Detection and diversity of expressed denitrification genes in estuarine sediments after reverse transcription-PCR amplification from mRNA

Dynamics of nitrogen genes in intertidal sediments of Darwin Harbour and their connection to N-biogeochemistry

Microbial mediated nitrogen (N) transformation is subject to multiple controlling factors such as prevailing physical and chemical conditions, and little is known about these processes in sediments of wet-dry tropical macrotidal systems such as Darwin Harbour in North Australia. To understand key transformations, we assessed the association between the relative abundance of nitrogen cycling genes with trophic status, sediment partition and benthic nitrogen fluxes in Darwin Harbour. We analysed nitrogen cycling gene abundance using a functional gene microarray and quantitative PCRs targeting the denitrification gene (nosZ) and archaeal ammonia oxidation (AOA.1). We found a significant negative correlation between archaeal ammonia oxidation and silicate flux (P = 0.004), an indicator for diatom and benthic microalgal activity. It is suggested that the degradation of the diatomaceous organic matter generates localised anoxic conditions and inhibition of nitrification. Abundance of the nosZ gene was negatively correlated with nutrient load. The lowest nosZ gene levels were in hyper-eutrophic tidal creeks with anoxic conditions and increased levels of sulphide limiting the coupling of nitrification-denitrification (P = 0.016). Significantly higher levels of nosZ genes were measured in the surface (top 2 cm) compared to bulk sediment (top 10 cm) and there was a positive association with di-nitrogen flux (N2) in surface (P = 0.024) but not bulk sediment. This suggests that denitrifiers are most active in surficial sediment at the sediment-water interface. Elevated levels of nosZ genes also occurred in the sediments of tidal creek mouths and mudflats with these depositional zones combining the diffuse and seaward supply of nitrogen and carbon supporting denitrifiers. N-cycle molecular assays using surface sediments show promise as a rapid monitoring technique for impact assessment and measuring ecosystem function. This is particularly pertinent for tropical macrotidal systems where systematic monitoring is sparse and in many cases challenged by climatic extremes and remoteness.

Activation of indigenous denitrifying bacteria and enhanced nitrogen removal via artificial mixing in a drinking water reservoir: Insights into gene abundance, community structure, and co-existence model

Nitrogen pollution poses a severe threat to aquatic ecosystems and human health. This study investigated the use of water lifting aerators for in situ nitrogen reduction in a drinking water reservoir. The reservoir was thoroughly mixed and oxygenated after using water-lifting aerators for 42 days. The average total nitrogen concentration, nitrate nitrogen, and ammonium nitrogen-in all water layers-decreased significantly (P < 0.01), with a reduction efficiency of 35 ± 3%, 34 ± 2%, and 70 ± 6%, respectively. Other pollutants, including organic matter, phosphorus, iron, and manganese, were also effectively removed. Quantitative polymerase chain reactions indicated that bacterial nirS gene abundance was enhanced 26.34-fold. High-throughput sequencing, phylogenetic tree, and network analysis suggested that core indigenous nirS-type denitrifying bacteria, such as Dechloromonas, Simplicispira, Thauera, and Azospira, played vital roles in nitrogen and other pollutant removal processes. Furthermore, structural equation modeling revealed that nitrogen removal responded positively to WT, DO, and nirS gene abundance. Our findings provide a promising strategy for nitrogen removal in oligotrophic drinking water reservoirs with carbon deficiencies.

