In a company, some competition is good for selecting the best employees but too much competition discourages cooperation and reduces productivity. The same trade-off between individual competitive traits and collective performance applies to a flock of chickens or a field of corn. Only recently has this insight been applied to increase the yield of domesticated organisms in a developing field called ?Darwinian Agriculture?. Indeed, selection of less aggressive animals and less competitive plants has resulted in increases in yield. These implementations are based on informed decisions, but the tradeoffs between individual competitive traits and collective performance resulting in the highest yield are not always intuitive Therefore, I propose a completely different approach to address the maximization of yield in a sustainable way: by studying an ancient non-human form of agriculture. Agriculture is not unique to our own species: a group of social insects in Africa, the fungus-growing termites, also have developed a sophisticated form of agriculture. In contrast to the evolutionarily recent human agriculture, this agricultural symbiosis has been shaped by millions of years of evolution and may thus reveal principles of sustainable agriculture not yet discovered by humans. The overall aim of this project is to identify the key factors that stabilize cooperative systems and that maximize the yield of domesticated organisms in agriculture and symbiosis. The termites cultivate their fungi by continuously inoculating spores, which form a colony of hyphae, cooperating in plant degradation and production of fungal biomass and new spores. However, the details of the cultivation mode that maximizes and stabilizes yield and the potential trade-off between competition and collective performance for the highest yield are unknown. Analogous to the challenges human farmers face, I will subsequently ask i) how termites select productive crop varieties to start a fungus farm; ii) by which cultivation mode they maximize yield; and iii) how they maintain crops of high genetic quality during long-term clonal propagation. I will use an integrative approach including theoretical modelling, experimental evolution and genomics. The proposed work will generate fundamental answers to the long-standing questions on the evolutionary stability of colony growth and mutualistic symbiosis. Moreover, this crucial knowledge will have direct relevance for human agriculture for stable maximization of yield. Finally, a better understanding of Termitomyces cultivation might provide the first steps for secondary human domestication of its highly prized edible mushrooms.

The increasingly available plant genome information reveals evidence that gene copy number expansion and subsequent copy number variation (CNV) lie at the basis of plant adaptation to adverse environmental conditions. Such CNV appears to be highly dynamic, already apparent upon only a few generations of selection. Rapid evolution of plant adaptation traits will be very attractive to apply in plant breeding. In this project, we will investigate the role of CNV in the evolution of plant adaptations to environment and the traces it leaves in plant genomes. To this end we will develop novel, sensitive CNV analysis tools based on next-generation whole genome (re)sequencing (WGS) data from available crop and wild plant diversity panels. The key challenge is to reliably detect CNV on (very) low coverage datasets, to link this CNV to observed phenotypes, and to detect recurrent CNV by integrating measurements across populations. In addition, we will experimentally evolve Arabidopsis thaliana under two severely adverse abiotic conditions (high salt and high Zn exposure) and apply the developed CNV analysis tools on WGS data of evolved lines. Overall, the project will provide detailed information on newly generated (Arabidopsis) as well as standing CNV (diversity panels), which will be used to determine the frequency and distribution of de novo CNVs and the genome sequence requirements for CNV. This will help understand the mechanisms permitting extensive CNV to occur and will allow us to find ways to exploit it for rapid improvement of crop stress tolerance through plant breeding.

Cooperation is omnipresent in the living world at various levels and has been called the third fundamental principle of evolution beside mutation and natural selection. However, the evolution of cooperation presents a paradox: why would an individual show costly helping behaviour for the benefit of another individual? Kin selection is one of the prevailing theories to explain cooperation within species: by helping a close relative reproduce, an individual indirectly still passes on its own genes to the next generation. No such single dominant explanation has yet generally been accepted for the evolution and stability of cooperative behaviour between different species in symbiotic relationships. Recently developed theory predicts that within-species relatedness in groups is also one of the key factors to explain stable among-species cooperation. This proposal tests this hypothesis for the mutualistic symbiosis between fungus-growing termites and their fungal symbionts. Fungi are unique because they show a range of social behaviours upon contact between individuals, ranging from mutually beneficial if somatic fusion leads to synergy, to spite if mutual growth inhibition leads to a zone of ?no-man?s land?. This proposal aims at, first, testing the relevance of somatic fusion for various aspects of cooperation and conflict between the symbionts of fungus-growing termites. A second aim of this proposal, addressed in a separate PhD project, is to address functional questions of somatic incompatibility between basidiomycetes as well as the genetic basis and expression of somatic incompatibility in Termitomyces. The termite-fungus symbiosis provides not only an interesting model for the evolution and stability of agriculture, but more generally offers possibilities for detailed studies of conflicts and cooperation between mutually dependent species. Interestingly, this symbiosis links cooperation within a species (Termitomyces spp.) with cooperation between species. A large culture collection of Termitomyces has recently been established so that experiments can readily be performed.

Applying the principles of circularity to agriculture is widely believed to hold much promise. Central to this approach is closing the various residue output-input loops either at a local, regional, or global scale for which the volumes of resources/materials can vary substantially. Whatever the scale, to increase efficiency and to further reduce losses, each of the loops involves the aggregation and accumulation of residues. Therefore, it is alarming that no attention has thus far been given to the associated accumulation of chemicals in these residues that pose potential health risks to natural and managed populations of organisms, including humans. In this proposal we address the One-Health consequences of circularity through the resistance development to environmental and medical azoles in the fungus Aspergillus fumigatus in accumulated organic residues. Our objectives are to (i) use the diversity of organic waste disposal in the bulb-sector to discern the key factors driving resistance development, (ii) use these factors to draw up an intervention plan that will be tested in the laboratory and on-site, and (iii) extend the obtained knowledge to general organic waste disposal to assess resistance and health risk across the system. Throughout, patient-risk will be monitored via local, regional, and national spore-trapping. Our project will deliver a quantitative and qualitative One-Health risk-assessment for the pressing problem of rapidly spreading azole-resistance. It will provide valuable lessons and actions to be taken to prevent similar problems arising in other parts of circular agriculture – in an effort to design health-risk free circular systems.