Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification

Elucidating functional microorganisms and metabolic mechanisms in a novel engineered ecosystem integrating C, N, P and S biotransformation by metagenomics

Denitrifying sulfur conversion-associated enhanced biological phosphorous removal (DS-EBPR) system is not only a novel wastewater treatment process, but also an ideal model for microbial ecology in a community context. However, it exists the knowledge gap on the roles and interactions of functional microorganisms in the DS-EBPR system for carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) bioconversions. We use genome-resolved metagenomics to build up an ecological model of microbial communities in a lab-scale DS-EBPR system with stable operation for more than 400 days. Our results yield 11 near-complete draft genomes that represent a substantial portion of the microbial community (39.4%). Sulfate-reducing bacteria (SRB) and sulfide-oxidizing bacteria (SOB) promote complex metabolic processes and interactions for C, N, P and S conversions. Bins 1-4 and 10 are considered as new potential polyphosphate-accumulating organisms (PAOs), in which Bins 1-4 can be considered as S-related PAOs (S-PAOs) with no previously cultivated or reported members. Our findings give an insight into a new ecological system with C, N, P and S simultaneous bioconversions and improve the understanding of interactions among SRB, SOB, denitrifiers and PAOs within a community context.

Understanding urban stormwater denitrification in bioretention internal water storage zones

Conventional free-draining bioretention systems promote nitrate production and continual leaching to receiving waters. In this study, laboratory tests demonstrated the efficacy of an internal water storage zone (IWSZ) to target nitrate removal via denitrification. Experimental results confirmed that the carbon substrate characteristics (Willow Oak woodchip media) and the hydraulic retention time of nitrified stormwater affected nitrate removal performance. A 2.6-day batch treatment time reduced 3.0 mg-N/L to <0.01 mg/L, corresponding to a first-order denitrification rate constant of 0.0011 min^-1 . Under various flow conditions, the associated hydraulic retention time may be used as a predictive measurement of nitrate removal performance. Scanning electron microscopy and 16S rRNA analysis of the woodchips showed that biofilms were present that could be responsible for anaerobic lignocellulose degradation and denitrification. This knowledge, along with evaluation of the biofilm community composition, reinforced the notion of a heterogeneous structure due to nutrient availability and hydrodynamic conditions. PRACTITIONER POINTS: Denitrification can occur using woodchips in a bioretention internal water storage zone. The denitrification rate is slow and may be limited during field-scale applications. A woodchip pretreatment did not provide long-term enhancement to the denitrification rate. Denitrification bacteria were found in the internal water storage zone.

Evidences of N2O Emissions in Chloropicrin-Fumigated Soil

The mechanism of N₂O production following chloropicrin (CP) fumigation was investigated in this study. Our results showed that CP fumigation increased N₂O production from 23 to 25 times in comparison with the control and significantly decreased the abundance of 16S rRNA and N-cycling functional genes. CP also decreased the soil bacterial diversity and caused a shift in the community composition. The N₂O emissions in fumigated soil were significantly correlated with soil environmental factors (NH₄⁺, dissolved amino acid, microbial biomass nitrogen, and NO₃^-) but were not correlated with the abundance of functional genes. Metatranscriptomes and dual-label ¹⁵N-¹⁸O isotope analysis revealed that CP fumigation inhibited the expression of gene families involved in N₂O production and sink processes and shifted the main pathway of N₂O production from nitrification to denitrification. These results provided useful information for environmental safety assessments of CP in China, to improve our understanding of the N-cycling pathways in fumigated soils.

Nitrous oxide from chemodenitrification: A possible missing link in the Proterozoic greenhouse and the evolution of aerobic respiration

The potent greenhouse gas nitrous oxide (N₂ O) may have been an important constituent of Earth's atmosphere during Proterozoic (~2.5-0.5 Ga). Here, we tested the hypothesis that chemodenitrification, the rapid reduction of nitric oxide by ferrous iron, would have enhanced the flux of N₂ O from ferruginous Proterozoic seas. We empirically derived a rate law, d N 2 O d t = 7.2 × 10 - 5 [ Fe 2 + ] 0.3 [ NO ] 1 , and measured an isotopic site preference of +16‰ for the reaction. Using this empirical rate law, and integrating across an oceanwide oxycline, we found that low nM NO and μM-low mM Fe²⁺ concentrations could have sustained a sea-air flux of 100-200 Tg N₂ O-N year^-1 , if N₂ fixation rates were near-modern and all fixed N₂ was emitted as N₂ O. A 1D photochemical model was used to obtain steady-state atmospheric N₂ O concentrations as a function of sea-air N₂ O flux across the wide range of possible pO₂ values (0.001-1 PAL). At 100-200 Tg N₂ O-N year^-1 and >0.1 PAL O₂ , this model yielded low-ppmv N₂ O, which would produce several degrees of greenhouse warming at 1.6 ppmv CH₄ and 320 ppmv CO₂ . These results suggest that enhanced N₂ O production in ferruginous seawater via a previously unconsidered chemodenitrification pathway may have helped to fill a Proterozoic "greenhouse gap," reconciling an ice-free Mesoproterozoic Earth with a less luminous early Sun. A particularly notable result was that high N₂ O fluxes at intermediate O₂ concentrations (0.01-0.1 PAL) would have enhanced ozone screening of solar UV radiation. Due to rapid photolysis in the absence of an ozone shield, N₂ O is unlikely to have been an important greenhouse gas if Mesoproterozoic O₂ was 0.001 PAL. At low O₂ , N₂ O might have played a more important role as life's primary terminal electron acceptor during the transition from an anoxic to oxic surface Earth, and correspondingly, from anaerobic to aerobic metabolisms.

