Phylogenetic analysis of nitric oxide reductase gene homologues from aerobic ammonia-oxidizing bacteria

Autotrophic denitrification under anoxic conditions by newly discovered mixotrophic sulfide-oxidizing bacterium

Autotrophic denitrification (AutoDN) using sulfur represents a promising strategy for treating wastewater characterized by low carbon-to-nitrogen ratios (C/N). However, its widespread application is constrained by operational instability and the excessive sulfate accumulation. This study reports the isolation of Thauera sp. AutoDN2, a novel autotrophic denitrifier coupling nitrate reduction with sulfide oxidation while minizing sulfate production. AutoDN2 achieved nitrate removal of 99 ± 1 % at a sulfide-to-nitrogen ratio (S/N) of 4.8, primarily reducing nitrate to nitrite - a substrate for anaerobic ammonium oxidation (anammox), with minimal further reduction observed at S/N ratios ≥ 6.4. Unlike conventional sulfide-driven autotrophic denitrifiers, AutoDN2 predominantly generated elemental sulfur rather than sulfate, thereby mitigating secondary pollution. It also exhibited mixotrophic denitrification, indicating metabolic adaptability across a wide range of C/N ratios (0.3-5.0). These findings highlight AutoDN2's capability for sustainable treatment of organic-deficient, nitrate-rich wastewater, contributing to an integrated carbon-nitrogen-sulfur (CNS) cycle with reduced sulfate release.

Formation and Fate of Reactive Nitrogen during Biological Nitrogen Removal from Water: Important Yet Often Ignored Chemical Aspects of the Nitrogen Cycle

Hydroxylamine, nitrous acid, and nitric oxide are obligate intermediates or side metabolites in different nitrogen-converting microorganisms. These compounds are unstable and susceptible to the formation of highly reactive nitrogen species, including nitrogen dioxide, dinitrogen trioxide, nitroxyl, and peroxynitrite. Due to the high reactivity and cytotoxicity, the buildup of reactive nitrogen can affect the interplay of microorganisms/microbial processes, stimulate the reactions with organic compounds like organic micropollutants (OMP) and act as the precursors of nitrous oxide (N2O). However, there is little understanding of the occurrence and significance of reactive nitrogen during biological nitrogen conversions in engineered water systems. In this review, we evaluate the formation and fate of reactive nitrogen produced by microorganisms involved in biological nitrogen removal (BNR) processes, i.e., nitritation/nitrification, denitratation/denitrification, anammox, and the combined processes. While the formation of reactive nitrogen intermediates is entirely controlled by microbial activities, the consumption can be either biological or purely chemical. Changes in environmental conditions, such as redox transition, pH, and substrate availability, can imbalance the production and consumption of these reactive intermediates, thus leading to the transient accumulation of species. Based on previous experimental evidence, environmental relevance of reactive nitrogen in BNR systems, particularly related to abiotic N2O production and OMP transformation, is demonstrated.

Deoxygenation turns the coastal Red Sea lagoons into sources of nitrous oxide

Direct measurements of dissolved N₂O concentrations, fluxes and saturation percentages undertaken for the first time in two coastal lagoons - Al-Shabab and Al-Arbaeen, along the east coast of the Red Sea, revealed the region as a significant source of N₂O to the atmosphere. The exacerbated dissolved inorganic nitrogen (DIN) from various anthropogenic sources led to substantial oxygen depletion in both the lagoons, which turned to bottom anoxia at Al-Arbaeen lagoon during the spring season. We assume that the accumulation of N₂O is caused by nitrifier-denitrification in the hypoxic/anoxic boundaries. In fact, the results indicated that oxygen-depleted bottom waters favoured denitrification when the oxygenated surface waters recorded nitrification signals. Overall, the N₂O concentration ranged from 109.4 to 788.6 nM (40.6-325.6 nM) in spring and 58.7 to 209.8 nM (35.8-89.9 nM) in winter in the Al-Arbaeen (Al-Shabab) lagoon. The N₂O flux ranged from 647.1 to 1763.2 μmol m^-2 day^-1 (85.9 to 160.2 μmol m^-2 day^-1) and 112.5 to 150.8 μmol m^-2 day^-1 (76.1 to 88.7 μmol m^-2 day^-1) in the spring and winter respectively, in the Al-Arbaeen (Al-Shabab) lagoons. The ongoing developmental activities may worsen the current situation of hypoxia and associated biogeochemical feedbacks; therefore, the present results underline the need for continuous monitoring of both lagoons to restrict more severe oxygen depletion in future.

A novel Pseudomonas aeruginosa strain performs simultaneous heterotrophic nitrification-aerobic denitrification and aerobic phosphate removal

Nitrogen and phosphate removal from wastewater relies on different functional bacteria. In this study, a novel strain affiliated with Pseudomonas aeruginosa was isolated from activated sludge by gradient dilution and performed heterotrophic nitrification-aerobic denitrification and aerobic phosphate removal (HNADPR). The strain showed an ammonium removal efficiency of 87% and a phosphate removal efficiency of 97% under optimal conditions, such as C/N ratio of 10, P/N ratio of 0.1, temperature of 30°C, and pH of 7.5-8.5. The modified Gompertz model could fit well the heterotrophic ammonium nitrification, aerobic nitrite/nitrate denitrification, and aerobic phosphate removal processes. Functional gene amplification indicated that ammonium removal followed the complete HN-AD pathway (NH₄⁺ → NH₂OH → NO₂^- → NO₃^- → NO₂^- → NO → N₂O → N₂). Phosphate removal only occurred under aerobic conditions and ceased under anaerobic conditions. In successive aerobic cycles, the strain persistently took up phosphate. In wastewater, phosphate was aerobically converted into cell membrane, intracellular and extracellular polymeric substrates (EPS). Phosphorus in the form of phosphate monoester was pooled in EPS. A hypothetic aerobic phosphate removal model for strain SNDPR-01 is proposed to improve our understanding of the novel bacterial function of HNADPR.

