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The UN General Assembly proclaimed that 2020 is the International Year of Plant Health to recognize and protect plant health, and to raise awareness of the crucial role of plant health in ecosystem health, food security and human health. Plants host diverse microbial communities that are associated with plant roots, the phyllosphere, rhizosphere and the endosphere, and comprise bacteria, fungi, protists, nematodes and viruses. Numerous studies from different fields of research have expanded our knowledge of the complex interactions between the plant, the associated microbial communities as well as the environment, and provided insights into the ecology and functions of this co-association, including the appreciation that the plant microbiota is important for plant growth, fitness, stress resilience and health. Such an increased understanding opens up the possibility to harness plant-associated communities for sustainable plant production and agricultural practises and to protect plants from the effects of climate change and human activities that lead to a decrease in biodiversity and the spread of plant diseases. This Collection contains Reviews and Research articles from across the Nature group of journals that cover the latest advances in plant microbiome research, addressing critical knowledge gaps that need to be addressed, such as a better understanding of the assembly of the plant-associated microbial communities, their dynamics, metabolic interactions or functional properties.