Composition and Dynamics of the Activated Sludge Microbiome during Seasonal Nitrification Failure

Wastewater-effluent discharge and incomplete denitrification drive riverine CO2, CH4 and N2O emissions

Rivers are well-known sources of the greenhouse gasses (GHG) carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O). These emissions from rivers can increase because of anthropogenic activities, such as agricultural fertilizer input or the discharge of treated wastewater, as these often contain elevated nutrient concentrations. Yet, the specific effects of wastewater effluent discharge on river GHG emissions remain poorly understood. Here, we studied two lowland rivers which both receive municipal wastewater effluent: river Linge and river Kromme Rijn. Dissolved concentrations and fluxes of CH4, N2O and CO2 were measured upstream, downstream and at discharge locations, alongside water column properties and sediment composition. Microbial communities in the sediment and water column were analysed using 16S rRNA gene sequencing. In general, observed GHG emissions from Linge and Kromme Rijn were comparable to eutrophic rivers in urban and agricultural environments. CO2 emissions peaked at most discharge locations, likely resulting from dissolved CO2 present in the effluent. CH4 emission was highest 2 km downstream, suggesting biological production by methanogenic activity stimulated by the effluents' carbon and nutrient supply. Dissolved N2O concentrations were strongly related to NO3- content of the water column which points towards incomplete riverine denitrification. Notably, methanogenic archaea were more abundant downstream of effluent discharge locations. However, overall microbial community composition remained relatively unaffected in both rivers. In conclusion, we demonstrate a clear link between wastewater effluent discharge and enhanced downstream GHG emission of two rivers. Mitigating the impact of wastewater effluent on receiving rivers will be crucial to reduce riverine GHG contributions.

Resilience towards organic load and activated sludge variations in co-fermentation for carboxylic acid production

Two perturbations were investigated in acidogenic co-fermentation of waste activated sludge (WAS) and food waste in continuous mesophilic fermenters: increasing the organic loading rate (OLR) and changing the WAS. A control reactor maintained an OLR of 11 gVS/(L·d), while a test reactor had a prolonged OLR change to 18 gVS/(L·d). For each OLR, two WAS were studied. The change in OLR led to differentiated fermentation product profile without compromising the fermentation yields (∼300 mgCOD/gVS). At 11 gVS/(L·d), the product profile was dominated by acetic, butyric, and propionic acids while at 18 gVS/(L·d) it shifted to acetic acid, ethanol, and caproic acid. Reverting the OLR also reverted the fermentation profile. The biomass immigration with the WAS changed the fermentation microbial structure and introduced acetic acid-consuming methanogens, which growth was only delayed by the OLR increase. Microbial monitoring and post-fermentation tests can be used for early detection of acetic acid-consuming events.

Impact of long-term temperature shifts on activated sludge microbiome dynamics and micropollutant removal

Micropollutants removal efficiency strongly vary across different aerobic wastewater treatment plants, resulting in their frequent detection in surface and ground waters. Seasonal temperature variation is a major factor influencing plant performance, but it is still unclear how prolonged periods of temperature change impact microbiome and micropollutant biotransformation. This work investigates the effect of long-term temperature variation on the microbial dynamics in an activated sludge system, and the impact on micropollutant biotransformation. Sequencing batch reactors were used as model system and 4-40 °C temperature range was studied. 16S rRNA amplicon sequencing showed that temperature drives microbial structure (gDNA) and activity (RNA), rather than time, and this was stronger below 15 °C and above 25 °C. The microbial community was richest and more diverse at 20 °C, while rarer and more specific taxa became predominant over time, at more extreme temperatures. This suggested that less abundant taxa might be responsible for maintaining the biotransformation capability in the activated sludge at extreme temperatures. Micropollutant biotransformation rates mostly deviated from the classic Arrhenius model below 15 °C and above 25 °C, indicating that prolonged exposure to temperature changes leads to temperature-induced taxonomic shifts, resulting in the emerging of different sets of biotransformation pathways over different temperature ranges.

Nitrite accumulation performance and microbial community of Algal-Bacterial symbiotic system constructed by Chlorella sp. And Navicula sp

Chlorella sp. and Navicula sp. were separately used to construct an algal-bacterial symbiotic system in two identical sequencing batch reactors (R1 and R2) to explore the influence of algal species differences on nitrite accumulation. The Navicula-bacterial symbiotic system showed a higher nitrite accumulation efficiency of 85% and a stronger resistance to ammonia load. It secreted twice as many extracellular polymeric substances than the Chlorella-bacterial symbiotic system. Nitrospira and SM1A02 were the dominant functional genera of nitrite-oxidizing bacteria in R1. The dominant functional genus of ammonium-oxidizing bacteria and the dominant functional genus of denitrifying bacteria were Ellin6067 and unclassified_Saprospiraceae in R2, respectively. In general, this research provided some reference for the construction of an algal-bacterial symbiotic system and achieving nitrite accumulation through an algal-bacterial symbiotic system.

Effects of operational parameters on bacterial communities in Hong Kong and global wastewater treatment plants

Wastewater treatment plants (WWTPs) are indispensable biotechnology facilities for modern cities and play an essential role in modern urban infrastructure by employing microorganisms to remove pollutants in wastewater, thus protecting public health and the environment. This study conducted a 13-month bacterial community survey of six full-scale WWTPs in Hong Kong with samples of influent, activated sludge (AS), and effluent to explore their synchronism and asynchronism of bacterial community. Besides, we compared AS results of six Hong Kong WWTPs with data from 1,186 AS amplicon data in 269 global WWTPs and a 9-year metagenomic sequencing survey of a Hong Kong WWTP. Our results showed the compositions of bacterial communities varied and the bacterial community structure of AS had obvious differences across Hong Kong WWTPs. The co-occurrence analysis identified 40 pairs of relationships that existed among Hong Kong WWTPs to show solid associations between two species and stochastic processes took large proportions for the bacterial community assembly of six WWTPs. The abundance and distribution of the functional bacteria in worldwide and Hong Kong WWTPs were examined and compared, and we found that ammonia-oxidizing bacteria had more diversity than nitrite-oxidizing bacteria. Besides, Hong Kong WWTPs could make great contributions to the genome mining of microbial dark matter in the global "wanted list." Operational parameters had important effects on OTUs' abundance, such as the temperature to the genera of Tetrasphaera, Gordonia and Nitrospira. All these results obtained from this study can deepen our understanding of the microbial ecology in WWTPs and provide foundations for further studies.

IMPORTANCE

Wastewater treatment plants (WWTPs) are an indispensable component of modern cities, as they can remove pollutants in wastewater to prevent anthropogenic activities. Activated sludge (AS) is a fundamental wastewater treatment process and it harbors a highly complex microbial community that forms the main components and contains functional groups. Unveiling "who is there" is a long-term goal of the research on AS microbiology. High-throughput sequencing provides insights into the inventory diversity of microbial communities to an unprecedented level of detail. At present, the analysis of communities in WWTPs usually comes from a specific WWTP and lacks comparisons and verification among different WWTPs. The wide-scale and long-term sampling project and research in this study could help us evaluate the AS community more accurately to find the similarities and different results for different WWTPs in Hong Kong and other regions of the world.

Temporal metagenomic characterization of microbial community structure and nitrogen modification genes within an activated sludge bioreactor system

IMPORTANCE

Wastewater treatment plays an essential role in minimizing negative impacts on downstream aquatic environments. Microbial communities are known to play a vital role in the wastewater treatment process, particularly in the removal of nitrogen and phosphorus, which can be especially damaging to aquatic ecosystems. There is limited understanding of how these microbial communities may change in response to fluctuating temperatures or how seasonality may impact their ability to participate in the treatment process. The findings of this study indicate that the microbial communities of wastewater are relatively stable both compositionally and functionally across fluctuating temperatures.

Full-scale demonstration of a floating seal for enhanced biological nutrient removal in a sequencing batch reactor establishing chemical-free environment in wastewater treatment at low carbon source availability

Due to the cyclical nature and changing water levels in the sequencing batch reactor (SBR), oxygen diffusion and utilization can be difficult to control particularly in light of the need to conserve the limited quantity of carbon source required to optimize biological nutrient removal. During the fill period, oxygen penetration may be undesirable since heterotrophic and autotrophic organisms cause a reduction in the readily biodegradable carbon source (rbCOD). This carbon source is essential and often limited in the anaerobic and anoxic periods. As a consequence, unwanted oxygen penetration can hinder efficient biological phosphorus and nitrogen removal. The purpose of the present research was to verify the advantage of a floating seal on the continuously moving surface of an SBR reactor to minimize undesirable oxygen penetration. In the floating seal-covered SBR both nitrification and denitrification efficiency proved to be higher due to insulation, and even during wintertime biological phosphorus removal met target removals without chemical dosing. The SVI values in the two SBR trains proved to be close to each other, despite the high difference in chemical dosing. Having experienced the higher efficiency of the seal-covered train, microbiome compositions of the two differently operated systems were investigated to determine potential differences via 16S rRNA gene amplicon sequencing experiments. In the samples taken from the seal-covered system, higher ratios of fermentative bacteria and phosphate accumulating organisms (PAOs) as well as glycogen accumulating organisms (GAOs) could be observed as compared to the samples deriving from the uncovered system.HighlightsSeal-covering the periodically decreasing open water surface increased SBR efficiencySeal-covering the open water surface increased nitrification efficiency by insulationNo chemical dosing was necessary for phosphorous removal in the Test systemMetagenome investigations provided almost doubled amount of fermentative bacteriaProduction of GAOs indicated nutrient deficiency due to phosphorous removal.

