Electron Flow Shifts from Anode Respiration to Nitrate Reduction During Electroactive Biofilm Thickening

As electrons generated through substrate oxidation compete with electrodes, dissimilatory nitrate reduction to ammonium (DNRA), denitrification in bioelectrochemical systems in the presence of nitrate, and nitrate reduction through an electroactive biofilm (EAB) are unpredictable. We find that pathways of nitrate reduction are related to EAB thickness and that 76 ± 2 μm is the critical thickness of a biofilm at which both the inner and outer layers simultaneously include DNRA, leading to a maximum level of DNRA efficiency of 42%. Fractions of electrons flowing during nitrate reduction are relatively stable, but their distributions between DNRA and denitrification vary with biofilm thickness. Electrons prefer denitrification in an EAB that is 66 ± 2 μm, while DNRA reversely surpasses denitrification when the thickness increases in the range of 76 ± 2 to 210 ± 2 μm. Biofilm thickening enhances the DNRA of all biofilms close to solution, where nirK remains constant and nrfA is significantly upregulated. However, nrfA is downregulated in layers close to the electrode when the biofilm is thicker than 76 ± 2 μm. These findings reveal the spatially heterogeneous reduction of nitrate in thick EABs, highlighting the importance of biofilm thickness to the regulation of end products of nitrate reduction.

Selective carbon sources influence the end products of microbial nitrate respiration

Respiratory and catabolic genes are differentially distributed across microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content, and function.

Wastewater treatment plant upgrade induces the receiving river retaining bioavailable nitrogen sources

Currently, wastewater treatment plant (WWTP) upgrades have been implemented in various countries to improve the water quality of the receiving ecosystems and protect aquatic species from potential deleterious effects. The impact of WWTP upgrades on biological communities and functions in receiving waters is a fundamental issue that remains largely unaddressed, especially for microbial communities. Here, we selected two wastewater-dominant rivers in Beijing (China) as study sites, i.e., one river receiving water from an upgraded WWTP to explore the impacts of upgrade on aquatic ecosystems and another river receiving water from a previously upgraded WWTP as a reference. After a five-year investigation, we found that WWTP upgrade significantly decreased total organic nitrogen (N) in the receiving river. As a biological response, N-metabolism-related bacterioplankton are accordingly altered in composition and tend to intensively interact according to the network analysis. Metagenomic analysis based on the N-cycling genes and metagenomic-assembled genomes revealed that WWTP upgrade decreased the abundance of nitrifying bacteria but increased that of denitrifying and dissimilatory nitrate reduction to ammonium (DNRA) bacteria in the receiving river, according to their marker gene abundances. After calculation of the ratios between DNRA and denitrifying bacteria and quantification of genes/bacteria related to ammonium cycling, we deduced the changes in N-metabolism-related bacteria are likely an attempt to provide enough bioavailable N for plankton growth as conservation of ammonium was enhanced in receiving river after WWTP upgrade.

Nitrate as a potential prebiotic for the oral microbiome

The salivary glands actively concentrate plasma nitrate, leading to high salivary nitrate concentrations (5–8 mM) after a nitrate-rich vegetable meal. Nitrate is an ecological factor that can induce rapid changes in structure and function of polymicrobial communities, but the effects on the oral microbiota have not been clarified. To test this, saliva of 12 healthy donors was collected to grow in vitro biofilms with and without 6.5 mM nitrate. Samples were taken at 5 h (most nitrate reduced) and 9 h (all nitrate reduced) of biofilm formation for ammonium, lactate and pH measurements, as well as 16S rRNA gene Illumina sequencing. Nitrate did not affect biofilm growth significantly, but reduced lactate production, while increasing the observed ammonium production and pH (all p < 0.01). Significantly higher levels of the oral health-associated nitrate-reducing genera Neisseria (3.1 ×) and Rothia (2.9 ×) were detected in the nitrate condition already after 5 h (both p < 0.01), while several caries-associated genera (Streptococcus, Veillonella and Oribacterium) and halitosis- and periodontitis-associated genera (Porphyromonas, Fusobacterium, Leptotrichia, Prevotella, and Alloprevotella) were significantly reduced (p < 0.05 at 5 h and/or 9 h). In conclusion, the addition of nitrate to oral communities led to rapid modulation of microbiome composition and activity that could be beneficial for the host (i.e., increasing eubiosis or decreasing dysbiosis). Nitrate should thus be investigated as a potential prebiotic for oral health.

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.

Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) pathway dominates nitrate reduction processes in rhizosphere and non-rhizosphere of four fertilized farmland soil

Nitrate (NO₃^-) reduction partitioning between denitrification, anaerobic ammonium oxidation (anammox), denitrifying anaerobic methane oxidation (DAMO), and dissimilatory nitrate reduction to ammonium (DNRA), can influence the nitrogen (N) use efficiency and crop production in arid farmland. The microbial structure, function and potential rates of denitrification, anammox, DAMO and DNRA, and their respective contributions to total NO₃^- reduction were investigated in rhizosphere and non-rhizosphere soil of four typical crops in north China by functional gene amplification, high-throughput sequencing, network analysis and isotopic tracing technique. The measured denitrification and DNRA rate varied from 0.0294 to 20.769 nmol N g^-1 h^-1and 2.4125-58.682 nmol N g^-1 h^-1, respectively, based on which DNRA pathway contributed to 84.44 ± 14.40% of dissimilatory NO₃^- reduction, hence dominated NO₃^- reduction processes compared to denitrification. Anammox and DAMO were not detected. High-throughput sequencing analysis on DNRA nrfA gene, and denitrification nirS and nirK genes demonstrated that these two processes did not correlate to corresponding gene abundance or dominant genus. RDA and Pearson's correlation analysis illustrated that DNRA rate was significantly correlated with the abundance of Chthiniobacter, as well as total organic matter (TOM); denitrification rate was significantly correlated with the abundance of Lautropia, so did TOM. Network analysis showed that the genus performed DNRA was the key connector in the microbial community of dissimilatory nitrate reducers. This study simultaneously investigated the dissimilatory nitrate reduction processes in rhizosphere and non-rhizosphere soils in arid farmland, highlighting that DNRA dominated NO₃^- reduction processes against denitrification. As denitrification results in N loss, whereas DNRA contributes to N retention, the relative contributions of DNRA versus denitrification activities should be considered appropriately when assessing N transformation processes and N fertilizer management in arid farmland fields.

Survey of dissimilatory nitrate reduction to ammonium microbial community at national wetland of Shanghai, China

Dissimilatory nitrate reduction to ammonia (DNRA) process is an important nitrate reduction pathway in the environment. Numerous studies focused on the DNRA, especially in various natural habitats. However, little is known about the envrionmental parameters driving the DNRA process in anthropogenic ecosystem. Human activities put forward significant influence on nitrogen cycle and bacterial communities of sediment. This study aimed to assess the DNRA potential rates, nrfA gene abundance, DNRA bacterial community's diversity and influencing factors in a national wetland park near the Yangtze River estuary, Shanghai. The results of ¹⁵N isotope tracer experiments showed that DNRA potential rates from 0.13 to 0.44 μmol N/kg/h and contribution of nitrate reduction varied from 1.56% to 7.47%. The quantitative real-time PCR results showed that DNRA functional gene nrfA abundances ranged from 9.87E+10 to 1.98E+11 copies/g dry weight. The results of nrfA gene pyrosequencing analysis showed that Lacunisphaera (10.4-13.4%), Sorangium (7.1-10.7%), Aeromonas (4.2-6.8%), Corallococcus (1.8-6.9%), and Geobacter (3.3-6.6%) showed higher relative abundances in their genus levels. Combined with environmental parameters of sediments, redundancy analysis indicated that the nrfA functional gene was positively correlated with moisture content, the concentration of NO₂^--N and NO₃^-N; the DNRA rates was positively correlated with sediment organic carbon (SOC), C/NO₃^- ratio and salinity (ranked by explains %). This study is the first simultaneous determination of nitrate reduction pathways including denitrification, anammox and DNRA rates to assess the role of DNRA in a national wetland park and revealed the community abundance, diversity of DNRA bacteria and its relationship with environmental factors.