Dynamics of bacterial functional genes and community structures during rhizoremediation of diesel-contaminated compost-amended soil

The objective of this study was to characterize the effects of organic soil amendment (compost) on bacterial populations associated with petroleum hydrocarbon (PH) degradation and nitrous oxide (N₂O) dynamics via pot experiments. Soil was artificially contaminated with diesel oil at total petroleum hydrocarbon (TPH) concentration of 30,000 mg·kg-soil^-1 and compost was mixed with the contaminated soil at a 1:9 ratio (w/w). Maize seedlings were planted in each pot and a total of ten pots with two treatments (compost-amended and unamended) were prepared. The pot experiment was conducted for 85 days. The compost-amended soil had a significantly higher TPH removal efficiency (51.1%) than unamended soil (21.4%). Additionally, the relative abundance of the alkB gene, which is associated with PH degradation, was higher in the compost-amended soil than in the unamended soil. Similarly, cnorB and nosZ (which are associated with nitric oxide (NO) and N₂O reduction, respectively) were also highly upregulated in the compost-amended soil. Moreover, the compost-amended soil exhibited higher richness and evenness indices, indicating that bacterial diversity was higher in the amended soil than in the unamended soil. Therefore, our findings may contribute to the development of strategies to enhance remediation efficiency and greenhouse gas mitigation during the rhizoremediation of diesel-contaminated soils.

Effects of environmental factors on denitrifying bacteria and functional genes in sediments of Bohai Sea, China

The ability of denitrifying microorganisms to respond to different ecological pressures remains unknown, especially in marine sediments rich in various heavy metals. Here, gene abundance and transcriptional abundance of five functional denitrification genes (narG, nirK, nirS, norB, and nosZ) in Bohai Sea sediments were examined, and high-throughput Illumina sequencing was used to analyze the community structure of nirK and nirS denitrifying bacteria. The nirS- and nirK-type denitrifying bacteria were classified into different genera. The heavy metal content in sediments was negatively correlated with transcriptional abundance of denitrifying genes, and RNA: DNA ratio for each gene was highest in central Bohai Sea. These results indicated the distribution of nitrite reductase denitrifying bacterial communities was affected by depth, total nitrogen, total phosphorus and sediment grain size. Heavy metal contamination in sediment environment may negatively regulate the transcriptional abundance of denitrifying genes and cause geographical differences in the denitrifying bacterial community structure.

An evaluation of primers for detecting denitrifiers via their functional genes

Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers.

C:N ratio shaped both taxonomic and functional structure of microbial communities in livestock and poultry breeding wastewater treatment reactor

C:N ratios play critical roles in determining the stability and performance of the wastewater treatment reactor. Here, we investigated bacterial and archaeal community composition, diversity, association networks, and functional profiles in livestock and poultry breeding wastewater (LPBW) with C:N gradients from 7.8 to 18.9 using 16S rRNA gene amplicon sequencing. Highest total nitrogen (TN) and total phosphorous (TP) removal rates were detected in the wastewater with high C:N ratios, while bacterial and archaeal communities in the wastewater varied across the four C:N ratios. Proteobacteria, Acidobacteria, and Bacteroides were generally the dominant phyla in the wastewater across treatments, with Candidatus Saccharibacteria being more enriched in the wastewater with high C:N ratios. Association network analysis showed that specific bacterial and archaeal taxa likely have similar metabolic activities allowing them to respond similarly to different C:N ratios. Bacteroidetes, Actinobacteria, Verrucomicrobia, Candidatus Saccharibacteria, and Proteobacteria were the keystone species found in the networks. Most dominant bacterial functions in the wastewater were chemoheterotrophy and aerobic chemoheterotrophy. Nitrite respiration, nitrous oxide denitrification, nitrate denitrification and nitrite denitrification were up-regulated with increased C:N ratios. Our findings provide new insights into our understanding of the compositions, potential associations, and predicted functional profiles of the microbial community in LPBW treated with different C:N ratios.

Effects of carbon source, C/N ratio, nitrate, temperature, and pH on N2O emission and functional denitrifying genes during heterotrophic denitrification

The effects of operational parameters such as carbon source, C/N ratio, initial nitrate concentration, temperature, and pH value on heterotrophic denitrification and functional denitrifying genes were evaluated. When methanol was used as the sole carbon source, complete denitrification was performed in a short time without nitrous oxide (N₂O) emission. Complete denitrification was performed at high C/N ratios (5.14 and 12.85) and low initial nitrate concentrations (75.9 and 151.6 mg N L^-1). The denitrification rate was not temperature-sensitive in the range of 25-35 °C, but tended to decrease at a low pH of 5-6. The relationships between N₂O emission and functional genes under various operational conditions were investigated by Pearson correlation and association network analyses. The C/N ratio was a key factor for N₂O emission during the heterotrophic denitrification process. This information on the denitrification performance and its association with functional gene dynamics under various operational conditions is useful for N₂O mitigation strategies for wastewater treatment processes.

