Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater

Regulation of nitrite-dependent anaerobic methane oxidation bacteria by available phosphorus and microbial communities in lake sediments of cold and arid regions

As global anthropogenic nitrogen inputs continue to rise, nitrite-dependent anaerobic methane oxidation (N-DAMO) plays an increasingly significant role in CH4 consumption in lake sediments. However, there is a dearth of knowledge regarding the effects of anthropogenic activities on N-DAMO bacteria in lakes in the cold and arid regions. Sediment samples were collected from five sampling areas in Lake Ulansuhai at varying depth ranges (0-20, 20-40, and 40-60 cm). The ecological characterization and niche differentiation of N-DAMO bacteria were investigated using bioinformatics and molecular biology techniques. Quantitative PCR confirmed the presence of N-DAMO bacteria in Lake Ulansuhai sediments, with 16S rRNA gene abundances ranging from 1.72 × 104 to 5.75 × 105 copies·g-1 dry sediment. The highest abundance was observed at the farmland drainage outlet with high available phosphorus (AP). Anthropogenic disturbances led to a significant increase in the abundance of N-DAMO bacteria, though their diversity remained unaffected. The heterogeneous community of N-DAMO bacteria was affected by interactions among various environmental characteristics, with AP and oxidation-reduction potential identified as the key drivers in this study. The Mantel test indicated that the N-DAMO bacterial abundance was more readily influenced by the presence of the denitrification genes (nirS and nirK). Network analysis revealed that the community structure of N-DAMO bacteria generated numerous links (especially positive links) with microbial taxa involved in carbon and nitrogen cycles, such as methanogens and nitrifying bacteria. In summary, N-DAMO bacteria exhibited sensitivity to both environmental and microbial factors under various human disturbances. This study provides valuable insights into the distribution patterns of N-DAMO bacteria and their roles in nitrogen and carbon cycling within lake ecosystems.

Removal of nitrate and pesticides from groundwater by nano zero-valent iron injection pulses under biostimulation and bioaugmentation scenarios in continuous-flow packed soil columns

This study evaluates the NO₃^- removal from groundwater through Heterotrophic Denitrification (HDN) (promoted by the addition of acetate and/or an inoculum rich in denitrifiers) and Abiotic Chemical Nitrate Reduction (ACNR) (promoted by pulse injection of zerovalent iron nanoparticles (nZVI)). HDN and ACNR were applied, separately or combined, in packed soil column experiments to complement the scarce research on pulse-injected nZVI in continuous-flow systems mimicking a Well-based Denitrification Barrier. Together with NO₃^-, the removal of two common pesticides (dieldrin and lindane) was evaluated. Results showed that total NO₃^- removal (>97%) could be achieved by either bioestimulation with acetate (converting NO₃^- to N₂(g) via HDN) or by injecting nZVI (removing NO₃^- via ACNR). In the presence of nZVI, NO₃^- was partially converted to N₂(g) and to a lower extent NO₂^-, with unreacted NO₃^- being likely adsorbed onto Fe-(oxy)hydroxides. Combination of both HDN and ACNR resulted in even a higher NO₃^- removal (>99%). Interestingly, nZVI did not seem to pose any toxic effect on denitrifiers. These results showed that both processes can be alterned or combined to take advantage of the benefits of each individual process while overcoming their disadvantages if applied alone. With regard to the target pesticides, the removal was high for dieldrin (>93%) and moderate for lindane (38%), and it was not due to biodegradation but to adsorption onto soil. When nZVI was applied, the removal increased (generally >91%) due to chemical degradation by nZVI and/or adsorption onto formed Fe-(oxy)hydroxides.

Investigation of nitrite accumulation by hydrogenotrophic denitrification in a moving bed biofilm reactor for partial denitrification and anammox process

The partial denitrification and anammox (PDA) process has received attention for its ability to optimize treatment of wastewater containing a low NH₄⁺-N concentration. This study investigated the suitable operational conditions for NO₂^--N accumulation by hydrogenotrophic denitrification (HD) in operation of a laboratory-scale moving bed biofilm reactor, for future application in the PDA process. NO₂^--N accumulation was achieved by minimizing the H₂ flow rate under optimized conditions (i.e., 15 mL/min H₂ flow rate, 40 mg-N/L influent NO₃^--N, 7.0 h hydraulic retention time, and 2 L working volume). Hydrogenophaga comprised 39.2% of the bacterial abundance after NO₂^--N accumulated, indicating its contribution to the NO₂^--N accumulation. In addition, an intermittent H₂ supply maintained the NO₂^--N accumulation rate (NAR) and maximized the nitrite accumulation efficiency (NAE). A H₂ supply ratio of 0.7 (i.e., ON: 7 min, OFF: 3 min) was optimal, which induced increases in NAR, NAE, and the NO₃^--N removal efficiency that reached 0.07±0.01 kg-N/m³/d, 64.4±14.5%, and 89.2±8.9%, respectively. The ratio of H₂ supply rate to the NO₃^--N loading rate was calculated as 4.3 in this experiment, which may represent the optimal balance for maximization of NO₂^--N accumulation by HD.

Black Truffles Affect Quercus aliena Physiology and Root-Associated nirK- and nirS-Type Denitrifying Bacterial Communities in the Initial Stage of Inoculation

Truffles (Tuber spp.) are edible ectomycorrhizal fungi with high economic value. Bacteria in ectomycorrhizosphere soils are considered to be associated with the nutrient uptake of truffles and hosts. Whether Tuber spp. inoculation can affect the growth of Quercus aliena, the ectomycorrhizosphere soil, and the rhizosphere nirK and nirS-denitrifier communities at the ectomycorrhizae formation stage is still unclear. Therefore, we inoculated Q. aliena with the black truffles Tuber melanosporum and Tuber indicum, determined the physiological activity and morphological indices of Q. aliena seedlings, analyzed the physicochemical properties of ectomycorrhizosphere soils, and applied DNA sequencing to assess the nirK and nirS- denitrifier community structure in ectomycorrhizosphere soils. Peroxidase activity was higher in the seedlings inoculated with T. melanosporum than in the T. indicum inoculation and uninoculated control treatments. The available phosphorus contents were lower and nitrate contents were higher in those with truffle inoculation, and T. melanosporum treatment differed more from the control than the T. indicum treatment. The richness of the nirK-community was highest in the T. indicum treatment and lowest in the uninoculated treatment. The differences in nirK-community composition across treatments were not statistically significant, but the nirS communities were different. The nirS-type bacteria correlated with three environmental factors (pH, available phosphorus, and nitrate contents), whereas the nirK-type bacteria were only associated with the nitrate contents. Generally, this work revealed that inoculation with Tuber spp. would change a few nutrient contents and richness of nirK-type bacteria and had little effects on growth of Q. aliena seedlings in the initial stage of inoculation. The results of this study may provide in-depth insights into the relationships between Tuber spp. and hosts, which should be taken into account when developing truffle production methods.