A novel strategy for accelerating the recovery of a Fe(II)-inhibited anammox reactor by intermittent addition of betaine: Performance, kinetics and statistical analysis

In this manuscript, Fe(II) inhibition of anammox and its recovery were investigated, and the performance, kinetics and statistical features were comprehensively studied simultaneously. Anammox was suppressed and completely inhibited by the addition of 109.29 and 378.57 mg/L Fe(II), respectively, via uncompetitive inhibition. Nitrite inhibition of anammox was best fitted by the Edwards model and Aiba model. EDTA-2Na wash (0.5, 1.0, 1.5, and 2.0 mM) had a limited effect on anammox recovery, while the addition of 2.0 mM betaine accelerated anammox recovery. Prolonged betaine addition caused an unintended reduction of anammox activity, though it self-recovered after the withdrawal of betaine. The modified Boltzmann model most accurately simulated the processes of anammox recovery using the EDTA-2Na wash, betaine regulation and self-recovery, and the modified Stover-Kincannon model was able to assess the results of anammox recovery. The one-sample t-test was successfully applied to determine the effects of these three recovery strategies on inhibited anammox, which were short-term disinhibition or long-term recovery effects. The above-mentioned results demonstrate that an intermittent addition of betaine, which is a better alternative to frequently-used but poorly-degradable EDTA, may be a useful and environmentally friendly recovery strategy for Fe(II)-inhibited anammox reactor.

Nitrate removal microbiology in woodchip bioreactors: A case-study with full-scale bioreactors treating aquaculture effluents

Woodchip bioreactors are viable low-cost nitrate (NO₃^-) removal applications for treating agricultural and aquaculture discharges. The active microbial biofilms growing on woodchips are conducting nitrogen (N) removal, reducing NO₃^- while oxidizing the carbon (C) from woodchips. However, bioreactor age, and changes in the operating conditions or in the microbial community might affect the NO₃^- removal as well as potentially promote nitrous oxide (N₂O) production through either incomplete denitrification or dissimilatory NO₃^- reduction to ammonium (DNRA). Here, we combined stable isotope approach, amplicon sequencing, and captured metagenomics for studying the potential NO₃^- removal rates, and the abundance and community composition of microbes involved in N transformation processes in the three different full-scale woodchip bioreactors treating recirculating aquaculture system (RAS) effluents. We confirmed denitrification producing di‑nitrogen gas (N₂) to be the primary NO₃^- removal pathway, but found that 6% of NO₃^- could be released as N₂O under high NO₃^- concentrations and low amounts of bioavailable C, whereas DNRA rates tend to increase with the C amount. The abundance of denitrifiers was equally high between the studied bioreactors, yet the potential NO₃^- removal rates were linked to the denitrifying community diversity. The same core proteobacterial groups were driving the denitrification, while Bacteroidetes dominated the DNRA carrying microbes in all the three bioreactors studied. Altogether, our results suggest that woodchip bioreactors have a high genetic potential for NO₃^- removal through a highly abundant and diverse denitrifying community, but that the rates and dynamics between the NO₃^- removal pathways depend on the other factors (e.g., bioreactor design, operating conditions, and the amount of bioavailable C in relation to the incoming NO₃^- concentrations).

Controls of H2S, Fe2 +, and Mn2 + on Microbial NO3 --Reducing Processes in Sediments of an Eutrophic Lake

Understanding the biogeochemical controls on the partitioning between nitrogen (N) removal through denitrification and anaerobic ammonium oxidation (anammox), and N recycling via dissimilatory nitrate (NO3 -) reduction to ammonium (DNRA) is crucial for constraining lacustrine N budgets. Besides organic carbon, inorganic compounds may serve as electron donors for NO3 - reduction, yet the significance of lithotrophic NO3 - reduction in the environment is still poorly understood. Conducting incubation experiments with additions of 15N-labeled compounds and reduced inorganic substrates (H2S, Fe2+, Mn2+), we assessed the role of alternative electron donors in regulating the partitioning between the different NO3 --reducing processes in ferruginous surface sediments of Lake Lugano, Switzerland. In sediment slurry incubations without added inorganic substrates, denitrification and DNRA were the dominant NO3 --reducing pathways, with DNRA contributing between 31 and 46% to the total NO3 - reduction. The contribution of anammox was less than 1%. Denitrification rates were stimulated by low to moderate additions of ferrous iron (Fe2+ ≤ 258 μM) but almost completely suppressed at higher levels (≥1300 μM). Conversely, DNRA was stimulated only at higher Fe2+ concentrations. Dissolved sulfide (H2S, i.e., sum of H2S, HS- and S2-) concentrations up to ∼80 μM, strongly stimulated denitrification, but did not affect DNRA significantly. At higher H2S levels (≥125 μM), both processes were inhibited. We were unable to find clear evidence for Mn2+-supported lithotrophic NO3 - reduction. However, at high concentrations (∼500 μM), Mn2+ additions inhibited NO3 - reduction, while it did not affect the balance between the two NO3 - reduction pathways. Our results provide experimental evidence for chemolithotrophic denitrification or DNRA with Fe2+ and H2S in the Lake Lugano sediments, and demonstrate that all tested potential electron donors, despite the beneficial effect at low concentrations of some of them, can inhibit NO3 - reduction at high concentration levels. Our findings thus imply that the concentration of inorganic electron donors in lake sediments can act as an important regulator of both benthic denitrification and DNRA rates, and suggest that they can exert an important control on the relative partitioning between microbial N removal and N retention in lakes.

The impact of biodegradable carbon sources on nutrients removal in post-denitrification biofilm reactors

Wastewater from households wastewater treatment plants (HWWTP) is discharged to the ground or to the surface waters. Special consideration should be given to the improvement of HWWTP effectiveness, particularly in relation to nutrients. The addition of biodegradable carbon sources to biofilm reactor, can enhance microbial activity but may also lead to filling clogging. The study aimed to compare 3 different organic substrates: acetic acid (commonly applied)and two untypical - citric acid and waste beer, under the same operational conditions in a post-denitrification biofilm reactor. The study investigated the impact of a type of organic substrate, low pH and time on: (1) biofilm growth, (2) the characteristics of extracellular polymeric substances (EPS), (3) the kinetics of nutrients removal and (4) reactor clogging. Results were referred to (5) the effectiveness of nutrients removal. The study demonstrated that low pH assured the development of a thinbiofilm. Citric acid ensured the lowest biomass volume, being by 53% lower than in the reactor with acetic acid and by as much as 61% lower than in the reactor with waste beer. The soluble EPS fraction prevailed in the total EPS in all reactors. The content of the tightly bound EPS fraction ranged from 26.93% (citric acid) to 36.32% (waste beer). Investigations showed also a high ratio of exoproteins to polysaccharide in all fractions, which indicated a significant role of proteins in developing a highly-proliferating biofilm. The treated wastewater met requirements of Polish regulations concerning COD and nitrogen concentrations.

Enhanced long-term advanced denitrogenation from nitrate wastewater by anammox consortia: Dissimilatory nitrate reduction to ammonium (DNRA) coupling with anammox in an upflow biofilter reactor equipped with EDTA-2Na/Fe(II) ratio and pH control

A long-term experiment in an anaerobic ammonium oxidation (anammox) reactor showed that anammox consortia could perform a stable and efficient Fe(II)-dependent dissimilatory nitrate reduction to ammonium (DNRA) coupled to the anammox (DNRA-anammox) process by controlling the EDTA-2Na/Fe(II) ratio and pH, with a total nitrogen removal rate (TNRR) of 0.23 ± 0.01 kg-N/m3/d. Anammox bacteria (Candidatus Kuenenia) were the dominant and functional microbes in such a nitrate wastewater treatment system. Visual MINTEQ analysis showed that the EDTA-2Na/Fe(II) molar ratio affected the influent composition of Fe and EDTA species and hence nitrate removal, while pH influenced both nitrate removal and the coupling degree of the Fe(II)-dependent DNRA-anammox process due to its own physiology. The kinetic simulation results showed that excess EDTA-2Na imposed a competitive inhibition on the Fe(II)-dependent DNRA-anammox process, and the Bell-shaped (A), (B), (C) and Ratkowsky models could be used to explore the pH dependency of the Fe(II)-dependent DNRA-anammox process.