A novel whole-cell biosensor of Pseudomonas aeruginosa to monitor the expression of quorum sensing genes

A novel whole-cell biosensor was developed to noninvasively and simultaneously monitor the in situ genetic activities of the four quorum sensing (QS) networks in Pseudomonas aeruginosa PAO1, including the las, rhl, pqs, and iqs systems. P. aeruginosa PAO1 is a model bacterium for studies of biofilm and pathogenesis while both processes are closely controlled by the QS systems. This biosensor worked well by selectively monitoring the expression of one representative gene from each network. In the biosensor, the promoter regions of lasI, rhlI, pqsA, and ambB (QS genes) controlled the fluorescent reporter genes of Turbo YFP, mTag BFP2, mNEON Green, and E2-Orange, respectively. The biosensor was successful in monitoring the impact of an important environmental factor, salt stress, on the genetic regulation of QS networks. High salt concentrations (≥ 20 g·L^-1) significantly downregulated rhlI, pqsA, and ambB after the biosensor was incubated for 17 h to 18 h at 37 °C, resulting in slow bacterial growth.

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.

Analysis of multiple haloarchaeal genomes suggests that the quinone-dependent respiratory nitric oxide reductase is an important source of nitrous oxide in hypersaline environments

Microorganisms, including Bacteria and Archaea, play a key role in denitrification, which is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. While the enzymology of denitrification is well understood in Bacteria, the details of the last two reactions in this pathway, which catalyse the reduction of nitric oxide (NO) via nitrous oxide (N₂ O) to nitrogen (N₂ ), are little studied in Archaea, and hardly at all in haloarchaea. This work describes an extensive interspecies analysis of both complete and draft haloarchaeal genomes aimed at identifying the genes that encode respiratory nitric oxide reductases (Nors). The study revealed that the only nor gene found in haloarchaea is one that encodes a single subunit quinone dependent Nor homologous to the qNor found in bacteria. This surprising discovery is considered in terms of our emerging understanding of haloarchaeal bioenergetics and NO management.

Quantifying nitrous oxide production pathways in wastewater treatment systems using isotope technology - A critical review

Nitrous oxide (N₂O) is an important greenhouse gas and an ozone-depleting substance which can be emitted from wastewater treatment systems (WWTS) causing significant environmental impacts. Understanding the N₂O production pathways and their contribution to total emissions is the key to effective mitigation. Isotope technology is a promising method that has been applied to WWTS for quantifying the N₂O production pathways. Within the scope of WWTS, this article reviews the current status of different isotope approaches, including both natural abundance and labelled isotope approaches, to N₂O production pathways quantification. It identifies the limitations and potential problems with these approaches, as well as improvement opportunities. We conclude that, while the capabilities of isotope technology have been largely recognized, the quantification of N₂O production pathways with isotope technology in WWTS require further improvement, particularly in relation to its accuracy and reliability.

Nutrient variability and its influence on nitrogen processes in a highly turbid tropical estuary (Bangpakong, Gulf of Thailand)

Estuarine ecosystems in SE Asia have been poorly studied when compared to other tropical environments. Important gaps exist particularly in the understanding of their biogeochemical function and contribution to global change. In this work we looked into N-turnover in the water column and sediments of the Bangpakong estuary (13°N). A seasonal sampling program was performed along the salinity gradient covering different stretches of the estuary (68km). Key physical and chemical characteristics were also monitored in order to unravel possible environmental controls. Results showed the occurrence of active denitrification in sediments (5.7-50.9nmol N-N2/(cm(3)·hr)), and water column (3.5-1044pmol N-N2/(cm(3)·hr)). No seasonal or spatial variability was detected for denitrification potential in sediment samples. However, in the water column, the denitrification activity peaked during the transition season in the downstream sites coinciding with high turbidity levels. Therefore, in that period of the year, the water column compartment may be an important contributor to nitrate reduction within the estuary. The rather low nitrification rates detected were not always measurable, probably due to the reduced oxygen content and high siltation. This study is one of the few dealing simultaneously with sediments and water column processes in a highly turbid tropical estuary. Therefore, it emerges as a valuable contribution for the understanding of the dynamics of the nitrogen cycle in tropical environments by exploring the role of estuarine N microbial activity in reducing the effects of increased nitrogen loads.

New Dimensions in Microbial Ecology-Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment

During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5'phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane monooxygenase (pmoA) for methane oxidizing bacteria.

Diversity, structure, and size of N(2)O-producing microbial communities in soils--what matters for their functioning?

Nitrous oxide (N(2)O) is mainly generated via nitrification and denitrification processes in soils and subsequently emitted into the atmosphere where it causes well-known radiative effects. How nitrification and denitrification are affected by proximal and distal controls has been studied extensively in the past. The importance of the underlying microbial communities, however, has been acknowledged only recently. Particularly, the application of molecular methods to study nitrifiers and denitrifiers directly in their habitats enabled addressing how environmental factors influence the diversity, community composition, and size of these functional groups in soils and whether this is of relevance for their functioning and N(2)O production. In this review, we summarize the current knowledge on community-function interrelationships. Aerobic nitrification (ammonia oxidation) and anaerobic denitrification are clearly under different controls. While N(2)O is an obligatory intermediate in denitrification, its production during ammonia oxidation depends on whether nitrite, the end product, is further reduced. Moreover, individual strains vary strongly in their responses to environmental cues, and so does N(2)O production. We therefore conclude that size and structure of both functional groups are relevant with regard to production and emission of N(2)O from soils. Diversity affects on function, however, are much more difficult to assess, as it is not resolved as yet how individual nitrification or denitrification genotypes are related to N(2)O production. More research is needed for further insights into the relation of microbial communities to ecosystem functions, for instance, how the actively nitrifying or denitrifying part of the community may be related to N(2)O emission.

