Recent mechanistic developments for cytochrome c nitrite reductase, the key enzyme in the dissimilatory nitrate reduction to ammonium pathway

Cytochrome c nitrite reductase, NrfA, is a soluble, periplasmic pentaheme cytochrome responsible for the reduction of nitrite to ammonium in the Dissimilatory Nitrate Reduction to Ammonium (DNRA) pathway, a vital reaction in the global nitrogen cycle. NrfA catalyzes this six-electron and eight-proton reduction of nitrite at a single active site with the help of its quinol oxidase partners. In this review, we summarize the latest progress in elucidating the reaction mechanism of ammonia production, including new findings about the active site architecture of NrfA, as well as recent results that elucidate electron transfer and storage in the pentaheme scaffold of this enzyme.

Relating the carbon sources to denitrifying community in full-scale wastewater treatment plants

Carbon source is a key factor determining the denitrifying effectiveness and efficiency in wastewater treatment plants (WWTPs). Whereas, the relationships between diverse and distinct denitrifying communities and their favorable carbon sources in full-scale WWTPs were not well-understood. This study performed a systematic analysis of the relationships between the denitrifying community and carbon sources by using 15 organic compounds from four categories and activated sludge from 8 full-scale WWTPs. Results showed that, diverse denitrifying bacteria were detected with distinct relative abundances in 8 WWTPs, such as Haliangium (1.98-4.08%), Dechloromonas (2.00-3.01%), Thauera (0.16-1.06%), Zoogloea (0.09-0.43%), and Rhodoferax (0.002-0.104%). Overall, acetate resulted in the highest denitrifying activities (1.21 to 4.62 mg/L/h/gMLSS), followed by other organic acids (propionate, butyrate and lactate, etc.). Detectable dissimilatory nitrate reduction to ammonium (DNRA) was observed for all 15 carbon sources. Methanol and glycerol resulted in the highest DRNA. Acetate, butyrate, and lactate resulted in the lowest DNRA. Redundancy analysis and 16S cDNA amplicon sequencing suggested that carbon sources within the same category tended to correlate to similar denitrifiers. Methanol and ethanol were primarily correlated to Haliangium. Glycerol and amino acids (glutamate and aspartate) were correlated to Inhella and Sphaerotilus. Acetate, propionate, and butyrate were positively correlated to a wide range of denitrifiers, explaining the high efficiency of these carbon sources. Additionally, even within the same genus, different amplicon sequence variants (ASVs) performed distinctly in terms of carbon source preference and denitrifying capabilities. These findings are expected to benefit carbon source formulation and selection in WWTPs.

Cyanobacterial Genomes from a Brackish Coastal Lagoon Reveal Potential for Novel Biogeochemical Functions and Their Evolution

Cyanobacteria are recognised for their pivotal roles in aquatic ecosystems, serving as primary producers and major agents in diazotrophic processes. Currently, the primary focus of cyanobacterial research lies in gaining a more detailed understanding of these well-established ecosystem functions. However, their involvement and impact on other crucial biogeochemical cycles remain understudied. This knowledge gap is partially attributed to the challenges associated with culturing cyanobacteria in controlled laboratory conditions and the limited understanding of their specific growth requirements. This can be circumvented partially by the culture-independent methods which can shed light on the genomic potential of cyanobacterial species and answer more profound questions about the evolution of other key biogeochemical functions. In this study, we assembled 83 cyanobacterial genomes from metagenomic data generated from environmental DNA extracted from a brackish water lagoon (Chilika Lake, India). We taxonomically classified these metagenome-assembled genomes (MAGs) and found that about 92.77% of them are novel genomes at the species level. We then annotated these cyanobacterial MAGs for all the encoded functions using KEGG Orthology. Interestingly, we found two previously unreported functions in Cyanobacteria, namely, DNRA (Dissimilatory Nitrate Reduction to Ammonium) and DMSP (Dimethylsulfoniopropionate) synthesis in multiple MAGs using nirBD and dsyB genes as markers. We validated their presence in several publicly available cyanobacterial isolate genomes. Further, we identified incongruities between the evolutionary patterns of species and the marker genes and elucidated the underlying reasons for these discrepancies. This study expands our overall comprehension of the contribution of cyanobacteria to the biogeochemical cycling in coastal brackish ecosystems.