Relationships between environmental factors and N-cycling microbes reveal the indirect effect of further eutrophication on denitrification and DNRA in shallow lakes

Traditional views indicate that eutrophication and subsequent algal blooms favor denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in lake ecosystems. However, lakes tend to show an increasing propensity for inorganic nitrogen (N) limitation as they become more eutrophic. Thus, the influence of further eutrophication on denitrification and DNRA in eutrophic lakes are unclear due to the uncertainty of N availability. To fill this gap, we investigated the genes abundance (AOA, AOB, nirS, nirK and nrfA) and the composition of N-cycling microbes through quantitative PCR and 16S rRNA sequencing analysis, respectively, in 15 shallow eutrophic lakes of the Yangtze-Huaihe River basin, China. The results indicated that denitrification and DNRA rates could be modulated mainly by their functional gene abundances (nirS, nirK and nrfA), followed by the environmental factors (sediment total organic carbon and nitrogen). Denitrification rates significantly increased from slightly to highly eutrophic lakes, but DNRA rates were not. An explanation is that nitrification provided ample nitrate for denitrification, and this cooperative interaction was indicated by the positive correlation of their gene abundances. In addition, Pseudomonas and Anaeromyxobacter was the dominant genus mediated denitrification and DNRA, showing the potential to perform facultative anaerobic and strict anaerobic nitrate reduction, respectively. High level of dissolved oxygen might favor the facultatively aerobic denitrifiers over the obligately anaerobic fermentative DNRA bacteria in these shallow lakes. Chlorophyll a had a weak but positive effect on the gene abundances for nitrification (AOA and AOB). Further eutrophication had an indirect effect on denitrification and DNRA rates through modulating the genes abundances of N-cycling microbes.

Denitrification in hypersaline and coastal environments

As the association of denitrification with global warming and nitrogen removal from ecosystems has gained attention in recent decades, numerous studies have examined denitrification rates and the distribution of denitrifiers across different environments. In this minireview, reported studies focused on coastal saline environments, including estuaries, mangroves, and hypersaline ecosystems, have been analysed to identify the relationship between denitrification and saline gradients. The analyses of the literature and databases stated the direct effect of salinity on the distribution patterns of denitrifiers. However, few works do not support this hypothesis thus making this topic controversial. The specific mechanisms by which salinity influences denitrifier distribution are not fully understood. Nevertheless, several physical and chemical environmental parameters, in addition to salinity, have been shown to play a role in structuring the denitrifying microbial communities. The prevalence of nirS or nirK denitrifiers in ecosystems is a subject of debate in this work. In general terms, in mesohaline environments, the predominant nitrite reductase is NirS type and, NirK is found predominantly in hypersaline environments. Moreover, the approaches used by different researchers are quite different, resulting in a huge amount of unrelated information, making it difficult to establish comparative analysis. The main techniques used to analyse the distribution of denitrifying populations along salt gradients have been also discussed.

The Contribution of Nitrate Dissimilation to Nitrate Consumption in narG- and napA-Containing Nitrate Reducers with Various Oxygen and Nitrate Supplies

Nitrate reducers containing narG or napA play an important role in the nitrogen cycle, but little is known about their functional differentiations in relation to environmental changes. In this study, three types of nitrate reducers in the genus Pseudomonas, including strains containing narG (G type), napA (A type) and both narG and napA (GA type), were selected to explore their functional performances under varied nitrate and oxygen concentrations. Their growth characteristics, nitrate consumption, and dissimilatory nitrate-reducing activity were investigated. Growth and nitrate consumption of all three types of strains were generally promoted with increasing oxygen and nitrate concentrations. However, their dissimilatory nitrate-reducing activities were restricted by oxygen supply. When supplied with 0.25 mM KNO₃, A-type strains showed a higher growth rate but lower activity of dissimilatory nitrate reduction (DNR) than G-type strains, regardless of oxygen concentration. However, when nitrate concentration increased to 0.75 mM or 5 mM, G-type strains displayed stronger capability of nitrate consumption and DNR than A-type strains under anaerobic conditions, whereas under oxygenated conditions, A-type strains exhibited higher growth and nitrate consumption but weaker DNR than G-type strains. The GA-type strains appeared similar to G type under anaerobic conditions but performed more similarly to A type in aerobic environments. In summary, the nitrate consumption of narG-containing nitrate reducers is mainly caused by DNR in both anaerobic and aerobic environments, while the large proportion of nitrate consumption in A-type nitrate reducers under the aerobic condition is attributed to the assimilation by cell growth. IMPORTANCE Nitrate reducers containing narG or napA are ubiquitous, but little is known about their functional performance in various environments. Our study provides an important clue that the nitrate consumption of narG-containing strains is mainly caused by dissimilatory reduction in the environments, while that of napA-containing nitrate reducers under anaerobic conditions is ascribed to nitrate dissimilation but under the aerobic condition is attributed to the assimilation by cell growth. This finding broadens the understanding of aerobic nitrate reduction in the nitrogen cycle and highlights the important role of narG-containing bacteria in nitrate reduction under aerobic conditions.