Investigation of dissimilatory nitrate reduction to ammonium (DNRA) in urban river network along the Huangpu River, China: rates, abundances, and microbial communities

Dissimilatory nitrate reduction to ammonium (DNRA) is an essential intermediate step in the nitrogen cycle, and different sediment physicochemical properties can affect the DNRA process. But the detailed research on the environmental nitrogen cycling in urban river networks based on DNRA communities and the functional gene nrfA is lacking. In this study, the flow line of the Huangpu River in Shanghai was analyzed using isotope tracer, quantitative real-time PCR, and high-throughput sequencing techniques to evaluate the role of DNRA on the stability of the river network and marine. The significant positive correlation between the rate of DNRA and sediment organic carbon was identified. At the genus level, Anaeromyxobacter is the most dominant. Notably, both heterotrophic and autotrophic DNRA species were discovered. This study added diversity to the scope of urban freshwater river network ecosystem studies by investigating the distribution of DNRA bacteria along the Huangpu River. It provided new insights into the biological nitrogen cycle of typical urban inland rivers in eastern China.

Are nitrogen and carbon cycle processes impacted by common stream antibiotics? A comparative assessment of single vs. mixture exposures

A variety of antibiotics are ubiquitous in all freshwater ecosystems that receive wastewater. A wide variety of antibiotics have been developed to kill problematic bacteria and fungi through targeted application, and their use has contributed significantly to public health and livestock management. Unfortunately, a substantial fraction of the antibiotics applied to humans, pets and livestock end up in wastewater, and ultimately many of these chemicals enter freshwater ecosystems. The effect of adding chemicals that are intentionally designed to kill microbes, on freshwater microbial communities remains poorly understood. There are reasons to be concerned, as microbes play an essential role in nutrient uptake, carbon fixation and denitrification in freshwater ecosystems. Chemicals that reduce or alter freshwater microbial communities might reduce their capacity to degrade the excess nutrients and organic matter that characterize wastewater. We performed a laboratory experiment in which we exposed microbial community from unexposed stream sediments to three commonly detected antibiotics found in urban wastewater and urban streams (sulfamethoxazole, danofloxacin, and erythromycin). We assessed how the form and concentration of inorganic nitrogen, microbial carbon, and nitrogen cycling processes changed in response to environmentally relevant doses (10 μg/L) of each of these antibiotics individually and in combination. We expected to find that all antibiotics suppressed rates of microbial mineralization and nitrogen transformations and we anticipated that this suppression of microbial activity would be greatest in the combined treatment. Contrary to our expectations we measured few significant changes in microbially mediated functions in response to our experimental antibiotic dosing. We found no difference in functional gene abundance of key nitrogen cycling genes nosZ, mcrA, nirK, and amoA genes, and we measured no treatment effects on NO3- uptake or N2O, N2, CH4, CO2 production over the course of our seven-day experiment. In the mixture treatment, we measured significant increases in NH4+ concentrations over the first 24 hours of the experiment, which were indistinguishable from controls within six hours. Our results suggest remarkable community resistance to pressure antibiotic exposure poses on naïve stream sediments.

Recent advances in partial denitrification-anaerobic ammonium oxidation process for mainstream municipal wastewater treatment

To solve the bottleneck of the unstable accumulation of nitrite in the partial nitrification (PN)-anammox (AMX) in municipal wastewater treatment, a novel process called partial denitrification (PD)-AMX has been developed. PD-AMX, which is known for cost-efficiency and environmental friendliness, has currently exhibited a promising potential for the removal of biological nitrogen from municipal wastewater and has attracted much research interest regarding its process mechanisms, as well as its practical applications. Here, we review the recent advances in the PD process and its coupling to the anammox process, including the development, basic principles, main characteristics, and critical process parameters of the stable operation of the PD-AMX process. We also explore the microbial community and its characteristics in the system and summarize the knowledge of the dominant bacteria to clarify the key factors affecting PD-AMX. Then, we introduce the engineering feasibility and economic feasibility as well as the potential challenges of the process. The induction and implementation of partial denitrification and maintenance of mainstream anammox are critical issues to be urgently solved. Meanwhile, the implementation of a full mainstream anammox application remains burdensome, while the mechanism of partial denitrification coupled to anammox needs to be further studied. Additionally, stable operation performance and process control¹ methods need to be optimized or developed for the PD-AMX system for better engineering practice. This review can help to accelerate the research and application of the PD-AMX process for municipal wastewater treatment.

Integrating experiments with system-level biogeochemical modeling to understand nitrogen cycling of reservoir sediments at elevated hydrostatic pressure

Impoundment of rivers to construct reservoirs for hydropower and irrigation greatly increase the hydrostatic pressure acting on river sediments with potential repercussions for ecosystem-level microbial activity and metabolism. Understanding the functioning and responses of key biogeochemical cycles such as that of nitrogen cycling to shifting hydrostatic pressure is needed to estimate and predict the systemic nutrient dynamics in deep-water reservoirs. We studied the functioning of bacterial communities involved in nitrogen transformation in bioreactors maintained under contrasting hydrostatic pressures (0.5 MPa-3.0 MPa) and complemented the experimental approach with a functional gene-informed biogeochemical model. The model predictions were broadly consistent with observations from the experiment, suggesting that the rates of N₂O production decreased while the sediment concentration of nitrite increased significantly with increasing pressure, at least when exceeding 1.0 MPa. Changes in nitrite reduction (nirS) and aerobic ammonia oxidation (amoA) genes abundances were in accordance with the observed changes in N₂O production and nitrite levels. Moreover, the model predicted that the higher pressures (P > 1.5 MPa) would intensify the inhibition of N₂ production via denitrification and result in an accumulation of ammonia in the sediment along with a decrease in dissolved oxygen. The results imply that increased hydrostatic pressure caused by dam constructions may have a strong effect on microbial nitrogen conversion, and that this may result in lower nitrogen removal.

Pathways and mechanisms of nitrogen transformation during co-composting of pig manure and diatomite

The aim of this study was to investigate the pathways and mechanisms of nitrogen transformation during the composting process, by adding diatomite (0%, 2.5%, 5%, 10%, 15% and 20%) into initial mixtures of pig manure and sawdust. The results revealed that diatomite facilitated the conversion from NH₄⁺-N to amino acid nitrogen and hydrolysis undefined nitrogen, then reduced NH₃ and N₂O emission by 8.63-35.29% and 14.34-73.21%, respectively. Moreover, the structure and abundance of nitrogen functional genes provided evidence for nitrogen loss. Furthermore, compared with the control (0.03), the treatment blended with 10% diatomite (T3) had the highest value in composting score (-1.27). Additionally, the ratio of carbon and nitrogen (57.30%) was vital for reducing nitrogen loss among all physio-chemical parameters in this study. In conclusion, adding diatomite was a practical way to enhance nitrogen conservation and increase quality of end products, and the optimum added dosage was at 10%.

