Insight into the effects of regulating denitrification on composting: Strategies to simultaneously reduce environmental pollution risk and promote aromatic humic substance formation

Denitrification during composting is a hidden danger that causes environmental pollution risk and aromatic humic substance damage, which needs to be better regulate urgently. In this study, two denitrification regulation methods, moisture and biochar amendment, were conducted during chicken manure composting. Denitrification performance data showed two regulation methods obviously reduced NO₃^--N, NO₂^--N and N₂ contents. Humic substance increased by 25.3 % and 29.1 % under two regulations. Microbiological analysis indicated that two regulation methods could decreasing denitrifying functional microbes with aroma degradation capability. Subsequently, denitrification gene narG, nirS, nosZ were significantly inhibited (p < 0.05) and the aromatic degradation metabolism pathways were down-regulated. Correlation analysis further revealed the important influence of interspecific interactions and non-biological characteristics on functional microbes. These results provided important scientific basis to denitrification regulation in the practice of composting, which achieved the purpose of simultaneously controlling environmental pollution risk and conducing end-product formation.

Giant sulfur bacteria (Beggiatoaceae) from sediments underlying the Benguela upwelling system host diverse microbiomes

Due to their lithotrophic metabolisms, morphological complexity and conspicuous appearance, members of the Beggiatoaceae have been extensively studied for more than 100 years. These bacteria are known to be primarily sulfur-oxidizing autotrophs that commonly occur in dense mats at redox interfaces. Their large size and the presence of a mucous sheath allows these cells to serve as sites of attachment for communities of other microorganisms. But little is known about their individual niche preferences and attached microbiomes, particularly in marine environments, due to a paucity of cultivars and their prevalence in habitats that are difficult to access and study. Therefore, in this study, we compare Beggiatoaceae strain composition, community composition, and geochemical profiles collected from sulfidic sediments at four marine stations off the coast of Namibia. To elucidate community members that were directly attached and enriched in both filamentous Beggiatoaceae, namely Ca. Marithioploca spp. and Ca. Maribeggiatoa spp., as well as non-filamentous Beggiatoaceae, Ca. Thiomargarita spp., the Beggiatoaceae were pooled by morphotype for community analysis. The Beggiatoaceae samples collected from a highly sulfidic site were enriched in strains of sulfur-oxidizing Campylobacterota, that may promote a more hospitable setting for the Beggiatoaceae, which are known to have a lower tolerance for high sulfide to oxygen ratios. We found just a few host-specific associations with the motile filamentous morphotypes. Conversely, we detected 123 host specific enrichments with non-motile chain forming Beggiatoaceae. Potential metabolisms of the enriched strains include fermentation of host sheath material, syntrophic exchange of H₂ and acetate, inorganic sulfur metabolism, and nitrite oxidation. Surprisingly, we did not detect any enrichments of anaerobic ammonium oxidizing bacteria as previously suggested and postulate that less well-studied anaerobic ammonium oxidation pathways may be occurring instead.

Crab bioturbation alters nitrogen cycling and promotes nitrous oxide emission in intertidal wetlands: Influence and microbial mechanism

Intertidal wetlands provide important ecosystem functions by acting as nitrogen (N) cycling hotspots, which can reduce anthropogenic N loading from land to coastal waters. Benthic bioturbations are thought to play an important role in mediating N cycling in intertidal marshes. However, how the burrowing activity of benthos and their microbial symbionts affect N transformation and greenhouse gas nitrous oxide (N₂O) emission remains unclear in these environments. Here, we show that bioturbation of crabs reshaped the structure of intertidal microbial communities and their N cycling function. Molecular analyses suggested that the microbially-driven N cycling might be accelerated by crab bioturbation, as the abundances of most of the N related functional genes were higher on the burrow wall than those in the surrounding bulk sediments, except for genes involved in N fixation, dissimilatory nitrate reduction to ammonium (DNRA), and N₂O reduction, which were further confirmed by isotope-tracing experiments. Especially, the potential rates of the main N₂O production pathways, nitrification and denitrification, were 2-3 times higher in the burrow wall sediments. However, even higher N₂O emission rates (approximately 6 times higher) were observed in this unique microhabitat, which was due to a disproportionate increase in N₂O production over N₂O consumption driven by burrowing activity. In addition, the sources of N₂O were also significantly affected by crab bioturbation, which increased the contribution of hydroxylamine oxidation pathway. This study reveals the mechanism through which benthic bioturbations mediate N cycling and highlights the importance of considering burrowing activity when evaluating the ecological function of intertidal wetlands.

Simultaneous removal of phosphorous and nitrogen by ammonium assimilation and aerobic denitrification of novel phosphate-accumulating organism Pseudomonas chloritidismutans K14

Pseudomonas chloritidismutans K14, a novel phosphate-accumulating organism with the capacity to perform ammonium assimilation, aerobic denitrification, and phosphorus removal, was isolated from aquaculture sediments. It produced no hemolysin, and showed susceptibility to most antibiotics. Optimum conditions were achieved with sodium pyruvate as a carbon source, a C/N ratio of 10, pH of 7.5, temperature of 27 °C, P/N ratio of 0.26, and shaking at 140 rpm. Under optimum conditions, the highest removal efficiencies of ammonium, nitrite, and nitrate were 99.82%, 99.11%, and 99.78%, respectively; the corresponding removal rates were 6.27, 4.51, and 4.99 mg/L/h. The strain removed over 98% of phosphorus, and over 87% of chemical oxygen demand. The highest biomass nitrogen during ammonium assimilation was 99.18 mg/L; no gaseous nitrogen was produced. The genes involved in nitrogen and phosphorus removal were amplified by PCR. This study demonstrated the potential application prospects of strain K14 for nitrogen and phosphorus removal.

Activities and metabolic versatility of distinct anammox bacteria in a full-scale wastewater treatment system

Anaerobic ammonium oxidation (anammox) is a key N₂-producing process in the global nitrogen cycle. Major progress in understanding the core mechanism of anammox bacteria has been made, but our knowledge of the survival strategies of anammox bacteria in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Here, by combining metagenomics with in situ metatranscriptomics, complex anammox-driven nitrogen cycles in an anoxic tank and a granular activated carbon (GAC) biofilm module of a full-scale WWTP treating landfill leachate were constructed. Four distinct anammox metagenome-assembled genomes (MAGs), representing a new genus named Ca. Loosdrechtii, a new species in Ca. Kuenenia, a new species in Ca. Brocadia, and a new strain in "Ca. Kuenenia stuttgartiensis", were simultaneously retrieved from the GAC biofilm. Metabolic reconstruction revealed that all anammox organisms highly expressed the core metabolic enzymes and showed a high metabolic versatility. Pathways for dissimilatory nitrate reduction to ammonium (DNRA) coupled to volatile fatty acids (VFAs) oxidation likely assist anammox bacteria to survive unfavorable conditions and facilitate switches between lifestyles in oxygen fluctuating environments. The new Ca. Kuenenia species dominated the anammox community of the GAC biofilm, specifically may be enhanced by the uniquely encoded flexible ammonium and iron acquisition strategies. The new Ca. Brocadia species likely has an extensive niche distribution that is simultaneously established in the anoxic tank and the GAC biofilm, the two distinct niches. The highly diverse and impressive metabolic versatility of anammox bacteria revealed in this study advance our understanding of the survival and application of anammox bacteria in the full-scale wastewater treatment system.

Coupling oxidation of acid volatile sulfide, ferrous iron, and ammonia nitrogen from black-odorous sediment via autotrophic denitrification-anammox by nitrate addition

The coupling removal of acid volatile sulfide (AVS), ferrous iron, and ammonia nitrogen has been applied for black-odorous sediment remediation. In this study, calcium nitrate with different N/(S + Fe) ratios (0.45, 0.90, 1.20 and 1.80) was added into black-odorous sediment in four systems named R1, R2, R3, and R4. Results showed that the removal rate of AVS was 76.40% in the R1, which was lower compared with rates in R2-R4 around 96.70%. The ferrous oxidation rate was approximately 87.00% in R2-R4, which was considerably higher than that in the R1 (24.62%). And the ammonia was reduced by 81.02%, 88.00%, 100%, and 57.18% in R1, R2, R3 and R4, respectively. During the reaction, nitrite accumulation was observed, indicating partial denitrification. Moreover, microbes related to autotrophic denitrification (e.g., genus Thiobacillus, Dok59, GOUTA19, Gallionella, with the highest abundance of 15.40%, 13.21%, 8.79%, 9.44%, respectively) were detected in all systems. Furthermore, the anammox bacteria Candidatus_Brocadia with the highest abundance of 3.44% and 4.00% in R2 and R3, respectively was also found. These findings confirmed that AVS, ferrous iron, and ammonia nitrogen could be simultaneously removed via autotrophic denitrification coupled with anammox in black-odorous sediment by nitrate addition.

