Unravelling riverine microbial communities under wastewater treatment plant effluent discharge in large urban areas

Nature-based bioreactors: Tackling antibiotic resistance in urban wastewater treatment

The overuse and misuse of antibiotics have accelerated the selection of antibiotic-resistant bacteria, significantly impacting human, animal, and environmental health. As aquatic environments are vulnerable to antibiotic resistance, suitable management practices should be adopted to tackle this phenomenon. Here we show an effective, nature-based solution for reducing antibiotic resistance from actual wastewater. We utilize a bioreactor that relies on benthic (biofilms) and planktonic microbial communities to treat secondary effluent from a small urban wastewater treatment plant (<10,000 population equivalent). This treated effluent is eventually released into the local aquatic ecosystem. We observe high removal efficiency for genes that provide resistance to commonly used antibiotic families, as well as for mobile genetic elements that could potentially aid in their spread. Importantly, we notice a buildup of sulfonamide (sul1 and sul2) and tetracycline (tet(C), tet(G), and tetR) resistance genes specifically in biofilms. This advancement marks the initial step in considering this bioreactor as a nature-based, cost-effective tertiary treatment option for small UWWTPs facing antibiotic resistance challenges.

Composition of the microbial community in surface flow-constructed wetlands for wastewater treatment

Traditionally constructed wetlands face significant limitations in treating tailwater from wastewater treatment plants, especially those associated with sugar mills. However, the advent of novel modified surface flow constructed wetlands offer a promising solution. This study aimed to assess the microbial community composition and compare the efficiencies of contaminant removal across different treatment wetlands: CW1 (Brick rubble, lignite, and Lemna minor L.), CW2 (Brick rubble and lignite), and CW3 (Lemna minor L.). The study also examined the impact of substrate and vegetation on the wetland systems. For a hydraulic retention time of 7 days, CW1 successfully removed more pollutants than CW2 and CW3. CW1 demonstrated removal rates of 72.19% for biochemical oxygen demand (BOD), 74.82% for chemical oxygen demand (COD), 79.62% for NH4 +-N, 77.84% for NO3 --N, 87.73% for ortho phosphorous (OP), 78% for total dissolved solids (TDS), 74.1% for total nitrogen (TN), 81.07% for total phosphorous (TP), and 72.90% for total suspended solids (TSS). Furthermore, high-throughput sequencing analysis of the 16S rRNA gene revealed that CW1 exhibited elevated Chao1, Shannon, and Simpson indices, with values of 1324.46, 8.8172, and 0.9941, respectively. The most common bacterial species in the wetland system were Proteobacteria, Spirochaetota, Bacteroidota, Desulfobacterota, and Chloroflexi. The denitrifying bacterial class Rhodobacteriaceae also had the highest content ratio within the wetland system. These results confirm that CW1 significantly improves the performance of water filtration. Therefore, this research provides valuable insights for wastewater treatment facilities aiming to incorporate surface flow-constructed wetland tailwater enhancement initiatives.

High-proportions of tailwater discharge alter microbial community composition and assembly in receiving sediments

The tailwater from wastewater treatment plants serves as an important water resource in arid regions, alleviating the conflict between supply and demand. However, the effects of different tailwater discharge proportions on microbial community dynamics remain unclear. In this study, we investigated the effects of different tailwater discharge proportions on the water quality and microbial community characteristics of sediments in receiving water bodies under controlled conditions (WF-1, WF-2, WF-3, WF-4, and WF-5, containing 0% tailwater + 100% natural water, 25% tailwater + 75% natural water, 50% tailwater + 50% natural water, 75% tailwater + 25% natural water, and 100% tailwater + 0% natural water, respectively). Microbial co-occurrence networks and structural equation model were used to unveil the relationship between microbial communities and their shaping factors. Results showed that distinct microbial community compositions were found in the sediments with low- (< 50%) and high- (> 50%) proportions of tailwater. Specifically, WCHB1-41 and g_4-29-1, which are involved in organic degradation-related functions, were the key genera in the high-proportion cluster. A total of 21 taxa were more abundant in the low-proportion (< 50%) cluster than that in high-proportion (> 50%). Moreover, higher modularity was observed in the low-proportion. Total phosphorus directly affected while ammonia nitrogen indirectly affected the microbial community structure. Our findings support the distinct heterogeneity of microbial communities driven by tailwater discharge in receiving water bodies, and further confirmed that high-proportion tailwater depletes sensitive microbial communities, which may be avoided through scientific management.