Role of sulfide on DNRA distribution and the microbial community structure in a sulfide-driven nitrate reduction process

Microbial nitrate reduction processes involve two competing pathways: denitrification (DEN) and dissimilatory nitrate reduction to ammonium (DNRA). This study investigated the distribution of DNRA in a sole sulfur-driven nitrogen conversion process using a laboratory-scale sequencing biofilm batch reactor (SBBR) through a series of batch tests with varying sulfide/nitrate (S/N) ratios. The results showed that DNRA became more dominant in the sulfide-oxidizing autotrophic denitrification (SOAD) process as the S/N ratio increased to 1.5:1, 1.7:1, and 2:1, reaching a peak of 35.3% at the S/N ratio of 1.5:1. Oxidation-reduction potential (ORP) patterns demonstrated distinct inflection points for nitrate and nitrite consumption under the SOAD-only conditions, whereas these points overlapped when DNRA coexisted with SOAD. Analysis of 16S ribosomal RNA identified Ignavibacterium, Hydrogenophaga, and Geobacter as the dominant genera responsible for DNRA during autotrophic nitrate reduction. The findings of the DNRA divergence investigation provided valuable insights into enhancing biological nitrogen removal processes, particularly when coupled with the anammox.

Sediment organic matter properties facilitate understanding nitrogen transformation potentials in East African lakes

East African lakes include the most productive and alkaline lake group in the world. Yet, they generally receive fewer nutrient inputs than the densely populated subtropical and temperate lakes in the northern hemisphere. In these lakes with insufficient supplies of inorganic nitrogen, the mineralization of benthic organic matter can play an important role in driving the nutrient cycle and nitrogen loss. Using a suite of stable ¹⁵N isotope dilution and tracer techniques, we examined five main processes of the sediment nitrogen cycle in 16 lakes and reservoirs of Tanzania and Kenya, East Africa: gross nitrogen mineralization, ammonium immobilization, dissimilatory nitrate reduction to ammonium (DNRA), and the dinitrogen (N₂) production via denitrification and anaerobic ammonium oxidation (anammox). Gross nitrogen mineralization and ammonium immobilization showed the maximum values of 9.84 and 12.39 μmol N kg^-1 h^-1, respectively. Potential DNRA rates ranged from 0.22 to 8.15 μmol N kg^-1 h^-1 and accounted for 10 %-74 % (average 25 %) of the total dissimilatory nitrate reduction. Potential nitrate reduction rates in most lakes were dominated by denitrification with a contribution of 26 %-85 % and a mean of 65 %. We further found that the sediment nitrogen transformations were driven mainly by benthic organic matter properties and water column phosphate concentrations, reflecting microbial metabolic responses to the changing carbon and nutrients availability. For instance, autochthonous production of protein-like organic matter attributed to active sediment nitrogen mineralization, DNRA, and denitrification. In contrast, the high degree of humification caused by the inputs of terrestrial humic-like substances slowed down the sediment nitrogen transformations. The contribution of DNRA to total dissimilatory nitrate reduction was significantly positively correlated to sediment C: N ratios. These results indicate that predictions of sediment N supply and loss in East African lakes can be improved by incorporating sediment organic matter properties.

Dissimilatory nitrate reduction to ammonium (DNRA) potentially facilitates the accumulation of phosphorus in lake water from sediment

Nitrogen (N) and phosphorus (P) are crucial nutrients for eutrophication in the lacustrine ecosystem and attract the attention worldwide. However, the interaction between them need further clarification. This study aimed to assess the influence of dissimilatory nitrate reduction to ammonia (DNRA) on the cycle of P in lacustrine sediment. Different fractions of N and P in the pore water were measured using high-resolution in-situ measurement techniques, HR-Peeper and DGT, coupling with sequential extraction for solid sediment from a shallow freshwater lake. The results showed that elevated nitrate (NO₃^-) reduction via DNRA rather than denitrification was verified at deeper sediment layer, suggesting the generation of inorganic ammonia (NH₄⁺) as electron donor under anaerobic episodes. High abundance of DNRA bacteria (nrfA gene) obtained using high-throughput sequencing analysis were detected at upper layer and responsible for the accumulation of NH₄⁺ in the sediment coupling with chemolithoautotrophic metabolism. Additionally, significant desorption of ionic ferrous iron (Fe²⁺) and dissolved reactive phosphate (DRP) from solid phase and the enrichment in the solution was simultaneously detected. Higher concentration of solid Fe bound P (Fe-P) at deeper layer indicated the potential re-oxidation of Fe²⁺ as electron donor during DNRA process and sorption of DRP toward the Fe-containing minerals. However, obvious evidence of desorption proved by DGT indicated that higher NH₄⁺ concentrations favored the reduction of Fe(III) oxy(hydr)oxides and the desorption of DRP into the pore water and diffusion toward the overlying water. Finally, noteworthy S^2- release from solid sediment was speculated to stimulate the DNRA and facilitated the accumulation of NH₄⁺ in the solution, which further induced the enrichment of DRP in water from the solid phase. Overall, DNRA potentially facilitates the accumulation of P in lake water, and the synchronous control of N and P is important for the eutrophication management and restoration of lake eutrophication.

