Denitrification

Orbital-scale denitrification changes in the Eastern Arabian Sea during the last 800 kyrs

Denitrification in the Arabian Sea is closely related to the monsoon-induced upwelling and subsequent phytoplankton production in the surface water. The δ¹⁵N values of bulk sediments collected at Site U1456 of the International Ocean Discovery Program (IODP) Expedition 355 reveal the orbital-scale denitrification history in response to the Indian Monsoon. Age reconstruction based on the correlation of planktonic foraminifera (Globigerinoides ruber) δ¹⁸O values with the LR04 stack together with the shipboard biostratigraphic and paleomagnetic data assigns the study interval to be 1.2 Ma. Comparison of δ¹⁵N values during the last 800 kyrs between Site U1456 (Eastern Arabian Sea) and Site 722B (Western Arabian Sea) showed that δ¹⁵N values were high during interglacial periods, indicating intensified denitrification, while the opposite was observed during glacial periods. Taking 6‰ as the empirical threshold of denitrification, the Eastern Arabian Sea has experienced a persistent oxygen minimum zone (OMZ) to maintain strong denitrification whereas the Western Arabian Sea has undergone OMZ breakdown during some glacial periods. The results of this study also suggests that five principal oceanographic conditions were changed in response to the Indian Monsoon following the interglacial and glacial cycles, which controls the degree of denitrification in the Arabian Sea.

Denitrification rates in estuarine sediments of Ashtamudi, Kerala, India

Estuarine sediments are important sites for denitrification, which is microbially mediated reduction of nitrate to dinitrogen that also influences global climate change by co-production of nitrous oxide, a potent greenhouse gas. Physicochemical properties and nutrients of sediment samples that influence denitrification rate were studied in Ashtamudi estuarine sediments. They were pH, electrical conductivity (EC), salinity, nitrate-nitrogen (NO₃^--N), exchangeable ammonia (NH₃^--N), total kjeldahl nitrogen (TKN) and organic carbon (Corg). Sediment samples were collected from six stations during summer, monsoon of 2013 and 13 stations from monsoon 2014 and summer 2015. The sedimentary denitrification potential ranged from 0.49 ± 0.05 to 4.85 ± 0.782 mmol N₂O m^-2 h^-1. Maximum denitrification was observed in S4, which is attributed to a local anthropogenic source coupled with intense rainfall episode preceding the sampling season of monsoon 2013. However, this trend was not repeated in the subsequent monsoon samples. This shows that in Ashtamudi, monsoonal effects do not influence sedimentary denitrification. Among the various environmental variables, NO₃^--N, Corg and NH₃-N were the key factors that influence denitrification in the Ashtamudi estuarine sediments. Among these key factors, NO₃^--N was the limiting factor for denitrification, and hence, it is of prime importance to understand the source of NO₃^--N that fuel denitrification in the sediments. In Ashtamudi, the concentration of NO₃^--N in overlying water was very less, which suggests reduced nitrogen yield in the estuary from the fluvial input of Kallada River and agricultural runoff. Sedimentary NO₃^--N correlated with denitrification which reveals that denitrification is coupled with nitrification in the sediments. This is further explained by the fact that NH₃-N positively correlated with denitrification. The anoxic sediments were the source of ammonia for nitrous oxide production by nitrogen mineralisation. Also, the Corg in sediment samples were sufficient to support denitrification and Corg was an important factor favouring but not limiting denitrification. The results of sediment denitrification in Ashtamudi can be a model for tropical estuaries experiencing unpredictable rainfall as well as high temperature than temperate systems.

Bioelectroremediation of perchlorate and nitrate contaminated water: A review

Fresh water is a fundamental source for humans, hence the recent shrinkage in freshwater and increase in water pollution are imperative problems that vigorously affect the people and the environment worldwide. The breakneck industrialization contributes to the procreation of substantial abundance of wastewater and its treatment becomes highly indispensable. Perchlorate and nitrate containing wastewaters poses a serious threat to human health and environment. Conventional biological treatment methods are expensive and also not effective for treating wastewater effectively and incapable of in situ bioremediation. Bioelectrochemical systems are emerging as a new technology platform for a sustainable removal of such contaminants from wastewater streams. This article reviews the state of art of bioelectroremediation of contaminated waters with perchlorate and nitrate. Different aspects of this technology such as configuration and design, mode of operation and type of substrate are considered in detail.

Potential of dissimilatory nitrate reduction pathways in polycyclic aromatic hydrocarbon degradation

This study investigates the potential of an indigenous estuarine microbial consortium to degrade two polycyclic aromatic hydrocarbons (PAHs), naphthalene and fluoranthene, under nitrate-reducing conditions. Two physicochemically diverse sediment samples from the Lima Estuary (Portugal) were spiked individually with 25 mg L^-1 of each PAH in laboratory designed microcosms. Sediments without PAHs and autoclaved sediments spiked with PAHs were run in parallel. Destructive sampling at the beginning and after 3, 6, 12, 30 and 63 weeks incubation was performed. Naphthalene and fluoranthene levels decreased over time with distinct degradation dynamics varying with sediment type. Next-generation sequencing (NGS) of 16 S rRNA gene amplicons revealed that the sediment type and incubation time were the main drivers influencing the microbial community structure rather than the impact of PAH amendments. Predicted microbial functional analyses revealed clear shifts and interrelationships between genes involved in anaerobic and aerobic degradation of PAHs and in the dissimilatory nitrate-reducing pathways (denitrification and dissimilatory nitrate reduction to ammonium - DNRA). These findings reinforced by clear biogeochemical denitrification signals (NO₃^- consumption, and NH₄⁺ increased during the incubation period), suggest that naphthalene and fluoranthene degradation may be coupled with denitrification and DNRA metabolism. The results of this study contribute to the understanding of the dissimilatory nitrate-reducing pathways and help uncover their involvement in degradation of PAHs, which will be crucial for directing remediation strategies of PAH-contaminated anoxic sediments.

The effect of bio-irrigation by the polychaete Lanice conchilega on active denitrifiers: Distribution, diversity and composition of nosZ gene

The presence of large densities of the piston-pumping polychaete Lanice conchilega can have important consequences for the functioning of marine sediments. It is considered both an allogenic and an autogenic ecosystem engineer, affecting spatial and temporal biogeochemical gradients (oxygen concentrations, oxygen penetration depth and nutrient concentrations) and physical properties (grain size) of marine sediments, which could affect functional properties of sediment-inhabiting microbial communities. Here we investigated whether density-dependent effects of L. conchilega affected horizontal (m-scale) and vertical (cm-scale) patterns in the distribution, diversity and composition of the typical nosZ gene in the active denitrifying organisms. This gene plays a major role in N2O reduction in coastal ecosystems as the last step completing the denitrification pathway. We showed that both vertical and horizontal composition and richness of nosZ gene were indeed significantly affected when large densities of the bio-irrigator were present. This could be directly related to allogenic ecosystem engineering effects on the environment, reflected in increased oxygen penetration depth and oxygen concentrations in the upper cm of the sediment in high densities of L. conchilega. A higher diversity (Shannon diversity and inverse Simpson) of nosZ observed in patches with high L. conchilega densities (3,185-3,440 ind. m-2) at deeper sediment layers could suggest a downward transport of NO3- to deeper layers resulting from bio-irrigation as well. Hence, our results show the effect of L. conchilega bio-irrigation activity on denitrifying organisms in L. conchilega reefs.

