Survival strategy of comammox bacteria in a wastewater nutrient removal system with sludge fermentation liquid as additional carbon source

Comparative enrichment of complete ammonium oxidation bacteria in floccular sludge reactors: Sequencing batch reactor vs. continuous stirred tank reactor

This study attempted to compare the enrichment of complete ammonium oxidation (comammox) bacteria, which are affiliated with Nitrospira and not able to generate nitrous oxide (N2O, a potent greenhouse gas) through biological pathways, in two commonly-utilized configurations of floccular sludge reactors, i.e., sequencing batch reactor (SBR) and continuous stirred tank reactor (CSTR), under the ammonium condition of mainstream wastewater (i.e., 40.0 g-N/m3). The results in terms of nitrification performance and microbial analyses during 216-d operation showed that compared with SBR offering a fluctuating but generally higher in-situ ammonium concentration (i.e., 1.0-6.0 g-N/m3) which was favorable for the growth of ammonium-oxidizing bacteria (AOB, belonging to Nitrosomonas in this study), CSTR managed to lower the in-situ ammonium level to < 2.0 g-N/m3, thus creating a competitive advantage for comammox bacteria with a highly oligotrophic lifestyle. Such an argument was further supported by dedicated batch tests which revealed that Nitrospira-dominant sludge had a lower maximum ammonium oxidation rate and lower apparent ammonium and oxygen affinity constants than Nitrosomonas-dominant sludge (i.e., 33.5 ± 2.1 mg-N/h/g-MLVSS vs. 139.9 ± 26.7 mg-N/h/g-MLVSS, 1.1 ± 0.1 g-N/m3 vs. 17.6 ± 4.6 g-N/m3, and 0.017 ± 0.002 g-O2/m3 vs. 0.037 ± 0.013 g-O2/m3, respectively), proving the nature of comammox bacteria as a K-strategist. Overall, this study not only provided useful insights into the effective enrichment of comammox bacteria in floccular sludge but also further revealed the interactions between comammox bacteria and AOB, thereby contributing to the future development of comammox-inclusive biological nitrogen removal technologies for sustainable wastewater treatment.

Response of comammox Nitrospira clades A and B communities to long-term fertilization and rhizosphere effects and their relative contribution to nitrification in a subtropical paddy field of China

The recently discovered complete ammonia oxidation (comammox Nitrospira) containing clade A and clade B has further complemented our understanding of nitrification process. Nevertheless, understanding the community feature of comammox Nitrospira clades A and B and their relative contribution to nitrification in paddy rhizosphere are still in its infancy. In this study, we assessed the community diversity and structure of comammox Nitrospira clades A and B in paddy rhizosphere and bulk soils under thirty years of different fertilization strategies, i.e., non-fertilization control (CK), chemical fertilizers application (NPK), and NPK plus swine manure (NPKM), respectively. NPKM significantly increased the a-diversity (Chao1 and Shannon indices) of comammox Nitrospira clade A and altered the community structure (P < 0.05) but had little effect on clade B. A two-way analysis of variance (ANOVA) showed that the effect of long-term fertilization on soil comammox Nitrospira community and nitrification potential rate (PNR) was much greater than that of rhizosphere. Compared with NPK, soil PNR was greatly increased by 51.0% under the NPKM treatment in the rhizosphere (P < 0.05). Phylogenetic analysis showed that NPKM improved the relative abundances of sub-clade A.2.1 and sub-clade A.3.2 of the comammox clade A community, with an average increase of 212.2 and 210.4% in both rhizosphere and bulk soils relative to the NPK treatment. Soil organic matter, NH4+-N, and pH were significant soil drivers of comammox Nitrospira clades A and B community. Furthermore, linear regression and structural equation modeling clearly showed that comammox Nitrospira clade A a-diversity were significantly associated with soil PNR (P < 0.05). Our results suggest (i) that comammox Nitrospira clade A are sensitive to the organic fertilization; and (ii) that comammox Nitrospira clade A contribute more to nitrification than clade B under the long-term organic fertilized paddy soil.