Accelerated nitrogen consumption in sediment by Tubifex tubifex and its significance in eutrophic sediment remediation

Sediment remediation in eutrophic aquatic ecosystems is imperative, but effective ecological measures are scarce. A pilot-scale trial investigated sediment remediation by the addition of Tubifex tubifex. The results showed that the addition of T. tubifex accelerated sediment organic matter (OM) and nitrogen (N) loss, with averages of 7.7% and 75.1% increased loss (IL) compared to treatments without T. tubifex in the 60-day experiment, respectively. The percentages of the increased in water to the IL in sediment were only 0.6%, 0.21%, 2.1% and 6.3% for NH₄⁺-N, NO_x^--N, TN and COD, respectively, at the end of the experiment. The absolute abundances of the nitrifying genes AOA and AOB; the denitrifying genes napA, nirS, nirK, cnorB and nosZ; and the anaerobic ammonia oxidation gene anammox increased 2.3- to 11.0-fold with the addition of T. tubifex. Therefore, the addition of T. tubifex is an effective strategy for sediment remediation by accelerating OM and N loss in sediment without substantially increasing the water N concentration.

The distribution of dissimilatory nitrate reduction to ammonium bacteria in multistage constructed wetland of Jining, Shandong, China

Dissimilatory nitrate reduction to ammonium (DNRA) is an important process of nitrate reduction in the environment. The distribution of DNRA bacteria and the relationships with environmental factors in multistage constructed wetland were investigated in this study. The quantitative real-time polymerase chain reaction analysis showed that the abundance of DNRA bacteria at all sites ranged from 2.10 × 10¹⁰ to 1.10 × 10¹¹ copies/g of dry sediments. The Anaeromyxobacter (belong to Deltaproteobacteria) was the most abundant DNRA bacteria at all sites. The Geobater known as DNRA bacteria was also identified in this study. The abundances of DNRA bacteria, denitrifying bacteria, and anammox bacteria were conspicuously negatively correlated with Eh and positively correlated with the NO₃^--N removal efficency by statistical analysis.

Win-win: Application of sawdust-derived hydrochar in low fertility soil improves rice yield and reduces greenhouse gas emissions from agricultural ecosystems

As a good soil synergist, biochar has a wide prospect in improving soil fertility and crop production. Although hydrochar, produced by hydrothermal carbonization process has attracted attention due to production advantages, hydrochar application in low fertility soils as well as its impact to the associated greenhouse gas (GHG) emissions in farmlands is rarely reported. To advance our understanding on the effect of hydrochar addition on grain yield from low fertility soils and the corresponding CH₄ and N₂O emissions, a soil-column experiment, with two hydrochar types (sawdust-derived hydrochar (SDH), microbial-aged hydrochar (A-SDH)) at two application rates (5‰, 15‰; (w/w)), was conducted. The results showed that hydrochar addition evidently increased rice yield. The N₂O emissions were mainly related to the substrate supply of the hydrochar itself and less affected by the denitrifiers (functional genes) present. Hydrochar amendment at low application rate (5‰; SDH05, A-SDH05) significantly decreased the cumulative N₂O emissions by 26.32% ~ 36.84%. Additionally, hydrochar amendment could not increase the CH₄ emissions due to the substrate limitation; the cumulative emissions were similar with those from the control, ranging between 11.1-12.8 g m^-2. Regarding grain yield and global warming potential, greenhouse gas intensity from the soils subjected to hydrochar (SDH05, A-SDH05, A-SDH15) were significantly lower than that of the control, observation attributed to the high yield and low N₂O emissions. Overall, hydrochar addition is an effective strategy to ensure grain yield in low fertility soils with relatively low/controlled GHG emissions, especially when the amendment is applied at low application rate.

The effect of re-startup strategies on the recovery of constructed wetlands after long-term resting operation

The objective of this study was to identify the proper re-startup strategies (RSSs) for constructed wetlands (CWs) after long-term resting operation in terms of the recovery of pollutant removal efficiency (RE) and N-cycle gene abundance. The results suggested that backwashing increased the gene abundance without shortening the recovery time of gene abundance. The RSS involving excavation and washing performed better in terms of chemical oxygen demand (COD) RE, especially at the beginning, and performed slightly better or similarly in terms of N-cycle gene abundance and the REs of ammonia nitrogen (NH₄⁺-N) and total nitrogen (TN). The abundance of the Amox gene was 66.1-92.8, 76.3-161.8 and 1550-2492 times larger than that of the napA, narG and amoA genes, respectively, and the anammox process was the dominant N removal pathway. Therefore, excavation and washing is recommended as the RSS for CWs with a long-term rest period.

Nitrogen Removal Ability and Characteristics of the Laboratory-Scale Tidal Flow Constructed Wetlands for Treating Ammonium-Nitrogen Contaminated Groundwater

Constructed wetlands (CWs) are an effective technology to remove organic compounds and nitrogen (N) from wastewaters and contaminated environmental waters. However, the feasibility of CWs for ammonium-N (NH4+-N)-contaminated groundwater treatment is unclear. In this study, zeolite-based laboratory-scale CW was operated as a tidal flow CW with a cycle consisting of 21-h flooded and 3-h rest, and used to treat NH4+-N (30 mg L−1) contaminated groundwater. In addition to NH4+-N, nitrite (NO2−-N) and nitrate (NO3−-N) were also not detected in the effluents from the tidal flow CW. The N removal constant remained high for a longer period of time compared to the continuous flow CW. The higher and more sustainable N removal of the tidal flow CW was due to the in-situ biological regeneration of zeolite NH4+-N adsorption capacity. Vegetation of common reeds in tidal flow zeolite-based CW enhanced nitrification and heterotrophic denitrification activities, and increased the functional genes of nitrification (AOB-amoA and nxrA) and denitrification (narG, nirK, nirS, and nosZ) by 2‒3 orders of magnitude, compared to CW without vegetation. The results suggest that the combination of zeolite substrate, tidal flow, and vegetation is key for the highly efficient and sustainable N removal from NH4+-N contaminated groundwater.

