adolf meyer-abich but most frequently associated with and popularized by lynn margulis and rigorously explored by bordenstein and theis. while the phytomicrobiome includes parasitic and commensal microbes, it also includes mutualists, or beneficial microbes, such as mycorrhizal fungi (mf) and plant growth-promoting bacteria (pgpb) that enable the plant holobiont to survive within a wide range of environments. beneficial microbes mediate plant holobiont responses to abiotic and biotic stresses and allow the plant holobiont to adapt to environmental variations. the plant host can then modify the abundance and composition of beneficial microbial species within the phytomicrobiome, at least in part, by secreting biochemical compounds. this selection occurs most strongly in the endosphere, followed by the rhizoplane, and finally the rhizosphere. for example, root exudates can select for and promote the growth of certain beneficial microbes by serving as carbon and/or energy sources for microbial metabolism. the origin of mitochondria and chloroplasts ...as modified prokaryotes that have become plant organelles, the endosymbiotic relationship between chloroplast, mitochondrion, and plant itself, and the symbiotic relationships between the beneficial microbes and the host plant. beneficial microbes include plant growth promoting bacteria and fungi. the shelter and habitat created by the plant host provide a regulated environment and energy source, enhancing the survival of the symbionts and endosymbionts. the earliest and arguably most essential example of a specific symbiotic function within the plant holobiome arose from the endosymbiosis of an alphaproteobacterium and a cyanobacterium. these microbes are now the mitochondrion and chloroplast, respectively, and are microbes that have been fully integrated into plant cells (see diagram). these endosymbionts did not replace particular functions of the ancestral organism, but rather provided new functions, giving an evolutionarily competitive edge to the newly evolving plants. in this paper, we focus on how beneficial bacteria and fungi, a relatively small fraction of the phytomicrobiome, have had a disproportionately large influence on plant holobiont evolution. we also review the fundamental roles that the phytomicrobiome plays in plant holobiont development and survival. finally, we propose that a greater integration of holobiont theory should be incorporated into the plant sciences. origin of the plant holobiont endosymbiosis of prokaryotes and the rise of plant holobionts life on earth is believed to stem from a single origin, the microbial ancestor that emerged as early as 3.5 billion years ago. according to endosymbiosis theory, about 1.5 billion years ago, a proto-eukaryotic cell engulfed an alphaproteobacteria, forming an endosymbiotic relationship, and gradually developed into what is now recognized as the mitochondrion (see diagram). mitochondria use alternative electron acceptors to generate adenosine triphosphate (atp) and are now the most important organelle for plant respiration since they enable metabolic reactions to convert energy into usable forms. approximately half of a billion years later, eukaryotic cells containing mitochondria engulfed cyanobacteria (photosynthetic prokaryotes), which like the alphaproteobacteria became fully incorporated into and dependent on plant cells, resulting in the chloroplast (diagram). chloroplasts convert energy from the sun into carbohydrates, using water as the electron donor. however, large-scale gene loss from plastids has occurred during the course of evolution, and higher plant chloroplasts now contain only 120–130 genes compared with the 1700 to 7500 genes contained in cyanobacterial genomes. in spite of their reduced genome size, chloroplasts and cyanobacteria still carry out some of the same functions, ranging from gene expression to metabolism. for example, it is clear that the protein targeting system of cyanobacteria is similar to that of the chloroplast. organisms have been described as entities evolved from constituent elements that are highly cooperative and minimally conflicting; however, there is ongoing debate regarding the levels of cooperation and conflict within holobionts. in plants, chloroplasts and mitochondria are highly cooperative with plant cells while relationships between the plant and the phytomicrobiome are more varied including the mutualistic and parasitic interactions. for example, relationships between plants and pgpb are organismal given that they are highly cooperative and low conflict in nature. on the other hand, some plant-microbe interactions are more opportunistic for one member and therefore are not organismal. the plant is therefore a eukaryotic organism, with prokaryotic constituents (entrained microbes), that interacts with its phytomicrobiome to form the plant holobiont. as a result, the difference between the plant and the phytomicrobiome blurs and the concept of the holobiont becomes pre-eminent. it can then be argued that the influence of microbes on the evolution of plants is so profound that without microbes, the concept of the “plant” fails. transition to land the phytomicrobiome helps the plant holobiont survive in a variety of environments. in fact, early in their evolution, plants could not have successfully transitioned from the aquatic environments inhabited by their ancestors without functional support from the phytomicrobiome. the phytomicrobiome has likely been shaped to impart additional genes to the holobiont, therefore altering the niches available to the plant; this allows the plant to adjust its behavior to suit the conditions of its immediate environment. a selective advantage provides the plant holobiont with functional plasticity, allowing it to better access resources and improve its nutrition, growth, and stress tolerance. for further analysis on the roles in which the phytomicrobiome plays in plant holobiont evolution, see several recent reviews.