Microbial Nitrogen Metabolism in Chloraminated Drinking Water Reservoirs

Ammonia availability due to chloramination can promote the growth of nitrifying organisms, which can deplete chloramine residuals and result in operational problems for drinking water utilities. In this study, we used a metagenomic approach to determine the identity and functional potential of microorganisms involved in nitrogen biotransformation within chloraminated drinking water reservoirs. Spatial changes in the nitrogen species included an increase in nitrate concentrations accompanied by a decrease in ammonium concentrations with increasing distance from the site of chloramination. This nitrifying activity was likely driven by canonical ammonia-oxidizing bacteria (i.e., Nitrosomonas) and nitrite-oxidizing bacteria (i.e., Nitrospira) as well as by complete-ammonia-oxidizing (i.e., comammox) Nitrospira-like bacteria. Functional annotation was used to evaluate genes associated with nitrogen metabolism, and the community gene catalogue contained mostly genes involved in nitrification, nitrate and nitrite reduction, and nitric oxide reduction. Furthermore, we assembled 47 high-quality metagenome-assembled genomes (MAGs) representing a highly diverse assemblage of bacteria. Of these, five MAGs showed high coverage across all samples, which included two Nitrosomonas, Nitrospira, Sphingomonas, and Rhizobiales-like MAGs. Systematic genome-level analyses of these MAGs in relation to nitrogen metabolism suggest that under ammonia-limited conditions, nitrate may be also reduced back to ammonia for assimilation. Alternatively, nitrate may be reduced to nitric oxide and may potentially play a role in regulating biofilm formation. Overall, this study provides insight into the microbial communities and their nitrogen metabolism and, together with the water chemistry data, improves our understanding of nitrogen biotransformation in chloraminated drinking water distribution systems.IMPORTANCE Chloramines are often used as a secondary disinfectant when free chlorine residuals are difficult to maintain. However, chloramination is often associated with the undesirable effect of nitrification, which results in operational problems for many drinking water utilities. The introduction of ammonia during chloramination provides a potential source of nitrogen either through the addition of excess ammonia or through chloramine decay. This promotes the growth of nitrifying microorganisms and provides a nitrogen source (i.e., nitrate) for the growth for other organisms. While the roles of canonical ammonia-oxidizing and nitrite-oxidizing bacteria in chloraminated drinking water systems have been extensively investigated, those studies have largely adopted a targeted gene-centered approach. Further, little is known about the potential long-term cooccurrence of complete-ammonia-oxidizing (i.e., comammox) bacteria and the potential metabolic synergies of nitrifying organisms with their heterotrophic counterparts that are capable of denitrification and nitrogen assimilation. This study leveraged data obtained for genome-resolved metagenomics over a time series to show that while nitrifying bacteria are dominant and likely to play a major role in nitrification, their cooccurrence with heterotrophic organisms suggests that nitric oxide production and nitrate reduction to ammonia may also occur in chloraminated drinking water systems.

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⁺.

Denitrification and dissimilatory nitrate reduction to ammonium in freshwater lakes of the Eastern Plain, China: Influences of organic carbon and algal bloom

Denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) are critical dissimilatory nitrate reduction pathways that determine nitrogen (N) removal and internal recycling in aquatic environments. However, the relative important of DNRA, and the influences of environmental factors on DNF and DNRA, have not been widely studied in freshwater lakes. In our study, we used N isotope-tracing to investigate the potential rates of DNF and DNRA in 27 lakes from the Eastern Plain Lake Zone (EPL), China. In the EPL lakes, DNF was the dominant nitrate reduction process, however DNRA was still important, accounting for around 4.3%-21.9% of total nitrate reduction. The sediment organic carbon was the primary factor controlling the rates of dissimilatory nitrate reduction, accounting for 28.3% and 37.9% of the variance in DNF and DNRA rates, respectively. High algal biomass accelerated DNF rates, while indirectly affected DNRA via changing the quality of organic carbon. The greater contributions of DNRA to dissimilatory nitrate reduction were found in lakes with higher sulfate concentrations. DNRA coupled to sulfur cycling may play an important role in lakes with high sulfate concentrations and high sediment organic carbon. This study highlights the important role played by DNRA in total nitrate reduction pathways of freshwater lakes. Mitigation strategies for N pollution and algal blooms should not only target decrease of nutrient input, strategies should also create a suitable environment for improving N removal and inhibit N recycling.

Bioelectrochemical Ammoniation Coupled with Microbial Electrolysis for Nitrogen Recovery from Nitrate in Wastewater

Nitrate-N in wastewaters is hard to be recovered because it is difficult to volatilize with an opposite charge to ammonium. Here, we have proved the feasibility of dissimilatory nitrate reduction to ammonia (DNRA) by the easy-acclimated mixed electroactive bacteria, achieving the highest DNRA efficiency of 44%. It was then coupled with microbial electrolysis to concentrate ammonium by a factor of 4 in the catholyte for recovery. The abundance of electroactive bacteria in the biofilm before nitrate addition, especially Geobacter spp., was found to determine the DNRA efficiency. As the main competitors of DNRA bacteria, the growth of denitrifiers was more sensitive to C/N ratios. The DNRA microbial community contrarily showed a stable and recoverable ammoniation performance over C/N ratios ranging from 0.5 to 8.0. A strong competition of the electrode and nitrate on electron donors was observed at the early stage (15 d) of electroactive biofilm formation, which can be weakened when the biofilm was mature on 40 d. Quantitative PCR showed a significant increase in nirS and nrfA transcripts in the ammoniation process. nirS was inhibited significantly after nitrate depletion while nrfA was still upregulated. These findings provided a novel way to recover nitrate-N using organic wastes as both electron donor and power, which has broader implications on the sustainable wastewater treatment and the ecology of nitrogen cycling.

Nitrogen loss process in hypoxic seawater based on the culture experiment

The oxygen minimum zones (OMZs) and other hypoxic seawaters are considered as the main areas of oceanic nitrogen loss. The laboratory simulation culture was conducted to study the main reactions, rates and proportions of dissolved inorganic nitrogen (DIN) in different dissolved oxygen concentrations seawater, with aim of clarifying the process of nitrogen loss in hypoxic seawater. The results showed that the change of DIN in hypoxic water could be divided into three stages. In the first stage, the main reactions were the dissimilatory nitrate reduction to ammonium (DNRA) and denitrification. In the second stage, anammox and denitrification were main reactions. In the last stage, anammox was the most important nitrogen loss reaction; nitrogen loss eventually reached a relative balance with the input from sediment mineralization. Based on the data obtained from the last stage, the annual nitrogen loss could be estimated to be about 240-260 Tg in the global OMZs.

Nitrate reduction in the reed rhizosphere of a riparian zone: From functional genes to activity and contribution

The increased nitrogen (N) fertilizer usage caused substantial nitrate (NO₃^-) leaching into groundwater and eutrophication in downstream aquatic systems. Riparian zones positioned as the link interfaces of terrestrial and aquatic environments are effective in NO₃^- removal. However, the microbial mechanisms regulating NO₃^- reduction in riparian zones are still unclear. In this study, four microbial NO₃^- reduction processes were explored in fine-scale riparian soil horizons by isotopic tracing technique, qPCR of functional gene, high-throughput amplicon sequencing, and phylogenetic molecular ecological network analysis. Interestingly, anaerobic ammonium oxidation (anammox) contributed to NO₃^- removal of up to 48.2% only in waterward sediments but not in landward soil. Denitrification was still the most significant contributor to NO₃^- reduction (32.0-91.8%) and N-losses (51.7-100%). Additionally, dissimilatory nitrate reduction to ammonium (DNRA) played a key role in NO₃^- reduction (4.4-67.5%) and was even comparable to denitrification. Community structure analysis of denitrifying, anammox, and DNRA bacterial communities targeting the related functional gene showed that spatial heterogeneity played a greater role than both temporal and soil type (rhizosphere and non-rhizosphere soil) variability in microbial community structuring. Denitrification and DNRA communities were diverse, and their activities did not depend on gene abundance but were significantly related to organic matter, suggesting that gene abundance alone was insufficient in assessing their activity in riparian zones. Based on networks, DNRA plays a keystone role among the microbial NO₃^- reducers. As the last line of defense in the interception of terrestrial NO₃^-, these findings contribute to our understanding of NO₃^- removal mechanisms in riparian zones, and could potentially be exploited to reduce the diffusion of NO₃^- pollution.

