Microbial synthesis structures organic compound composition in anaerobic digestion

TL;DR

This study explores how microbes shape organic compound composition during anaerobic digestion, revealing key metabolite-microbe interactions that influence system performance.

Contribution

The study identifies a conserved core of metabolites and their microbial associations, offering new insights into microbe-metabolite dynamics in anaerobic digestion.

Findings

A conserved core of 1154 metabolites was identified across seven full-scale digesters.

Microbial community and feedstock explained 30.1%–43.4% of spatiotemporal variation in metabolite dynamics.

Microbial metabolite accumulation and turnover were strongly linked to methane production and system performance.

Abstract

Anaerobic digestion (AD) is a cornerstone technology for sustainable waste treatment and renewable energy recovery, yet its complex microbe–metabolite interactions remain poorly understood. Here, we combined high-resolution molecular profiling and microbial community sequencing in a three-month study across seven full-scale digesters to resolve dissolved organic matter (DOM) and microbiome dynamics. A total of 28 925 DOM molecules, including a conserved core of 1154 metabolites, were identified. By disentangling metabolic pathways, we observed complex transformation patterns that extend beyond simple substrate breakdown. Molecules within a mass window (183.57–390.81 m/z) exhibited high persistence, strong microbial associations, and distinct transformation trajectories. Within this mass window, microbial community composition and feedstock input, together explained ~30.1%–43.4% of the observed spatiotemporal variation. In each digester, 1260–2108 molecules were closely associated with microbial metabolism, forming 7.77–24.52 microbe–metabolite associations on average. The accumulation and turnover of these microbial metabolites were strongly linked to methane production and system performance, highlighting microbial processing of DOM as a significant factor shaping microbe–metabolite interactions. This perspective emphasizes the importance of microbe–metabolite interplay in AD, providing a conceptual framework for predictive monitoring and optimization of engineered biotechnologies.

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