Exploring the microbial influence on seasonal nitrous oxide concentration in a full-scale wastewater treatment plant using metagenome assembled genomes

Metabolic labour division trade-offs in denitrifying microbiomes

Division of metabolic labour is a defining trait of natural and engineered microbiomes. Denitrification-the stepwise reduction of nitrate and nitrite to nitrogenous gases-is inherently modular, catalysed either by a single microorganism (termed complete denitrifier) or by consortia of partial denitrifiers. Despite the pivotal role of denitrification in biogeochemical cycles and environmental biotechnologies, the ecological factors selecting for complete versus partial denitrifiers remain poorly understood. In this perspective, we critically review over 1500 published metagenome-assembled genomes of denitrifiers from diverse and globally relevant ecosystems. Our findings highlight the widespread occurrence of labour division and the dominance of partial denitrifiers in complex ecosystems, contrasting with the prevalence of complete denitrifiers only in simple laboratory cultures. We challenge current labour division theories centred around catabolic pathways, and discuss their limits in explaining the observed niche partitioning. Instead, we propose that labour division benefits partial denitrifiers by minimising resource allocation to denitrification, enabling broader metabolic adaptability to oligotrophic and dynamic environments. Conversely, stable, nutrient-rich laboratory cultures seem to favour complete denitrifiers, which maximise energy generation through denitrification. To resolve the ecological significance of metabolic trade-offs in denitrifying microbiomes, we advocate for mechanistic studies that integrate mixed-culture enrichments mimicking natural environments, multi-meta-omics, and targeted physiological characterisations. These undertakings will greatly advance our understanding of global nitrogen turnover and nitrogenous greenhouse gases emissions.

Diversity and physiology of abundant Rhodoferax species in global wastewater treatment systems

Wastewater treatment plants rely on complex microbial communities for bioconversion and removal of pollutants, but many process-critical species are still poorly investigated. One of these genera is Rhodoferax, an abundant core genus in wastewater treatment plants across the world. The genus has been associated with many metabolic traits such as iron reduction and oxidation and denitrification. We used 16S rRNA gene amplicon data to uncover the diversity and abundance of Rhodoferax species in Danish and global treatment plants. Publicly available metagenome-assembled genomes were analyzed based on phylogenomics to delineate species and assign taxonomies based on the SeqCode. The phylogenetic analysis of "Rhodoferax" revealed that species previously assigned to Rhodoferax in wastewater treatment plants should be considered as at least eight different genera, with five representing previously undescribed genera. Genome annotation showed potential for several key-bioconversions in wastewater treatment, such as nitrate reduction, carbohydrate degradation, and accumulations of various storage compounds. Iron oxidation and reduction capabilities were not predicted for abundant species. Species-resolved FISH-Raman was performed to gain an overview of the morphology and ecophysiology of selected taxa to clarify their potential role in global wastewater treatment systems. Our study provides a first insight into the functional and ecological characteristics of several novel genera abundant in global wastewater treatment plants, previously assigned to the Rhodoferax genus.

Green manuring combined with zeolite reduced nitrous oxide emissions in maize field by targeting microbial nitrogen transformations

Green manure is a crucial strategy for increasing cereal yield and mitigating environmental burden while reducing chemical N fertilizer. To effectively tackle climate change, finding ways to reduce nitrous oxide (N2O) emissions from green manuring systems is vital. Herein, field and 15N labeled microcosm experiments were arranged to investigate the effect and mechanisms of green manuring and zeolite application on N2O emission. Both experiments comprised four treatments: conventional chemical N (N100), 70 % chemical N (N70), N70 with green manure (N70 + CV), and N70 + CV combined with zeolite (N70 + CV + Z). Compared with N100, both N70 + CV and N70 + CV + Z maintained maize yield, cumulative N2O emissions decreased by 37.7 % and 34.9 % in N70 + CV + Z in 2022-yr and 2023-yr, and by 12.8 % in N70 + CV in 2022-yr. Moreover, the reduction of N2O emission primarily occurred after incorporating green manure. The N100 and N70 + CV demonstrated a similar transformed proportion of chemical N to N2O (i.e., 4.9 % and 4.7 %) while reducing it to 2.7 % in N70 + CV + Z. Additionally, a mere 0.7 % of green manure N was transformed to N2O in both N70 + CV and N70 + CV + Z treatments. Compared with N100, both N70 + CV and N70 + CV + Z decreased the relative abundances of ammonia oxidation microbes, increased denitrifier and the ratios of (nirK + nirS)/nosZ and norBC/nosZ. Furthermore, compared with N70 + CV, N70 + CV + Z decreased the relative abundances of N2O-producer and the ratios of (nirK + nirS)/nosZ and norBC/nosZ in denitrification. These findings revealed that the reduction of N2O emissions resulting from green manure replaced chemical N was mainly due to weakened nitrification, while zeolite reduced N2O emissions attributed to enhanced conversion of N2O to N2. Moreover, certain key N-cycling functional bacteria, such as Phycisphaerae, Rubrobacteria, and Thermoflexia, were positively correlated with N2O emission. In contrast, Dehalococcoidia, Gammaproteobacteria, and Betaproteobacteria were negatively correlated with N2O emission. This investigation uncovered the underlying mechanisms for effectively reducing N2O emissions through green manuring combined with zeolite.

