Research often seeks to simplify the incredibly complex so that we can make sense of it. Complexity in science is reality, however, trying to interpret overly complex data can lead to uncertainly, or just plain wrong conclusions.
A research team from the US have developed a new model that, for some applications, strikes a sweet spot between complexity and simplicity. The team took 3 species from the rhizosphere, Bacillus cereus and two so-called hitchhikers, Pseudomonas koreensis & Flavobacterium johnsoniae. The reason being that B. cereus is often isolated from the rhizosphere with these two tagging along. This hitchhiking behaviour led to the memorable name for the community, THOR or The Hitchhikers Of the Rhizosphere.
The results from these in vitro communities gave some striking insights into how the organisms might behave in the rhizosphere. For example, the three organisms together promote dendritic expansion of B. cereus which led to more robust biofilms. The researchers also found that P. koreensis was capable of killing F. johnsoniae through the production of an alkaloid antibiotic. However, the production of this antibiotic was inhibited by B. cereus allowing the three species to coexist.
Of course, the criticism of a study like this is that it is over simplistic as well as being conducted in vitro making it difficult to draw solid conclusions about the real situation. However, while I agree that it's hard to draw conclusions about the natural rhizosphere, I think studies like this have tremendous value. They present incredibly specific hypotheses that can be used to interrogate more complex data sets, such as metagenomes, which can be used to gather evidence to support or challenge the hypothesis.
The full study was published in mBio on March 5th.
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.
Lozano GL, Bravo JI, Garavito Diago MF, Park HB, Hurley A, Peterson SB, Stabb EV, Crawford JM, Broderick NA, Handelsman J. 2019. Introducing THOR, a model microbiome for genetic dissection of community behavior. mBio 10:e02846-18. https://doi.org/10.1128/mBio.02846-18.