Microbial assembly, metabolic activity, and interactions in microbiome of biological wastewater treatment systems

Abstract

The effective assembly, metabolic activities, and interactions of microorganisms are vital to the process’s stability and efficiency in biological wastewater treatment plants (WWTPs). In addition, the bacteriophages also play important roles in adjusting the treatment process by mediating microbial metabolism. However, the niche differentiation, activities, and interactions of these microorganisms in wastewater treatment systems with remarkable variations in physicochemical characteristics are not well studied. In my thesis, I first studied how anammox consortia respond to and recover from short-term nutrient starvation (three days) in a lab-scale reactor by employing integrated metagenomics and metatranscriptomics. The results demonstrated that the remarkable changes in transcriptional patterns were associated with nutritional stress. Many factors have been proven to benefit microbes’ survival during starvation and the ensuing recovery of the anammox process. Anammox bacteria was highly resilient and quickly returned to its pre-starvation state. The niche differentiation and symbiotic associations of ammonia/nitrite oxidizers were investigated in a concatenated full-scale rotating biological contactor (RBC) using integrated metagenomics and metatranscriptomics. Nineteen metagenome-assembled genomes (MAGs) of ammonia/nitrite oxidizers were recovered using a hybrid assembly approach, demonstrating that diverse AOB and anammox dominated Stage-A, and comammox Nitrospira and AOA appeared and increased in relative abundance in Stage-B. Viruses likely act as a biotic factor mediating ammonia/nitrite oxidizer populations in this system. In addition, multi-omics, including metagenomics, metatranscriptomics, metaviromics, and the Hi-C approach, was used to disclose the ecological niche and interactions of microbes in the biofilm microbiome. A total of 525 MAGs were recovered to investigate the microbial distribution and substrate-dependent contrasts in biogeochemical cycling. Metaviromic sequencing and assembly reconstructed 17,695 phage genomes, and 548 host-virus pairs were identified using multiple identification approaches. A total of 3,213 viral genes were predicted as auxiliary metabolic genes (AMGs), implying their crucial roles in this system. In addition to the single biofilm system, the distribution and metabolic activities of functional microbes in a full-scale hybrid activated sludge and biofilm reactor were also revealed. Distinct dissimilarities in microbial composition between suspended sludge and biofilm were demonstrated by 454 recovered MAGs. Microbes involved in the nitrification and anammox processes are enriched in the biofilm metagenome, including two comammox Nitrospira genomes that were recovered. Distinct metabolic activities of these microbes were observed in suspended sludge and carrier biofilm. Finally, Illumina and Nanopore sequencing of enriched virus-like particles (VLPs) were combined to establish a phage catalog from a full-scale hybrid activated sludge and biofilm reactor. 18,645 viral operational taxonomic units (vOTUs) were reconstructed from this system, with a longer average length of 28,038 bp. Distinct phage compositions between carrier biofilm and suspended sludge were observed. The combination of advanced Hi-C sequencing and in silico analysis approaches significantly improves the resolution of host-phage associations. Overall, my study provides deep insights into the microbial assembly, metabolic activities, and interactions in microbiomes of both the label-scale and full-scale wastewater treatment systems. Furthermore, this study highlights that efficient microbiome assembly and interactions among members contribute to the stable and efficient process in sewage treatment systems.