Metabolic specialization of denitrifiers in permeable sediments controls N2 O emissions

Coastal oceans receive large amounts of anthropogenic fixed nitrogen (N), most of which is denitrified in the sediment before reaching the open ocean. Sandy sediments, which are common in coastal regions, seem to play an important role in catalysing this N-loss. Permeable sediments are characterized by advective porewater transport, which supplies high fluxes of organic matter into the sediment, but also leads to fluctuations in oxygen and nitrate concentrations. Little is known about how the denitrifying communities in these sediments are adapted to such fluctuations. Our combined results indicate that denitrification in eutrophied sandy sediments from the world's largest tidal flat system, the Wadden Sea, is carried out by different groups of microorganisms. This segregation leads to the formation of N₂ O which is advectively transported to the overlying waters and thereby emitted to the atmosphere. At the same time, the production of N₂ O within the sediment supports a subset of Flavobacteriia which appear to be specialized on N₂ O reduction. If the mechanisms shown here are active in other coastal zones, then denitrification in eutrophied sandy sediments may substantially contribute to current marine N₂ O emissions.

Genomic organization, gene expression and activity profile of Marinobacter hydrocarbonoclasticus denitrification enzymes

Background

Denitrification is one of the main pathways of the N-cycle, during which nitrate is converted to dinitrogen gas, in four consecutive reactions that are each catalyzed by a different metalloenzyme. One of the intermediate metabolites is nitrous oxide, which has a global warming impact greater then carbon dioxide and which atmospheric concentration has been increasing in the last years. The four denitrification enzymes have been isolated and biochemically characterized from Marinobacter hydrocarbonoclasticus in our lab.

Methods

Bioinformatic analysis of the M. hydrocarbonoclasticus genome to identify the genes involved in the denitrification pathway. The relative gene expression of the gene encoding the catalytic subunits of those enzymes was analyzed during the growth under microoxic conditions. The consumption of nitrate and nitrite, and the reduction of nitric oxide and nitrous oxide by whole-cells was monitored during anoxic and microoxic growth in the presence of 10 mM sodium nitrate at pH 7.5.

Results

The bioinformatic analysis shows that genes encoding the enzymes and accessory factors required for each step of the denitrification pathway are clustered together. An unusual feature is the co-existence of genes encoding a q- and a c-type nitric oxide reductase, with only the latter being transcribed at similar levels as the ones encoding the catalytic subunits of the other denitrifying enzymes, when cells are grown in the presence of nitrate under microoxic conditions. Using either a batch- or a closed system, nitrate is completely consumed in the beginning of the growth, with transient formation of nitrite, and whole-cells can reduce nitric oxide and nitrous oxide from mid-exponential phase until being collected (time-point 50 h).

Discussion

M. hydrocarbonoclasticus cells can reduce nitric and nitrous oxide in vivo, indicating that the four denitrification steps are active. Gene expression profile together with promoter regions analysis indicates the involvement of a cascade regulatory mechanism triggered by FNR-type in response to low oxygen tension, with nitric oxide and nitrate as secondary effectors, through DNR and NarXL, respectively. This global characterization of the denitrification pathway of a strict marine bacterium, contributes to the understanding of the N-cycle and nitrous oxide release in marine environments.

Nitrifying and Denitrifying Bacterial Communities in Advanced Nitrogen-Removal Onsite Wastewater Treatment Systems

Advanced N-removal onsite wastewater treatment systems (OWTS) rely on nitrification and denitrification to remove N from wastewater. Despite their use to reduce N contamination, we know little about microbial communities controlling N removal in these systems. We used quantitative polymerase chain reaction and high-throughput sequencing targeting nitrous oxide reductase () and bacterial ammonia monooxygenase () to determine the size, structure, and composition of communities containing these genes. We analyzed water samples from three advanced N-removal technologies in 38 systems in five towns in Rhode Island in August 2016, and in nine systems from one town in June, August, and October 2016. Abundance of ranged from 9.1 × 10 to 9 × 10 copies L and differed among technologies and over time, whereas bacterial abundance ranged from 0 to 1.9 × 10 copies L and was not different among technologies or over time. Richness and diversity of -but not -differed over time, with median Shannon diversity indices ranging from 2.61 in October to 4.53 in August. We observed weak community similarity patterns driven by geography and technology in The most abundant and containing bacteria were associated with water distribution and municipal wastewater treatment plants, such as and species. Our results show that communities in N-removal OWTS technologies differ slightly in terms of size and diversity as a function of time, but not geography, whereas communities are similar across time, technology, and geography. Furthermore, community composition appears to be stable across technologies, geography, and time for .

Response of the denitrifier community and its relationship with multiple N2O emission peaks after mature compost addition into dairy manure compost with forced aeration

Animal manure is a source of the greenhouse gas nitrous oxide (N₂O), therefore understanding the mechanisms underlying its production is essential for developing mitigating strategies and sustainable livestock production system. In this study, microbial communities potentially involved in multiple emission peaks during initial stage of laboratory-scale dairy manure composting with forced aeration system were investigated. Mature compost was used for the bulking agent. Change of overall bacterial community and nitrification-denitrification gene abundance were monitored by using 16S rRNA gene amoA, nirS, nirK or nosZ genes, respectively. Three N₂O emission peaks were observed when the temperature reached at 45, 60 and 72 °C, at the same timing of oxygen consumption peaks. The maximum N₂O emission peak was 3.86 mg h^-1 kg^-1 TS when the temperature reached at 60 °C. The shift of bacterial community among these experimental periods was significant, orders Flavobacteriales, Burkholderiales and Xanthomonadales increased, while orders belong to Bacillales, Lactobacillales, Clostridiales and Bacteroidales decreased. In addition, abundance of two denitrification genes (nirS and nosZ) significantly increased during this period. Clone library analysis of these genes showed that significantly increased sequences belonged to Pseudomonas-like clusters for both genes, indicates that denitrifiers possesses these genes are involved for these N₂O emission peaks caused by mature compost addition.