Soil moisture and pH control relative contributions of fungi and bacteria to N2O production

Fungal N(2)O production has been progressively recognized, but its controlling factors remain unclear. This study examined the impacts of soil moisture and pH on fungal and bacterial N(2)O production in two ecosystems, conventional farming and plantation forestry. Four treatments, antibiotic-free soil and soil amended with streptomycin, cycloheximide, or both were used to determine N(2)O production of fungi versus bacteria. Soil moisture and pH effects were assessed under 65-90 % water-filled pore space (WFPS) and pH 4.0-9.0, respectively. Irrespective of antibiotic treatments, soil N(2)O fluxes peaked at 85-90 % WFPS and pH 7.0 or 8.0, indicating that both fungi and bacteria preferred more anoxic and neutral or slightly alkaline conditions in producing N(2)O. However, compared with bacteria, fungi contributed more to N(2)O production under sub-anoxic and acidic conditions. Real-time polymerase chain reaction of 16S, ITS rDNA, and denitrifying genes for quantifications of bacteria, fungi, and denitrifying bacteria, respectively, showed that fungi were more abundant at acidic pH, whereas total and denitrifying bacteria favored neutral conditions. Such variations in the abundance appeared to be related to the pH effects on the relative fungal and bacterial contribution to N(2)O production.

Effects of water-saving irrigation on emissions of greenhouse gases and prokaryotic communities in rice paddy soil

The effects of water-saving irrigation on emissions of greenhouse gases and soil prokaryotic communities were investigated in an experimental rice field. The water layer was kept at 1-2 cm in the water-saving (WS) irrigation treatment and at 6 cm in the continuous flooding (CF) irrigation treatment. WS irrigation decreased CH(4) emissions by 78 % and increased N(2)O emissions by 533 %, resulting in 78 % reduction of global warming potential compared to the CF irrigation. WS irrigation did not affect the abundance or phylogenetic distribution of bacterial/archaeal 16S rRNA genes and the abundance of bacterial/archaeal 16S rRNAs. The transcript abundance of CH(4) emission-related genes generally followed CH(4) emission patterns, but the difference in abundance between mcrA transcripts and amoA/pmoA transcripts best described the differences in CH(4) emissions between the two irrigation practices. WS irrigation increased the relative abundance of 16S rRNAs and functional gene transcripts associated with Anaeromyxobacter and Methylocystis spp., suggesting that their activities might be important in emissions of the greenhouse gases. The N(2)O emission patterns were not reflected in the abundance of N(2)O emission-related genes and transcripts. We showed that the alternative irrigation practice was effective for mitigating greenhouse gas emissions from rice fields and that it did not affect the overall size and structure of the soil prokaryotic community but did affect the activity of some groups.

Identification of key nitrous oxide production pathways in aerobic partial nitrifying granules

The identification of the key nitrous oxide (N2O) production pathways is important to establish a strategy to mitigate N2O emission. In this study, we combined real-time gas-monitoring analysis, (15)N stable isotope analysis, denitrification functional gene transcriptome analysis and microscale N2O concentration measurements to identify the main N2O producers in a partial nitrification (PN) aerobic granule reactor, which was fed with ammonium and acetate. Our results suggest that heterotrophic denitrification was the main contributor to N2O production in our PN aerobic granule reactor. The heterotrophic denitrifiers were probably related to Rhodocyclales bacteria, although different types of bacteria were active in the initial and latter stages of the PN reaction cycles, most likely in response to the presence of acetate. Hydroxylamine oxidation and nitrifier denitrification occurred, but their contribution to N2O emission was relatively small (20-30%) compared with heterotrophic denitrification. Our approach can be useful to quantitatively examine the relative contributions of the three pathways (hydroxylamine oxidation, nitrifier denitrification and heterotrophic denitrification) to N2O emission in mixed microbial populations.

Denitrifier community in the oxygen minimum zone of a subtropical deep reservoir

Denitrification is an important pathway for nitrogen removal from aquatic systems and this could benefit water quality. However, little is known about the denitrifier community composition and key steps of denitrification in the freshwater environments, and whether different bacteria have a role in multiple processes of denitrification reduction. In this study, quantitative PCR, quantitative RT-PCR, clone library and 454 pyrosequencing were used together to investigate the bacterial and denitrifier community in a subtropical deep reservoir during the strongly stratified period. Our results indicated that the narG gene recorded the highest abundance among the denitrifying genes (2.76×10⁹ copies L⁻¹ for DNA and 4.19×10⁸ copies L⁻¹ for RNA), and the lowest value was nosZ gene (7.56×10⁵ copies L⁻¹ for DNA and undetected for RNA). The RNA: DNA ratios indicated that narG gene was the most active denitrifying gene in the oxygen minimum zone of Dongzhen Reservoir. Further, α-, β- and γ- Proteobacteria were the overwhelmingly dominant classes of denitrifier communities. Each functional gene had its own dominant groups which were different at the genus level: the narG gene was dominated by Albidiferax, while nirS gene was dominated by Dechloromonas. The main OTU of nirK gene was Rhodopseudomonas palustris, but for norB and nosZ genes, they were Bacillus and Bradyrhizobium, respectively. These results contribute to the understanding of linkages between denitrifier community, function and how they work together to complete the denitrification process. Studies on denitrifier community and activity may be useful in managing stratified reservoirs for the ecosystem services and aiding in constructing nitrogen budgets.