Quantitative analysis of soil sustainability after applying stabilizing amendments in long-term Cd-contaminated paddy soils

Considering the biomagnification in food chains, cadmium (Cd) contamination in paddy fields has become concerning. The remediation of soil cadmium by the addition of amendments is a common agricultural practice. However, it remains ambiguous whether amendment use decreases soil environmental quality (SEQ) and sustainability. In this study, five compound amendments with different pH were utilized in long-term Cd-contaminated paddy soils. The SEQ of all treatments was quantitatively assessed according to a comprehensive evaluation mathematical model (Criteria Importance Through Inter-criteria Correlation (CRITIC)-Technique for Order Preference by Similarity to Ideal Solution (TOPSIS)), and the indicators involved in microbial functional gene (MFG) abundance, soil physicochemical and microbiological properties (CMP) and soil microbial function (N-related enzyme and transformation rate, N-ET) were measured. The results show that the SQE and remediation effect (expressed by the decrease in available Cd (A_Cd), %) in our treatments were alkaline > natural > acidic except for D alkaline treatment. The significant contradiction between soil SQE and remediation effect in D treatment attribute to its dose effects, which inhibiting microbial nitrogen assimilation and dissimilation and therefore counteracts the promoting effect of the decrease in A_Cd. Based on this discussion, three alkaline amendments (A, B and D) with similar effective remediation effect were employed in four other Cd-contaminated soils. Results indicated that both negative effect (D treatment) and promoting effect (A and B treatment) existed in the next 3 years.

Shift of DNRA bacterial community composition in sediment cores of the Pearl River Estuary and the impact of environmental factors

Dissimilatory nitrate reduction to ammonia (DNRA) process, competing with denitrification and anaerobic ammonia oxidation (anammox) for nitrate, is an important nitrogen retention pathway in the environment. Previous studies on DNRA bacterial diversity and composition focused on the surface sediments in estuaries, but studies on the deep sediments are limited, and the linkage between DNRA community structure and complex estuarine environment remains unclear. In this study, through high-throughput sequencing of nrfA gene followed by high-resolution sample inference, we examined spatially and temporally the composition and diversity of DNRA bacteria along a salinity gradient in five sediment cores of the Pearl River Estuary (PRE). We found a higher diversity and richness of DNRA bacteria in sediments with lower organic carbon, where sea water intersects fresh water. Moreover, the DNRA bacterial communities had the specific spatially distribution coupling with their metabolic difference along the salinity gradient of the Pearl River Estuary, but no obvious difference along the sediment depth. The distribution of DNRA bacteria in the PRE was largely driven by various environmental factors, including salinity, Oxidation-Reduction Potential (ORP), ammonium, nitrate and C_org/NO₃^-. Furthermore, dominant DNRA bacteria were found to be the key populations of DNRA communities in the PRE sediments by network analysis. Collectively, our results showed that niche difference of DNRA bacteria indeed occurs in the Pearl River Estuary.

Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling

BACKGROUND

Coastal aquatic ecosystems include chemically distinct, but highly interconnected environments. Across a freshwater-to-marine transect, aquatic communities are exposed to large variations in salinity and nutrient availability as tidal cycles create periodic fluctuations in local conditions. These factors are predicted to strongly influence the resident microbial community structure and functioning, and alter the structure of aquatic food webs and biogeochemical cycles. Nevertheless, little is known about the spatial distribution of metabolic properties across salinity gradients, and no study has simultaneously surveyed the sediment and water environments. Here, we determined patterns and drivers of benthic and planktonic prokaryotic and microeukaryotic community assembly across a river and tidal lagoon system by collecting sediments and planktonic biomass at nine shallow subtidal sites in the summer. Genomic and transcriptomic analyses, alongside a suite of complementary geochemical data, were used to determine patterns in the distribution of taxa, mechanisms of salt tolerance, and nutrient cycling.

RESULTS

Taxonomic and metabolic profiles related to salt tolerance and nutrient cycling of the aquatic microbiome were found to decrease in similarity with increasing salinity, and distinct trends in diversity were observed between the water column and sediment. Non-saline and saline communities adopted divergent strategies for osmoregulation, with an increase in osmoregulation-related transcript expression as salinity increased in the water column due to lineage-specific adaptations to salt tolerance. Results indicated a transition from phosphate limitation in freshwater habitats to nutrient-rich conditions in the brackish zone, where distinct carbon, nitrogen and sulfur cycling processes dominated. Phosphorus acquisition-related activity was highest in the freshwater zone, along with dissimilatory nitrate reduction to ammonium in freshwater sediment. Activity associated with denitrification, sulfur metabolism and photosynthesis were instead highest in the brackish zone, where photosynthesis was dominated by distinct microeukaryotes in water (Cryptophyta) and sediment (diatoms). Despite microeukaryotes and archaea being rare relative to bacteria, results indicate that they contributed more to photosynthesis and ammonia oxidation, respectively.

CONCLUSIONS

Our study demonstrates clear freshwater-saline and sediment-water ecosystem boundaries in an interconnected coastal aquatic system and provides a framework for understanding the relative importance of salinity, planktonic-versus-benthic habitats and nutrient availability in shaping aquatic microbial metabolic processes, particularly in tidal lagoon systems. Video abstract.

In situ characterization of benthic fluxes and denitrification efficiency in a newly re-established mussel farm

Mussel farming has been proposed as a mechanism to mitigate eutrophication in coastal waters. However, localizing the intensive filtration of organic matter by mussels can cause a concomitant enrichment of organic matter in sediments below farms, which may influence biogeochemical processes and fates of nutrients in the system. In the context of mitigating eutrophication, it is important to quantify sedimentary changes induced at early life stages of mussel farms. Accordingly, this study investigated how a newly re-established mussel farm affected sedimentation rates, sediment characteristics, sediment-water solute fluxes and nitrate (NO₃^-) reduction rates (measured in situ) during the first year of production. Sedimentation rates were enhanced at the farm relative to a reference station, and both organic and inorganic carbon accumulated in the sediment with time. Increased organic matter input likely drove the slightly elevated sedimentary effluxes of ammonium (NH₄⁺) and dissolved inorganic phosphorus (DIP) in the farm. Denitrification was the main NO₃^- reduction process, however, there was a relative increase in the remobilization of bioavailable nitrogen underneath the farm as dissimilatory nitrate reduction to ammonium (DNRA) rates were enhanced by >200% and the denitrification efficiency was 49% lower compared to the reference station. The sedimentary methane (CH₄) release tended to be higher at the farm, but fluxes were not significantly different from reference conditions. Low sedimentary pigment concentrations indicated a reduced presence of benthic microalgae at the farm, which likely influenced sediment-water solute fluxes. Over the production cycle, the release of dissolved inorganic nitrogen (DIN) and DIP underneath the farm were respectively 426% and 510% relative to reference conditions. Impacts of the mussel farm were thus measurable already during the first year of establishment. These immediate changes to the sediment biogeochemistry, as well as long-term effects, should be considered when estimating the environmental impact of mussel aquaculture.

Functional analysis of pristine estuarine marine sediments

Traditional environmental monitoring techniques are well suited to resolving acute exposure effects but lack resolution in determining subtle shifts in ecosystem functions resulting from chronic exposure(s). Surveillance with sensitive omics-based technologies could bridge this gap but, to date, most omics-based environmental studies have focused on previously degraded environments, identifying key metabolic differences resulting from anthropogenic perturbations. Here, we apply omics-based approaches to pristine environments to establish blueprints of microbial functionality within healthy estuarine sediment communities. We collected surface sediments (n = 50) from four pristine estuaries along the Western Cape York Peninsula of Far North Queensland, Australia. Sediment microbiomes were analyzed for 16S rRNA amplicon sequences, central carbon metabolism metabolites and associated secondary metabolites via targeted and untargeted metabolic profiling methods. Multivariate statistical analyses indicated heterogeneity among all the sampled estuaries, however, taxa-function relationships could be established that predicted community metabolism potential. Twenty-four correlated gene-metabolite pathways were identified and used to establish sediment microbial blueprints of essential carbon metabolism and amino acid biosynthesis that were positively correlated with community metabolic function outputs (2-oxisocapraote, tryptophan, histidine citrulline and succinic acid). In addition, an increase in the 125 KEGG genes related to metal homeostasis and metal resistance was observed, although, none of the detected metabolites related to these specific genes upon integration. However, there was a correlation between metal abundance and functional genes related to Fe and Zn metabolism. Our results establish a baseline microbial blueprint for the pristine sediment microbiome, one that drives important ecosystem services and to which future ecosurveillance monitoring can be compared.

Coupled relationships among anammox, denitrification, and dissimilatory nitrate reduction to ammonium along salinity gradients in a Chinese estuarine wetland

Salinization in estuarine wetlands significantly alters the balance between their nitrogen (N) removal and retention abilities but these processes have not yet been characterized effectively. In the present study, the potential rates of sediment denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) were mapped using N isotope tracing methods along salinity gradients across the Yellow River Delta wetland (YRDW) in China. The contribution of anammox to total dissimilatory N transformations in YRDW was merely 6.8%, whereas denitrification and DNRA contributed 52.3% and 40.9%, respectively. The potential rate of denitrification (5.82 μmol/kg/h) decreased significantly along salinity gradients and markedly exceeded DNRA potential rate (2.7 μmol/kg/h) in fresh wetlands, but was lower than that of DNRA in oligohaline wetlands (3.06 and 3.18 μmol/kg/h, respectively). Moreover, a significantly positive relationship between salinity and DNRA/denitrification was obeserved, indicating that increased salinity may favor DNRA over denitrification. Furthermore, total sulfur (TS) content and ratio of total organic carbon to total nitrogen (C/N) increased with the salinity gradient and showed evident positive relationships with the DNRA/denitrification ratio. In this study, we proved that increased salinization resulted in the dominance of DNRA over denitrification, possible through the addition of S and alteration of the C/N in estuarine wetlands, leading to increased N retention in estuarine wetlands during salinization, which would enhance the eutrophication potential within wetlands and in downstream ecosystems.