Treated and untreated wastewater effluents alter river sediment bacterial communities involved in nitrogen and sulphur cycling

Studying the dynamics of nitrogen and sulphur cycling bacteria in river surface sediments is essential to better understand their contribution to global biogeochemical cycles. Evaporitic rocks settled at the headwater of the Deba River catchment (northern Spain) lead to high values of sulphate concentration in its waters. Besides, the discharge of effluents from untreated and treated residual (urban and industrial) wastewaters increases the concentration of metals, nutrients and organic compounds in its mid- and low-water courses. The aim of this study was to assess the impact of anthropogenic contamination from untreated and treated residual and industrial wastewaters on the structure and function of bacterial communities present in surface sediments of the Deba River catchment. The application of a quantitative functional approach (qPCR) based on denitrification genes (nir: nirS+nirK; and nosZ), together with a 16S rRNA gene metabarcoding structural analysis, revealed (i) the high relevance of the sulphur cycle at headwater surface sediments (as reflected by the abundance of members of the Syntrophobacterales order, and the Sulfuricurvum and Thiobacillus genera) and (ii) the predominance of sulphide-driven autotrophic denitrification over heterotrophic denitrification. Incomplete heterotrophic denitrification appeared to be predominant in surface sediments strongly impacted by treated and untreated effluents, as reflected by the lower values of the nosZ/nir ratio, thus favouring N₂O emissions. Understanding nitrogen and sulphur cycling pathways has profound implications for the management of river ecosystems, since this knowledge can help us determine whether a specific river is acting or not as a source of greenhouse gases (i.e., N₂O).

Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States

The North American prairie covered about 3.6 million-km2 of the continent prior to European contact. Only 1-2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis. At the Wisconsin site, we also sampled adjacent restored prairie and switchgrass plots. We found that agricultural practices drove differences in community composition and diversity across the transect. Microbial biomass in prairie samples was twice that of cultivated soils, but alpha diversity was higher with cultivation. Metagenome analyses revealed denitrification and starch degradation genes were abundant across all soils, as were core genes involved in response to osmotic stress, resource transport, and environmental sensing. Together, these data indicate that cultivation shifted the microbiome in consistent ways across different regions of the prairie, but also suggest that many functions are resilient to changes caused by land management practices - perhaps reflecting adaptations to conditions common to tallgrass prairie soils in the region (e.g., soil type, parent material, development under grasses, temperature and rainfall patterns, and annual freeze-thaw cycles). These findings are important for understanding the long-term consequences of land management practices to prairie soil microbial communities and their genetic potential to carry out key functions.

Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake

Oxygen-stratified lakes are typical for the boreal zone and also a major source of greenhouse gas emissions in the region. Due to shallow light penetration, restricting the growth of phototrophic organisms, and large allochthonous organic carbon inputs from the catchment area, the lake metabolism is expected to be dominated by heterotrophic organisms. In this study, we test this assumption and show that the potential for autotrophic carbon fixation and internal carbon cycling is high throughout the water column. Further, we show that during the summer stratification carbon fixation can exceed respiration in a boreal lake even below the euphotic zone. Metagenome-assembled genomes and 16S profiling of a vertical transect of the lake revealed multiple organisms in an oxygen-depleted compartment belonging to novel or poorly characterized phyla. Many of these organisms were chemolithotrophic, potentially deriving their energy from reactions related to sulfur, iron, and nitrogen transformations. The community, as well as the functions, was stratified along the redox gradient. The autotrophic potential in the lake metagenome below the oxygenic zone was high, pointing toward a need for revising our concepts of internal carbon cycling in boreal lakes. Further, the importance of chemolithoautotrophy for the internal carbon cycling suggests that many predicted climate change-associated fluctuations in the physical properties of the lake, such as altered mixing patterns, likely have consequences for the whole-lake metabolism even beyond the impact to the phototrophic community.

Autotrophic organisms at the base of the food web are the only life form capable of turning inorganic carbon into the organic form, facilitating the survival of all other organisms. In certain environments, the autotrophic production is limited by environmental conditions and the food web is supported by external carbon inputs. One such environment is stratified boreal lakes, which are one of the biggest natural sources of greenhouse gas emissions in the boreal region. Thus, carbon cycling in these habitats is of utmost importance for the future climate. Here, we demonstrate a high potential for internal carbon cycling via phototrophic and novel chemolithotrophic organisms in the anoxic, poorly illuminated layers of a boreal lake. Our results significantly increase our knowledge on the microbial communities and their metabolic potential in oxygen-depleted freshwaters and help to understand and predict how climate change-induced alterations could impact the lake carbon dynamics.

Expression of nirK and nirS genes in two strains of Pseudomonas stutzeri harbouring both types of NO-forming nitrite reductases

Reduction of nitrite to nitric oxide in denitrification is catalysed by two different nitrite reductases, encoded by nirS or nirK. Long considered mutually exclusive and functionally redundant in denitrifying bacteria, we show expression of both genes co-occurring in Pseudomonas stutzeri. The differential expression patterns between strain AN10 and JM300 in relation to oxygen and nitrate and their different denitrification phenotypes, with AN10 reducing nitrate more rapidly and accumulating nitrite, suggest that nirS and nirK can have different roles. Dissimilar gene arrangements and transcription factors in the nir gene neighbourhoods could explain the observed differences in gene expression and denitrification activity.

