Characterization of comammox bacteria in wastewater secondary treatment systems

Abstract

Until the discovery of the complete ammonia oxidizing (comammox) bacteria, microorganisms able to accomplish complete ammonia oxidation to nitrate, aerobic nitrification was considered an obligate two-step process carried out by two different groups, i.e., ammonia-oxidizing archaea (AOA) or bacteria (AOB) and nitrite-oxidizing bacteria (NOB). Previous studies have reported that comammox bacteria are adapted to low ammonia dissolved oxygen environments and prefer the biofilm niche. This suggests that comammox bacteria could significantly impact the process performance and economic feasibility of nitrogen removal systems in the wastewater industry. In contrast to the multiple co-existing populations of strict ammonia and nitrite oxidizers in wastewater, several studies have found that Ca. Nitrospira nitrosa is the principal or sole comammox bacteria in the nitrogen removal systems of wastewater secondary treatment. This apparent lack of diversity and redundancy challenges the practicality of designing operational strategies that rely on the comammox bacteria activity. This doctoral research (1) developed a qPCR assay for the rapid and reliable detection and quantification of comammox bacteria in the complex microbial communities in nitrogen removal systems and determined the process parameters influencing their presence and abundance, (2) explored the diversity and microdiversity of comammox bacteria compared to strict nitrifiers using a combination of full-length 16S rRNA gene amplicon sequencing and genome-resolved metagenomics and (3) determined the ability of different assembly methods (e.g., hybrid assembly, reassembly and Hi-C assembly) to improve the quality of nitrifiers metagenome assembled genomes (MAGs) recovered from complex environments (e.g., wastewater).--Author's abstract