Bacterial monospecies metabolic niches predict community interactions and metabolism

Ying Wang, Nicholas R. Saichek, Tami L. Swenson, Anita Silver and Trent R. Northen, Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA

Background/Question/Methods
Substrate utilization by microbial species with varying nutritional needs is important in structuring microbial communities. However, it remains unclear how individual species substrate preferences drive interspecific interactions and the overall metabolic activity of a consortium. If monospecies metabolic niches are conserved in a community, we could better link community structure to overall metabolism based on abundances and activities of the constituent members. This would provide a powerful tool for designing synthetic communities to achieve desirable microbiome services, for example promoting soil health and crop productivity.
To explore this, we chose soil bacterial isolates of different ecological attributes. We characterized the substrate niches of each species grown individually in a defined medium containing a diversity of carbon substrates using exometabolite profiling. To evaluate interspecific interactions, we performed sequential growth experiments where pairs of bacteria were grown in each other’s spent media. To examine interactions and substrate use in a mixed community, we applied ribosomal marker protein profiling combined with stable isotope probing to simultaneously measure the structure and substrate incorporation of a five-member community.

Results/Conclusions
Monospecies exometabolomic analysis showed that each bacterial monospecies had different preferences for various substrates present in the growth medium. Bacteria from different phylogenetic or trait groups varied in their substrate utilization patterns. Through sequential growth experiments, we quantified directional, pairwise interaction strengths. These experimentally determined interaction strengths agreed with those predicted from monospecies exometabolomes based on metabolite biochemistry and niche theory. We also found monospecies substrate preferences were conserved in the five-member bacterial community. The overall substrate use by the community could be predicted from that of each constituent monospecies using a weighted-sum model. Our results suggest that monospecies substrate preference is a major force governing interspecific interactions. Characterizing monospecies exometabolite niches would provide useful information to predict microbial interactions and community metabolism.