Anaerobic Microbial Degradation of Polycyclic Aromatic Hydrocarbons: A Comprehensive Review

Polycyclic aromatic hydrocarbons (PAHs) are a class of hazardous organic contaminants that are widely distributed in nature, and many of them are potentially toxic to humans and other living organisms. Biodegradation is the major route of detoxification and removal of PAHs from the environment. Aerobic biodegradation of PAHs has been the subject of extensive research; however, reports on anaerobic biodegradation of PAHs are so far limited. Microbial degradation of PAHs under anaerobic conditions is difficult because of the slow growth rate of anaerobes and low energy yield in the metabolic processes. Despite the limitations, some anaerobic bacteria degrade PAHs under nitrate-reducing, sulfate-reducing, iron-reducing, and methanogenic conditions. Anaerobic biodegradation, though relatively slow, is a significant process of natural attenuation of PAHs from the impacted anoxic environments such as sediments, subsurface soils, and aquifers. This review is intended to provide comprehensive details on microbial degradation of PAHs under various reducing conditions, to describe the degradation mechanisms, and to identify the areas that should receive due attention in further investigations.

Stable aerobic and anaerobic coexistence in anoxic marine zones

Mechanistic description of the transition from aerobic to anaerobic metabolism is necessary for diagnostic and predictive modeling of fixed nitrogen loss in anoxic marine zones (AMZs). In a metabolic model where diverse oxygen- and nitrogen-cycling microbial metabolisms are described by underlying redox chemical reactions, we predict a transition from strictly aerobic to predominantly anaerobic regimes as the outcome of ecological interactions along an oxygen gradient, obviating the need for prescribed critical oxygen concentrations. Competing aerobic and anaerobic metabolisms can coexist in anoxic conditions whether these metabolisms represent obligate or facultative populations. In the coexistence regime, relative rates of aerobic and anaerobic activity are determined by the ratio of oxygen to electron donor supply. The model simulates key characteristics of AMZs, such as the accumulation of nitrite and the sustainability of anammox at higher oxygen concentrations than denitrification, and articulates how microbial biomass concentrations relate to associated water column transformation rates as a function of redox stoichiometry and energetics. Incorporating the metabolic model into an idealized two-dimensional ocean circulation results in a simulated AMZ, in which a secondary chlorophyll maximum emerges from oxygen-limited grazing, and where vertical mixing and dispersal in the oxycline also contribute to metabolic co-occurrence. The modeling approach is mechanistic yet computationally economical and suitable for global change applications.

Effects of shrimp-aquaculture reclamation on sediment nitrate dissimilatory reduction processes in a coastal wetland of southeastern China

The conversion of natural saltmarshes to shrimp aquaculture ponds can potentially influence the biogeochemical cycling of nutrients in coastal wetlands, but its impact on the dynamics of sediment dissimilatory nitrate (NO₃^-) reduction remains poorly understood. In this study, three sediment NO₃^- reduction processes including denitrification (DNF), anaerobic ammonium oxidation (ANAMMOX), and dissimilatory NO₃^- reduction to ammonium (DNRA) were examined simultaneously in a natural saltmarsh and two shrimp culture ponds (5- and 18-year-old) in July and November, using nitrogen (N) isotope-tracing experiments. Our results showed that sediment potential DNF, ANAMMOX and DNRA rates were generally higher in the shrimp culture ponds than the natural saltmarsh in the two seasons. The rates of all three processes generally increased with the age of shrimp ponds, with the magnitude of increase being less pronounced for DNF and ANAMMOX than DNRA. The contribution of DNRA to total NO₃^- reduction increased significantly following saltmarsh conversion to shrimp ponds, suggesting that DNRA became an increasingly important biogeochemical process under shrimp culture. DNRA competed with DNF and limited reactive N loss to some extent after natural saltmarshes converted to shrimp culture ponds. The results of redundancy analysis revealed that the availability of substrates and sulfides in sediments, rather than the bacteria gene abundance, were the most important factor influencing the NO₃^- reduction processes. Overall, our findings highlighted that shrimp-aquaculture reclamation may aggravate nitrogen loading in coastal wetlands by promoting the production of bioavailable ammonium.

Increasing oxygen deficiency changes rare and moderately abundant bacterial communities in coastal soft sediments

Coastal hypoxia is a major environmental problem worldwide. Hypoxia-induced changes in sediment bacterial communities harm marine ecosystems and alter biogeochemical cycles. Nevertheless, the resistance of sediment bacterial communities to hypoxic stress is unknown. We investigated changes in bacterial communities during hypoxic-anoxic disturbance by artificially inducing oxygen deficiency to the seafloor for 0, 3, 7, and 48 days, with subsequent molecular biological analyses. We further investigated relationships between bacterial communities, benthic macrofauna and nutrient effluxes across the sediment-water-interface during hypoxic-anoxic stress, considering differentially abundant operational taxonomic units (OTUs). The composition of the moderately abundant OTUs changed significantly after seven days of oxygen deficiency, while the abundant and rare OTUs first changed after 48 days. High bacterial diversity maintained the resistance of the communities during oxygen deficiency until it dropped after 48 days, likely due to anoxia-induced loss of macrofaunal diversity and bioturbation. Nutrient fluxes, especially ammonium, correlated positively with the moderate and rare OTUs, including potential sulfate reducers. Correlations may reflect bacteria-mediated nutrient effluxes that accelerate eutrophication. The study suggests that even slightly higher bottom-water oxygen concentrations, which could sustain macrofaunal bioturbation, enable bacterial communities to resist large compositional changes and decrease the harmful consequences of hypoxia in marine ecosystems.

Effects of carbon availability in a woody carbon source on its nitrate removal behavior in solid-phase denitrification

Woody biomass is the most common natural carbon source applied in solid-phase denitrification (SPD). However, its denitrification ability is low in the SPD process due to its poor carbon availability. In this study, sawdust samples were pretreated to various degrees, and then filled into SPD bioreactors to reveal the relationship between carbon availability and denitrification behaviors. The behaviors include the denitrification process, internal effects of major factors (carbon availability, pH and temperature), and the presence of bacterial communities. Results shown that the long-term denitrification rate of pretreated sawdust was increased by 4.5-4.8 times over that of untreated sawdust (29.3 mg N L^-1 sawdust d^-1). However, despite improving the pretreatment degree of the sawdust in the bioreactor, the long-term denitrification rate shown no further increase. The denitrification rate was most influenced by the temperature, followed by the pH, and then the sawdust pretreatment degree. The denitrification rate increased with decreasing pH and rising temperature of the pretreated sawdust. The removed nitrate was rarely converted into nitrite or nitrous oxide, but ammonium was produced at high pH and temperature for the pretreated sawdust. The adverse effects of ammonium and dissolved organic carbon (DOC) reduced when the pH of the pretreated sawdust was lowered to 6.5. Hydrolytic and denitrifying bacteria formed the main SPD bioreactor bacteria, whose abundances increased with increasing sawdust pretreatment degree. The results were beneficial to reduce the hydrolytic retention time and adverse products for the SPD system using woody carbon source.

Denitrification characterization of dissolved oxygen microprofiles in lake surface sediment through analyzing abundance, expression, community composition and enzymatic activities of denitrifier functional genes

The responses of denitrifiers and denitrification ability to dissolved oxygen (DO) concent in different layers of surface lake sediments are still poorly understood. Here, the optimal denitrification condition was constructed based on response surface methodology (RSM) to analyze the denitrification characteristics of surface sediments. The aerobic zone (AEZ), hypoxic zone (HYZ), up-anoxic zone (ANZ-1) and sub-anoxic zone (ANZ-2) were partitioned based on the oxygen contents, and sediments were collected using a customized-designed sub-millimeter scale sampling device. Integrated real-time quantitative PCR, Illumina Miseq-based sequencing and denitrifying enzyme activities analysis revealed that denitrification characteristics varied among different DO layers. Among the four layers, the DNA abundance and RNA expression levels of norB, nirS and nosZ were the highest at the aerobic layer, hypoxic layer and up-axoic layer, respectively. The hypoxia and up-anaerobic layer were the active nitrogen removal layers, since these two layers displayed the highest DNA abundance, RNA expression level and enzyme activities of denitrification functional genes. The abundance of major denitrifying bacteria showed significant differences among layers, with Azoarcus, Pseudogulbenkiania and Rhizobium identified as the main nirS, nirK and nosZ-based denitrifiers. Pearson’s correlation revealed that the response of denitrifiers to environmental factors differed greatly among DO layers. Furthermore, napA showed higher DNA abundance and RNA expression level in the aerobic and hypoxic layers than anaerobic layers, indicating that aerobic denitrifiers might play important roles at these layers.

