The Use of Synthetic Microbial Communities to Improve Plant Health

Abstract

Despite the numerous benefits plants receive from probiotics, maintaining consistent results across applications is still a challenge. Cultivation-independent methods associated with reduced sequencing costs have considerably improved the overall understanding of microbial ecology in the plant environment. As a result, now it is possible to engineer a consortium of microbes aiming for improved plant health. Such synthetic microbial communities (SynComs) contain carefully chosen microbial species to produce the desired microbiome function. Microbial biofilm formation, production of secondary metabolites and ability to induce plant resistance are some of the microbial traits to take into consideration when designing SynComs. Plant-associated microbial communities are not assembled randomly. Ecological theories suggest that these communities have a defined phylogenetic organization structured by general community assembly rules. Using machine learning, we can study these rules and target microbial functions that generate desired plant phenotypes. Well-structured assemblages are more likely to lead to a stable SynCom that thrives under environmental stressors, as compared to the classical selection of single microbial activities or taxonomy. However, ensuring microbial colonization and long-term plant phenotype stability are still some of the challenges to overcome with SynComs, as the synthetic community may change over time with microbial horizontal gene transfer and retained mutations. Here, we explored the advances made in SynCom research regarding plant health focusing on bacteria, as they are the most dominant microbial form compared with other members of the microbiome and the most commonly found in SynCom studies.

The Underground World of Plant Disease: How Does Rhizosphere Dysbiosis Affect Plant Health Above-ground?

“…The Alpha and Inverse Simpson diversity indexes were calculated using the default parameters of Volant et al (2020). For the network analysis, the OTUs obtained from the soils as input and considering both biological associations and niche (Martins et al 2023, Poudel et al 2021), network analysis was applied to integrate microbes, plant phenotypes, and soil proprieties as a system to investigate how phytobiome structure influences crop health using the methods and codes adapted from Poudel et al (2021). Raw read data was submitted to the NCBI SRA under the accession number PRJNA1046511.…”

“…As a result of this relationship, plants and microbes have evolved very sophisticated beneficial communication. For instance, under stress (e.g., a pathogen infection), plants change their root chemical composition by releasing modified root exudates and “ cry for help ” to recruit beneficial microbes from the soil to cope with the stress (Martins et al 2023, Rolfe et al 2019). Like the human gut microbiome, the plant rhizosphere, the narrow soil area around the root, is colonized by diverse microbes (Ravelo-Ortega et al 2023).…”

Harnessing Emergent Properties of Microbial Consortia: Assembly of the Xilonen SynCom

“…Synthetic communities (SynComs) have emerged as valuable tools for establishing causal relationships between members (or their genes) and community functions (phenotypes) (42,43). These laboratory-assembled communities can be designed to represent natural communities but with reduced complexity (42), thereby enabling precise experimental manipulation aimed at generating microbial consortia for enhancing plant health and productivity (44)(45)(46). However, the design of simplified, tractable and ecologically relevant SynComs is still challenging (39)(40)(41).…”

Integration of Phenotypes in Microbiome Networks for Designing Synthetic Communities: a Study of Mycobiomes in the Grafted Tomato System

“…Interactions among microbes as well as with the host are important, and the net outcome of these complex interactions defines host health and ecosystem functions ( 23 ). Thus, it is critical to understand the ecology of microbes selected for biological applications, and systems approaches centered on host-microbe interaction can help guide the selection of microbes for synthetic communities ( 24 , 25 ).…”