Genome-enabled elucidation of nitrogen removal pathways in Thauera sp. strain SND5

Conventional nutrients removal processes generally require separate tanks for nitrification/denitrification reactions and release large volumes of greenhouse gases. A Thauera sp. strain SND5 was discovered previously to mitigate emission of nitrous oxide during wastewater treatment and alleviate carbon source competition among heterotrophic bacteria in wastewater treatment plants (WWTPs). Here we report nutrients removal performance by strain SND5 in a 3.6-L sequencing batch reactor (SBR) and identification of novel functional gene homologs encoding enzymes likely responsible for the unique metabolic activity of strain SND5. The SBR containing SND5 removed 90.6±1.2% TIN and 59.4±4.9% phosphorus at representative operational conditions (DO ∼0.5 ppm and C/N = 2). The genome of strain SND5 harbors characteristic variants of the ammonia monooxygenase (amo) and polyphosphate kinase (ppk) genes that may support nutrients removal at low C/N ratios and DO. SND5 or SND5-like amo- and ppk-specific primers targeting amo_SND5 and ppk_SND5 were designed (SND5_ppk-757F/1100R and SND5_amo-322F/937R) and used to quantify SND5 and SND5-like functional populations in a demonstration-scale WWTP. In this real-world system, meaningful correlations were found between abundance of amo gene and ppk gene, aeration rate, DO, or ammonium concentration (Pearson's values r=0.65, -0.48, -0.32, and -0.57, respectively). This study provides insights into the biological mechanisms underlying nutrients removal by strain SND5, guiding the development of low DO wastewater treatment processes with lower greenhouse gas emissions, contributing to reduced energy consumption and environmental footprint of wastewater treatment plants.