Role of organic/sulfide ratios on competition of DNRA and denitrification in a co-driven sequencing biofilm batch reactor

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two competing pathways in nitrate-reducing process. In this study, a series of C/S ratios from 8:1 to 2:4 were investigated in a sequencing biofilm batch reactor (SBBR) to determine the role of reducers (sulfide and acetate) on their competition. The results showed that the proportion of DNRA increased in high electron system, either in organic-rich system or in sulfide-rich system. The highest DNRA ratio increased to 16.4% at the C/S ratio of 2:3. Excess electron donors, particularly sulfide, were favorable for DNRA in a limited nitrate environment. Moreover, a higher reductive environment could facilitate DNRA, especially, when ORP was lower than - 400 mV in this system. 16S rRNA gene sequencing analysis demonstrated that Geobacter might be the important participant involved in DNRA process in organic-rich system, while Desulfomicrobium might be the dominant DNRA bacteria in sulfide-rich system. DNRA cultivation could enrich nitrogen conversion pathways in conventional denitrification systems and deepen the insight into nitrogen removal at low C/N.

Organic carbon quantity and quality jointly triggered the switch between dissimilatory nitrate reduction to ammonium (DNRA) and denitrification in biofilters

The effect of organic carbon (OC) quality and quantity on switch between dissimilatory nitrate reduction to ammonium (DNRA) and denitrification (DEN) was studied in biofilter systems. High OC in matrix could promote significantly nitrate (NO₃^--N) removal due to the reinforce of DEN. Sodium acetate (SA) addition in influent further fueled NO₃^--N removal in groups with low OC in matrix but increased ammonium (NH₄⁺-N) and nitrite (NO₂^--N) accumulation in groups with high OC in matrix. This indicated that high OC combined different species, facilitated the DNRA over DEN. Compared to bagasse, corncob was the better suitable OC source in matrix for DEN due to slow and continuous release of OC. Hence, in order to promote NO₃^--N removal and decline NH₄⁺-N accumulation in biofilters, it is very important to screen suitable OC source (mixed utilization of multiple C sources is recommended) and regulate its dosage (below 80 mg L^-1).

Dissimilatory nitrate reduction to ammonium (DNRA) in traditional municipal wastewater treatment plants in China: Widespread but low contribution

Recent reports on the occurrence and contribution of dissimilatory nitrate reduction to ammonium (DNRA) in marine, inland water, and soil systems have greatly improved our understanding of the global nitrogen (N) cycle. This also promoted the investigation of the role and ecological features of DNRA in anthropogenic ecosystems. However, so far, the use of DNRA in municipal wastewater treatment plants (WWTPs), which are one of the most common and largest biotechnologically artificial water ecosystems, has not been investigated. Accordingly, this study focused on the abundance, activity, community structure, and diversity of DNRA bacteria in full-scale WWTPs. DNRA bacteria were detected in all treatment units in six tested municipal WWTPs, even in aerobic zones (dissolved oxygen > 2 mg L^-1). Although the relative abundance of DNRA bacteria (0.2-4.0%) was less than that of denitrifying bacteria (0.7-10.1%) among all investigated samples, the abundance of DNRA bacteria still reaches 10⁹ gene copies g^-1. However, ¹⁵N-isotope tracing indicated that the potential DNRA rates were significantly lower (0.4-2.1 nmol N g^-1 h^-1) than those of denitrification (9.5-15.7 nmol N g^-1 h^-1), but higher than anammox rate (0.3-1.3 nmol N g^-1 h^-1). The DNRA bacterial community structure was primarily affected by temperature gradient despite the treatment process. High-throughput sequencing analysis targeting the DNRA nrfA gene showed that Nitrospira accounted for the largest proportion of nrfA genes among all samples (6.2-36.3%), followed by Brocadia (5.9-22.1%). Network analysis further indicated that Nitrospira played an important role in both the DNRA bacterial community and entire bacterial community in municipal WWTPs. These results suggest that the ecological habitats of DNRA bacteria in anthropogenic ecosystems were far more abundant than previously assumed. However, the contribution to N transformation by the widespread DNRA was not significant in traditional municipal WWTPs.