Microbial community at transcription level in the synergy of GAOs and Candidatus Accumulibacter for saving carbon source in wastewater treatment

The microbial community in endogenous denitrification and denitrifying phosphorus removal treatment at transcription level was unknown. This study first confirmed the expression of actually active bacteria in endogenous denitrification and denitrifying phosphorus removal system to treat low C/N municipal wastewater. No external carbon source was added to influent wastewater. The cDNA high throughput sequencing showed that Candidatus Accumulibacter was the most effective polyphosphate accumulating organisms (PAOs) that actually worked rather than Dechloromonas, which was different from the result at gene level. Reverse transcriptional PCR (RT-PCR) and analysis of Variance (ANOVA) suggested that the ratios of dead or dormant bacteria could monitor wastewater treatment process. Identification of active microbial community at transcription level demonstrated that the synergy of endogenous denitrification by glycogen accumulating organisms (GAOs) and denitrifying phosphorus removal by Candidatus Accumulibacter fully utilized the internal carbon source, and effectively solved the problem of carbon source deficiency in municipal wastewater treatment.

Nitrogen Fertilizer Amendment Alter the Bacterial Community Structure in the Rhizosphere of Rice (Oryza sativa L.) and Improve Crop Yield

Availability of nitrogen (N) in soil changes the composition and activities of microbial community, which is critical for the processing of soil organic matter and health of crop plants. Inappropriate application of N fertilizer can alter the rhizosphere microbial community and disturb the soil N homeostasis. The goal of this study was to assess the effect of different ratio of N fertilizer at various early to late growth stages of rice, while keeping the total N supply constant on rice growth performance, microbial community structure, and soil protein expression in rice rhizosphere. Two different N regimes were applied, i.e., traditional N application (NT) consists of three sessions including 60, 30 and 10% at pre-transplanting, tillering and panicle initiation stages, respectively, while efficient N application (NF) comprises of four sessions, i.e., 30, 30, 30, and 10%), where the fourth session was extended to anthesis stage. Soil metaproteomics combined with Terminal Restriction Fragment Length Polymorphism (T-RFLP) were used to determine the rhizosphere biological process. Under NF application, soil enzymes, nitrogen utilization efficiency and rice yield were significantly higher compared to NT application. T-RFLP and qPCR analysis revealed differences in rice rhizosphere bacterial diversity and structure. NF significantly decreased the specific microbes related to denitrification, but opposite result was observed for bacteria associated with nitrification. Furthermore, soil metaproteomics analysis showed that 88.28% of the soil proteins were derived from microbes, 5.74% from plants, and 6.25% from fauna. Specifically, most of the identified microbial proteins were involved in carbohydrate, amino acid and protein metabolisms. Our experiments revealed that NF positively regulates the functioning of the rhizosphere ecosystem and further enabled us to put new insight into microbial communities and soil protein expression in rice rhizosphere.

Analysis of microbial community in a continuous flow process at gene and transcription level to enhance biological nutrients removal from municipal wastewater

In biological municipal wastewater treatment, gene level analysis of community structure could not determine functional genes that actually played a role and expression of viable microorganism. In this study, reverse transcriptional PCR (RT-PCR), cDNA high throughput sequencing and transcriptional activity analysis were conducted to investigate active microbial community with nitrogen and phosphorus removal from municipal wastewater. RT-PCR and correlation heatmap analysis suggested that transcriptional activities of bacteria had strong correlation with performance of nitrogen and phosphorus removal, they might be therefore regarded as an indicator for wastewater treatment monitoring. When DO concentration were raised from 0.6 mg/L to 2 mg/L and C/N ratio from 3-4 to 5, the increase of population abundance and transcriptional activities of denitrifying genes improved the removal efficiencies of COD and TN. The species with relatively high abundance at gene level were not really active species at transcription level, and vice versa.

Effects of Oenanthe javanica on Nitrogen Removal in Free-Water Surface Constructed Wetlands under Low-Temperature Conditions

To investigate the role and microorganism-related mechanisms of macrophytes and assess the feasibility of Oenanthe javanica (Blume) DC. in promoting nitrogen removal in free-water surface constructed wetlands (FWS-CWS) under low temperatures (<10 °C), pilot-scale FWS-CWS, planted with O. javanica, were set up and run for batch wastewater treatment in eastern China during winter. The presence of macrophytes observably improved the removal rates of ammonia nitrogen (65%-71%) and total nitrogen (41%-48%) (p < 0.05), with a sharp increase in chemical oxygen demand concentrations (about 3-4 times). Compared to the unplanted systems, the planted systems not only exhibited higher richness and diversity of microorganisms, but also significantly higher abundances of bacteria, ammonia monooxygenase gene (amoA), nitrous oxide reductase gene (nosZ), dissimilatory cd1-containing nitrite reductase gene (nirS), and dissimilatory copper-containing nitrite reductase gene (nirK) in the substrate. Meanwhile, the analysis of the microbial community composition further revealed significant differences. The results indicate that enhanced abundances of microorganisms, and the key functional genes involved with nitrogen metabolism in the planted systems played critical roles in nitrogen removal from wastewater in FWS-CWS. Furthermore, abundant carbon release from the wetland macrophytes could potentially aid nitrogen removal in FWS-CWS during winter.

Roles and correlations of functional bacteria and genes in the start-up of simultaneous anammox and denitrification system for enhanced nitrogen removal

Simultaneous anammox and denitrification (SAD) is a newly developed wastewater treatment process efficient in nitrogen removal, but its underlying microbiological mechanisms during start-up remains unknown. This study investigated the changing patterns of functional bacteria and genes, as well as their correlation during the start-up (260 d) of the SAD systems in two lab-scale up-flow anaerobic sludge blanket bioreactors separately inoculated with anaerobic granular sludge (R1) and aerobic floccular sludge (R2). Results showed that high total nitrogen removal was achieved in the SAD systems of both R1 (88.25%) and R2 (89.42%). High-throughput sequencing of 16S rRNA gene amplicons revealed that Armatimonadetes phylum had a high abundance (44.34%) in R2, while was not detectable in R1 during the anammox stage. However, the SAD bioreactors retained inherent microbial community and the inoculation with different sludge showed less notable effects on their microbial composition. In the SAD systems, Candidatus Brocadia had high abundance in R1 (2.93%) and R2 (4.64%) and played important role in anammox. Network analysis indicated that Denitratisoma and Dokdonella were positively correlated with nitrite reductase genes nirS and nirK (p < 0.05), while Thermomonas and Pseudomonas showing a positive correlation with nitrate reductase gene narG (p < 0.05) were mainly responsible for the nitrate reduction in the SAD systems. Moreover, the overwhelming dominance of narG v.s. napA revealed the crucial roles of respiratory nitrate reduction in the bioreactors. The results extend our knowledge regarding the microbial ecology of the SAD system, which might be practically helpful for application of the process in wastewater treatment.

