The loss of a single species can sometimes trigger cascading effects that reshape entire ecosystems. In such cases, that species is termed a keystone species, reflecting its disproportionately large influence relative to its abundance. While keystone species have been identified in some macroscopic ecosystems, how common they are and what determines their emergence remain uncertain. This question is particularly unexplored in microbial systems, where species interactions are numerous and complex, and where functional redundancy is often considered prevalent.
This study developed a comprehensive experimental framework to directly test how microbial communities respond to the absence of individual species. Synthetic marine microcosms were assembled from 16 bacterial isolates, and a full set of “Ecological Knock-Out” (EKO) communities was generated by omitting each species in turn. Across all environments tested, the communities showed striking stability, with no species removal producing the cascading changes expected of keystone behavior. Modeling revealed that while a neutral generalized Lotka–Volterra framework predicted multiple secondary impacts, incorporating structured, hierarchical interactions reproduced the observed resilience. Such a structure may arise from variation in species’ carrying capacities or growth rates coupled with system-level processes such as dilution or mortality, collectively buffering microbial communities against secondary extinctions and invasions.
These findings suggest that keystone species may be rarer than predicted by classical theory and that structured interspecies interactions provide a stabilizing framework in microbial ecosystems. By combining systematic experiments with theory, this work offers a new lens on how microbial communities maintain stability in the face of species loss.
Read the full journal article titled Structured interactions explain the absence of keystone species in synthetic microcosms in The ISME Journal. This article has been selected as Editor’s Choice for the month of September 2025.
Authors
- Sivan Pearl Mizrahi, MIT, USA and Hebrew University of Jerusalem, Israel
- Hyunseok Lee, MIT, USA
- Akshit Goyal, MIT, USA, and Tata Institute of Fundamental Research, India
- Erik Owen, MIT, USA
- Jeff Gore, MIT, USA