Biokinetic Characterization and Activities of N2O-Reducing Bacteria in Response to Various Oxygen Levels

Nitrous oxide (N₂O)-reducing bacteria, which reduce N₂O to nitrogen in the absence of oxygen, are phylogenetically spread throughout various taxa and have a potential role as N₂O sinks in the environment. However, research on their physiological traits has been limited. In particular, their activities under microaerophilic and aerobic conditions, which severely inhibit N₂O reduction, remain poorly understood. We used an O₂ and N₂O micro-respirometric system to compare the N₂O reduction kinetics of four strains, i.e., two strains of an Azospira sp., harboring clade II type nosZ, and Pseudomonas stutzeri and Paracoccus denitrificans, harboring clade I type nosZ, in the presence and absence of oxygen. In the absence of oxygen, the highest N₂O-reducing activity, V_m,N2O, was 5.80 ± 1.78 × 10^-3 pmol/h/cell of Azospira sp. I13, and the highest and lowest half-saturation constants were 34.8 ± 10.2 μM for Pa. denitirificans and 0.866 ± 0.29 μM for Azospira sp. I09. Only Azospira sp. I09 showed N₂O-reducing activity under microaerophilic conditions at oxygen concentrations below 110 μM, although the activity was low (10% of V_m,N2O). This trait is represented by the higher O₂ inhibition coefficient than those of the other strains. The activation rates of N₂O reductase, which describe the resilience of the N₂O reduction activity after O₂ exposure, differ for the two strains of Azospira sp. (0.319 ± 0.028 h^-1 for strain I09 and 0.397 ± 0.064 h^-1 for strain I13) and Ps. stutzeri (0.200 ± 0.013 h^-1), suggesting that Azospira sp. has a potential for rapid recovery of N₂O reduction and tolerance against O₂ inhibition. These physiological characteristics of Azospira sp. can be of promise for mitigation of N₂O emission in industrial applications.

Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys

At hydrothermal vent sites, chimneys consisting of sulfides, sulfates, and oxides are formed upon contact of reduced hydrothermal fluids with oxygenated seawater. The walls and surfaces of these chimneys are an important habitat for vent-associated microorganisms. We used community proteogenomics to investigate and compare the composition, metabolic potential and relative in situ protein abundance of microbial communities colonizing two actively venting hydrothermal chimneys from the Manus Basin back-arc spreading center (Papua New Guinea). We identified overlaps in the in situ functional profiles of both chimneys, despite differences in microbial community composition and venting regime. Carbon fixation on both chimneys seems to have been primarily mediated through the reverse tricarboxylic acid cycle and fueled by sulfur-oxidation, while the abundant metabolic potential for hydrogen oxidation and carbon fixation via the Calvin–Benson–Bassham cycle was hardly utilized. Notably, the highly diverse microbial community colonizing the analyzed black smoker chimney had a highly redundant metabolic potential. In contrast, the considerably less diverse community colonizing the diffusely venting chimney displayed a higher metabolic versatility. An increased diversity on the phylogenetic level is thus not directly linked to an increased metabolic diversity in microbial communities that colonize hydrothermal chimneys.

Urea Amendment Decreases Microbial Diversity and Selects for Specific Nitrifying Strains in Eight Contrasting Agricultural Soils

Application of nitrogen (N) fertilizers, predominantly as urea, is a major source of reactive N in the environment, with wide ranging effects including increased greenhouse gas accumulation in the atmosphere and aquatic eutrophication. The soil microbial community is the principal driver of soil N cycling; thus, improved understanding of microbial community responses to urea addition has widespread implications. We used next-generation amplicon sequencing of the 16S rRNA gene to characterize bacterial and archaeal communities in eight contrasting agricultural soil types amended with 0, 100, or 500 μg N g^-1 of urea and incubated for 21 days. We hypothesized that urea amendment would have common, direct effects on the abundance and diversity of members of the microbial community associated with nitrification, across all soils, and would further affect the broader heterotrophic community resulting in decreased diversity and variation in abundances of specific taxa. Significant (P < 0.001) differences in bacterial community diversity and composition were observed by site, but amendment with only the greatest urea concentration significantly decreased Shannon indices. Expansion in the abundances of members of the families Microbacteriaceae, Chitinophagaceae, Comamonadaceae, Xanthomonadaceae, and Nitrosomonadaceae were also consistently observed among all soils (linear discriminant analysis score ≥ 3.0). Analysis of nitrifier genera revealed diverse, soil-specific distributions of oligotypes (strains), but few were correlated with nitrification gene abundances that were reported in a previous study. Our results suggest that the majority of the bacterial and archaeal community are likely unassociated with N cycling, but are significantly negatively impacted by urea application. Furthermore, these results reveal that amendment with high concentrations of urea may reduce nitrifier diversity, favoring specific strains, specifically those within the nitrifying genera Nitrobacter, Nitrospira, and Nitrosospira, that may play significant roles related to N cycling in soils receiving intensive urea inputs.

Nitrogen-rich organic soils under warm well-drained conditions are global nitrous oxide emission hotspots

Nitrous oxide (N₂O) is a powerful greenhouse gas and the main driver of stratospheric ozone depletion. Since soils are the largest source of N₂O, predicting soil response to changes in climate or land use is central to understanding and managing N₂O. Here we find that N₂O flux can be predicted by models incorporating soil nitrate concentration (NO₃⁻), water content and temperature using a global field survey of N₂O emissions and potential driving factors across a wide range of organic soils. N₂O emissions increase with NO₃⁻ and follow a bell-shaped distribution with water content. Combining the two functions explains 72% of N₂O emission from all organic soils. Above 5 mg NO₃⁻-N kg⁻¹, either draining wet soils or irrigating well-drained soils increases N₂O emission by orders of magnitude. As soil temperature together with NO₃⁻ explains 69% of N₂O emission, tropical wetlands should be a priority for N₂O management.

In a global field survey across a wide range of organic soils, the authors find that N₂O flux can be predicted by models incorporating soil nitrate concentration (NO₃^–), water content and temperature. N₂O emission increases with NO₃^– and temperature and follows a bell-shaped distribution with water content.

Community Composition of Nitrous Oxide-Related Genes in Salt Marsh Sediments Exposed to Nitrogen Enrichment

Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated profiles of microbial communities and communities of micro-organisms containing specific nitrogen cycling genes that encode several enzymes (amoA, norB, nosZ) related to nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms involved in the production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that previously measured rates of nitrous oxide production and consumption are likely the result of changes in community structure, not simply changes in microbial activity.

