Delineation of the complex microbial nitrogen-transformation network in an anammox-driven full-scale wastewater treatment plant

A positive contribution to nitrogen removal by a novel NOB in a full-scale duck wastewater treatment system

Nitrite-oxidizing bacteria (NOB) are undesirable in the anaerobic ammonium oxidation (anammox)-driven nitrogen removal technologies in the modern wastewater treatment plants (WWTPs). Diverse strategies have been developed to suppress NOB based on their physiological properties that we have understood. But our knowledge of the diversity and mechanisms employed by NOB for survival in the modern WWTPs remains limited. Here, Three NOB species (NOB01-03) were recovered from the metagenomic datasets of a full-scale WWTP treating duck breeding wastewater. Among them, NOB01 and NOB02 were classified as newly identified lineage VII, tentatively named Candidatus (Ca.) Nitrospira NOB01 and Ca. Nitrospira NOB02. Analyses of genomes and in situ transcriptomes revealed that these two novel NOB were active and showed a high metabolic versatility. The transcriptional activity of Ca. Nitrospira could be detected in all tanks with quite different dissolved oxygen (DO) (0.01-5.01 mg/L), illustrating Ca. Nitrospira can survive in fluctuating DO conditions. The much lower Ca. Nitrospira abundance on the anammox bacteria-enriched sponge carrier likely originated from the intensification substrate (NO2 -) competition from anammox and denitrifying bacteria. In particular, a highlight is that Ca. Nitrospira encoded and treanscribed cyanate hydratase (CynS), amine oxidase, urease (UreC), and copper-containing nitrite reductase (NirK) related to ammonium and NO production, driving NOB to interact with the co-existed AOB and anammox bacteria. Ca. Nitrospira strains NOB01 and NOB02 showed quite different niche preference in the same aerobic tank, which dominanted the NOB communities in activated sludge and biofilm, respectively. In addition to the common rTCA cycle for CO2 fixation, a reductive glycine pathway (RGP) was encoded and transcribed by NOB02 likely for CO2 fixation purpose. Additionally, a 3b group hydrogenase and respiratory nitrate reductase were uniquely encoded and transcribed by NOB02, which likely confer a survival advantage to this strain in the fluctuant activated sludge niche. The discovery of this new genus significantly broadens our understanding of the ecophysiology of NOB. Furthermore, the impressive metabolic versatility of the novel NOB revealed in this study advances our understanding of the survival strategy of NOB and provides valuable insight for suppressing NOB in the anammox-based WWTP.

A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota

Research on the microbial community and function of the anammox process for environmentally friendly wastewater treatment has achieved certain success, which may mean more universal insights are needed. However, the comprehensive understanding of the anammox process is constrained by the limited taxonomic assignment and functional characterization of anammox microbiota, primarily due to the scarcity of high-quality genomes for most organisms. This study reported a global genome catalog of anammox microbiotas based on numerous metagenomes obtained from both lab- and full-scale systems. A total of 1376 candidate species from 7474 metagenome-assembled genomes were used to construct the genome catalog, providing extensive microbial coverage (averaged of 92.40 %) of anammox microbiota. Moreover, a total of 64 core genera and 44 core species were identified, accounting for approximately 64.25 % and 43.97 %, respectively, of anammox microbiota. The strict core genera encompassed not only functional bacteria (e.g., Brocadia, Desulfobacillus, Zeimonas, and Nitrosomonas) but also two candidate genera (UBA12294 and OLB14) affiliated with the order Anaerolineales. In particular, core denitrifying bacteria with observably taxonomic diversity exhibited diverse functional profiles; for instance, the potential of carbohydrate metabolism in Desulfobacillus and Zeimonas likely improves the mixotrophic lifestyle of anammox microbiota. Besides, a noteworthy association was detected between anammox microbiota and system type. Microbiota in coupling system exhibited complex diversity and interspecies interactions by limiting numerous core denitrifying bacteria. In summary, the constructed catalog substantially expands our understanding of the core community and their functions of anammox microbiota, providing a valuable resource for future studies on anammox systems.

