Exploiting the relationship between plant genotypes and soil microbial communities for agricultural benefit
The Microbiology Society is undertaking a project entitled A Sustainable Future as part of our 75th Anniversary, which aims to highlight the Sustainable Development Goals (SDGs) to our members and empower them to use their research to evidence and impact the goals. Earlier this year, we put a call out to our members to submit case studies in the following three areas: antimicrobial resistance, soil health and the circular economy.
This case study was written by Alba Pacheco-Moreno, who is a PhD student and by Dr Jacob Malone, who is Group Leader in Molecular Microbiology; both are based at the John Innes Centre, UK. It focuses on Soil Health; maintaining the health of our soils has gained increasing prominence in recent years. Soils are essential for the global food system and regulate water, carbon and nitrogen cycles but are put under pressure from population growth and climate change.
What are the challenges that this research addresses?
As the global population grows, food security is becoming an increasingly urgent research challenge. For example, by 2050 worldwide demand for wheat is expected to increase by 60% due to population growth and shifting patterns of consumption. During the Green Revolution in the latter half of the 20th century, cereal crop yields were markedly enhanced through a combination of more productive crop varieties and liberal use of pesticides and chemical fertilisers. In recent years however, yield increases have begun to plateau alongside an increased awareness of the harmful consequences of agrochemical overuse. Thus, the challenge for the second Green Revolution is to further increase agricultural productivity in sustainable manner, while minimising the harmful effects of chemical fertilisers and pesticides on the environment.
How can this research support the transition to a more sustainable future?
All plants secrete a large proportion (more than 20%) of their fixed carbon into the surrounding soil in the form of sugars, amino acids, and other metabolites. As a consequence, the soil surrounding plant roots (the rhizosphere) is home to an enormously complex community of bacteria, fungi, and other micro-organisms that live on these exudates. This community contains commensal, beneficial, and pathogenic microbes, all interacting with one another and with the plant. Needless to say, the impact of the rhizosphere microbiota on plant fitness and yield is highly significant.
Many rhizosphere-associated bugs can fight off harmful microbes and/or insect pests or have impressive biofertilisation and growth-promoting abilities. Therefore, a potential route to sustainably increasing crop yields is to harness the positive attributes of these rhizosphere dwelling microbes. This can be achieved in several ways: by adding beneficial microbes to seeds or soil, by tweaking soil conditions to increase the abundance of beneficial microbes, or potentially by breeding crop plants that preferentially recruit beneficial microbes from soil.
An increasing array of natural fertilisers, growth stimulants and natural pesticides are becoming commercially available. However, these products often have issues with consistency, stemming from our incomplete knowledge of the complex rhizosphere ecosystem. Likewise, we have some way to go before breeding for beneficial microbial association becomes routine. A better understanding of the relationship between crop root architecture, exudate secretion and rhizosphere microbiome assembly is crucial to achieve the goal of sustainable crop yield enhancement.
What findings and solutions were provided by this research?
Research from several different labs has shown that different plant species recruit markedly different populations of soil bacteria. Our lab is building on these findings in collaboration with our industrial partner, New Heritage Barley, and crop geneticists at the John Innes Centre, to understand how elite and land-race cultivars of the same cereal species differ in their ability to recruit plant growth-promoting soil bacteria. We are analysing how patterns of root exudate secretion vary between different crop cultivars, and how this translates into different microbial recruitment in the rhizosphere. This work has allowed us to identify bacterial genes and phenotypes that contribute to particularly successful colonisation of elite and land-race cereal rhizospheres. We can also show why this matters: cereal cultivars grow substantially better when inoculated with their own recruited microbiota than with bugs taken from a different cultivar.
What is the future for research and innovation in this area?
Recently, differences in the preference of certain microbes to colonise model plant roots have been linked to specific, secreted plant natural products. A major goal for this research going forward is to identify the genetic loci in cereal crops that are responsible for recruiting beneficial soil microbes. Fortunately for us, the JIC has fantastic genetic resources and world-class expertise in this area, which will support our efforts to identify plant gene targets for beneficial microbial recruitment. Ultimately, we hope this will allow breeders to develop new crop cultivars that enable sustainable growth promotion and disease suppression with less environmentally damaging chemical inputs.
About the authors
Dr Jacob Malone is a Group Leader at the John Innes Centre, who studies the signalling pathways that control plant colonisation and infection by pathogenic and beneficial Pseudomonas species. Alba Pacheco-Moreno is a final year PhD student at the John Innes Centre and her research focuses on understanding the plant–microbe recognition process in the rhizosphere.