Unveiling Microbial Nitrogen Metabolism in Rivers using a Machine Learning Approach

Microbial nitrogen metabolism is a complicated and key process in mediating environmental pollution and greenhouse gas emissions in rivers. However, the interactive drivers of microbial nitrogen metabolism in rivers have not been identified. Here, we analyze the microbial nitrogen metabolism patterns in 105 rivers in China driven by 26 environmental and socioeconomic factors using an interpretable causal machine learning (ICML) framework. ICML better recognizes the complex relationships between factors and microbial nitrogen metabolism than traditional linear regression models. Furthermore, tipping points and concentration windows were proposed to precisely regulate microbial nitrogen metabolism. For example, concentrations of dissolved organic carbon (DOC) below tipping points of 6.2 and 4.2 mg/L easily reduce bacterial denitrification and nitrification, respectively. The concentration windows for NO3--N (15.9-18.0 mg/L) and DOC (9.1-10.8 mg/L) enabled the highest abundance of denitrifying bacteria on a national scale. The integration of ICML models and field data clarifies the important drivers of microbial nitrogen metabolism, supporting the precise regulation of nitrogen pollution and river ecological management.

Assessing impacts of municipal wastewater treatment plant upgrades on bacterial hazard contributions to the receiving urban river using SourceTracker

Upgrading municipal wastewater treatment plants (MWTPs) has been implemented in many megacities of China to reduce the discharges of nutrients and other pollutants and improve water quality of highly urbanized rivers. However, the contribution of MWTP discharge to bacterial hazards in the receiving rivers after upgrades has been largely unknown. In this study, high-throughput sequencing and shotgun metagenomics were applied to investigate the changes in the abundance, composition, potential risks, and contributions of bacteria and antibiotic resistance genes (ARGs) from effluent to receiving river after upgrading the third-largest MWTP in China with denitrification biofilters, ultrafiltration, ozonation, and disinfection processes. The annual loadings of total nitrogen and 27 types of pharmaceuticals were reduced by 42.4% ± 13.2% and 46.2% ± 15.4%, respectively. Bacterial biomass decreased from (3.58 ± 0.49) to (1.23 ± 0.27) × 107 16S rRNA gene copies/mL, and identified biomarkers in effluent and downstream shifted due to the adopted processes. Opportunistic pathogen bacteria downstream were also reduced. Although the relative abundance of total ARGs in MWTP effluent increased from 1.10 ± 0.02 to 2.19 ± 0.03 copies/16S rRNA gene after upgrades, that of total and high-risk ARGs downstream showed no significant difference. More importantly, the Bayesian-based SourceTracker method provided valuable insight by revealing that the contributions of MWTP discharge to downstream bacteria (from 44.2% ± 1.5%-31.4% ± 0.9%) and ARGs (from 61.2% ± 5.3%-47.6% ± 4.1%) were significantly reduced following the upgrades, indicating upgrading MWTP showed integrated benefits to the bacterial hazards in the receiving river. This study provides useful information for better control of bacterial hazard risks and operational strategy for the improvement of the urban aquatic ecosystem.

