Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE

Soil nitrogen substances and denitrifying communities regulate the anaerobic oxidation of methane in wetlands of Yellow River Delta, China

Anaerobic oxidation of methane (AOM) in wetland soils is widely recognized as a key sink for the greenhouse gas methane (CH₄). The occurrence of this reaction is influenced by several factors, but the exact process and related mechanism of this reaction remain unclear, due to the complex interactions between multiple influencing factors in nature. Therefore, we investigated how environmental and microbial factors affect AOM in wetlands using laboratory incubation methods combined with molecular biology techniques. The results showed that wetland AOM was associated with a variety of environmental factors and microbial factors. The environmental factors include such as vegetation, depth, hydrogen ion concentration (pH), oxidation-reduction potential (ORP), electrical conductivity (EC), total nitrogen (TN), nitrate (NO₃^-), sulfate (SO₄^2-), and nitrous oxide (N₂O) flux, among them, soil N substances (TN, NO₃^-, N₂O) have essential regulatory roles in the AOM process, while NO₃^- and N₂O may be the key electron acceptors driving the AOM process under the coexistence of multiple electron acceptors. Moreover, denitrification communities (narG, nirS, nirK, nosZI, nosZII) and anaerobic methanotrophic (ANME-2d) were identified as important functional microorganisms affecting the AOM process, which is largely regulated by the former. In the environmental context of growing global anthropogenic N inputs to wetlands, these findings imply that N cycle-mediated AOM processes are a more important CH₄ sink for controlling global climate change. This studying contributes to the knowledge and prediction of wetland CH₄ biogeochemical cycling and provides a microbial ecology viewpoint on the AOM response to global environmental change.

Climate-induced salinization may lead to increased lake nitrogen retention

Salinization caused by climate change and nitrogen (N) pollution are both important environmental threats for inland lakes. However, evaluating their interactive effects continues to be challenging. Here, field observation and microcosmic experiments were conducted in six lakes of East Asia with the different salinity and climate characteristics, to explore the response of the key N cycle processes related to N fate to the climate-induced change in salinity. The results indicated that increased salinity inhibited denitrification, which was the outcome of two cumulative effects: the long-term microbial adaptation effect and the direct salinity stress. Whereas increased salinity had unsignificant or positive effects on dissimilatory nitrate reduction to ammonium. It had caused that N retention capacity is relatively stronger in saline than freshwater lakes. Inland lakes are long-term basin-wide integrators of climatic conditions that drying (salinization) and wetting (desalination) with climate change. In semi-arid regions of East Asia, lake shrinkage, salinization and increasing temperature driven by climate warming and drying may exert a negative impact on N pollution through concentrating, decreasing denitrification and increasing ammonium release from sediment. The threat of climate change on these lakes is not just the quantity of water, but its quality.

The Effect of Mealworm Frass on the Chemical and Microbiological Properties of Horticultural Peat in an Incubation Experiment

Insect farming is growing in popularity, and in addition to insect meal, it generates waste products such as exuviae and frass, which can be recycled in agriculture. The aim of this incubation experiment was to evaluate the effect of Tenebrio molitor L. frass on selected chemical and biological properties of deacidified peat, which is widely used in horticulture. The optimal rate of frass fertilizer in peat for growing vegetables and ornamental plants was determined, with special emphasis on mineral nitrogen levels. Peat was fertilized with five nitrogen rates, 0, 50, 100, 200, and 400 mg dm^-3, and supplied with frass or urea. The study demonstrated that frass can be used as organic fertilizer. An increase in the nitrogen rate significantly increased mineral nitrogen content and electrical conductivity and decreased Ca content in peat. Both frass and urea increased the ammonification rate at the beginning of incubation and the nitrification rate from the second week of the experiment. Higher frass rates (5 and 10 g dm^-3) increased the content of plant-available nutrients (nitrogen, phosphorus, magnesium, potassium, and sodium) in peat as well as the abundance of microorganisms supporting organic matter mineralization. Unlike frass, urea increased the counts of nitrogen-fixing bacteria in peat.

Environmental and anthropogenic factors affect bacterial community and nitrogen removal in the Yarlung Zangbo River

Microorganisms play a critical role in the process of nitrogen removal in aquatic environment, which is regulated by multiple environmental factors. As a high-altitude region, the Qinghai-Tibet Plateau has unique composition of bacterial communities due to its unique geographical conditions, which may affect the nitrogen conversion of Plateau rivers. However, the regulation of nitrogen removal by environmental factors and bacterial community in high-altitude rivers has been rarely reported. This study investigated denitrification, anammox, and dissimilatory nitrate reduction to ammonium rates as well as the community of bacteria and denitrifiers in the Yarlung Zangbo River. The results showed that denitrification was the dominant nitrate removal process. Redundancy analysis revealed that environmental factors including suspended particulate matter, chemical oxygen demand, dissolved oxygen, nitrogen and phosphorus content, electrical conductivity, and pH explained a large amount of the variance in bacterial community. Denitrifiers carrying nitrite reductase-related gene were an important driver of denitrification in the Yarlung Zangbo River. The low water temperature brought by high altitude significantly reduced the denitrification rate. The cascade dams on the river affected the particle size distribution of sediment, changed the community composition of bacteria and denitrifying bacteria, and increased the denitrification rate in the downstream. Our findings highlight that nitrogen removal processes in high-altitude rivers are jointly regulated by environmental and anthropogenic factors through shaping denitrifier abundance.

Black Plastic Film Mulching Increases Soil Nitrous Oxide Emissions in Arid Potato Fields

Black plastic film mulching is a common practice for potato production in the arid area of Northwest China. Many studies have reported the significant positive effect of black plastic film mulch on potato harvest, while the effect of black plastic film mulch treatment on soil nitrous oxide (N₂O) emissions is still unclear. As a consequence, this study aimed to examine the effect of black plastic film mulch treatment on N₂O emission from arid upland potato fields. With the static chamber-gas chromatography method, soil N₂O emissions were measured. The results showed that black plastic film mulching treatment significantly increased cumulative soil N₂O emissions by 21-26% compared with non-mulched treatment. Cumulative N₂O emission positively correlated with soil temperature, soil moisture, soil CO₂ concentration, and amoA-AOB abundance. This study indicated that black plastic film mulching, mainly through increasing soil temperature and soil moisture, increasing soil carbon dioxide (CO₂) concentration, and promoting the abundance of nitrification-related functional gene of amoA-AOB, regulated N₂O emissions. This study also highlighted that the specific soil environment under black plastic film mulch is conducive to N₂O emissions and lay the foundation for settling the contradiction between food production and greenhouse gas mitigation in upland soils. The negative effects of black plastic film mulching on the environment should be considered in future applications in food production.

High importance of coupled nitrification-denitrification for nitrogen removal in a large periodically low-oxygen estuary

The coupling between nitrification and denitrification/anammox (nitrate/nitrite used in denitrification/anammox derives from nitrification) is a significant process of reactive nitrogen (N) removal that has attracted much attention. However, the dynamics of coupled nitrification-denitrification/anammox in the periodically low-oxygen estuaries and coasts remain unclear. Here, continuous-flow experiments combined with isotope tracing techniques were conducted in periodically low-oxygen areas of the Yangtze Estuary to reveal the changes in benthic sediment denitrification and anammox as well as their coupling with nitrification. Our results showed that denitrification increased but anammox decreased during low-oxygen summer. The occurrence of low oxygen also promoted coupled nitrification-denitrification but decreased coupled nitrification-anammox. These results implied that decreased dissolved oxygen in summer did not largely restrict nitrification activity, and anaerobic denitrification/anammox regulated the magnitude of coupled nitrification-denitrification/anammox rates. Denitrification (74.95-100 %) was the dominant process in total N removal, while coupled nitrification-denitrification accounted for a higher proportion (45.68-97.05 %) of denitrification, indicating that coupling between nitrification and denitrification played a dominant role in N removal. In addition to dissolved oxygen levels, carbon and N substrate availabilities were also important variables to regulate N transformations. Overall, this study advanced our knowledge of the distribution patterns and controlling factors of N removal processes and highlighted that coupled nitrification-denitrification might have a significant but neglected role in N removal from periodically low-oxygen estuaries.

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.

