Soil health and the rhizosphere microbiome: from bench to field and back again

Humanity’s continued reliance on soil has led to its extensive degradation. Stakeholders in the farming community recognise the need for sustainable soil use and are concerned about improving soil health whilst maintaining agricultural productivity. Land management practices that aim to build and maintain a diverse and active soil microbiome and restore soil health are critical for our soil's continued productivity. Grass-clover leys are an example of such practices that are gaining prominence in pursuit of better soil health. However, the soil microbiome associated with such systems and their roles in the ecosystem is yet to be fully understood. This study employed an interdisciplinary approach to investigate how soils under contrasting management practices categorised as “healthy” and “poor” influence plant growth and disease response. The general hypothesis was that “healthy” soils possess beneficial microbiomes that promote plant growth and disease suppression. Farmers were consulted at sampling, and soil samples were categorised as “healthy” or “poor” based on their perceptions of soil health. Characterisation of these soils showed that Arabidopsis and tomato plants grown in the “healthy” soils of two out of four farms were consistently smaller than plants grown in the “poor” soil. Infection of these plants with Hyaloperonospora arabidopsidis and Pseudomonas syringae pv tomato showed that plants grown in the “healthy” soil were resistant to diseases. Further manipulation of these soil using soil microbiome transplants showed that the soil microbiome in these “healthy” soil caused disease suppression, whilst the water-soluble chemical fraction of the soils caused growth repression, indicating allelopathy activity in the soil. Metataxonomic profiling of the soil identified taxa associated with disease suppression and a Pseudomonas spp. commonly occurred in the three suppressive treatments. This study highlighted the complexity of the microbiome but also harnessed the beneficial properties of the soil microbiome. Focus group discussions with stakeholders in the farming community showed that the growth repression observed in this study was not unique, as farmers experience similar issues. The discussions with stakeholders also highlighted that many key areas of soil microbiome research remain “undone science” due to funding and practicality challenges. However, various stakeholders are optimistic about the place of the soil microbiome in farming and are enthusiastic about harnessing it, be it through land management practices or microbial manipulations. Overall, this research shows that categorising soils as “healthy” and “poor” can be very complex and should be conducted with caution. Furthermore, researchers and the farming community should consider the biochemical indicators of soil health and pursue harnessing them for sustainable soil use.