Spatial and temporal distribution of the microbial community structure in the receiving rivers of the middle and lower reaches of the Yangtze River under the influence of different wastewater types

The gradual intensification of human activity has caused severe negative impacts on the ecosystems of the Yangtze River Basin. Treated effluents still affect the environment and health of receiving rivers, particularly in terms of microbial community structure. However, relatively few studies have been conducted on the differences in the effects of wastewater types on microbial community structure. Three sampling campaigns (237 samples) were conducted in the Nanjing and Wuhan sections of the Yangtze River Basin. Our results showed that the microbial community structure differed significantly among the water periods and could recover to its original state at > 500 m downstream of the outfall. The diversity of the receiving rivers under the influence of industrial wastewater was higher than that of the other wastewater types, although the number of taxa was lower than that of other wastewater types. Cyanobium_PCC-6307 and Rhodoferax were screened for biomarkers in samples affected by domestic and industrial wastewater, respectively. Although different kinds of wastewater influenced the microbial community structure, environmental factors, and geographical distance were still the main drivers. This study suggests that treated wastewater still poses a risk to ecosystems and highlights the importance of effective management strategies for assessing ecosystem health.

Subsurface constructed wetlands with modified biochar added for advanced treatment of tailwater: Performance and microbial communities

The limitations of conventional substrates in treating wastewater treatment plant tailwater are evident in subsurface flow constructed wetlands, and the emergence of biochar presents a solution to this problem. The objective of this study was to assess and prioritize the efficacy of various modified reed biochar in removing pollutants when used as fillers in wetland systems. To achieve this, we established multiple simulation systems of vertical groundwater flow wetlands, each filled with different modified reed biochar. The reed biochar was prepared and modified using Pingluo reed poles from Ningxia. We monitored the quality of the effluent water and the diversity of the microbial community in order to evaluate the pollutant removal performance of the modified biochar under different hydraulic retention times in a laboratory setting. The findings indicated that a hydraulic retention time of 24-48 h was found to be optimal for each wetland system. Furthermore, the composite modified biochar system with KMnO4 and ZnCl2 exhibited higher levels of dissolved oxygen and lower conductivity, resulting in superior pollutant removal performance. Specifically, the system achieved removal rates of 89.94 % for COD, 85.88 % for TP, 91.05 % for TN, and 92.76 % for NH3-N. Additionally, the 16S rRNA high-throughput sequencing analysis revealed that the system displayed high Chao1, Shannon, and Simpson indices of 6548.75, 10.1965, and 0.9944, respectively. The predominant bacterial phyla observed in the wetland system were Proteobacteria, Bacteroidetes, Chloroflexi, Patescibacteria, Firmicutes, and Actinobacteria. Additionally, the denitrifying bacterial class, Rhodobacteriaceae, was found to have the highest content ratio in this system. This finding serves as confirmation that the KMnO4 and ZnCl2 composite modified biochar can significantly enhance water purification performance. Consequently, this study offers valuable insights for wastewater treatment plants seeking to implement vertical submersible artificial wetland tailwater improvement projects.

Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems

Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.

Impacts of municipal wastewater treatment plant discharge on microbial community structure and function of the receiving river in Northwest Tibetan Plateau

Wastewater treatment plant (WWTP) effluents carrying plenty of nutrients and micropollutants pose serious threats to receiving rivers, however, the response of microbial community structure and function to WWTP effluents discharge is still poorly understood. To address this knowledge gap, paired water and sediment samples from 17 sites of the Huangshui River, and effluents from 6 WWTPs were collected to investigate the effect of WWTP discharge on riverine microbial communities. Our results revealed that WWTP effluents exerted significant effects on planktonic rather than sedimentary microorganisms in the receiving river. Notably, lower diversity and richness of planktonic communities were observed in the effluent-influenced section (WRW) than other river sections (RW) along the urban river. Meanwhile, network analysis potentially revealed lower stability of co-occurrence patterns of microbial communities in WRW. The remarkably higher antibiotics, nitrate-nitrogen, and water temperature in WRW samples caused by WWTPs played essential roles in shaping the structure and function of planktonic microbial communities. This study suggested the enrichment of multiple-drug resistance genes and destruction of energy metabolisms were caused by sewage effluents, and highlighted the importance of effective management strategies for protecting the ecological health of the receiving river.