Importance of denitrification driven by the relative abundances of microbial communities in coastal wetlands

Excessive nitrogen (N) loadings from human activities have led to increased eutrophication and associated water quality impacts in China's coastal wetlands. Denitrification accounts for significant reduction of inorganic N to nitrous oxide (N₂O) or dinitrogen gas (N₂), and thereby curtails harmful effects of N pollution in coastal and marine ecosystems. However, the molecular drivers and limiting steps of denitrification in coastal wetlands are not well understood. Here, we quantified the abundances of functional genes involved in N cycling and determined denitrification rates using ¹⁵N paring technique in the coastal wetland sediments of Bohai Economic Rim in eastern China. Denitrification accounting for 80.7 ± 12.6% of N removal was the dominant pathway for N removal in the coastal wetlands. In comparison, anaerobic ammonium oxidation (ANAMMOX) removed up to 36.9 ± 7.3% of inorganic N. Structural equation modeling analysis indicated that the effects of ammonium on denitrification potential were mainly mediated by the relative abundances of nosZ/nirS, nirS/(narG + napA) and amoA/nirK. Denitrification was limited by the relative strength of two steps, namely N₂O reduction to N₂ and nitrite (NO₂^-) reduction to nitric oxide (NO). Our results suggest that the relative abundances of functional genes which are more stable than sediment chemical compounds in the context of environmental changes are indictive of denitrification potential in coastal wetlands.

Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments

Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.

Quantitative responses of potential nitrification and denitrification rates to the size of microbial communities in rice paddy soils

Nitrification and denitrification are important to nitrogen balance in agricultural ecosystems. However, the molecular drivers and limiting steps for these microbial processes in rice paddy soils are not well understood. Here, we assessed soil properties and abundances of functional genes affiliated with nitrification (amoA and nxrA), denitrification (nirS, nirK and nosZ), nitrate reduction (narG and napA) processes, and measured potential nitrification and denitrification rates (PNRs and PDRs) at 15 sites in Xiamen, China. The soil properties imposed indirect impacts on the potential rates by mediating the relative abundances of microbial communities. No significant relationships between the size of microbial communities and the potential rates were observed. Instead, we found the variables that best explained the variations in the PNRs and PDRs were AOB/nirS and (nirK + nirS)/nosZ, respectively. The PNRs were mainly limited by the relative strength of two steps, namely bacterial ammonium oxidation and nitrite into nitric oxide reduction, whereas the PDRs were mainly limited by the relative strength of the second and last denitrification steps. These results indicated that the dynamics of microbial communities based on the relative gene abundances are valuable in integrating fluctuations in soil physicochemical properties and are indictive of potential rates in paddy soils. Results of this study contribute to our quantitative understanding of the relative importance of soil physicochemical and biological factors in driving microbial potential in paddy soils.

Effect of trace elements on the development of co-cultured nitrite-dependent anaerobic methane oxidation and methanogenic bacteria consortium

The aim of this work was to study the effects of key trace elements (i.e., iron, copper and molybdenum) on the development of co-cultured n-damo and methanogenic bacteria consortium, which could realize in situ CH₄ production and utilization. The results showed that rational dosage, which was 50 mg/L of Fe, 1 mg/L of Cu and 5 mg/L of Mo, significantly stimulated the removal of NO₂^-. However, the activity of microbes was noticeably inhibited at 5 mg/L of Cu and 1 mg/L of Mo. Microbial community analysis indicated that the abundances of n-damo bacteria and methanogens showed a positive response to the rational dosage. Furthermore, the expression of key functional genes was enhanced under the rational dosage condition.

Nitrogen removal performance and functional genes distribution patterns in solid-phase denitrification sub-surface constructed wetland with micro aeration

An up-flow vertical flow constructed wetland (AC-VFCW) filled with ceramsite and 5% external carbon source poly(3-hydroxybutyrate-hydroxyvalerate) (PHBV) as substrate was set for nitrogen removal with micro aeration. Simultaneous nitrification and denitrification process was observed with 90.4% NH₄⁺-N and 92.1% TN removal efficiencies. Nitrification and denitrification genes were both preferentially enriched on the surface of PHBV. Nitrogen transformation along the flow direction showed that NH₄⁺-N was oxidized to NO₃^--N at the lowermost 10 cm of the substrate and NO₃^--N gradually degraded over the depth. AmoA gene was more enriched at -10 and -50 cm layers. NirS gene was the dominant functional gene at the bottom layer with the abundance of 2.05 × 10⁷ copies g^-1 substrate while nosZ gene was predominantly abundant with 7.51 × 10⁶ and 2.64 × 10⁶ copies g^-1 substrate at the middle and top layer, respectively, indicating that functional division of dominant nitrogen functional genes forms along the flow direction in AC-VFCW.

Microbial Community and in situ Bioremediation of Groundwater by Nitrate Removal in the Zone of a Radioactive Waste Surface Repository

The goal of the present work was to investigate the physicochemical and radiochemical conditions and the composition of the microbial community in the groundwater of a suspended surface repository for radioactive waste (Russia) and to determine the possibility of in situ groundwater bioremediation by removal of nitrate ions. Groundwater in the repository area (10-m depth) had elevated concentrations of strontium, tritium, nitrate, sulfate, and bicarbonate ions. High-throughput sequencing of the V3-V4/V4 region of the 16S rRNA gene revealed the presence of members of the phyla Proteobacteria (genera Acidovorax, Simplicispira, Thermomonas, Thiobacillus, Pseudomonas, Brevundimonas, and uncultured Oxalobacteraceae), Firmicutes (genera Bacillus and Paenibacillus), and Actinobacteria (Candidatus Planktophila, Gaiella). Canonical correspondence analysis suggested that major contaminant - nitrate, uranium, and sulfate shaped the composition of groundwater microbial community. Groundwater samples contained culturable aerobic organotrophic, as well as anaerobic fermenting, iron-reducing, and denitrifying bacteria. Pure cultures of 33 bacterial strains belonging to 15 genera were isolated. Members of the genera Pseudomonas, Rhizobium, Cupriavidus, Shewanella, Ensifer, and Thermomonas reduced nitrate to nitrite and/or dinitrogen. Application of specific primers revealed the nirS and nirK genes encoding nitrite reductases in bacteria of the genera Pseudomonas, Rhizobium, and Ensifer. Nitrate reduction by pure bacterial cultures resulted in decreased ambient Eh. Among the organic substrates tested, sodium acetate and milk whey were the best for stimulation of denitrification by the microcosms with groundwater microorganisms. Injection of these substrates into the subterranean horizon (single-well push-pull test) resulted in temporary removal of nitrate ions in the area of the suspended radioactive waste repository and confirmed the possibility for in situ application of this method for bioremediation.