Response of soil microbial communities to petroleum hydrocarbons at a multi-contaminated industrial site in Lanzhou, China

Total petroleum hydrocarbon (TPH) contamination poses threats to ecological systems and human health. Many studies have reported its negative impacts on soil microbes, but limited information is known about microbial change and response to multiple TPH contamination events. In this study, we investigated TPH contamination level, microbial community structure and functional genes at a multi-contaminated industrial site in Lanzhou, where a benzene spill accident caused the drinking water crisis in 2014. TPHs distribution in soils and groundwater indicated multiple TPH contamination events in history, and identified the spill location where high TPH level (6549 mg kg^-1) and high ratio of low-molecular-weight TPHs (>80%) were observed. In contrast, TPH level was moderate (349 mg kg^-1) and the proportion of low-molecular-weight TPHs was 44% in soils with a long TPH contamination history. After the spill accident, soil bacterial communities became significant diverse (p = 0.047), but the dominant microbes remained the same as Pseudomonadaceae and Comamonadaceae. The abundance of hydrocarbon-degradation related genes increased by 10-1000 folds at the site where the spill accident occurred in multi-contaminated areas and was significantly related to 2-ring PAHs. Such changes of microbial community and hydrocarbon-degradation related genes together indicated the resilience of soil indigenous microbes toward multiple contamination events. Our results proved the significant change of bacterial community and huge shift of hydrocarbon-degradation related genes after the spill accident (multiple contamination events), and provided a deep insight into microbial response at industrial sites with a long period of contamination history.

Effects of biochar addition on nitrous oxide emission during soil freeze–thaw cycles

Biochar applied to soil can reduce nitrous oxide (N2O) emissions produced by freeze–thaw processes. Nonetheless, how biochar modification affects N2O emissions during freeze–thaw cycles is not completely clear. In our research, during freeze–thaw cycles, microcosm experiments were conducted to investigate the effects of maize straw biochar (MB) or rice straw biochar (RB) addition on soil N2O emissions under different water conditions. The N2O emissions peaked at the initial stage of thawing in all the soils, and the total N2O emissions were considerably greater in the flooded soils than in the nonflooded soils. Compared with the soils without biochar addition, RB and MB amendments inhibited N2O emissions by 69 and 67%, respectively. Moreover, after biochar addition, the abundance of AOB amoA genes decreased by 9–13%. Biochar addition significantly decreased the content of microbial biomass nitrogen (MBN) in flooded soil during thawing, which was significantly correlated with N2O emissions and nitrification and denitrification communities. The PLS-PM further revealed that biochar can inhibit the production and emission of soil N2O by reducing soil MBN during soil thawing. In addition, soil moisture directly significantly affects N2O emissions and indirectly affects N2O emissions through its influence on soil physicochemical properties. Our results revealed the important function of biochar in decreasing the emission of N2O in flooded soil during freeze–thaw cycles.

Nitrogen optimization coupled with alternate wetting and drying practice enhances rhizospheric nitrifier and denitrifier abundance and rice productivity

Optimizing nitrogen (N) fertilization without sacrificing grain yield is a major concern of rice production system because most of the applied N has been depleted from the soil and creating environmental consequences. Hence, limited information is available about nutrient management (NM) performance at a specific site under alternate wetting and drying (AWD) irrigation compared to conventional permanent flooding (PF). We aimed to inquire about the performance of NM practices compared to the farmer's fertilizer practice (FFP) under PF and AWD on rhizospheric nitrifier and denitrifier abundance, rice yield, plant growth, and photosynthetic parameters. Two improved NM practices; nutrient management by pig manure (NMPM); 40% chemical N replaced by pig manure (organic N), and nutrient management by organic slow-release fertilizer (NMSR); 40% chemical N replaced by organic slow-release N were compared. The results showed an increased total grain yield (16.06%) during AWD compared to PF. Compared to conventional FFP, NMPM, and NMSR significantly increased the yields by 53.84 and 29.67%, respectively, during AWD. Meanwhile, PF prompted a yield increase of 45.07 and 28.75% for NMPM and NMSR, respectively, (p < 0.05) compared to FFP. Besides, a significant correlation was observed between grain yield and nitrogen content during AWD (R ² = 0.58, p < 0.01), but no significant correlation was observed during PF. The NMPM contributed to photosynthetic attributes and the relative chlorophyll content under both watering events. Moreover, relatively higher abundances of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were observed during AWD, and the highest value was found after the late panicle stage. Our results suggest that the AWD-NMPM model is the best option to stimulate nitrifier and denitrifier gene abundance and promote rice production.

Diversity of Microbial Functional Genes Should Be Considered During the Interpretation of the qPCR Melting Curves

Soil microorganisms play an essential role in biogeochemical cycles. One approach to study these microbial communities is quantifying functional genes by quantitative PCR (qPCR), in which a melting curve analysis is usually assessed to confirm that a single PCR product is being quantified. However, the high diversity of functional genes in environmental samples could generate more than one peak in those curves, so the presence of two or multiple peaks does not always indicate nonspecific amplification. Here, we analyzed the taxonomic diversity of soil microorganisms harboring functional genes involved in nitrogen (N) and phosphorus (P) cycles, based on a database of genomes and metagenomes, and predicted the melting curve profiles of these genes. These functional genes were spread across many bacterial phyla, but mainly Proteobacteria and Actinobacteria. In general, the melting curves exhibited more than one peak or peaks with shoulders, mainly related to the variation of the nucleotide composition of the genes and the expected size of the amplicons. These results indicate that the melting curves of functional genes from environmental samples should be carefully evaluated, being in silico analyses a cost-effective way to identify inherent sequence diversity and avoid interpreting multiple peaks always as unspecific amplifications.

Nitrogen removal and mechanism of an extremely high-ammonia tolerant heterotrophic nitrification-aerobic denitrification bacterium Alcaligenes faecalis TF-1

A novel heterotrophic nitrifying bacterium with high salt and high ammonia nitrogen tolerance, Alcaligenes faecalis TF-1, was isolated from the leachate of a landfill. The verification of nitrogen removal efficiency of different nitrogen sources and PCR amplification electrophoresis results showed that the HN-AD pathway of the strain TF-1 was NH₄⁺ → NH₂OH → NO → N₂O → N₂. The results of parameter optimization showed that the optimal nitrogen removal conditions were as follows: sodium citrate as carbon source, C/N = 16, pH = 7, and NH₄⁺-N loading of 808.21 mg/L. The strain TF-1 could remove about 94.60% of ammonia nitrogen (1963.94 mg/L). The salinity tolerance range of the strain TF-1 was 0-70 g/L, and the removal efficiency was 52.87% at salinity 70 g/L and NH₄⁺-N concentration 919.20 mg/L and 55.67% at pH = 10 and NH₄⁺-N concentration 994.82 mg/L. The extreme environmental adaptability and remarkable nitrogen removal performance make this strain a promising candidate in leachate treatment.

Nitrogen deposition stimulated winter nitrous oxide emissions from bare sand more than biological soil crusts in cold desert ecosystem

Dryland ecosystems are often nitrogen-limited, and small nitrogen inputs may produce large responses to dryland ecological processes, such as gaseous nitrogen emission. The effect of increased anthropogenic nitrogen deposition on N₂O and NO emissions in desert ecosystems is unclear, especially in non-growing seasons when the surface is covered with snow. In this study, nitrogen applications were performed on biological soil crusts (lichen crust and moss crust, bare sand for control) in the Gurbantunggut Desert, Northwest China. We measured the fluxes of N₂O and NO and related nitrogen cycle functional gene abundances in winter for three-years period. Nitrogen addition significantly affected N₂O emissions and increased the abundances of key functional gene for nitrogen cycle, while it only slightly influenced NO emissions. These effects of nitrogen addition depended on composition of biological soil crusts. For bare sand and lichen crust, nitrogen addition significantly increased N₂O emissions, whereas for moss crust, only a negligible effect was observed. Meanwhile, significant differences in nitrogen cycle functional gene abundances were found among different composition of biological soil crusts. Abundance of amoA, narG, and nosZ genes were highly related to N₂O and NO emissions. Thus, our results indicate that gaseous nitrogen emissions were generally increased by nitrogen addition through their effects on related functional microbial groups. The effects were regulated by composition of biological soil crusts which can buffer the effects of increasing nitrogen addition during winter.

