Understanding these processes requires a solid theory-based approach to integrate across levels of organisation and spatio-temporal scales, combined with experimental platforms and ‘-omics’ technologies. Work thus far at iDiv has addressed this question using agent-based models and experiments exploring the role of traits and feedbacks among microbes and plants in determining coexistence, examining co-evolutionary processes between hosts and parasites, and determining the genomic and biochemical factors that mediate plant-herbivore interactions. Our challenge is to integrate these approaches and to scale-up – from the genome to the individual and from the individual to the ecosystem and global patterns of biodiversity.