Dissolved oxygen drives heterotrophic microorganism succession to regulate low carbon source wastewater treatment enhanced by slurry

The limited availability of carbon sources in low carbon source wastewater has always hindered nitrogen removal efficiency. The residual slurry liquid after anaerobic digestion has the potential to be used as a carbon source. This study investigated the optimal parameters of dissolved oxygen (DO) for enhancing the treatment of low carbon source wastewater using slurry, and revealed the characteristics of carbon metabolism gene enrichment and carbon fixation potential driven by DO. The results indicated that treating wastewater under high DO concentrations (3-4 mg/L) conditions could meet the emission standards set by wastewater treatment plants in China. However, the lower-cost DO concentration of 3 mg/L is considered a more cost-effective parameter, effectively removing 85.68% of chemical oxygen demand and 91.56% of total nitrogen. Mechanistic analysis suggested that reducing DO concentration increased the diversity of microbial communities. Regulating DO concentration reshaped the co-metabolic network of microorganisms with different DO sensitivities by influencing Hydrogenophaga and Chlorobium. This ultimately led to the reconstruction of heterotrophic microbial communities dominated by Sphaerotilus and Acidovorax under high DO conditions, and heterotrophic-autotrophic co-enriched microbial communities dominated by Chlorobium under low DO conditions (1-2 mg/L). Additionally, under high DO conditions, high microbial mass transfer efficiency and the enrichment of functional genes were crucial for achieving high nitrogen removal performance. Further, the microbial carbon fixation potential was relatively high under the DO 3 mg/L condition, helping to reduce the consumption of additional carbon sources. This study provided innovative ideas for the sustainable and low-carbon development of wastewater treatment technology.

Metatranscriptomic Analysis Reveals Synergistic Activities of Comammox and Anammox Bacteria in Full-Scale Attached Growth Nitrogen Removal System

Leveraging comammox Nitrospira and anammox bacteria for shortcut nitrogen removal can drastically lower the carbon footprint of wastewater treatment facilities by decreasing aeration energy, carbon, alkalinity, and tank volume requirements while also potentially reducing nitrous oxide emissions. However, their co-occurrence as dominant nitrifying bacteria is rarely reported in full-scale wastewater treatment. As a result, there is a poor understanding of how operational parameters, in particular, dissolved oxygen, impact their activity and synergistic behavior. Here, we report the impact of dissolved oxygen concentration (DO = 2, 4, 6 mg/L) on the microbial community's transcriptomic expression in a full-scale integrated fixed film activated sludge (IFAS) municipal wastewater treatment facility where nitrogen removal is predominantly performed by comammox Nitrospira and anammox bacterial populations. 16S rRNA transcript compositions revealed anammox bacteria and Nitrospira were significantly more active in IFAS biofilms compared to suspended sludge biomass. In IFAS biofilms, anammox bacteria significantly increased hzo expression at lower dissolved oxygen concentrations and this increase was highly correlated with the amoA expression levels of comammox bacteria. Interestingly, the genes involved in nitrite oxidation by comammox bacteria were significantly more upregulated, relative to the genes involved in ammonia oxidation with decreasing dissolved oxygen concentrations. Ultimately, our findings suggest that comammox Nitrospira supplies anammox bacteria with nitrite via ammonia oxidation and that this synergistic behavior is dependent on dissolved oxygen concentrations.

A critical review of comammox and synergistic nitrogen removal coupling anammox: Mechanisms and regulatory strategies

Nitrification is highly crucial for both anammox systems and the global nitrogen cycle. The discovery of complete ammonia oxidation (comammox) challenges the inherent concept of nitrification as a two-step process. Its wide distribution, adaptability to low substrate environments, low sludge production, and low greenhouse gas emissions may make it a promising new nitrogen removal treatment process. Meanwhile, anammox technology is considered the most suitable process for future wastewater treatment. The diverse metabolic capabilities and similar ecological niches of comammox bacteria and anammox bacteria are expected to achieve synergistic nitrogen removal within a single system. However, previous studies have overlooked the existence of comammox, and it is necessary to re-evaluate the conclusions drawn. This paper outlined the ecophysiological characteristics of comammox bacteria and summarized the environmental factors affecting their growth. Furthermore, it focused on the enrichment, regulatory strategies, and nitrogen removal mechanisms of comammox and anammox, with a comparative analysis of hydroxylamine, a particular intermediate product. Overall, this is the first critical overview of the conclusions drawn from the last few years of research on comammox-anammox, highlighting possible next steps for research.

