Periodic Reporting for period 1 - Apple-Biome (The origin, distribution, and dissemination of the apple microbiome)
Reporting period: 2020-01-01 to 2021-12-31
• What is the problem/issue being addressed?
Virtually all organisms, including plant, are associated with a diverse community of microorganisms, collectively call the microbiome. These organisms are only recently are being intensively described in many systems, thanks to the development of DNA high throughput sequencing which was developed less than two decades ago. Although the role of these organisms is being elucidated, questions regarding the origin, distribution, and dissemination of these microorganisms remain unanswered. Therefore, Apple-Biome aims to understand where does the plant microbiome come from and how they are distributed within the plant.
• Why is it important for society?
The microbiome is currently being studied and analyzed to be exploited in numerous sectors such as plant protection, production, and biotechnology. Understanding the origin and distribution of the plant microbiome. These exploitations will help reduce or rather eliminate the use of chemical pesticides and fertilizers, which translates into environmentally friendly and sustainable plant protection solutions with reduced effects on non-target organisms, and natural resources. Therefore, Apple-Biome measures are in line with the EU policies e.g. Directive 2009/128/EC and Directive 98/8/EC that focus on sustainable agriculture and the use of plant protection products, as well as environmental and human health initiatives e.g. the One Health Initiative and Eco-Innovation Initiative. Accordingly, this project should contribute in the fulfillment and reinforcement of the current EU directives as well as influence the policy-making decisions in the future.
• What are the overall objectives?
Objective 1: identifying the origin and source(s) of the apple microbiome.
Objective 2: investigating the colonization and the distribution pattern of the microbiome within the plant.
Objective 3: identifying the mechanisms of dissemination/transmission of the microbiome
Virtually all organisms, including plant, are associated with a diverse community of microorganisms, collectively call the microbiome. These organisms are only recently are being intensively described in many systems, thanks to the development of DNA high throughput sequencing which was developed less than two decades ago. Although the role of these organisms is being elucidated, questions regarding the origin, distribution, and dissemination of these microorganisms remain unanswered. Therefore, Apple-Biome aims to understand where does the plant microbiome come from and how they are distributed within the plant.
• Why is it important for society?
The microbiome is currently being studied and analyzed to be exploited in numerous sectors such as plant protection, production, and biotechnology. Understanding the origin and distribution of the plant microbiome. These exploitations will help reduce or rather eliminate the use of chemical pesticides and fertilizers, which translates into environmentally friendly and sustainable plant protection solutions with reduced effects on non-target organisms, and natural resources. Therefore, Apple-Biome measures are in line with the EU policies e.g. Directive 2009/128/EC and Directive 98/8/EC that focus on sustainable agriculture and the use of plant protection products, as well as environmental and human health initiatives e.g. the One Health Initiative and Eco-Innovation Initiative. Accordingly, this project should contribute in the fulfillment and reinforcement of the current EU directives as well as influence the policy-making decisions in the future.
• What are the overall objectives?
Objective 1: identifying the origin and source(s) of the apple microbiome.
Objective 2: investigating the colonization and the distribution pattern of the microbiome within the plant.
Objective 3: identifying the mechanisms of dissemination/transmission of the microbiome
• To understand the origin of the plant microbiome, we first started by testing the hypothesis that members of the plant microbiome are partially inherited from through seeds and partially acquired from the environment.
• Using culturing device, called Microcosms, for growing plants in microbe-free condition was developed specifically for this work by the ER, we provided experimental evidence of microbial inheritance in plants, from seed to seedling.
• We then identified that the origin of seed microbiome to be combination of both sexual and asexual, i.e. pollen and ovules, and shoot endosphere.
• Based on these results, which provided experimental proof the vertical transmission in plants from parents to offspring (seeds), and from seed to seedling, we tested the hypothesis that this continuous transmission can be tracked back to plant ancestors.
• At this stage, we further aimed to identify the spatial distribution of the plant microbiome at local scale (within the plant) and geographical scale (across the globe). The spatial variation within the plant was evaluated in both fruit and root system.
• To evaluate the geographical distribution of the apple microbiome, we used Gala cultivar sampled from 21 orchards across the globe and analyzed the microbial community associated to its calyx-end, stem-end, and peel using amplicon sequencing. We showed that all apples are not the same.
• The spatial variation within the plant was evaluated in both fruit and root system. The fruit: here we tested the how different part of the fruit vary in their microbial diversity and community composition and how simple agricultural practices such as washing, waxing, and storage time, affect these communities.
• To identify the spatial variation within the root system and examine if these effect are persistent in different genotypes, the microbiota associated with four different apple rootstocks planted in the same soil environment were analyzed.
• Using culturing device, called Microcosms, for growing plants in microbe-free condition was developed specifically for this work by the ER, we provided experimental evidence of microbial inheritance in plants, from seed to seedling.
• We then identified that the origin of seed microbiome to be combination of both sexual and asexual, i.e. pollen and ovules, and shoot endosphere.
• Based on these results, which provided experimental proof the vertical transmission in plants from parents to offspring (seeds), and from seed to seedling, we tested the hypothesis that this continuous transmission can be tracked back to plant ancestors.
• At this stage, we further aimed to identify the spatial distribution of the plant microbiome at local scale (within the plant) and geographical scale (across the globe). The spatial variation within the plant was evaluated in both fruit and root system.
• To evaluate the geographical distribution of the apple microbiome, we used Gala cultivar sampled from 21 orchards across the globe and analyzed the microbial community associated to its calyx-end, stem-end, and peel using amplicon sequencing. We showed that all apples are not the same.
• The spatial variation within the plant was evaluated in both fruit and root system. The fruit: here we tested the how different part of the fruit vary in their microbial diversity and community composition and how simple agricultural practices such as washing, waxing, and storage time, affect these communities.
• To identify the spatial variation within the root system and examine if these effect are persistent in different genotypes, the microbiota associated with four different apple rootstocks planted in the same soil environment were analyzed.
Apple-Biome have provided the first experimental proof of vertical transmission of the plant microbiome and showed that this community can be tracked back to its ancestry. 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. On the other hand, the interdisciplinary nature of the project makes its outcomes exploitable in different sectors and at various levels; from seed health and production, to the development of synthetic microbial communities and the use of biocontrol agents against plant diseases. For instance, the germ-free system represents a tool that can be used for several applications, ranging from the discovery of new microbes with biotechnological potential to the study of the plant holobiont. Therefore, it will likely interest scientists and stakeholders working in similar fields, which in turn will increase its chances of reaching commercial viability.