Application potential of aerobic denitrifiers coupled with a biostimulant for nitrogen removal from urban river sediment

Aerobic denitrifiers coupled with a denitrification agent were applied in the sediment of an urban river for the bioremediation of nitrogen pollution. The results revealed that 14.7% of the total nitrogen in the sediment was removed after 115 days of treatment and the nitrate nitrogen concentration removal rate was enhanced in the overlying water. Compared with the control, the total transferable nitrogen in the sediment increased from 0.097 to 0.166 mg/g, indicating that more nitrogen is likely to be involved in the biogeochemical cycling of nitrogen. Increased urease activity indicated the possible further potential of nitrogen biodegradation, while the decreased protease pointed to the low concentration of protein remaining in the sediment. Sequencing revealed that the bacterial community diversity in the sediment increased significantly after 43 days of treatment and that the effect persisted. Compared with other microcosms, the dominant phyla in the sediment after 43 days were Firmicutes, Elusimicrobia, Spirochaetae and Fibrobacteres; whereas, after 115 of treatment, the dominant bacteria were Nitrospirae, Deferribacteres and Chloroflexi. The dominant bacteria in the sediment are mainly associated with nitrogen cycling and thus contributed considerably to nitrogen removal in the sediment. Overall, the direction of species succession was similar to natural succession; namely, there were no undesirable ecological risks involved. This study highlights the possible benefits and feasibility of using bioaugmentation technology coupled with biostimulation to remediate nitrogen-polluted sediments.

Tracing the role of endogenous carbon in denitrification using wine industry by-product as an external electron donor: Coupling isotopic tools with mathematical modeling

Nitrate removal through enhanced biological denitrification (EBD), consisting of the inoculation of an external electron donor, is a feasible solution for the recovery of groundwater quality. In this context, liquid waste from wine industries (wine industry by-products, WIB) may be feasible for use as a reactant to enhance heterotrophic denitrification. To address the feasibility of WIB as electron donor to promote denitrification, as well as to evaluate the role of biomass as a secondary organic C source, a flow-through experiment was carried out. Chemical and isotopic characterization was performed and coupled with mathematical modeling. Complete nitrate attenuation with no nitrite accumulation was successfully achieved after 10 days. Four different C/N molar ratios (7.0, 2.0, 1.0 and 0) were tested. Progressive decrease of the C/N ratio reduced the remaining C in the outflow and favored biomass migration, producing significant changes in dispersivity in the reactor, which favored efficient nitrate degradation. The applied mathematical model described the general trends for nitrate, ethanol, dissolved organic carbon (DOC) and dissolved inorganic carbon (DIC) concentrations. This model shows how the biomass present in the system is degraded to dissolved organic C (DOC_en) and becomes the main source of DOC for a C/N ratio between 1.0 and 0. The isotopic model developed for organic and inorganic carbon also describes the general trends of δ¹³C of ethanol, DOC and DIC in the outflow water. The study of the evolution of the isotopic fractionation of organic C using a Rayleigh distillation model shows the shift in the organic carbon source from the WIB to the biomass and is in agreement with the isotopic fractionation values used to calibrate the model. Isotopic fractionations (ε) of C-ethanol and C-DOC_en were -1‰ and -5‰ (model) and -3.3‰ and -4.8‰ (Rayleigh), respectively. In addition, an inverse isotopic fractionation of +10‰ was observed for biomass degradation to DOC_en. Overall, WIB can efficiently promote nitrate reduction in EBD treatments. The conceptual model of the organic C cycle and the developed mathematical model accurately described the chemical and isotopic transformations that occur during this induced denitrification.

Organic carbon availability limiting microbial denitrification in the deep vadose zone

Microbes in the deep vadose zone play an essential role in the mitigation of nitrate leaching; however, limited information is available on the mechanisms of microbial denitrification due to sampling difficulties. We experimentally studied the factors that affect denitrification in soils collected down to 10.5 meters deep along the soil profile. After an anoxic pre-incubation, denitrification rates moderately increased and the N₂ O/(N₂ O + N₂ ) ratios declined while the microbial abundance and diversity did not change significantly in most of the layers. Denitrification rate was significantly enhanced and the abundance of the denitrification genes was simultaneously elevated by the increased availability of organic carbon in all studied layers, to a greater extent in the subsurface layers than in the surface layers, suggesting the severe scarcity of carbon in the deep vadose zone. The genera Pseudomonas and Bacillus, which are made up of a number of species that have been previously identified as denitrifiers in soil, were the major taxa that respond to carbon addition. Overall, our results suggested that the limited denitrification in the deep vadose zone is not because of the lack of denitrifiers, but due to the low abundance of denitrifiers which is caused by low carbon availability.

Management Practices Used in Agricultural Drainage Ditches to Reduce Gulf of Mexico Hypoxia

Agricultural non-point sources of nutrients and sediments have caused eutrophication and other water quality issues in aquatic and marine ecosystems, such as the annual occurrence of hypoxia in the Gulf of Mexico. Management practices have been implemented adjacent to and in agricultural drainage ditches to promote their wetland characteristics and functions, including reduction of nitrogen, phosphorus, and sediment losses downstream. This review: (1) summarized studies examining changes in nutrient and total suspended solid concentrations and loads associated with management practices in drainage ditches (i.e., riser and slotted pipes, two-stage ditches, vegetated ditches, low-grade weirs, and organic carbon amendments) with emphasis on the Lower Mississippi Alluvial Valley, (2) quantified management system effects on nutrient and total suspended solid concentrations and loads and, (3) identified information gaps regarding water quality associated with these management practices and research needs in this area. In general, management practices used in drainage ditches at times reduced losses of total suspended solids, N, and P. However, management practices were often ineffective during storm events that were uncommon and intense in duration and volume, although these types of events could increase in frequency and intensity with climate change. Studies on combined effects of management practices on drainage ditch water quality, along with research towards improved nutrient and sediment reduction efficiency during intense storm events are urgently needed.

The roles of cyanobacterial bloom in nitrogen removal

Annually occurred cyanobacterial bloom aggravated eutrophication situation and changed the lacustrine ecosystem components. Recently, high concentration of bloom cyanobacteria had been found to accelerate total nitrogen (TN) removal. However, the contribution of cyanobacterial bloom to TN removal remained unclear. In this study, microcosms with different density of bloom cyanobacteria were constructed and quantitative PCR and structural equation modelling (SEM) were used to analyze the microbes, environmental variables and the causal relationship to TN removal. Total bacteria, ammonia-oxidizing archaea and nirS gene abundances were indirectly influenced by cyanobacteria biomass and all of them had a direct effect on TN removal. SEM confirmed that cyanobacteria made a direct contribution to ammonium‑nitrogen (NH₄⁺-N) level in water and induced nitrification activity, which favored the process of denitrification by supplying substrate and aggravating the anoxic status. These results strongly suggested that an increased cyanobacteria biomass had strong impacts on mineralization, nitrification and denitrification by mediating TN, dissolved organic carbon and dissolved oxygen directly and subsequently influenced the nitrifiers and denitrifiers.

