Exploiting the potential of genotype microbiome interactions to promote sustainable soil health in southern Africa

Lead Research Organisation: University of Edinburgh
Department Name: Roslin Institute


Maize is the most important cereal crop in southern Africa but without new management practices in the face of increasing occurrence and severity of drought and low soil nutrient availability, yields which are already low are predicted to further decline. It is critical that new approaches are developed to ensure food security, and help alleviate poverty of smallholder farmers. Breeding for new maize cultivars with greater tolerance to drought and enhanced ability to take up nitrogen holds much promise to transform these cropping systems, but first we need to understand how these crop plants interact with the soil, the microorganisms in the soil, and with management to confer benefits for crop production, that will help ensure food security.

Aims and objectives
Our research aims to address whether considering the nature of interactions between crop genetic make-up (genotype), soil microorganisms and the processes they undertake provides a viable approach for future maize breeding programmes to help ensure yield stability and resilience to low nutrient availability and drought in southern Africa. We will firstly undertake, under controlled environment conditions, a detailed screening of a wide range of maize genotypes from the CIMMYT germplasm collection to establish the extent of variation in influence on soil nitrogen and carbon processes. This screen will include varieties characterised by CIMMYT as being tolerant of low soil nitrogen or drought stress conditions. From this screen we will select lines to examine in more detail, and look at how they shape the microbial populations that undertake these processes, and gain understanding of plant-soil interactions underpinning sustainable production and soil health. We will then select six maize lines to establish consistency of interactions, established in controlled environments, under field conditions across CIMMYT farmer's network in Zimbabwe. Understanding these interactions will tell us if there is potential in using different maize genotypes to influence the soil microbial community, or future breeding for particular characteristics, to promote more effective nitrogen use and to confer greater resilience to drought.

Potential applications and benefits
Demonstrating variation of maize for impacts on soil microbiota and processes is an essential step to developing strategies to exploit these traits for enhancing crop yields in combination with sustainable management practices. We anticipate that this foundation award will lead in the future to the development of a framework to inform future maize breeding initiatives or cultivar selection for southern Africa, that is based on the ability of crops to enhance and capitalise on soil health in terms of sustainable nutrient acquisition thereby helping ensure more reliable yields and greater resilience to changing environmental conditions.

Technical Summary

In partnership with CIMMYT, Zimbabwe, we will demonstrate the potential for variation between maize genotypes to influence the rhizosphere microbiome for function. Our detailed assessments of genotype-soil interactions will characterise maize varieties in use at the CIMMYT on-station trial sites (including drought- and non-drought-tolerant varieties) and additionally CIMMYT lines (in testcross) that are genetically characterised. This will provide information of use both in the short-term for current practices and will demonstrate whether there is the potential in the longer-term for cultivar breeding to further enhance effective nutrient use and drought tolerance through shaping the rhizosphere community.

We will examine these interactions under controlled environment conditions adopting stable isotope (13C, 15N) and molecular (16S for total bacteria and amoA, nirS, nirK functional genes) approaches to better understand the influence of characterised maize lines on the soil microbial community involved in key nitrogen and carbon processes (nitrification, denitrification and mineralisation). The first step will be a wide screen of genotypic variation across 100 CIMMYT maize lines to a range of soil indicators of N-use and soil C cycling. We will then test root interaction traits in more depth for a selection of these lines, utilising soils from the two CIMMYT stations that have been under 3 management regimes: conservation, conventional with inputs match to the conservation management, and conventional with low nitrogen input that represents typical smallholder management. This will generate greater mechanistic understanding of processes underpinning the responses and generate process validated molecular indices of these functions. Finally we will determine the robustness of these yield and process responses to varying soil characteristics and managements in on-farm trials in Zimbabwe.

Planned Impact

We anticipate the main outcomes of this foundation award to be increased scientific understanding of maize genotype, management and environment interactions in shaping the soil microbiome underpinning C and N processes and the potential of an approach of crop cultivar selection to promote functioning of the soil biota in the context of water and N-limited systems. By working closely with CIMMYT, we maximise the likelihood of positive discoveries from this award to be taken forward into future maize breeding programs and to maximise the likelihood of new maize varieties, or varieties proven for optimal performance under specific site conditions and management to be adopted by smallholder farmers.