Comparison of performance of two large-scale vertical-flow constructed wetlands treating wastewater treatment plant tail-water: Contaminants removal and associated microbial community

The removal efficiency of contaminants in large-scale integrated vertical-flow constructed wetland (IVCW) and vertical-flow constructed wetland (VCW) for wastewater treatment plant (WWTP) tail-water was evaluated, and the microbial community was also investigated in this study. The results for 14 months study period indicated that 40.05% chemical oxygen demand (COD), 45.47% ammonia nitrogen (NH₄⁺-N), 62.55% total phosphorus (TP), 55.53% total nitrogen (TN) and 57.20% total suspended solids (TSS) average removal efficiencies were achieved in the IVCW. There was a poor performance of TN removal in the VCW, with an average removal efficiency of 38.13%. There was no significant seasonal difference in TP removal, and a strong positive correlation between influent TP load and removed load. The high-throughput sequencing analysis revealed that Proteobacteria, Planctomycetes, Bacteroidetes and Acidobacteria were dominant in nature and wetland systems. The relative abundance of nitrifying bacteria, denitrifying bacteria and anammox bacteria confirmed that nitrification, denitrification and anammox may be the main processes for nitrogen removal in the IVCW.

The effects of C/N (10-25) on the relationship of substrates, metabolites, and microorganisms in "inhibited steady-state" of anaerobic digestion

The carbon/nitrogen ratio (C/N) is a key parameter that affects the performance of anaerobic digestion (AD). Recent AD research has focused on optimizing the C/N of feedstock. The so-called "inhibited steady-state" refers to a special state of ammonia inhibition of AD that often occurs at low-C/N (below 25) when degradable nitrogen-rich substrates, such as livestock manure, are used as feedstock. However, the mechanism behind the "inhibited steady-state" is still unknown. In the current study, co-digestion and recirculation were used to create a C/N gradient in the influent to explore the relationship between substrates, metabolites, and microorganisms in the "inhibited steady-state." Data were collected at the macro, microbial, and genetic levels. Three CSTRs were successfully made run into the "inhibited steady-state" using influent C/Ns of 10-12. Digestion performance levels of R10-R12 were low and stable, transitioning from an aceticlastic methane-producing pathway to a hydrogenotrophic pathway as the C/N gradually decreased. As the abundance of the hydrogenophilic methanogens increased, the abundance of syntrophic acetate-oxidizing bacteria (SAOB) also increased. The succession between populations of Methanosaeta and Methanosarcina may be used as a microbiological indicator of ammonia inhibition. Under high-C/Ns, cooperation among bacteria was high, while under low-C/Ns, competition among bacteria was high. These results clarify the processes underlying the "inhibited steady-state," which is a condition often faced in actual large-scale biogas facilities that use degradable nitrogen-rich substrates. Moreover, practical guidelines for evaluating ammonia inhibition are provided, and strategies to alleviate ammonia suppression are developed.

Impact assessment of bioaugmented tannery effluent discharge on the microbiota of water bodies

Effluents are commonly discharged into water bodies, and in order for the process to be as environmentally sound as possible, the potential effects on native water communities must be assessed alongside the quality parameters of the effluents themselves. In the present work, changes in the bacterial diversity of streamwater receiving a tannery effluent were monitored by high-throughput MiSeq sequencing. Physico-chemical and microbiological parameters and acute toxicity were also evaluated through different bioassays. After the discharge of treated effluents that had been either naturally attenuated or bioaugmented, bacterial diversity decreased immediately in the streamwater samples, as evidenced by the over-representation of taxa such as Brachymonas, Arcobacter, Marinobacterium, Myroides, Paludibacter and Acinetobacter, typically found in tannery effluents. However, there were no remarkable changes in diversity over time (after 1 day). In terms of the physico-chemical and microbiological parameters analyzed, chemical oxygen demand and total bacterial count increased in response to discharge of the treated effluents. No lethal effects were observed in Lactuca sativa L. seeds or Rhinella arenarum embryos exposed to the streamwater that had received the treated effluents. All of these results contribute to the growing knowledge about the environmental safety of effluent discharge procedures.

