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Plants live with a diversity of microorganisms throughout their lifespan. Plants recruit and shape microbiome structures through topological and chemical strategies. Meanwhile, plant growth and resilience are heavily impacted by associated microbiomes. Studies of plant microbiomes not only shed light on principles underlying the assembly and dynamics of plant-associated microbiomes but also provide strategic insights into microbiome engineering to boost plant health and sustainable agriculture. The editors of Nature Communications, Communications Biology and Scientific Reports invite submissions on plant microbiomes.