Periodic Reporting for period 1 - HoloE2Plant (Exploring the Holobiont concept through a Plant Evolutionary Experiment study)
Reporting period: 2022-04-01 to 2024-09-30
The microbiome is a key determinant in maintaining animal and plant health. With the increasing evidence of the effect of microbiomes on host phenotypic traits, host-associated microbes have been factored into evolutionary studies by the modern hologenome theory of evolution, considering all living organisms as polygenomic entities (holobionts), on which natural selection and drift can operate. The holobiont/hologenome theory has important implications on evolutionary studies, animal health and agronomy. Nevertheless, we currently lack a tangible proof of the synergic evolution of holobionts to be able to effectively deploy this concept for developing novel and actionable research perspectives. Importantly, identifying the genetic bases behind this interaction under an evolutionary perspective is the first step in categorizing and engineering microbial consortia associated with plant fitness and health. In other words, decrypting the hologenome concept will help to formulate novel bio-sourced strategies to manage crop production by reducing pesticide use. In this context, the overall aim of HoloE2Plant is to provide evidence for the holobiont theory by identifying the genetic signatures that are under rapid evolution in both plant host and microbiota and affecting resistance to pathogens.
To address this main question and bring solutions applicable in the short-term to agriculture HoloE2Plant scientific objectives are:
i) To deeply characterize, by genomic and biochemical methodologies, bacterial and fungal communities isolated from natural Brassica rapa populations. Compared to agricultural lands, non-cultivated habitats harbor a wider diversity of wild plants and by consequence a larger species microbial diversity.
ii) To develop methods to reconstruct Synthetic Microbial Communities (SynComs) by using the genomic and biochemical information obtained from bacteria and fungi. SynComs are microbial assemblages’ representative of the host microbiota. SynComs can be used in agronomy to protect plants or to restore soil microbial biodiversity associated with ecosystems functioning. In HoloE2Plant, the obtained SynComs have a biostimulant and biocontrol properties conferring resistance to the soil-born fungal pathogen Rhizoctonia solani when applied to B. rapa plants.
iii) To use SynComs conferring a different degree of resistance to R. solani, in a cutting-edge experimental evolution study. For this, HoloE2Plant is using fast-cycling B. rapa plants that have the peculiarity to produce seeds in 40 days. These plants are extremely rapid when we compare to a natural Brassica life cycle (6 months). We make co-evolve these fast-cycling plants with SynComs and R. solani over 10 plant cycles. At each cycle, we monitor the impact of the SynComs on plant resistance and other phenotypes and we collect the evolved microbial populations and seeds.
At the end of the experimental evolution, we will be able to compare the genomic evolution of both plants and microbes and study the coevolutionary traits conferring resistance to R. solani.
To address this main question and bring solutions applicable in the short-term to agriculture HoloE2Plant scientific objectives are:
i) To deeply characterize, by genomic and biochemical methodologies, bacterial and fungal communities isolated from natural Brassica rapa populations. Compared to agricultural lands, non-cultivated habitats harbor a wider diversity of wild plants and by consequence a larger species microbial diversity.
ii) To develop methods to reconstruct Synthetic Microbial Communities (SynComs) by using the genomic and biochemical information obtained from bacteria and fungi. SynComs are microbial assemblages’ representative of the host microbiota. SynComs can be used in agronomy to protect plants or to restore soil microbial biodiversity associated with ecosystems functioning. In HoloE2Plant, the obtained SynComs have a biostimulant and biocontrol properties conferring resistance to the soil-born fungal pathogen Rhizoctonia solani when applied to B. rapa plants.
iii) To use SynComs conferring a different degree of resistance to R. solani, in a cutting-edge experimental evolution study. For this, HoloE2Plant is using fast-cycling B. rapa plants that have the peculiarity to produce seeds in 40 days. These plants are extremely rapid when we compare to a natural Brassica life cycle (6 months). We make co-evolve these fast-cycling plants with SynComs and R. solani over 10 plant cycles. At each cycle, we monitor the impact of the SynComs on plant resistance and other phenotypes and we collect the evolved microbial populations and seeds.
