Chakraverti-Wuerthwein, M. S.

bioRxiv2026

Phylogenetic coherence in microbiome composition across environmental gradients

Global surveys of microbial communities across biomes have shown that environmental variables such as depth and pH are strong determinants of community composition. However, we do not understand how the traits of individual taxa, and their evolutionary conservation, conspire to give rise to these patterns. Exploiting large-scale surveys of top soil and marine microbiomes, we use canonical correlation analysis (CCA) to concurrently infer directions of environmental variation and the associated compositional changes. We find that the primary canonical direction, capturing the dominant environmental gradient, exhibits a strong phylogenetic signal: individual species responses to environmental shifts along this direction are similar among taxa with shared evolutionary history. In contrast, secondary canonical directions show weak or no phylogenetic structure. Together, these results suggest a two-scale view of microbial community assembly. Deeply evolutionarily conserved traits govern community reorganization along the main environmental driver of community composition. Additional environmentally driven changes in community composition then reflect traits that are more evolutionarily labile.

ecology↗

bioRxiv2026

Minimizing co-growth as a broad predictor of community robustness

Microbial communities rarely remain in a fixed physiological state. Instead, they progress through internal life cycles in which changing metabolites, spatial organization, and physiological states reshape ecological interactions over time. Despite extensive theory on coexistence with fixed interactions, we lack simple quantitative predictors of robustness for communities undergoing repeated growth and dispersal cycles. Here we show that a single quantity, the temporal co-growth of community members, predicts robustness across several models of community maturation, including chemotactic spatial patterning, cross-feeding with toxicity, and a phenomenological many-species model with prescribed growth trajectories. Communities in which different species grow at distinct times persist far longer under stochastic reseeding than communities with overlapping growth, with average community lifetime increasing approximately exponentially as co-growth decreases. Across the systems studied here, diverse mechanisms such as spatial organization, metabolic cascades, and physiological programs promote robustness insofar as they reduce the temporal overlap of rapid growth across species. These results identify co-growth as a common quantitative feature of robust dynamically maturing communities and suggest that minimizing co-growth may provide a broader organizing principle for ecological robustness.

ecology↗