Anaerobic Neutrophilic Pyrite Oxidation by a Chemolithoautotrophic Nitrate-Reducing Iron(II)-Oxidizing Culture Enriched from a Fractured Aquifer

Neutrophilic microbial pyrite (FeS₂) oxidation coupled to denitrification is thought to be an important natural nitrate attenuation pathway in nitrate-contaminated aquifers. However, the poor solubility of pyrite raises questions about its bioavailability and the mechanisms underlying its oxidation. Here, we investigated direct microbial pyrite oxidation by a neutrophilic chemolithoautotrophic nitrate-reducing Fe(II)-oxidizing culture enriched from a pyrite-rich aquifer. We used pyrite with natural abundance (NA) of Fe isotopes (^NAFe-pyrite) and ⁵⁷Fe-labeled siderite to evaluate whether the oxidation of the more soluble Fe(II)-carbonate (FeCO₃) can indirectly drive abiotic pyrite oxidation. Our results showed that in setups where only pyrite was incubated with bacteria, direct microbial pyrite oxidation contributed ca. 26% to overall nitrate reduction. The rest was attributed to the oxidation of elemental sulfur (S⁰), present as a residue from pyrite synthesis. Pyrite oxidation was evidenced in the ^NAFe-pyrite/⁵⁷Fe-siderite setups by maps of ⁵⁶FeO and ³²S obtained using a combination of SEM with nanoscale secondary ion MS (NanoSIMS), which showed the presence of ⁵⁶Fe(III) (oxyhydr)oxides that could solely originate from ⁵⁶FeS₂. Based on the fit of a reaction model to the geochemical data and the Fe-isotope distributions from NanoSIMS, we conclude that anaerobic oxidation of pyrite by our neutrophilic enrichment culture was mainly driven by direct enzymatic activity of the cells. The contribution of abiotic pyrite oxidation by Fe³⁺ appeared to be negligible in our experimental setup.

Niche partitioning of bacterial communities along the stratified water column in the Black Sea

The Black Sea is the largest semi‐closed permanently anoxic basin on our planet with long‐term stratification. The study aimed at describing the Black Sea microbial community taxonomic and functional composition within the range of depths spanning across oxic/anoxic interface, and to uncover the factors behind both their vertical and regional differentiation. 16S rRNA gene MiSeq sequencing was applied to get the data on microbial community taxonomy, and the PICRUSt pipeline was used to infer their functional profile. The normoxic zone was mainly inhabited by primary producers and heterotrophic prokaryotes (e.g., Flavobacteriaceae, Rhodobacteraceae, Synechococcaceae) whereas the euxinic zone—by heterotrophic and chemoautotrophic taxa (e.g., MSBL2, Piscirickettsiaceae, and Desulfarculaceae). Assimilatory sulfate reduction and oxygenic photosynthesis were prevailing within the normoxic zone, while the role of nitrification, dissimilatory sulfate reduction, and anoxygenic photosynthesis increased in the oxygen‐depleted water column part. Regional differentiation of microbial communities between the Ukrainian shelf and offshore zone was detected as well, yet it was significantly less pronounced than the vertical one. It is suggested that regional differentiation within a well‐oxygenated zone is driven by the difference in phytoplankton communities providing various substrates for the prokaryotes, whereas redox stratification is the main driving force behind microbial community vertical structure.

Responses of microbial structures, functions and metabolic pathways for nitrogen removal to different hydraulic retention times in anaerobic side-stream reactor coupled membrane bioreactors

Synchronous sludge reduction and nitrogen removal have attracted increasing attention, while the underlying mechanisms of diverse nitrogen metabolism within the complicated processes remain unclear. Four anoxic/oxic membrane bioreactors, three of which were upgraded by anaerobic side-stream reactors (ASSR) and carriers (APSSR-MBRs), were operated to determine effects of hydraulic retention time of ASSRs. APSSR-MBRs achieved more significant nitrogen removal and higher nitrate uptake rate because of more denitrifying bacteria and the supernumerary release of secondary substrates. Ammonia uptake rate showed the diverse Nitrospira preceded over anaerobic decay and sulfide inhibition in the ASSR, and made the reactor exhibit higher nitrification capacity. Metagenomic analysis indicated that APSSR-MBRs showed higher abundances of genes related to nitrogen consumption processes, and higher abundances on the carriers, confirming their pivotal roles in nitrogen metabolism. This study provided novel perspectives to build a bridge between process model and nitrogen metabolism in the sludge reduction system..

Factoring distinct materials and nitrogen-related microbes into assessments of nitrogen pollution risks during composting

The aim of this study was to evaluate nitrogen pollution risks from distinct materials composting with the discrepancy of component, including chicken manure, municipal solid and straw waste (CM, MSW, SW). Results showed total nitrogen maximum mean concentrations were observed in CM (39.57 g/kg). Pollution risks in CM were continuous, while MSW and SW mainly concentrated during heating phases. Microbial analysis confirmed that pollution risks from ammonification and nitrification were more prevalent in CM. The risks of pollution caused by nitrate reduction accompanied N₂O were the most serious in MSW. The multifunctional nitrogen-related microbes Pseudomonas and Bacillus were affected by microenvironments and contributed to different pollution risks. Furthermore, PICRUSt analysis identified the "inferred" key genes (pmoC-amoC, nrfH, nifD etc.) related to nitrogen pollution risks. This study evaluated nitrogen pollution risks and proposed the future directions, providing theoretical basis and feasible optimization measures for the mitigation of nitrogen pollution during composting.

Estuarine microbial diversity and nitrogen cycling increase along sand-mud gradients independent of salinity and distance

Estuaries are depositional environments prone to terrigenous mud sedimentation. While macrofaunal diversity and nitrogen retention are greatly affected by changes in sedimentary mud content, its impact on prokaryotic diversity and nitrogen cycling activity remains understudied. We characterized the composition of estuarine tidal flat prokaryotic communities spanning a habitat range from sandy to muddy sediments, while controlling for salinity and distance. We also determined the diversity, abundance and expression of ammonia oxidizers and N₂ O-reducers within these communities by amoA and clade I nosZ gene and transcript analysis. Results show that prokaryotic communities and nitrogen cycling fractions were sensitive to changes in sedimentary mud content, and that changes in the overall community were driven by a small number of phyla. Significant changes occurred in prokaryotic communities and N₂ O-reducing fractions with only a 3% increase in mud, while thresholds for ammonia oxidizers were less distinct, suggesting other factors are also important for structuring these guilds. Expression of nitrogen cycling genes was substantially higher in muddier sediments, and results indicate that the potential for coupled nitrification-denitrification became increasingly prevalent as mud content increased. Altogether, results demonstrate that mud content is a strong environmental driver of diversity and N-cycling dynamics in estuarine microbial communities.

Dechloromonas and close relatives prevail during hydrogenotrophic denitrification in stimulated microcosms with oxic aquifer material

Globally occurring nitrate pollution in groundwater is harming the environment and human health. In situ hydrogen addition to stimulate denitrification has been proposed as a remediation strategy. However, observed nitrite accumulation and incomplete denitrification are severe drawbacks that possibly stem from the specific microbial community composition. We set up a microcosm experiment comprising sediment and groundwater from a nitrate polluted oxic oligotrophic aquifer. After the microcosms were sparged with hydrogen gas, samples were taken regularly within 122 h for nitrate and nitrite measurements, community composition analysis via 16S rRNA gene amplicon sequencing and gene and transcript quantification via qPCR of reductase genes essential for complete denitrification. The highest nitrate reduction rates and greatest increase in bacterial abundance coincided with a 15.3-fold increase in relative abundance of Rhodocyclaceae, specifically six ASVs that are closely related to the genus Dechloromonas. The denitrification reductase genes napA, nirS and clade I nosZ also increased significantly over the observation period. We conclude that taxa of the genus Dechloromonas are the prevailing hydrogenotrophic denitrifiers in this nitrate polluted aquifer and the ability of hydrogenotrophic denitrification under the given conditions is species-specific.

Active DNRA and denitrification in oxic hypereutrophic waters

Since the start of synthetic fertilizer production more than a hundred years ago, the coastal ocean has been exposed to increasing nutrient loading, which has led to eutrophication and extensive algal blooms. Such hypereutrophic waters might harbor anaerobic nitrogen (N) cycling processes due to low-oxygen microniches associated with abundant organic particles, but studies on nitrate reduction in coastal pelagic environments are scarce. Here, we report on ¹⁵N isotope-labeling experiments, metagenome, and RT-qPCR data from a large hypereutrophic lagoon indicating that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were active processes, even though the bulk water was fully oxygenated (> 224 µM O₂). DNRA in the bottom water corresponded to 83% of whole-ecosystem DNRA (water + sediment), while denitrification was predominant in the sediment. Microbial taxa important for DNRA according to the metagenomic data were dominated by Bacteroidetes (genus Parabacteroides) and Proteobacteria (genus Wolinella), while denitrification was mainly associated with proteobacterial genera Pseudomonas, Achromobacter, and Brucella. The metagenomic and microscopy data suggest that these anaerobic processes were likely occurring in low-oxygen microniches related to extensive growth of filamentous cyanobacteria, including diazotrophic Dolichospermum and non-diazotrophic Planktothrix. By summing the total nitrate fluxes through DNRA and denitrification, it results that DNRA retains approximately one fifth (19%) of the fixed N that goes through the nitrate pool. This is noteworthy as DNRA represents thus a very important recycling mechanism for fixed N, which sustains algal proliferation and leads to further enhancement of eutrophication in these endangered ecosystems.

