Environmental selection constrains metabolic network architecture despite taxonomic turnover in anaerobic digestion communities
Microbial ecosystems often sustain stable metabolic functions despite pronounced taxonomic turnover, yet the mechanisms that give rise to such reproducible functional states remain poorly understood. Here, we investigated how physicochemical constraints shape functional convergence in anaerobic digestion (AD) communities using replicated serial enrichments seeded from four distinct inocula. Across three pH levels and six substrate regimes, communities converged toward reproducible metabolite profiles, with pH emerging as the dominant organizing factor. Community composition became progressively environment-driven over time, and after ~30 generations, pH explained the largest fraction of compositional variance (R² = 0.214, p = 0.001), followed by feed regime. Genome-resolved metagenomics further showed that this convergence was associated with strong pH-dependent structuring of redox-balancing and terminal electron-disposal pathways, whereas upstream carbon-entry pathways remained broadly conserved across conditions. Taxonomic convergence was nevertheless incomplete and scale-dependent: predictability of inoculum identity declined from 75% at the genus level to 53% at the phylum level, indicating partial homogenization at coarse taxonomic resolution while finer-scale variability persisted. Despite this taxonomic flexibility, communities exposed to identical environments consistently assembled similar sets of metabolic functions organized into comparable pathway-level configurations. Quantification of within- and between-community functional redundancy revealed high redundancy and flexible taxonomic implementation for upstream fermentative functions, contrasted with lower redundancy and stronger convergence for terminal methanogenic processes. Pathway-resolved network analyses further showed that communities selectively retained a restricted subset of pre-existing metabolic routes encoded in the inocula, rather than assembling alternative pathway-level solutions capable of producing equivalent functional outcomes. Together, these results indicate that reproducible function in AD emerges from environmentally enforced stabilization of shared metabolic network architectures, imposed by physicochemical constraints on redox balance and energy conservation, rather than from deterministic fixation of species composition or flexible reassembly of distinct pathway organizations.
Microbial ecosystems often sustain stable metabolic functions despite pronounced taxonomic turnover, yet the mechanisms that give rise to such reproducible functional states remain poorly understood. Here, we investigated how physicochemical constraints shape functional convergence in anaerobic digestion (AD) communities using replicated serial enrichments seeded from four distinct inocula. Across three pH levels and six substrate regimes, communities converged toward reproducible metabolite profiles, with pH emerging as the dominant organizing factor. Community composition became progressively environment-driven over time, and after ~30 generations, pH explained the largest fraction of compositional variance (R² = 0.214, p = 0.001), followed by feed regime. Genome-resolved metagenomics further showed that this convergence was associated with strong pH-dependent structuring of redox-balancing and terminal electron-disposal pathways, whereas upstream carbon-entry pathways remained broadly conserved across conditions. Taxonomic convergence was nevertheless incomplete and scale-dependent: predictability of inoculum identity declined from 75% at the genus level to 53% at the phylum level, indicating partial homogenization at coarse taxonomic resolution while finer-scale variability persisted. Despite this taxonomic flexibility, communities exposed to identical environments consistently assembled similar sets of metabolic functions organized into comparable pathway-level configurations. Quantification of within- and between-community functional redundancy revealed high redundancy and flexible taxonomic implementation for upstream fermentative functions, contrasted with lower redundancy and stronger convergence for terminal methanogenic processes. Pathway-resolved network analyses further showed that communities selectively retained a restricted subset of pre-existing metabolic routes encoded in the inocula, rather than assembling alternative pathway-level solutions capable of producing equivalent functional outcomes. Together, these results indicate that reproducible function in AD emerges from environmentally enforced stabilization of shared metabolic network architectures, imposed by physicochemical constraints on redox balance and energy conservation, rather than from deterministic fixation of species composition or flexible reassembly of distinct pathway organizations.
Ecole Polytechnique Federale de Lausanne