Effects of aeration control strategies on nitrous oxide emissions in alternating anoxic-oxic sequencing batch reactor systems

Reducing N2O emissions is key to controlling greenhouse gases (GHG) in wastewater treatment plants (WWTPs). Although studies have examined the effects of dissolved oxygen (DO) on N2O emissions during nitrogen removal, the precise effects of aeration rate remain unclear. This study aimed to fill this research gap by investigating the influence of dynamic aeration rates on N2O emissions in an alternating anoxic-oxic sequencing batch reactor system. The emergence of DO breakthrough points indicated that the conversion of ammonia nitrogen to nitrite and the release of N2O were nearly complete. Approximately 91.73 ± 3.35% of N2O was released between the start of aeration and the DO breakthrough point. Compared to a fixed aeration rate, dynamically adjusting the aeration rates could reduce N2O production by up to 48.6%. Structural equation modeling revealed that aeration rate and total nitrogen directly or indirectly had significant effects on the N2O production. A novel regression model was developed to estimate N2O production based on energy consumption (aeration flux), water quality (total nitrogen), and GHG emissions (N2O). This study emphasizes the potential of optimizing aeration strategies in WWTPs to significantly reduce GHG and improve environmental sustainability.

Ammonia oxidizing bacteria (AOB) denitrification and bacterial denitrification as the main culprit of high N2O emission in SBR with low C/N ratio wastewater

A large amount of greenhouse gas nitrous oxide (N2O) will be produced during the biological nitrogen removal process for organic wastewater of low C/N ratio. One of the effective methods to solve this problem is to incorporate inexpensive carbon source. In this study, raw wastewater (RW) from pig farm, that was not anaerobically digested, was utilized as exogenous carbon in both A/O and SBR aerobic reactor to treat liquid digestate with high ammonia nitrogen and low C/N ratio. The results showed that N2O emission in SBR was higher than that of A/O process under the same nitrogen load. The N2O conversion in the biological nitrogen removal process was investigated by the strategy of integrating stable isotope method and metagenomics. The δO18-N2O, δN15-N2O, and SP values of the SBR were closer to the denitrification values of Ammonia-Oxidizing Bacteria (AOB) than those of A/O. The abundance of AOB in the SBR reactor was higher than that in the A/O reactor, while the abundance of denitrifying bacteria was lower. The amoA/B/C gene abundance in the SBR was greater than that in the A/O, and the NOS gene abundance was the opposite. The results indicated that both AOB denitrification and bacterial denitrification led to the increase of N2O emissions of the SBR.

Future directions in microbial nitrogen cycling in wastewater treatment

Discoveries in the past decade of novel reactions, processes, and micro-organisms have altered our understanding of microbial nitrogen cycling in wastewater treatment systems. These advancements pave the way for a transition toward more sustainable and energy-efficient wastewater treatment systems that also minimize greenhouse gas emissions. This review highlights these innovative directions in microbial nitrogen cycling within the context of wastewater treatment. Processes such as comammox, Feammox, electro-anammox, and nitrous oxide mitigation offer innovative approaches for sustainable, energy-efficient nitrogen removal. However, while these emerging processes show promise, advancing from laboratory research to practical applications, particularly in decentralized systems, remains a critical next step toward a sustainable and efficient wastewater management.