Sphagnum capillifolium holobiont from a subarctic palsa bog aggravates the potential of nitrous oxide emissions

Melting permafrost mounds in subarctic palsa mires are thawing under climate warming and have become a substantial source of N2O emissions. However, mechanistic insights into the permafrost thaw-induced N2O emissions in these unique habitats remain elusive. We demonstrated that N2O emission potential in palsa bogs was driven by the bacterial residents of two dominant Sphagnum mosses especially of Sphagnum capillifolium (SC) in the subarctic palsa bog, which responded to endogenous and exogenous Sphagnum factors such as secondary metabolites, nitrogen and carbon sources, temperature, and pH. SC's high N2O emission activity was linked with two classes of distinctive hyperactive N2O emitters, including Pseudomonas sp. and Enterobacteriaceae bacteria, whose hyperactive N2O emitting capability was characterized to be dominantly pH-responsive. As the nosZ gene-harboring emitter, Pseudomonas sp. SC-H2 reached a high level of N2O emissions that increased significantly with increasing pH. For emitters lacking the nosZ gene, an Enterobacteriaceae bacterium SC-L1 was more adaptive to natural acidic conditions, and N2O emissions also increased with pH. Our study revealed previously unknown hyperactive N2O emitters in Sphagnum capillifolium found in melting palsa mound environments, and provided novel insights into SC-associated N2O emissions.

Effects of whole-orchard recycling on nitrate leaching potential in almond production systems

Inefficient nitrogen (N) fertilization and irrigation have led to unhealthy nitrate levels in groundwater bodies of agricultural areas in California. Simultaneously, high commodity prices and drought have encouraged perennial crop growers to turnover less-productive orchards, providing opportunities to recycle tree biomass in situ and to use high-carbon (C) residues to conserve soil and water resources. Although climate change adaptation and mitigation benefits of high-C soil amendments have been shown, uncertainties remain regarding the benefits and trade-offs of this practice for N cycling and retention. We used established almond [Prunus dulcis (Mill.) D. A. Webb] orchard trials on Hanford fine sandy loam with short-term and long-term biomass recycling legacies to better understand the changes in N dynamics and retention capacity associated with this practice. In a soil column experiment, labeled N fertilizer was added and traced into various N pools, including microbial biomass and inorganic fractions in soil and leachate. Shifts in microbial communities were characterized using the abundance of key N cycling functional genes regulating nitrification and denitrification processes. Our findings showed that, in the short term, biomass recycling led to N immobilization within the orchard biomass incorporation depth zone (0-15 cm) without impacts on N leaching potential. However, this practice drastically reduced nitrate leaching potential by 52%, 10 yr after biomass incorporation without an increase in N immobilization. Although the timing of these potential benefits as a function of microbial population and C and N biogeochemical cycles still needs to be clarified, our results highlight the potential of this practice to meaningfully mitigate nitrate discharges into groundwater while conserving soil resources.

Nitrogen process in stormwater bioretention: effect of the antecedent dry days on the relative abundance of nitrogen functional genes

In this study, we evaluated the relative abundance of nitrogen functional genes (amoA, nirK and nirS) involved in ammonia oxidation and denitrification bacteria in laboratory-scale bioretention columns in response to environmental factors (e.g., moisture content, pH, soil organic matter, soil nitrogen) under different antecedent dry days (ADDs). We observed a decrease tendency of the relative abundance of ammonia-oxidizing bacteria at first and then increased when increasing ADDs from 1 to 22 day, while the relative abundance of denitrifying bacteria showed a downward trend. The abundance of bacteria gene amoA was positively associated with soil ammonia nitrogen concentration (r² = 0.389, p < 0.05) and soil organic matter concentration (r² = 0.334, p < 0.05), while the abundance of bacteria gene nirS was positively correlated with soil ammonia nitrogen (r² = 0.730, p < 0.01), soil organic matter (r² = 0.901, p < 0.01) and soil total nitrogen (r² = 0.779, p < 0.01). Furthermore, gene counts for bacteria gene nirS were correlated negatively with plant root length (r² = 0.364, p < 0.05) and plant biomass (r² = 0.381, p < 0.05). Taken together, these results suggest that both nitrification and denitrification can occur in bioretention systems, which can be affected by environmental factors.

Underestimation about the Contribution of Nitrate Reducers to Iron Cycling Indicated by Enterobacter Strain

Nitrate-reducing iron(II) oxidation (NRFO) has been intensively reported in various bacteria. Iron(II) oxidation is found to be involved in both enzymatic and chemical reactions in nitrate-reducing Fe(II)-oxidizing microorganisms (NRFOMs). However, little is known about the relative contribution of biotic and abiotic reactions to iron(II) oxidation for the common nitrate reducers during the NRFO process. In this study, the typical nitrate reducers, four Enterobacter strains E. hormaechei, E. tabaci, E. mori and E. asburiae, were utilized as the model microorganisms. The comparison of the kinetics of nitrate, iron(II) and nitrite and N₂O production in setups with and without iron(II) indicates a mixture of enzymatic and abiotic oxidation of iron(II) in all four Enterobacter strains. It was estimated that 22−29% of total oxidized iron(II) was coupled to microbial nitrate reduction by E. hormaechei, E. tabaci, E. mori, and E. asburiae. Enterobacter strains displayed an metabolic inactivity with heavy iron(III) encrustation on the cell surface in the NRFOmedium during days of incubation. Moreover, both respiratory and periplasmic nitrate-reducing genes are encoded by genomes of Enterobacter strains, suggesting that cell encrustation may occur with periplasmic iron(III) oxide precipitation as well as the surface iron(II) mineral coating for nitrate reducers. Overall, this study clarified the potential role of nitrate reducers in the biochemical cycling of iron under anoxic conditions, in turn, re-shaping their activity during denitrification because of cell encrustation with iron(III) minerals.

Diverse nirS-type Denitrifying Bacteria Contribute to Vital Nitrogen Loss in Natural Acidic Red Soils

Denitrifying bacteria, playing a key role in nitrogen removal in ecosystem, are highly diverse and complex in their community composition. However, there were few reports on the abundance, community composition, and the contribution to nitrogen loss of denitrifiers in natural acidic red soils. In this study, we investigated the structure and function of nirS-type denitrifying bacteria in ten natural red soil samples collected from nine provinces in southern China, based on quantitative polymerase chain reaction (qPCR) and high-throughput sequencing techniques. Nitrogen loss from microbial denitrification in red soils of southern China was estimated up to 9.86 Tg N per year based on ¹⁵N isotope tracing method. The abundance of nirS-type denitrifiers varied from 8.41 × 10⁵ to 2.55 × 10⁹ copies per gram of dry weight. The community of nirS-type denitrifying bacterial was revealed, which contained 50 dominant OTUs assigned to 9 clusters phylogenetically related to Marinobacter, Rhodobacter, and other uncultured species. pH was the key factor affecting both denitrification rates and community composition. Our results demonstrate that nirS-type denitrifying bacteria have higher abundance, diversity, and contribution to the nitrogen loss in natural acidic red soils of southern China.

Effects of Caffeine and COD from Coffee Wastewater on Anaerobic Ammonium Oxidation (Anammox) Activities

An anaerobic ammonium oxidation (anammox) process was employed to remove nitrogen from wastewater generated from a coffee brewing facility. The effects of caffeine and chemical oxygen demand (COD) in coffee wastewater on anammox activity were investigated. The anammox activity was inhibited in synthetic wastewater with a caffeine concentration greater than 350 mg/L. Daily additions of caffeine at 2.5 mg/L for 28 days to the same substrate did not inhibit anammox activity. However, daily additions of coffee wastewater with COD of ≥387 mg/L and caffeine at 2.5 mg/L significantly inhibited anammox activity. Because the pH was increased in the system, resulting in an increase in free ammonia (FA) concentration, one could postulate that FA is an inhibitor of anammox activity. Quantitative polymerase chain reaction (qPCR) analysis was employed to determine the populations of anammox and denitrifying bacteria. Coffee wastewater with bacterial COD to total nitrogen (bCOD:TN) ratios of 0.3–0.6:1 did not have any effect on the abundances of anammox and denitrifying bacteria. The results from this work suggest that biodegradable COD (bCOD) rather than total COD (TCOD) should be used for calculating the COD:TN ratio during the study of the effects of nitrogen removal from real wastewaters using the anammox process. A not-competitive model could fit the anammox inhibition with caffeine concentrations at 50–500 mg/L with maximum specific anammox activity (SAAmax) of 0.594 mg-N/mg-volatile suspended solids (VSS)/d and inhibitory constant (Ki) of 480.97 mg/L.

