A call to arms for cell–cell interactions between bacteria in the plant microbiome

Plant microbiomes in the different host compartments are significantly more dominated by the bacterial phyla Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes. Phylogenetic organisation of members of plant microbiomes infers that grouping and assembly mechanisms must occur in the microbiome, including cell–cell interactions among bacteria. In the last two decades microbiologists have discovered several mechanisms of bacterial cell–cell interactions. These include metabolic interactions, competition for resources, cell–cell signalling, cell–cell contacts, and production of secondary metabolites. Their function in shaping plant microbial communities is currently unknown. Bacteria–bacteria interactions in plant microbiomes now need to be studied using biologically pertinent models via traditional genetics combined with meta-omics, computational biology, mass spectroscopy, and imaging. Next-generation sequencing and computational biology has unravelled the different bacterial groups populating plant microbiomes. In addition, microbiologists have discovered many different mechanisms of cell–cell interactions that take place between bacteria. Bacteria use four prevalent mechanisms for intercellular interactions; however, their pertinent role in the formation and maintenance of plant microbiomes is currently unknown. We argue that it is overdue to speed up research on the biotic cell–cell interactions that take place between bacteria in plant microbiomes. This research will have a major impact on both fundamental sciences and translational agriculture via the development of bacterial prebiotic compounds as well probiotics competence, resulting in a more sustainable agriculture of economically important crops. Next-generation sequencing and computational biology has unravelled the different bacterial groups populating plant microbiomes. In addition, microbiologists have discovered many different mechanisms of cell–cell interactions that take place between bacteria. Bacteria use four prevalent mechanisms for intercellular interactions; however, their pertinent role in the formation and maintenance of plant microbiomes is currently unknown. We argue that it is overdue to speed up research on the biotic cell–cell interactions that take place between bacteria in plant microbiomes. This research will have a major impact on both fundamental sciences and translational agriculture via the development of bacterial prebiotic compounds as well probiotics competence, resulting in a more sustainable agriculture of economically important crops. a complex and multispecies assemblage of microbial cells that is irreversibly attached to a surface and is enclosed in a self-produced extracellular matrix primarily composed of polysaccharides, DNA, and other components. methods widely used in ecology to infer the possible connections or relationships (either positive, neutral, or negative) between two species based on pairwise comparisons of the abundance profiles of individual taxa. microbial habitat/compartment inside plant tissues. also called ‘integrative omics approaches,’ this technique combines sets of different omic technologies, such as genomics, proteomics, transcriptomics, and metabolomics, to study biological entities in a concerted way. not only refers to the totality of micro-organisms and their genetic material (genome, plasmid, and mobile elements) present in a particular environment (e.g., soil, rhizosphere, phyllosphere, endosphere, or seeds) but also encompasses the sum of their activities, which results in the formation of a specific microecosystem. an interaction between two species at the population level rather than in a single organism, in which each species derives a benefit. Also referred to as ‘cooperation’ or ‘symbiosis.’ a kind of peptide secondary metabolite synthesized by multidomain megaenzymes called ‘nonribosomal peptide synthetases’ without the use of cell ribosomal machinery and mRNAs. a large class of structurally diverse acetate- or propionate-derived natural products that are often created by a series of modular enzymes and exhibit a wide range of bioactivities. mechanism of bacterial cell-to-cell communication that regulates specific gene expression in response to population cell density, mediated by the production, release, and detection of chemical signal molecules. low-molecular-weight organic chelators with a very specific affinity for ferric iron, they scavenge iron from the surrounding environment and make it available to microbial cells and/or the plant host. setups of communities formed by individually isolated micro-organisms for controlled microbiome engineering.