Culturomics of the plant microbiota: the emerging in situ similis cultivation strategies to meet the complexity of nutritional requirements of microbiota associated with plants of multiple species, growth stages and compartments

Abstract Background The holobiont" refers to the plant and its associated microbiota that are pivotal to the plant's health, fitness, and survival. By in vitro culturing and functionally characterizing members of the plant microbiota, their specific roles in influencing plant responses to environmental changes can be determined and manipulated to foster sustainable agriculture and ecosystem management. Aims The review presents a comprehensive survey and current updates on culturomics of plant microbiota within the overall context of: a) the importance of understanding the plant holobiont composition and functioning; b) the necessity to in vitro track down and explore environmental microbiomes, entailing the plant microbiome with its myriad composition and spatio-temporal dynamics and mobility in various plant species, compartments and growth stages and c) the recent developments of the emerging in-situ similis cultivation strategies grounded on plant-based culture media. Conclusions The review highlights the urgent need to explore in vitro cultivation strategies built on compatible plant-based culture media, and the transformative role of omics technologies in refining these strategies. By bridging fundamental research and cultivation-based applications, such tools offer a gateway towards more sustainable and efficient in vitro cultivation systems, leading to a deeper understanding and potential manipulation of the plant holobiont. Graphical Abstract