Let the Core Microbiota Be Functional

Recent advances in next-generation sequencing technology have boosted the field of plant–microorganism interactions, especially in rhizosphere ecology. The principle of a core microbiota has been proposed to describe the microbial community that is systematically associated with a given plant genotype. So far, this core microbiota was mostly defined on the basis of DNA sequences with taxonomic value, and not on their functional relevance. However, biogeography studies suggest that microbial reservoirs may differ depending upon soil types, thus questioning the universal distribution of the taxonomic core microbiota under various environmental conditions. The microbiota recruited by a given plant genotype in different environments seems to share greater functional similarity than taxonomic similarity. The microbial community that is systematically associated with a given host plant is called the core microbiota. The definition of the core microbiota was so far based on its taxonomic composition, but we argue that it should also be based on its functions. This so-called functional core microbiota encompasses microbial vehicles carrying replicators (genes) with essential functions for holobiont (i.e., plant plus microbiota) fitness. It builds up from enhanced horizontal transfers of replicators as well as from ecological enrichment of their vehicles. The transmission pathways of this functional core microbiota vary over plant generations according to environmental constraints and its added value for holobiont fitness. The microbial community that is systematically associated with a given host plant is called the core microbiota. The definition of the core microbiota was so far based on its taxonomic composition, but we argue that it should also be based on its functions. This so-called functional core microbiota encompasses microbial vehicles carrying replicators (genes) with essential functions for holobiont (i.e., plant plus microbiota) fitness. It builds up from enhanced horizontal transfers of replicators as well as from ecological enrichment of their vehicles. The transmission pathways of this functional core microbiota vary over plant generations according to environmental constraints and its added value for holobiont fitness. survival and reproductive success of an individual in a given environment. a subset of the microbiota associated with a given host irrespective of the macroenvironment (e.g., soil type) and that encompasses microbial vehicles carrying replicators with essential functions for holobiont fitness (Table 1). an entity encompassing an individual host (e.g., a plant) and its associated microbial community (i.e., the microbiota). On the basis of its properties, the holobiont may be assimilated into a superorganism. an adaptation to microorganisms of the ecological concept of biome, the latter being defined as a set of biotic communities typical of a biogeographical area and named on the basis of plant (and animal) taxa emblematic of this area. On this basis, a microbiome encompasses the microbiota present in a given environment (e.g., in the rhizosphere). the ecological community of commensal, symbiotic, and pathogenic microorganisms as characterized by their abundance, taxonomic diversity, and functional diversity. an entity (e.g., a DNA sequence) able to reproduce itself exactly [8], thus representing a fundamental unit of natural selection, the basic unit that survives or fails to survive. a multispecies community that functions as an organizational unit [17,18]. This unit of functional organization [17] corresponds to a unit whose subsets have stronger and more numerous interactions with one another than with the environment of the system. a subset of the microbiota associated with a given host irrespective of the macroenvironment (e.g., soil type), as characterized by taxonomic markers (e.g., 16S rRNA sequences). an entity (i.e., an individual organism, or group of organisms) that carries replicators. In contrast to replicators, vehicles do not reproduce themselves exactly, but they represent the phenotypic level at which selection occurs. Vehicles that are more successful than others in ensuring the survival of their replicators are selected preferentially by the plant.