Nitrogen loading effects on nitrification and denitrification with functional gene quantity/transcription analysis in biochar packed reactors at 5 °C

This study investigated the nitrogen transformation rates of different nitrogen-loading (20, 30, and 50 mg TN/L) biochar packed reactors (C:N:P = 100:5:1) within 125 days at 5 °C. The results showed that high nitrogen loading resulted in an NH4+ (TN) removal efficiency decline from 98% (57%) to 83% (29%), with biochar yielding a higher NH4+, TN and DON removal rate than conventional activated sludge. Moreover, all biochar packed reactors realized a quick start-up by dropping in temperature stage by stage, and the effluent dissolved organic nitrogen (DON) concentrations of R20, R30, and R50 were 0.44 ± 0.18, 0.85 ± 0.35, and 0.66 ± 0.26 mg/L, respectively. The nirS/amoA, nxrA/amoA, and amoA/(narG + napA) were deemed to be the markers of ammonium oxidation rate (SAOR), specific nitrite oxidation rate (SNOR), and specific nitrate reduction rate (SNRR), respectively. Compared with functional gene quantity data, transcription data (mRNA) introduced into stepwise regression analyses agreed well with nitrogen transformation rates. High nitrogen loading also resulted in the cell viability decreased in R50. Nitrogen loadings and operation time both led to a significant variation in cell membrane composition, and unsaturated fatty acids (UFAs) significantly increased in R30 (46.49%) and R50 (36.34%). High-throughput sequencing revealed that nitrogen loadings increased the abundance of nitrifying bacteria (e.g., Nitrospira) and reduced the abundance of denitrifying bacteria (e.g., Nakamurella, Thermomonas, and Zoogloea) through linear discriminant analysis (LDA).

Pathway and mechanism of nitrogen transformation during composting: Functional enzymes and genes under different concentrations of PVP-AgNPs

Polyvinylpyrrolidone coated silver nanoparticles (PVP-AgNPs) were applied at different concentrations to reduce total nitrogen (TN) losses and the mechanisms of nitrogen bio-transformation were investigated in terms of the nitrogen functional enzymes and genes. Results showed that mineral N in pile 3 which was treated with AgNPs at a concentration of 10 mg/kg compost was the highest (6.58 g/kg dry weight (DW) compost) and the TN loss (47.07%) was the lowest at the end of composting. Correlation analysis indicated that TN loss was significantly correlated with amoA abundance. High throughput sequencing showed that the dominant family of ammonia-oxidizing bacteria (AOB) was Nitrosomonadaceae, and the number of Operational Taxonomic Units (OTUs) reduced after the beginning of composting when compared with day 1. In summary, treatment with AgNPs at a concentration of 10 mg/kg compost was considerable to reduce TN losses and reserve more mineral N during composting.

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning

Contamination from anthropogenic activities has significantly impacted Earth’s biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P < 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning.

Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as uranium or nitrate increased. These key microbial functional genes could be used to successfully predict environmental contamination and ecosystem functioning. This study represents a significant advance in using functional gene markers to predict the spatial distribution of environmental contaminants and ecosystem functioning toward predictive microbial ecology, which is an ultimate goal of microbial ecology.

nirS-type denitrifying bacterial assemblages respond to environmental conditions of a shallow estuary

Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered 'generalist' and 'specialist' archetypes based on the distribution of archetypes within these assemblages. Generalists, archetypes detected in all samples during at least one season, were commonly world-wide found in estuarine and marine ecosystems, comprised 8%-29% of the abundant NRE archetypes. Archetypes found in a particular site, 'specialists', were found to co-vary based on site specific conditions. Archetypes specific to the lower estuary in winter were designated Cluster I and significantly correlated by sediment Chl a and porewater Fe²⁺ . A combination of specialist and more widely distributed archetypes formed Clusters II and III, which separated based on salinity and porewater H₂ S respectively. The co-occurrence of archetypes correlated with different environmental conditions highlights the importance of habitat type and niche differentiation among nirS-type denitrifying communities and supports the essential role of individual community members in overall ecosystem function.

Attached and Suspended Denitrifier Communities in Pristine Limestone Aquifers Harbor High Fractions of Potential Autotrophs Oxidizing Reduced Iron and Sulfur Compounds

Oxygen and nitrate availability as well as the presence of suitable organic or inorganic electron donors are strong drivers of denitrification; however, the factors influencing denitrifier abundance and community composition in pristine aquifers are not well understood. We explored the denitrifier community structure of suspended and attached groundwater microorganisms in two superimposed limestone aquifer assemblages with contrasting oxygen regime in the Hainich Critical Zone Exploratory (Germany). Attached communities were retrieved from freshly crushed parent rock material which had been exposed for colonization in two groundwater wells (12.7 and 48 m depth). Quantitative PCR and amplicon pyrosequencing of nirK and nirS genes encoding copper-containing or cytochrome cd1 heme-type nitrite reductase, respectively, and of bacterial 16S ribosomal RNA genes showed a numerical predominance of nirS-type denitrifiers in both attached and suspended groundwater communities and a dominance of nirS-type denitrifiers closely related to the autotrophic thiosulfate- and hydrogen-oxidizing Sulfuritalea hydrogenivorans and the iron- and sulfide-oxidizing Sideroxydans lithotrophicus ES-1. Potential rates of nitrate reduction in association with exposed crushed rock material were higher with an inorganic electron donor (thiosulfate) compared to an organic electron donor (fumarate/acetate) in the upper aquifer assemblage but similar in the lower, oxic aquifer. Our results have clearly demonstrated that groundwater from pristine limestone aquifers harbors diverse denitrifier communities which appear to selectively attach to rock surfaces and harbor a high potential for nitrate reduction. Our findings suggest that the availability of suitable inorganic versus organic electron donors rather than oxygen availability shapes denitrifier communities and their potential activity in these limestone aquifers.

A comparison of denitrifying bacterial community structures and abundance in acidic soils between natural forest and re-vegetated forest of Nanling Nature Reserve in southern China

Denitrification plays a key role in converting reactive nitrogen species to dinitrogen gas back into the atmosphere to maintain the equilibrium of nitrogen cycling in ecosystems. In this study, functional genes of nirK and nosZ were used to detect the community structure and abundance of denitrifying microorganisms in acidic forest soils in southern China. Three sets of factors were considered for a comparison among 5 forests, including forest types (natural vs. re-vegetated), depths (surface layer vs. lower layer) and seasons (winter vs. summer). The community of nirK gene detected from these acidic forest soils was closely related to Proteobacteria especially α-Proteobacteria and uncultured soil sequences, while that of nosZ gene was affiliated with the α-, β- and γ-Proteobacteria. Higher diversity of denitrifiers was observed in re-vegetated forest soils than natural ones. Not only the community but also the abundance showed significant differences between forest types as well as depths. The abundance of denitrifiers ranged from 10⁵ to 10⁷ gene copies g^-1 dry soil in this study. For nirK gene, the abundance was much higher in the lower layer than surface layer in both forest types, and the differences between winter and summer in natural forest soils were higher than those in re-vegetated forest soils. The abundance of nosZ and nirK genes showed a similar trend in natural forest, but the former was higher in matured forest than re-vegetated forest. This study provided a direct comparison on community composition and abundance of denitrifying bacteria in natural and re-vegetated acidic forest soils to allow further assessment of the nitrogen cycling.

