Structural Dynamics and Structure from Dynamics in Complex Ecosystems

[eng] This thesis uses a complex network perspective in ecological systems. Within this approach it explores the dynamics of two classes of ecological systems under perturbations: bipartite mutualistic networks with extinctions and rewiring, and microbial mesocosm communities under nutrient addition treatments. First, we examine how the community structure of bipartite mutualistic networks changes under different extinction scenarios, such as plant-pollinator and seed-dispersal systems. Extinctions are modeled as either node or interaction removals, with scenarios including random, directed, and sequential extinctions. Our analysis reveals that the network undergoes a significant reorganization in response to species loss, characterized by an increase in effective modularity and a rapid decline in species persistence within their original communities as extinction events accumulate. Furthermore, we explore the concept of network plasticity, specifically how adaptive rewiring modifies network characteristics like stability, modularity, or robustness following species loss. Through the analysis of over one hundred empirical mutualistic networks, we evaluated two rewiring strategies: random rewiring, representing a baseline adaptive mechanism, and resource affinity-driven rewiring, which accounts for phylogenetic similarity and functional redundancy between species. Our results show that network modularity generally increases with the frequency of extinction events. Interestingly, the effect of extinctions on modularity is more pronounced than the impact of the rewiring strategy itself. Notably, resource affinity-driven rewiring enhances modularity, robustness, and stability, suggesting an evolutionary mechanism that could help prevent cascading co-extinctions and support ecosystem resilience. The second part of this thesis focuses on microbial communities, specifically on the abundance dynamics and interaction patterns of microbial consortia in marine ecosystems. Microbial communities are crucial for ecosystem function, yet their responses to nutrient gradients and environmental changes are not fully understood. To address this gap, we use data from a series of experiments in mesocosms to directly test ecological theories regarding how patterns of interaction types correlate with community dynamics under different regimes of nutrient addition. Our findings show that, regardless of the nutrient additions, microbial consortium networks exhibit significant fluctuations in species abundance and a lower network connectance than expected, with a higher prevalence of negative interactions compared to expectations based on null models. These fluctuations suggest that microbial communities respond idiosyncratically to nutrient changes, driven by non-random patterns in species abundance correlations and connectivity. Despite strong temporal correlations among operational taxonomic units (OTUs) and substantial turnover in microbial composition across experiments, the networks maintain complex structures that reflect a dynamic interplay between stabilizing and destabilizing forces. Furthermore, our results indicate that certain triplets exhibit greater co-fluctuations compared to pairs, suggesting the presence of higher-order fluctuations within the community. These findings imply that biotically driven first-order and higher-order interactions in mesocosm experiments are key predictors of high turnover in OTU community composition and interaction specificity. Further analysis reveals that these communities possess inherent adaptive mechanisms that allow them to reorganize their interaction networks in response to nutrient addition. This plasticity, however, does not always follow predictable patterns and often manifests through a range of community-specific strategies shaped by ecological and evolutionary pressures. By integrating theoretical modeling with empirical data, this study advances our understanding of how different nutrient regimes influence the composition of microbial communities and the interaction networks, providing new insights into the factors driving ecological stability and resilience. Overall, this thesis advances our understanding of how ecological networks respond to different types of perturbations, including species extinctions and changes in nutrient availability. By highlighting the roles of modularity and network plasticity in supporting ecosystem resilience, the findings offer new insights into the mechanisms that sustain ecosystem function in the face of environmental challenges.