Hierarchical Control of Nitrite Respiration by Transcription Factors Encoded within Mobile Gene Clusters of Thermus thermophilus

Denitrification in Thermus thermophilus is encoded by the nitrate respiration conjugative element (NCE) and nitrite and nitric oxide respiration (nic) gene clusters. A tight coordination of each cluster’s expression is required to maximize anaerobic growth, and to avoid toxicity by intermediates, especially nitric oxides (NO). Here, we study the control of the nitrite reductases (Nir) and NO reductases (Nor) upon horizontal acquisition of the NCE and nic clusters by a formerly aerobic host. Expression of the nic promoters PnirS, PnirJ, and PnorC, depends on the oxygen sensor DnrS and on the DnrT protein, both NCE-encoded. NsrR, a nic-encoded transcription factor with an iron–sulfur cluster, is also involved in Nir and Nor control. Deletion of nsrR decreased PnorC and PnirJ transcription, and activated PnirS under denitrification conditions, exhibiting a dual regulatory role never described before for members of the NsrR family. On the basis of these results, a regulatory hierarchy is proposed, in which under anoxia, there is a pre-activation of the nic promoters by DnrS and DnrT, and then NsrR leads to Nor induction and Nir repression, likely as a second stage of regulation that would require NO detection, thus avoiding accumulation of toxic levels of NO. The whole system appears to work in remarkable coordination to function only when the relevant nitrogen species are present inside the cell.

Watershed vs. within-lake drivers of nitrogen: phosphorus dynamics in shallow lakes

Research on lake eutrophication often identifies variables affecting amounts of phosphorus (P) and nitrogen (N) in lakes, but understanding factors influencing N:P ratios is important given its influence on species composition and toxin production by cyanobacteria. We sampled 80 shallow lakes in Minnesota (USA) for three years to assess effects of watershed size, proportion of watershed as both row crop and natural area, fish biomass, and lake alternative state (turbid vs. clear) on total N : total P (TN : TP), ammonium, total dissolved phosphorus (TDP), and seston stoichiometry. We also examined N:P stoichiometry in 20 additional lakes that shifted states during the study. Last, we assessed the importance of denitrification by measuring denitrification rates in sediment cores from a subset of 34 lakes, and by measuring seston δ¹⁵ N in four additional experimental lakes before and after they were experimentally manipulated from turbid to clear states. Results showed alternative state had the largest influence on overall N:P stoichiometry in these systems, as it had the strongest relationship with TN : TP, seston C:N:P, ammonium, and TDP. Turbid lakes had higher N at given levels of P than clear lakes, with TN and ammonium 2-fold and 1.4-fold higher in turbid lakes, respectively. In lakes that shifted states, TN was 3-fold higher in turbid lakes, while TP was only 2-fold higher, supporting the notion N is more responsive to state shifts than is P. Seston δ¹⁵ N increased after lakes shifted to clear states, suggesting higher denitrification rates may be important for reducing N levels in clear states, and potential denitrification rates in sediment cores were among the highest recorded in the literature. Overall, our results indicate lake state was a primary driver of N:P dynamics in shallow lakes, and lakes in clear states had much lower N at a given level of P relative to turbid lakes, likely due to higher denitrification rates. Shallow lakes are often managed for the clear-water state due to increased value as wildlife habitat. However, our results indicate lake state also influences N biogeochemistry, such that managing shallow lakes for the clear-water state may also mitigate excess N levels at a landscape scale.

Greenhouse Gas Emissions after Application of Landfilled Paper Mill Sludge for Land Reclamation of a Nonacidic Mine Tailings Site

Large areas of mine tailings are reclaimed by applying organic amendments such as paper mill sludge (PMS). Although mining industries can use PMS freshly generated by paper mills, operational constraints on paper industries make temporary landfilling of this material an unavoidable alternative for the paper industries, creating the most prominent PMS source for mining industries. This study aimed to quantify soil greenhouse gas (GHG) emissions (NO, CO, and CH) after application of landfilled PMS (LPMS; i.e., excavated from a landfill site at a paper mill) and LPMS combined with a seeding treatment of white clover ( L.) on nonacidic mine tailings site prior to reforestation. Soil NO, CO, and CH fluxes were measured after applications of 50 and 100 Mg dry LPMS ha during two consecutive snow-free seasons on two adjacent sites; LPMS was applied once in the first season. The LPMS application increased NO emissions (7.6 to 34.7 kg NO-N ha, comprising 1.04 to 2.43% of applied N) compared with the unamended control during the first season; these emissions were negligible during the second season. The LPMS application increased CO emissions (∼5800 to 11,400 kg CO-C ha, comprising 7 to 27% of applied C) compared with the unamended control on both sites and in both seasons. Fluxes of CH were negligible. White clover combined with LPMS treatments did not affect soil GHG emissions. These new GHG emission factors should be integrated into life-cycle analyses to evaluate the C footprint of potential symbioses between the mining and paper industries. Future research should focus on the effect of PMS applications on soil GHG emissions from a variety of mine tailings under various management practices and climatic conditions to plan responsible and sustainable land reclamation.

How Plant Root Exudates Shape the Nitrogen Cycle

Although the global nitrogen (N) cycle is largely driven by soil microbes, plant root exudates can profoundly modify soil microbial communities and influence their N transformations. A detailed understanding is now beginning to emerge regarding the control that root exudates exert over two major soil N processes - nitrification and N2 fixation. We discuss recent breakthroughs in this area, including the identification of root exudates as nitrification inhibitors and as signaling compounds facilitating N-acquisition symbioses. We indicate gaps in current knowledge, including questions of how root exudates affect newly discovered microbial players and N-cycle components. A better understanding of these processes is urgent given the widespread inefficiencies in agricultural N use and their links to N pollution and climate change.

Denitrifying bacterial communities display different temporal fluctuation patterns across Dutch agricultural soils

Considering the great agronomic and environmental importance of denitrification, the aim of the present study was to study the temporal and spatial factors controlling the abundance and activity of denitrifying bacterial communities in a range of eight agricultural soils over 2 years. Abundance was quantified by qPCR of the nirS, nirK and nosZ genes, and the potential denitrification enzyme activity (DEA) was estimated. Our data showed a significant temporal variation considerably high for the abundance of nirK-harboring communities, followed by nosZ and nirS communities. Regarding soil parameters, the abundances of nosZ, nirS and nirK were mostly influenced by organic material, pH, and slightly by NO₃^-, respectively. Soil texture was the most important factor regulating DEA, which could not be explained by the abundance of denitrifiers. Analyses of general patterns across lands to understand the soil functioning is not an easy task because the multiple factors influencing processes such as denitrification can skew the data. Careful analysis of atypical sites are necessary to classify the soils according to trait similarity and in this way reach a better predictability of the denitrifiers dynamics.