Metagenomics and metatranscriptomics suggest pathways of 3-chloroaniline degradation in wastewater reactors

Biological wastewater treatment systems are often affected by shifts in influent quality, including the input of toxic chemicals. Yet the mechanisms underlying the adaptation of activated sludge process performance are rarely studied in a controlled and replicated experimental setting, particularly when challenged with a sustained toxin input. Three replicate bench-scale bioreactors were subjected to a chemical disturbance in the form of 3-chloroaniline (3-CA) over 132 days, after an acclimation period of 58 days, while three control reactors received no 3-CA input. Ammonia oxidation was initially affected by 3-CA. Within three weeks of the experiment, microbial communities in all three treatment reactors adapted to biologically degrade 3-CA resulting in partial ammonia oxidation recovery. Combining process and microbial community data from amplicon sequencing with potential functions gleaned from assembled metagenomics and metatranscriptomics data, two putative degradation pathways for 3-CA were identified. The first pathway, determined from metagenomics data, involves a benzoate dioxygenase and subsequent meta-cleavage of the aromatic ring. The second, determined from intensive short-term sampling for gene expression data in tandem with 3-CA degradation, involves a phenol monooxygenase followed by ortho-cleavage of the aromatic ring. The relative abundances of amplicon sequence variants associated with the genera Gemmatimonas, OLB8, and Taibaiella correlated significantly with 3-CA degradation. Metagenome-assembled genome data also showed the genus OLB8 to be differentially enriched in treatment reactors, making it a strong candidate as 3-CA degrader. Using replicated reactors, this study has demonstrated the impact of a sustained stress on the activated sludge process. The unique and novel features of this study include the identification of putative pathways and potential degraders of 3-CA using long-term and short-term sampling in tandem with multiple methods in a controlled and replicated experiment.

Ammonium oxidizing bacterial populations in South African activated sludge wastewater treatment plants

This is the first study that describes ammonium oxidizing bacterial populations and correlations of these populations with a range of criteria in activated sludge wastewater treatment plants in South Africa. In this study, not only the influent but also the activated sludge chemistry was comprehensively characterized. Multivariate statistical analyses were used to determine the relative significances of the geographical location (factor: site), wastewater treatment plant process (factor: configuration), seasonality (factor: season), and environmental parameters on the ammonium oxidizing bacterial genera in six municipal activated sludge wastewater treatments plants from two sites (the cities of Cape Town and Ekurhuleni). The geographical location (site) was significant for selection of the ammonium oxidizing genera (Global ANOSIM R value = 0.538, p = 0.001). It was established that the inter-site differences were not climatic in origin, nor related to the composition of the influent, but were rather driven by the activated sludge chemistry. It was found using BEST analysis that the activated sludge ammonia, activated sludge total phosphate, and activated sludge total chemical oxygen demand were the most significant (p < 0.001) drivers for ammonium oxidizing bacterial selection (ANOSIM Global R value 0.419) and were significantly higher in the activated sludge from the City of Cape Town wastewater treatment plants. Nitrosospira was the most abundant ammonium oxidizing bacterial genus, with notably higher relative and estimated actual abundances in the City of Cape Town wastewater treatment plants than the City of Ekurhuleni wastewater treatment plants. The strong selection of Nitrosospira in the City of Cape Town wastewater treatment plants with higher nutrient concentrations strongly suggests that high concentrations of activated sludge ammonia, activated sludge total phosphate, and activated sludge total chemical oxygen demand are key selective drivers for this genus. PRACTITIONER POINTS: First comprehensive study describing ammonium oxidizing bacterial populations in Southern African domestic activated sludge wastewater treatment plants. The geographical location (site) was significant for selection of different ammonium oxidizing genera (Global ANOSIM R value = 0.538, p = 0.001). Inter-site differences driven by the activated sludge chemistry, not climate or influent wastewater composition. Selection of Nitrosospira driven by high concentrations of activated sludge ammonia, total phosphate and total chemical oxygen demand.

The role of the core microorganisms in the microbial interactions in activated sludge

In order to gain a deeper understanding of the microbial interactions in wastewater treatment plants (WWTPs) in China and clarify the role of the core community in the microbial interactions in activated sludge (AS), this study used a molecular ecological network approach based on random matrix theory to construct co-occurrence networks of the core microorganisms (CoreN), the whole AS community (WholeN) and the microbial communities without the core microorganisms (OtherN), respectively. It was shown that the WholeN had more complex and tighter connections compared with the OtherN, because of its higher total number of nodes, higher average clustering coefficient, and shorter average geodesic distance. The proportions of positive links in the CoreN, WholeN and OtherN were gradually decreased, indicating that the core microorganisms promoted cooperation between AS microorganisms. Moreover, higher robustness after random removal of 50% of the nodes of the WholeN (0.2836 ± 0.0311) was observed than the robustness of the OtherN (0.1152 ± 0.0263). In addition, the vulnerability of OtherN (0.0514) is significantly higher than WholeN (0.0225). Meanwhile, the average ratio of negative/positive cohesion, was significantly decreased when the core microorganisms were removed. These results demonstrated that core community could strengthen the stability of the ecological network in AS. By discerning the key factors affecting ecological network, AS temperature was observed to have a strong correlation with all three networks. Moreover, pollutants in wastewater shown stronger correlations with the CoreN and WholeN, supporting the point that core community play a critical role in pollutant removal in WWTPs to a certain extent.

Toward Integrating EBPR and the Short-Cut Nitrogen Removal Process in a One-Stage System for Treating High-Strength Wastewater

Enhanced biological phosphorus removal (EBPR) is an economical and sustainable process for phosphorus removal from wastewater. Despite the widespread application of EBPR for low-strength domestic wastewater treatment, limited investigations have been conducted to apply EBPR to the high-strength wastewaters, particularly, the integration of EBPR and the short-cut nitrogen removal process in the one-stage system remains challenging. Herein, we reported a novel proof-of-concept demonstration of integrating EBPR and nitritation (oxidation of ammonium to nitrite) in a one-stage sequencing batch reactor to achieve simultaneous high-strength phosphorus and short-cut nitrogen removal. Excellent EBPR performance of effluent 0.8 ± 1.0 mg P/L and >99% removal efficiency was achieved fed with synthetic high-strength phosphorus wastewater. Long-term sludge acclimation proved that the dominant polyphosphate accumulating organisms (PAOs), Candidatus Accumulibacter, could evolve to a specific subtype that can tolerate the nitrite inhibition as revealed by operational taxonomic unit (OTU)-based oligotyping analysis. The EBPR kinetic and stoichiometric evaluations combined with the amplicon sequencing proved that the Candidatus Competibacter, as the dominant glycogen accumulating organisms (GAOs), could well coexist with PAOs (15.3-24.9% and 14.2-33.1%, respectively) and did not deteriorate the EBPR performance. The nitrification activity assessment, amplicon sequencing, and functional-based gene marker quantification verified that the unexpected nitrite accumulation (10.7-21.0 mg N/L) in the high-strength EBPR system was likely caused by the nitritation process, in which the nitrite-oxidizing bacteria (NOB) were successfully out-selected (<0.1% relative abundance). We hypothesized that the introduction of the anaerobic phase with high VFA concentrations could be the potential selection force for achieving nitritation based on the literature review and our preliminary batch tests. This study sheds light on developing a new feasible technical route for integrating EBPR with short-cut nitrogen removal for efficient high-strength wastewater treatment.

Seasonal prevalence of bacteria in the outflow of two full-scale municipal wastewater treatment plants

Despite many modern wastewater treatment solutions, the most common is still the use of activated sludge (AS). Studies indicate that the microbial composition of AS is most often influenced by the raw sewage composition (especially influent ammonia), biological oxygen demand, the level of dissolved oxygen, technological solutions, as well as the temperature of wastewater related to seasonality. The available literature mainly refers to the relationship between AS parameters or the technology used and the composition of microorganisms in AS. However, there is a lack of data on the groups of microorganisms leaching into water bodies whose presence is a signal for possible changes in treatment technology. Moreover, sludge flocs in the outflow contain less extracellular substance (EPS) which interferes microbial identification. The novelty of this article concerns the identification and quantification of microorganisms in the AS and in the outflow by fluorescence in situ hybridization (FISH) method from two full-scale wastewater treatment plants (WWTPs) in terms of 4 key groups of microorganisms involved in the wastewater treatment process in the context of their potential technological usefulness. The results of the study showed that Nitrospirae, Chloroflexi and Ca. Accumulibacter phosphatis in treated wastewater reflect the trend in abundance of these bacteria in activated sludge. Increased abundance of betaproteobacterial ammonia-oxidizing bacteria and Nitrospirae in the outflow were observed in winter. Principal component analysis (PCA) showed that loadings obtained from abundance of bacteria in the outflow made larger contributions to the variance in the PC1 factorial axis, than loadings obtained from abundance of bacteria from activated sludge. PCA confirmed the reasonableness of conducting studies not only in the activated sludge, but also in the outflow to find correlations between technological problems and qualitative and quantitative changes in the outflow microorganisms.

