The Citrus Microbiome: From Structure and Function to Microbiome Engineering and Beyond

Abstract

Individual microbes often have defined relationships with their hosts that include beneficial, commensal, and pathogenic interactions. However, at the community level, plant microbiomes are considered to play a beneficial role in protecting the plant from potential pathogens, acquiring nutrients, and improving growth and production. Citrus is a globally important perennial fruit crop and its production faces many challenges. There has been tremendous interest in exploring the structure and function of the citrus microbiome and engineering the citrus microbiome to address various challenges. In this review, we summarized recent advances in understanding the citrus microbiome, including the composition and function of the microbiome in the rhizosphere, rhizoplane, endorhiza, and core members, and their functional traits. We conducted comparisons of the citrus root-associated microbiome with other plant root-associated microbiomes. We also present a perspective on how incoming pathogens interact with the resident microbial community and their outcomes. Despite the promising potential of the citrus microbiome to combat disease, harnessing the citrus microbiome for beneficial applications remains in its infancy. We envision that rapid development of high-throughput sequencing and multiomics technologies, artificial intelligence, consortia of microbes, genome editing technology, and high-throughput culturing present many exciting opportunities for citrus microbiome research and microbial engineering to improve citrus health and productivity.