Enhancement of the complete autotrophic nitrogen removal over nitrite process in a modified single-stage subsurface vertical flow constructed wetland: Effect of saturated zone depth

This study was conducted to explore enhancement of the complete autotrophic nitrogen removal over nitrite (CANON) process in a modified single-stage subsurface vertical flow constructed wetland (VSSF) with saturated zone, and nitrogen transformation pathways in the VSSF treating digested swine wastewater were investigated at four different saturated zone depths (SZDs). SZD significantly affected nitrogen transformation pathways in the VSSF throughout the experiment. As the SZD was 45cm, the CANON process was enhanced most effectively in the system owing to the notable enhancement of anammox. Correspondingly, the VSSF had the best TN removal performance [(76.74±7.30)%] and lower N₂O emission flux [(3.50±0.22)mg·(m²·h)^-1]. It could be concluded that autotrophic nitrogen removal via CANON process could become a primary route for nitrogen removal in the VSSF with optimized microenvironment that developed as a result of the appropriate SZD.

Effect of plant-based carbon sources on denitrifying microorganisms in a vertical flow constructed wetland

The effects of supplementing plant-based carbon sources, fermented tissues of Arundo donax and Pontederia cordata, and a combination of the two plants, on the nitrogen removal efficiency and microbial composition in a vertical flow constructed wetland (VFCW) were examined. The results showed that the addition of the composite carbon source produced the highest removal efficiencies of NH₄⁺-N 91.5%, NO₃^--N 94.5% and TN 92.8% in VFCW. The detected abundance of amoA, nirS, and nxrA genes indicated that ammonia oxidation bacteria and denitrifying bacteria were more abundant than the nitrite oxidation bacteria. Furthermore, the addition of the composite carbon source significantly promoted the growth of the denitrifying bacteria in VFCW. The results indicated that supplementing the system with plant-based carbon sources achieved partial nitrification and denitrification, as well as classic denitrification in VFCWs. The study suggested that multiple nitrogen removal pathways were required to feasibly and efficiently remove nitrogen.

Microbial community and metabolism activity in a bioelectrochemical denitrification system under long-term presence of p-nitrophenol

Bioelectrochemical denitrification system (BEDS) is a promising technology for nitrate removal from wastewaters. The hazards and effects concerning p-nitrophenol (PNP) towards BEDS lack enough investigations and possess great research prospects. This study investigated how PNP affected the nitrate removal efficiency, microbial communities, functional denitrifying genes abundances, nitrate and nitrite reductase activities, diffusible signal factors (DSF) release, and extracellular polymeric substances (EPS) production in the BEDS. Results indicated that nitrate removal efficiency decreased with initial PNP concentration increased from 0 to 100mg/L. Phylum Firmicutes and class Clostridia were the main contributors for denitrification process in this BEDS. The abundances of the denitrifying genes nirS, nirK, napA, and narG all presented decreased trends with increasing PNP. In addition, the concentrations of nitrate reductase (NR), nitrite reductase (NIR), and EPS obviously decreased, while the concentration of DSF increased with increasing PNP, which demonstrated that higher PNP would inhibit the biofilm formation.

Altitude-scale variation in nitrogen-removal bacterial communities from municipal wastewater treatment plants distributed along a 3600-m altitudinal gradient in China

Microbial ecological information on the nitrogen removal processes in wastewater treatment plants (WWTPs) has been of considerable importance as a means for diagnosing the poor performance of nitrogen removal. In this study, the altitude-scale variations in the quantitative relationships and community structures of betaproteobacteria ammonia-oxidizing bacteria (βAOB) and nitrite-reducing bacteria containing the copper-containing nitrite reductase gene (nirK-NRB) and the cytochrome cd1-containing nitrite reductase gene (nirS-NRB) were investigated in 18 municipal WWTPs distributed along a 3660-masl altitude gradient in China. An altitude threshold associated with the proportions of NRB to total bacteria, NRB to βAOB and nirK-NRB to nirS-NRB was detected at approximately 1500m above sea level (masl). Compared with the stable proportions below 1500masl, the proportions exhibited a pronounced decreasing trend with increased altitude above 1500masl. Spearman correlation analysis indicated that the trend was significantly driven by altitude as well as multiple wastewater and operational variables. The community structure dissimilarity of βAOB, nirK-NRB and nirS-NRB showed significant and positive correlations with altitudinal distance between WWTPs. Redundancy analyses indicated that the variation in community structures above 1500masl were predominantly associated with wastewater, followed by operation and altitude. In summary, although the variations of nitrogen-removal bacterial community in WWTPs were driven dominantly by wastewater and operational variables, altitude was also an important variable influencing the quantitative relationships and community structures of nitrogen-removal bacteria in WWTPs particularly above 1500masl.

Distribution patterns of nitrogen micro-cycle functional genes and their quantitative coupling relationships with nitrogen transformation rates in a biotrickling filter

The present study explored the distribution patterns of nitrogen micro-cycle genes and the underlying mechanisms responsible for nitrogen transformation at the molecular level (genes) in a biotrickling filter (biofilter). The biofilter achieved high removal efficiencies for ammonium (NH4(+)-N) (80-94%), whereas nitrate accumulated at different levels under a progressive NH4(+)-N load. Combined analyses revealed the anammox, nas, napA, narG, nirS, and nxrA genes were the dominant enriched genes in different treatment layers. The presence of simultaneous nitrification, ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) were the primary factors accounted for the robust NH4(+)-N treatment performance. The presence of DNRA, nitrification, and denitrification was determined to be a pivotal pathway that contributed to the nitrate accumulation in the biofilter. The enrichment of functional genes at different depth gradients and the multi-path coupled cooperation at the functional gene level are conducive to achieving complete nitrogen removal.

Denitrifying phosphorus removal from municipal wastewater and dynamics of "Candidatus Accumulibacter" and denitrifying bacteria based on genes of ppk1, narG, nirS and nirK

Relevance of clade-level population dynamics of "Candidatus Accumulibacter" to performance of denitrifying phosphorus (P) removal from municipal wastewater was investigated. Stable denitrifying P removal in anoxic zone of continuous-flow reactor was achieved, accounting for 90% of total P removal. Clades IIC and IIF affiliated with Accumulibacter lineage were the dominant clades during denitrifying P removal, reaching 90% of ppk1 clone library. NarG gene library indicated Gamma and Beta-proteobacteria played an important role in nitrate reduction. Diversity and abundance of nirS library was much more than nirK, and thus became the main functional gene to execute nitrite reduction. Based on abundance of nirS, nirK and ppk1, the ratio of Accumulibacter capable of denitrifying P removal to total Accumulibacter was 22%. No matter whether Accumulibacter had narG gene or not, high abundance of narG at a level of 10(9)cells/(g dried-sludge) promoted nitrate reduced to nitrite, ensuring performance of denitrifying P removal.