Universal Dynamics of Microbial Communities in Full-Scale Textile Wastewater Treatment Plants and System Prediction by Machine Learning

The performance of full-scale biological wastewater treatment plants (WWTPs) depends on the operational and environmental conditions of treatment systems. However, we do not know how much these conditions affect microbial community structures and dynamics across systems over time and predictability of the treatment performance. For over a year, the microbial communities of four full-scale WWTPs processing textile wastewater were monitored. During temporal succession, the environmental conditions and system treatment performance were the main drivers, which explained up to 51% of community variations within and between all plants based on the multiple regression models. We identified the universality of community dynamics in all systems using the dissimilarity-overlap curve method, with the significant negative slopes suggesting that the communities containing the same taxa from different plants over time exhibited a similar composition dynamic. The Hubbell neutral theory and the covariance neutrality test indicated that all systems had a dominant niche-based assembly mechanism, supporting that the communities had a similar composition dynamic. Phylogenetically diverse biomarkers for the system conditions and treatment performance were identified by machine learning. Most of the biomarkers (83%) were classified as generalist taxa, and the phylogenetically related biomarkers responded similarly to the system conditions. Many biomarkers for treatment performance perform functions that are crucial for wastewater treatment processes (e.g., carbon and nutrient removal). This study clarifies the relationships between community composition and environmental conditions in full-scale WWTPs over time.

Ammonia-Oxidizing Bacteria Maintain Abundance but Lower amoA-Gene Expression during Cold Temperature Nitrification Failure in a Full-Scale Municipal Wastewater Treatment Plant

In this study, we explore the relationship between community structure and transcriptional activity of ammonia-oxidizing bacteria during cold temperature nitrification failure in three parallel full-scale sequencing batch reactors (SBRs) treating municipal wastewater. In the three reactors, ammonia concentrations increased with declines in wastewater temperature below 15°C. We quantified and sequenced 16S rRNA and ammonia monooxygenase (amoA) gene fragments in DNA and RNA extracts from activated sludge samples collected from the SBRs during the warmer seasons (summer and fall) and when water temperatures were below 15°C (winter and spring). Taxonomic community composition of amoA genes and transcripts did not vary much between the warmer and colder seasons. However, we observed significant differences in amoA transcript copy numbers between fall (highest) and spring (lowest). Ammonia-oxidizing bacteria of the genus Nitrosomonas sp. could maintain their population abundance despite lowering their amoA gene expression during winter and spring. In spite of relatively low population abundance, an amoA amplicon sequence variant (ASV) cluster identified as most similar to the amoA gene of Nitrosospira briensis showed the highest amoA transcript-to-gene ratio throughout all four seasons, indicating that some nitrifiers remain active at wastewater temperatures below 15°C. Our results show that 16S rRNA and amoA gene copy numbers are limited predictors of cell activity. To optimize function and performance of mixed community bioprocesses, we need to collect high-resolution quantitative transcriptomic and potentially proteomic data to resolve the response of individual species to changes in environmental parameters in engineered systems. IMPORTANCE The diverse microbial community of activated sludge used in biological treatment systems exhibits dynamic seasonal shifts in community composition and activity. Many wastewater treatment plants in temperate/continental climates experience seasonal cold temperature nitrification failure. "Seasonal nitrification failure" is the discharge of elevated concentrations of ammonia (greater than 4 mg/liter) with treated wastewater during the winter (influent wastewater temperatures below 13°C). This study aims at expanding our understanding of how ammonia-oxidizing bacteria in activated sludge change in activity and growth across seasons. We quantified the ammonia monooxygenase (amoA) gene and transcript copy numbers using real-time PCR and sequenced the amoA amplicons to reveal community structure and activity changes of nitrifying microbial populations during seasonal nitrification failure in three full-scale sequencing batch reactors (SRBs) treating municipal wastewater. Relevant findings presented in this study contribute to explain seasonal nitrification performance variability in SRBs.

Multi-omics analysis on seasonal variations of the biofilm microbial community in a full-scale pre-denitrification biofilter

The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.

Full-scale activated sludge transplantation reveals a highly resilient community structure

Well-functioning and stable microbial communities are critical for the operation of activated sludge (AS) wastewater treatment plants (WWTPs). Bioaugmentation represents a potentially useful approach to recover deteriorated systems or to support specific AS processes, but its application in full-scale WWTPs is generally problematic. We conducted a massive transplantation (in one day) exchanging AS from a donor to a recipient full-scale WWTP with similar process type (biological removal of nitrogen and phosphorus) and performance, but with differences in microbial community structure. The treatment performance in the recipient plant was not compromised and the effluent quality remained stable. The AS community structure of the recipient plant was initially very similar to the donor AS, but it almost completely restored the pre-transplantation structure approximately 40 days after transplantation, corresponding to 3 times the solid retention time. Most of the unique species of donor AS added to recipient AS disappeared quickly, although some disappeared more slowly the following months, indicating some survival and potentially a time limited function in the recipient plant. Moreover, the addition in higher abundance of most species already present in the recipient AS (e.g., the polyphosphate accumulating organisms) or the reduction of the abundance of unwanted bacteria (e.g., filamentous bacteria) in the recipient plant was not successful. Moreover, we observed similar abundance patterns after transplantation for species belonging to different functional guilds, so we did not observe an increase of the functional redundancy. Investigations of the microbial community structure in influent wastewater revealed that for some species the abundance trends in the recipient plant were closely correlated to their abundance in the influent. We showed that a very resilient microbial community was responsible for the outcome of the transplantation of AS at full-scale WWTP, potentially as a consequence of mass-immigration from influent wastewater. The overall results imply that massive transplantation of AS across different WWTPs is not a promising strategy to permanently solve operational problems. However, by choosing a compatible AS donor, short term mitigation of serious operational problems may be possible.

Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge

The recovery of metagenome-assembled genomes is biased towards the most abundant species in a given community. To improve the identification of species, even if only dominant species are recovered, we investigated the integration of flow cytometry cell sorting with bioinformatics tools to recover metagenome-assembled genomes. We used a cell culture of a wastewater microbial community as our model system. Cells were separated based on fluorescence signals via flow cytometry cell sorting into sub-communities: dominant gates, low abundant gates, and outer gates into subsets of the original community. Metagenome sequencing was performed for all groups. The unsorted community was used as control. We recovered a total of 24 metagenome-assembled genomes (MAGs) representing 11 species-level genome operational taxonomic units (gOTUs). In addition, 57 ribosomal operational taxonomic units (rOTUs) affiliated with 29 taxa at species level were reconstructed from metagenomic libraries. Our approach suggests a two-fold increase in the resolution when comparing sorted and unsorted communities. Our results also indicate that species abundance is one determinant of genome recovery from metagenomes as we can recover taxa in the sorted libraries that are not present in the unsorted community. In conclusion, a combination of cell sorting and metagenomics allows the recovery of MAGs undetected without cell sorting.

Seasonal characterization of the prokaryotic microbiota of full-scale anaerobic UASB reactors treating domestic sewage in southern Brazil

Upflow Anaerobic Sludge Blanket (UASB) reactors are alternatives in the anaerobic treatment of sanitary sewage in different parts of the world; however, in temperate environments, they are subject to strong seasonal influence. Understanding the dynamics of the microbial community in these systems is essential to propose operational alternatives, improve projects and increase the quality of treated effluents. In this study, for one year, high-performance sequencing, associated with bioinformatics tools for taxonomic annotation and functional prediction was used to characterize the microbial community present in the sludge of biodigesters on full-scale, treating domestic sewage at ambient temperature. Among the most representative phyla stood out Desulfobacterota (20.21-28.64%), Proteobacteria (7.48-24.90%), Bacteroidota (10.05-18.37%), Caldisericota (9.49-17.20%), and Halobacterota (3.23-6.55%). By performing a Canonical Correspondence Analysis (CCA), Methanolinea was correlated to the efficiency in removing Chemical Oxygen Demand (COD), Bacteroidetes_VadinHA17 to the production of volatile fatty acids (VFAs), and CI75cm.2.12 at temperature. On the other hand, Desulfovibrio, Spirochaetaceae_uncultured, Methanosaeta, Lentimicrobiaceae_unclassified, and ADurb.Bin063-1 were relevant in shaping the microbial community in a co-occurrence network. Diversity analyses showed greater richness and evenness for the colder seasons, possibly, due to the lesser influence of dominant taxa. Among the principal metabolic functions associated with the community, the metabolism of proteins and amino acids stood out (7.74-8.00%), and the genes related to the synthesis of VFAs presented higher relative abundance for the autumn and winter. Despite the differences in diversity and taxonomic composition, no significant changes were observed in the efficiency of the biodigesters.

Comparing with oxygen, nitrate simplifies microbial community assembly and improves function as an electron acceptor in wastewater treatment

Biochemical oxidation and reduction are key processes in treating biological wastewater and they require the presence of electron acceptors. The functional impact of electron acceptors on microbiomes provides strategies for improving the treatment efficiency. This research focused on two of the most important electron acceptors, nitrate and oxygen. Molecule ecological network, null model, and functional prediction based on high-throughput sequencing were used to analyze the microbiomes features and assembly mechanism. The results revealed nitrate via the homogeneous selection (74.0%) decreased species diversity, while oxygen via the homogeneous selection (51.1%) and dispersal limitation (29.6%) increased the complexity of community structure. Microbes that were more strongly homogeneously selected for assembly included polyphosphate accumulating organisms (PAOs), such as Pseudomonas and variovorax in the nitrate impacted community; Pseudomonas, Candidatus_Accumulibacter, Thermomonas and Dechloromonas, in the oxygen impacted community. Nitrate simplified species interaction and increased the abundance of functional genes involving in tricarboxylic acid cycle (TCA cycle), electron transfer, nitrogen metabolism, and membrane transport. These findings contribute to our knowledge of assembly process and interactions among microorganisms and lay a theoretical basis for future microbial regulation strategies in wastewater treatment.