Applying the Nernst Equation to Control ORP in Denitrification Process for Uranium-Containing Nuclear Effluent with High Loads of Nitrogen and COD

Several reviews of denitrification have shown it to be an efficient process for treating high nitrate-loaded effluents from nuclear industries. However, stressful conditions adversely affect biological kinetic parameters and performance. Additionally, actual nuclear effluents contain multiple pollutants and radioactive emissions that could render implementation difficult. The objective of this study was to treat and recycle water from nuclear industries by using a mixture of blended real nuclear wastewater (BRNW). The process was carried out under physicochemical parameters control in a biological model to established a technical setup and to model the denitrification process in a real nuclear wastewater effluent. Denitrification processes were carried out in the wastewater sample under controlled ORP conditions by the Hill model to establish the kinetic model. The results show a complete elimination of nitrate by the bacteria. Indicators of biochemical reactions were used to obtain a model based on Monod and controlled ORP. The good fit of the proposed model was verified under empirical and simulated conditions. To establish optimal performance, it was necessary to add 3% v/v of methanol, as a carbon source, to remove the nitrate in BRNW. Isolation techniques confirmed that Pseudomonas spp. was the dominant bacteria. Gene expression demonstrated the lack of inhibition of the NosZ gene responsible for the reduction in nitric oxide, a “greenhouse gas”. Finally, COD and uranium were removed from the liquid by precipitation. At the end of the process, the treated effluent could potentially be reused in industrial processes, recycling most of the wastewater effluents.

Salinity-Linked Denitrification Potential in Endorheic Lake Bosten (China) and Its Sensitivity to Climate Change

Endorheic lakes in arid regions of Northwest China are generally vulnerable and sensitive to accelerated climate change and extensive human activities. Therefore, a better understanding of the self-purification capacity of ecosystems, such as denitrification, is necessary to effectively protect these water resources. In the present study, we measured unamended and amended denitrification rates of Lake Bosten by adding the ambient and extra nitrate isotopes in slurry incubations. Meanwhile, we investigated the abundances and community structure of nitrous oxide-reducing microorganisms using qPCR and high-throughput sequencing, respectively, in the surface sediments of Lake Bosten to study denitrification potential in endorheic lakes of arid regions as well as the response of those denitrifiers to climatically induced changes in lake environments. Amended denitrification rates increased by one order of magnitude compared to unamended rates in Lake Bosten. The great discrepancy between unamended and amended rates was attributed to low nitrate availability, indicating that Lake Bosten is not operating at maximum capacity of denitrification. Salinity shaped the spatial heterogeneity of denitrification potential through changes in the abundances and species diversity of denitrifiers. Climate change had a positive effect on the water quality of Lake Bosten so far, through increased runoff, decreased salinity, and enhanced denitrification. But the long-term trajectories of water quality are difficult to predict alongside future glacier shrinkage and decreased snow cover.

Insights into the microbial community of treated wastewater, its year-round variability and impact on the receiver, using cultivation, microscopy and amplicon-based methods

Apart from chemical constituents, wastewater treatment plant (WWTP) effluents also release microorganisms that can be important to the receiving water bodies either from a sanitary point of view, or taking to the account the biogeochemical potential of the recipients. However, little is known about the treated wastewater microbial community, its composition, seasonal changes, functions and fate in the waters of the receiver. Thus, this study presents a synergistic approach coupling new and traditional methods: analytical chemistry, classical microbiology (cultivation- and microscopy-based methods), as well as Next Generation Sequencing and a quantitative real-time polymerase chain reaction (qPCR). The results show that in terms of bacterial community composition, treated wastewater differed from the environmental samples, irrespectively if they were related or unrelated to the WWTP effluent discharge. The canonical correspondence analysis (CCA) taking into account chemical parameters and taxonomical biodiversity indirectly confirmed the seasonal deterioration of the treated wastewater quality as a result of temperature-driven change of activated sludge community structure and biomass washout (observed also by DAPI staining). Despite seasonal fluctuations of total suspended solids and inter-related parameters (such as COD, BOD, TN, TP), the treated wastewater quality remained within current discharge limits. It was due to treatment processes intensively adjusted by WWTP operators, particularly those necessary to maintain an appropriate rate of autotrophic processes of nitrification and to support biological phosphorus removal. This can explain the observed microbiome composition similarity among WWTP effluents at high taxonomic levels. Obtained data also suggest that besides wastewater treatment efficiency, WWTP effluents are still sources of both human-related microorganisms as well as bacteria equipped in genes involved in N-cycling. Their potential of participation in nutrients cycling in the receivers is widely unknown and require critical attention and better understanding.

Incomplete denitrification phenotypes in diverse Thermus species from diverse geothermal spring sediments and adjacent soils in southwest China

A few members of the bacterial genus Thermus have been shown to be incomplete denitrifiers, terminating with nitrite (NO₂⁻) or nitrous oxide (N₂O). However, the denitrification abilities of the genus as a whole remain poorly characterized. Here, we describe diverse denitrification phenotypes and genotypes of a collection of 24 strains representing ten species, all isolated from a variety of geothermal systems in China. Confirmed terminal products of nitrate reduction were nitrite or N₂O, while nitric oxide (NO) was inferred as the terminal product in some strains. Most strains produced N₂O; complete denitrification was not observed. Denitrification phenotypes were largely consistent with the presence of denitrification genes, and strains of the same species often had the same denitrification phenotypes and largely syntenous denitrification gene clusters. Genes for nirS and nirK coexisted in three Thermus brockianus and three Thermus oshimai genomes, which is a unique hallmark of some denitrifying Thermus strains and may be ecologically important. These results show that incomplete denitrification phenotypes are prominent, but variable, within and between Thermus species. The incomplete denitrification phenotypes described here suggest Thermus species may play important roles in consortial denitrification in high-temperature terrestrial biotopes where sufficient supply of oxidized inorganic nitrogen exists.

Rhizosphere and Straw Return Interactively Shape Rhizosphere Bacterial Community Composition and Nitrogen Cycling in Paddy Soil

Currently, how rice roots interact with straw return in structuring rhizosphere communities and nitrogen (N) cycling functions is relatively unexplored. In this study, paddy soil was amended with wheat straw at 1 and 2% w/w and used for rice growth. The effects of the rhizosphere, straw, and their interaction on soil bacterial community composition and N-cycling gene abundances were assessed at the rice maturity stage. For the soil without straw addition, rice growth, i.e., the rhizosphere effect, significantly altered the bacterial community composition and abundances of N-cycling genes, such as archaeal and bacterial amoA (AOA and AOB), nirK, and nosZ. The comparison of bulk soils between control and straw treatments showed a shift in bacterial community composition and decreased abundance of AOA, AOB, nirS, and nosZ, which were attributed to sole straw effects. The comparison of rhizosphere soils between control and straw treatments showed an increase in the nifH gene and a decrease in the nirK gene, which were attributed to the interaction of straw and the rhizosphere. The number of differentially abundant genera in bulk soils between control and straw treatments was 13-23, similar to the number of 16-22 genera in rhizosphere soil between control and straw treatment. However, the number of genera affected by the rhizosphere effect was much lower in soil amended with straw (3-4) than in soil without straw addition (9). Results suggest possibly more pronounced impacts of straw amendments in shaping soil bacterial community composition.

Impact of influent strengths on nitrous oxide emission and its molecular mechanism in constructed wetlands treating swine wastewater

Constructed wetlands (CWs) can remove nitrogen (N) through plant assimilation and microbial nitrification and denitrification, while it also releases large greenhouse gas nitrous oxide (N₂O) into the atmosphere. However, N₂O emissions and the underlying microbial mechanisms of CWs when treating high-strength wastewater have not been systematically surveyed. Here, the effect of three influent strengths on N₂O emissions in a pilot-scale CW treatment of swine wastewater was determined and the underlying microbial mechanisms were explored. The results showed that the removal rates of ammonium (NH₄⁺) and total nitrogen (TN) increased significantly with the increasing influent strengths, however, the ratio of N₂O emission/TN removal rose by 1.5 times at the same time. Quantitation of microorganisms responsible for N-cycle in the sediment indicated that the abundance of ammonia-oxidizing bacteria (AOB) in high influent strengths (COD, 962.38 ± 3.05 mg/L; NH₄⁺, 317.89 ± 4.24 mg/L) was 51.6-fold compared with that in low influent strengths (COD, 516.94 ± 4.18 mg/L; NH₄⁺, 100.65 ± 2.65), and AOB gradually replaced ammonia-oxidizing archaea (AOA) to dominate ammonia oxidizers. Structural equation models demonstrated that NO₂^- accumulations promoted the ratio of AOB/AOA, which further led to an increase in the ratio of N₂O emission/TN removal. It is worth noting both the N removal rates and N₂O emissions increased with the increasing influent strength. To obtain reduced N₂O emissions, pretreatment technology for strength reduction should be supplemented before high-strength wastewater enters the CWs. This study may shed new light on the sustainable operation and application of CWs.