Wastewater treatment plant upgrade induces the receiving river retaining bioavailable nitrogen sources

Currently, wastewater treatment plant (WWTP) upgrades have been implemented in various countries to improve the water quality of the receiving ecosystems and protect aquatic species from potential deleterious effects. The impact of WWTP upgrades on biological communities and functions in receiving waters is a fundamental issue that remains largely unaddressed, especially for microbial communities. Here, we selected two wastewater-dominant rivers in Beijing (China) as study sites, i.e., one river receiving water from an upgraded WWTP to explore the impacts of upgrade on aquatic ecosystems and another river receiving water from a previously upgraded WWTP as a reference. After a five-year investigation, we found that WWTP upgrade significantly decreased total organic nitrogen (N) in the receiving river. As a biological response, N-metabolism-related bacterioplankton are accordingly altered in composition and tend to intensively interact according to the network analysis. Metagenomic analysis based on the N-cycling genes and metagenomic-assembled genomes revealed that WWTP upgrade decreased the abundance of nitrifying bacteria but increased that of denitrifying and dissimilatory nitrate reduction to ammonium (DNRA) bacteria in the receiving river, according to their marker gene abundances. After calculation of the ratios between DNRA and denitrifying bacteria and quantification of genes/bacteria related to ammonium cycling, we deduced the changes in N-metabolism-related bacteria are likely an attempt to provide enough bioavailable N for plankton growth as conservation of ammonium was enhanced in receiving river after WWTP upgrade.

Sediment Microbial Diversity in Urban Piedmont North Carolina Watersheds Receiving Wastewater Input

Urban streams are heavily influenced by human activity. One way that this occurs is through the reintroduction of treated effluent from wastewater treatment plants. We measured the microbial community composition of water, sediment, and soil at sites upstream and downstream from two Charlotte treatment facilities. We performed 16S rRNA gene sequencing to assay the microbial community composition at each site at four time points between the late winter and mid-summer of 2016. Despite the location of these streams in an urban area with many influences and disruptions, the streams maintain distinct water, sediment, and soil microbial profiles. While there is an overlap of microbial species in upstream and downstream sites, there are several taxa that differentiate these sites. Some taxa characteristics of human-associated microbial communities appear elevated in the downstream sediment communities. In the wastewater treatment plant and to a lesser extent in the downstream community, there are high abundance amplicon sequence variants (ASVs) which are less than 97% similar to any sequence in reference databases, suggesting that these environments contain an unexplored biological novelty. Taken together, these results suggest a need to more fully characterize the microbial communities associated with urban streams, and to integrate information about microbial community composition with mechanistic models.

Tuning up microbiome analysis to monitor WWTPs' biological reactors functioning

Wastewater treatment plants (WWTPs) are necessary to protect ecosystems quality and human health. Their function relies on the degradation of organic matter and nutrients from a water influent, prior to the effluent release into the environment. In this work we studied the bacterial community dynamics of a municipal WWTP with a membrane bioreactor through 16S rRNA gene sequencing. The main phyla identified in the wastewater were Proteobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Actinobacteria. The WWTP is located in Spain and, like other studied WWTP in temperate climate zones, the temperature played a major role in community assembly. Seasonal community succession is observed along the two years sampling period, in addition to a continual annual drift in the microbial populations. The core community of the WWTP bioreactor was also studied, where a small fraction of sequence variants constituted a large fraction of the total abundance. This core microbiome stability along the sampling period and the likewise dissimilarity patterns along the temperature gradient makes this feature a good candidate for a new process control in WWTPs.