Natural flocculant chitosan inhibits short-chain fatty acid production in anaerobic fermentation of waste activated sludge

Chitosan (CTS) serves as an excellent natural flocculant in wastewater purification and sludge conditioning, but its potential impact on anaerobic fermentation of waste-activated sludge is unclear. The current study investigated the role of CTS in short-chain fatty acids (SCFAs) generation via sludge alkaline anaerobic fermentation. The results showed a drastic reduction in SCFA production with CTS, showing a maximum inhibition of 33 % at 6 mg/g of total suspended solids. CTS hindered sludge solubilization through flocculation, and acted as a humus precursor, promoting humus formation, and consequently reduced the amount of available substrates. Further, CTS promoted free ammonia production, posing a challenge to enzymes and cell viability. Additionally, CTS increased the population of Rikenellaceae sp. and weakened the dominance of hydrolyzing and acidifying bacteria. This study deepens the understanding of the potential impact of CTS on anaerobic fermentation and provides a theoretical basis for reducing the risk of polymeric flocculants.

Complete long-term monitoring of greenhouse gas emissions from a full-scale industrial wastewater treatment plant with different cover configurations

The greenhouse gas (GHG) emissions from wastewater treatment plants (WWTPs), consisting mainly of methane (CH4) and nitrous oxide (N2O), have been constantly increasing and become a non-negligible contributor towards carbon neutrality. The precise evaluation of plant-specific GHG emissions, however, remains challenging. The current assessment approach is based on the product of influent load and emission factor (EF), of which the latter is quite often a single value with huge uncertainty. In particular, the latest default Tier 1 value of N2O EF, 0.016 ± 0.012 kgN2O-N kgTN-1, is estimated based on the measurement of 30 municipal WWTPs only, without involving any industrial wastewater. Therefore, to resolve the pattern of GHG emissions from industrial WWTPs, this work conducted a 14-month monitoring campaign covering all the process units at a full-scale industrial WWTP in Shanghai, China. The total CH4 and N2O emissions from the whole plant were, on average, 447.7 ± 224.5 kgCO2-eq d-1 and 1605.3 ± 2491.0 kgCO2-eq d-1, respectively, exhibiting a 5.2- or 3.9-times more significant deviation than the influent loads of chemical oxygen demand (COD) or total nitrogen (TN). The resulting EFs, 0.00072 kgCH4 kgCOD-1 and 0.00211 kgN2O-N kgTN-1, were just 0.36% of the IPCC recommended value for CH4, and 13.2% for N2O. Besides, the parallel anoxic-oxic (A/O) lines of this industrial WWTP were covered in two configurations, allowing the comparison of GHG emissions from different odor control setup. Unit-specific analysis showed that the replacement of enclosed A/open O with enclosed A/O reduced the CH4 EF by three times, from 0.00159 to 0.00051 kgCH4 kgCOD-1, and dramatically decreased the N2O EF by an order of magnitude, from 0.00376 to 0.00032 kgN2O-N kgTN-1, which was among the lowest of all full-scale WWTPs.

Competitive bio-augmentation overcoming unusual direct inhibitor inefficacy in mainstream nitrite-oxidizing bacteria suppression: Unveiling the underpinnings in microbial and nitrogen metabolism aspects

The long-stabilized mainstream partial nitritation/Anammox (PN/A) process continues to encounter significant challenges from nitrite-oxidizing bacteria (NOB). Therefore, this study aimed to determine an efficient, rapid, and easily implementable strategy for inhibiting NOB. A laboratory-scale reactor was operated continuously for 325 days, experiencing NOB outbreak in mainstream and recovery with simulated sidestream support. The results show that direct inhibitory strategies including intermittent aeration and approximately 35 mg/L free ammonia had unusual weak inhibitory effects on NOB activity. Subsequently, the exogenous Anammox from sidestream employed as a competitive bio-augmentation approach rapidly inhibited NOB dynamics. Evidence suggests that the damaged hydroxyapatite granules under low pH conditions might have contributed to NOB dominance by diminishing Anammox bacteria activity, thereby creating a substrate-rich environment favoring NOB survival. In contrast, the introduction of exogenous Candidatus Kuenenia facilitated the nitrogen removal efficiency from 32.5 % to over 80 %. This coincided with a decrease in the relative abundance of Nitrospira from 16.5 % to 2.7 % and NOB activity from 0.34 to 0.07 g N/(g mixed liquor volatile suspended solid)/d. Metagenomic analysis reveals a decrease in the functional potential of most nitrite transport proteins, coupled with a significant increase in eukaryotic-like serine/threonine-protein kinase involved in cellular regulation, during the Anammox activity recovery. This study's findings reveal the feasibility of the bio-augmentation based on substrate competition, wherein sidestream processes support the mainstream PN/A integration, offering significant potential for practical applications.