Beyond an Applicable Rate in Low-Strength Wastewater Treatment by Anammox: Motivated Labor at an Extremely Short Hydraulic Retention Time

The application of anammox technology in low-strength wastewater treatment is still challenging due to unstable nitrite (NO₂^--N) generation. Partial denitrification (PD) of nitrate (NO₃^--N) reduction ending with NO₂^--N provides a promising solution. However, little is known about the feasibility of accelerating nitrogen removal toward the practical application of anammox combined with heterotrophic denitrification. In this work, an ultrafast, highly stable, and impressive nitrogen removal performance was demonstrated in the PD coupling with an anammox (PD/A) system. With a low-strength influent [50 mg/L each of ammonia (NH₄⁺-N) and NO₃^--N] at a low chemical oxygen demand/NO₃^--N ratio of 2.2, the hydraulic retention time could be shortened from 16.0 to 1.0 h. Remarkable nitrogen removal rates of 1.28 kg N/(m³ d) and excellent total nitrogen removal efficiency of 94.1% were achieved, far exceeding the applicable capacity for mainstream treatment. Stimulated enzymatic reaction activity of anammox was obtained due to the fast NO₂^--N jump followed by a famine condition with limited organic carbon utilization. This high-rate PD/A system exhibited efficient renewal of bacteria with a short sludge retention time. The 16S rRNA sequencing unraveled the rapid growth of the genus Thauera, possibly responsible for the incomplete reduction of NO₃^--N to NO₂^--N and a decreasing abundance of anammox bacteria. This provides new insights into the practical application of the PD/A process in the energy-efficient treatment of low-strength wastewater with less land occupancy and desirable effluent quality.

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.

Nitrite removal by Acinetobacter sp.TX: a candidate of curbing N2O emission

The nitrite removal pathway in Acinetobacter sp. TX5 was explored through the key gene identification and the corresponding enzyme purification, after which the capability to reduce nitrite by immobilized beads was investigated in a fixed-bed reactor. Results revealed that a nosZ gene encoding nitrous oxide reductase (N₂OR) exists in TX5 cells, and a N₂OR responsible for the reduction of N₂O to N₂ was purified successfully with a molecular weight of 70.05 kDa, a purification fold of 16.30 and a recovery rate of 5.17%. For TX5 immobilization, the optimal values of polyvinyl alcohol (PVA), spent mushroom substrate (SMS) and Aci (TX5) obtained by response surface methodology (RSM) were 6.32%, 2.92% and 4.57%, respectively. In a fixed-bed reactor packed with immobilized TX5, the removal efficiency (RE) achieved 90% (at 50 h) for NO2--N and 85% (at 96 h) for total nitrogen (TN). On the basis of these results, a nitrite removal pathway in TX5 was proposed. Overall, Acinetobacter sp. TX5 might be a promising candidate for nitrite removal with an ability to suppress N₂O accumulation.

Sediment Nitrate Dissimilatory Reduction Processes along a Salinity Gradient in an Estuarine and Coastal Wetland, China

Nitrate (NO3−) dissimilatory reduction processes (denitrification, anammox and dissimilatory NO3− reduction to ammonium (DNRA)) in estuarine and coastal ecosystems play a crucial role in regulating reactive nitrogen loadings. However, nitrate reduction process rates and relative proportions along the estuarine salinity gradient remain poorly understood. Here, denitrification, anammox and DNRA were explored simultaneously along a salinity gradient in Yangtze Estuary based on nitrogen isotope-tracing experiments. Measured denitrification, anammox and DNRA process rates were in the range of 2.33–28.21 nmol g−1 h−1, 0.43–1.87 nmol g−1 h−1 and 0.28–0.74 nmol g−1 h−1, respectively, with a large spatio-temporal variation. The changes in these nitrate reduction process rates were mainly affected by the TOC, TN, NH4+ and NOx− concentrations, rather than salinity and related functional gene abundance. Denitrification dominated the total NO3− reduction process (67.52 to 93.85%), while anammox (3.67 to 25.01%) and DNRA (2.48 to 11.21%) also played a substantially important role in nitrate reduction. The proportions of denitrification to gross nitrate reduction in high-salinity areas were generally lower than those in freshwater, but the opposite was true for DNRA. Overall, our study reported the simultaneous observation of nitrate dissimilatory reduction processes along the salinity gradient of the estuary and highlighted that changes in sediment environmental variables affected by human activities can alter the distribution patterns of NO3− reduction processes.

Nitrogen Removal Capacity of Microbial Communities Developing in Compost- and Woodchip-Based Multipurpose Reactive Barriers for Aquifer Recharge With Wastewater

Global water supplies are threatened by climate changes and the expansion of urban areas, which have led to an increasing interest in nature-based solutions for water reuse and reclamation. Reclaimed water is a possible resource for recharging aquifers, and the addition of an organic reactive barrier has been proposed to improve the removal of pollutants. There has been a large focus on organic pollutants, but less is known about multifunctional barriers, that is, how barriers also remove nutrients that threaten groundwater ecosystems. Herein, we investigated how compost- and woodchip-based barriers affect nitrogen (N) removal in a pilot soil aquifer treatment facility designed for removing nutrients and recalcitrant compounds by investigating the composition of microbial communities and their capacity for N transformations. Secondary-treated, ammonium-rich wastewater was infiltrated through the barriers, and the changes in the concentration of ammonium, nitrate, and dissolved organic carbon (DOC) were measured after passage through the barrier during 1 year of operation. The development and composition of the microbial community in the barriers were examined, and potential N-transforming processes in the barriers were quantified by determining the abundance of key functional genes using quantitative PCR. Only one barrier, based on compost, significantly decreased the ammonium concentration in the infiltrated water. However, the reduction of reactive N in the barriers was moderate (between 21 and 37%), and there were no differences between the barrier types. All the barriers were after 1 year dominated by members of Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria, although the community composition differed between the barriers. Bacterial classes belonging to the phylum Chloroflexi showed an increased relative abundance in the compost-based barriers. In contrast to the increased genetic potential for nitrification in the compost-based barriers, the woodchip-based barrier demonstrated higher genetic potentials for denitrification, nitrous oxide reduction, and dissimilatory reduction of nitrate to ammonium. The barriers have previously been shown to display a high capacity to degrade recalcitrant pollutants, but in this study, we show that most barriers performed poorly in terms of N removal and those based on compost also leaked DOC, highlighting the difficulties in designing barriers that satisfactorily meet several purposes.

Synergistic Inorganic Carbon and Denitrification Genes Contributed to Nitrite Accumulation in a Hydrogen-Based Membrane Biofilm Reactor

Partial denitrification, the termination of NO3−-N reduction at nitrite (NO2−-N), has received growing interest for treating wastewaters with high ammonium concentrations, because it can be coupled to anammox for total-nitrogen removal. NO2− accumulation in the hydrogen (H2)-based membrane biofilm reactor (MBfR) has rarely been studied, and the mechanisms behind its accumulation have not been defined. This study aimed at achieving the partial denitrification with H2-based autotrophic reducing bacteria in a MBfR. Results showed that by increasing the NO3− loading, increasing the pH, and decreasing the inorganic-carbon concentration, a nitrite transformation rate higher than 68% was achieved. Community analysis indicated that Thauera and Azoarcus became the dominant genera when partial denitrification was occurring. Functional genes abundances proved that partial denitrification to accumulate NO2− was correlated to increases of gene for the form I RuBisCo enzyme (cbbL). This study confirmed the feasibility of autotrophic partial denitrification formed in the MBfR, and revealed the inorganic carbon mechanism in MBfR denitrification.