Nitrous oxide emissions from wastewater treatment processes

Nitrous oxide (N(2)O) emissions from wastewater treatment plants vary substantially between plants, ranging from negligible to substantial (a few per cent of the total nitrogen load), probably because of different designs and operational conditions. In general, plants that achieve high levels of nitrogen removal emit less N(2)O, indicating that no compromise is required between high water quality and lower N(2)O emissions. N(2)O emissions primarily occur in aerated zones/compartments/periods owing to active stripping, and ammonia-oxidizing bacteria, rather than heterotrophic denitrifiers, are the main contributors. However, the detailed mechanisms remain to be fully elucidated, despite strong evidence suggesting that both nitrifier denitrification and the chemical breakdown of intermediates of hydroxylamine oxidation are probably involved. With increased understanding of the fundamental reactions responsible for N(2)O production in wastewater treatment systems and the conditions that stimulate their occurrence, reduction of N(2)O emissions from wastewater treatment systems through improved plant design and operation will be achieved in the near future.

Spatial distribution of prokaryotic symbionts and ammoxidation, denitrifier bacteria in marine sponge Astrosclera willeyana

The present knowledge of microbial community mainly focus on total sponge, the spatial distribution of microbes in sponges is rarely known, especially those with potential ecological functions. In this study, based on gene library and ∫-LIBSHUFF analysis, the spatial distribution of prokaryotic symbionts and nitrogen cycling genes in the cortex and endosome sections of sponge Astrosclera willeyana were investigated. A significance difference of bacterial phylotypes between the cortex and endosome was revealed. For example Bacteroidetes, Frankineae and Propionibacterineae were detected only in the endosome, whereas Cyanobacteria, Planctomycetacia and Micrococcineae were only associated with the cortex. Some branches of α-Proteobacteria, γ-Proteobacteria, Corynebacterineae, Acidimicobidae, Crenarchaeota and Euryarchaeota also showed distribution difference. Bacterial denitrifiers and ammonia oxidizing bacteria (AOB) were observed using nirS and amoA genes as markers. Particularly, AOB were only associated with the endosome. This study highlighted the spatial distribution of bacterial symbionts especially those with ammonia oxidization function.

N2O production rate of an enriched ammonia-oxidising bacteria culture exponentially correlates to its ammonia oxidation rate

The relationship between the ammonia oxidation rate (AOR) and nitrous oxide production rate (N(2)OR) of an enriched ammonia-oxidising bacteria (AOB) culture was investigated. The AOB culture was enriched in a nitritation system fed with synthetic anaerobic digester liquor. The AOR was controlled by adjusting the dissolved oxygen (DO) and pH levels and also by varying the initial ammonium (NH(4)(+)) concentration in batch experiments. Tests were also performed directly on the parent reactor where a stepwise decrease/increase in DO was implemented to alter AOR. The experimental data indicated a clear exponential relationship between the biomass specific N(2)OR and AOR. Four metabolic models were used to analyse the experimental data. The metabolic model formulated based on aerobic N(2)O production from the decomposition of nitrosyl radical (NOH) predicted the exponential correlation observed experimentally. The experimental data could not be reproduced by models developed on the basis of N(2)O production through nitrite (NO(2)(-)) and nitric oxide (NO) reduction by AOB.

Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil

Nitrification of excess ammonia in soil causes eutrophication of water resources and emission of atmospheric N(2) O gas. The first step of nitrification, ammonia oxidation, is mediated by Archaea as well as Bacteria. The physiological reactions mediated by ammonia-oxidizing archaea (AOA) and their contribution to soil nitrification are still unclear. Results of non-culture-based studies have shown the thaumarchaeotal group I.1b lineage of AOA to be dominant over both AOA of group I.1a and ammonia-oxidizing bacteria in various soils. We obtained from an agricultural soil a highly enriched ammonia-oxidizing culture dominated by a single archaeal population [c. 90% of total cells, as determined microscopically (by fluorescence in situ hybridization) and by quantitative PCR of its 16S rRNA gene]. The archaeon (termed 'strain JG1') fell within thaumarchaeotal group I.1b and was related to the moderately thermophilic archaeon, Candidatus Nitrososphaera gargensis, and the mesophilic archaeon, Ca. Nitrososphaera viennensis with 97.0% and 99.1% 16S rRNA gene sequence similarity respectively. Strain JG1 was neutrophilic (growth range pH 6.0-8.0) and mesophilic (growth range temperature 25-40°C). The optimum temperature of strain JG1 (35-40°C) is > 10°C higher than that of ammonia-oxidizing bacteria (AOB). Membrane analysis showed that strain JG1 contained a glycerol dialkyl glycerol tetraether, GDGT-4, and its regioisomer as major core lipids; this crenarchaeol regioisomer was previously detected in similar abundance in the thermophile, Ca. N. gargensis and has been frequently observed in tropical soils. Substrate uptake assays showed that the affinity of strain JG1 for ammonia and oxygen was much higher than those of AOB. These traits may give a competitive advantage to AOA related to strain JG1 in oligotrophic environments. (13) C-bicarbonate incorporation into archaeal lipids of strain JG1 established its ability to grow autotrophically. Strain JG1 produced a significant amount of N(2) O gas - implicating AOA as a possible source of N(2) O emission from soils. Sequences of archaeal amoA and 16S rRNA genes closely related to those of strain JG1 have been retrieved from various terrestrial environments in which lineage of strain JG1 is likely engaged in autotrophic nitrification.