New insights into modeling two-step nitrification in activated sludge systems - The effects of initial biomass concentrations, comammox and heterotrophic activities

In this study, the conventional two-step nitrification model was extended with complete ammonia oxidation (comammox) and heterotrophic denitrification on soluble microbial products. The data for model calibration/validation were collected at four long-term washout experiments when the solid retention time (SRT) and hydraulic retention time (HRT) were progressively reduced from 4 d to 1 d, with mixed liquor suspended solids (MLSS) of approximately 2000 mg/L at the start of each trial. A new calibration protocol was proposed by including a systematic calculation of the initial biomass concentrations and microbial relationships as the calibration targets. Moreover, the impact assessment of initial biomass concentrations (X) and maximum growth rates (μ) for ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), comammox Nitrospira, and heterotrophs on the calibration accuracy were investigated using the response surface methodology (RSM). The RSM results revealed the strongest interaction of X_AOB and μ_AOB on the model calibration accuracy. All the examined model efficiency measures confirmed that the extended model was accurately calibrated and validated. The estimated μ values were as follows: μ_AOB = 0.38 ± 0.005 d^-1, μ_NOB = 0.20 ± 0.01 d^-1, μ_CMX = 0.20 ± 0.01 d^-1, μ_HET = 1.0 ± 0.03 d^-1. For comparison, when using the conventional model, μ_AOB and μ_NOB increased respectively by 26 and 15 % (μ_AOB = 0.48 ± 0.02 d^-1 and μ_NOB = 0.23 ± 0.005 d^-1). This study provides better understanding of the effects of the initial biomass composition and the accompanying processes (comammox and heterotrophic denitrification) on modeling two-step nitrification.

Initial pH Conditions Shape the Microbial Community Structure of Sewage Sludge in Batch Fermentations for the Improvement of Volatile Fatty Acid Production

Conversion of wastewater treatment plants into biorefineries is a sustainable alternative for obtaining valuable compounds, thus reducing pollutants and costs and protecting the environment and human health. Under specific operating conditions, microbial fermentative products of sewage sludge are volatile fatty acids (VFA) that can be precursors of polyhydroxyalkanoate thermoplastic polyesters. The role of various operating parameters in VFA production has yet to be elucidated. This study aimed to correlate the levels of VFA yields with prokaryotic microbiota structures of sewage sludge in two sets of batch fermentations with an initial pH of 8 and 10. The sewage sludge used to inoculate the batch fermentations was collected from a Sicilian WWTP located in Marineo (Italy) as a case study. Gas chromatography analysis revealed that initial pH 10 stimulated chemical oxygen demands (sCOD) and VFA yields (2020 mg COD/L) in comparison with initial pH 8. Characterization of the sewage sludge prokaryotic community structures—analyzed by next-generation sequencing of 16S rRNA gene amplicons—demonstrated that the improved yield of VFA paralleled the increased abundance of fermenting bacteria belonging to Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes phyla and, conversely, the reduced abundance of VFA-degrading strains, such as archaeal methanogens.

Insights into the microbial community of treated wastewater, its year-round variability and impact on the receiver, using cultivation, microscopy and amplicon-based methods

Apart from chemical constituents, wastewater treatment plant (WWTP) effluents also release microorganisms that can be important to the receiving water bodies either from a sanitary point of view, or taking to the account the biogeochemical potential of the recipients. However, little is known about the treated wastewater microbial community, its composition, seasonal changes, functions and fate in the waters of the receiver. Thus, this study presents a synergistic approach coupling new and traditional methods: analytical chemistry, classical microbiology (cultivation- and microscopy-based methods), as well as Next Generation Sequencing and a quantitative real-time polymerase chain reaction (qPCR). The results show that in terms of bacterial community composition, treated wastewater differed from the environmental samples, irrespectively if they were related or unrelated to the WWTP effluent discharge. The canonical correspondence analysis (CCA) taking into account chemical parameters and taxonomical biodiversity indirectly confirmed the seasonal deterioration of the treated wastewater quality as a result of temperature-driven change of activated sludge community structure and biomass washout (observed also by DAPI staining). Despite seasonal fluctuations of total suspended solids and inter-related parameters (such as COD, BOD, TN, TP), the treated wastewater quality remained within current discharge limits. It was due to treatment processes intensively adjusted by WWTP operators, particularly those necessary to maintain an appropriate rate of autotrophic processes of nitrification and to support biological phosphorus removal. This can explain the observed microbiome composition similarity among WWTP effluents at high taxonomic levels. Obtained data also suggest that besides wastewater treatment efficiency, WWTP effluents are still sources of both human-related microorganisms as well as bacteria equipped in genes involved in N-cycling. Their potential of participation in nutrients cycling in the receivers is widely unknown and require critical attention and better understanding.

Microbial response on the first full-scale DEMON® biomass transfer for mainstream deammonification

Sidestream partial nitritation and deammonification (pN/A) of high-strength ammonia wastewater is a well-established technology. Its expansion to the mainstream is, however mainly impeded by poor retention of anaerobic ammonia oxidizing bacteria (AnAOB), insufficient repression of nitrite oxidizing bacteria (NOB) and difficult control of soluble chemical oxygen demand and nitrite levels. At the municipal wastewater treatment plant in Strass (Austria) the microbial consortium was exhaustively monitored at full-scale over one and a half year with regular transfer of sidestream DEMON® biomass and further retention and enrichment of granular anammox biomass via hydrocyclone operation. Routine process parameters were surveyed and the response and evolution of the microbiota was followed by molecular tools, ex-situ activity tests and further, AnAOB quantification through particle tracking and heme measurement. After eight months of operation, the first anaerobic, simultaneous depletion of ammonia and nitrite was observed ex-situ, together with a direction to higher nitrite generation (68% of total NO_x-N) as compared to nitrate under aerobic conditions. Our dissolved oxygen (DO) scheme allowed for transient anoxic conditions and had a strong influence on nitrite levels and the NOB community, where Nitrobacter eventually dominated Nitrospira. The establishment of a minor but stable AnAOB biomass was accompanied by the rise of Chloroflexi and distinct emergence of Chlorobi, a trend not seen in the sidestream system. Interestingly, the most pronounced switch in the microbial community and noticeable NOB repression occurred during unfavorable conditions, i.e. the cold winter season and high organic load. Further abatement of NOB was achieved through bioaugmentation of aerobic ammonia oxidizing bacteria (AerAOB) from the sidestream-DEMON® tank. Performance of the sidestream pN/A was not impaired by this operational scheme and the average volumetric nitrogen removal rate of the mainstream even doubled in the second half of the monitoring campaign. We conclude that a combination of both, regular sidestream-DEMON® biomass transfer and granular SRT increase via hydrocyclone operation was crucial for AnAOB establishment within the mainstream.

Variations of nitrogen-metabolizing enzyme activity and microbial community under typical loading conditions in full-scale leachate anoxic/aerobic system

Influent loading determines the performance of leachate treatment plant (LTP) facing the dynamic conditions, but enzyme expression in microbial community is unclear. Here, six nitrogen-metabolizing enzymes were detected during nitrification failures (NF), high loading (HL), low loading (LL), and low carbon/nitrogen (LCN) in a 500 m³/d LTP. Nitrogen removal in LL was 15 ± 5% higher than that in HL. The activity of hydroxylamine oxidoreductase decreased by 90% as the influent total nitrogen increased from 2450 mg/L to 3100 mg/L, which might be a critical enzyme causing the nitrification failure. Denitrifying enzyme abated by 1.3% as the carbon/nitrogen dropped by 1% in LCN. With the influent chemical oxygen demand decreased from 22000 mg/L to 12000 mg/L, the relative abundance of norank_f_Saprospiraceae dropped from 33.66% to 11.94%, and finally disappeared, which seems to be an indicator of the high load operation. These findings provide the basis for improving the efficiency of LTPs.

Occurrence of antibiotic resistance genes and multidrug-resistant bacteria during wastewater treatment processes

Wastewater treatment plants (WWTPs) constantly receive a wide variety of contaminants, including pharmaceuticals, and are potential reservoirs of antibiotic resistance genes (ARGs). This favors the development of multidrug-resistant bacteria (MRB) through horizontal gene transfer. Samples from five different WWTP processes were collected in September 2020 and January 2021 to monitor ARG resistomes and culturable MRB in the presence of eight different antibiotics. Nanopore-based ARG abundance and bacterial community analyses suggested that ARG accumulation favors the generation of MRB. Activated and mixed sludges tended to have lower bacterial diversity and ARG abundance because of selective forces that favored the growth of specific microorganisms during aeration processes. Escherichia strains enriched in WWTPs (up to 71%) were dominant in all the samples, whereas Cloacamonas species were highly abundant only in anaerobically digested sludge samples (60%-79%). Two ARG types [sulfonamide resistance genes (sul1) and aminoglycoside resistance genes (aadA1, aadA13, and aadA2)] were prevalent in all the processes. The total counts of culturable MRB, such as Niabella, Enterococcus, Bacillus, and Chryseobacterium species, gradually increased during aerobic WWTP processes. Genomic analyses of all MRB isolated from the samples revealed that the resistome of Enterococcus species harbored the highest number of ARGs (7-18 ARGs), commonly encoding ant(6)-la, lnu(B), erm(B), and tet(S/M). On the other hand, Niablella strains possibly had intrinsic resistant phenotypes without ARGs. All MRB possessed ARGs originating from the same mobile genetic elements, suggesting that WWTPs are hotspots for the migration of ARGs and emergence of MRB.