Indicator species drive the key ecological functions of microbiota in a river impacted by acid mine drainage generated by rare earth elements mining in South China

Acid mine drainage (AMD) generated by rare earth elements (REEs) deposits exploration contains high concentrations of REEs, ammonium and sulfates, which is quite different from typical metallic AMD. Currently, microbial responses and ecological functions in REEs-AMD impacted rivers are unknown. Here, 16S rRNA analysis and genome-resolved metagenomics were performed on microbial community collected from a REEs-AMD contaminated river. The results showed that REEs-AMD significantly changed river microbial diversity and shaped unique indicator species (e.g. Thaumarchaeota, Methylophilales, Rhodospirillales and Burkholderiales). The main environmental factors regulating community were pH, ammonium and REEs, among which high concentration of REEs increased REEs-dependent enzyme-encoding genes (XoxF and ExaF/PedH). Additionally, we reconstructed 566 metagenome-assembled genomes covering 70.4% of identifying indicators. Genome-centric analysis revealed that the abundant archaea Thaumarchaeota and Xanthomonadaceae were often involved in nitrification and denitrification, while family Burkholderiaceae were capable of sulfide oxidation coupled with dissimilatory nitrate reduction to ammonium. These indicators play crucial roles in nitrogen and sulfur cycling as well as REEs immobilization in REEs-AMD contaminated rivers. This study confirmed the potential dual effect of REEs on microbial community at the functional gene level. Our investigation on the ecological roles of indicators further provided new insights for the development of REEs-AMD bioremediation.

Shift in nitrogen transformation in peatland soil by nitrogen inputs

Inputs of nitrogen (N) to peatlands in the form of fertilizers have rapidly increased due to the intensification of agricultural systems, impacting ecological processes, and the carbon storage function of peatland. However, detailed information on the impacts of long-term N inputs on the individual steps of N transformation processes in peatland soils still needs to be fully understood. We investigated N mineralization and nitrification rates as well as nitrite dependent anaerobic methane oxidation (n-damo), anaerobic ammonium oxidation (anammox), denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) in a peatland affected by N inputs for >50 years, using isotope tracing technique and quantitative PCR. Based on the results, N inputs increased N mineralization and nitrification rates by 77 and 43%, respectively. Notably, the contributions of n-damo and anammox to N₂ production were enhanced by 242 and 170%, accounting for 30 and 12%, respectively. The contributions of denitrification and DNRA to N₂ production decreased by 27 and 52%, accounting for 48 and 10% of N₂ production, respectively. Nitrifier abundance increased significantly, with AOA being the dominant prokaryote (from 696 to 1090 copies g^-1), but AOB responded more strongly to N inputs (from 5 to 68 copies g^-1). The N inputs also promoted the growth of n-damo and anammox bacteria, whose abundances increased by 3.7% (from 565 to 586 copies g^-1) and 85.7% (from 305 to 567 copies g^-1), respectively, while denitrifier abundance was significantly reduced, with nirK and nirS abundances decreasing by 58% (from 738 to 308 copies g^-1) and 50% (from 218 to 109 copies g^-1), respectively. Soil pH was the key environmental factor influencing N transformations. We show that n-damo plays important roles in N cycling in peatland subjected to N inputs, providing a scientific basis for improved peatland management.

Strategies to Overcome Intermediate Accumulation During in situ Nitrate Remediation in Groundwater by Hydrogenotrophic Denitrification

Bioremediation of polluted groundwater is one of the most difficult actions in environmental science. Nonetheless, the clean-up of nitrate polluted groundwater may become increasingly important as nitrate concentrations frequently exceed the EU drinking water limit of 50 mg L-1, largely due to intensification of agriculture and food production. Denitrifiers are natural catalysts that can reduce increasing nitrogen loading of aquatic ecosystems. Porous aquifers with high nitrate loading are largely electron donor limited and additionally, high dissolved oxygen concentrations are known to reduce the efficiency of denitrification. Therefore, denitrification lag times (time prior to commencement of microbial nitrate reduction) up to decades were determined for such groundwater systems. The stimulation of autotrophic denitrifiers by the injection of hydrogen into nitrate polluted regional groundwater systems may represent a promising remediation strategy for such environments. However, besides high costs other drawbacks, such as the transient or lasting accumulation of the cytotoxic intermediate nitrite or the formation of the potent greenhouse gas nitrous oxide, have been described. In this article, we detect causes of incomplete denitrification, which include environmental factors and physiological characteristics of the underlying bacteria and provide possible mitigation approaches.

Nitrogen removal through collaborative microbial pathways in tidal flow constructed wetlands

Constructed wetlands are efficient in removing nitrogen from water; however, little is known about nitrogen-cycling pathways for nitrogen loss from tidal flow constructed wetlands. This study conducted molecular and stable isotopic analyses to investigate potential dissimilatory nitrate reduction to ammonium (DNRA), denitrification, nitrification, anaerobic ammonium oxidation (anammox), and their contributions to nitrogen removal by two tidal wetland mesocosms, PA (planted with Phragmites australis) and NP (unplanted), designated to treat Yangtze River Estuary water. Our results show the mesocosms removed ~22.6% of TN from nitrate-dominated river water (1.19 mg·L^-1), with better performance obtained in PA than that in NP, which was consistent with the molecular and stable isotopic data. The potential activities of DNRA, anammox, denitrification and nitrification varied between 0.6 and 1.6, 4.6-37.3, 36.4-305.7, and 463.7-945.9 nmol N₂ g^-1 dry soil d^-1, respectively, with higher values obtained in PA than NP. Nitrification accounted for 94.3-99.4% of NH₄⁺ oxidation, with the rest through anammox. Denitrification contributed to 77.9-90.3% of NO_x^- reduction, compared to 9.2-21.6% and 0.5-1.5% via anammox and DNRA, respectively; 78.4-90.9% of N₂ was produced through denitrification, with the rest via anammox. Pearson correlation analyses suggest NH₄⁺ was the major factor regulating nitrification, while NO₃^- played an important role in the competition between denitrification and DNRA, and NO₂^- was a key restrictive factor for anammox. Overall, this study reveals the importance of nitrification, denitrification, anammox and DNRA in nitrogen removal, providing new insight into the nitrogen-cycling mechanisms in natural/artificial tidal wetlands.

Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments

Large amounts of methane, a potent greenhouse gas, are produced in anoxic sediments by methanogenic archaea. Nonetheless, over 90% of the produced methane is oxidized via sulfate-dependent anaerobic oxidation of methane (S-AOM) in the sulfate-methane transition zone (SMTZ) by consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Coastal systems account for the majority of total marine methane emissions and typically have lower sulfate concentrations, hence S-AOM is less significant. However, alternative electron acceptors such as metal oxides or nitrate could be used for AOM instead of sulfate. The availability of electron acceptors is determined by the redox zonation in the sediment, which may vary due to changes in oxygen availability and the type and rate of organic matter inputs. Additionally, eutrophication and climate change can affect the microbiome, biogeochemical zonation, and methane cycling in coastal sediments. This review summarizes the current knowledge on the processes and microorganisms involved in methane cycling in coastal sediments and the factors influencing methane emissions from these systems. In eutrophic coastal areas, organic matter inputs are a key driver of bottom water hypoxia. Global warming can reduce the solubility of oxygen in surface waters, enhancing water column stratification, increasing primary production, and favoring methanogenesis. ANME are notoriously slow growers and may not be able to effectively oxidize methane upon rapid sedimentation and shoaling of the SMTZ. In such settings, ANME-2d (Methanoperedenaceae) and ANME-2a may couple iron- and/or manganese reduction to AOM, while ANME-2d and NC10 bacteria (Methylomirabilota) could couple AOM to nitrate or nitrite reduction. Ultimately, methane may be oxidized by aerobic methanotrophs in the upper millimeters of the sediment or in the water column. The role of these processes in mitigating methane emissions from eutrophic coastal sediments, including the exact pathways and microorganisms involved, are still underexplored, and factors controlling these processes are unclear. Further studies are needed in order to understand the factors driving methane-cycling pathways and to identify the responsible microorganisms. Integration of the knowledge on microbial pathways and geochemical processes is expected to lead to more accurate predictions of methane emissions from coastal zones in the future.

Combined removal of organic micropollutants and ammonium in reactive barriers developed for managed aquifer recharge

Groundwater is an important drinking water resource. To ensure clean drinking water, managed aquifer recharge (MAR) could be an attractive solution when recharging with treated wastewater. The installation of reactive barriers, e.g. with compost or other organic materials at MAR facilities, may improve pollutant removal. To link pollutant transformation processes and microbiology in reactive barriers, we simulated infiltration through different sand-compost mixtures using laboratory columns with depth-specific sampling of water and barrier material. We also evaluated the effect of inoculation with activated sludge. Our focus was on the simultaneous removal of organic micropollutants and nitrogen species, with parallel monitoring of the development of microbial communities. During 17 weeks of operation, the columns were fed with synthetic wastewater containing five organic micropollutants (1-2 µg/L each) and ammonium (2 mg N/L). Unique communities developed in the columns in relation to barrier material, with high effects of compost addition and minor effect of inoculation. Removal of the micropollutant paracetamol (acetaminophen) occurred in all columns, while sulfamethoxazole was only removed in columns with 50% compost. By contrast, limited removal was observed for sulfadiazine, carbamazepine and diuron, with the latter two displaying transient removal, attributed sorption. Oxygen was depleted within the top few cm of the columns when compost was present, but this was sufficient to remove all ammonium through nitrification. The fate of accumulated nitrate at deeper layers depended on the fraction of compost, with more compost leading to removal of nitrate by denitrification, but also by dissimilatory nitrate reduction to ammonium, hampering the overall nitrogen removal efficiency. Introducing compost as reactive barrier in MAR facilities has a large effect on the microbial communities and processes, but whether it will provide overall cleaner water to the underlying aquifer is uncertain and will depend very much on the type of pollutant.

