Genome-Resolved Metagenomics Reveals Dominant Enrichment and Metabolic Adaptations of Thauera sp. in Activated Sludge under Carbon Limitation

Abstract

Partial denitrification has been proposed as an alternative route to supply nitrite for anammox bacteria. The genus Thauera is frequently dominant in this process, yet the genomic basis for its ecological success within activated sludge remains unclear. Here, genome-resolved metagenomics was used to elucidate the genomic traits favoring its dominance under carbon (acetate)-limited conditions. Stable nitrite accumulation was achieved during treatment of low-strength ammonium wastewater (∼30 mg N/L) only under carbon limitation, whereas no nitrite accumulation occurred under carbon-sufficient conditions. The dominant high-quality metagenome-assembled genomes (MAGs) differed markedly between the two reactors. A near-complete MAG, affiliated with T. aminoaromatica (98.9% completeness and 0.4% contamination), dominated the carbon-limited reactor (27.0 ± 3.2%) but was rare in the carbon-sufficient reactor (0.6 ± 0.5%). The Thauera MAG encoded 4 copies of the acetate transporter genes (actP), a complete gene set for denitrification and internal carbon synthesis. Consistently, acetate limitation significantly increased both polyhydroxyalkanoate (PHA) content and the abundance of PHA-encoding microbes. Comparative genomics with 39 Thauera reference genomes further indicated selective enrichment of narG-containing Thauera lineages associated with nitrite accumulation. This study provides genomic insights into the ecological dominance of Thauera, highlighting its metabolic versatility and adaptive advantages in low-carbon wastewater treatment systems.