Collecting microbial network members and hub species

As microbial ecology has advanced in recent decades, the importance and incredible diversity of microbial communities has become apparent. However, the processes that determine the composition of microbial communities remain poorly understood. Determining what gives rise to a certain community composition may help us manipulate microbial communities into healthier or more productive forms.

To gather candidates for our synthetic microbial community studies, we are coordinating two A. thaliana microbial collections: one from Sweden and one from the Midwestern United States.  We are attempting to collect as many microbes from our samples as possible, creating a permanent “living library” for future research. We are collecting microbes primarily from internal leaf tissue. However, collections from the Midwest also include microbes from roots and siliques.

We are currently processing over 5000 new bacterial and hundreds of fungal isolates (we already hold >6,000 Midwestern bacterial and 50 fungal isolates).  We seek taxa that match hub OTUs that have not been previously cultured in order test them in controlled growth chamber experiments with sterile plants and ultimately combine them with other OTUs to form synthetic communities in which the network of interactions among microbes has been empirically verified.  Such a community will be used to assess the accuracy of various interaction inference approaches. This evaluation of our ability to identify microbial interactions is fundamental for our continued application of network science to microbial communities.             Future work will expand the application of this experimental community to address questions and hypotheses from network science and ecology. This may include topics such as: the importance of competitive interactions in community stability, and the effect of higher order interactions on community dynamics and composition.