Plant growth-promoting rhizobacteria Burkholderia vietnamiensis B418 inhibits root-knot nematode on watermelon by modifying the rhizosphere microbial community

Burkholderia vietnamiensis B418 is a multifunctional plant growth-promoting rhizobacteria (PGPR) strain with nitrogen-fixing and phosphate-solubilizing capability which can be employed for root-knot nematode (RKN) management on various crops and vegetables. Here we investigated the control efficacy of B. vietnamiensis B418 inoculation against RKN on watermelon, applied either alone or combined with nematicides fosthiazate or avermectin, and their effects on bacterial and fungal microbiomes in rhizosphere soil. The results of field experiments showed individual application of B418 displayed the highest control efficacy against RKN by 71.15%. The combinations with fosthiazate and avermectin exhibited slight incompatibility with lower inhibitory effects of 62.71% and 67.87%, respectively, which were still notably higher than these nematicides applied separately. Analysis of microbiome assemblages revealed B418 inoculation resulted in a slight reduction for bacterial community and a significant increment for fungal community, suggesting that B418 could compete with other bacteria and stimulate fungal diversity in rhizosphere. The relative abundance of Xanthomonadales, Gemmatimonadales and Sphingomonadales increased while that of Actinomycetales reduced with B418 inoculation. The predominate Sordariomycetes of fungal community decreased dramatically in control treatment with B418 inoculation whereas there were increments in fosthiazate and avermectin treatments. Additionally, nitrogen (N) cycling by soil microbes was estimated by quantifying the abundance of microbial functional genes involved in N-transformation processes as B418 has the capability of N-fixation. The copy number of N-fixing gene nifH increased with B418 inoculation, and the highest increment reached 35.66% in control treatment. Our results demonstrate that B. vietnamiensis B418 is an effective biological nematicide for nematode management, which acts through the modulation of rhizosphere microbial community.

A hydroponic plants and biofilm combined treatment system efficiently purified wastewater from cold flowing water aquaculture

Recently, more and more cold flowing water aquaculture has been adopted, but its wastewater treatment is always ignored, which causes great pressure on the environment. In this study, a compound in-situ treatment system that applied hydroponic plants and biofilm was constructed to treat the wastewater produced by cold flowing water culture of sturgeon. The removal efficiency of the nutrients from culture and the microbial composition in water and biofilm were tested, the correlation between the water quality indexes and bacterium was analyzed, and the abundance of nitrogen and phosphorus cycling genes was quantified. The results show that the system respectively achieved 90%, 100%, 100%, 100% and 48% removal efficiency of NH₄⁺-N, NO₃^--N, TN, TP and COD which were produced by experimental sturgeon culture. Chinese cabbage (Brassica rapa var. chinensis) and water dropwort (Oenanthe javanica) showed obvious growth in the four plants, which contributed to the removal of nutrients from wastewater. Besides, in the biofilm, Proteobacteria, Bacteroidetes and Verrucomicrobia became the top three dominant flora at the phylum level, and Flavobacterium, Rhodoferax, Sphaerotilus and Chitinimonas became the top four dominant flora at the genus level, which promoted the removal of nitrogen in the wastewater. The FAPROTAX analysis result shows that the highest functions within the carbon and nitrogen metabolisms were significantly identified in the biofilm, such as chemoheterotrophy, aerobic chemoheterotrophy and nitrate reduction. Further, the abundance of denitrifying genes (narG and napA) was higher than the nitrifying related genes (nxrB and amoA), indicating the more active denitrifying process. In summary, the compound in-situ treatment system efficiently removed nutrients from cold flowing water aquaculture. And the combined purification of hydroponic plants and biofilm which is rich in denitrifying bacterium plays an essential role in this process.

Effect of remediation reagents on bacterial composition and ecological function in black-odorous water sediments

Black-odorous urban water bodies and sediments pose a serious environmental problem. In this study, we conducted microcosm batch experiments to investigate the effect of remediation reagents (magnesium hydroxide and calcium nitrate) on native bacterial communities and their ecological functions in the black-odorous sediment of urban water. The dominant phyla (Proteobacteria, Actinobacteria, Chloroflexi, and Planctomycetes) and classes (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, Actinobacteria, Anaerolineae, and Planctomycetia) were determined under calcium nitrate and magnesium hydroxide treatments. Functional groups related to aerobic metabolism, including aerobic chemoheterotrophy, dark sulfide oxidation, and correlated dominant genera (Thiobacillus, Lysobacter, Gp16, and Gaiella) became more abundant under calcium nitrate treatment, whereas functional genes potentially involved in dissimilatory sulfate reduction became less abundant. The relative abundance of chloroplasts, fermentation, and correlated genera (Desulfomonile and unclassified Cyanobacteria) decreased under magnesium hydroxide treatment. Overall, these results indicated that calcium nitrate addition improved hypoxia-related reducing conditions in the sediment and promoted aerobic chemoheterotrophy.

Selective pressure on microbial communities in a drinking water aquifer - Geochemical parameters vs. micropollutants

Groundwater quality is crucial for drinking water production, but groundwater resources are increasingly threatened by contamination with pesticides. As pesticides often occur at micropollutant concentrations, they are unattractive carbon sources for microorganisms and typically remain recalcitrant. Exploring microbial communities in aquifers used for drinking water production is an essential first step towards understanding the fate of micropollutants in groundwater. In this study, we investigated the interaction between groundwater geochemistry, pesticide presence, and microbial communities in an aquifer used for drinking water production. Two groundwater monitoring wells in The Netherlands were sampled in 2014, 2015, and 2016. In both wells, water was sampled from five discrete depths ranging from 13 to 54 m and was analyzed for geochemical parameters, pesticide concentrations and microbial community composition using 16S rRNA gene sequencing and qPCR. Groundwater geochemistry was stable throughout the study period and pesticides were heterogeneously distributed at low concentrations (μg L^-1 range). Microbial community composition was also stable throughout the sampling period. Integration of a unique dataset of chemical and microbial data showed that geochemical parameters and to a lesser extent pesticides exerted selective pressure on microbial communities. Microbial communities in both wells showed similar composition in the deeper aquifer, where pumping results in horizontal flow. This study provides insight into groundwater parameters that shape microbial community composition. This information can contribute to the future implementation of remediation technologies to guarantee safe drinking water production.

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.

Thiocyanate increases the nitrous oxide formation process through modifying the soil bacterial community

BACKGROUND

Nitrous oxide (N₂ O) is a potent greenhouse gas depleting the stratospheric ozone. Previous studies reported that the thiocyanate (TC) excretion in the urine of cattle fed rapeseed meals containing glucosinolates was positively correlated with the N₂ O-nitrogen (N) emissions. The objectives of the experiment were to verify the effects and the mechanism of TC on the N₂ O-N emissions from the soil applied with artificial urine using static incubation technique. Four levels of TC, that is 0.00, 0.26, 0.78 and 2.33 mmol L^-1 were composited in artificial urine as experimental treatments. Soil inorganic N and bacterial community were analyzed to elucidate the effects of TC on the N₂ O-N emissions of artificial urine.

RESULTS

Adding TC increased the N₂ O-N fluxes, the N₂ O-N to N application ratio, and the estimated N₂ O-N emissions from the soil applied with artificial urine both linearly and quadratically. The estimated N₂ O-N emission (Y, in μmol) was increased with the TC adding level (X, in μmol) in a quadratic manner: Y = 52.57 + 4.47 X - 0.123 X 2 (R ²  = 0.70). Adding TC did not affect the soil bacterial diversity and richness, but increased the relative abundances of Nitrosomonas (both for nitrification and denitrification) and Hyphomicrobium, Lysobacter and Terrimonas (for denitrification), and tended to increase the relative abundances of denitrification and dissimilatory nitrate reduction to ammonium.

CONCLUSION

TC increased the N₂ O-N emissions of the soil applied with artificial urine possibly through enhancing the denitrification of nitrifiers in the soil. Field experiments are necessary to verify the laboratory results. © 2021 Society of Chemical Industry.