Microbial community assembly in engineered bioreactors

Microbial community assembly (MCA) processes that shape microbial communities in environments are being used to analyze engineered bioreactors such as activated sludge systems and anaerobic digesters. The goal of studying MCA is to be able to understand and predict the effect of design and operation procedures on bioreactor microbial composition and function. Ultimately, this can lead to bioreactors that are more efficient, resilient, or resistant to perturbations. This review summarizes the ecological theories underpinning MCA, evaluates MCA analysis methods, analyzes how these MCA-based methods are applied to engineered bioreactors, and extracts lessons from case studies. Furthermore, we suggest future directions in MCA research in engineered bioreactor systems. The review aims to provide insights and guidance to the growing number of environmental engineers who wish to design and understand bioreactors through the lens of MCA.

Direct and indirect monitoring methods for nitrous oxide emissions in full-scale wastewater treatment plants: A critical review

Mitigation of nitrous oxide (N2O) emissions in full-scale wastewater treatment plant (WWTP) has become an irreversible trend to adapt the climate change. Monitoring of N2O emissions plays a fundamental role in understanding and mitigating N2O emissions. This paper provides a comprehensive review of direct and indirect N2O monitoring methods. The techniques, strengths, limitations, and applicable scenarios of various methods are discussed. We conclude that the floating chamber technique is suitable for capturing and interpreting the spatiotemporal variability of real-time N2O emissions, due to its long-term in-situ monitoring capability and high data acquisition frequency. The monitoring duration, location, and frequency should be emphasized to guarantee the accuracy and comparability of acquired data. Calculation by default emission factors (EFs) is efficient when there is a need for ambiguous historical N2O emission accounts of national-scale or regional-scale WWTPs. Using process-specific EFs is beneficial in promoting mitigation pathways that are primarily focused on low-emission process upgrades. Machine learning models exhibit exemplary performance in the prediction of N2O emissions. Integrating mechanistic models with machine learning models can improve their explanatory power and sharpen their predictive precision. The implementation of the synergy of nutrient removal and N2O mitigation strategies necessitates the calibration and validation of multi-path mechanistic models, supported by long-term continuous direct monitoring campaigns.

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.

Optimized start-up strategies for elemental sulfur packing bioreactor achieving effective autotrophic denitrification

The start-up efficiency of the elemental sulfur packing bioreactor (S0PB) is constrained by the slow growth kinetics of autotrophic microorganisms, which is essentially optimized. This study aims to optimize start-up procedures and offer scientific guidance for the practical applications of S0PB. Through comparing the start-up efficiencies under various conditions related to inoculation, backwashing, and EBCT, it was found that these conditions did not significantly influence start-up time, but they did impact denitrification performance in detail. Using activated sludge as the inoculum was not recommended as the 2.5 ± 0.2 mg-N/L higher nitrite accumulation and 26.0 ± 5.1 % lower TN removal rate, compared to self-enrichment. Starting with a long-to-short EBCT (1 → 0.33 h) achieved higher nitrate removal of 11.5 ± 0.6 mg-N/L and eliminated nitrite accumulation compared to constantly short EBCT (0.33 h) conditions. Daily and postponed backwashing were suggested for long-to-short EBCT and constantly short EBCT start-up, respectively. Enrichment of Sulfurimonas was beneficial for the effective nitrite reduction process.

Biotrickling Filtration for the Reduction of N2O Emitted during Wastewater Treatment: Results from a Long-Term In Situ Pilot-Scale Testing

Wastewater treatment plants (WWTPs) are a major source of N₂O, a potent greenhouse gas with 300 times higher global warming potential than CO₂. Several approaches have been proposed for mitigation of N₂O emissions from WWTPs and have shown promising yet only site-specific results. Here, self-sustaining biotrickling filtration, an end-of-the-pipe treatment technology, was tested in situ at a full-scale WWTP under realistic operational conditions. Temporally varying untreated wastewater was used as trickling medium, and no temperature control was applied. The off-gas from the covered WWTP aerated section was conveyed through the pilot-scale reactor, and an average removal efficiency of 57.9 ± 29.1% was achieved during 165 days of operation despite the generally low and largely fluctuating influent N₂O concentrations (ranging between 4.8 and 96.4 ppmv). For the following 60-day period, the continuously operated reactor system removed 43.0 ± 21.2% of the periodically augmented N₂O, exhibiting elimination capacities as high as 5.25 g N₂O m^-3·h^-1. Additionally, the bench-scale experiments performed abreast corroborated the resilience of the system to short-term N₂O starvations. Our results corroborate the feasibility of biotrickling filtration for mitigating N₂O emitted from WWTPs and demonstrate its robustness toward suboptimal field operating conditions and N₂O starvation, as also supported by analyses of the microbial compositions and nosZ gene profiles.