The role of sulfur cycle and enzyme activity in dissimilatory nitrate reduction processes in heterotrophic sediments

The dissimilatory nitrate (NO₃^-) reduction processes (DNRPs) play an important role in regulating the nitrogen (N) balance of aquatic ecosystem. Organic carbon (OC) and sulfur are important factors that influence the DNRPs. In this study, we investigated the effects of sulfur cycle and enzyme activity on DNRPs in the natural and human-modified heterotrophic sediments. Quarterly monitoring of anaerobic ammonium oxidation, denitrification (DNF), and dissimilatory NO₃^- reduction to ammonium (DNRA) in sediments was conducted using ¹⁵N isotope tracing method. qPCR and high-throughput sequencing were applied to characterize the DNF and DNRA microbial abundances and communities. Results showed that instead of the OC, the glucosidase activity (GLU) was the key driver of the DNRPs. Furthermore, instead of the ratio of OC to NO₃^-, the GLU and the ratio of OC to sulfide (C/S) correctly indicated the partitioning of DNRPs in this study. We deduced that the sulfur reduction processes competed with the DNRPs for the available OC. In addition, the inhibitory effect of sulfide (final product of the sulfur reduction processes) on the DNRPs bacterial community were observed, which suggested a general restrictive role of the sulfur cycle in the regulation and partitioning of the DNRPs in heterotrophic sediments.

Ubiquity and Diversity of Cold Adapted Denitrifying Bacteria Isolated From Diverse Antarctic Ecosystems

Nitrogen cycle has been poorly investigated in Antarctic ecosystems. In particular, how extreme conditions of low temperature, dryness, and high radiation select the microorganisms involved in the cycle is not yet understood. Denitrification is an important step in the nitrogen cycle in which nitrate is reduced stepwise to the gases NO, N2O, and N2. Denitrification is carried out by a wide group of microorganisms spread in the phylogenetic tree. The aim of this work was to isolate and characterize denitrifying bacteria present in different cold environments from Antarctica. Bacterial isolates were obtained from lake, meltwater, sea, glacier ice, ornithogenic soil, and penguin feces samples from King George Island, Fildes peninsula in the Antarctic. Samples were taken during the deicing season in five sampling campaigns. From all the samples we were able to isolate denitrifying strains. A total of 199 bacterial isolates with the capacity to grow in anaerobic mineral media reducing nitrate at 4°C were obtained. The characterization of the isolates by 16S rRNA gene sequence analysis showed a high predominance of the genus Pseudomonas, followed by Janthinobacterium, Flavobacterium, Psychrobacter, and Yersinia. Other minor genera detected were Cryobacterium, Iodobacter, Kaistella, and Carnobacterium. The capacity to denitrify was not previously described for most of the bacteria related to our isolates and in many of them denitrifying genes were not present suggesting the presence of new genes in this extreme environment. Our work demonstrates the ubiquity of denitrification in the Maritime Antarctica and gives important information linking denitrification at cold temperature with taxa in an unequivocal way.