Influence of infrastructure on water quality and greenhouse gas dynamics in urban streams

Streams and rivers are significant sources of nitrous oxide (N₂O), carbon dioxide (CO₂), and methane (CH₄) globally, and watershed management can alter greenhouse gas (GHG) emissions from streams. We hypothesized that urban infrastructure significantly alters downstream water quality and contributes to variability in GHG saturation and emissions. We measured gas saturation and estimated emission rates in headwaters of two urban stream networks (Red Run and Dead Run) of the Baltimore Ecosystem Study Long-Term Ecological Research project. We identified four combinations of stormwater and sanitary infrastructure present in these watersheds, including: (1) stream burial, (2) inline stormwater wetlands, (3) riparian/floodplain preservation, and (4) septic systems. We selected two first order catchments in each of these categories and measured GHG concentrations, emissions, and dissolved inorganic and organic carbon (DIC and DOC) and nutrient concentrations biweekly for 1 year. From a water quality perspective, the DOC : NO₃ ^- ratio of streamwater was significantly different across infrastructure categories. Multiple linear regressions including DOC : NO₃ ^- and other variables (dissolved oxygen, DO; total dissolved nitrogen, TDN; and temperature) explained much of the statistical variation in nitrous oxide (N₂O, r² = 0.78), carbon dioxide (CO₂, r² = 0.78) and methane (CH4, r 2 = 0.50) saturation in stream water. We measured N₂O saturation ratios, which were among the highest reported in the literature for streams, ranging from 1.1 to 47 across all sites and dates. N₂O saturation ratios were highest in streams draining watersheds with septic systems and strongly correlated with TDN. The CO₂ saturation ratio was highly correlated with the N₂O saturation ratio across all sites and dates, and the CO₂ saturation ratio ranged from 1.1 to 73. CH₄ was always supersaturated, with saturation ratios ranging from 3.0 to 2157. Longitudinal surveys extending form headwaters to third-order outlets of Red Run and Dead Run took place in spring and fall. Linear regressions of these data yielded significant negative relationships between each gas with increasing watershed size as well as consistent relationships between solutes (TDN or DOC, and DOC : TDN ratio) and gas saturation. Despite a decline in gas saturation between the headwaters and stream outlet, streams remained saturated with GHGs throughout the drainage network, suggesting that urban streams are continuous sources of CO₂, CH₄, and N₂O. Our results suggest that infrastructure decisions can have significant effects on downstream water quality and greenhouse gases, and watershed management strategies may need to consider coupled impacts on urban water and air quality.

Nitrate-rich agricultural runoff treatment by Vallisneria-sulfur based mixotrophic denitrification process

Vallisneria-sulfur based mixotrophic denitrification (VSMD) process was put forward for the treatment of nitrate-rich agricultural runoff with low COD/TN (C/N) ratio in free water surface constructed wetland mesocosms, whose feasibility and mechanism were thoroughly studied through 273-day operation. The results showed that the average NO₃^--N removal efficiency and denitrification rate of VSMD mesocosms were 97.7% and 1.5gNO₃^--Nm^-3d^-1 under 5.0 or higher C/N ratio conditions in phase II (7-117d), which were similar with those of Vallisneria packed heterotrophic denitrification (VHD) mesocosms. However, VSMD mesocosms with 2.0 average C/N ratio in phase III (118-273d) were more stable and efficient than VHD mesocosms. More than 49.4mg NO₃^--N was reduced by VSMD mesocosms than that by VHD mesocosms throughout the operation. NO₂^--N accumulation in phase I (0-6d) had no influence on denitrification performance of VSMD mesocosms. In phase II and III, effluent COD, NH₄⁺-N and NO₂^--N could meet the Class II standard of Environmental quality for surface water (GB3838-2002) if the experiment was carried out in batch mode. pH in VSMD mesocosms fluctuated between 7.0 and 8.9 throughout the operation without any pH buffer. The abundance of three denitrifying genes coding for nitrate (narG), nitrite (nirS), and nitrous oxide (nosZ) reductases in bottom soil and mixture from litter bags was quantified. VSMD could supply more favorable circumstances for the growth of denitrificans containing narG (3.1×10⁸±7.9×10⁷copiesg^-1mixture^-1) and nirS (2.1×10⁸±2.0×10⁶copiesg^-1mixture^-1) in litter bags than VHD, i.e., 8.7×10⁷±1.4×10⁷ and 1.4×10⁸±1.5×10⁷copiesg^-1mixture^-1 for narG and nirS respectively. Sulfur addition in VSMD mesocosms might increase the abundance of denitrificans containing narG and nirS, thus led to better denitrification performance.

Responses of denitrifying bacterial communities to short-term waterlogging of soils

Agricultural soil is often subjected to waterlogging after heavy rainfalls, resulting in sharp and explosive increases in the emission of nitrous oxide (N₂O), an important greenhouse gas primarily released from agricultural soil ecosystems. Previous studies on waterlogged soil examined the abundance of denitrifiers but not the composition of denitrifier communities in soil. Also, the PCR primers used in those studies could only detect partial groups of denitrifiers. Here, we performed pyrosequencing analyses with the aid of recently developed PCR primers exhibiting high coverage for three denitrification genes, nirK, nirS, and nosZ to examine the effect of short-term waterlogging on denitrifier communities in soil. We found that microbial communities harboring denitrification genes in the top 5 cm of soil distributed according to soil depth, water-soluble carbon, and nitrate nitrogen. Short-term waterlogging scarcely affected abundance, richness, or the alpha-diversities of microbial communities harboring nirK, nirS, and nosZ genes, but significantly affected their composition, particularly in microbial communities at soil depths of 0 to 1 cm. Our results indicated that the composition of denitrifying microbial communities but not the abundance of denitrifiers in soil was responsive to short-term waterlogging of an agricultural soil ecosystem.

Diversity and Abundance of the Denitrifying Microbiota in the Sediment of Eastern China Marginal Seas and the Impact of Environmental Factors

Investigating the environmental influence on the community composition and abundance of denitrifiers in marine sediment ecosystem is essential for understanding of the ecosystem-level controls on the biogeochemical process of denitrification. In the present study, nirK-harboring denitrifying communities in different mud deposit zones of eastern China marginal seas (ECMS) were investigated via clone library analysis. The abundance of three functional genes affiliated with denitrification (narG, nirK, nosZ) was assessed by fluorescent quantitative PCR. The nirK-harboring microbiota were dominated by a few operational taxonomic units (OTUs), which were widely distributed in different sites with each site harboring their unique phylotypes. The mean abundance of nirK was significantly higher than that of narG and nosZ genes, and the abundance of narG was higher than that of nosZ. The inconsistent abundance profile of different functional genes along the process of denitrification might indicate that nitrite reduction occurred independently of denitrification in the mud deposit zones of ECMS, and sedimentary denitrification was accomplished by cooperation of different denitrifying species rather than a single species. Such important information would be missed when targeting only a single denitrifying functional gene. Analysis of correlation between abundance ratios and environmental factors revealed that the response of denitrifiers to environmental factors was not invariable in different mud deposit zones. Our results suggested that a comprehensive analysis of different denitrifying functional genes may gain more information about the dynamics of denitrifying microbiota in marine sediments.

