Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior

Abstract

The quest to manipulate microbiomes has intensified, but many microbial communities have proven to be recalcitrant to sustained change. Developing model communities amenable to genetic dissection will underpin successful strategies for shaping microbiomes by advancing an understanding of community interactions. We developed a model community with representatives from three dominant rhizosphere taxa, the Firmicutes, Proteobacteria, and Bacteroidetes. We chose Bacillus cereus as a model rhizosphere firmicute and characterized 20 other candidates, including “hitchhikers” that coisolated with B. cereus from the rhizosphere. Pairwise analysis produced a hierarchical interstrain-competition network. We chose two hitchhikers, Pseudomonas koreensis from the top tier of the competition network and Flavobacterium johnsoniae from the bottom of the network, to represent the Proteobacteria and Bacteroidetes, respectively. The model community has several emergent properties, induction of dendritic expansion of B. cereus colonies by either of the other members, and production of more robust biofilms by the three members together than individually. Moreover, P. koreensis produces a novel family of alkaloid antibiotics that inhibit growth of F. johnsoniae, and production is inhibited by B. cereus. We designate this community THOR, because the members are the hitchhikers of the rhizosphere. The genetic, genomic, and biochemical tools available for dissection of THOR provide the means to achieve a new level of understanding of microbial community behavior. IMPORTANCE The manipulation and engineering of microbiomes could lead to improved human health, environmental sustainability, and agricultural productivity. However, microbiomes have proven difficult to alter in predictable ways, and their emergent properties are poorly understood. The history of biology has demonstrated the power of model systems to understand complex problems such as gene expression or development. Therefore, a defined and genetically tractable model community would be useful to dissect microbiome assembly, maintenance, and processes. We have developed a tractable model rhizosphere microbiome, designated THOR, containing Pseudomonas koreensis, Flavobacterium johnsoniae, and Bacillus cereus, which represent three dominant phyla in the rhizosphere, as well as in soil and the mammalian gut. The model community demonstrates emergent properties, and the members are amenable to genetic dissection. We propose that THOR will be a useful model for investigations of community-level interactions.

Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome

“…It is possible that difficult-to-cultivate species may only emerge in the context of a community, requiring interactions with other members and precluding their growth as axenic strains without more biochemical information. Species that co-isolate together is a phenomenon that has been seen previously (Lozano et al, 2019). These "hitchhikers" have been used to build consortia that have a high probability of containing interacting organisms.…”

“…One approach to investigate the high diversity and complexity of the soil microbiome is to develop reduced complexity model consortia. Ideally, a model consortium would have a tractable and reproducible number of species that are amenable to genetic manipulation and that would enable experimental analysis of population dynamics and specific metabolic and signaling interactions between members (Lozano et al, 2019;Zengler et al, 2019). Ultimately, knowledge gained by analysis of these reduced complexity communities should help to reveal details of metabolic and interspecies interactions that may take place in the native soil community.…”

Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome

“…Recent studies of interactions within synthetic communities based on plant microbiomes found widespread inhibitory interactions and led to the discovery of novel antimicrobial compounds. For example, the THOR model rhizosphere microbiome, presented by Lozano and coworkers ( 16 ), was found to contain Pseudomonas koreensis , the producer of koreenceines A to C. These molecules had inhibitory activity against another member, Flavobacterium johnsoniae . In another example, in a phyllosphere model presented by Helfrich and coworkers ( 15 ), binary interaction networks were created and bioactivity-guided fractionation led to the discovery of multiple novel molecules produced by Brevibacillus sp.…”

“…Specialized metabolites produced by microbes, including molecules with antibacterial, antifungal, and siderophore activities, have been hypothesized to play a role in shaping plant microbiomes. For example, specialized metabolites may influence interactions between members of plant microbiomes ( 15 – 17 ) and may be a mechanism of protection from pathogen invasion ( 7 , 17 ). Thus, there is interest in leveraging specialized metabolism by plant-associated microbes in agriculture and for discovery of novel compounds.…”

“…Multiple reports have demonstrated that plant microbiomes contain members with strong potential as sources of novel specialized metabolites in vitro (2,15,16,18,19); however, relatively few studies have examined microbial specialized metabolism in planta (17,(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32). Members of the genus Pseudomonas and the order Rhizobiales are notable exceptions, as genetic approaches have been used in these organisms to demonstrate the effect of specialized metabolites which inhibited fungal pathogens (33,34) and mediated microbe/host plant communication (35,36), respectively.…”