Who will benefit?
The primary beneficiaries of this approach will be smallholder farmers in southern Africa, farmers' groups, particularly initially CIMMYT's farmers' network across southern Africa, national agricultural research and extension services (NARES), small and medium enterprise (SME) seed companies, non-governmental organizations (NGOs), and community-based organizations (CBOs). Specifically within Zimbabwe our findings will be of interest to research institutes (such as the Department of Agriculture Extension (AGRITEX), the Department of Research and Specialized Services (DR&SS), the Plant Protection Research Institute and the Genebank of Zimbabwe), NGOs (such as Development Aid from People to People, DAPP), private sector organisations (such as AGRITEX and seed companies), and regional organisations (such as the Community Technology Development Trust). CIMMYT's maize research program is also collaborative with CIAT, ICRISAT, IITA, IFPRI and the World Agroforestry Centre, which will widen the impact at the latter stages of the impact pipeline.
Our project will also benefit the scientific community (see section on academic beneficiaries), the general public with interests in how soils underpin food production/security, and those aligned to the One Health Initiative where multiple disciplines working locally, nationally, and globally seek to attain optimal health for people, animals and the environment.

How will they benefit?
The potential for plant trait informed selection of genotypes, and genotype microbiome interactions is a hot topic amongst the UK research community, but as yet relationships have not been tested in the field. Given the specific pressures of climate change, low income levels and food insecurity in southern Africa, the potential to support delivery of sustainable crop yield (and consequent alleviation of poverty and greater food security), using a low cost approach while also promoting health and resilience of fragile soils, by provision of seed tailored for these purposes, and for these agricultural systems, is an attractive option. Partnerships, such as with CIMMYT, are essential to take this research area forward. Consideration of maize belowground traits will facilitate major advances for CIMMYT in helping understanding of what controls low nitrogen and drought tolerances in current maize varieties and wider germplasm collections. This understanding will help target future trials and breeding initiatives.
Description Our results have demonstrated that there is significant variation in the impact of different maize cultivars on soil processes. This has allowed us to make selections of contrasting cultivars from which we are establishing the mechanistic bases for this variation and validating their interaction with management in the field in Zimbabwe.
Exploitation Route This funding has enabled us to demonstrate that different maize genotypes have different abilities to source N from soil organic matter. This is now being taken forward, with further funding, to translate this to practical outcomes through farmer engagement, out-scaling experiences to promote uptake of conservation agriculture, and by knowledge transfer within maize breeding programmes for southern Africa. This is a "win-win-win" strategy: conservation agriculture is best suited to degraded, low fertility soils under drought conditions; we now know that some drought tolerant maize varieties are excellent utilisers of soil organic matter replenished during conservation agriculture, which is anticipated to incur both economic and environmental benefits; and we are now able to embed this into variety selection criteria, taking us a critical step further towards future breeding for sustainability that is best suited to the local context in southern Africa and conservation agriculture practices. This will help ensure greater yield stability under changing conditions particularly drought, lowered dependence on inorganic fertiliser input, mitigating the associated economic and environmental impacts of this practice, and averting further soil degradation through enhanced soil structure. It will be transformative for smallholder farmers in southern Africa, who will benefit socially and economically from more sustainable maize yields, livelihood benefits and safe and nutritious food under a changing climate.
Sectors Agriculture, Food and Drink,Environment

Description Our research findings have generated significant interest in the potential to introduce beneficial root-soil interaction traits into maize breeding programmes, establishing a strong basis for future collaboration to translate findings of this research into practical outcomes. We anticipate this will lead in the future to the embedding of ability to utilise soil organic matter (SOM) nitrogen into variety selection criteria, taking us a critical step further towards future breeding for sustainability that is best suited to the local context in southern Africa and conservation agriculture practices. We are now taking forward our dialogues with maize breeders and seed companies about selection for this additional criterion, and jointly developing a pathway for implementation and wider promotion. Our aim here is to develop a strategy for incorporating SOM exploitation into their breeding pipeline. To our knowledge this will be the first time a joint climate- and environment-smart technology has been embedded in this way. This approach is closely aligned with UN SDGs 1, 2, 13, 15, through promoting more productive food systems without compromising wider ecosystem services. The primary beneficiaries of this research are smallholder farmers in Zimbabwe, who will benefit socially and economically from more sustainable maize yields, livelihood benefits and safe and nutritious food under a changing climate.
First Year Of Impact 2019
Sector Agriculture, Food and Drink,Environment
Impact Types Societal

Description Africa SOIL: Soil Organic matter Improves Livelihoods
Amount £271,490 (GBP)
Funding ID BB/T012552/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2020 
End 01/2024
Description Presentation to the Zimbabwe Plant Breeders Association, hosted by the University of Zimbabwe 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Three presentations were given to the Zimbabwe Plant Breeders Association on the potential of different barley and maize genotypes to source and utilise soil organic matter carbon and nitrogen. Results included those from genotypes of some of the breeders present. This was followed by discussion about embedding sustainability criteria into breeding programmes for climate smart agriculture. This has led to collaboration with one of the seed companies in the follow on translation grant. It also led to a lot of interest in other potential research opportunities and applications for PhD study.
Year(s) Of Engagement Activity 2019