About this Research Topic
Research on plant microbiome diversity, community assembly, evolution, ecology, and functional roles is booming. Approaches in investigating microbiome structure and discerning their functions are continuously evolving. Leveraging the power of advancing techniques in omics and multi-omics, computational throughput and biostatistics, as well as remodeling biological and evolutionary theories are all making it possible to obtain deeper insights into plant–microbiome interactions.
Extensive microbiome surveys have been made for several model species, and a few agriculturally important plants, but the vast majority remains to be discovered. Identifying microbiomes of other plant species, including crop and non-crop plant species, will give us a broader understanding of core, hub, and rare taxa and the host functions they provide.
Available findings suggest that bacteria and fungi constitute the majority of the plant microbiome by abundance. However, we still have a paucity of information regarding the abundance, drivers of assembly, and functionals of other fractions of the plant microbiome such as viruses, archaea, protists, and nematodes. Genome-wide association and meta-omics studies have identified key factors that impact the assembly of microbiome. Roles of individual taxa and genes on plant colonization, plant growth, and fitness have been investigated. However, these studies highlighted that large proportions of the variation in community assembly and microbiomes' effects on plant fitness remain unexplained.
Larger-scale investigations are being carried out on plant microbiomes with consideration of spatial and temporal dynamics and host-microbe and microbe-microbe interactions. Elucidation of multipartite interaction of the phytobiome such as plant-animal–soil or plant– microbe–soil-climate interactions are also gaining momentum. In addition, efforts are being made in understanding the functional roles of the microbiome to translate microbiome potentials in sustainable plant production and protection. Currently, microbiome engineering, and advances in the application of synthetic community (SynComs) approaches have revealed important roles of microbes in plant fitness and productivity. The standardization of SynComs is rapidly expanding, and microbiome-optimized plants are envisioned to develop by using microbiome selection breeding. Integrated efforts in translating sequence data into phenotypic links, experimental modeling using co-culture or gnotobiotics, and multiscale computational approaches are giving an increased understanding of microbiomes application.
With the pace of current development in plant microbiome research, this Research Topic looks to explore this important area of research by accepting original research articles and reviews on:
• Investigation of identity, diversity and community assembly of culturable and non-culturable plant-associated microorganisms (bacteria, fungi, virus, protists, algae, etc.), including legume-rhizobium and mycorrhizae
• Identification of the factors involved in the assembly and structure of the microbial community in plants
• Studies related to endosphere, episphere, phyllosphere, rhizoplane, and rhizosphere microbiome.
• Meta-omics in microbial identity, functions, and ecology.
• Evolution and co-evolution of microbes and plants
• Synthetic microbial community, microbial consortia, and application in plant production
• Mathematical and computational modeling developed for increased plant microbiome understanding
• Meta-analysis to synthesize novel hypothesis and findings
But following will not be considered:
• Studies focused on the effects and mechanisms that single strains of microbes have on the host plant, unless its impact on the microbiome is considered.
• Effect of pathogenic strains on plant growth unless the impact on the microbiome is described.
• Description of only soil microbiome unless their effects on plant growth are investigated.
Extensive microbiome surveys have been made for several model species, and a few agriculturally important plants, but the vast majority remains to be discovered. Identifying microbiomes of other plant species, including crop and non-crop plant species, will give us a broader understanding of core, hub, and rare taxa and the host functions they provide.
Available findings suggest that bacteria and fungi constitute the majority of the plant microbiome by abundance. However, we still have a paucity of information regarding the abundance, drivers of assembly, and functionals of other fractions of the plant microbiome such as viruses, archaea, protists, and nematodes. Genome-wide association and meta-omics studies have identified key factors that impact the assembly of microbiome. Roles of individual taxa and genes on plant colonization, plant growth, and fitness have been investigated. However, these studies highlighted that large proportions of the variation in community assembly and microbiomes' effects on plant fitness remain unexplained.
Larger-scale investigations are being carried out on plant microbiomes with consideration of spatial and temporal dynamics and host-microbe and microbe-microbe interactions. Elucidation of multipartite interaction of the phytobiome such as plant-animal–soil or plant– microbe–soil-climate interactions are also gaining momentum. In addition, efforts are being made in understanding the functional roles of the microbiome to translate microbiome potentials in sustainable plant production and protection. Currently, microbiome engineering, and advances in the application of synthetic community (SynComs) approaches have revealed important roles of microbes in plant fitness and productivity. The standardization of SynComs is rapidly expanding, and microbiome-optimized plants are envisioned to develop by using microbiome selection breeding. Integrated efforts in translating sequence data into phenotypic links, experimental modeling using co-culture or gnotobiotics, and multiscale computational approaches are giving an increased understanding of microbiomes application.
With the pace of current development in plant microbiome research, this Research Topic looks to explore this important area of research by accepting original research articles and reviews on:
• Investigation of identity, diversity and community assembly of culturable and non-culturable plant-associated microorganisms (bacteria, fungi, virus, protists, algae, etc.), including legume-rhizobium and mycorrhizae
• Identification of the factors involved in the assembly and structure of the microbial community in plants
• Studies related to endosphere, episphere, phyllosphere, rhizoplane, and rhizosphere microbiome.
• Meta-omics in microbial identity, functions, and ecology.
• Evolution and co-evolution of microbes and plants
• Synthetic microbial community, microbial consortia, and application in plant production
• Mathematical and computational modeling developed for increased plant microbiome understanding
• Meta-analysis to synthesize novel hypothesis and findings
But following will not be considered:
• Studies focused on the effects and mechanisms that single strains of microbes have on the host plant, unless its impact on the microbiome is considered.
• Effect of pathogenic strains on plant growth unless the impact on the microbiome is described.
• Description of only soil microbiome unless their effects on plant growth are investigated.
Keywords: amplicon sequencing, bioinformatics, community assembly, meta-omics, microbial ecology plant-microbe interactions, plant microbiology
Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.