Trace metal requirements for microbial enzymes involved in the production and consumption of methane and nitrous oxide

Fluxes of greenhouse gases to the atmosphere are heavily influenced by microbiological activity. Microbial enzymes involved in the production and consumption of greenhouse gases often contain metal cofactors. While extensive research has examined the influence of Fe bioavailability on microbial CO(2) cycling, fewer studies have explored metal requirements for microbial production and consumption of the second- and third-most abundant greenhouse gases, methane (CH(4)), and nitrous oxide (N(2)O). Here we review the current state of biochemical, physiological, and environmental research on transition metal requirements for microbial CH(4) and N(2)O cycling. Methanogenic archaea require large amounts of Fe, Ni, and Co (and some Mo/W and Zn). Low bioavailability of Fe, Ni, and Co limits methanogenesis in pure and mixed cultures and environmental studies. Anaerobic methane oxidation by anaerobic methanotrophic archaea (ANME) likely occurs via reverse methanogenesis since ANME possess most of the enzymes in the methanogenic pathway. Aerobic CH(4) oxidation uses Cu or Fe for the first step depending on Cu availability, and additional Fe, Cu, and Mo for later steps. N(2)O production via classical anaerobic denitrification is primarily Fe-based, whereas aerobic pathways (nitrifier denitrification and archaeal ammonia oxidation) require Cu in addition to, or possibly in place of, Fe. Genes encoding the Cu-containing N(2)O reductase, the only known enzyme capable of microbial N(2)O conversion to N(2), have only been found in classical denitrifiers. Accumulation of N(2)O due to low Cu has been observed in pure cultures and a lake ecosystem, but not in marine systems. Future research is needed on metalloenzymes involved in the production of N(2)O by enrichment cultures of ammonia oxidizing archaea, biological mechanisms for scavenging scarce metals, and possible links between metal bioavailability and greenhouse gas fluxes in anaerobic environments where metals may be limiting due to sulfide-metal scavenging.

Enrichment and characterization of an autotrophic ammonia-oxidizing archaeon of mesophilic crenarchaeal group I.1a from an agricultural soil

Soil nitrification is an important process for agricultural productivity and environmental pollution. Though one cultivated representative of ammonia-oxidizing Archaea from soil has been described, additional representatives warrant characterization. We describe an ammonia-oxidizing archaeon (strain MY1) in a highly enriched culture derived from agricultural soil. Fluorescence in situ hybridization microscopy showed that, after 2 years of enrichment, the culture was composed of >90% archaeal cells. Clone libraries of both 16S rRNA and archaeal amoA genes featured a single sequence each. No bacterial amoA genes could be detected by PCR. A [¹³C]bicarbonate assimilation assay showed stoichiometric incorporation of ¹³C into Archaea-specific glycerol dialkyl glycerol tetraethers. Strain MY1 falls phylogenetically within crenarchaeal group I.1a; sequence comparisons to "Candidatus Nitrosopumilus maritimus" revealed 96.9% 16S rRNA and 89.2% amoA gene similarities. Completed growth assays showed strain MY1 to be chemoautotrophic, mesophilic (optimum at 25°C), neutrophilic (optimum at pH 6.5 to 7.0), and nonhalophilic (optimum at 0.2 to 0.4% salinity). Kinetic respirometry assays showed that strain MY1's affinities for ammonia and oxygen were much higher than those of ammonia-oxidizing bacteria (AOB). The yield of the greenhouse gas N₂O in the strain MY1 culture was lower but comparable to that of soil AOB. We propose that this new soil ammonia-oxidizing archaeon be designated "Candidatus Nitrosoarchaeum koreensis."

Denitrification in Gram-positive bacteria: an underexplored trait

Denitrifying organisms are essential in removing fixed nitrogen pollutants from ecosystems (e.g. sewage sludge). They can be detrimental (e.g. for agricultural soil) and can also produce the greenhouse gas N2O (nitrous oxide). Therefore a more comprehensive understanding of this process has become increasingly important regarding its global environmental impact. Even though bacterial genome sequencing projects may reveal new data, to date the denitrification abilities and features in Gram-positive bacteria are still poorly studied and understood. The present review evaluates current knowledge on the denitrification trait in Gram-positive bacteria and addresses the likely existence of unknown denitrification genes. In addition, current molecular tools to study denitrification gene diversity in pure cultures and environmental samples seem to be highly biased, and additional novel approaches for the detection of denitrifying (Gram-positive) bacteria appear to be crucial in re-assessing the real diversity of denitrifiers.

Determining the distribution of marine and coastal ammonia-oxidizing archaea and bacteria using a quantitative approach

The oxidation of ammonia to nitrite is the first and often rate-limiting step in nitrification and plays an important role in both nitrogen and carbon cycling. This process is carried out by two distinct groups of microorganisms: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This chapter describes methods for measuring the abundance of AOA and AOB using ammonia monooxygenase subunit A (amoA) genes, with a particular emphasis on marine and coastal systems. We also describe quantitative measures designed to target two specific clades of marine AOA: the "shallow" (group A) and "deep" (group B) water column AOA.

Microbial nitrogen cycling processes in oxygen minimum zones

Oxygen minimum zones (OMZs) harbor unique microbial communities that rely on alternative electron acceptors for respiration. Conditions therein enable an almost complete nitrogen (N) cycle and substantial N-loss. N-loss in OMZs is attributable to anammox and heterotrophic denitrification, whereas nitrate reduction to nitrite along with dissimilatory nitrate reduction to ammonium are major remineralization pathways. Despite virtually anoxic conditions, nitrification also occurs in OMZs, converting remineralized ammonium to N-oxides. The concurrence of all these processes provides a direct channel from organic N to the ultimate N-loss, whereas most individual processes are likely controlled by organic matter. Many microorganisms inhabiting the OMZs are capable of multiple functions in the N- and other elemental cycles. Their versatile metabolic potentials versus actual activities present a challenge to ecophysiological and biogeochemical measurements. These challenges need to be tackled before we can realistically predict how N-cycling in OMZs, and thus oceanic N-balance, will respond to future global perturbations.