Bacterial Diversity in Submarine Groundwater along the Coasts of the Yellow Sea

Submarine groundwater (SGD) is one of the most significant pathways for the exchange of groundwater and/or source of nutrients, metals and carbon to the ocean, subsequently cause deleterious impacts on the coastal ecosystems. Microorganisms have been recognized as the important participators in the biogeochemical processes in the SGD. In this study, by utilizing 16S rRNA-based Illumina Miseq sequencing technology, we investigated bacterial diversity and distribution in both fresh well water and brackish recirculated porewater along the coasts in the Yellow Sea. The results showed that Actinobacteria and Betaproteobacteria, especially Comamonas spp. and Limnohabitans spp. were dominated in fresh well samples. Distinct patterns of bacterial communities were found among the porewater samples due to different locations, for examples, Cyanbacteria was the most abundant in the porewater samples far from the algal bloomed areas. The analysis of correlation between representative bacterial taxonomic groups and the contexture environmental parameters showed that fresh well water and brackish porewater might provide different nutrients to the coastal waters. Potential key bacterial groups such as Comamonas spp. may be excellent candidates for the bioremediation of the natural pollutants in the SGD. Our comprehensive understanding of bacterial diversity in the SGD along the coasts of the Yellow Sea will create a basis for designing the effective clean-up approach in-situ, and provide valuable information for the coastal management.

Cold Temperature Effects on Long-Term Nitrogen Transformation Pathway in a Tidal Flow Constructed Wetland

The present study investigated long-term treatment performance and nitrogen transformation mechanisms in tidal flow constructed wetlands (TFCWs) under 4, 8, and 12 °C temperature regimes. High and stable ammonium (NH4(+)-N) removal efficiency (93-96%) was achieved in our TFCWs, whereas nitrate (NO3(-)-N) was accumulated at different levels under different temperatures. Quantitative response relationships showed anammox/amoA, (narG+napA)/amoA, and (narG+napA)/bacteria were the respective key functional gene groups determining 4, 8, and 12 °C NO3(-)-N reduction. Pathway analysis revealed the contribution of these functional gene groups along a depth gradient. In addition, denitrification process increased, while anammox process decreased consistent with a rise in temperature from 4 to 12 °C. Furthermore, cold temperatures exhibited different effects on anammox and denitrification and their long-term acclimatization capacities changed with temperature.

Response of Spatial Patterns of Denitrifying Bacteria Communities to Water Properties in the Stream Inlets at Dianchi Lake, China

Streams are an important sink for anthropogenic N owing to their hydrological connections with terrestrial systems, but main factors influencing the community structure and abundance of denitrifiers in stream water remain unclear. To elucidate the potential impact of varying water properties of different streams on denitrifiers, the abundance and community of three denitrifying genes coding for nitrite (nirK, nirS) and nitrous oxide (nosZ) reductase were investigated in 11 streams inlets at the north part of Dianchi Lake. The DGGE results showed the significant pairwise differences in community structure of nirK, nirS, and nosZ genes among different streams. The results of redundancy analysis (RDA) confirmed that nitrogen and phosphorus concentrations, pH, and temperature in waters were the main environmental factors leading to a significant alteration in the community structure of denitrifiers among different streams. The denitrifying community size was assessed by quantitative PCR (qPCR) of the nirS, nirK, and nosZ genes. The abundance of nirK, nirS, and nosZ was positively associated with concentrations of total N (TN) and PO4 (3-) (p < 0.001). The difference in spatial patterns between nirK and nirS community diversity, in combination with the spatial distribution of the nirS/nirK ratio, indicated the occurrence of habitat selection for these two types of denitrifiers in the different streams. The results indicated that the varying of N species and PO4 (3-) together with pH and temperature would be the main factors shaping the community structure of denitrifiers. Meanwhile, the levels of N in water, together with PO4 (3-), tend to affect the abundance of denitrifiers.

Diversity, Abundance, and Distribution of nirS-Harboring Denitrifiers in Intertidal Sediments of the Yangtze Estuary

Denitrification plays a critical role in nitrogen removal in estuarine and coastal ecosystems. In this study, the community composition, diversity, abundance, and distribution of cytochrome cd1-type nitrite reductase gene (nirS)-harboring denitrifiers in intertidal sediments of the Yangtze Estuary were analyzed using polymerase chain reaction (PCR)-based clone libraries and quantitative PCR techniques. Clone library analysis showed that the nirS-encoding bacterial biodiversity was significantly higher at the lower salinity sites than at the higher salinity sites. However, there was no significant seasonal difference in the nirS gene diversity between summer and winter. Phylogenetic analysis revealed that the nirS-harboring denitrifier communities at the study area had distinctive spatial heterogeneity along the estuary. At the lower salinity sites, the nirS-harboring bacterial community was co-dominated by clusters III and VII; while at the higher salinity sites, it was dominated by cluster I. Canonical correspondence analysis indicated that the community compositions of nirS-type denitrifiers were significantly correlated with salinity, ammonium, and nitrate. Quantitative PCR results showed that the nirS gene abundance was in the range of 1.01 × 10(6) to 9.00 × 10(7) copies per gram dry sediment, without significant seasonal variation. Among all the environmental factors, the nirS gene abundance was only significantly related to the change of salinity. These results can extend our current knowledge about the composition and dynamics of denitrification microbial community in the estuarine ecosystem.

Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils

Microorganisms are capable of producing N2 and N2O gases as the end products of denitrification. Copper-containing nitrite reductase (NirK), a key enzyme in the microbial N-cycle, has been found in bacteria, archaea and fungi. This study seeks to assess the diversity of nirK genes in the prokaryotic and fungal communities of agricultural soils in the United States. New primers targeting the nirK genes in fungi were developed, while nirK genes in archaea and bacteria were detected using previously published methods. The new primers were able to detect fungal nirK genes as well as bacterial nirK genes from a group that could not be observed with previously published primers. Based on the sequence analyses from three different primer sets, five clades of nirK genes were identified, which were associated with soil archaea, ammonium-oxidizing bacteria, denitrifying bacteria and fungi. The diversity of nirK genes in the two denitrifying bacteria clades was higher than the diversity found in other clades. Using a newly designed primer set, this study showed the detection of fungal nirK genes from environmental samples. The newly designed PCR primers in this study enhance the ability to detect the diversity of nirK-encoding microorganisms in soils.

Soil-borne microbial functional structure across different land uses

Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.