IntroductionThe soil is what supports and feeds our crops, but with each successive harvest of the same crop, the yieldt in a field goes down. This phenomenon, known as ‘yield decline’ occurs almost universally across crop plants and can have a substantial effect; oilseed rape, for example, shows a 25% decline in yield in the second year of growth. A team of researchers led by Gary Bending (University of Warwick) believe that the root of this problem is in the soil itself.

Previous work by the team showed that microbial communities living in the soil change with repeated harvests of the same crop, and linked yield decline to a greater number of harmful microbes. In their latest project, the team collected soil samples and conducted field trials, and sequenced the genes and proteins being expressed in the roots and soil to better understand how the network of soil microbes influences crop yield, and identify key players in the microbiome. “We’re trying to understand the fundamental processes that control the types of microbes that live in association with plants”, said Bending.

MethodologyBending and colleagues collected samples of soil from 37 oilseed rape (Brassica napus) fields across the UK that varied

in their climate, soil properties, land management and crop rotation. They sequenced DNA samples from the soil, the plant roots, and the rhizosphere to identify the different species of bacteria, fungi and protist microbes. The team grew a rotation of four oilseed rape varieties, selected for different root properties. They monitored how the microbial community changed through this rotation by sequencing the genes and proteins expressed in the roots and by the microbes in the soil.

Many crops experience a decline in yield when the same crop is grown year after year. Professor Gary Bending and colleagues investigated the role of soil microbes in this phenomenon using molecular techniques to better understand how the composition of the soil community affects yield decline in oilseed rape. They found that repeated crops of oilseed rape fundamentally changed the microbes present in the soil around the roots, linked to a reduction in yield. They found an increase in the signs of harmful bacteria and identified new microbial species that are associated with good and poor soil microbiomes.

Profiling soil communities at the root of yield decline

A crucial zone for both plant and soil health is the interface between the roots and the soil, known as the ‘rhizosphere’. This is where most of the biological activity occurs in the soil – plants take up water, roots engineer soil structure, and microbes recycle nutrients.

Although they are small and seemingly insignificant, soil microbes are incredibly numerous and play crucial roles in many soil processes. They include bacteria, fungi, nematodes and protists, some of which are beneficial to plants and others that are harmful.

Field experiments in Wellebourne, Warwickshire, testing different oilseed rape cultivars (foreground) and different frequences of wheat and oilseed rape rotation (background). The researchers found that the frequency of oil seed rape rotation affected the composition of fungi in the soil.

•The roots and surrounding soil harbour a distinct community of soil bacteria and fungi.

•The soil microbiome changed when the same crop was grown repeatedly.

•An increase in harmful bacteria and fungi was linked to lower yield.

= harmful microbes

= beneficial microbes

= neutral microbes= crop yield

ResultsThe team found that there was a distinctive community of microbes that lived in the rhizosphere soil and the roots themselves, which was constant across different soil types and climatic conditions.

“Right across the country no matter where you took your samples from, the community that’s assembled into the roots and the rhizosphere soil has a similar composition”, said Bending. The team say this is evidence that the plant itself is carefully cultivating it’s own rhizosphere community, which is distinct from the soil in the rest of the field.

The frequency with which oilseed rape had been planted in a field’s crop rotation had a significant impact on the fungal species present in the rhizosphere. Including a fallow year in crop rotations, or using break crops like faba beans (Vicia faba) or wheat (Triticum aestivum), doubled oil seed rape yeild compared to continously cropping the land.

The researchers identified several new species of fungi and protists that are only found in the rhizosphere soil. In some cases, these species are most closely related to pathogenic microbes found in marine environments, suggesting that their soil-dwelling relatives may be harmful, too.

Some microbial species emerged as key ‘nodes’ in the soil community that are characteristic of either a good or a poor soil microbiome, affecting crop yield. For example, the root-dwelling fungus Tetracladium becomes increasingly common as the frequency of

oilseed rape is decreased in t he rotation, and is associated with higher yields.

The results showed that the composition of microbial species and their relative abundance in the soil had a large effect on the crop yield produced. “The way the community was assembled was quite tightly linked to yield”, said Bending.

Analysing the pattern of genes being expressed in plant roots and by microbes in the soil, the researchers found that there was a distinct transcriptomic signature of a good or bad microbiome, providing further support for the idea that a poor microbiome is characterised by more pathogenic microbes. The researchers were also able to detect the presence of a harmful microbiome just by looking at the genes expressed by the plant.

A network showing the most common bacterial, fungal and protist species in the root soil community and their relationship to crop yield. The composition of the soil microbial community was strongly linked to yield.

•Poor soils tend to harbour more harmful bacteria and fungi that can reduce crop yield, so restoring healthy soil microbial communities is a win-win for farmers and the environment.

•Certain break crops, particularly beans or cereals can help restore the soil microbiome and improve yield.

•As our understanding of how the root microbiome affects yield decline we may be able to selectively breed for crop varieties that promote the development healthier, more productive soils.

“The power of ‘omic approaches to unravel the complexity of the microbiome is advancing incredibly rapidly and our work show it has great promise to provide practical approaches to improve crop yield” - Gary Bending

Contact Details: Professor Gary Bending (Gary.Bending@warwick.ac.uk)

ReferencesHilton, S., Bennett, A. J., Chandler, D., Mills, P., & Bending, G. D. (2018). Preceding crop and seasonal effects influence fungal, bacterial and nematode diversity in wheat and oilseed rape rhizosphere and soil. Applied soil ecology, 126, 34-46.

Bass, D., van der Gast, C., Thomson, S., Neuhauser, S., Hilton, S., & Bending, G. D. (2018). Plant Rhizosphere Selection of Plasmodiophorid Lineages from Bulk Soil: The Importance of “Hidden” Diversity. Frontiers in microbiology, 9, 168.