From Genes to Nitrogen Removal: Determining the Impacts of Poultry Industry Wastewater on Tidal Creek Denitrification

The intensification of the poultry industry in the last decades has led to a sharp increase in the number of animal processing plants discharging wastewater to water bodies. These discharges may have a significant effect on environmental quality and on important ecosystem functions, such as denitrification. We conducted a seasonal survey and a microcosm experiment in an impacted and a reference tidal creek to investigate the impacts of wastewater discharge from a poultry processing plant on sedimentary microbial communities, denitrification activity, and nitrate removal. Denitrification potential was measured using slurry incubations, and the microbial community was examined with 16S rDNA MiSeq sequencing and quantitative polymerase chain reaction of denitrification genes. The lowest denitrification rates were observed in the impacted creek, especially near the wastewater discharge, and denitrification inhibition by impacted creek water was clearly observed in the microcosm experiment. Denitrification rates were associated with changes in the microbial community composition and gene abundance. Estimated nitrate removal was lower in the impacted creek, and higher chlorophyll levels were observed in a downstream coastal bay through remote sensing. This study demonstrates denitrification inhibition by wastewater discharge from a poultry processing plant with potential consequences to coastal eutrophication.

Assessing the spatial and temporal variability of bacterial communities in two Bardenpho wastewater treatment systems via Illumina MiSeq sequencing

Next generation sequencing provides new insights into the diversity and ecophysiology of bacteria communities throughout wastewater treatment plants (WWTP), as well as the fate of pathogens in wastewater treatment system. In the present study, we investigated the bacterial communities and human-associated Bacteroidales (HF183) marker in two WWTPs in North America that utilize Bardenpho treatment processes. Although, most pathogens were eliminated during wastewater treatment, some pathogenic bacteria were still observed in final effluents. The HF183 genetic marker demonstrated significant reductions between influent and post-Bardenpho treated samples in each WWTP, which coincided with changes in bacteria relative abundances and community compositions. Consistent with previous studies, the major phyla in wastewater samples were predominantly comprised by Proteobacteria (with Gammaproteobacteria and Alphaproteobacteria among the top two classes), Actinobacteria, Bacteroidetes, and Firmicutes. Dominant genera were often members of Proteobacteria and Firmicutes, including several pathogens of public health concern, such as Pseudomonas, Serratia, Streptococcus, Mycobacterium and Arcobacter. Pearson correlations were calculated to observe the seasonal variation of relative abundances of gene sequences at different levels based on the monthly average temperature. These findings profile how changes in bacterial communities can function as a robust method for monitoring wastewater treatment quality and performance for public and environmental health purposes.

From Pig Breeding Environment to Subsequently Produced Pork: Comparative Analysis of Antibiotic Resistance Genes and Bacterial Community Composition

It is well verified that pig farms are an important reservoir and supplier of antibiotic resistance genes (ARGs). However, little is known about the transmission of ARGs between the breeding environment and subsequently produced pork. This study was conducted to investigate if ARGs and associated host bacteria spread from the breeding environment onto the meat through the food production chain. We thus analyzed the occurrence and abundance of ARGs, as well as comparing both ARG and bacterial community compositions in farm soil, pig feces and pork samples from a large-scale pig farm located in Xiamen, People's Republic of China. Among the 26 target ARGs, genes conferring resistance to sulfonamide, trimethoprim, aminoglycoside, chloramphenicol, macrolide, florfenicol, and tetracycline were observed at high frequency in both the pig breeding environment and pork. The prevalence of ARGs in pork was surprisingly consistent with breeding environments, especially between the pork and feces. The relative abundance of 10 representative ARGs conferring resistance to six classes of antibiotics ranged from 3.01 × 10-1 to 1.55 × 10-6 copies/16S rRNA copies. The ARGs conferring resistance to sulfanilamide (sulI and sulII), aminoglycoside (aadA), and tetracycline [tet(A) and tet(M)] were most highly abundant across most samples. Samples from feces and meat possessed a higher similarity in ARG compositions than samples from the farms soil. Enterobacteriaceae found on the meat samples were further identical with previously isolated multidrug-resistant bacteria from the same pig farm. Our results strongly indicate that ARGs can be potentially spreading from pig breeding environment to meat via the pork industry chain, such as feed supply, pig feeding and pork production.