Comammox and unknown ammonia oxidizers contribute to nitrite accumulation in an integrated A-B stage process that incorporates side-stream EBPR (S2EBPR)

A novel integrated pilot-scale A-stage high rate activated sludge, B-stage short-cut biological nitrogen removal and side-stream enhanced biological phosphorus removal (A/B-shortcut N-S2EBPR) process for treating municipal wastewater was demonstrated with the aim to achieve simultaneous and carbon- and energy-efficient N and P removal. In this studied period, an average of 7.62 ± 2.17 mg-N/L nitrite accumulation was achieved through atypical partial nitrification without canonical known NOB out-selection. Network analysis confirms the central hub of microbial community as Nitrospira, which was one to two orders of magnitude higher than canonical aerobic oxidizing bacteria (AOB) in a B-stage nitrification tank. The contribution of comammox Nitrospira as AOB was evidenced by the increased amoB/nxr ratio and higher ammonia oxidation activity. Furthermore, oligotyping analysis of Nitrospira revealed two dominant sub-clusters (microdiveristy) within the Nitrospira. The relative abundance of oligotype II, which is phylogenetically close to Nitrospira_midas_s_31566, exhibited a positive correlation with nitrite accumulation in the same operational period, suggesting its role as comammox Nitrospira. Additionally, the phylogenetic investigation suggested that heterotrophic organisms from the family Comamonadacea and the order Rhodocyclaceae embedding ammonia monooxygenase and hydroxylamine oxidase may function as heterotrophic nitrifiers. This is the first study that elucidated the impact of integrating the S2EBPR on nitrifying populations with implications on short-cut N removal. The unique conditions in the side-stream reactor, such as low ORP, favorable VFA concentrations and composition, seemed to exert different selective forces on nitrifying populations from those in conventional biological nutrient removal processes. The results provide new insights for integrating EBPR with short-cut N removal process for mainstream wastewater treatment.

Competitive enrichment of comammox Nitrospira in floccular sludge

The discovery of complete ammonium oxidation (comammox) has subverted the traditional perception of two-step nitrification, which plays a key role in achieving biological nitrogen removal from wastewater. Floccular sludge-based treatment technologies are being applied at the majority of wastewater treatment plants in service where detection of various abundances and activities of comammox bacteria have been reported. However, limited efforts have been made to enrich and subsequently characterize comammox bacteria in floccular sludge. To this end, a lab-scale sequencing batch reactor (SBR) in the step-feeding mode was applied in this work to enrich comammox bacteria through controlling appropriate operational conditions (dissolved oxygen of 0.5 ± 0.1 g-O2/m3, influent ammonium of 40 g-N/m3 and uncontrolled longer sludge retention time). After 215-d operation, comammox bacteria gradually gained competitive advantages over counterparts in the SBR with a stable nitrification efficiency of 92.2 ± 2.2 %: the relative abundance of Nitrospira reached 42.9 ± 1.3 %, which was 13 times higher than that of Nitrosomonas, and the amoA gene level of comammox bacteria increased to 7.7 ± 2.1 × 106 copies/g-biomass, nearly 50 times higher than that of conventional ammonium-oxidizing bacteria. The enrichment of comammox bacteria, especially Clade A Candidatus Nitrospira nitrosa, in the floccular sludge led to (i) apparent affinity constants for ammonium and oxygen of 3.296 ± 0.989 g-N/m3 and 0.110 ± 0.004 g-O2/m3, respectively, and (ii) significantly low N2O and NO production, with emission factors being 0.136 ± 0.026 % and 0.023 ± 0.013 %, respectively.

N-methyl pyrrolidone manufacturing wastewater as the electron donor for denitrification: From bench to pilot scale

Actual wastewater generated from N-methylpyrrolidone (NMP) manufacture was used as electron donor for tertiary denitrification. The organic components of NMP wastewater were mainly NMP and monomethylamine (CH3NH2), and their biodegradation released ammonium that was nitrified to nitrate that also had to be denitrified. Bench-scale experiments documented that alternating denitrification and nitrification realized effective total‑nitrogen removal. Ammonium released from NMP was nitrified in the aerobic reactor and then denitrified when actual NMP wastewater was used as the electron donor for endogenous and exogenous nitrate. Whereas TN and NMP removals occurred in the denitrification step, dissolved organic carbon (DOC) and CH3NH2 removals occurred in the denitrification and nitrification stages. The genera Thauera and Paracoccus were important for NMP biodegradation and denitrification in the denitrification reactor; in the nitrification stage, Amaricoccus and Sphingobium played key roles for biodegrading intermediates of NMP, while Nitrospira was responsible for NH4+ oxidation to NO3-. Pilot-scale demonstration was achieved in a two-stage vertical baffled bioreactor (VBBR) in which total‑nitrogen removal was realized sequential anoxic-oxic treatment without biomass recycle. Although the bench-scale reactors and the VBBR had different configurations, both effectively removed total nitrogen through the same mechanisms. Thus, an N-containing organic compound in an industrial wastewater could be used to drive total-N removal in a tertiary-treatment scenario.

