What is the microbiome?

The microbiome refers to a collection of microorganisms possessing distinct physicochemical characteristics, occupying well-defined and reasonable habitats. This term encompasses not only the microorganisms themselves but also their active zones, which establish specific ecological niches. This dynamic and interactive microecosystem undergoes changes over time and scale and holds crucial importance for the functioning and health of its host. Comprising microorganisms from various domains such as prokaryotes (bacteria, archaea) and eukaryotes (protozoa, fungi, algae), the microbiome's 'active zone' includes microbial structures, metabolites, mobile genetic elements (such as transposons, phages, and viruses), as well as residual DNA embedded within the habitat's environment.

The Microbiome's Role in Plants

Microbial communities within plants exhibit marked differences in terms of their composition compared to those in animals. Due to the greater abundance and diversity of plant communities, the microorganisms found in plants are relatively more intricate. These plant microorganisms can be categorized into surface microorganisms and intra-tissue microorganisms based on their colonization sites.

Plants are firmly rooted in the soil, and their root system, along with its apoptosis, abscission, and secretions, serves as a vital source of nutrients and energy for microorganisms. The root system's intricate structure also results in improved water status and aeration conditions within the approximately 1 mm thickness close to the root, forming what is known as the inter-root region. This inter-root region stands as the primary site for nutrient and information exchange between plants and soil, harboring microorganisms known as inter-root microorganisms.

Some microorganisms manage to overcome the host's barriers and enter the root, becoming intra-root microorganisms. Additionally, microorganisms residing on the leaf's surface, particularly around stomata, are called interleaf microorganisms. Those capable of penetrating stomata or other barriers to infiltrate plant tissues are known as intraleaf microorganisms. Notably, the microorganisms recruited from diverse species or even different tissue parts of the same species exhibit distinct profiles, though certain patterns emerge. Bacterial populations are primarily dominated by groups like Ascomycetes, Anaplasma, Posterobacteria, and Actinobacteria, while fungi are mainly represented by Ascomycetes and Stamenomycetes.

What factors influence the structure of plant microorganisms?

The structure of the plant microbiome is shaped by a multitude of factors. The physical and chemical attributes of the soil act as the initial determinant, influencing the scope of the community that plant roots can directly engage with. Environmental fluctuations, insect activity, and herbivorous feeding exert a significant influence on the microbial assembly accessible to the above-ground parts of the plant. The specific plant species and its growth phase play a direct role in selecting the microbiome associated with the plant. These dynamics collectively impact the lateral dispersion of the plant microbiome. In the case of flowering plants, microorganisms also hitch a ride through pollen, nectar, and eventually seeds, transmitting vertically as seed microorganisms to the subsequent life cycle.

Simultaneously, plants actively assess environmental microbes based on specific requirements. Initially, primary compounds generated through photosynthesis, like sugars and amino acids, are secreted into the surrounding milieu via the roots. This prompts recruitment of microorganisms from the soil's microbial seed bank, facilitated by nutrient provisions. Furthermore, secondary metabolites such as coumarins, phenolic compounds, and post compounds are synthesized, prompting a screening process for appropriate microbial partners. Some partners seek to establish a closer rapport and infiltrate tissues via cortical cells. The plant exercises a more meticulous screening here, activating its own immune responses to expel unwelcome partners. Ultimately, diverse levels of cooperation are established with microorganisms that fulfill distinct functions, contingent on the plant's requirements."