Substrate type determines microbial activity and community composition in bioreactors for nitrate removal by denitrification at low temperature

High levels of nitrogen originating from blasting operations, for example at mining sites or quarries, risk contaminating water bodies through leaching from waste rock dumps. Woodchip bioreactors can be a simple and cost-effective way of reducing nitrate concentrations in the leachate. In this study we investigated how bottle sedge, barley straw, and pine woodchips used as electron donors for denitrification influenced microbial community composition and nitrate removal in lab-scale bioreactors during 270 days. The reactors were operated to ensure that nitrate was never limiting and to achieve similar nitrate removal (%). Distinct bacterial communities developed due to the different substrates, as determined by sequencing of the 16S rRNA gene. Sedge and straw reactors shared more taxa with each other than with woodchips and throughout the experimental period, sedge and straw were more diverse than woodchips. Cellulose degrading bacteria like Fibrobacteres and Verrucomicrobia were detected in the substrates after 100-150 days of operation. Nitrate removal rates were highest in the sedge and straw reactors. After initial fluctuations, these reactors removed 5.1-6.3 g N m^-3 water day^-1, which was 3.3-4.4 times more than in the woodchip reactors. This corresponded to 48%, 42%, and 44% nitrate removal for the sedge, straw, and woodchip reactors respectively. The functional communities were characterized by quantitative PCR and denitrification was the major nitrate removing process based on genetic potential and water chemistry, although sedge and straw developed a capacity for ammonification. Gene ratios suggested that denitrification was initially incomplete and terminating with nitrous oxide. An increase in abundances of nitrous oxide reducing capacity in all substrate types towards the end increased the potential for less emissions of the greenhouse gas nitrous oxide.

The long-term effects of using nitrite and urea on the enrichment of comammox bacteria

The discovery of complete ammonia oxidizer (comammox) was a breakthrough in the study of nitrification. However, slow growth of comammox bacteria makes it challenging to distinguish them from traditional ammonia oxidizing microorganisms. Genomic data indicated that comammox bacteria encoded genes that can metabolize urea and had higher nitrite tolerance, which could only be found in several ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This implies that using nitrite and urea as nitrogen sources may accelerate comammox bacteria's enrichment efficiency. In this study, two reactors using nitrite and urea as substrates, respectively, were operated for 390 days. At the end of cultivation, the reactor fed with urea exhibited higher nitrification potential than the reactor fed with nitrite. Comammox bacteria outcompeted AOA and AOB, regardless of whether they were cultured with nitrite or urea. Using nitrite can improve the proportion of comammox amoA to total amoA of 92%, while using urea may increase the proportion of comammox bacteria among total bacteria to 14.2%. Metagenomic results implied that nitrite was converted to ammonia by nitrate reduction and absorbed by comammox bacteria. On the other hand, urea may be directly utilized as substrate. These results demonstrated that using different nitrogen sources caused niche differentiation of comammox bacteria, AOA, and AOB. Using nitrite can increase the relative abundance of comammox amoA to total amoA, while using urea can increase the quantity of comammox amoA. Comammox bacteria were dominant among ammonia oxidizing microorganisms for both nitrite and urea cultures.

Effects of submerged vegetation on sediment nitrogen-cycling bacterial communities in Honghu Lake (China)

Sediment nitrogen (N) cycling is an important biological removal process for N permanently and driven by N-cycling microbial community. There is a growing interest in interactions between submerged vegetation (SV) and sediment N-cycling bacterial community, because of the close link between rooted aquatic plants and the sediment microbes. However, the effects of SV on the sediment N-cycling bacterial community are still controversial. Furthermore, the discrimination of direct and indirect effects of SV on the N-cycling bacterial community remains unclear. Here, we investigated the biomass and species richness of SV and determined the corresponding environment factors (water quality and sediment properties) in Honghu Lake (China). We also used functional genes as markers to unveil the bacterial diversity and community composition and abundance in lake sediments. Our results showed that biomass and species richness of SV affected the composition, diversity and abundance of sediment N-cycling bacterial communities through improving lake water quality and sediment properties. With the increasing richness and abundance of SV, the diversity of most N-cycling bacterial assemblages including nitrifying, denitrifying and DNRA bacteria decreased, while the abundance increased. However, the anammox bacterial assemblage in sediments showed inverse trends. Sediment carbon vs. nitrogen (C:N) ratio negatively affected the abundance of amoA and nirS + nirK + nosZ bacterial assemblages. Additionally, due to the presence of SV, positive interactions among N-cycling bacterial assemblages were found, such as amoA and nrfA bacterial assemblages. Overall, our findings confirmed the significant effects of SV on the N-cycling bacterial community structure and abundance. Moreover, the direct effects of SV on the N-cycling bacterial community and the indirect effects through altering the sediment C were clarified in our study. Our results casted a new light on the negative effects of high C:N ratio. From the study, we made a conclusion that the better SV develops, the greater nitrogen removal occurs in lake sediments.

Long-term sulfide input enhances chemoautotrophic denitrification rather than DNRA in freshwater lake sediments

Partitioning between nitrate reduction pathways, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) determines the fate of nitrate removal and thus it is of great ecological importance. Sulfide (S^2-) is a potentially important factor that influences the role of denitrification and DNRA. However, information on the impact of microbial mechanisms for S^2- on the partitioning of nitrate reduction pathways in freshwater environments is still lacking. This study investigated the effects of long-term (108 d) S^2- addition on nitrate reduction pathways and microbial communities in the sediments of two different freshwater lakes. The results show that the increasing S^2- addition enhanced the coupling of S^2- oxidation with denitrification instead of DNRA. The sulfide-oxidizing denitrifier, Thiobacillus, was significantly enriched in the incubations of both lake samples with S^2- addition, which indicates that it may be the key genus driving sulfide-oxidizing denitrification in the lake sediments. During S^2- incubation of the Hongze Lake sample, which had lower inherent organic carbon (C) and sulfate (SO₄^2-), Thiobacillus was more enriched and played a dominant role in the microbial community; while during that of the Nansi Lake sample, which had higher inherent organic C and SO₄^2-, Thiobacillus was less enriched, but increasing abundances of sulfate reducing bacteria (Desulfomicrobium, Desulfatitalea and Geothermobacter) were observed. Moreover, sulfide-oxidizing denitrifiers and sulfate reducers were enriched in the Nansi Lake control treatment without external S^2- input, which suggests that internal sulfate release may promote the cooperation between sulfide-oxidizing denitrifiers and sulfate reducers. This study highlights the importance of sulfide-driven denitrification and the close coupling between the N and S cycles in freshwater environments, which are factors that have often been overlooked.

Anaerobic Oxidation of Methane Coupled with Dissimilatory Nitrate Reduction to Ammonium Fuels Anaerobic Ammonium Oxidation

Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) is critical for mitigating methane emission and returning reactive nitrogen to the atmosphere. The genomes of n-DAMO archaea show that they have the potential to couple anaerobic oxidation of methane to dissimilatory nitrate reduction to ammonium (DNRA). However, physiological details of DNRA for n-DAMO archaea were not reported yet. This work demonstrated n-DAMO archaea coupling the anaerobic oxidation of methane to DNRA, which fueled Anammox in a methane-fed membrane biofilm reactor with nitrate as only electron acceptor. Microelectrode analysis revealed that ammonium accumulated where nitrite built up in the biofilm. Ammonium production and significant upregulation of gene expression for DNRA were detected in suspended n-DAMO culture with nitrite exposure, indicating that nitrite triggered DNRA by n-DAMO archaea. ¹⁵N-labeling batch experiments revealed that n-DAMO archaea produced ammonium from nitrate rather than from external nitrite. Localized gradients of nitrite produced by n-DAMO archaea in biofilms induced ammonium production via the DNRA process, which promoted nitrite consumption by Anammox bacteria and in turn helped n-DAMO archaea resist stress from nitrite. As biofilms predominate in various ecosystems, anaerobic oxidation of methane coupled with DNRA could be an important link between the global carbon and nitrogen cycles that should be investigated in future research.

Soil gross nitrogen transformations in forestland and cropland of Regosols

Soil gross nitrogen (N) transformations could be influenced by land use change, however, the differences in inherent N transformations between different land use soils are still not well understood under subtropical conditions. In this study, an ¹⁵N tracing experiment was applied to determine the influence of land uses on gross N transformations in Regosols, widely distributed soils in Southwest China. Soil samples were taken from the dominant land use types of forestland and cropland. In the cropland soils, the gross autotrophic nitrification rates (mean 14.54 ± 1.66 mg N kg^-1 day^-1) were significantly higher, while the gross NH₄⁺ immobilization rates (mean 0.34 ± 0.10 mg N kg^-1 day^-1) were significantly lower than those in the forestland soils (mean 1.99 ± 0.56 and 6.67 ± 0.74 mg N kg^-1 day^-1, respectively). The gross NO₃^- immobilization and dissimilatory NO₃^- reduction to NH₄⁺ (DNRA) rates were not significantly different between the forestland and cropland soils. In comparison to the forestland soils (mean 0.51 ± 0.24), the cropland soils had significantly lower NO₃^- retention capacities (mean 0.01 ± 0.01), indicating that the potential N losses in the cropland soils were higher. The correlation analysis demonstrated that soil gross autotrophic nitrification rate was negatively and gross NH₄⁺ immobilization rate was positively related to the SOC content and C/N ratio. Therefore, effective measures should be taken to increase soil SOC content and C/N ratio to enhance soil N immobilization ability and NO₃^- retention capacity and thus reduce NO₃^- losses from the Regosols.