Redirecting carbon to recover VFA to facilitate biological short-cut nitrogen removal in wastewater treatment: A critical review

Wastewater treatment plants (WWTPs) are facing a great challenge to transition from energy-intensive to carbon-neutral and energy-efficient systems. Biological nutrient removal (BNR) can be severely impacted by carbon limitation, particularly for wastewater with a low carbon-to-nitrogen (C/N) ratio, which can significantly increase the operational costs. Waste activated sludge (WAS) is a valuable byproduct of WWTPs, as it contains high levels of organic matter that can be utilized to improve BNR management by recovering and reusing the fermentative volatile fatty acids (VFAs). This review provides a comprehensive examination of the recovery and reuse of VFAs in wastewater management, with a particular focus on advancing the preferable biological short-cut nitrogen removal process for carbon-insufficient municipal wastewaters. First, the method of carbon redirection for recovering VFAs was reviewed. Carbon could be captured through the two-stage A/B process or via sludge fermentation with different sludge pretreatment and process control strategies to accelerate sludge hydrolysis and inhibit methanogens to enhance VFA production. Second, VFAs can support the metabolism of autotrophic N-cycling microorganisms involved in wastewater treatment, such as AOB, NOB, anammox, and comammox bacteria. However, VFAs can also cause inhibition at high concentrations, leading to the partition of AOB and NOB; and can promote partial denitrification as an efficient carbon source for heterotrophic denitrifiers. Third, the lab- and pilot-scale engineering practices with different configurations (i.e., A²O, SBR, UASB) were summarized that have shown the feasibility of utilizing the fermentate to achieve superior nitrogen removal performance without the need for external carbon addition. Lastly, the future perspectives on leveraging the relationships between mainstream and sidestream, nitrogen and phosphorus, autotrophs and heterotrophs were given for sustainable and efficient BNR management.

Low diversity and microdiversity of comammox bacteria in wastewater systems suggest specific adaptations within the Ca. Nitrospira nitrosa cluster

Studies have found Ca. Nitrospira nitrosa-like bacteria to be the principal or sole comammox bacteria in nitrogen removal systems for wastewater treatment. In contrast, multiple populations of strict ammonia and nitrite oxidizers co-exist in similar systems. This apparent lack of diversity is surprising and could impact the feasibility of leveraging comammox bacteria for nitrogen removal. We used full-length 16S rRNA gene sequencing and genome-resolved metagenomics to compare the species-level diversity of comammox bacteria with that of strict nitrifiers in full-scale wastewater treatment systems and assess whether this comparison is consistent or diverged at the strain-level. Full-length 16S rRNA gene sequencing indicated that Nitrosomonas-like bacteria exhibited higher species-level diversity in comparison with other nitrifying bacteria, while the strain-level diversity (also called microdiversity) of most Nitrospira-like bacteria were higher than Nitrosomonas-like bacteria with few exceptions (one Nitrospira lineage II population). Comammox bacterial metagenome assembled genomes (MAGs) were associated with Ca. Nitrospira nitrosa. The average amino acid identity between principal comammox bacterial MAGs (93% ± 3) across systems was significantly higher than that of the Nitrosomonas-like ammonia oxidizers (73% ± 8), the Nitrospira_A-like nitrite oxidizer (85% ± 4), and the Nitrospira_D-like nitrite oxidizer (83% ± 1). This demonstrated the low species-level diversity of comammox bacteria compared with strict nitrifiers and further suggests that the same comammox population was detected in all systems. Comammox bacteria (Nitrospira lineage II), Nitrosomonas and, Nitrospira_D (Nitrospira lineage II) MAGs were significantly less microdiverse than the Nitrospira_A (lineage I) MAGs. Interestingly, strain-resolved analysis also indicates that different nitrogen removal systems harbor different comammox bacterial strains within the Ca. Nitrospira nitrosa cluster. These results suggest that comammox bacteria associated with Ca. Nitrospira nitrosa have low species- and strain-level diversity in nitrogen removal systems and may thus harbor specific adaptations to the wastewater ecosystem.