Enhancement of microbial nitrogen removal pathway by vegetation in Integrated Vertical-Flow Constructed Wetlands (IVCWs) for treating reclaimed water

Constructed wetland is an efficient way to lower N load from wastewater treatment plants. Here, the nitrogen removal rate and nitrogen balance, as well as the microbial community structure in IVCWs planted with different vegetation for treating reclaimed water were investigated. The results showed that IVCWs planted with vegetation generally achieved a higher TN removal rate than unplanted treatment, especially for Canna indica L. with 10.35% enhancement. Moreover, the microbial process proportion (83.87-87.94%) is the main N removal pathway in IVCW, and vegetation planting could increase 8.16% of it in average. The combination of quantitative polymerase chain reaction (qPCR) and high-throughput sequencing analysis revealed that IVCW planted with Canna indica L. showed the highest microbial abundant and biodiversity. The related denitrification genus Pseudomonas, Acinetobacter, Rhizobium, Bacillus and Rhodopseudomonas might be responsible for the high biological removal rate of nitrogen.

Isotope and microbiome data provide complementary information to identify natural nitrate attenuation processes in groundwater

Natural attenuation processes alleviate the impact of fertilization practices on groundwater resources. Therefore, identifying the occurrence of denitrification has become a requirement for water quality management. Several approaches are useful for this purpose, such as isotopic and microbiological methods, each of them providing distinct but complementary information about denitrification reactions, attenuation rates and their occurrence in the aquifer. In this paper, we investigate the contribution of both approaches to describe denitrification in a consolidated rock aquifer (limestone and marls), with a porosity related to fracture networks located in the northeastern sector of the Osona basin (NE Spain). Isotopic methods indicated the origin of nitrate (fertilization using manure) and that denitrification occurred, reaching a reduction of near 25% of the nitrate mass in groundwater. The studied area could be divided in two zones with distinct agricultural pressures and, consequently, nitrate concentrations in groundwater. Denitrification occurred in both zones and at different levels, indicating that attenuation processes took place all along the whole hydrogeological unit, and that the observed levels could be attributed to a larger flow path or, in a minor extent, to mixing processes that mask the actual denitrification rates. Microbiological data showed a correlation between denitrifier genes and the isotopic composition. However, the groundwater microbiome and the distribution of denitrifying bacteria did not reveal a major influence on the denitrification level observed by isotopic methods. This focuses the interest of microbiological analysis to identify functional genes within the bacteria present in the aquifer. Results indicated that isotopic methods provide information of the overall denitrification ability of the hydrogeological unit, and that genomic data represent the processes actually acting nearby the well. A combination of both approaches is advised to support induced in situ attenuation actions in polluted sites.

Nitrous oxide emission and denitrifier communities in drip-irrigated calcareous soil as affected by chemical and organic fertilizers

The effects of consecutive application of chemical fertilizer with or without organic fertilizer on soil N₂O emissions and denitrifying community structure in a drip-irrigated field were determined. The four fertilizer treatments were (i) unfertilized, (ii) chemical fertilizer, (iii) 60% chemical fertilizer plus cattle manure, and (iv) 60% chemical fertilizer plus biofertilizer. The treatments with organic amendments (i.e. cattle manure and biofertilizer) reduced cumulative N₂O emissions by 4.9-9.9%, reduced the N₂O emission factor by 1.3-42%, and increased denitrifying enzyme activities by 14.3-56.2%. The nirK gene copy numbers were greatest in soil which received only chemical fertilizer. In contrast, nirS- and nosZ-copy numbers were greatest in soil amended with chemical fertilizer plus biofertilizer. Chemical fertilizer application with or without organic fertilizer significantly changed the community structure of nirK-type denitrifiers relative to the unfertilized soil. In comparison, the nirS- and nosZ-type denitrifier genotypes varied in treatments receiving organic fertilizer but not chemical fertilizer alone. The changes in the denitrifier communities were closely associated with soil organic carbon (SOC), NO₃^-, NH₄⁺, water holding capacity, and soil pH. Modeling indicated that N₂O emissions in this soil were primarily associated with the abundance of nirS type denitrifying bacteria, SOC, and NO₃^-. Overall, our findings indicate that (i) the organic fertilizers increased denitrifying enzyme activity, increased denitrifying-bacteria gene copy numbers, but reduced N₂O emissions, and (ii) nirS- and nosZ-type denitrifiers were more sensitive than nirK-type denitrifiers to the organic fertilizers.

Seasonality distribution of the abundance and activity of nitrification and denitrification microorganisms in sediments of surface flow constructed wetlands planted with Myriophyllum elatinoides during swine wastewater treatment

Surface flow constructed wetlands (SFCWs) planted with Myriophyllum elatinoides for treatment of swine wastewater were examined to evaluate the effect of season, segment (site S1, S2, and S3), and treatment (100mgL^-1 TN, T1; 300mgL^-1 TN, T2; 500mgL^-1 TN, T3) on the activity, and abundances of nitrifying and, denitrifying microorganisms, and on the abundance of sediment bacteria. The activity and abundances of nitrifiers, denitrifiers, and the abundance of bacteria were the highest in T3 samples, especially in S1 (P<0.05). The potential nitrification rate (PNR) was highest in the summer and potential denitrification rate (PDR) showed an increasing trend over seasons. The abundance of ammonia-oxidizing bacteria (AOB) was strongly correlated with PNR, while abundance of denitrifying gene (nirK) was strongly correlated with PDR. These results indicate that M. elatinoides SFCWs for swine wastewater treatment stimulate the growth of nitrifiers, denitrifiers and bacteria in sediments.

Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone

Microbial communities in marine oxygen deficient zones (ODZs) are responsible for up to half of marine N loss through conversion of nutrients to N2O and N2. This N loss is accomplished by a consortium of diverse microbes, many of which remain uncultured. Here, we characterize genes for all steps in the anoxic N cycle in metagenomes from the water column and >30 μm particles from the Eastern Tropical North Pacific (ETNP) ODZ. We use an approach that allows for both phylogenetic identification and semi-quantitative assessment of gene abundances from individual organisms, and place these results in context of chemical measurements and rate data from the same location. Denitrification genes were enriched in >30 μm particles, even in the oxycline, while anammox bacteria were not abundant on particles. Many steps in denitrification were encoded by multiple phylotypes with different distributions. Notably three N2O reductases (nosZ), each with no cultured relative, inhabited distinct niches; one was free-living, one dominant on particles and one had a C terminal extension found in autotrophic S-oxidizing bacteria. At some depths >30% of the community possessed nitrite reductase nirK. A nirK OTU linked to SAR11 explained much of this abundance. The only bacterial gene found for NO reduction to N2O in the ODZ was a form of qnorB related to the previously postulated "nitric oxide dismutase," hypothesized to produce N2 directly while oxidizing methane. However, similar qnorB-like genes are also found in the published genomes of many bacteria that do not oxidize methane, and here the qnorB-like genes did not correlate with the presence of methane oxidation genes. Correlations with N2O concentrations indicate that these qnorB-like genes likely facilitate NO reduction to N2O in the ODZ. In the oxycline, qnorB-like genes were not detected in the water column, and estimated N2O production rates from ammonia oxidation were insufficient to support the observed oxycline N2O maximum. However, both qnorB-like and nosZ genes were present within particles in the oxycline, suggesting a particulate source of N2O and N2. Together, our analyses provide a holistic view of the diverse players in the low oxygen nitrogen cycle.

Field-Scale Pattern of Denitrifying Microorganisms and N2O Emission Rates Indicate a High Potential for Complete Denitrification in an Agriculturally Used Organic Soil

More than 50% of all anthropogenic N₂O emissions come from the soil. Drained Histosols that are used for agricultural purposes are particularly potent sources of denitrification due to higher stocks of organic matter and fertiliser application. However, conditions that favour denitrification can vary considerably across a field and change significantly throughout the year. Spatial and temporal denitrifier dynamics were assessed in a drained, intensely managed Histosol by focusing on the genetic nitrite and N₂O reduction potential derived from the abundance of nirK, nirS and nosZ genes. These data were correlated with soil properties at two different points in time in 2013. N₂O emissions were measured every 2 weeks over three vegetation periods (2012-2014). Very low N₂O emission rates were measured throughout the entire period of investigation in accordance with the geostatistical data that revealed an abundance of microbes carrying the N₂O reductase gene nosZ. This, along with neutral soil pH values, is indicative of high microbial denitrification potential. While the distribution of the microbial communities was strongly influenced by total organic carbon and nitrogen pools in March, the spatial distribution pattern was not related to the distribution of soil properties in October, when higher nutrient availability was observed. Different nitrite reducer groups prevailed in spring and autumn. While nirS, followed by nosZ and nirK, was most abundant in March, the latter was the dominant nitrite reductase in October.

Counter-diffusion biofilms have lower N2O emissions than co-diffusion biofilms during simultaneous nitrification and denitrification: Insights from depth-profile analysis

The goal of this study was to investigate the effectiveness of a membrane-aerated biofilm reactor (MABR), a representative of counter-current substrate diffusion geometry, in mitigating nitrous oxide (N₂O) emission. Two laboratory-scale reactors with the same dimensions but distinct biofilm geometries, i.e., a MABR and a conventional biofilm reactor (CBR) employing co-current substrate diffusion geometry, were operated to determine depth profiles of dissolved oxygen (DO), nitrous oxide (N₂O), functional gene abundance and microbial community structure. Surficial nitrogen removal rate was slightly higher in the MABR (11.0 ± 0.80 g-N/(m² day) than in the CBR (9.71 ± 0.94 g-N/(m² day), while total organic carbon removal efficiencies were comparable (96.9 ± 1.0% for MABR and 98.0 ± 0.8% for CBR). In stark contrast, the dissolved N₂O concentration in the MABR was two orders of magnitude lower (0.011 ± 0.001 mg N₂O-N/L) than that in the CBR (1.38 ± 0.25 mg N₂O-N/L), resulting in distinct N₂O emission factors (0.0058 ± 0.0005% in the MABR vs. 0.72 ± 0.13% in the CBR). Analysis on local net N₂O production and consumption rates unveiled that zones for N₂O production and consumption were adjacent in the MABR biofilm. Real-time quantitative PCR indicated higher abundance of denitrifying genes, especially nitrous oxide reductase (nosZ) genes, in the MABR versus the CBR. Analyses of the microbial community composition via 16S rRNA gene amplicon sequencing revealed the abundant presence of the genera Thauera (31.2 ± 11%), Rhizobium (10.9 ± 6.6%), Stenotrophomonas (6.8 ± 2.7%), Sphingobacteria (3.2 ± 1.1%) and Brevundimonas (2.5 ± 1.0%) as potential N₂O-reducing bacteria in the MABR.

Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing

A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA gene amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly.IMPORTANCE Through highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection and enrichment of specific organisms. Additionally, we provide a method for estimating the number of cultivable units of each OTU in the original sample through the MPN approach.

Design and Feasibility Analysis of a Self-Sustaining Biofiltration System for Removal of Low Concentration N2O Emitted from Wastewater Treatment Plants

N₂O is a potent greenhouse gas and ozone-depletion agent. In this study, a biofiltration system was designed for removal of N₂O emitted at low concentrations (<200 ppmv) from wastewater treatment plants. The proposed biofiltration system utilizes untreated wastewater from the primary sedimentation basin as the source of electron donor and nutrients and energy requirement is minimized by utilizing gravitational force and pressure differential to direct liquid medium and gas through the biofilter. The experiments performed with laboratory-scale biofilter in two different configurations confirmed the feasibility of the biofiltration system. The biofilter operated with cycling of raw wastewater exhibited up to 94% and 53% removal efficiency with 100 ppmv N₂O in N₂ and air, respectively, as the feed gas, corroborating that untreated wastewater can serve as a robust source of electron donor and nutrients. The laboratory-scale biofilter operated with a continuous flow-through of synthetic wastewater attained >99.9% removal of N₂O from N₂ background at the gas flow rate up to 2,000 mL·min^-1 and >50% N₂O removal from air background at the gas flow rate of 200 mL·min^-1. nosZ-containing bacterial genera including Flavobacterium (5.92%), Pseudomonas (4.26%) and Bosea (2.39%) were identified in the biofilm samples collected from the oxic biofilter, indicating these organisms were responsible for N₂O removal.

