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

Context
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.

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.

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.