Advanced nutrient removal and external sludge reduction: Demonstration in a pilot-scale sequencing batch reactor

Although the addition of excess sludge fermentation products to improve nutrient removal from sewage is cost-effective, its application has rarely been demonstrated. In this study, the external sludge was first collected and fermented under a sludge retention time of 10 days, then introduced into SBR with a 1:15 sewage ratio. The results revealed a gradual increase in the nitrite accumulation ratio to 34.7% in the SBR at the end of the oxic stage after 64 days of adding fermented sludge products. In addition, the average effluent total nitrogen and phosphorous decreased to 7.3 and 0.5 mg/L, corresponding to removal efficiencies of 86.7% and 95.5%, respectively. On the other hand, the use of the fermented sludge products as external organic carbon sources in the SBR increased the external sludge reduction ratio to 42.5%. High-throughput sequencing demonstrated that the increase in the endogenous denitrifier community, polyphosphate-accumulating organisms, and fermentation bacteria were the main factors contributing to the increase in nutrient removal and excess sludge reduction. The economic evaluation indicated that the operational cost of the pilot-scale system saves 0.011$/m³ of sewage treated. PRACTITIONER POINTS: Fermented sludge addition effectively enhanced nutrient removal in pilot-scale SBR. Average effluent TN and PO₄ ^3- -P decreased to 7.3 and 0.5 mg/L, respectively. Highest external sludge reduction rate was 42.5% in pilot-scale reactor. Sewage treatment cost can save 0.011$/m³ under advanced nutrient removal.

Removal of Mg2+ inhibition benefited the growth and isolation of ammonia-oxidizing bacteria: An inspiration from bacterial interaction

Ammonia-oxidizing bacteria (AOB) play an important role in the global nitrogen cycle and have broad applications in the nitrogen removal from wastewater. However, the AOB species are sensitive to environmental factors and usually form tight relationships with other microbes, making the AOB isolation and maintenance are difficult and time-consuming. In this study, the relationship that occurred between AOB and their bacterial partners was found to be able to improve the ammonia oxidation; during the co-cultivation, the magnesium ions (Mg²⁺) with removal rate as high as 36.7% was removed from culture medium by the concomitant bacterial species, which was regarded as the main reason for improving ammonia oxidation. During the pure cultivation of AOB isolate, when the concentration of Mg²⁺ reduced to low levels, the ammonia-oxidizing activity was more than 5 times and the amoA gene expression was more than 12 times higher than that grown in the initial culture medium. Based on a newly designed culture medium, the ammonia oxidation of AOB isolate grown in liquid culture was significantly promoted and the visible AOB colonies with much more number and larger diameter were observed to form on agar plates. With the addition of high concentration of calcium carbonate (CaCO₃), AOB colonies could be easily and specifically identified by following the hydrolytic zones that formed around AOB colonies. Another AOB isolates were successively obtained from different samples and within a short time, suggesting the feasibility and effectivity of this culture medium and strategy on the AOB isolation from environments.

Comammox Nitrospira bacteria outnumber canonical nitrifiers irrespective of electron donor mode and availability in biofiltration systems

Complete ammonia oxidizing bacteria coexist with canonical ammonia and nitrite oxidizing bacteria in a wide range of environments. Whether this is due to competitive or cooperative interactions, or a result of niche separation is not yet clear. Understanding the factors driving coexistence of nitrifiers is critical to manage nitrification processes occurring in engineered and natural ecosystems. In this study, microcosm-based experiments were used to investigate the impact of nitrogen source and loading on the population dynamics of nitrifiers in drinking water biofilter media. Shotgun sequencing of DNA followed by co-assembly and reconstruction of metagenome assembled genomes revealed clade A2 comammox bacteria were likely the primary nitrifiers within microcosms and increased in abundance over Nitrsomonas-like ammonia and Nitrospira-like nitrite oxidizing bacteria irrespective of nitrogen source type or loading. Changes in comammox bacterial abundance did not correlate with either ammonia or nitrite oxidizing bacterial abundance in urea amended systems where metabolic reconstruction indicated potential for cross feeding between ammonia and nitrite oxidizing bacteria. In contrast, comammox bacterial abundance demonstrated a negative correlation with nitrite oxidizers in ammonia amended systems. This suggests potentially weaker synergistic relationships between ammonia and nitrite oxidizers might enable comammox bacteria to displace nitrite oxidizers from complex nitrifying communities.