Partition of Anammox and Nitrifiers Through Bio-Carriers for Full-Scale Sidestream Partial Nitrification–Anammox Plant

This study assessed the activity and community structure in different types of sludge to reveal the partition mechanism of anammox and nitrifiers in a full-scale partial nitrification–anammox plant. Batch experiments confirmed that suspended sludge had higher partial nitrification capacity, and biofilm sludge had higher anammox activity, 16.9 times higher than suspended sludge. qPCR analysis confirmed that the amoA gene was mainly present in suspended sludge, and the highest abundance of the Amx gene was observed in biofilm sludge, reaching 1.01 × 107 copies/ng DNA. High-throughput results revealed that Nitrosomonas was the main ammonia-oxidizing bacteria with high activity in suspended sludge, and Candidatus Brocadia had the highest abundance of 13.4% in biofilm sludge. This is the exploration of the microbial community of three different sludge types in the full-scale sidestream PN/A system for the first time, which can guide the construction and replication of full-scale PN/A plants.

Effects of marine produced organic matter on the potential estuarine capacity of NOx- removal

Dissolved inorganic nitrogen (DIN) is very high in the Pearl River Estuary (PRE) and nitrate (NO_x^-) removal processes such as denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) are important for determining export of DIN to coastal waters. However, fluxes of NO_x^- removal and influencing factors in the PRE are still unclear. We conducted 4 cruises at 11 sites in the PRE to investigate potential NO_x^- removal rates, their contributions, and corresponding gene abundances, and controlling factors in surface sediments (0-5 cm). The results showed that the potential rates of denitrification, anammox, and DNRA as well as their contributions varied spatially and seasonally. Denitrification (1.98 ± 1.7 μg N g^-1 d^-1) was the major NO_x^- removal processes (68.43 ± 14.61%) while DNRA (0.45 ± 0.28 μg N g^-1 d^-1) contributed 22.61 ± 14.89% in NO_x^- removal. The NO_x^- removal processes and corresponding gene abundances were correlated with the chlorophyll concentrations in both overlying water and sediment, indicating that marine-produced organic matter was the major driver for benthic NO_x^- removal processes. In addition, water column turbidity had important effects on primary production, which affects benthic N processes. Our study provides evidences for that the turbidity-regulated primary production in overlying water is the primary driver for benthic NO_x^- removal processes. The contribution of sediment NO_x^- removal fluxes to water column NO_x^- concentration was low in the upper estuary and increased in the lower estuary where marine produced chlorophyll a was higher. However, daily fluxes of NO_x^- removal were estimated to account for only 0.18-7.22% (mean 1.85 ± 1.62%) of NO_x^- in the whole overlying water column. This suggests that most riverine NO_x^- was exported out into the adjacent coastal waters.

Effects of water level on nitrous oxide emissions from vegetated ditches

Nitrous oxide (N₂O) is considered a powerful greenhouse gas. Vegetated ditches are an important source of N₂O emissions in the agricultural systems. However, few studies have examined on the relationship between N₂O emissions and the water level in vegetated ditches. To investigate the effect of water level on the N₂O emissions, three pilot-scale ditches vegetated with Myriophyllum aquaticum were constructed with low (LW), medium (MW), and high (HW) water levels. The examined results indicated that the M. aquaticum ditches decreased N₂O emissions by 38.4% and 67.9% in MW and HW, respectively, as compared to the LW ditch. In addition, the N₂O emission factor decreased with increasing water level in the order of: LW (0.18%) > MW (0.11%) > HW (0.06%). The MW and HW ditches reduced the N₂O emissions by controlling the sediment nitrogen contents, in which the ammonia nitrogen increased with increasing the level of water, while nitrate nitrogen decreased with increasing the level of water. The increase in the level of water significantly reduced the gene abundance of ammonia-oxidizing archaea (AOA) (p < 0.05), thereby reducing the N₂O emissions in the MW and HW conditions due to the positive correlation between N₂O emissions and AOA gene abundances. The unclassified_k_norank_d_Bacteria was the dominant denitrifying bacterial genus observed in the M. aquaticum ditches, and its highly relative abundance yielded low N₂O emissions in the HW ditch. These findings indicate that reducing N₂O emissions may be achieved by controlling the water level in vegetated ditches.

Mixed Effects of Soil Compaction on the Nitrogen Cycle Under Pea and Wheat

Soil compaction caused by highly mechanized agriculture can constrain soil microbial diversity and functioning. Physical pressure on the soil decreases macropores and thereby limits oxygen diffusion. The associated shift from aerobic to anaerobic conditions can reduce nitrification and promote denitrification processes, leading to nitrogen (N) losses and N depletion that affect plant productivity. High soil moisture content during trafficking can exacerbate the negative effects of soil compaction. However, the extent to which soil moisture amplifies the effects of compaction on the soil microbiome and its control over N cycling is not well understood. Using a controlled greenhouse experiment with two different crops (pea and wheat), we compared the effects of compaction at three different soil moisture levels on soil physicochemical properties, microbial diversity, and the abundance of specific N species and quantification of associated microbial functional groups in the N cycle. Soil compaction increased bulk density from 15% (light compaction) to 25% (severe compaction). Compaction delayed germination in both crops and reduced yield by up to 60% for pea and 40% for wheat. Compaction further induced crop-specific shifts in microbial community structures. After compaction, the relative abundance of denitrifiers increased along with increased nitrate (NO3–) consumption and elevated nitrous oxide (N2O) concentrations in the soil pores. Conversely, the relative abundance of nitrifiers remained stable under compaction, but potentially decelerated nitrification rates, resulting in ammonium (NH4+) accumulation in the soil. This study showed that soil compaction effects are proportional to the initial soil moisture content, which could serve as a good indicator of compaction severity on agricultural fields. However, the impact of soil compaction on crop performance and on microbial communities and functions associated with the N cycle were not necessarily aligned. These findings demonstrate that not only the soil physical properties but also various biological indicators need to be considered in order to provide more precise recommendations for developing sustainable farming systems.

Synergistic Effects of Aquatic Plants and Cyanobacterial Blooms on the Nitrous Oxide Emission from Wetlands

Wetlands provide a habitat for the symbiosis of multiple plants and play a significant role in global N₂O emissions. The metabolic traits and effects on microorganisms, which regulate the conversion of nitrogen to N₂O, varies with plant species. The frequent occurrences of cyanobacterial blooms in wetlands can also have a positive or negative effect on denitrification, entangling N₂O emissions. In situ observations of the Dongting Lake reveal that the fluxes in N₂O emissions vary with the vegetation. Maximum emissions occurred in the mud flat, while the zone with the minimum emissions was populated with carex. In 210-day batch cultures, the addition of cyanobacteria synergistically enhanced N₂O production during the degredation of phalaris and reed. The abundance of the nirS and nirK genes decreased over time except in the phalaris-algae group. To mitigate the N₂O emissions from wetlands, the macrophyte communities need to be protected, and the cyanobacterial blooms need to be avoided by reducing the nitrogen pollution.

Efficacies of Nitrogen Removal and Comparisons of Microbial Communities in Full-Scale (Pre-Anoxic Systems) Municipal Water Resource Recovery Facilities at Low and High COD:TN Ratios

At a low COD:TN ratio (≤5) in influent, maintaining a longer HRT (≥9 h) and longer SRT (≥30 d) are suggested to improve higher N removal efficiency in case of operation at low DO (Dissolved oxygen) level (0.9 ± 0.2 mg-O2/L). However, in case of operation at high DO level (4.0 ± 0.5 mg-O2/L), short HRT (1 h) and typical SRT (17 d) make it possible to achieve nitrogen removal. On the other hand, at a high COD:TN ratio (≥8.4), a typical HRT (9–15 h), SRT (12–19 d), and DO level (1.3–2.6 mg-O2/L) would be applied. Microbial distribution analysis showed an abundance of AOA (Ammonia-oxidizing archaea) under conditions of low DO (≤0.9 mg-O2/L). Nitrosomonas sp. are mostly found in the all investigated water resource recovery facilities (WRRFs). Nitrosospira sp. are only found under operating conditions of longer SRT for WRRFs with a low COD:TN ratio. In comparison between abundances of Nitrobacter sp. and Nitrospira sp., abundances of Nitrobacter sp. are proportional to low DO concentration rather than abundance of Nitrospira sp. A predominance of nosZ-type denitrifiers were found at low DO level. Abundance of denitrifiers by using nirS genes showed an over-abundance of denitrifiers by using nirK genes at low and high COD:TN ratios.