Feasibility of two low-cost organic substrates for inducing denitrification in artificial recharge ponds: Batch and flow-through experiments

Anaerobic batch and flow-through experiments were performed to assess the capacity of two organic substrates to promote denitrification of nitrate-contaminated groundwater within managed artificial recharge systems (MAR) in arid or semi-arid regions. Denitrification in MAR systems can be achieved through artificial recharge ponds coupled with a permeable reactive barrier in the form of a reactive organic layer. In arid or semi-arid regions, short-term efficient organic substrates are required due to the short recharge periods. We examined the effectiveness of two low-cost, easily available and easily handled organic substrates, commercial plant-based compost and crushed palm tree leaves, to determine the feasibility of using them in these systems. Chemical and multi-isotopic monitoring (δ¹⁵N_NO3, δ¹⁸O_NO3, δ³⁴S_SO4, δ¹⁸O_SO4) of the laboratory experiments confirmed that both organic substrates induced denitrification. Complete nitrate removal was achieved in all the experiments with a slight transient nitrite accumulation. In the flow-through experiments, ammonium release was observed at the beginning of both experiments and lasted longer for the experiment with palm tree leaves. Isotopic characterisation of the released ammonium suggested ammonium leaching from both organic substrates at the beginning of the experiments and pointed to ammonium production by DNRA for the palm tree leaves experiment, which would only account for a maximum of 15% of the nitrate attenuation. Sulphate reduction was achieved in both column experiments. The amount of organic carbon consumed during denitrification and sulphate reduction was 0.8‰ of the total organic carbon present in commercial compost and 4.4% for the palm tree leaves. The N and O isotopic fractionation values obtained (ε_N and ε_O) were -10.4‰ and -9.0‰ for the commercial compost (combining data from both batch and column experiments), and -9.9‰ and -8.6‰ for the palm tree column, respectively. Both materials showed a satisfactory capacity for denitrification, but the palm tree leaves gave a higher denitrification rate and yield (amount of nitrate consumed per amount of available C) than commercial compost.

Coupled molecular and isotopic evidence for denitrifier controls over terrestrial nitrogen availability

Denitrification removes ecologically available nitrogen (N) from the biosphere and influences both the pace and magnitude of global climate change. Disagreements exist over the degree to which this microbial process influences N-availability patterns across Earth's ecosystems. We combine natural stable isotope methods with qPCR to investigate how denitrifier gene abundance is related to variations in nitrate (NO3-) pool sizes across diverse terrestrial biomes and conditions. We analyze NO3- isotope composition (15N/14N, 18O/16O) and denitrifier gene nirS in 52 soil samples from different California ecosystems, spanning desert, chaparral, oak-woodland/savanna and forest. δ15N-NO3- correlates positively with δ18O-NO3- (P⩽0.03) and nirS abundance (P=0.00002) across sites, revealing the widespread importance of isotopic discrimination by soil denitrifiers. Furthermore, NO3- concentrations correlate negatively to nirS (P=0.002) and δ15N-NO3- (P=0.003) across sites. We also observe these spatial relationships in short-term (7-day), in situ soil-incubation experiments; NO3--depletion strongly corresponds with increased nirS, nirS/16 rRNA, and enrichment of heavy NO3- isotopes over time. Overall, these findings suggest that microbial denitrification can consume plant-available NO3- to low levels at multiple time scales, contributing to N-limitation patterns across sites, particularly in moist, carbon-rich soils. Furthermore, our study provides a new approach for understanding the relationships between microbial gene abundance and terrestrial ecosystem functioning.

Pyrosequencing reveals microbial community dynamics in integrated simultaneous desulfurization and denitrification process at different influent nitrate concentrations

Integrated simultaneous desulfurization and denitrification (ISDD) process has proven to be feasible for the coremoval of sulfate, nitrate, and chemical oxygen demand (COD). In this study, we aimed to reveal the microbial community dynamics in the ISDD process with different influent nitrate (NO₃^-) concentrations. For all tested scenarios, full denitrification was accomplished while sulfate removal efficiency decreased along with increased influent NO₃^- concentrations. The proportion of S⁰ to influent SO₄^2- maintained a low level (5.6-17.0%) regardless of the increased influent NO₃^- concentrations. Microbial community analysis results showed that higher influent NO₃^- concentrations affected the microbial community structure greatly. Phyla Proteobacteria, Spirochaetae, Firmicutes, Synergistetes, and Chloroflexi dominated in all the community compositions, of which Proteobacteria exhibited a clear difference among eight microbial samples. Members of δ-Proteobacteria, with 16S rRNA gene sequences related to Desulfobulbus, were clearly decreased at influent NO₃^- = 3000 and 3500 mg/L, suggesting an inhibitory effect of NO₃^- on sulfate reduction. In contrast, as influent NO₃^- concentration increased, microbial community was notably enriched in γ-Proteobacteria and ε-Proteobacteria, which revealed the enrichment of 16S rRNA gene sequences related to Pseudomonas (γ-Proteobacteria), and Arcobacteria and Sulfurospirillum (ε-Proteobacteria).

Dissolved nitrous oxide and emission relating to denitrification across the Poyang Lake aquatic continuum

Most aquatic ecosystems contribute elevated N₂O to atmosphere due to increasing anthropogenic nitrogen loading. To further understand the spatial heterogeneity along an aquatic continuum from the upriver to wetland to lake to downriver, the study was conducted on spatial variations in N₂O emission along Poyang Lake aquatic continuum during the flood season from 15 July 2013 to 10 August 2013. The results showed the N₂O concentrations, the ratio of N₂O/dinitrogen (N₂) gases production, N₂O emission and denitrification rates ranged from 0.10 to 1.11μgN/L, -0.007% to 0.051%, -9.73 to 127μgN/m²/hr and 1.33×10⁴ to 31.9×10⁴μgN₂/m²/hr, respectively, across the continuum. The average N₂O concentrations, the ratio of N₂O/N₂ and N₂O emission was significantly lower in wetlands as compared to the rivers and lake (p<0.01). The significantly high denitrification rate and low N₂O emission together highlighted that most N₂O can be converted into N₂ via near complete denitrification in the Poyang Lake wetlands. Our study suggests that the wetlands might impact N₂O budget in an integrated aquatic ecosystems. Moreover, N₂O emission from different aquatic ecosystem should be considered separately when quantifying the regional budget in aquatic ecosystem.

Small Reservoirs as a Beneficial Management Practice for Nitrogen Removal

There are few beneficial management practices (BMPs) with demonstrated efficacy in snowmelt-dominated regions. Small reservoirs are a BMP that can help mitigate flooding and reduce sediment transport, while reducing export of dissolved nutrients. To understand controls on nitrate removal and assess how this ecosystem service can be optimized, denitrification activity was measured in reservoirs and stream pools of the Tobacco Creek Model Watershed (Manitoba, Canada) via the chloramphenicol-amended acetylene block technique. Denitrification activity was positively correlated with nitrate and sediment organic carbon (SOC), and negatively correlated with sediment particle size and pH. Reservoirs exhibited higher denitrification activity than stream pools and were associated with higher levels of SOC, higher nitrate in early summer, and lower concentrations of dissolved oxygen. Nitrate was added to a set of samples to test for nitrate saturation, an indicator of poor ecological status, where nitrate concentrations exceed the denitrification capacity of microbes. Forty-nine percent of measurements demonstrated nitrate saturation, indicative of the need for additional remediation activity. Findings from this research suggest this BMP has higher capacity for nitrogen removal than stream pools because of higher denitrification rates and a higher apparent threshold for nitrate saturation, coupled with increased residence times. Results also inform the construction of additional reservoirs, which have been identified as a priority BMP in this region. Siting reservoirs in areas where conditions contribute to buildup of fine sediments and planting riparian vegetation to foster high organic C availability may help optimize denitrification, although tradeoffs in terms of other ecosystem services must be considered.