Hotspot of dissimilatory nitrate reduction to ammonium (DNRA) process in freshwater sediments of riparian zones

Dissimilatory nitrate reduction to ammonium (DNRA), an important intermediate process in the N-cycle, links N-compound oxidation and reduction processes. Hence, the oxic-anoxic interface would be the hotspot of the DNRA process. In freshwater ecosystems, the riparian zone is the most typical carrier of the oxic-anoxic interface. Here we report spatio-temporal evidence of a higher abundance and rate of DNRA in the riparian zone than in the open water sediments based on molecular and ¹⁵N isotopic-tracing technologies, hence signifying a hotspot for the DNRA process. These abudance and rates were significantly higher than those in open water sediments. ¹⁵N isotopic paring technology revealed that the DNRA hotspot promoted higher rates of N-compound oxidation (NO₂^-), reduction (NO₃^- and DNRA), and N₂ production (anammox and denitrification) in the riparian zone than those in open water sediment. However, high-through sequencing analysis showed that the DNRA bacteria in the riparian zone and openwater sediments were insignificantly different. Network and correlation analysis showed that the DNRA abundance and rates were significantly positively correlated with TOM, TC/NH₄⁺, and TC/NO₂^-, but not with the dominant genera (Anaeromyxobacter, Lacunisphaera, and Sorangium), which played different roles on the connection in the respective community networks. The DNRA process in the riparian zone could be driven mainly by the related environmental biogeochemical characteristics induced by anthropogenic changes, followed by microbial processes. This result provides valuable information for the management of riparian zones because anthropogenic changes in the riparian water table are expected to increase, inducing consequent changes in the reduction from NO₃^- to NH₄⁺.

Analysis of enhanced nitrogen removal mechanisms in a validation wastewater treatment plant containing anammox bacteria

Anammox bacteria have attracted attention due to their apparent importance in saving energy and reducing organic chemical demands. Here, we report the detection and quantification of anammox bacteria with an improved primer set in a validation wastewater treatment plant. The improved primer set was shown to detect a broad range of anammox bacteria (47.3%) facilitating more accurate analyses of nitrogen removal mechanisms. Nitrogen removal efficiency and dominant nitrogen removal mechanisms were compared in the modification-Johannesburg (Mod-JHB), modified Ludzack-Ettinger (MLE) single-feed, and anoxic-oxic-anoxic-oxic (AOAO) step-feed modes. In the Mod-JHB configuration, simultaneous nitrification and denitrification (SND) and anammox were found to be responsible for more than 80% of total inorganic nitrogen (TIN) removal (98.5 ± 0.8% of TIN removal). Decrease of anoxic SRT from 5 to 2.5 days did not have any obvious effect on nitrogen removal or the abundance of functional microorganisms. Microbial batch tests demonstrated that both partial nitrification and dissimilatory nitrate reduction to ammonium (DNRA) were responsible for maintaining the anammox process. Short SRT (2 days) in the aerobic zone may explain the presence of partial nitrification. This study provides insights to the analysis of nitrogen removal mechanisms in validation wastewater treatment plants (WWTPs) aiming for high nitrogen removal efficiency.

Dissimilatory nitrate reduction to ammonium conserves nitrogen in anthropogenically affected subtropical mangrove sediments in Southeast China

In this study, basic sediment properties, nutrient flux, and nitrogen cycle (including denitrification, anaerobic ammonium oxidation [anammox], nitrification, and dissimilatory nitrate reduction to ammonium [DNRA]) were investigated at two sampling sites with different tree ages in the mangrove region of the Jiulong River Estuary, China. The results show that sediments at mangrove flat area have relatively strong capability to reduce NO3(-), in which the DNRA rate is relatively high (204.53±48.32μmolNm(-2)h(-1)), which is approximately 75.7-85.9% of the total NO3(-) reduction, while the denitrification and anammox rates are relatively low - only approximately 5.6-9.5% and 8.5-14.8% of the total NO3(-) reduction, respectively. Thus, in the nitrogen-enriched subtropical mangrove system, DNRA is the main pathway to reduce NO3(-), and most of the input nitrogen is conserved as NH4(+) in the system, which assures high productivity of the mangrove system.