Freshwater copepod carcasses as pelagic microsites of dissimilatory nitrate reduction to ammonium

A considerable fraction of freshwater zooplankton was recently found to consist of dead specimens that sink to the lake bottom. Such carcasses host intense microbial activities that may promote oxygen depletion at the microscale. Therefore, we tested the hypothesis that sinking zooplankton carcasses are microsites of anaerobic nitrogen cycling that contribute to pelagic fixed-nitrogen loss even in the presence of ambient oxygen. Incubation experiments were performed with the ubiquitous copepods Eudiaptomus sp. and Megacyclops gigas at different ambient oxygen levels that sinking carcasses encounter during their descent in stratified lakes. ¹⁵N-stable-isotope incubations revealed intense carcass-associated anaerobic nitrogen cycling only at low ambient oxygen levels (<25% air saturation). Dissimilatory nitrate reduction to ammonium (DNRA) dominated over denitrification and thus the potential for fixed-nitrogen loss was low. Consistent with this partitioning of anaerobic nitrogen cycling, the relative abundance of the carcass-associated marker gene for DNRA (nrfA) was ∼20–400 times higher than that for denitrification (nirS). Additionally, the relative nrfA and nirS abundances were ∼90–180 times higher on copepod carcasses than in lake water. This functional distinctiveness of carcass-associated bacterial communities was further substantiated by 16S rDNA-based fingerprinting. We conclude that the unique bacterial communities and microenvironments provided by zooplankton carcasses influence pelagic nitrogen cycling in lakes, but mainly at seasonally low ambient O₂ levels in the bottom water.

The DNRA-Denitrification Dichotomy Differentiates Nitrogen Transformation Pathways in Mountain Lake Benthic Habitats

Effects of nitrogen (N) deposition on microbially-driven processes in oligotrophic freshwater ecosystems are poorly understood. We quantified guilds in the main N-transformation pathways in benthic habitats of 11 mountain lakes along a dissolved inorganic nitrogen gradient. The genes involved in denitrification (nirS, nirK, nosZ), nitrification (archaeal and bacterial amoA), dissimilatory nitrate reduction to ammonium (DNRA, nrfA) and anaerobic ammonium oxidation (anammox, hdh) were quantified, and the bacterial 16S rRNA gene was sequenced. The dominant pathways and associated bacterial communities defined four main N-transforming clusters that differed across habitat types. DNRA dominated in the sediments, except in the upper layers of more productive lakes where nirS denitrifiers prevailed with potential N₂O release. Loss as N₂ was more likely in lithic biofilms, as indicated by the higher hdh and nosZ abundances. Archaeal ammonia oxidisers predominated in the isoetid rhizosphere and rocky littoral sediments, suggesting nitrifying hotspots. Overall, we observed a change in potential for reactive N recycling via DNRA to N losses via denitrification as lake productivity increases in oligotrophic mountain lakes. Thus, N deposition results in a shift in genetic potential from an internal N accumulation to an atmospheric release in the respective lake systems, with increased risk for N₂O emissions from productive lakes.

Role of organic carbon, nitrate and ferrous iron on the partitioning between denitrification and DNRA in constructed stormwater urban wetlands

Denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) are two competing nitrate reduction pathways that remove or recycle nitrogen, respectively. However, factors controlling the partitioning between these two pathways are manifold and our understanding of these factors is critical for the management of N loads in constructed wetlands. An important factor that controls DNRA in an aquatic ecosystem is the electron donor, commonly organic carbon (OC) or alternatively ferrous iron and sulfide. In this study, we investigated the role of natural organic carbon (NOC) and acetate at different OC/NO₃^- ratios and ferrous iron on the partitioning between DNF and DNRA using the ¹⁵N-tracer method in slurries from four constructed stormwater urban wetlands in Melbourne, Australia. The carbon and nitrate experiments revealed that DNF dominated at all OC/NO₃^- ratios. The higher DNF and DNRA rates observed after the addition of NOC indicates that nitrate reduction was enhanced more by NOC than acetate. Moreover, addition of NOC in slurries stimulated DNRA more than DNF. Interestingly, slurries amended with Fe²⁺ showed that Fe²⁺ had significant control on the balance between DNF and DNRA. From two out of four wetlands, a significant increase in DNRA rates (p < .05) at the cost of DNF in the presence of available Fe²⁺ suggests DNRA is coupled to Fe²⁺ oxidation. Rates of DNRA increased 1.5-3.5 times in the Fe²⁺ treatment compared to the control. Overall, our study provides direct evidence that DNRA is linked to Fe²⁺ oxidation in some wetland sediments and highlights the role of Fe²⁺ in controlling the partitioning between removal (DNF) and recycling (DNRA) of bioavailable N in stormwater urban constructed wetlands. In our study we also measured anammox and found that it was always <0.05% of total nitrate reduction in these sediments.

The electrifying physiology of Geobacter bacteria, 30 years on

The family Geobacteraceae, with its only valid genus Geobacter, comprises deltaproteobacteria ubiquitous in soil, sediments, and subsurface environments where metal reduction is an active process. Research for almost three decades has provided novel insights into environmental processes and biogeochemical reactions not previously known to be carried out by microorganisms. At the heart of the environmental roles played by Geobacter bacteria is their ability to integrate redox pathways and regulatory checkpoints that maximize growth efficiency with electron donors derived from the decomposition of organic matter while respiring metal oxides, particularly the often abundant oxides of ferric iron. This metabolic specialization is complemented by versatile metabolic reactions, respiratory chains, and sensory networks that allow specific members to adaptively respond to environmental cues to integrate organic and inorganic contaminants in their oxidative and reductive metabolism, respectively. Thus, Geobacteraceae are important members of the microbial communities that degrade hydrocarbon contaminants under iron-reducing conditions and that contribute, directly or indirectly, to the reduction of radionuclides, toxic metals, and oxidized species of nitrogen. Their ability to produce conductive pili as nanowires for discharging respiratory electrons to solid-phase electron acceptors and radionuclides, or for wiring cells in current-harvesting biofilms highlights the unique physiological traits that make these organisms attractive biological platforms for bioremediation, bioenergy, and bioelectronics application. Here we review some of the most notable physiological features described in Geobacter species since the first model representatives were recovered in pure culture. We provide a historical account of the environmental research that has set the foundation for numerous physiological studies and the laboratory tools that had provided novel insights into the role of Geobacter in the functioning of microbial communities from pristine and contaminated environments. We pay particular attention to latest research, both basic and applied, that has served to expand the field into new directions and to advance interdisciplinary knowledge. The electrifying physiology of Geobacter, it seems, is alive and well 30 years on.

Ecological and physiological implications of nitrogen oxide reduction pathways on greenhouse gas emissions in agroecosystems

Microbial reductive pathways of nitrogen (N) oxides are highly relevant to net emissions of greenhouse gases (GHG) from agroecosystems. Several biotic and abiotic N-oxide reductive pathways influence the N budget and net GHG production in soil. This review summarizes the recent findings of N-oxide reduction pathways and their implications to GHG emissions in agroecosystems and proposes several mitigation strategies. Denitrification is the primary N-oxide reductive pathway that results in direct N2O emissions and fixed N losses, which add to the net carbon footprint. We highlight how dissimilatory nitrate reduction to ammonium (DNRA), an alternative N-oxide reduction pathway, may be used to reduce N2O production and N losses via denitrification. Implications of nosZ abundance and diversity and expressed N2O reductase activity to soil N2O emissions are reviewed with focus on the role of the N2O-reducers as an important N2O sink. Non-prokaryotic N2O sources, e.g. fungal denitrification, codenitrification and chemodenitrification, are also summarized to emphasize their potential significance as modulators of soil N2O emissions. Through the extensive review of these recent scientific advancements, this study posits opportunities for GHG mitigation through manipulation of microbial N-oxide reductive pathways in soil.