Recent structural insights into the function of copper nitrite reductases

Copper nitrite reductases (CuNiRs) catalyse the reduction of nitrite to nitric oxide as part of the denitrification pathway. In this review, we describe insights into CuNiR function from structural studies.

Genome sequence and overview of Oligoflexus tunisiensis Shr3T in the eighth class Oligoflexia of the phylum Proteobacteria

Oligoflexus tunisiensis Shr3^T is the first strain described in the newest (eighth) class Oligoflexia of the phylum Proteobacteria. This strain was isolated from the 0.2-μm filtrate of a suspension of sand gravels collected in the Sahara Desert in the Republic of Tunisia. The genome of O. tunisiensis Shr3^T is 7,569,109 bp long and consists of one scaffold with a 54.3% G + C content. A total of 6,463 genes were predicted, comprising 6,406 protein-coding and 57 RNA genes. Genome sequence analysis suggested that strain Shr3^T had multiple terminal oxidases for aerobic respiration and various transporters, including the resistance-nodulation-cell division-type efflux pumps. Additionally, gene sequences related to the incomplete denitrification pathway lacking the final step to reduce nitrous oxide (N₂O) to nitrogen gas (N₂) were found in the O. tunisiensis Shr3^T genome. The results presented herein provide insight into the metabolic versatility and N₂O-producing activity of Oligoflexus species.

An integrated biological approach for treatment of cyanidation wastewater

The cyanidation process has been, and still remains, a profitable and highly efficient process for the recovery of precious metals from ores. However, this process has contributed to environmental deterioration and potable water reserve contamination due to the discharge of poorly treated, or untreated, cyanide containing wastewater. The process produces numerous cyanide complexes in addition to the gold cyanocomplex. Additionally, the discharge constituents also include hydrogen cyanide (HCN) - metallic complexes with iron, nickel, copper, zinc, cobalt and other metals; thiocyanate (SCN); and cyanate (CNO). The fate of these complexes in the environment dictates the degree to which these species pose a threat to living organisms. This paper reviews the impact that the cyanidation process has on the environment, the ecotoxicology of the cyanidation wastewater and the treatment methods that are currently utilised to treat cyanidation wastewater. Furthermore, this review proposes an integrated biological approach for the treatment of the cyanidation process wastewater using microbial consortia that is insensitive and able to degrade cyanide species, in all stages of the proposed process.

Disentangling gross N2O production and consumption in soil

The difficulty of measuring gross N2O production and consumption in soil impedes our ability to predict N2O dynamics across the soil-atmosphere interface. Our study aimed to disentangle these processes by comparing measurements from gas-flow soil core (GFSC) and 15N2O pool dilution (15N2OPD) methods. GFSC directly measures soil N2O and N2 fluxes, with their sum as the gross N2O production, whereas 15N2OPD involves addition of 15N2O into a chamber headspace and measuring its isotopic dilution over time. Measurements were conducted on intact soil cores from grassland, cropland, beech and pine forests. Across sites, gross N2O production and consumption measured by 15N2OPD were only 10% and 6%, respectively, of those measured by GFSC. However, 15N2OPD remains the only method that can be used under field conditions to measure atmospheric N2O uptake in soil. We propose to use different terminologies for the gross N2O fluxes that these two methods quantified. For 15N2OPD, we suggest using 'gross N2O emission and uptake', which encompass gas exchange within the 15N2O-labelled, soil air-filled pores. For GFSC, 'gross N2O production and consumption' can be used, which includes both N2O emitted into the soil air-filled pores and N2O directly consumed, forming N2, in soil anaerobic microsites.

Physical Factors Correlate to Microbial Community Structure and Nitrogen Cycling Gene Abundance in a Nitrate Fed Eutrophic Lagoon

Nitrogenous run-off from farmed pastures contributes to the eutrophication of Lake Ellesmere, a large shallow lagoon/lake on the east coast of New Zealand. Tributaries periodically deliver high loads of nitrate to the lake which likely affect microbial communities therein. We hypothesized that a nutrient gradient would form from the potential sources (tributaries) creating a disturbance resulting in changes in microbial community structure. To test this we first determined the existence of such a gradient but found only a weak nitrogen (TN) and phosphorous gradient (DRP). Changes in microbial communities were determined by measuring functional potential (quantification of nitrogen cycling genes via nifH, nirS, nosZI, and nosZII using qPCR), potential activity (via denitrification enzyme activity), as well as using changes in total community (via 16S rRNA gene amplicon sequencing). Our results demonstrated that changes in microbial communities at a phylogenetic (relative abundance) and functional level (proportion of the microbial community carrying nifH and nosZI genes) were most strongly associated with physical gradients (e.g., lake depth, sediment grain size, sediment porosity) and not nutrient concentrations. Low nitrate influx at the time of sampling is proposed as a factor contributing to the observed patterns.

Source, variability, and transformation of nitrate in a regional karst aquifer: Edwards aquifer, central Texas

Many karst regions are undergoing rapid population growth and expansion of urban land accompanied by increases in wastewater generation and changing patterns of nitrate (NO3(-)) loading to surface and groundwater. We investigate variability and sources of NO3(-) in a regional karst aquifer system, the Edwards aquifer of central Texas. Samples from streams recharging the aquifer, groundwater wells, and springs were collected during 2008-12 from the Barton Springs and San Antonio segments of the Edwards aquifer and analyzed for nitrogen (N) species concentrations and NO3(-) stable isotopes (δ(15)N and δ(18)O). These data were augmented by historical data collected from 1937 to 2007. NO3(-) concentrations and discharge data indicate that short-term variability (days to months) in groundwater NO3(-) concentrations in the Barton Springs segment is controlled by occurrence of individual storms and multi-annual wet-dry cycles, whereas the lack of short-term variability in groundwater in the San Antonio segment indicates the dominance of transport along regional flow paths. In both segments, longer-term increases (years to decades) in NO3(-) concentrations cannot be attributed to hydrologic conditions; rather, isotopic ratios and land-use change indicate that septic systems and land application of treated wastewater might be the source of increased loading of NO3(-). These results highlight the vulnerability of karst aquifers to NO3(-) contamination from urban wastewater. An analysis of N-species loading in recharge and discharge for the Barton Springs segment during 2008-10 indicates an overall mass balance in total N, but recharge contains higher concentrations of organic N and lower concentrations of NO3(-) than does discharge, consistent with nitrification of organic N within the aquifer and consumption of dissolved oxygen. This study demonstrates that subaqueous nitrification of organic N in the aquifer, as opposed to in soils, might be a previously unrecognized source of NO3(-) to karst groundwater or other oxic groundwater systems.

