Unraveling Keystone Taxa: Interactions Within Microbial Networks and Environmental Dynamics in Lake Mendota

Microbial communities in freshwater ecosystems drive critical biogeochemical cycles, nutrient transformations, and energy flows essential for ecosystem stability. Yet, in the face of accelerating environmental changes, the responses of these microbial networks to spatial and temporal shifts remain underexplored, particularly with rising anoxia. We investigated the microbial ecosystems of Lake Mendota, Wisconsin, USA, through comprehensive metagenomic and metatranscriptomic analyses to elucidate their adaptations to environmental fluctuations across temporal and spatial dimensions. Employing tools like Sparse Inverse Covariance Estimation for Ecological Association Inference (SPIEC-EASI) and Conditional Auto-Regressive Least Absolute Shrinkage and Selection Operator (CARlasso), we identified key microbial taxa and their interactions with environmental parameters such as depth, temperature, pH, and dissolved oxygen. Our findings reveal that biological interactions more than environmental variables shape microbial community assembly and function. Specifically, keystone taxa from the phylum Bacteroidota emerged as pivotal in nutrient cycling and organic matter decomposition, processes crucial for sustaining water quality. Notably, these keystone taxa demonstrate dynamic adaptability, suggesting that microbial networks can rapidly adjust to changes in composition, a trait essential for resilience in the face of warming temperatures and altered precipitation patterns. This study provides critical insights into the resilience and adaptability of freshwater microbiomes, highlighting the role of microbial interactions in maintaining ecosystem health. By understanding how these microbial networks respond to environmental pressures, we can better predict shifts in microbial dynamics and anticipate the broader ecological impacts of climate change on freshwater systems. ImportanceThis research underscores the critical role of keystone taxa in freshwater ecosystems, highlighting how these organisms maintain water quality and contribute to the stability of aquatic environments. Understanding the ecological roles of these taxa is essential for developing strategies to manage ecosystems and conserve freshwater resources, particularly in the face of ongoing environmental challenges like climate change. The insights provided by this study not only enhance our comprehension of microbial interactions but also support effective ecosystem management and conservation efforts.