricated new fluidics systems for soil control of soil conditions under a microscope.
Computational modelling work for simulation of root development in soil is extremely promising. We anticipate we will be possible to make simulation of entire roots at cellular resolutions while at the same time model the soil at the particle level. The model and algorithms are being implemented in DualSPHysics, an open source community led simulation tool.
Work focused on understanding factors affecting microbial activity in the rhizosphere is, and is just starting to benefit from the technological development from the project. In particular, we expect to be able to quantify accurately the mobility coefficient of soil microbes surrounding plant roots and predict what contributes to maintenance of certain microbes in the rhizosphere.
Bacillus subtilis colonising a lettuce root