The Potential of Sewage Sludge to Predict and Evaluate the Human Chemical Exposome

Chemicals are part of our daily lives, and we are exposed to numerous chemicals through multiple pathways. Relevant scientific evidence contributing to the regulation of hazardous chemicals require a holistic approach to assess simultaneous exposure to multiple compounds. Biomonitoring provides an accurate estimation of exposure to chemicals through very complex and costly sampling campaigns. Finding efficient proxies to predict the risk of chemical exposure in humans is an urgent need to cover large areas and populations at a reasonable cost. We conducted an exploratory study to characterize the human chemical exposome in maternal blood and placenta samples of a population-based birth cohort in Barcelona (2018-2021). Ultimate HRMS-based approaches were applied including wide-scope target, suspect, and nontarget screening. Forty-two chemicals were identified including pesticides, personal care products, or industrial compounds, among others, in the range of ng/mL and ng/g. In parallel, sewage sludge from the wastewater treatment plants serving the residence areas of the studied population were also screened, showing correlations with the type and concentrations of chemicals found in humans. Our findings were suggestive for the potential use of sewage sludge as a proxy of the human exposure and its application in early warning systems to prevent bioaccumulation of hazardous chemicals.

Evaluating acute toxicity in enriched nitrifying cultures: Lessons learned

Toxicological batch assays are essential to assess a compound's acute effect on microorganisms. This methodology is frequently employed to evaluate the effect of contaminants in sensitive microbial communities from wastewater treatment plants (WWTPs), such as autotrophic nitrifying populations. However, despite nitrifying batch assays being commonly mentioned in the literature, their experimental design criteria are rarely reported or overlooked. Here, we found that slight deviations in culture preparations and conditions impacted bacterial community performance and could skew assay results. From pre-experimental trials and experience, we determined how mishandling and treatment of cultures could affect nitrification activity. While media and biomass preparations are needed to establish baseline conditions (e.g., biomass washing), we found extensive centrifugation selectively destabilised nitrification activities. Further, it is paramount that the air supply is adjusted to minimise nitrite build-up in the culture and maintain suitable aeration levels without sparging ammonia. DMSO and acetone up to 0.03% (v/v) were suitable organic solvents with minimal impact on nitrification activity. In the nitrification assays with allylthiourea (ATU), dilute cultures exhibited more significant inhibition than concentrated cultures. So there were biomass-related effects; however, these differences minimally impacted the EC₅₀ values. Using different nutrient-media compositions had a minimal effect; however, switching mineral media for the toxicity test from the original cultivation media is not recommended because it reduced the original biomass nitrification capacity. Our results demonstrated that these factors substantially impact the performance of the nitrifying inoculum used in acute bioassays, and consequently, affect the response of AOB-NOB populations during the toxicant exposure. These are not highlighted in operation standards, and unfortunately, they can have significant consequential impacts on the determinations of toxicological endpoints. Moreover, the practical procedures tested here could support other authors in developing testing methodologies, adding quality checks in the experimental framework with minimal waste of time and resources.

Pharmaceuticals and personal care products' (PPCPs) impact on enriched nitrifying cultures

The impact of pharmaceutical and personal care products (PPCPs) on the performance of biological wastewater treatment plants (WWTPs) has been widely studied using whole-community approaches. These contaminants affect the capacity of microbial communities to transform nutrients; however, most have neither honed their examination on the nitrifying communities directly nor considered the impact on individual populations. In this study, six PPCPs commonly found in WWTPs, including a stimulant (caffeine), an antimicrobial agent (triclosan), an insect repellent ingredient (N,N-diethyl-m-toluamide (DEET)) and antibiotics (ampicillin, colistin and ofloxacin), were selected to assess their short-term toxic effect on enriched nitrifying cultures: Nitrosomonas sp. and Nitrobacter sp. The results showed that triclosan exhibited the greatest inhibition on nitrification with EC₅₀ of 89.1 μg L^-1. From the selected antibiotics, colistin significantly affected the overall nitrification with the lowest EC₅₀ of 1 mg L^-1, and a more pronounced inhibitory effect on ammonia-oxidizing bacteria (AOB) compared to nitrite-oxidizing bacteria (NOB). The EC₅₀ of ampicillin and ofloxacin was 23.7 and 12.7 mg L^-1, respectively. Additionally, experimental data suggested that nitrifying bacteria were insensitive to the presence of caffeine. In the case of DEET, moderate inhibition of nitrification (<40%) was observed at 10 mg L^-1. These findings contribute to the understanding of the response of nitrifying communities in presence of PPCPs, which play an essential role in biological nitrification in WWTPs. Knowing specific community responses helps develop mitigation measures to improve system resilience.

Microbial Community Composition in Municipal Wastewater Treatment Bioreactors Follows a Distance Decay Pattern Primarily Controlled by Environmental Heterogeneity

Understanding spatiotemporal patterns in microbial community composition is a central goal of microbial ecology. The objective of this study was to better understand the biogeography of activated sludge microbial communities, which are important for the protection of surface water quality. Monthly samples were collected from 20 facilities (25 bioreactors) within 442 km of each other for 1 year. Microbial community composition was characterized by sequencing of PCR-amplified 16S rRNA gene fragments. Statistically significant distance decay of community similarity was observed in these bioreactors independent of clustering method (operational taxonomic units [OTUs] at 97% similarity, genus-level phylotypes) and community dissimilarity metric (Sørensen, Bray-Curtis, and weighted Unifrac). Universal colonizers (i.e., detected in all samples) and ubiquitous genus-level phylotypes (i.e., detected in every facility at least once) also exhibited a significant distance decay relationship. Variation partitioning analysis of community composition showed that environmental characteristics (temperature, influent characteristics, etc.) explained more of the variance in community composition than geographic distance did, suggesting that environmental heterogeneity is more important than dispersal limitation as a mechanism for determining microbial community composition. Distance decay relationships also became stronger with increasing distance between facilities. Seasonal variation in community composition was also observed from selected bioreactors, but there was no clear seasonal pattern in the distance decay relationships.

IMPORTANCE Understanding the spatiotemporal patterns of biodiversity is a central goal of ecology. The distance decay of community similarity is one of the spatial scaling patterns observed in many forms of life, including plants, animals, and microbial communities. Municipal wastewater treatment relies on microorganisms to prevent the release of excessive quantities of nutrients and other pollutants, but relatively few studies have explored distance decay relationships in wastewater treatment bioreactors. Our results demonstrate a strong distance decay pattern in wastewater treatment bioreactors, regardless of the sequence clustering method or the community dissimilarity metric. Our results suggest that microbial communities in wastewater treatment bioreactors are not randomly assembled but rather exhibit a statistically significant spatial pattern.

Tracking de novo protein synthesis in the activated sludge microbiome using BONCAT-FACS

In order to ensure stable performance of engineered biotechnologies that rely on mixed microbial community systems, it is important to identify process-specific microbial traits and study their in-situ activity and responses to changing environmental conditions and system operational parameters. We used BioOrthogonal Non-Canonical Amino acid Tagging (BONCAT) in combination with Fluorescence-Activated Cell Sorting (FACS) and 16S rRNA gene amplicon sequencing to identify translationally active cells in activated sludge. We found that only a subset of the activated sludge microbiome is translationally active during the aerobic treatment phase of a full-scale sequencing batch reactor designed to enhance biological phosphorus removal from municipal wastewater. Relative abundance of amplicon sequence variants was not a reliable predictor of species activity. BONCAT-positive and -negative cells revealed a broad range of population-wide and taxa-specific translational heterogeneity. BONCAT-FACS in combination with amplicon sequencing can provide new insights into the ecophysiology of highly dynamic microbiomes in activated sludge systems.

Relevance of Candidatus Nitrotoga for nitrite oxidation in technical nitrogen removal systems

Abstract

Many biotechnological applications deal with nitrification, one of the main steps of the global nitrogen cycle. The biological oxidation of ammonia to nitrite and further to nitrate is critical to avoid environmental damage and its functioning has to be retained even under adverse conditions. Bacteria performing the second reaction, oxidation of nitrite to nitrate, are fastidious microorganisms that are highly sensitive against disturbances. One important finding with relevance for nitrogen removal systems was the discovery of the mainly cold-adapted Cand. Nitrotoga, whose activity seems to be essential for the recovery of nitrite oxidation in wastewater treatment plants at low temperatures, e.g., during cold seasons. Several new strains of this genus have been recently described and ecophysiologically characterized including genome analyses. With increasing diversity, also mesophilic Cand. Nitrotoga representatives have been detected in activated sludge. This review summarizes the natural distribution and driving forces defining niche separation in artificial nitrification systems. Further critical aspects for the competition with Nitrospira and Nitrobacter are discussed. Knowledge about the physiological capacities and limits of Cand. Nitrotoga can help to define physico-chemical parameters for example in reactor systems that need to be run at low temperatures.

Key points

• Characterization of the psychrotolerant nitrite oxidizer Cand. Nitrotoga

• Comparison of the physiological features of Cand. Nitrotoga with those of other NOB

• Identification of beneficial environmental/operational parameters for proliferation

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11487-5.