Nutrient removal through pyrrhotite autotrophic denitrification: Implications for eutrophication control

This study investigated nutrient removal kinetics and main influencing factors of natural pyrrhotite autotrophic denitrification (PAD), and nutrient removal performance and the microbial community in the PAD biofilter (PADB). Results demonstrated that both NO₃^- and PO₄^3- in wastewater were nearly completely removed, and biological N removal and chemical P removal took place simultaneously in the PAD process. NO₃^- removal kinetics of the PAD can be described with half-order kinetics. The PAD was effective across a wide temperature range of 11-34 °C, initial NO₃^--N range of 13-52 mg·L^-1 and PO₄^3--P below 60 mg·L^-1. Both NO₃^- and PO₄^3- decreased gradually with wastewater flowing along the PADB. The PADB operation results show that at 12 h HRT, when the PADB treated wastewater containing 30.95 ± 0.97 mg·L^-1 of NO₃^- and 3.02 ± 0.10 mg·L^-1 of PO₄^3--P, the effluent contained 1.15 ± 2.08 and 0.09 ± 0.11 mg·L^-1 of NO₃^--N and PO₄^3--P on average, respectively. In the PADB the dominant bacteria were Thiobacillus and Sulfurimonas, which used pyrrhotite as the electron donor to reduce NO₃^-. The relative abundance of Thiobacillus at the bottom of the PADB increased from 0.81% to 58.65% and that of Sulfurimonas decreased from 97.22% to 12.30%, with exposure to pyrrhotite. From the bottom to the top of the PADB, the relative abundance of Thiobacillus increased from 58.65% to 86.23% and Sulfurimonas decreased from 12.30% to 0.52%. Technologies based on the PAD are promising ways to control eutrophication.

High-throughput sequence analysis of bacterial communities in commercial biofertiliser products marketed in South Africa: an independent snapshot quality assessment

The genetic and predicted functional diversity of bacterial communities in 12 commercial biofertiliser products were evaluated using high-throughput sequencing of the 16S rRNA gene. Proteobacteria, Firmicutes and Bacteroides dominated the bacterial communities, with the genera Pseudomonas, Lactobacillus, Bacillus, Bradyrhizobium and Rhizobium being prevalent. The manufacturer-specified species were detected in relatively high abundance in two of the products while a few or none of the specified species were detected in some products. A number of unspecified microbes were detected, including potential human and crop pathogens such as Alcaligenes, Clostridium, Escherichia-Shigella and Proteus. The functional prediction unravelled high prevalence of enzyme-coding genes such as nitrogenase, NifT, alkaline phosphatase and reductases of nitric oxide, nitrate and nitrite which contribute to nitrogen-fixation, phosphorus solubilisation and degradation of nitrates and nitrites. In addition, toxins such as leukocidin/hemolysin and colicin V protein that cause product quality damage were highly predicted in over 67% of the products. Overall, high-throughput sequence analysis of bacterial communities in biofertiliser products revealed that majority of the products were of poor quality. This result justifies the need for regular quality assessment and improvement in quality control systems during biofertiliser formulation.

Resource Concentration Modulates the Fate of Dissimilated Nitrogen in a Dual-Pathway Actinobacterium

Respiratory ammonification and denitrification are two evolutionarily unrelated dissimilatory nitrogen (N) processes central to the global N cycle, the activity of which is thought to be controlled by carbon (C) to nitrate (NO3 -) ratio. Here we find that Intrasporangium calvum C5, a novel dual-pathway denitrifier/respiratory ammonifier, disproportionately utilizes ammonification rather than denitrification when grown under low C concentrations, even at low C:NO3 - ratios. This finding is in conflict with the paradigm that high C:NO3 - ratios promote ammonification and low C:NO3 - ratios promote denitrification. We find that the protein atomic composition for denitrification modules (NirK) are significantly cost minimized for C and N compared to ammonification modules (NrfA), indicating that limitation for C and N is a major evolutionary selective pressure imprinted in the architecture of these proteins. The evolutionary precedent for these findings suggests ecological importance for microbial activity as evidenced by higher growth rates when I. calvum grows predominantly using its ammonification pathway and by assimilating its end-product (ammonium) for growth under ammonium-free conditions. Genomic analysis of I. calvum further reveals a versatile ecophysiology to cope with nutrient stress and redox conditions. Metabolite and transcriptional profiles during growth indicate that enzyme modules, NrfAH and NirK, are not constitutively expressed but rather induced by nitrite production via NarG. Mechanistically, our results suggest that pathway selection is driven by intracellular redox potential (redox poise), which may be lowered when resource concentrations are low, thereby decreasing catalytic activity of upstream electron transport steps (i.e., the bc1 complex) needed for denitrification enzymes. Our work advances our understanding of the biogeochemical flexibility of N-cycling organisms, pathway evolution, and ecological food-webs.

Lactobacillus Dominate in the Intestine of Atlantic Salmon Fed Dietary Probiotics

Probiotics, the live microbial strains incorporated as dietary supplements, are known to provide health benefits to the host. These live microbes manipulate the gut microbial community by suppressing the growth of certain intestinal microbes while enhancing the establishment of some others. Lactic acid bacteria (LAB) have been widely studied as probiotics; in this study we have elucidated the effects of two fish-derived LAB types (RII and RIII) on the distal intestinal microbial communities of Atlantic salmon (Salmo salar). We employed high-throughput 16S rRNA gene amplicon sequencing to investigate the bacterial communities in the distal intestinal content and mucus of Atlantic salmon fed diets coated with the LABs or that did not have microbes included in it. Our results show that the supplementation of the microbes shifts the intestinal microbial profile differentially. LAB supplementation did not cause any significant alterations in the alpha diversity of the intestinal content bacteria but RIII feeding increased the bacterial diversity in the intestinal mucus of the fish. Beta diversity analysis revealed significant differences between the bacterial compositions of the control and LAB-fed groups. Lactobacillus was the dominant genus in LAB-fed fish. A few members of the phyla Tenericutes, Proteobacteria, Actinobacteria, and Spirochaetes were also found to be abundant in the LAB-fed groups. Furthermore, the bacterial association network analysis showed that the co-occurrence pattern of bacteria of the three study groups were different. Dietary probiotics can modulate the composition and interaction of the intestinal microbiota of Atlantic salmon.

Nitrate Removal via a Formate Radical-Induced Photochemical Process

Removal of excess nitrate is critical to balance the nitrogen cycle in aquatic systems. This study investigated a novel denitrification process by tailoring photochemistry of nitrate with formate. Under UV light irradiation, short-lived radicals (i.e., HO^•, NO₂^•, and CO₃^•-) generated from nitrate photolysis partially oxidized formate to highly reductive formate radical (CO₂^•-). CO₂^•- further reduced nitrogen intermediates generated during photochemical denitrification (mainly NO^•, HNO, and N₂O) to gas-phase nitrogen (i.e., N₂O and N₂). The degradation kinetics of total dissolved nitrogen was mainly controlled by the photolysis rates of nitrate and nitrite. The distribution of final products was controlled by the reaction between CO₂^•- and N₂O. To achieve a simultaneous and complete removal of dissolved nitrogen (i.e., nitrate, nitrite, and ammonia) and organic carbon, the formate-to-nitrate stoichiometry was determined as 3.1 ± 0.2 at neutral pH in deionized water. Solution pH impacted the removal rates of nitrate and nitrite but not that of total dissolved nitrogen or formate. The presence of dissolved organic matter at levels similar to those in groundwater had a negligible impact on the photochemical denitrification process. A high denitrification efficiency was also achieved in a synthetic groundwater matrix. Outcome from this study provides a potential denitrification technology for decentralized water treatment and reuse facilities to abate nitrate in local water resources.

Nitrogen Fertilization Reduces the Capacity of Soils to Take up Atmospheric Carbonyl Sulphide

Soils are an important carbonyl sulphide (COS) sink. However, they can also act as sources of COS to the atmosphere. Here we demonstrate that variability in the soil COS sink and source strength is strongly linked to the available soil inorganic nitrogen (N) content across a diverse range of biomes in Europe. We revealed in controlled laboratory experiments that a one-off addition of ammonium nitrate systematically decreased the COS uptake rate whilst simultaneously increasing the COS production rate of soils from boreal and temperate sites in Europe. Furthermore, we found strong links between variations in the two gross COS fluxes, microbial biomass, and nitrate and ammonium contents, providing new insights into the mechanisms involved. Our findings provide evidence for how the soil–atmosphere exchange of COS is likely to vary spatially and temporally, a necessary step for constraining the role of soils and land use in the COS mass budget.