Potential for aerobic NO2- reduction and corresponding key enzyme genes involved in Alcaligenes faecalis strain NR

The potential for aerobic NO₂^- removal by Alcaligenes faecalis strain NR was investigated. 35 mg/L of NO₂^--N was removed by strain NR under aerobic conditions in the presence of NH₄⁺. ¹⁵N-labeling experiment demonstrated that N₂O and N₂ were possible products during the aerobic nitrite removal process by strain NR. The key enzyme genes of nirK, norB and nosZ, which regulate the aerobic nitrite denitrification process, were successfully amplified from strain NR. The gene sequence analysis indicates that copper-containing nitrite reductase (NIRK) and periplasmic nitrous oxide reductase (NOSZ) were both hydrophilic protein and the transmembrane structures were absent, while nitric oxide reductase large subunit (NORB) was a hydrophobic and transmembrane protein. According to the three-dimensional structure and binding site analysis, the bulky and hydrophobic methionine residue proximity to the nitrite binding sites of NIRK was speculated to be related to the oxygen tolerance of NIRK from strain NR.

Use of oxygen isotopes to differentiate between nitrous oxide produced by fungi or bacteria during denitrification

RATIONALE

Fungal denitrifiers can contribute substantially to N₂ O emissions from arable soil and show a distinct site preference for N₂ O (SP(N₂ O)). This study sought to identify another process-specific isotopic tool to improve precise identification of N₂ O of fungal origin by mass spectrometric analysis of the N₂ O produced.

METHODS

Three pure bacterial and three fungal species were incubated under denitrifying conditions in treatments with natural abundance and stable isotope labelling to analyse the N₂ O produced. Combining different applications of isotope ratio mass spectrometry enabled us to estimate the oxygen (O) exchange accelerated by denitrifying enzymes and the ongoing microbial pathway in parallel. This experimental set-up allowed the determination of δ¹⁸ O(N₂ O) values and isotopic fractionation of O, as well as SP(N₂ O) values, as a perspective to differentiate between microbial denitrifiers.

RESULTS

Oxygen exchange during N₂ O production was lower for bacteria than for fungi, differed between species, and depended also on incubation time. Apparent O isotopic fractionation during denitrification was in a similar range for bacteria and fungi, but application of the fractionation model indicated that different enzymes in bacteria and fungi were responsible for O exchange. This difference was associated with different isotopic fractionation for bacteria and fungi.

CONCLUSIONS

δ¹⁸ O(N₂ O) values depend on isotopic fractionation and isotopic fractionation may differ between processes and organism groups. By comparing SP(N₂ O) values, O exchange and the isotopic signature of precursors, we propose here a novel tool for differentiating between different sources of N₂ O.

Genomics and Ecology of Novel N2O-Reducing Microorganisms

Microorganisms with the capacity to reduce the greenhouse gas nitrous oxide (N₂O) to harmless dinitrogen gas are receiving increased attention due to increasing N₂O emissions (and our need to mitigate climate change) and to recent discoveries of novel N₂O-reducing bacteria and archaea. The diversity of denitrifying and nondenitrifying microorganisms with capacity for N₂O reduction was recently shown to be greater than previously expected. A formerly overlooked group (clade II) in the environment include a large fraction of nondenitrifying N₂O reducers, which could be N₂O sinks without major contribution to N₂O formation. We review the recent advances about fundamental understanding of the genomics, physiology, and ecology of N₂O reducers and the importance of these findings for curbing N₂O emissions.

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

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

Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment

Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.

Microbial community shift in a suspended stuffing biological reactor with pre-attached aerobic denitrifier

Bioaugmentation is substantially determined by pre-attached communities in biological stuffing systems. However, the inevitable changes of microbial community shift occurred between pre-attached microorganisms on stuffing material and other existing communities in wastewater. Targeting at nitrogen removal in aerobic denitrification reactors, biological augmentation was built by polyurethane supporting material and aerobic denitrification bacteria of Pseudomonas stutzeri strains were primarily colonized. The total nitrogen removal reached a high efficiency of 77 ± 6%, resulting from a relative high nitrate removal (90%) and a low nitrite production of 24 mg l^-1. The nitrate removal was kept 10% higher using preattached strains than that using wastewater communities. During the bioaugmentation process, abundant bacteria related to nitrogen removal were evolutively enriched to compete with preattached Pseudomonas stutzeri. The most abundant bacteria growing up in the biofilm belonged to various Classes of Proteobacteria Phylum. A noticeable nitrite production with a relative low TN removal efficiency occurred when Brucella sp. and Brevundimonas sp. were simultaneously enriched in place of Pseudomonas, because Brevundimonas also accumulated nitrite during denitrification under an aerobic condition. The results indicated that pre-attached denitrifiers in comprehensive communities on stuffing material can be established for the efficient nitrogen and COD removal in aerobic denitrification reactors.

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.