Microbial controls on net production of nitrous oxide in a denitrifying woodchip bioreactor

Denitrifying woodchip bioreactors are potential low-cost technologies for the removal of nitrate (NO₃ ^- ) in water through denitrification. However, if environmental conditions do not support microbial communities performing complete denitrification, other N transformation processes will occur, resulting in the export of nitrite (NO₂ ^- ), nitrous oxide (N₂ O), or ammonium (NH₄ ⁺ ). To identify the factors controlling the relative accumulation of NO₂ ^- , N₂ O, and/or NH₄ ⁺ in denitrifying woodchip bioreactors, porewater samples were collected over two operational years from a denitrifying woodchip bioreactor designed for removing NO₃ ^- from mine water. Woodchip samples were collected at the end of the operational period. Changes in the abundances of functional genes involved in denitrification, N₂ O reduction, and dissimilatory NO₃ ^- reduction to NH₄ ⁺ were correlated with porewater chemistry and temperature. Temporal changes in the abundance of the denitrification gene nirS were significantly correlated with increases in porewater N₂ O concentrations and indicated the preferential selection of incomplete denitrifying pathways ending with N₂ O. Temperature and the total organic carbon/NO₃ ^- ratio were strongly correlated with NH₄ ⁺ concentrations and inversely correlated with the ratio between denitrification genes and the genes indicative of ammonification (Σnir/nrfA), suggesting an environmental control on NO₃ ^- transformations. Overall, our results for a denitrifying woodchip bioreactor operated at hydraulic residence times of 1.0-2.6 d demonstrate the temporal development in the microbial community and indicate an increased potential for N₂ O emissions with time from the denitrifying woodchip bioreactor.

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

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

Nitrate respiration and diel migration patterns of diatoms are linked in sediments underneath a microbial mat

Diatoms are among the few eukaryotes known to store nitrate (NO₃ ^- ) and to use it as an electron acceptor for respiration in the absence of light and O₂ . Using microscopy and ¹⁵ N stable isotope incubations, we studied the relationship between dissimilatory nitrate/nitrite reduction to ammonium (DNRA) and diel vertical migration of diatoms in phototrophic microbial mats and the underlying sediment of a sinkhole in Lake Huron (USA). We found that the diatoms rapidly accumulated NO₃ ^- at the mat-water interface in the afternoon and 40% of the population migrated deep into the sediment, where they were exposed to dark and anoxic conditions for ~75% of the day. The vertical distribution of DNRA rates and diatom abundance maxima coincided, suggesting that DNRA was the main energy generating metabolism of the diatom population. We conclude that the illuminated redox-dynamic ecosystem selects for migratory diatoms that can store nitrate for respiration in the absence of light. A major implication of this study is that the dominance of DNRA over denitrification is not explained by kinetics or thermodynamics. Rather, the dynamic conditions select for migratory diatoms that perform DNRA and can outcompete sessile denitrifiers.

Understanding Microbial Community Dynamics in Up-Flow Bioreactors to Improve Mitigation Strategies for Oil Souring

Oil souring occurs when H2S is generated in oil reservoirs. This not only leads to operational risks and health hazards but also increases the cost of refining crude oil. Sulfate-reducing microorganisms are considered to be the main source of the H2S that leads to oil souring. Substrate competition between nitrate-reducing and sulfate-reducing microorganisms makes biosouring mitigation via the addition of nitrate salts a viable strategy. This study explores the shift in microbial community across different phases of biosouring and mitigation. Anaerobic sand-filled columns wetted with seawater and/or oil were used to initiate the processes of sulfidogenesis, followed by mitigation with nitrate, rebound sulfidogenesis, and rebound control phases (via nitrate and low salinity treatment). Shifts in microbial community structure and function were observed across different phases of seawater and oil setups. Marine bacterial taxa (Marinobacter, Marinobacterium, Thalassolituus, Alteromonas, and Cycloclasticus) were found to be the initial responders to the application of nitrate during mitigation of sulfidogenesis in both seawater- and oil- wetted columns. Autotrophic groups (Sulfurimonas and Desulfatibacillum) were found to be higher in seawater-wetted columns compared to oil-wetted columns, suggesting the potential for autotrophic volatile fatty acid (VFA) production in oil-field aquifers when seawater is introduced. Results indicate that fermentative (such as Bacteroidetes) and oil-degrading bacteria (such as Desulfobacula toluolica) play an important role in generating electron donors in the system, which may sustain biosouring and nitrate reduction. Persistence of certain microorganisms (Desulfobacula) across different phases was observed, which may be due to a shift in metabolic lifestyle of the microorganisms across phases, or zonation based on nutrient availability in the columns. Overall results suggest mitigation strategies for biosouring can be improved by monitoring VFA concentrations and microbial community dynamics in the oil reservoirs during secondary recovery of oil.

Research on enhancement of zero-valent iron on dissimilatory nitrate/nitrite reduction to ammonium of Desulfovibrio sp. CMX

The process of nitrate dissimilation to ammonium (DNRA) is an important way for storing nitrogen in nature and DNRA is a key step in efficient recovery of nitrogen in wastewater. However, in view of the low conversion efficiency of DNRA, zero-valent iron (ZVI) was used to enhance the DNRA process of Desulfovibrio sp. CMX. ZVI can obviously promote the nitrate/nitrite reduction. The experiment indicated that 5 g/L 300 mesh ZVI could convert 5 mmol/L nitrate or nitrite to ammonium in 48 h or 36 h respectively, and the conversion ratio of NO₂^- to NH₄⁺ could reach more than 90%. The ZVI provided a suitable growth environment for the Desulfovibrio sp. CMX through chemical reduction of nitrite, production of divalent iron (Fe²⁺), reduction of oxidation-reduction potential (ORP) and adjustment of pH, which strengthened the DNRA performance. This experiment is advantageous for increasing efficiency of DNRA and provides a new idea for efficient recovery of nitrogen resources.

Effects of exposure to anionic surfactants (SDBS and SDS) on nitrogen removal of aerobic denitrifier

In order to explain the effect of anionic surfactants on aerobic denitrification in the urban river, sodium dodecyl benzene sulfonate (SDBS) and sodium dodecyl sulfonate (SDS) were added in aerobic denitrifier and the efficiency of nitrogen removal, microbial mechanisms, and enzyme activity was investigated in this study. The results showed that the total nitrogen (TN) and the nitrate nitrogen ( NO 3 - - N ) removal efficiency decreased as an increase of SDBS concentration. In contrast, 59.70% of the TN and 75.12% of NO 3 - - N were removed as the SDBS was 0 mg/L (Control). When SDBS was 200 mg/L (SDBS-200), the removal efficiency of TN and NO 3 - - N was reduced to 4.92% and 4.00%, respectively. However, the denitrification efficiency was significantly accelerated when the concentration of SDS increased, except for 200 mg/L treatment (SDS-200). As the SDS increased from 0 to 100 mg/L (SDS-100), the removal efficiency of TN and NO 3 - - N raised from 59.70% to 70.8% and from 75.12% to 85.08%, respectively. The community structure of aerobic denitrifiers was significantly affected in the SDBS and SDS. While the Cupriavidus and Achromobacter were dominant genera in the group of Control (39.59%, and 42.45%) and SDS-100 (44.40% and 34.86%), the relative abundance of Cupriavidus increased to 84.06% and 59.45% in the group of SDBS-200 and SDS-200, respectively. Enzyme activity assays proved that the nitrite reductase (NiR) relative activity of aerobic denitrification was suppressed by both SDBS and SDS. The increase in the SDS concentrations (from 0 to 50 mg/L) resulted in sharp growth of the nitrate reductase (NR) relative activities (from 100% to 146.86%). These findings demonstrated that SDBS and SDS affected aerobic denitrification efficiency of the aerobic denitrifiers by changing its microbial community structure and enzyme activity. PRACTITIONER POINTS: SDS strengthened aerobic denitrification at low concentration, but the aerobic denitrifiers were inhibited in SDBS. The variation of community structure played a vital role in the aerobic denitrification system. The enzyme activity was seriously affected by SDBS and SDS. Microorganisms and enzyme activity were synergistically involved in the aerobic denitrification.

