From shielding effect to hierarchical structures: a coarse-grained description of diversity

The shared trade-off in microbial resource-utilization strategies has been proposed to resolve the paradox of the plankton, which states that the diversity observed in nature greatly exceeds the theoretically predicted upper bound that limits the number of coexisting species to the number of available resources. However, three important aspects remain unaddressed in this line of work. First, trade-offs have been quantified not only for phenotypes associated with alternative resource utilization, but also for other modes of microbial interaction. Second, in natural systems, not all taxa are subjected to the same trade-offs. Third, existing trade-off-based models do not explain the empirically observed clustering of taxa according to functional similarity. Here, we extend the trade-off-based framework to incorporate multiple types of resources. We assume that different subsets of taxa are constrained by distinct sets of trade-offs. Under this framework, our model predicts the emergence of clusters: while taxa with similar strategies can belong to the same cluster, each cluster is sustained by taxa with substantially different strategies. The resulting system supports high diversity with an effectively unlimited number of coexisting taxa, yet can still be described as a low-diversity community in which the number of coexisting functional clusters does not exceed the theoretical upper bound.