Field application of nitrogen and phenylacetylene to mitigate greenhouse gas emissions from landfill cover soils: effects on microbial community structure

Landfills are large sources of CH(4), but a considerable amount of CH(4) can be removed in situ by methanotrophs if their activity can be stimulated through the addition of nitrogen. Nitrogen can, however, lead to increased N(2)O production. To examine the effects of nitrogen and a selective inhibitor on CH(4) oxidation and N(2)O production in situ, 0.5 M of NH(4)Cl and 0.25 M of KNO(3), with and without 0.01% (w/v) phenylacetylene, were applied to test plots at a landfill in Kalamazoo, MI from 2007 November to 2009 July. Nitrogen amendments stimulated N(2)O production but had no effect on CH(4) oxidation. The addition of phenylacetylene stimulated CH(4) oxidation while reducing N(2)O production. Methanotrophs possessing particulate methane monooxygenase and archaeal ammonia-oxidizers (AOAs) were abundant. The addition of nitrogen reduced methanotrophic diversity, particularly for type I methanotrophs. The simultaneous addition of phenylacetylene increased methanotrophic diversity and the presence of type I methanotrophs. Clone libraries of the archaeal amoA gene showed that the addition of nitrogen increased AOAs affiliated with Crenarchaeal group 1.1b, while they decreased with the simultaneous addition of phenylacetylene. These results suggest that the addition of phenylacetylene with nitrogen reduces N(2)O production by selectively inhibiting AOAs and/or type II methanotrophs.

Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment

The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments.

Effect of nutrient and selective inhibitor amendments on methane oxidation, nitrous oxide production, and key gene presence and expression in landfill cover soils: characterization of the role of methanotrophs, nitrifiers, and denitrifiers

Methane and nitrous oxide are both potent greenhouse gasses, with global warming potentials approximately 25 and 298 times that of carbon dioxide. A matrix of soil microcosms was constructed with landfill cover soils collected from the King Highway Landfill in Kalamazoo, Michigan and exposed to geochemical parameters known to affect methane consumption by methanotrophs while also examining their impact on biogenic nitrous oxide production. It was found that relatively dry soils (5% moisture content) along with 15 mg NH (4) (+) (kg soil)(-1) and 0.1 mg phenylacetylene(kg soil)(-1) provided the greatest stimulation of methane oxidation while minimizing nitrous oxide production. Microarray analyses of pmoA showed that the methanotrophic community structure was dominated by Type II organisms, but Type I genera were more evident with the addition of ammonia. When phenylacetylene was added in conjunction with ammonia, the methanotrophic community structure was more similar to that observed in the presence of no amendments. PCR analyses showed the presence of amoA from both ammonia-oxidizing bacteria and archaea, and that the presence of key genes associated with these cells was reduced with the addition of phenylacetylene. Messenger RNA analyses found transcripts of pmoA, but not of mmoX, nirK, norB, or amoA from either ammonia-oxidizing bacteria or archaea. Pure culture analyses showed that methanotrophs could produce significant amounts of nitrous oxide, particularly when expressing the particulate methane monooxygenase (pMMO). Collectively, these data suggest that methanotrophs expressing pMMO played a role in nitrous oxide production in these microcosms.

Effects of heavy metal contamination upon soil microbes: lead-induced changes in general and denitrifying microbial communities as evidenced by molecular markers

Lead (Pb) is a common environmental contaminant found in soils. Unlike other metals, Pb has no biological role, and is potentially toxic to microorganisms. Effects of low (1 ppm) and high (500–2000) levels of lead (Pb) upon the soil microbial community was investigated by the PCR/DGGE analysis of the 16S and nirK gene markers, indicative of general microbial community and denitrifying community, respectively. Community analysis by use of those markers had shown that Pb has detectable effects upon the community diversity even at the lowest concentration tested. Analysis of sample diversity and similarity between the samples suggested that there are several thresholds crossed as metal concentration increase, each causing a substantial change in microbial diversity. Preliminary data obtained in this study suggest that the denitrifying microbial community adapts to elevated levels of Pb by selecting for metal-resistant forms of nitrite reductases.

New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation

Microbial activities drive the global nitrogen cycle, and in the past few years, our understanding of nitrogen cycling processes and the micro-organisms that mediate them has changed dramatically. During this time, the processes of anaerobic ammonium oxidation (anammox), and ammonia oxidation within the domain Archaea, have been recognized as two new links in the global nitrogen cycle. All available evidence indicates that these processes and organisms are critically important in the environment, and particularly in the ocean. Here we review what is currently known about the microbial ecology of anaerobic and archaeal ammonia oxidation, highlight relevant unknowns and discuss the implications of these discoveries for the global nitrogen and carbon cycles.