Evaluating the effect of seasonal temperature changes on the efficiency of a rhizofiltration system in nitrogen removal from urban runoff

The study presents an evaluation of nitrogen removal efficiency of a pilot-scale rhizofiltration system in Pretoria, South Africa. The rhizofiltration system was divided into two sections, one side planted with common reeds (Phragmites australis) and the other side was without plants kept as a control. The objective of the study was to evaluate the influence of seasonal temperature on the removal of nitrogen species from the simulated urban runoff using the rhizofiltration system. The final effluent from the filter was collected bimonthly at different sampling points for 10 months after an application time of 5 min and 25 min. Duplicate samples were taken to determine the concentrations of TKN (Total Kjeldahl nitrogen), ammonium, nitrate and chemical oxygen demand (COD) for the raw influent and final effluent from the rhizofiltration system. Temperature and pH were determined on-site. During the monitoring period, there was no significant difference in the inflow concentration of ammonium in colder and warmer months for both planted and control sides. Furthermore, the composition of the feed medium to the rhizofilter was kept the same in both cold and warm season and for both planted and control sides. The removal of ammonium in colder and warmer months was not significant in both systems. At an average temperature increase of 5.2 °C in the warmer months, the ammonium removal efficiency in the planted side increased by 7.5%, while for the control side the removal efficiency increased by 2.4%. The difference in removal was not significant between the averages of effluent ammonium after an application time of 25 min in colder versus warmer months for the planted and control sides of the system. Furthermore, an increased nitrification rate was more evident in the planted than in the control side, which was subsequently denitrified. It was observed that 60.4% of nitrate concentration was potentially removed in the planted side whereas 45.4% was potentially denitrified in the control side. These results suggest positive correlation between nitrate concentration and the potential for denitrification. The nitrate removal efficiency dropped to 32.2% for the planted site and to 26.1% for the control system in colder months. Temperature had an effect on nitrogen removal, since nitrogen removal efficiency decreased in colder months. Complete nitrogen removal could not be achieved under the operating conditions.

Elucidating the Competition between Heterotrophic Denitrification and DNRA Using the Resource-Ratio Theory

Heterotrophic denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two microbial processes competing for two shared resources, namely, nitrate and organic carbon (COD). Their competition has great implications for nitrogen loss, conservation, and greenhouse gas emissions. Nevertheless, a comprehensive and mechanistic understanding of the governing factors for this competition is still lacking. We applied the resource-ratio theory to study this competition and validated the theory with experimental data from continuous cultures reported in the literature. Based on this theory, we revealed that influent COD/N ratio alone was not sufficient to predict the competition outcome as the boundary values for different competition outcomes changed substantially with influent resource concentrations. The stoichiometry of the two processes was determinative for the boundaries, whereas the affinity for the shared resources (K_S), maximum specific growth rate (μ_max) of the two species, and the dilution rate had significant impacts as well but mainly at low influent resource concentrations (e.g., <100 μM nitrate). The presented approach allows for a more comprehensive understanding of the parameters controlling microbial competition. The computational comparison between continuous and batch cultures could explain seemingly conflicting experimental results as to the impact of the COD/N ratio. The results also include testable hypotheses and tools for understanding and managing the fate of nitrate in ecosystems, which could also be applied more widely to other species competing for two shared resources.

The key role of Geobacter in regulating emissions and biogeochemical cycling of soil-derived greenhouse gases

In the past two decades, more and more attentions have been paid to soil-derived greenhouse gases (GHGs) including carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) because there are signs that they have rising negative impacts on the sustainability of the earth surface system. Farmlands, particularly paddy soils, have been regarded as the most important emitter of GHGs (nearly 17%) due to a large influx of fertilization and the abundance in animals, plants and microorganisms. Geobacter, as an electroactive microorganism widely occurred in soil, has been well studied on electron transport mechanisms and the direct interspecies electron transfer. These studies on Geobacter illustrate that it has the ability to be involved in the pathways of soil GHG emissions through redox reactions under anaerobic conditions. In this review, production mechanisms of soil-derived GHGs and the amount of these GHGs produced had been first summarized. The cycling process of CH₄ and N₂O was described from the view of microorganisms and discussed the co-culture relationships between Geobacter and other microorganisms. Furthermore, the role of Geobacter in the production of soil-derived GHGs is defined by biogeochemical cycling. The complete view on the effect of Geobacter on the emission of soil-derived GHGs has been shed light on, and appeals further investigation.

Changes in the ballast water tank bacterial community during a trans-sea voyage: Elucidation through next generation DNA sequencing

Ballast water (BW) mediated bioinvasion is one of the greatest threats to the health of aquatic ecosystems. Bacteria, unlike higher organisms, are transferred in large numbers through BW. Owing to their abundance and potential pathogenicity, they pose a direct threat to the prevailing microbiome in the recipient waters and also to human health. This study investigated the changes in the BW tank bacterial community during a trans-sea voyage from Visakhapatnam port, located along the east coast of India (Bay of Bengal) to Mumbai port, located along the west coast of India (Arabian Sea). Next generation sequencing was used to explore the unculturable segment of bacteria. The BW tank conditions led to a decrease in photoautotrophs and non-spore forming bacteria. On the other hand, biofilm forming and antibiotic producing bacteria, nutrient limiting condition sustaining bacteria, and those capable of synthesizing enzymes prerequisite for active metabolism under stress, increased over time. The shifts in the bacterial community were dependent on mechanisms adopted by the clades to cope with the BW tank conditions. Functional prediction of the bacterial community revealed a significant increase in the core metabolic functions, which enabled the survival of such bacteria. As the voyage progressed, an increase in the total viable bacteria in BW tanks could be attributed to the decrease in the abundance of phytoplankton and zooplankton. At the end of the voyage, the bacterial community in the BW tanks was significantly different, and the species diversity and richness were higher than that of the natural seawater (source water). Pathogenic species were more abundant during mid-voyage than at the end of the voyage, suggesting that voyage duration influences the pathogenic bacterial community. Investigating the fate of the discharged bacterial population at the deballasting point is a way forward in the assessment of marine bioinvasion.

DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems

This paper reviews dissimilatory nitrate reduction to ammonium (DNRA) in soils - a newly appreciated pathway of nitrogen (N) cycling in the terrestrial ecosystems. The reduction of NO₃^- occurs in two steps; in the first step, NO₃^- is reduced to NO₂^-; and in the second, unlike denitrification, NO₂^- is reduced to NH₄⁺ without intermediates. There are two sets of NO₃^-/NO₂^- reductase enzymes, i.e., Nap/Nrf and Nar/Nir; the former occurs on the periplasmic-membrane and energy conservation is respiratory via electron-transport-chain, whereas the latter is cytoplasmic and energy conservation is both respiratory and fermentative (Nir, substrate-phosphorylation). Since, Nir catalyzes both assimilatory- and dissimilatory-nitrate reduction, the nrfA gene, which transcribes the NrfA protein, is treated as a molecular-marker of DNRA; and a high nrfA/nosZ (N₂O-reductase) ratio favours DNRA. Recently, several crystal structures of NrfA have been presumed to producee N₂O as a byproduct of DNRA via the NO (nitric-oxide) pathway. Meta-analyses of about 200 publications have revealed that DNRA is regulated by oxidation state of soils and sediments, carbon (C)/N and NO₂^-/NO₃^- ratio, and concentrations of ferrous iron (Fe²⁺) and sulfide (S^2-). Under low-redox conditions, a high C/NO₃^- ratio selects for DNRA while a low ratio selects for denitrification. When the proportion of both C and NO₃^- are equal, the NO₂^-/NO₃^- ratio modulates partitioning of NO₃^-, and a high NO₂^-/NO₃^- ratio favours DNRA. A high S^2-/NO₃^- ratio also promotes DNRA in coastal-ecosystems and saline sediments. Soil pH, temperature, and fine soil particles are other factors known to influence DNRA. Since, DNRA reduces NO₃^- to NH₄⁺, it is essential for protecting NO₃^- from leaching and gaseous (N₂O) losses and enriches soils with readily available NH₄⁺-N to primary producers and heterotrophic microorganisms. Therefore, DNRA may be treated as a tool to reduce ground-water NO₃^- pollution, enhance soil health and improve environmental quality.

Isolation and Characterization of Nitrate-Reducing Bacteria as Potential Probiotics for Oral and Systemic Health

Recent evidence indicates that the reduction of salivary nitrate by oral bacteria can contribute to prevent oral diseases, as well as increase systemic nitric oxide levels that can improve conditions such as hypertension and diabetes. The objective of the current manuscript was to isolate nitrate-reducing bacteria from the oral cavity of healthy donors and test their in vitro probiotic potential to increase the nitrate-reduction capacity (NRC) of oral communities. Sixty-two isolates were obtained from five different donors of which 53 were confirmed to be nitrate-reducers. Ten isolates were selected based on high NRC as well as high growth rates and low acidogenicity, all being Rothia species. The genomes of these ten isolates confirmed the presence of nitrate- and nitrite reductase genes, as well as lactate utilization genes, and the absence of antimicrobial resistance, mobile genetic elements and virulence genes. The pH at which most nitrate was reduced differed between strains. However, acidic pH 6 always stimulated the reduction of nitrite compared to neutral pH 7 or slightly alkaline pH 7.5 (p < 0.01). We tested the effect of six out of 10 isolates on in vitro oral biofilm development in the presence or absence of 6.5 mM nitrate. The integration of the isolates into in vitro communities was confirmed by Illumina sequencing. The NRC of the bacterial communities increased when adding the isolates compared to controls without isolates (p < 0.05). When adding nitrate (prebiotic treatment) or isolates in combination with nitrate (symbiotic treatment), a smaller decrease in pH derived from sugar metabolism was observed (p < 0.05), which for some symbiotic combinations appeared to be due to lactate consumption. Interestingly, there was a strong correlation between the NRC of oral communities and ammonia production even in the absence of nitrate (R = 0.814, p < 0.01), which indicates that bacteria involved in these processes are related. As observed in our study, individuals differ in their NRC. Thus, some may have direct benefits from nitrate as a prebiotic as their microbiota naturally reduces significant amounts, while others may benefit more from a symbiotic combination (nitrate + nitrate-reducing probiotic). Future clinical studies should test the effects of these treatments on oral and systemic health.