Differentiated Mechanisms of Biochar Mitigating Straw-Induced Greenhouse Gas Emissions in Two Contrasting Paddy Soils

Straw returns to the soil is an effective way to improve soil organic carbon and reduce air pollution by straw burning, but this may increase CH₄ and N₂O emissions risks in paddy soils. Biochar has been used as a soil amendment to improve soil fertility and mitigate CH₄ and N₂O emissions. However, little is known about their interactive effect on CH₄ and N₂O emissions and the underlying microbial mechanisms. In this study, a 2-year pot experiment was conducted on two paddy soil types (an acidic Utisol, TY, and an alkaline Inceptisol, BH) to evaluate the influence of straw and biochar applications on CH₄ and N₂O emissions, and on related microbial functional genes. Results showed that straw addition markedly increased the cumulative CH₄ emissions in both soils by 4.7- to 9.1-fold and 23.8- to 72.4-fold at low (S1) and high (S2) straw input rate, respectively, and significantly increased mcrA gene abundance. Biochar amendment under the high straw input (BS2) significantly decreased CH₄ emissions by more than 50% in both soils, and increased both mcrA gene and pmoA gene abundances, with greatly enhanced pmoA gene and a decreased mcrA/pmoA gene ratio. Moreover, methanotrophs community changed distinctly in response to straw and biochar amendment in the alkaline BH soil, but showed slight change in the acidic TY soil. Straw had little effect on N₂O emissions at low input rate (S1) but significantly increased N₂O emissions at the high input rate (S2). Biochar amendment showed inconsistent effect on N₂O emissions, with a decreasing trend in the BH soil but an increasing trend in the TY soil in which high ammonia existed. Correspondingly, increased nirS and nosZ gene abundances and obvious community changes in nosZ gene containing denitrifiers in response to biochar amendment were observed in the BH soil but not in the TY soil. Overall, our results suggested that biochar amendment could markedly mitigate the CH₄ and N₂O emissions risks under a straw return practice via regulating functional microbes and soil physicochemical properties, while the performance of this practice will vary depending on soil parent material characteristics.

Tetracycline and sulfamethazine alter dissimilatory nitrate reduction processes and increase N2O release in rice fields

Effects of antibiotics on the transformation of nitrate and the associated N₂O release in paddy fields are obscure. Using soil slurry experiments combined with ¹⁵N tracer techniques, the influence of tetracycline and sulfamethazine (applied alone and in combination) on the denitrification, anaerobic ammonium oxidation (anammox), dissimilatory nitrate reduction to ammonium (DNRA) and N₂O release rates in the paddy soil were investigated, while genes related to nitrate reduction and antibiotic resistance were quantified to explore the microbial mechanisms behind the antibiotics' effects. The potential rates of denitrification, anammox, and DNRA were significantly (p < 0.05) reduced, which were mainly attributed to the inhibitory effects of the antibiotics on nitrate-reducing microbes. However, the N₂O release rates were significantly (p < 0.05) stimulated by the antibiotic treatments (0.6-6000 μg kg^-1 soil dry weight), which were caused by the different inhibition effects of antibiotics on N₂O production and N₂O reduction as suggest by the changes in abundance of nirS (nitrite reduction step) and nosZ (N₂O reduction to N₂ step) genes. Antibiotic resistance gene (tetA, tetG, sulI, and sulIII) abundances were significantly (p < 0.05) increased under high antibiotic exposure concentrations (>600 μg kg^-1 soil dry weight). Our results suggest that the widespread occurrence of antibiotics in paddy soils may pose significant eco-environmental risks (nitrate accumulation and greenhouse effects) by altering nitrate transformation processes.

Copepod-Associated Gammaproteobacteria Respire Nitrate in the Open Ocean Surface Layers

Microbial dissimilatory nitrate reduction to nitrite, or nitrate respiration, was detected in association with copepods in the oxygenated water column of the North Atlantic subtropical waters. These unexpected rates correspond to up to 0.09 nmol N copepod-1 d-1 and demonstrate a previously unaccounted nitrogen transformation in the oceanic pelagic surface layers. Genes and transcripts for both the periplasmic and membrane associated dissimilatory nitrate reduction pathways (Nap and Nar, respectively) were detected. The napA genes and transcripts were closely related with sequences from several clades of Vibrio sp., while the closest relatives of the narG sequences were Pseudoalteromonas spp. and Alteromonas spp., many of them representing clades only distantly related to previously described cultivated bacteria. The discovered activity demonstrates a novel Gammaproteobacterial respiratory role in copepod association, presumably providing energy for these facultatively anaerobic bacteria, while supporting a reductive path of nitrogen in the oxygenated water column of the open ocean.

Seasonal function succession and biogeographic zonation of assimilatory and dissimilatory nitrate-reducing bacterioplankton

The dominance of different nitrate-reducing pathways determines nitrogen cycling patterns. Denitrification (DNF) has been widely studied, but assimilatory nitrate reduction (ANR) and dissimilatory nitrate reduction to ammonium (DNRA) have received much less attention. Their ecological patterns and responsible microbes are poorly understood. Here, we studied the structure and function succession of the three functional groups in the middle route of the South-to-North Water Diversion Project, which is a 1230 km canal spanning 8 degrees of latitude. The results reflected a nitrogen-removing pattern dominated by DNF in the summer and a nitrogen-retaining pattern dominated by ANR and DNRA in the winter. Stenotrophomonas, a typical denitrifier, was the keystone species in the summer and contributed to N₂O production. Clostridium, a genus able to conduct ANR and DNRA, was the keystone species in the winter. Notably, a significant zonation pattern was discovered. According to the community structure, the system could be separated into two biogeographic zones, and the Yellow River (about latitude 35°N) is an important cut-off line. This bacterial biogeography followed different water characteristics and ecological processes. ANR was found to be an important process and seasonally transformed its habitat from the northern zone to the southern zone. DNRA bacteria were acclimated to the northern zone and favored at this region in both seasons. The generation of N₂O, a strong greenhouse gas, also exhibited this zonation pattern. This is the first study to consider assimilatory and dissimilatory nitrate reducers together at a molecular level, and provides new insights into the underlying patterns of a nitrate-reducing bacterioplankton community.

Denitrification-Potential Evaluation and Nitrate-Removal-Pathway Analysis of Aerobic Denitrifier Strain Marinobacter hydrocarbonoclasticus RAD-2

An aerobic denitrifier was isolated from a long-term poly (3-hydroxybutyrate-co-3-hydroxyvalerate) PHBV-supported denitrification reactor that operated under alternate aerobic/anoxic conditions. The strain was identified as Marinobacter hydrocarbonoclasticus RAD-2 based on 16S rRNA-sequence phylogenetic analysis. Morphology was observed by scanning electron microscopy (SEM), and phylogenetic characteristics were analyzed with the API 20NE test. Strain RAD-2 showed efficient aerobic denitrification ability when using NO3−-N or NO2−-N as its only nitrogen source, while heterotrophic nitrification was not detected. The average NO3−-N and NO2−-N removal rates were 6.47 mg/(L·h)and 6.32 mg/(L·h), respectively. Single-factor experiments indicated that a 5:10 C/N ratio, 25–40 °C temperature, and 100–150 rpm rotation speed were the optimal conditions for aerobic denitrification. Furthermore, the denitrifying gene napA had the highest expression on a transcriptional level, followed by the denitrifying genes nirS and nosZ. The norB gene was found to have significantly low expression during the experiment. Overall, great aerobic denitrification ability makes the RAD-2 strain a potential alternative in enhancing nitrate management for marine recirculating aquaculture system (RAS) practices.

Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira in natural environments

Complete ammonia oxidizers (comammox), as novel microbial communities, are predicted to play an important role in the nitrogen cycle. Here we reported the presence of complete nitrification in tidal sediments and examined the diversity and abundance of comammox in natural ecosystems. Metagenome and metatranscriptome of the enrichment culture from tidal sediments harbored the genes of comammox. Near-complete comammox AmoA/B/C- and Hao-like sequences showed close relationships to the known comammox (with sequence identity from 79 to 99%) rather than classical betaproteobacterial ammonia-oxidizing bacteria (β-AOB) (57 to 66%) and ammonia-oxidizing archaea (AOA) (24 to 38%). To analyze the diversity of comammox in natural environments, a new primer set targeting clade A comammox Nitrospira (COM-A) amoA genes was designed based on sequences obtained in this study and sequences from published database. In silico evaluation of the primers showed the high coverage of 89 and 100% in the COM-A amoA database. Application of the primers in six different ecosystems proved their strong availability. Community composition of COM-A suggested a relatively higher diversity than β-AOB in similar environments. Quantification results showed that COM-A amoA genes accounted for about 0.4-5.6% in total amoA genes. These results provide novel insight into our perception of the enigmatic comammox and have significant implications for profound understanding of complex nitrification process.

Distinct Microbial Community Performing Dissimilatory Nitrate Reduction to Ammonium (DNRA) in a High C/NO3- Reactor

A dissimilatory nitrate reduction to ammonium (DNRA) microbial community was developed under a high organic carbon to nitrate (C/NO₃⁻) ratio in an anoxic semi-continuous sequencing batch reactor (SBR) fed with glucose as the source of carbon and NO₃⁻ as the electron acceptor. Activated sludge collected from a municipal wastewater treatment plant with good denitrification efficiency was used as the inoculum to start the system. The aim of this study was to examine the microbial populations in a high C/NO₃⁻ ecosystem for potential DNRA microorganisms, which are the microbial group with the ability to reduce NO₃⁻ to ammonium (NH₄⁺). A low C/NO₃⁻ reactor was operated in parallel for direct comparisons of the microbial communities that developed under different C/NO₃⁻ values. The occurrence of DNRA in the high C/NO₃⁻ SBR was evidenced by stable isotope-labeled nitrate and nitrite (¹⁵NO₃⁻ and ¹⁵NO₂⁻), which proved the formation of NH₄⁺ from dissimilatory NO₃⁻/NO₂⁻ reduction, in which both nitrogen oxides induced DNRA activity in a similar manner. An analysis of sludge samples with Illumina MiSeq 16S rRNA sequencing showed that the predominant microorganisms in the high C/NO₃⁻ SBR were related to Sulfurospirillum and the family Lachnospiraceae, which were barely present in the low C/NO₃⁻ system. A comparison of the populations and activities of the two reactors indicated that these major taxa play important roles as DNRA microorganisms under the high C/NO₃⁻ condition. Additionally, a beta-diversity analysis revealed distinct microbial compositions between the low and high C/NO₃⁻ SBRs, which reflected the activities observed in the two systems.

Filamentous Giant Beggiatoaceae from the Guaymas Basin Are Capable of both Denitrification and Dissimilatory Nitrate Reduction to Ammonium

Whether large sulfur bacteria of the family Beggiatoaceae reduce NO₃⁻ to N₂ via denitrification or to NH₄⁺ via DNRA has been debated in the literature for more than 25 years. We resolve this debate by showing that certain members of the Beggiatoaceae use both metabolic pathways. This is important for the ecological role of these bacteria, as N₂ production removes bioavailable nitrogen from the ecosystem, whereas NH₄⁺ production retains it. For this reason, the topic of environmental controls on the competition for NO₃⁻ between N₂-producing and NH₄⁺-producing bacteria is of great scientific interest. Recent experiments on the competition between these two types of microorganisms have demonstrated that the balance between electron donor and electron acceptor availability strongly influences the end product of NO₃⁻ reduction. Our results suggest that this is also the case at the even more fundamental level of enzyme system regulation within a single organism.

Filamentous large sulfur-oxidizing bacteria (FLSB) of the family Beggiatoaceae are globally distributed aquatic bacteria that can control geochemical fluxes from the sediment to the water column through their metabolic activity. FLSB mats from hydrothermal sediments of Guaymas Basin, Mexico, typically have a “fried-egg” appearance, with orange filaments dominating near the center and wider white filaments at the periphery, likely reflecting areas of higher and lower sulfide fluxes, respectively. These FLSB store large quantities of intracellular nitrate that they use to oxidize sulfide. By applying a combination of ¹⁵N-labeling techniques and genome sequence analysis, we demonstrate that the white FLSB filaments were capable of reducing their intracellular nitrate stores to both nitrogen gas and ammonium by denitrification and dissimilatory nitrate reduction to ammonium (DNRA), respectively. On the other hand, our combined results show that the orange filaments were primarily capable of DNRA. Microsensor profiles through a laboratory-incubated white FLSB mat revealed a 2- to 3-mm vertical separation between the oxic and sulfidic zones. Denitrification was most intense just below the oxic zone, as shown by the production of nitrous oxide following exposure to acetylene, which blocks nitrous oxide reduction to nitrogen gas. Below this zone, a local pH maximum coincided with sulfide oxidation, consistent with nitrate reduction by DNRA. The balance between internally and externally available electron acceptors (nitrate) and electron donors (reduced sulfur) likely controlled the end product of nitrate reduction both between orange and white FLSB mats and between different spatial and geochemical niches within the white FLSB mat.

IMPORTANCE Whether large sulfur bacteria of the family Beggiatoaceae reduce NO₃⁻ to N₂ via denitrification or to NH₄⁺ via DNRA has been debated in the literature for more than 25 years. We resolve this debate by showing that certain members of the Beggiatoaceae use both metabolic pathways. This is important for the ecological role of these bacteria, as N₂ production removes bioavailable nitrogen from the ecosystem, whereas NH₄⁺ production retains it. For this reason, the topic of environmental controls on the competition for NO₃⁻ between N₂-producing and NH₄⁺-producing bacteria is of great scientific interest. Recent experiments on the competition between these two types of microorganisms have demonstrated that the balance between electron donor and electron acceptor availability strongly influences the end product of NO₃⁻ reduction. Our results suggest that this is also the case at the even more fundamental level of enzyme system regulation within a single organism.

Sediment diffusion method improves wastewater nitrogen removal in the receiving lake sediments

Sediment microbes have a great potential to transform reactive N to harmless N₂, thus decreasing wastewater nitrogen load into aquatic ecosystems. Here, we examined if spatial allocation of the wastewater discharge by a specially constructed sediment diffuser pipe system enhanced the microbial nitrate reduction processes. Full-scale experiments were set on two Finnish lake sites, Keuruu and Petäjävesi, and effects on the nitrate removal processes were studied using the stable isotope pairing technique. All nitrate reduction rates followed nitrate concentrations, being highest at the wastewater-influenced sampling points. Complete denitrification with N₂ as an end-product was the main nitrate reduction process, indicating that the high nitrate and organic matter concentrations of wastewater did not promote nitrous oxide (N₂O) production (truncated denitrification) or ammonification (dissimilatory nitrate reduction to ammonium; DNRA). Using 3D simulation, we demonstrated that the sediment diffusion method enhanced the contact time and amount of wastewater near the sediment surface especially in spring and in autumn, altering organic matter concentration and oxygen levels, and increasing the denitrification capacity of the sediment. We estimated that natural denitrification potentially removed 3-10% of discharged wastewater nitrate in the 33 ha study area of Keuruu, and the sediment diffusion method increased this areal denitrification capacity on average 45%. Overall, our results indicate that sediment diffusion method can supplement wastewater treatment plant (WWTP) nitrate removal without enhancing alternative harmful processes.

Response of humic acid formation to elevated nitrate during chicken manure composting

Nitrate can stimulate microbes to degrade aromatic compounds, whereas humic acid (HA) as a high molecular weight aromatic compound, its formation may be affected by elevated nitrate during composting. Therefore, this study is conducted to determine the effect of elevated nitrate on HA formation. Five tests were executed by adding different nitrate concentrations to chicken manure composting. Results demonstrate that the concentration of HA in treatment group is significantly decreased compared with control group (p < 0.05), especially in the highest nitrate concentration group. RDA indicates that the microbes associated with HA and environmental parameters are influenced by elevated nitrate. Furthermore, structural equation model reveals that elevated nitrate reduces HA formation by mediating microbes directly, or by affecting ammonia and pH as the indirect drivers to regulate microbial community structure.