Selective genes expression and metabolites transformation drive a robust nitrite accumulation during nitrate reduction under alternating feast-famine condition

Nitrite production via denitrification has been regarded as a key approach for survival of anaerobic ammonium oxidation (anammox) bacteria. Despite the important carbon substrate, little is known about the role of differential genes expression and extracellular metabolite regulation among diverse microbial communities. In this study, a novel alternating feast-famine strategy was proposed and demonstrated to efficiently accumulate nitrite in a low-nitrogen loading rate (NLR) (0.2∼0.8 kg N/m3/d) denitrification system. Highly selective expression of denitrifying genes was revealed as key regulators. Interestingly, in absence of carbon source (ACS) condition, the expression of narG and narI/V genes responsible for reduction of nitrate to nitrite jumped to 2.5 and 5.1 times higher than that in presence of carbon source (PCS) condition with carbon to nitrate ratio of 3.0. This fortunately facilitated a rapid nitrite accumulation once acetate was added, despite a significantly down-regulated narG and narI/narV and up-regulated nirS/nirK. This strategy selected Thauera as the most dominant denitrifier (50.2 %) with the highest contribution to narG and narI/narV genes, responsible for the high nitrite accumulation. Additionally, extracellular xylose, pyruvate, and glucose jointly promoted carbon-central metabolic pathway of key denitrifiers in ACS stage, playing an important role in the process of self-growth and selective enrichment of functional bacteria. The relatively rapid establishment and robust performance obtained in this study shows an engineering-feasible and economically-favorable solution for the regulation of partial denitrification in practical application.

A multi-subsystem collaborative Bi-LSTM-based adaptive soft sensor for global prediction of ammonia-nitrogen concentration in wastewater treatment processes

Ammonia-nitrogen concentration is a key water quality indicator, which reflects changes in pollutant components during wastewater treatment processes. The timely and accurate detection results contribute to optimizing control and operational management of wastewater treatment plants (WWTPs), but current detection methods only focus on the effluent location. This paper proposes a multi-subsystem collaborative Bi-LSTM-based adaptive soft sensor to achieve the global prediction of ammonia-nitrogen concentration. Firstly, the wastewater treatment process is divided into several independent subsystems depending on the reaction mechanism, and the variable selection is performed using mutual information. Subsequently, the bidirectional long short-term memory network (Bi-LSTM) is employed to construct a model for predicting ammonia-nitrogen concentration within each subsystem, and the outputs between neighboring subsystems are incorporated as a set of new variables added into the training dataset to strengthen their connection. Finally, to address performance degradation caused by environmental factors, a probability density function (PDF)-based dynamic moving window method is proposed to enhance the robustness. The effectiveness and superiority of the proposed soft sensor are validated in the Benchmark Simulation Model no. 1 (BSM1). The experimental results demonstrate that the proposed soft sensor can accurately predict the global ammonia-nitrogen concentration in the face of different weather conditions including sunny, rainy, and stormy days. This study contributes to the stable operation of WWTPs with higher treatment efficiency and lower economic costs.

Micro-aeration and low influent C/N are key environmental factors for achieving ANAMMOX in livestock farming wastewater treatment plants

Anaerobic ammonium oxidation (ANAMMOX)-mediated system is a cost-effective green nitrogen removal process. However, there are few examples of successful application of this advanced wastewater denitrification process in wastewater treatment plants, and the understanding of how to implement anaerobic ammonia oxidation process in full-scale is still limited. In this study, it was found that the abundance of anaerobic ammonia-oxidizing bacteria (AnAOB) in the two livestock wastewater plants named J1 and J2, respectively, showed diametrically opposed trends of waxing and waning with time. The microbial communities of the activated sludge in the two plants at different time were sampled and analyzed by high-throughput sequencing of 16S rRNA genes. Structural equation models (SEMs) were used to reveal the key factors affecting the realization of the ANAMMOX. Changes in the concentration of dissolved oxygen and C/N had a significant effect on the relative abundance of anaerobic ammonia oxidation bacteria (AnAOB). The low concentration of DO (0.2∼0.5 mg/L) could inhibit the activity of nitrifying bacteria (NOB) to achieve partial oxidation of ammonia nitrogen and provide sufficient substrate for the growth of AnAOB, similar to the CANON (Completely Autotrophic Nitrogen removal Over Nitrite). Unlike CANON, heterotrophic denitrification is also a particularly critical part of the livestock wastewater treatment, and a suitable C/N of about 0.6 could reduce the competition risk of heterotrophic microorganisms to AnAOB and ensure a good ecological niche for AnAOB. Based on the results of 16S rRNA and microbial co-occurrence networks, it was discovered that microorganisms in the sludge not only had a richer network interaction, but also achieved a mutually beneficial symbiotic interaction network among denitrifying bacteria (Pseudomonas sp., Terrimonas sp., Dokdonella sp.), AnAOB (Candidatus Brocadia sp.) at DO of 0.2∼0.5 mg/L and C/N of 0.6. Among the top 20 in abundance of genus level, AnAOB had a high relative abundance of 27.66%, followed by denitrifying bacteria of 3.67%, AOB of 0.64% and NOB of 0.26%, which is an essential indicator for the emergence of an AnAOB-dominated nitrogen removal cycle. In conclusion, this study highlights the importance of dissolved oxygen and C/N regulation by analyzing the mechanism of ANAMMOX sludge extinction and growth in two plants under anthropogenic regulation of AnAOB in full-scale wastewater treatment systems.