Pelagic and benthic communities of the Antarctic ecosystem of Potter Cove: Genomics and ecological implications

Molecular technologies are more frequently applied in Antarctic ecosystem research and the growing amount of sequence-based information available in databases adds a new dimension to understanding the response of Antarctic organisms and communities to environmental change. We apply molecular techniques, including fingerprinting, and amplicon and metagenome sequencing, to understand biodiversity and phylogeography to resolve adaptive processes in an Antarctic coastal ecosystem from microbial to macrobenthic organisms and communities. Interpretation of the molecular data is not only achieved by their combination with classical methods (pigment analyses or microscopy), but furthermore by combining molecular with environmental data (e.g., sediment characteristics, biogeochemistry or oceanography) in space and over time. The studies form part of a long-term ecosystem investigation in Potter Cove on King-George Island, Antarctica, in which we follow the effects of rapid retreat of the local glacier on the cove ecosystem. We formulate and encourage new approaches to integrate molecular tools into Antarctic ecosystem research, environmental conservation actions, and polar ocean observatories.

Distinct distribution patterns of proteobacterial nirK- and nirS-type denitrifiers in the Yellow River estuary, China

Denitrification is considered to be the critical process in removing reactive nitrogen in estuarine ecosystems. In the present study, the abundance, diversity, and community structure of nirK- and nirS-type denitrifiers were compared in sediments from the Yellow River estuary. Quantitative polymerase chain reaction showed that the 2 types of denitrifiers exhibited different distribution patterns among the samples, indicating their distinct habitat preference. Phylogenetic analysis revealed that most of the sequences from clusters I, III, IV, and V for nirK-type denitrifiers were dominant and were distributed at sites where dissolved oxygen (DO) was lower, and the sequences in the other clusters were dominant at sites with higher DO. However, there was no spatially heterogeneous distribution for the nirS-type denitrifier community. Canonical correlation analysis and correlation analysis demonstrated that the community structure of nirK was more responsive to environmental factors than was that of nirS. Inversely, the abundance and α-diversity targeting nirS gene could be more easily influenced by environmental parameters. These findings can extend our current knowledge about the distribution patterns of denitrifying bacteria and provide a basic theoretical reference for the dynamics of denitrifying communities in estuarine ecosystem of China.

Identification of the autotrophic denitrifying community in nitrate removal reactors by DNA-stable isotope probing

Autotrophic denitrification has attracted increasing attention for wastewater with insufficient organic carbon sources. Nevertheless, in situ identification of autotrophic denitrifying communities in reactors remains challenging. Here, a process combining micro-electrolysis and autotrophic denitrification with high nitrate removal efficiency was presented. Two batch reactors were fed organic-free nitrate influent, with H¹³CO₃^- and H¹²CO₃^- as inorganic carbon sources. DNA-based stable-isotope probing (DNA-SIP) was used to obtain molecular evidence for autotrophic denitrifying communities. The results showed that the nirS gene was strongly labeled by H¹³CO₃^-, demonstrating that the inorganic carbon source was assimilated by autotrophic denitrifiers. High-throughput sequencing and clone library analysis identified Thiobacillus-like bacteria as the most dominant autotrophic denitrifiers. However, 88% of nirS genes cloned from the ¹³C-labeled "heavy" DNA fraction showed low similarity with all culturable denitrifiers. These findings provided functional and taxonomical identification of autotrophic denitrifying communities, facilitating application of autotrophic denitrification process for wastewater treatment.

Spatiotemporal Characterization of San Francisco Bay Denitrifying Communities: a Comparison of nirK and nirS Diversity and Abundance

Denitrifying bacteria play a critical role in the estuarine nitrogen cycle. Through the transformation of nitrate into nitrogen gas, these organisms contribute to the loss of bioavailable (i.e., fixed) nitrogen from low-oxygen environments such as estuary sediments. Denitrifiers have been shown to vary in abundance and diversity across the spatial environmental gradients that characterize estuaries, such as salinity and nitrogen availability; however, little is known about how their communities change in response to temporal changes in those environmental properties. Here, we present a 1-year survey of sediment denitrifier communities along the estuarine salinity gradient of San Francisco Bay. We used quantitative PCR and sequencing of functional genes coding for a key denitrifying enzyme, dissimilatory nitrite reductase, to compare two groups of denitrifiers: those with nirK (encoding copper-dependent nitrite reductase) and those with nirS (encoding the cytochrome-cd ₁-dependent variant). We found that nirS was consistently more abundant and more diverse than nirK in all parts of the estuary. The abundances of the two genes were tightly linked across space but differed temporally, with nirK peaking when temperature was low and nirS peaking when nitrate was high. Likewise, the diversity and composition of nirK- versus nirS-type communities differed in their responses to seasonal variations, though both were strongly determined by site. Furthermore, our sequence libraries detected deeply branching clades with no cultured isolates, evidence of enormous diversity within the denitrifiers that remains to be explored.

Kinetics and gene diversity of denitrifying biocathode in biological electrochemical systems

Biocathodic nitrogen degradation kinetics match Monod model and Pseudomonas play an important role on denitrification biocathodes with different nitrogen substrates.

Design and evaluation of primers targeting genes encoding NO-forming nitrite reductases: implications for ecological inference of denitrifying communities

The detection of NO-forming nitrite reductase genes (nir) has become the standard when studying denitrifying communities in the environment, despite well-known amplification biases in available primers. We review the performance of 35 published and 121 newly designed primers targeting the nirS and nirK genes, against sequences from complete genomes and 47 metagenomes from three major habitats where denitrification is important. There were no optimal universal primer pairs for either gene, although published primers targeting nirS displayed up to 75% coverage. The alternative is clade-specific primers, which show a trade-off between coverage and specificity. The test against metagenomic datasets showed a distinct performance of primers across habitats. The implications of clade-specific nir primers choice and their performance for ecological inference when used for quantitative estimates and in sequenced-based community ecology studies are discussed and our phylogenomic primer evaluation can be used as a reference along with their environmental specificity as a guide for primer selection. Based on our results, we also propose a general framework for primer evaluation that emphasizes the testing of coverage and phylogenetic range using full-length sequences from complete genomes, as well as accounting for environmental range using metagenomes. This framework serves as a guideline to simplify primer performance comparisons while explicitly addressing the limitations and biases of the primers evaluated.