Nitrogen Removal in Permeable Woodchip Filters Affected by Hydraulic Loading Rate and Woodchip Ratio

Unregulated and event-driven agricultural tile drainage discharge poses several challenges that potentially limit the nitrate (NO) removal performance of woodchip-based wetlands constructed to intercept subsurface tile drain flows. Laboratory column tests were conducted to evaluate the biogeochemical response of mixed reactive media (woodchips-seashells and woodchips-Filtralite mixtures) at two woodchip ratios to changes in hydraulic loading rate (HLR). The tests involved continuous loading of aerated artificial drainage water spiked with NO-N and tritium (HO) breakthrough experiments. Flow-normalized NO reduction rates ranged from 0.35 to 3.97 g N m L, corresponding to N removal efficiencies of 5 to 64%, depending on HLR and filter mixtures. At high HLRs, oxic conditions prevailed in the woodchip filters, resulting in reduced N removal. At low HLRs, progressively lower pore-water velocities extended the period for consumption of terminal electron acceptors, increasing N removal. When increasing the content of mineral material, N removal declined, probably due to a lower denitrifying biomass at lower woodchip mass. The effect of woodchip ratios on solute transport characteristics was difficult to assess. However, woodchip media including a mineral fraction of crushed seashells demonstrated the highest N removal rates and efficiencies, most likely due to the alkalizing effect of the seashells. In conclusion, filter mixtures consisting of woodchips and seashells were the most effective material for N removal in subsurface flow-constructed wetlands treating agricultural drainage water.

The effects of temperature and resource availability on denitrification and relative N2O production in boreal lake sediments

Anthropogenic environmental stressors (like atmospheric deposition, land use change, and climate warming) are predicted to increase inorganic nitrogen and organic carbon loading to northern boreal lakes, with potential consequences for denitrification in lakes. However, our ability to predict effects of these changes is currently limited as northern boreal lakes have been largely neglected in denitrification studies. The aim of this study was therefore to assess how maximum potential denitrification and N2O production rates, and the relationship between the two (relative N2O production), is controlled by availability of nitrate (NO3(-)), carbon (C), phosphorus (P), and temperature. Experiments were performed using the acetylene inhibition technique on sediments from a small, nutrient poor boreal lake in northern Sweden in 2014. Maximum potential denitrification and N2O production rates at 4°C were reached already at NO3(-) additions of 106-120μg NO3(-)-N/L, and remained unchanged with higher NO3 amendments. Higher incubation temperatures increased maximum potential denitrification and N2O production rates, and Q10 was somewhat higher for N2O production (1.77) than for denitrification (1.69). The relative N2O production ranged between 13% and 64%, and was not related to NO3(-) concentration, but the ratio increased when incubations were amended with C and P (from a median of 16% to 27%). Combined, our results suggests that unproductive northern boreal lakes currently have low potential for denitrification but are susceptible to small changes in NO3 loading especially if these are accompanied by enhanced C and P availability, likely promoting higher N2O production relative to N2.

Nitrous Oxide Fluxes, Soil Oxygen, and Denitrification Potential of Urine- and Non-Urine-Treated Soil under Different Irrigation Frequencies

Despite increased use of irrigation to improve forage quality and quantity for grazing cattle ( Linnaeus), there is a lack of data that assess how irrigation practices influence nitrous oxide (NO) emissions from urine-affected soils. Irrigation effects on soil oxygen (O) availability, a primary controller of NO fluxes, is poorly understood. It was hypothesized that increased irrigation frequency would result in lower NO emissions by increasing soil moisture and decreasing soil O concentrations. This would favor more NO reduction to dinitrogen (N). We examined effects of high (3-d) versus low (6-d) irrigation frequency with and without bovine urine addition to pasture. Nitrous oxide fluxes were measured daily for 35 d. Soil O, temperature, and water content were continuously measured at multiple depths. Inorganic nitrogen, organic carbon, and soil pH were measured at 6-d intervals. Measurements of denitrification enzyme activity with and without acetylene inhibition were used to infer the NO/(NO + N) ratio. The NO/(NO + N) ratio was lower under high- compared with low-frequency irrigation, suggesting greater potential for NO reduction to N with more frequent irrigation. Although NO fluxes were increased by urine addition, they were not affected by irrigation frequency. Soil O decreased temporarily after urine deposition, but O dynamics did not explain NO dynamics. Relative soil gas diffusivity (/) was a better predictor of NO fluxes than O concentration. On a free-draining soil, increasing irrigation frequency while providing the same total water volume did not enhance NO emissions under ruminant urine patches in a grazed pasture.

Nitrogen Stimulates the Growth of Subsurface Basalt-associated Microorganisms at the Western Flank of the Mid-Atlantic Ridge

Oceanic crust constitutes the largest aquifer system on Earth, and microbial activity in this environment has been inferred from various geochemical analyses. However, empirical documentation of microbial activity from subsurface basalts is still lacking, particularly in the cool (<25°C) regions of the crust, where are assumed to harbor active iron-oxidizing microbial communities. To test this hypothesis, we report the enrichment and isolation of crust-associated microorganisms from North Pond, a site of relatively young and cold basaltic basement on the western flank of the Mid-Atlantic Ridge that was sampled during Expedition 336 of the Integrated Ocean Drilling Program. Enrichment experiments with different carbon (bicarbonate, acetate, methane) and nitrogen (nitrate and ammonium) sources revealed significant cell growth (one magnitude higher cell abundance), higher intracellular DNA content, and increased Fe³⁺/ΣFe ratios only when nitrogen substrates were added. Furthermore, a Marinobacter strain with neutrophilic iron-oxidizing capabilities was isolated from the basalt. This work reveals that basalt-associated microorganisms at North Pond had the potential for activity and that microbial growth could be stimulated by in vitro nitrogen addition. Furthermore, iron oxidation is supported as an important process for microbial communities in subsurface basalts from young and cool ridge flank basement.

Microbiology and potential applications of aerobic methane oxidation coupled to denitrification (AME-D) process: A review

Aerobic methane oxidation coupled to denitrification (AME-D) is an important link between the global methane and nitrogen cycles. This mini-review updates discoveries regarding aerobic methanotrophs and denitrifiers, as a prelude to spotlight the microbial mechanism and the potential applications of AME-D. Until recently, AME-D was thought to be accomplished by a microbial consortium where denitrifying bacteria utilize carbon intermediates, which are excreted by aerobic methanotrophs, as energy and carbon sources. Potential carbon intermediates include methanol, citrate and acetate. This mini-review presents microbial thermodynamic estimations and postulates that methanol is the ideal electron donor for denitrification, and may serve as a trophic link between methanotrophic bacteria and denitrifiers. More excitingly, new discoveries have revealed that AME-D is not only confined to the conventional synergism between methanotrophic bacteria and denitrifiers. Specifically, an obligate aerobic methanotrophic bacterium, Methylomonas denitrificans FJG1, has been demonstrated to couple partial denitrification with methane oxidation, under hypoxia conditions, releasing nitrous oxide as a terminal product. This finding not only substantially advances the understanding of AME-D mechanism, but also implies an important but unknown role of aerobic methanotrophs in global climate change through their influence on both the methane and nitrogen cycles in ecosystems. Hence, further investigation on AME-D microbiology and mechanism is essential to better understand global climate issues and to develop niche biotechnological solutions. This mini-review also presents traditional microbial techniques, such as pure cultivation and stable isotope probing, and powerful microbial techniques, such as (meta-) genomics and (meta-) transcriptomics, for deciphering linked methane oxidation and denitrification. Although AME-D has immense potential for nitrogen removal from wastewater, drinking water and groundwater, bottlenecks and potential issues are also discussed.