At the end of the experimental evolution, we will be able to compare the genomic evolution of both plants and microbes and study the coevolutionary traits conferring resistance to R. solani.
In the first two years of HoloE2Plant, we created an incredible repertoire of information related to bacterial and fungal species covering a large microbial diversity. We sequenced whole-genomes to study the metabolic pathways that are written in the genetic code of microbes. We characterized the activity of these bacteria and fungi to inhibit the R. solani pathogen, the ability to produce beneficial molecules for plants and we estimated their potential to cooperate within themselves by studying the carbon sources degradation profiles. We integrated the obtained data in a pipeline helping to design SynComs with beneficial activities for plants.
We developed a bioinformatic method that can help scientists to construct SynComs producing molecules that were registered and are approved by EU as bio-stimulants and biocontrol compounds. Our methodology is considering the information that we can extract from whole microbial genomic sequences to identify whether the metabolic pathways for the production of a target molecule are present. We then consider the whole microbial metabolic potential to design communities that do not compete for niche resources when assembled together. We hope that these developments can accelerate the use of microbes in agriculture.
We developed a bioinformatic method that can help scientists to construct SynComs producing molecules that were registered and are approved by EU as bio-stimulants and biocontrol compounds. Our methodology is considering the information that we can extract from whole microbial genomic sequences to identify whether the metabolic pathways for the production of a target molecule are present. We then consider the whole microbial metabolic potential to design communities that do not compete for niche resources when assembled together. We hope that these developments can accelerate the use of microbes in agriculture.
Identifying host genes associated with microbiota is a first step to study the coevolution of holobionts and to breed crop varieties selecting for beneficial microbes. In our article “Plant genetic bases explaining microbiota diversity shed light into a novel holobiont generalist gene theory” https://doi.org/10.1101/2023.12.22.572874 we found for the first time holobiont generalist genes, i.e. genes shared among several microbial species. This is a relevant discovery with important implications in agronomy. In fact, we found that most of these generalist genes are associated with microbial species known to be biocontrol and biostimulant agents. Thanks to the collection we set up in the first year of HoloE2Plant we were able to validate the biocontrol activity of strains belonging to these species and found to be associated to plant genes involved in host defenses. This unexpected result, motivated us to further characterize the role of these holobiont generalist genes in regulating the interaction between plants and beneficial microbes.
We also found that as in the societies, cooperation is making the strength! In fact, the biocontrol effect of a bacterial or fungal species is enhanced when these microbes are co-inoculated with other microbial species with different metabolic profiles. Hence, we can improve current biopesticides by integrating microbial formulations that are able to cooperate. However, the use of microbial mixtures necessitates the evolution of the biocontrol legislation and also clarification on the Intellectual Properties of the strains used in the mixtures. Preliminary results from the first cycle of the evolutionary experiment are elucidating the effect of these SynComs over the time. We observed in the first three steps of evolution that the protective effect of the SynComs is increasing over the time for SynComs harboring biocontrol agents. At the end of the evolutionary experiment we hope to be informed on the resilience of SynComs, a relevant information in the development of novel biopesticides.
We also found that as in the societies, cooperation is making the strength! In fact, the biocontrol effect of a bacterial or fungal species is enhanced when these microbes are co-inoculated with other microbial species with different metabolic profiles. Hence, we can improve current biopesticides by integrating microbial formulations that are able to cooperate. However, the use of microbial mixtures necessitates the evolution of the biocontrol legislation and also clarification on the Intellectual Properties of the strains used in the mixtures. Preliminary results from the first cycle of the evolutionary experiment are elucidating the effect of these SynComs over the time. We observed in the first three steps of evolution that the protective effect of the SynComs is increasing over the time for SynComs harboring biocontrol agents. At the end of the evolutionary experiment we hope to be informed on the resilience of SynComs, a relevant information in the development of novel biopesticides.