Same Nodes, Different Flux: A Unified Microbial Framework for Nitrogen in Composting and Anaerobic Digestion

Nitrogen cycling during the biological treatment of organic waste is governed by a consortium of microorganisms whose activity determines whether nitrogen is conserved as a fertiliser resource or lost as ammonia, nitrous oxide, or dinitrogen. Composting and anaerobic digestion are the dominant biological platforms for organic waste valorisation, yet they impose contrasting selective pressures on nitrogen-cycling guilds. In composting, thermophilic conditions and fluctuating oxygen availability shape sequential communities of ammonifiers, ammonia oxidisers, and denitrifiers, with volatilisation and incomplete denitrification as principal loss pathways. In anaerobic digestion, nitrification is effectively absent and high organic nitrogen loading generates free ammonia that inhibits methanogenic archaea, constraining process stability and reshaping community structure toward ammonia-tolerant taxa. This review synthesises understanding of the functional guilds, enzymes, and regulatory genes involved in nitrogen mineralisation, nitrification, denitrification, and ammonia assimilation across both systems. It sets out the feedstock categories and regulatory frameworks that constrain treatment and product use, the operating parameters governing nitrogen retention, and the strategies used to mitigate loss, including additives, bioaugmentation, ammonia stripping, and struvite precipitation. We propose a comparative framework that positions the two systems along a shared continuum of microbial nitrogen regulation, in which redox regime determines which transformation pathways are available while pH, temperature, carbon-to-nitrogen ratio, moisture, and retention time govern the magnitude of loss. Attention is given to how upstream process outcomes determine nitrogen use efficiency and environmental risk after land application. We conclude by identifying research gaps, including paired cross-system studies, standardised molecular monitoring, field-scale validation, and harmonised quality standards.