Role of algal accumulations on the partitioning between N2 production and dissimilatory nitrate reduction to ammonium in eutrophic lakes

Cyanobacterial blooms change benthic nitrogen (N) cycling in eutrophic lake ecosystems by affecting organic carbon (OC) delivery and changing in nutrients availability. Denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) are critical dissimilatory nitrate reduction pathways that determine N removal and N recycling in aquatic environments. A mechanistic understanding of the influence of algal accumulations on partitioning among these pathways is currently lacking. In the present study, a manipulative experiment in aquarium tanks was conducted to determine the response of dissimilatory nitrate reduction pathways to changes in algal biomass, and the interactive effects of OC and nitrate. Potential dinitrogen (N₂) production and DNRA rates, and related functional gene abundances were determined during incubation of 3-4 weeks. The results indicated that high algal biomass promoted DNRA but not N₂ production. The concentrations of dissolved organic carbon were the primary factor affecting DNRA rates. Low nitrate availability limited N₂ production rates in treatments with algal pellets and without nitrate addition. Meanwhile, the AOAamoA gene abundance was significantly correlated with the nrfA and nirS gene abundances, suggesting that coupled nitrification-denitrification/DNRA was prevalent. Partitioning between N₂ production and DNRA was positively correlated with the ratios of dissolved organic carbon to nitrate. Correspondingly, in Lake Taihu during summer to fall, the relatively high organic carbon/nitrate might favorably facilitate DNRA over denitrification, subsequently sustaining cyanobacterial blooms.

Nitrate application decreased microbial biodiversity but stimulated denitrifiers in epiphytic biofilms on Ceratophyllum demersum

Among nitrogen species, nitrate is more stable than ammonium and nitrite, and it is an important nitrogenous pollutant in surface water. However, little is known about the characterization of epiphytic microbial communities on submersed macrophytes under nitrate loading. In this study, we investigated the co-occurring pattern and response of bacteria and microeukaryotes in epiphytic biofilms under nitrate loading. Nitrate loading significantly affected bacterial and eukaryotic communities, and turnover played greater contribution to the total dissimilarity than nestedness by partitioning beta-diversity analysis. Cyanobacteria, α-proteobacteria, β-proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, and γ-proteobacteria were dominant bacterial phyla/classes. Metazoan (phylum Arthropoda, Rotifera, Gastrotricha, Annelida, and Nematoda) and algae (phylum Bacillariophyta, Chlorophyta, and Streptophyta) were dominated in eukaryotic communities. The abundances of denitrifying bacteria (Rhodobacter, Acinetobacter, Bacillus, Flavobacterium, and Pseudomonas) and genes (nirS, cnorB, and nosZ) increased with nitrate loading. The network analysis showed there were complex interactions among photosynthetic microbes, metazoan, and bacteria (including denitrifiers) that they were potentially interrelated via photosynthesis, predation or feeding. This study provides new perspectives into understanding the factors affecting nitrate removal mechanisms in wetlands with submersed macrophytes.

N2 fixation dominates nitrogen cycling in a mangrove fiddler crab holobiont

Mangrove forests are among the most productive and diverse ecosystems on the planet, despite limited nitrogen (N) availability. Under such conditions, animal-microbe associations (holobionts) are often key to ecosystem functioning. Here, we investigated the role of fiddler crabs and their carapace-associated microbial biofilm as hotspots of microbial N transformations and sources of N within the mangrove ecosystem. 16S rRNA gene and metagenomic sequencing provided evidence of a microbial biofilm dominated by Cyanobacteria, Alphaproteobacteria, Actinobacteria, and Bacteroidota with a community encoding both aerobic and anaerobic pathways of the N cycle. Dinitrogen (N₂) fixation was among the most commonly predicted process. Net N fluxes between the biofilm-covered crabs and the water and microbial N transformation rates in suspended biofilm slurries portray these holobionts as a net N₂ sink, with N₂ fixation exceeding N losses, and as a significant source of ammonium and dissolved organic N to the surrounding environment. N stable isotope natural abundances of fiddler crab carapace-associated biofilms were within the range expected for fixed N, further suggesting active microbial N₂ fixation. These results extend our knowledge on the diversity of invertebrate-microbe associations, and provide a clear example of how animal microbiota can mediate a plethora of essential biogeochemical processes in mangrove ecosystems.

Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence

Social interaction between microbes can be described at many levels of details: from the biochemistry of cell-cell interactions to the ecological dynamics of populations. Choosing an appropriate level to model microbial communities without losing generality remains a challenge. Here we show that modeling cross-feeding interactions at an intermediate level between genome-scale metabolic models of individual species and consumer-resource models of ecosystems is suitable to experimental data. We applied our modeling framework to three published examples of multi-strain Escherichia coli communities with increasing complexity: uni-, bi-, and multi-directional cross-feeding of either substitutable metabolic byproducts or essential nutrients. The intermediate-scale model accurately fit empirical data and quantified metabolic exchange rates that are hard to measure experimentally, even for a complex community of 14 amino acid auxotrophies. By studying the conditions of species coexistence, the ecological outcomes of cross-feeding interactions, and each community’s robustness to perturbations, we extracted new quantitative insights from these three published experimental datasets. Our analysis provides a foundation to quantify cross-feeding interactions from experimental data, and highlights the importance of metabolic exchanges in the dynamics and stability of microbial communities.

The behavior of microbial communities such as the human microbiome is hard to predict by its species composition alone. Our efforts to engineer microbiomes—for example to improve human health—would benefit from mathematical models that accurately describe how microbes exchange metabolites with each other and how their environment shapes these exchanges. But what is an appropriate level of details for those models? We propose an intermediate level to model metabolic exchanges between microbes. We show that these models can accurately describe population dynamics in three laboratory communities and predicts their stability in response to perturbations such as changes in the nutrients available in the medium that they grow on. Our work suggests that a highly detailed metabolic network model is unnecessary for extracting ecological insights from experimental data and improves mathematical models so that one day we may be able to predict the behavior of real-world communities such as the human microbiome.

Availability of Nitrite and Nitrate as Electron Acceptors Modulates Anaerobic Toluene-Degrading Communities in Aquifer Sediments

Microorganisms are essential in the degradation of environmental pollutants. Aromatic hydrocarbons, e.g., benzene, toluene, ethylbenzene, and xylene (BTEX), are common aquifer contaminants, whose degradation in situ is often limited by the availability of electron acceptors. It is clear that different electron acceptors such as nitrate, iron, or sulfate support the activity of distinct degraders. However, this has not been demonstrated for the availability of nitrate vs. nitrite, both of which can be respired in reductive nitrogen cycling. Here via DNA-stable isotope probing, we report that nitrate and nitrite provided as electron acceptors in different concentrations and ratios not only modulated the microbial communities responsible for toluene degradation but also influenced how nitrate reduction proceeded. Zoogloeaceae members, mainly Azoarcus spp., were the key toluene degraders with nitrate-only, or both nitrate and nitrite as electron acceptors. In addition, a shift within Azoarcus degrader populations was observed on the amplicon sequence variant (ASV) level depending on electron acceptor ratios. In contrast, members of the Sphingomonadales were likely the most active toluene degraders when only nitrite was provided. Nitrate reduction did not proceed beyond nitrite in the nitrate-only treatment, while it continued when nitrite was initially also present in the microcosms. Likely, this was attributed to the fact that different microbial communities were stimulated and active in different microcosms. Together, these findings demonstrate that the availability of nitrate and nitrite can define degrader community selection and N-reduction outcomes. It also implies that nitrate usage efficiency in bioremediation could possibly be enhanced by an initial co-supply of nitrite, via modulating the active degrader communities.

Salt intrusion alters nitrogen cycling in tidal reaches as determined in field and laboratory investigations

Salinization is a growing problem throughout the world and poses a threat especially to freshwater ecosystems. However, much remains to be learned about the mechanisms by which salinity impacts microbially mediated biogeochemical processes. Elevated nitrogen (N) concentrations in estuarine ecosystems have led to their eutrophication, but the relationship between N transformation and the functional genes involved in the response to saltwater intrusion is poorly understood. Here, using the Minjiang River, a tidal river in southeastern China as an easily accessible natural laboratory, we conducted a 2-year field survey to investigate N speciation during ebb and flood tides. Then, in a laboratory experiment we simulated the varying degrees of salt intrusion that occur in natural tidal reaches. The microcosm study allowed quantitative assessments of N transformation and functional gene responses. The field surveys showed that concentrations of NH₄⁺ rose during flood tides, while the concentrations of NO₃^- and total N fluctuated. In the microcosms, NO₃^- concentrations decreased in response to salt pulses, due to simultaneous declines in the abundance of genes responsible for nitrification and increases in the abundance of those involved in dissimilatory nitrate reduction to ammonium (DNRA). The elevated salinity led to increased yields of NH₄⁺, a response that correlated positively with the abundance of nrfA genes, involved in DNRA. Furthermore, an increase in salinity promoted N₂O accumulation during the denitrification process. Altogether, our study suggests that saltwater intrusion leads to a decrease in nitrification while favoring N transformation via denitrification and DNRA and that N₂O accumulation in the water is dependent on the strength of the salt pulse.