The success of any agricultural system and sustainable production depends on the health of its plants. Pests and pathogens are responsible for the loss of almost one-third of the global crop production. However, microorganisms found in and on plants are not always the cause of disease. Instead, the naturally occurring microbial communities, the plant’s microbiome, play an essential role in the development of healthy plants. This project is based on a hypothesis-driven approach to address fundamental questions about the plant microbiome such as what is the source of a plant’s microbiome? What are the pathways of inheritance and acquisition? How does the microbiome move, disseminate, and enter a new host? Apple was selected as a plant model; a fruit that has been a principal component of a healthy diet, and played a major role in human evolution and survival. The proposed methodology employs cutting-edge and multidisciplinary techniques such as metagenomics, transcriptomics, and metabolomics, among others. Results of this project will help to understand the microbiome’s life cycle, associate microbes with specific organs and tissues, and identify microbial species that define a healthy host with healthy organs and offspring. From there, it will be easy to determine changes, understand disease and disorders, and find ways to correct unbalanced microbiomes. Identifying how the microbes are acquired and to which organs and tissues they are associated with, will help in understanding the optimal methods to introduce microbial species to the host. While the proposed approaches are novel, once the validity of the hypotheses is proven, they will serve as a foundation for future microbiome studies. These studies will drive the development and implementation of safe, environmentally-friendly strategies for global agriculture production. These innovations in the management of plant health have myriad positive and far-reaching implications for environmental and human health.

Objectives and aims

Identifying the origin and source(s) of the apple microbiome.

Proving the existence of the inheritance concept as well as identifying and differentiating between the “inherited” and “acquired” microbiome will increase our understanding of the role of these microbes during the early stages of the plant’s life, as well as the mechanisms in which the microbiome reaches a “mature” and stable stage. Determining how much of the “mature” microbiome is inherited from the parent plant, sexually or asexually, will establish parameters for the time needed to reach a mature state and provide foundation in studying the microbial succession in the host. Having this knowledge, particularly about the asexually inherited microbiome, will help us determine the optimal timing for collecting the vegetative material to ensure a mature, healthy, and stable microbiome for the offspring, thus improving cultivation strategies and ensuring higher production. Exploring the difference between the sexually and asexually inherited microbiome will uncover several aspects about the importance of sexual reproduction for the plant’s health, evolution, and the survival of both the microbiome and its host. Moreover, learning a new role of the microbiome in ensuring a healthy and successful fertilization could be of significant importance. Showing that sexual reproduction is not only important for the creation of genetically diverse individuals but also for providing more microbial diversity for the offspring, will have important practical implications since it will highlight that seed does not only contain a food supply (endosperm) but also a microbial source to ensure a healthy growth for the offspring.

Investigating the colonization and the distribution pattern of the microbiome within the plant.

Identifying the microbes associated with each organ will help in understanding their overall role in this specific niche. Perhaps microbes associated with leaves will have some role on the photosynthesis, or the ones colonizing the fruits play a part in fruits ripening and/or pomological characteristics such as color, firmness, and sugar content as well as in determining flavor and content of nutritive elements. Flower microbiome may be involved in the fertilization process, embryo development, or fruit setting. Identifying tissue-specific microbes will help us to predict their function within these tissues and to the overall well-being of the host. Microbes inhabiting the epidermis of the plant might be involved in the plant protection system, whereas the vascular microbiome may play a role in the water/nutrient transportation and/or metabolism. Moreover, results from the same experiments will be useful to predict the movement of the plant endophyte within and between the host tissues. Showing which microbes inhibit which tissue together with metabolites identified from these particular tissues, can help in understanding the actual role of these microorganisms and their interaction with each other and/or with the host. This information, do not only provide advancement in the field of action but also have a significant importance at both the agricultural and industrial level.

Identifying the mechanisms of dissemination/transmission of the microbiome.

Understating the pathways and mechanisms in which the plant microbiome is disseminated and transmitted to new host will shed the light on the microbe’s life cycle and their movement within and outside the host. Such information can be useful for future biological applications in restoring the host’s microbiome or in controlling plant diseases. Although the idea of microbes inhabiting the vascular system is not new, the idea of microbes using the plant vascular system to be transmitted is intriguing. It is not far-fetched then to hypothesize that some rhizosphere associated microbe like mycorrhiza can travel through the vascular system to colonize the plant reproductive tissues- ensuring an early developmental stage presence. This is more probable for strictly-symbiotic species that have been in a successful association with their hosts for thousands of years. The development of gnotobiotic plants and germ-free devices for their growth is expected to lead to a new paradigm in conducting microbiome experiments. The germ-free system will represent a tool for several important applications ranging from the discovery of new microbes with biotechnological potential to the study of the plant holobiont.