Nitric oxide microsensor for high spatial resolution measurements in biofilms and sediments

Nitric oxide (NO) is a ubiquitous biomolecule that is known as a signaling compound in eukaryotes and prokaryotes. In addition, NO is involved in all conversions of the biogeochemical nitrogen cycle: denitrification, nitrification, and the anaerobic oxidation of ammonium (Anammox). Until now, NO has not been measured with high spatial resolution within microbial communities, such as biofilms, sediments, aggregates, or microbial mats, because the available sensors are not robust enough and their spatial resolution is insufficient. Here we describe the fabrication and application of a novel Clark-type NO microsensor with an internal reference electrode and a guard anode. The NO microsensor has a spatial resolution of 60-80 microm, a sensitivity of 2 pA microM-1, and a detection limit of approximately 30 nM. Hydrogen sulfide (H2S) was found to be a major interfering compound for the electrochemical detection of NO. The application of the novel NO microsensor to nitrifying biofilms and marine sediments revealed dynamic NO concentration profiles with peaks in the oxic parts of the samples. The local concentrations suggested that NO may be an important bioactive compound in natural environments. The consumption and production of NO occurs in separate regions of stratified microbial communities and indicates that it is linked to distinct biogeochemical cycles.

Nitric oxide reductase (norB) gene sequence analysis reveals discrepancies with nitrite reductase (nir) gene phylogeny in cultivated denitrifiers

Gene sequence analysis of cnorB and qnorB, both encoding nitric oxide reductases, was performed on pure cultures of denitrifiers, for which previously nir genes were analysed. Only 30% of the 227 denitrifying strains rendered a norB amplicon. The cnorB gene was dominant in Alphaproteobacteria, and dominantly coexisted with the nirK gene, coding for the copper-containing nitrite reductase. Both norB genes were equally present in Betaproteobacteria but no linked distributional pattern of nir and norB genes could be observed. The overall cnorB phylogeny was not congruent with the widely accepted organism phylogeny based on 16S rRNA gene sequence analysis, with strains from different bacterial classes having identical cnorB sequences. Denitrifiers and non-denitrifiers could be distinguished through qnorB gene phylogeny, without further grouping at a higher taxonomic resolution. Comparison of nir and norB phylogeny revealed that genetic linkage of both genes is not widespread among denitrifiers. Thus, independent evolution of the genes for both nitrogen oxide reductases does also occur.

Oxygen exchange between (de)nitrification intermediates and H2O and its implications for source determination of NO3- and N2O: a review

Stable isotope analysis of oxygen (O) is increasingly used to determine the origin of nitrate (NO(3)-) and nitrous oxide (N(2)O) in the environment. The assumption underlying these studies is that the (18)O signature of NO(3)- and N(2)O provides information on the different O sources (O(2) and H(2)O) during the production of these compounds by various biochemical pathways. However, exchange of O atoms between H(2)O and intermediates of the (de)nitrification pathways may change the isotopic signal and thereby bias its interpretation for source determination. Chemical exchange of O between H(2)O and various nitrogenous oxides has been reported, but the probability and extent of its occurrence in terrestrial ecosystems remain unclear. Biochemical O exchange between H(2)O and nitrogenous oxides, NO(2)- in particular, has been reported for monocultures of many nitrifiers and denitrifiers that are abundant in nature, with exchange rates of up to 100%. Therefore, biochemical O exchange is likely to be important in most soil ecosystems, and should be taken into account in source determination studies. Failing to do so might lead to (i) an overestimation of nitrification as NO(3)- source, and (ii) an overestimation of nitrifier denitrification and nitrification-coupled denitrification as N(2)O production pathways. A method to quantify the rate and controls of biochemical O exchange in ecosystems is needed, and we argue this can only be done reliably with artificially enriched (18)O compounds. We conclude that in N source determination studies, the O isotopic signature of especially N(2)O should only be used with extreme caution.

Nitrogen transformations in stratified aquatic microbial ecosystems

New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a microm-mm scale. A large and ever-expanding knowledge base about nitrogen fixation, nitrification, denitrification, and dissimilatory reduction of nitrate to ammonium, and about the microorganisms performing the processes, has been produced by use of these techniques. During the last decade the discovery of anammmox bacteria and migrating, nitrate accumulating bacteria performing dissimilatory reduction of nitrate to ammonium have given new dimensions to the understanding of nitrogen cycling in nature, and the occurrence of these organisms and processes in stratified microbial communities will be described in detail.

Nitrosospira spp. can produce nitrous oxide via a nitrifier denitrification pathway

Nitrous oxide (N(2)O) emission from soils is a major contributor to the atmospheric loading of this potent greenhouse gas. It is thought that autotrophic ammonia oxidizing bacteria (AOB) are a significant source of soil-derived N(2)O and a denitrification pathway (i.e. reduction of NO(2) (-) to NO and N(2)O), so-called nitrifier denitrification, has been demonstrated as a N(2)O production mechanism in Nitrosomonas europaea. It is thought that Nitrosospira spp. are the dominant AOB in soil, but little information is available on their ability to produce N(2)O or on the existence of a nitrifier denitrification pathway in this lineage. This study aims to characterize N(2)O production and nitrifier denitrification in seven strains of AOB representative of clusters 0, 2 and 3 in the cultured Nitrosospira lineage. Nitrosomonas europaea ATCC 19718 and ATCC 25978 were analysed for comparison. The aerobically incubated test strains produced significant (P < 0.001) amounts of N(2)O and total N(2)O production rates ranged from 2.0 amol cell(-1) h(-1), in Nitrosospira tenuis strain NV12, to 58.0 amol cell(-1) h(-1), in N. europaea ATCC 19718. Nitrosomonas europaea ATCC 19718 was atypical in that it produced four times more N(2)O than the next highest producing strain. All AOB tested were able to carry out nitrifier denitrification under aerobic conditions, as determined by production of (15)N-N(2)O from applied (15)N-NO(2) (-). Up to 13.5% of the N(2)O produced was derived from the exogenously applied (15)N-NO(2) (-). The results suggest that nitrifier denitrification could be a universal trait in the betaproteobacterial AOB and its potential ecological significance is discussed.