Important soil microbiota's effects on plants and soils: a comprehensive 30-year systematic literature review

Clarifying the relationship between soil microorganisms and the plant-soil system is crucial for encouraging the sustainable development of ecosystems, as soil microorganisms serve a variety of functional roles in the plant-soil system. In this work, the influence mechanisms of significant soil microbial groups on the plant-soil system and their applications in environmental remediation over the previous 30 years were reviewed using a systematic literature review (SLR) methodology. The findings demonstrated that: (1) There has been a general upward trend in the number of publications on significant microorganisms, including bacteria, fungi, and archaea. (2) Bacteria and fungi influence soil development and plant growth through organic matter decomposition, nitrogen, phosphorus, and potassium element dissolution, symbiotic relationships, plant growth hormone production, pathogen inhibition, and plant resistance induction. Archaea aid in the growth of plants by breaking down low-molecular-weight organic matter, participating in element cycles, producing plant growth hormones, and suppressing infections. (3) Microorganism principles are utilized in soil remediation, biofertilizer production, denitrification, and phosphorus removal, effectively reducing environmental pollution, preventing soil pathogen invasion, protecting vegetation health, and promoting plant growth. The three important microbial groups collectively regulate the plant-soil ecosystem and help maintain its relative stability. This work systematically summarizes the principles of important microbial groups influence plant-soil systems, providing a theoretical reference for how to control soil microbes in order to restore damaged ecosystems and enhance ecosystem resilience in the future.

Transformation mechanisms of ammonium and nitrate in subsurface wastewater infiltration system: Implication for reducing greenhouse gas emissions

Subsurface wastewater infiltration system (SWIS) has been recognized as a cost-effective and environmentally friendly tool for wastewater treatment. However, there is a lack of knowledge on the transformation processes of nitrogen (N), hindering the improvement of the N removal efficiency in SWIS. Here, the migration and transformation mechanisms of ammonium (NH4+-N) and nitrate (NO3+-N) over 10 days were explored by 15N labeling technique. Over the study period, 49% of the added 15NH4+-N remained in the soil, 29% was removed via gaseous N emissions, and 14% was leaked with the effluent in the SWIS. In contrast, only 11% of the added 15NO3--N remained in the soil while 65% of the added 15NO3--N was removed via gaseous N emissions, and 12% with the effluent in the SWIS. The main pathway for N2O emission was denitrification (52-70%) followed by nitrification (15-28%) and co-denitrification (9-20%). Denitrification was also the predominant pathway for N loss as N2, accounting for 88-96% of the N2 emission. The dominant biological transformation processes were different at divergent soil depths, corresponding to nitrification zone and denitrification zone along the longitudinal continuum in SWIS, which was confirmed by the expression patterns of microbial gene abundance. Overall, our findings reveal the mechanism of N transformation in SWIS and provide a theoretical basis for establishing a pollutant management strategy and reducing greenhouse gas emissions from domestic wastewater treatment.

Nitrogen removal performance of improved subsurface wastewater infiltration system under various influent carbon-nitrogen ratios

Subsurface wastewater infiltration system (SWIS) has been recognized as a simple operation and environmentally friendly technology for wastewater purification. However, effectively removing nitrogen (N) remains a challenge, hindering the widespread application of SWIS. In this study, zero-valent iron (ZVI) and porous mineral material (PMM) were applied in SWIS to improve the soil matrix. Our results suggested that the addition of ZVI and PMM could simultaneously enhance N removal efficiency and reduce nitrous oxide emissions. This could be attributed to the abundant electrons generated by ZVI alleviating the electronic limitation of denitrification and the porous structure of PMM providing solid phase support for microbial growth. In addition, the abundance of microbial functional genes increased in modified SWIS, which could further explain the higher pollutant removal efficiency. Overall, this study provides new insights into the mitigation of wastewater pollution and greenhouse gas emissions in SWIS. PRACTITIONER POINTS: ZVI and PMM can adapt to different C loads and enhance pollutant removal efficiency in SWIS. Increasing C-N ratios positively affected the nitrate removal performance and negatively affected ammonium removal performance in SWIS. The amending soil matrix promoted the reduction of the N2 O to N2 and greenhouse gas emissions were well controlled. The abundance of microbial functional genes increased with the improvement of the soil matrix.