High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409(T) with an incomplete denitrification pathway

Thermus amyloliquefaciens type strain YIM 77409(T) is a thermophilic, Gram-negative, non-motile and rod-shaped bacterium isolated from Niujie Hot Spring in Eryuan County, Yunnan Province, southwest China. In the present study we describe the features of strain YIM 77409(T) together with its genome sequence and annotation. The genome is 2,160,855 bp long and consists of 6 scaffolds with 67.4 % average GC content. A total of 2,313 genes were predicted, comprising 2,257 protein-coding and 56 RNA genes. The genome is predicted to encode a complete glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle. Additionally, a large number of transporters and enzymes for heterotrophy highlight the broad heterotrophic lifestyle of this organism. A denitrification gene cluster included genes predicted to encode enzymes for the sequential reduction of nitrate to nitrous oxide, consistent with the incomplete denitrification phenotype of this strain.

Effect of particle size and composition of suspended sediment on denitrification in river water

Rivers with high suspended sediment (SPS) concentration are common worldwide, and previous studies reported the occurrence of denitrification on SPS. In this work, effect of particle size and composition of SPS on denitrification in river water was studied in laboratory. The (15)N isotope tracer technique was used to investigate the denitrification in water containing 8 g L(-1) SPS with different particle sizes, including <20 μm, 20-50 μm, 50-100 μm, and 100-200 μm. The results showed that the denitrification rate was negatively related to particle size, and the SPS with particle size below 20 μm had the highest (15)N2 emission rate of 0.27 mg-N/m(3) · d, which was twice that of 100-200 μm. The denitrifying bacteria population in the system decreased with the increase of particle size, which was positively correlated with denitrification rate (p<0.05). There was a positive correlation between organic carbon content of SPS and denitrifying bacteria population (p<0.01), indicating that organic carbon is a key factor influencing denitrifying bacteria. Different from the (15)N2 production, (15)N2O emission rate reached the highest of 1.02 μg-N/m(3) · d in the system containing SPS of 20-50 μm, which was 14.8 times that of 100-200 μm. This was due to the difference in denitrifying bacteria species in different systems due to different oxic/anoxic conditions around SPS. This study suggests that not only the SPS concentration but also the SPS size and composition should be considered in studying the nitrogen cycle in river systems, especially for the production of N2O.

Co-Regulations of Spartina alterniflora Invasion and Exogenous Nitrogen Loading on Soil N2O Efflux in Subtropical Mangrove Mesocosms

Both plant invasion and nitrogen (N) enrichment should have significant impact on mangrove ecosystems in coastal regions around the world. However, how N2O efflux in mangrove wetlands responds to these environmental changes has not been well studied. Here, we conducted a mesocosm experiment with native mangrove species Kandelia obovata, invasive salt marsh species Spartina alterniflora, and their mixture in a simulated tide rotation system with or without nitrogen addition. In the treatments without N addition, the N2O effluxes were relatively low and there were no significant variations among the three vegetation types. A pulse loading of exogenous ammonium nitrogen increased N2O effluxes from soils but the stimulatory effect gradually diminished over time, suggesting that frequent measurements are necessary to accurately understand the behavior of N-induced response of N2O emissions. With the N addition, the N2O effluxes from the invasive S. alterniflora were lower than that from native K. obovata mesocosms. This result may be attributed to higher growth of S. alterniflora consuming most of the available nitrogen in soils, and thus inhibiting N2O production. We concluded that N loading significantly increased N2O effluxes, while the invasion of S. alterniflora reduced N2O effluxes response to N loading in this simulated mangrove ecosystem. Thus, both plant invasion and excessive N loading can co-regulate soil N2O emissions from mangrove wetlands, which should be considered when projecting future N2O effluxes from this type of coastal wetland.

Bacterial Mobilization of Nutrients From Biochar-Amended Soils

Soil amendments with biochar to improve soil fertility and increase soil carbon stocks have received some high-level attention. Physical and chemical analyses of amended soils and biochars from various feedstocks are reported, alongside some evaluations of plant growth promotion capabilities. Fewer studies investigated the soil microbiota and their potential to increase cycling and mobilization of nutrients in biochar-amended soils. This review is discussing the latest findings in the bacterial contribution to cycling and mobilizing nitrogen, phosphorus, and sulfur in biochar-amended soils and potential contributions to plant growth promotion. Depending on feedstock, pyrolysis, soil type, and plant cover, changes in the bacterial community structure were observed for a majority of the studies using amplicon sequencing or genetic fingerprinting methods. Prokaryotic nitrification largely depends on the availability of ammonium and can vary considerably under soil biochar amendment. However, denitrification to di-nitrogen and in particular, nitrous oxide reductase activity is commonly enhanced, resulting in reduced nitrous oxide emissions. Likewise, bacterial fixation of di-nitrogen appears to be regularly enhanced. A paucity of studies suggests that bacterial mobilization of phosphorus and sulfur is enhanced as well. However, most studies only tested for extracellular sulfatase and phosphatase activity. Further research is needed to reveal details of the bacterial nutrient mobilizing capabilities and this is in particular the case for the mobilization of phosphorus and sulfur.

Effect of dissolved oxygen on elemental sulfur generation in sulfide and nitrate removal process: characterization, pathway, and microbial community analysis

Microaerobic bioreactor treatment for enriched sulfide and nitrate has been demonstrated as an effective strategy to improve the efficiencies of elemental sulfur (S(0)) generation, sulfide oxidation, and nitrate reduction. However, there is little detailed information for the effect and mechanism of dissolved oxygen (DO) on the variations of microbial community in sulfur generation, sulfide oxidation, and nitrate reduction systems. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was employed to evaluate the variations of microbial community structures in a sulfide oxidation and nitrate reduction reactor under different DO conditions (DO 0-0.7 mg · L(-1)). Experimental results revealed that the activity of sulfide-oxidizing bacteria (SOB) and nitrate-reducing bacteria (NRB) could be greatly stimulated in 0.1-0.3 mg-DO · L(-1). However, when the DO concentration was further elevated to more than 0.5 mg · L(-1), the abundance of NRB was markedly decreased, while the heterotrophic microorganisms, especially carbon degradation species, were enriched. The reaction pathways for sulfide and nitrate removal under microaerobic conditions were also deduced by combining batch experiments with functional species analysis. It was likely that the oxidation of sulfide to sulfur could be performed by both aerobic heterotrophic SOB and sulfur-based autotrophic denitrification bacteria with oxygen and nitrate as terminal electron acceptor, respectively. The nitrate could be reduced to nitrite by both autotrophic and heterotrophic denitrification, and then the generated nitrite could be completely converted to nitrogen gas via heterotrophic denitrification. This study provides new insights into the impacts of microaerobic conditions on the microbial community functional structures of sulfide-oxidizing, nitrate-reducing, and sulfur-producing bioreactors, which revealing the potential linkage between functional microbial communities and reactor performance.