Effects of Plastic versus Straw Mulching Systems on Soil Microbial Community Structure and Enzymes in Strawberry Cultivation

This study aimed to evaluate changes in abundance, structure, and enzyme activity of the soil microbiome in response to 4 years of mulching using either black polyethylene plastic film (PM) or wheat straw (SM). Soil samples (depth 0–5 and 5–10 cm) were collected from conventional strawberry plots, in two samplings: 1 week prior (S1) and 7 weeks after straw application (S2). Selected soil properties were monitored in each system and the abundance and structure of microbial communities were characterized via phospholipid fatty acid (PLFA) analysis. The investigation of soil microbial functions included activities of the enzymes chitinase, leucine aminopeptidase, and acid phosphatase, as well as function genes involved in nitrogen transformation. Each mulch system resulted in distinct physicochemical properties. In particular, a pH value higher by one-unit under PM (7.6 ± 0.3) compared to SM (6.5 ± 0.3) was observed. Values for SOC, DOC, and total-N were 15%, 22%, and 16% higher in PM than in SM. The microbial biomass (total PLFAs) was 1.5-fold higher in SM compared to PM. The abundance of soil fungi (F) and bacteria (B) increased by 37% and 44% after straw incorporation compared to PM (S2). In particular, Gram-negative bacteria (gr–) increased by twofold in SM. Consequently, wider F:B and gr+:gr– ratios were observed in PM. According to the shifts in microbial abundance, the activity of the enzyme chitinase was lower by 27% in PM, while the activity of the acid phosphatase increased by 32%. Denitrification genes were not affected by the mulching systems. In conclusion, the abundance and structure of the investigated microbial groups and the enzyme activities were strongly influenced by the mulching system. In detail, effects on microbiota were primarily attributed to the altered soil pH and probably the input of degradable organic matter with straw mulching in SM. This resulted in higher abundance of soil microorganisms in SM, although measures within this cultivation system such as fungicide application may have exerted adverse effects on the microbiota.

Intermittent aeration reducing N2O emissions from bioreactor landfills with gas-water joint regulation

Landfills are important emission sources of atmospheric N₂O, especially bioreactor landfills with leachate recirculation. In this study, N₂O emissions were characterized in four bioreactor landfills with different ventilation methods, including intermittent (2-h aeration per 12 h or 4 h/d in continuous) and continuous aeration (20 h/d), in comparison to a traditional landfill without aeration. During the experiment, the N₂O emissions from the landfill reactors with intermittent aeration were 7.48 and 7.15 mg, accounting for only 20.8% and 19.9% of those with continuous aeration, respectively. Continuous aeration was more favorable for the biodegradation of organic matter than intermittent aeration in the landfilled waste and leachate. Intermittent and continuous aeration could both effectively remove total nitrogen (TN) and NH₄⁺-N with removal efficiencies above 64% in the leachate. In the experimental landfill reactors with gas-water joint regulation, the proportion of N₂O-N to TN loss ranged from 0.02% to 0.75%. Luteimonas, Pseudomonas, Thauera, Pusillimonas and Comamonas were the dominant denitrifying bacteria in the landfill reactors. The denitrifying bacterial community in the landfilled waste was closely related to its degree of stabilization and nitrogenous compound concentrations in the landfilled waste and leachate. The NO₃^--N and NO₂^--N concentrations of leachate were the most important environmental factors affecting the succession of nirS-type and nirK-type denitrifying microbial communities in the landfilled waste. These findings indicated that intermittent aeration was an economical and effective way to accelerate the stabilization of landfilled waste and reduce the pollutants in leachate and N₂O emissions during landfill mining and reclamation.

Changes in Wastewater Treatment Performance and the Microbial Community during the Bioaugmentation of a Denitrifying Pseudomonas Strain in the Low Carbon–Nitrogen Ratio Sequencing Batch Reactor

The low carbon–nitrogen ratio (C/N) of influent wastewater results in the insufficient carbon source for the process of denitrification in urban wastewater treatment plants (WWTPs). A denitrifying bacterial strain, Pseudomonas sp. JMSTP, was isolated and demonstrated effective denitrification ability under a low C/N ratio of 1.5–4 (w/w) in anoxic conditions. Sequencing batch reactor (SBR) studies were conducted to test the bioaugmentation of JMSTP on total nitrogen (TN) removal under the influent COD/N ratio of 3/1. After the second bioaugmentation, the TN of effluent in the bioaugmented SBR was significantly lower than that in the control SBR. Redundancy analysis results showed that there was a positive correlation between Pseudomonas sp. abundance and TN removal in the bioaugmented SBR. Microbial community analysis showed that, especially after the second bioaugmentation, the abundance of Pseudomonas sp. decreased rapidly, but it was still much higher than that in the control SBR. Correlation network analysis showed that after the addition, Pseudomonas sp. had no significant co-occurrence relationship with other native bacteria, owing to the quick increase and decrease. Our results suggest that JMSTP shows the potential to enhance TN removal through bioaugmentation. Since the effect of bioaugmentation gradually diminishes, further research is still needed to investigate its long-lasting applications.

Microbial selenate detoxification linked to elemental sulfur oxidation: Independent and synergic pathways

Elevated selenium levels in the environment, with soluble selenate [Se(VI)] as the common chemical species, pose a severe threat to human health. Anaerobic Se(VI) bioreduction is a promising approach for selenium detoxification, and various organic/inorganic electron donors have proved effective in supporting this bioprocess. Nevertheless, autotrophic Se(VI) bioreduction driven by solid inorganic electron donors is still not fully understood. This work is the first to employ elemental sulfur [S(0)] as electron donor to support Se(VI) bioreduction. A batch trial with mixed culture demonstrated the feasibility of this bioprocess, with Se(VI) removal efficiency of 92.4 ± 0.7% at an initial Se(VI) concentration of 10 mg/L within 36 h. Continuous column tests showed that increased initial concentration, flow rate, and introduction of NO₃^--N depressed Se(VI) removal. Se(VI) was mainly bioreduced to solid elemental Se with trace selenite in the effluent, while S(0) was oxidized to SO₄^2-. Enrichment of Thiobacillus, Desulfurivibrio, and Sulfuricurvum combined with upregulation of genes serA, tatC, and soxB indicated Se(VI) bioreduction was coupled to S(0) oxidation. Thiobacillus performed S(0) oxidation and Se(VI) reduction independently. Intermediate metabolites as volatile fatty acids, hydrogen and methane from S(0) oxidation were utilized by heterotrophic Se(VI) reducers for Se(VI) detoxification, indicative of microbial synergy.

Adaptability of enhanced bioretention cell for nitrogen and phosphorus removal under two antibiotics stress

The overuse of antibiotics in the medical and aquaculture industries has led to the frequent detection of antibiotics in wastewater. Considering antibiotics would have an unknown impact on wastewater treatment in the future, the long-term effects of sulfamethoxazole (SMX) and tetracycline (TC) stress on the performance, functional genes and microbial community in three bioretention cells were investigated. The results showed that during the experiment, 0.8-1.2 mg/L of SMX would not destroy the water treatment capacity of the bioretention cells, and had a promoting effect on total nitrogen and ammonia nitrogen. 1.6 mg/L of SMX would cause the reduction of nitrogen removal efficiency and the phenomenon of phosphorus release, but it could be restored after a period of operation. TC of 0.8-1.2 mg/L did not have a significant impact on the removal of nutrients in AC-BRC (activated carbon-bioretention cell) and ACI-BRC (activated carbon and iron-bioretention cell), but TC of 1.2 mg/L caused the phenomenon of phosphorus release in BRC and the decrease of total nitrogen removal rate, 1.6 mg/L TC could make the bioretention cell lose its water treatment capacity. qPCR analysis of denitrification genes showed that the abundance of nirS, nirK, nosZ, and hzo had varying degrees of decrease before and after antibiotic stress, which meant the two antibiotics significantly inhibited the reduction of nitrite and nitrous oxide. But for the total number of bacteria, the relative abundance of the four genes has increased. The results of microbial community analysis also found that Proteobacteria, Bacteroidetes, Chloroflexi, and BIrii41, Denitratisoma, Ferritrophicum, Thiobacillus occupied the dominant species at the phylum level and the genus level respectively, which included most of the denitrifying bacteria. During the experiment, the nitrogen and phosphorus removal efficiency of AC-BRC and ACI-BRC were enhanced obviously, but ammonia nitrogen accumulated in ACI-BRC in the early stage of the reaction.