Time-series genome-centric analysis unveils bacterial response to operational disturbance in activated sludge

Abstract

Understanding ecosystem response to disturbances and identifying the most critical traits for the maintenance of ecosystem functioning are important goals for microbial community ecology. In this study, we used 16S rRNA amplicon sequencing and metagenomics to investigate the assembly of bacterial populations in a full-scale municipal activated sludge wastewater treatment plant over a period of three years, including a period of nine month of disturbance, characterized by short-term plant shutdowns. Following the reconstruction of 173 metagenome-assembled genomes, we assessed the functional potential, the number of rRNA gene operons and the in situ growth rate of microorganisms present throughout the time series. Operational disturbances caused a significant decrease in bacteria with a single copy of the ribosomal RNA (rrn) operon. Despite only moderate differences in resource availability, Understanding the drivers of community structure is important for developing predictive models and for guiding engineering and management practice of microbial community ecosystems (1-4). Activated sludge is the most widely used process for biological wastewater treatment worldwide (5). It involves highly diverse biomass aggregated into flocs, which can be separated from treated wastewater by gravity settling. The heterogeneous structure of activated sludge flocs is a result of physical, chemical, and biological processes. These include (a) physicochemical interactions between microorganisms, exopolymeric substances (EPS), inorganic particles and di-and trivalent cations, (b) biological interactions among diverse microorganisms within the community, and (c) physiological processes for nutrient uptake and resource allocation between biological activities in bacterial cells (6). The selection of microbial populations in these ecosystems is driven primarily by environmental and operational pressures (7).A great deal of knowledge has been achieved during the last two decades from research exploring how bacterial community composition is affected by process configuration, solid retention time (SRT), temperature, redox conditions, wastewater composition, pH, and other factors (8)(9)(10)(11)(12)(13)(14)(15)(16). Recent progress in high-throughput sequencing technology has facilitated a detailed characterization of the composition of microbial communities in a large number of wastewater treatment systems worldwide (12,(17)(18)(19). However, the ability to produce a precise ecological description of activated sludge based on the abundance of the species present is still elusive.Typically, wastewater treatment plants (WWTP) are able to perform reliably under fluctuating conditions. Given that the stability of microbial communities is affected by disturbance events, it is important to understand how ecosystems respond to disturbance and which traits are the most critical for the maintenance of functioning. To date few studies have addressed the response of microbial communities to disturbance in full-scale wastewater treatment systems (20...

Long-run bacteria-phage coexistence dynamics under natural habitat conditions in an environmental biotechnology system

“…The Gordonia metagenome-assembled genome (MAG) was one of the 173 MAGs obtained in a previous study using data from a time-series analysis of a municipal full-scale activated sludge plant [30]. The refined Gordonia sp.…”

“…Reads were recovered from the Gordonia MAG assembled in Perez 2019 [30]. We confirmed that all scaffolds belonged to the same MAG by calculating the abundance and tetranucleotide frequency correlation of each scaffold in the MAG.…”

“…Characteristics of the wastewater treatment plant, and full details of the sampling, nucleic acid extraction, and metagenomic analysis are provided in our previous article [30]. Briefly, samples were obtained from a full-scale municipal WWTP that provides sewage treatment for a population of ca.…”

“…DNA from sludge samples was extracted by a direct lysis procedure involving physical disruption of cells and a CTAB (cetyltrimethylammonium bromide) purification step [30]. The DNA extracted from the 60 sludge samples samples were sent to INDEAR (Rosario, Argentina) for Nextera DNA library preparation and sequencing.…”

“…A key challenge is to understand how phages and bacteria manage to coexist in complex natural environments, avoiding complete host and virus eradication [29]. To help bridge this gap, we conducted a detailed observational study of the dynamics of phage-bacteria interaction under natural habitat conditions, using a three-year data series of samples collected from a municipal full-scale activated sludge plant [30].…”