Migration of microorganisms between nitrification-denitrification flocs, anammox biofilms and blank carriers during mainstream anammox start-up

To solve the shortage of inoculum, the feasibility of establishing simultaneous partial nitrification, anammox, and denitrification (SNAD) reactor through inoculating nitrification-denitrification sludge, anammox biofilm and blank carriers was investigated. Advanced nitrogen removal efficiency of 91.2 ± 3.6 % was achieved. Bacteria related to nitrogen removal and fermentation were enriched in anammox biofilm, blank carriers and flocs, and the abundance of dominant anaerobic ammonia oxidizing bacteria (AnAOB), Candidatus Brocadia, reached 3.4 %, 0.5 % and 0.3 %, respectively. Candidatus Competibacter and Calorithrix became the dominant denitrifying bacteria (DNB) and fermentative bacteria (FB), respectively. The SNAD system was successfully established, and new mature biofilms formed in blank carriers, which could provide inoculum for other anammox processes. Partial nitrification, partial denitrification and aerobic_chemoheterotrophy were existed and facilitated AnAOB enrichment. Microbial correlation networks revealed the cooperation between DNB, FB and AnAOB that promoted nitrogen removal. Overall, the SNAD process was started up through inoculating more accessible inoculum.

Metagenomics insights into high-rate nitrogen removal from municipal wastewater by integrated nitrification, partial denitrification and Anammox at an extremely short hydraulic retention time

To achieve high-rate nitrogen removal in municipal wastewater treatment through anaerobic ammonia oxidation (Anammox), the nitrification, partial denitrification, and Anammox processes were integrated by a step-feed strategy. An exceptional nitrogen removal load of 0.224 kg N/(m3·d) was achieved by gradient-reducing the hydraulic retention time (HRT) to 5 h. Metagenomic analysis demonstrated that Nitrosospira could express all genes encoding ammonia oxidation under low nitrogen and dissolved oxygen conditions (less than 0.5 mg/L), enabling complete nitrification. With the short of HRT, the relative abundance of Thauera increased from 2.8 % to 6.4 %. Frequent substrate exchanges at such extremely short HRT facilitated enhanced synergistic interactions among Nitrosospira, Thauera, and Candidatus Brocadia. These findings provide a comprehensive understanding of the utilization of Anammox combined processes for high-speed nitrogen removal in municipal wastewater treatment and the microbial interactions involved.

Combination of Sequencing Batch Operation and A/O Process to Achieve Partial Mainstream Anammox: Pilot-Scale Demonstration and Microbial Ecological Mechanism

In this study, sequencing batch operation was successfully combined with a pilot-scale anaerobic biofilm-modified anaerobic/aerobic membrane bioreactor to achieve anaerobic ammonium oxidation (anammox) without inoculation of anammox aggregates for municipal wastewater treatment. Both total nitrogen and phosphorus removal efficiencies of the reactor reached up to 80% in the 250-day operation, with effluent concentrations of 4.95 mg-N/L and 0.48 mg-P/L. In situ enrichment of anammox bacteria with a maximum relative abundance of 7.86% was observed in the anaerobic biofilm, contributing to 18.81% of nitrogen removal, with denitrification being the primary removal pathway (38.41%). Denitrifying phosphorus removal (DPR) (40.54%) and aerobic phosphorus uptake (48.40%) played comparable roles in phosphorus removal. Metagenomic sequencing results showed that the biofilm contained significantly lower abundances of NO-reducing functional genes than the bulk sludge (p < 0.01), favoring anammox catabolism in the former. Interactions between the anammox bacteria and flanking community were dominated by cooperation behaviors (e.g., nitrite supply, amino acids/vitamins exchange) in the anaerobic biofilm community network. Moreover, the hydrolytic/fermentative bacteria and endogenous heterotrophic bacteria (Dechloromonas, Candidatus competibacter) were substantially enriched under sequencing batch operation, which could alleviate the inhibition of anammox bacteria by complex organics. Overall, this study provides a feasible and promising strategy for substantially enriching anammox bacteria and achieving partial mainstream anammox as well as DPR.