Different Engineering Designs Have Profoundly Different Impacts on the Microbiome and Nitrifying Bacterial Populations in Municipal Wastewater Treatment Bioreactors

Numerous wastewater treatment processes are designed by engineers to achieve specific treatment goals. However, the impact of these different process designs on bacterial community composition is poorly understood. In this study, 24 different municipal wastewater treatment facilities (37 bioreactors) with various system designs were analyzed by sequencing of PCR-amplified 16S rRNA gene fragments. Although a core microbiome was observed in all of the bioreactors, the overall microbial community composition (analysis of molecular variance; P = 0.001) as well as that of a specific population of Nitrosomonas spp. (P = 0.04) was significantly different between A/O (anaerobic/aerobic) systems and conventional activated sludge (CAS) systems. Community α-diversity (number of observed operational taxonomic units [OTUs] and Shannon diversity index) was also significantly higher in A/O systems than in CAS systems (Wilcoxon; P < 2 × 10^-16). In addition, wastewater bioreactors with short mean cell residence time (<2 days) had very low community α-diversity and fewer nitrifying bacteria compared to those of other system designs. Nitrospira spp. (0.71%) and Nitrotoga spp. (0.41%) were the most prominent nitrite-oxidizing bacteria (NOB); because these two genera were rarely prominent at the same time, these populations appeared to be functionally redundant. Weak evidence (AOB:NOB « 2; substantial quantities of Nitrospira sublineage II) was also obtained suggesting that complete ammonia oxidation by a single organism was occurring in system designs known to impose stringent nutrient limitation. This research demonstrates that design decisions made by wastewater treatment engineers significantly affect the microbiome of wastewater treatment bioreactors. IMPORTANCE Municipal wastewater treatment facilities rely on the application of numerous "activated sludge" process designs to achieve site-specific treatment goals. A plethora of microbiome studies on municipal wastewater treatment bioreactors have been performed previously; however, the role of process design on the municipal wastewater treatment microbiome is poorly understood. In fact, wastewater treatment engineers have attempted to control the microbiome of wastewater bioreactors for decades without sufficient empirical evidence to support their design paradigms. Our research demonstrates that engineering decisions with respect to system design have a significant impact on the microbiome of wastewater treatment bioreactors.

Resilience and life cycle assessment of ion exchange process for ammonium removal from municipal wastewater

This study was completed to understand the resilience of an ion exchange (IEX) process for its ability to remove variable ammonium (NH₄⁺-N) loads) and to prove its environmental benefits through a life cycle assessment (LCA). The tertiary 10 m³/day demonstration scale IEX was fed with variable NH₄⁺-N concentrations (<0.006-26 mg NH₄⁺-N /L) naturally found in municipal wastewater. Zeolite-N was used as ion exchange media and regeneration was completed with 10% potassium chloride (KCl). The influent NH₄⁺-N concentration impacted the ion exchange capacity, which ranged from 0.9-17.7 mg NH₄⁺-N/g media. When the influent concentration was <2.5 mg NH₄⁺-N/L, the Zeolite-N released NH₄⁺-N (up to 12%). However, the exchange increased up to 62% when the influent NH₄⁺-N load peaked, confirming the resilience of the process. A 94% regeneration efficiency was obtained with fresh regenerant, however, with the increase of the mass of NH₄⁺-N on the media, the regeneration efficiency decreased. An optimisation of the volume of brine and regeneration contact time is suggested. To further measure the benefits of the IEX process, an LCA was conducted, for a 10,000 population equivalent reference scenario, and compared with traditional nitrification-denitrification WWTP. The LCA revealed that IEX with regenerant re-use and NH₄⁺-N recovery through a membrane stripping process resulted in reductions of: 25% cumulative energy demand; 66% global warming potential and 62% marine eutrophication potential, when compared to traditional WWTP. This work demonstrated that the IEX process is an efficient and an environmentally benign technology that can be widely applied in WWTPs.

Dissolved oxygen concentrations affect the function but not the relative abundance of nitrifying bacterial populations in full-scale municipal wastewater treatment bioreactors during cold weather

This study aimed to understand the effect of different dissolved oxygen (DO) concentrations on the abundance and performance of nitrifying bacteria in full-scale wastewater treatment bioreactors, particularly during the winter when nitrifying bacterial activity is often negligible. Biomass samples were collected from three parallel full-scale bioreactors with low DO concentrations (<1.3 mg/ L) and from two full-scale bioreactors with higher DO concentrations (~4.0 and ~2.3 mg/ L). The relative abundance of nitrifying bacteria was determined by sequencing of PCR-amplified 16S rRNA gene fragments. In the three bioreactors with low DO concentrations, effluent ammonia concentrations sharply increased with a decline in temperature below approximately 17 °C, while the bioreactors with high DO concentrations showed stable nitrification regardless of temperature. Even with the decline in nitrification during the winter in the three low DO bioreactors, the relative abundance of ammonia oxidizing bacteria (mostly Nitrosomonas spp.) was curiously maintained. The relative abundance of nitrite oxidizing bacteria was similarly maintained, although there were substantial seasonal fluctuations in the relative abundance values of Nitrospira spp. versus Nitrotoga spp. This research suggests that nitrification activity can be controlled during the winter via DO to produce better effluent quality with high DO concentrations or to reduce aeration costs with a concomitant decline in nitrification activity.

Direct evidence for deterministic assembly of bacterial communities in full-scale municipal wastewater treatment facilities

In this study we investigated whether bacterial community composition in full-scale wastewater treatment bioreactors can be better explained by niche- or neutral- based theory (deterministic or stochastic) and whether bioreactor design (continuous-flow vs. fill-and-draw) affected community assembly. Four wastewater treatment facilities (one with quadruplicated continuous-flow bioreactors, two with one continuous-flow bioreactor each, one with triplicated fill-and-draw bioreactors) were investigated. Bioreactor community composition was characterized by sequencing of PCR-amplified 16S rRNA gene fragments. Replicate bioreactors at the same wastewater treatment facility had largely reproducible (i.e., deterministic) bacterial community composition, although bacterial community composition in continuous-flow bioreactors was significantly more reproducible (P < 0.001) than in fill-and-draw bioreactors (Bray-Curtis dissimilarity: μ = 0.48 ± 0.06 vs. 0.58 ± 0.08). Next, we compared our results to previously-used indirect methods for distinguishing between deterministic and stochastic community assembly mechanisms. Synchronicity was observed in the bacterial community composition among bioreactors within the same metropolitan region, consistent with deterministic community assembly. Similarly, a null model-based analysis also indicated that all wastewater bioreactor communities were controlled by deterministic factors and that continuous-flow bioreactors were significantly more deterministic (P < 0.001) than fill-and-draw bioreactors (nearest-taxon index: μ = 3.3 ± 0.6 vs. 2.7 ± 0.8). Our results indicate that bacterial community composition in wastewater treatment bioreactors is better explained by deterministic community assembly theory; simultaneously, our results validate previously-used but indirect methods to quantify whether microbial communities were assembled via deterministic or stochastic mechanisms. IMPORTANCE Understanding the mechanisms of bacterial community assembly is one of the grand challenges of microbial ecology. In environmental systems, this challenge is exacerbated because "replicate" experiments are typically impossible; that is, microbial ecologists cannot fabricate multiple field-scale experiments of identical, natural ecosystems. Our results directly demonstrate that deterministic mechanisms are more prominent than stochastic mechanisms in the assembly of wastewater treatment bioreactor communities. Our results also suggest that wastewater treatment bioreactor design is pertinent, such that the imposition of feast-famine conditions (i.e., fill-and-draw bioreactors) nudge bacterial community assembly more towards stochastic mechanisms compared to the imposition of stringent nutrient limitation (i.e., continuous-flow bioreactors). Our research also validates the previously-used indirect methods (synchronous community dynamics and an application of a null-model) for characterizing the relative importance of deterministic versus stochastic mechanisms of community assembly.

Seasonal dynamics of the microbial community in two full-scale wastewater treatment plants: Diversity, composition, phylogenetic group based assembly and co-occurrence pattern

The optimal operation and functional stability of a wastewater treatment plant (WWTP) strongly depend on the properties of its microbial community. However, a knowledge gap remains regarding the seasonal dynamics of microbial community properties, especially phylogenetic group based assembly and co-occurrence patterns. Accordingly, in this study, influent and activated sludge (AS) samples were weekly collected from 2 full-scale WWTPs for one year (89 influent and 103 AS samples in total) and examined by high-throughput Illumina-MiSeq sequencing. The results suggested that the microbial community diversity and composition in the influent fluctuated substantially with season, while those in the AS had a relatively more stable pattern throughout the year. The phylogenetic group based assembly mechanisms of AS community were identified by using "Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP)". The results showed that drift accounted for the largest proportion (52.8%), while homogeneous selection (18.2%) was the most important deterministic process. Deterministic processes dominated in 47 microbial groups (bins), which were also found (~40%) in the AS core taxa dataset. Moreover, the results suggested that Nitrospira were more susceptible to stochastic processes in winter, which may provide a possible explanation for nitrification failure in winter. Network analysis results suggested that the network structure of the AS community could be more stable in summer and autumn. In addition, there were no identical keystone taxa found in different networks (constructed from different plants, sources, and seasons), which supported the context dependency theory. The results of this study deepened our understanding of the microbial ecology in AS systems and provided a foundation for further studies on the community regulation strategy of WWTPs.

Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies

In recent years, multi-omic studies have enabled resolving community structure and interrogating community function of microbial communities. Simultaneous generation of metagenomic, metatranscriptomic, metaproteomic, and (meta) metabolomic data is more feasible than ever before, thus enabling in-depth assessment of community structure, function, and phenotype, thus resulting in a multitude of multi-omic microbiome datasets and the development of innovative methods to integrate and interrogate those multi-omic datasets. Specifically, the application of reference-independent approaches provides opportunities in identifying novel organisms and functions. At present, most of these large-scale multi-omic datasets stem from spatial sampling (e.g., water/soil microbiomes at several depths, microbiomes in/on different parts of the human anatomy) or case-control studies (e.g., cohorts of human microbiomes). We believe that longitudinal multi-omic microbiome datasets are the logical next step in microbiome studies due to their characteristic advantages in providing a better understanding of community dynamics, including: observation of trends, inference of causality, and ultimately, prediction of community behavior. Furthermore, the acquisition of complementary host-derived omics, environmental measurements, and suitable metadata will further enhance the aforementioned advantages of longitudinal data, which will serve as the basis to resolve drivers of community structure and function to understand the biotic and abiotic factors governing communities and specific populations. Carefully setup future experiments hold great potential to further unveil ecological mechanisms to evolution, microbe-microbe interactions, or microbe-host interactions. In this article, we discuss the challenges, emerging strategies, and best-practices applicable to longitudinal microbiome studies ranging from sampling, biomolecular extraction, systematic multi-omic measurements, reference-independent data integration, modeling, and validation.

Linking seasonal N2O emissions and nitrification failures to microbial dynamics in a SBR wastewater treatment plant

Nitrous oxide (N2O) is a strong greenhouse gas and causal for stratospheric ozone depletion. During biological nitrogen removal in wastewater treatment plants (WWTP), high N2O fluxes to the atmosphere can occur, typically exhibiting a seasonal emission pattern. Attempts to explain the peak emission phases in winter and spring using physico-chemical process data from WWTP were so far unsuccessful and new approaches are required. The complex and diverse microbial community of activated sludge used in biological treatment systems also exhibit substantial seasonal patterns. However, a potentially causal link between the seasonal patterns of microbial diversity and N2O emissions has not yet been investigated. Here we show that in a full-scale WWTP nitrification failure and N2O peak emissions, bad settleability of the activated sludge and a turbid effluent strongly correlate with a significant reduction in the microbial community diversity and shifts in community composition. During episodes of impaired performance, we observed a significant reduction in abundance for filamentous and nitrite oxidizing bacteria in all affected reactors. In some reactors that did not exhibit nitrification and settling failures, we observed a stable microbial community and no drastic loss of species. Standard engineering approaches to stabilize nitrification, such as increasing the aerobic sludge age and oxygen availability failed to improve the plant performance on this particular WWTP and replacing the activated sludge was the only measure applied by the operators to recover treatment performance in affected reactors. Our results demonstrate that disturbances of the sludge microbiome affect key structural and functional microbial groups, which lead to seasonal N2O emission patterns. To reduce N2O emissions from WWTP, it is therefore crucial to understand the drivers that lead to the microbial population dynamics in the activated sludge.

Changes in bacterial diversity of activated sludge exposed to titanium dioxide nanoparticles

The rapid growth of the use of nanomaterials in different modern industrial branches makes the study of the impact of nanoparticles on the human health and environment an urgent matter. For instance, it has been reported that titanium dioxide nanoparticles (TiO₂ NPs) can be found in wastewater treatment plants. Previous studies have found contrasting effects of these nanoparticles over the activated sludge process, including negative effects on the oxygen uptake. The non-utilization of oxygen reflects that aerobic bacteria were inhibited or decayed. The aim of this work was to study how TiO₂ NPs affect the bacterial diversity and metabolic processes on an activated sludge. First, respirometry assays of 8 h were carried out at different concentrations of TiO₂ NPs (0.5-2.0 mg/mL) to measure the oxygen uptake by the activated sludge. The bacterial diversity of these assays was determined by sequencing the amplified V3-V4 region of the 16S rRNA gene using Illumina MiSeq. According to the respirometry assays, the aerobic processes were inhibited in a range from 18.5 ± 4.8% to 37.5 ± 2.0% for concentrations of 0.5-2.0 mg/mL TiO₂ NPs. The oxygen uptake rate was affected mainly after 4.5 h for concentrations higher than 1.0 mg/mL of these nanoparticles. Results indicated that, in the presence of TiO₂ NPs, the bacterial community of activated sludge was altered mainly in the genera related to nitrogen removal (nitrogen assimilation, nitrification and denitrification). The metabolic pathways prediction suggested that genes related to biofilm formation were more sensitive than genes directly related to nitrification-denitrification and N-assimilation processes. These results indicated that TiO₂ NPs might modify the bacteria diversity in the activated sludge according to their concentration and time of exposition, which in turn impact in the performance of the wastewater treatment processes.

Effects of Clinical Wastewater on the Bacterial Community Structure from Sewage to the Environment

This study pertains to measure differences in bacterial communities along the wastewater pathway, from sewage sources through the environment. Our main focus was on taxa which include pathogenic genera, and genera harboring antibiotic resistance (henceforth referred to as "target taxa"). Our objective was to measure the relative abundance of these taxa in clinical wastewaters compared to non-clinical wastewaters, and to investigate what changes can be detected along the wastewater pathway. The study entailed a monthly sampling campaign along a wastewater pathway, and taxa identification through 16S rRNA amplicon sequencing. Results indicated that clinical and non-clinical wastewaters differed in their overall bacterial composition, but that target taxa were not enriched in clinical wastewater. This suggests that treatment of clinical wastewater before release into the wastewater system would only remove a minor part of the potential total pathogen load in wastewater treatment plants. Additional findings were that the relative abundance of most target taxa was decreased after wastewater treatment, yet all investigated taxa were detected in 68% of the treated effluent samples-meaning that these bacteria are continuously released into the receiving surface water. Temporal variation was only observed for specific taxa in surface water, but not in wastewater samples.

Microbial Population Dynamics in Model Sewage Treatment Plants and the Fate and Effect of Gold Nanoparticles

Adequate functioning of a sewage treatment plant (STP) is essential to protect the downstream aquatic environment (ECHA 2017), and information on the degradability of chemicals and their toxicity to activated sludge microorganisms is required. An environmental realistic higher tier test is a STP simulation test as described in OECD 303A (2001) which for nanoparticles can also be used to study their sorption behavior to activated sludge. However, information is limited on the influence of synthetic sewage on the microbial community of the activated sludge. A modified community can result in modifications of the sludge floccules affecting the sorption behavior. The main objective of our study was to show whether a representative microbial diversity remains under standardized test conditions as described in OECD 303A (2001) using synthetic sewage as influent. Furthermore, we investigated whether just considering the functional properties of a STP (elimination of dissolved organic carbon; nitrification), is sufficient for an assessment of gold nanoparticles (AuNPs) or whether the influence on microbial diversity also needs to be considered. AuNPs were used as a case study due to their rising medical applications and therefore increasing probability to reach the sewer and STP. The results can provide significant input for the interpretation of results from the regulatory point of view. To deliver these objectives, the general changes of the microbial population in activated sludge and its influence on the degradation activity (dissolved organic carbon (DOC) and inorganic nitrogen) using freshly collected sludge from the municipal STP in an artificial test system as a model STP in accordance with OECD 303A (2001) were assessed. Additionally, we evaluated the potential impact of AuNPs and its dispersant on the microbial composition and the overall impact on the function of the STP in terms of DOC degradation and nitrogen removal to observe if an assessment based on functional properties is sufficient. The bacteria composition in our study, evaluated at a class level, revealed commonly described environmental bacteria. Proteobacteria (β, α, δ) accounted for more than 50% but also nitrifying bacteria as Nitrospira were present. Our results show that mainly within the first 7 days of an acclimatization phase by addition of synthetic sewage, the bacterial community changed. Even though AuNPs can have antibacterial properties, no adverse effects on the function and structure of the microorganisms in the STP could be detected at concentrations of increased modeled PEC values by a factor of about 10,000. Complementary to other metallic nanomaterials, gold nanomaterials also sorb to a large extent to the activated sludge. If activated sludge is used as fertilizer on agricultural land, gold nanoparticles can be introduced into soils. In this case, the effect on soil (micro)organisms must be investigated more closely, also taking into account the structural diversity.

Annual dynamics of antimicrobials and resistance determinants in flocculent and aerobic granular sludge treatment systems

The occurrence and removal patterns of 24 antimicrobial agents and antimicrobial resistant determinants namely 6 antibiotic resistance genes (ARGs) and 2 mobile genetic elements (MGEs), and the fecal indicator E. coli were investigated in three full-scale wastewater treatment plants. Their waterlines and biosolids lines (including secondary treatment based on both granular and activated sludge) were sampled monthly throughout one year. Samples were analyzed by means of LC-MS/MS, qPCR and cell enumeration, respectively. The influence of rainfall, temperature, and turbidity on the occurrence and removal of the aforementioned agents was assessed through statistical linear mixed models. Ten of the antimicrobial agents (macrolides, fluoroquinolones, tetracyclines, and sulfonamides) were commonly found in influent in concentrations of 0.1-2 µg L^-1, and the predominant ARGs were ermB and sul1 (6.4 and 5.9 log₁₀ mL^-1 respectively). Warmer temperatures slightly reduced gene concentrations in influent whilst increasing that of E. coli and produced an uneven effect on the antimicrobial concentrations across plants. Rainfall diluted both E. coli (-0.25 logs, p < 0.001) and antimicrobials but not genes. The wastewater treatment reduced the absolute abundance of both genes (1.86 logs on average) and E. coli (2.31 logs on average). The antimicrobials agents were also partly removed, but 8 of them were still detectable after treatment, and 6 accumulated in the biosolids. ARGs were also found in biosolids with patterns resembling those of influent. No significant differences in the removal of antimicrobials, genes and E. coli were observed when comparing conventional activated sludge with aerobic granular sludge. Irrespective of the type of sludge treatment, the removal of genes was significantly reduced with increasing hydraulic loads caused by rainfall (-0.35 logs per ∆ average daily flow p < 0.01), and slightly decreased with increasing turbidity (-0.02 logs per ∆1 nephelometric turbidy unit p < 0.05) .

Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes

In the fight to limit the global spread of antibiotic resistance, the assembly of environmental metagenomes has the potential to provide rich contextual information (e.g., taxonomic hosts, carriage on mobile genetic elements) about antibiotic resistance genes (ARG) in the environment. However, computational challenges associated with assembly can impact the accuracy of downstream analyses. This work critically evaluates the impact of assembly leveraging short reads, nanopore MinION long-reads, and a combination of the two (hybrid) on ARG contextualization for ten environmental metagenomes using seven prominent assemblers (IDBA-UD, MEGAHIT, Canu, Flye, Opera-MS, metaSpades and HybridSpades). While short-read and hybrid assemblies produced similar patterns of ARG contextualization, raw or assembled long nanopore reads produced distinct patterns. Based on an in-silico spike-in experiment using real and simulated reads, we show that low to intermediate coverage species are more likely to be incorporated into chimeric contigs across all assemblers and sequencing technologies, while more abundant species produce assemblies with a greater frequency of inversions and insertion/deletions (indels). In sum, our analyses support hybrid assembly as a valuable technique for boosting the reliability and accuracy of assembly-based analyses of ARGs and neighboring genes at environmentally-relevant coverages, provided that sufficient short-read sequencing depth is achieved.

Strategy for denitrifying anaerobic methane-oxidizing bacteria growing under the oxygen-present condition

Denitrifying anaerobic methane oxidizing (DAMO) bacteria are newly discovered microorganisms that use methane as the electron donor to reduce nitrite into dinitrogen. They have potential value on nitrogen removal from wastewater. However, the oxygen exposure in engineering is considered one of the bottlenecks for DAMO engineering application. In this work, we cultured DAMO bacteria under oxic and anoxic conditions in a gas-lift sequencing batch reactor (GLSBR) to explore DAMO bacterial response to oxygen stress. Under oxic conditions (7.5-8 mg O₂/L), the extension of hydraulic retention time (HRT) from 2 days to 4 days increased DAMO bacterial abundance by 3.8 times. Under anoxic conditions (0.2-0.5 mg O₂/L), DAMO bacterial abundance increased by 30.1 times and were kept over 2.0 × 10¹¹ copies g^-1 wet sludge. During the enrichment, microbial aggregates were formed and DAMO bacteria tended to be distributed inside the aggregates. Notably, aerobic methanotrophs existed in the whole process, capable of consuming oxygen and providing a suitable environment for DAMO bacterial growth. Finally, DAMO bacteria were enriched and the relative abundance was 16.16%. This work provides new insights into DAMO bacterial enrichment and their application in wastewater treatment.

Seasonal Dynamics of the Activated Sludge Microbiome in Sequencing Batch Reactors, Assessed Using 16S rRNA Transcript Amplicon Sequencing

Activated sludge is comprised of diverse microorganisms which remediate wastewater. Previous research has characterized activated sludge using 16S rRNA gene amplicon sequencing, which can help to address questions on the relative abundance of microorganisms. In this study, we used 16S rRNA transcript sequencing in order to characterize "active" populations (via protein synthesis potential) and gain a deeper understanding of microbial activity patterns within activated sludge. Seasonal abundances of individual populations in activated sludge change over time, yet a persistent group of core microorganisms remains throughout the year which are traditionally classified on presence or absence without monitoring of their activity or growth. The goal of this study was to further our understanding of how the activated sludge microbiome changes between seasons with respect to population abundance, activity, and growth. Triplicate sequencing batch reactors were sampled at 10-min intervals throughout reaction cycles during all four seasons. We quantified the gene and transcript copy numbers of 16S rRNA amplicons using real-time PCR and sequenced the products to reveal community abundance and activity changes. We identified 108 operational taxonomic units (OTUs) with stable abundance, activity, and growth throughout the year. Nonproliferating OTUs were commonly human health related, while OTUs that showed seasonal abundance changes have previously been identified as being associated with floc formation and bulking. We observed significant differences in 16S rRNA transcript copy numbers, particularly at lower temperatures in winter and spring. The study provides an analysis of the seasonal dynamics of microbial activity variations in activated sludge based on quantifying and sequencing 16S rRNA transcripts.IMPORTANCE Sequencing batch reactors are a common design for wastewater treatment plants, particularly in smaller municipalities, due to their low footprint and ease of operations. However, like for most treatment plants in temperate/continental climates, the microbial community involved in water treatment is highly seasonal and its biological processes can be sensitive to cold temperatures. The seasonality of these microbial communities has been explored primarily in conventional treatment plants and not in sequencing batch reactors. Furthermore, most studies often only address which organisms are present. However, the activated sludge microbial community is very diverse, and it is often hard to discern which organisms are active and which organisms are simply present. In this study, we applied additional sequencing techniques to also address the issues of which organisms are active and which organisms are growing. By addressing these issues, we gained new insights into seasonal microbial populations dynamics and activity patterns affecting wastewater treatment.

Nitrifying and Denitrifying Microbial Communities in Centralized and Decentralized Biological Nitrogen Removing Wastewater Treatment Systems

Biological nitrogen removal (BNR) in centralized and decentralized wastewater treatment systems is assumed to be driven by the same microbial processes and to have communities with a similar composition and structure. There is, however, little information to support these assumptions, which may impact the effectiveness of decentralized systems. We used high-throughput sequencing to compare the structure and composition of the nitrifying and denitrifying bacterial communities of nine onsite wastewater treatment systems (OWTS) and one wastewater treatment plant (WTP) by targeting the genes coding for ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ). The amoA diversity was similar between the WTP and OWTS, but nosZ diversity was generally higher for the WTP. Beta diversity analyses showed the WTP and OWTS promoted distinct amoA and nosZ communities, although there is a core group of N-transforming bacteria common across scales of BNR treatment. Our results suggest that advanced N-removal OWTS have microbial communities that are sufficiently distinct from those of WTP with BNR, which may warrant different management approaches.

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.

Investigating Industrial Effluent Impact on Municipal Wastewater Treatment Plant in Vaal, South Africa

Industrial effluents with high concentrations of toxic heavy metals are of great concern because of their persistence and non-degradability. However, poor operation and maintenance of wastewater treatment infrastructure is a great concern in South Africa. In this study, physico-chemical parameters and heavy metals (HMs) concentration of wastewater from five different industries, Leeuwkuil wastewater treatment plant (WWTP) inflow and effluent, and Vaal River water samples were monitored between January and September 2017, to investigate the correlation between heavy metal pollution and the location of industries and ascertain the effectiveness of the municipal WWTP. Physico-chemical variables such as pH, biological oxygen demand (BOD), dissolved oxygen (DO), chemical oxygen demand (COD), total dissolved solids (TDS) and electrical conductivity (EC) exhibited both temporal and spatial variations with the values significantly higher in the industrial samples. Inductively coupled plasma optical emission spectrometry (ICP-OES) results also showed that aluminium (Al), copper (Cu), lead (Pb) and zinc (Zn) were significantly higher in industrial effluents (p < 0.05), with only Zn and Al exhibiting significant seasonal variability. Statistical correlation analysis revealed a poor correlation between physicochemical parameters and the HMs compositional quality of wastewater. However, toxic HMs (Zn, Cu and Pb) concentrations in treated wastewater from WWTP were above the permissible limits. Although the WWTP was effective in maintaining most of the wastewater parameters within South African Green drop Standards, the higher Cu, Zn, Pb and COD in its final effluent is a concern in terms of Vaal river health and biological diversity. Therefore, we recommend continuous monitoring and maintenance of the WWTPs infrastructure in the study area.

Increased replication of dissimilatory nitrate-reducing bacteria leads to decreased anammox bioreactor performance

BACKGROUND

Anaerobic ammonium oxidation (anammox) is a biological process employed to remove reactive nitrogen from wastewater. While a substantial body of literature describes the performance of anammox bioreactors under various operational conditions and perturbations, few studies have resolved the metabolic roles of their core microbial community members.

RESULTS

Here, we used metagenomics to study the microbial community of a laboratory-scale anammox bioreactor from inoculation, through a performance destabilization event, to robust steady-state performance. Metabolic analyses revealed that nutrient acquisition from the environment is selected for in the anammox community. Dissimilatory nitrate reduction to ammonium (DNRA) was the primary nitrogen removal pathway that competed with anammox. Increased replication of bacteria capable of DNRA led to the out-competition of anammox bacteria, and the loss of the bioreactor's nitrogen removal capacity. These bacteria were highly associated with the anammox bacterium and considered part of the core microbial community.

CONCLUSIONS

Our findings highlight the importance of metabolic interdependencies related to nitrogen- and carbon-cycling within anammox bioreactors and the potentially detrimental effects of bacteria that are otherwise considered core microbial community members.