Nitrate Water Contamination from Industrial Activities and Complete Denitrification as a Remediation Option

Freshwater is a scarce resource that continues to be at high risk of pollution from anthropogenic activities, requiring remediation in such cases for its continuous use. The agricultural and mining industries extensively use water and nitrogen (N)-dependent products, mainly in fertilizers and explosives, respectively, with their excess accumulating in different water bodies. Although removal of NO3 from water and soil through the application of chemical, physical, and biological methods has been studied globally, these methods seldom yield N2 gas as a desired byproduct for nitrogen cycling. These methods predominantly cause secondary contamination with deposits of chemical waste such as slurry brine, nitrite (NO2), ammonia (NH3), and nitrous oxide (N2O), which are also harmful and fastidious to remove. This review focuses on complete denitrification facilitated by bacteria as a remedial option aimed at producing nitrogen gas as a terminal byproduct. Synergistic interaction of different nitrogen metabolisms from different bacteria is highlighted, with detailed attention to the optimization of their enzymatic activities. A biotechnological approach to mitigating industrial NO3 contamination using indigenous bacteria from wastewater is proposed, holding the prospect of optimizing to the point of complete denitrification. The approach was reviewed and found to be durable, sustainable, cost effective, and environmentally friendly, as opposed to current chemical and physical water remediation technologies.

Dissimilatory nitrate reduction and functional genes in two subtropical rivers, China

Dissimilatory nitrate reduction processes, including denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA), are important pathways of nitrate transformation in the aquatic environments. In this study, we investigated potential rates of denitrification, anammox, and DNRA in the sediments of two subtropical rivers, Jinshui River and Qi River, with different intensities of human activities in their respective catchment, China. Our objectives were to assess the seasonality of dissimilatory nitrate reduction rates, quantify their respective contributions to nitrate reduction, and reveal the relationship between dissimilatory nitrate reduction rates, functional gene abundances, and physicochemicals in the river ecosystems. Our results showed higher rates of denitrification and anammox in the intensively disturbed areas in autumn and spring, and higher potential DNRA in the slightly disturbed areas in summer. Generally, denitrification, anammox, and DNRA were higher in summer, autumn, and spring, respectively. Relative contributions of nitrate reduction from denitrification, anammox, and DNRA were quite different in different seasons. Dissimilatory nitrate reduction rates and gene abundances correlated significantly with water temperature, dissolved organic carbon (DOC), sediment total organic carbon (SOC), NO₃^-, NH₄⁺, DOC/NO₃^-, iron ions, and sulfide. Understanding dissimilatory nitrate reduction is essential for restoring nitrate reduction capacity and improving and sustaining ecohealth of the river ecosystems.

Overlooked contribution of water column to nitrogen removal in estuarine turbidity maximum zone (TMZ)

Estuarine systems are important sites of eliminating reactive nitrogen (N) delivered from land to sea. Numerous studies have focused on N cycling in estuarine sediment. However, the N elimination role of suspended sediments in estuarine turbid water column, which might provide anaerobic microenvironment for N loss, is rarely considered. This study examined the community dynamics and activities of denitrifying and anaerobic ammonium oxidation (anammox) bacteria in the water column of the turbidity maximum zone (TMZ) of the Yangtze Estuary, using molecular and ¹⁵N isotope-tracing techniques. Results showed that the anammox bacterial community was dominated by Candidatus Kuenenia and Candidatus Brocadia in the TMZ water column, while the main nirS-harboring denitrifiers were affiliated with Rhodobacterales. The denitrifying nirS gene was two orders of magnitude more abundant than anammox bacterial 16S rRNA gene, ranging from 1.77 × 10⁵ to 1.42 × 10⁸ copies l^-1 and from 7.68 × 10⁴ to 4.27 × 10⁶ copies l^-1, respectively. Compared with anammox, denitrification, with rates of 0.88 to 20.83 μmol N l^-1 d^-1, overwhelmingly dominated the N removal in the TMZ water column and was significantly correlated to suspended sediment concentrations (SSC). Based on the measured N removal rates, it was estimated that about 2.5 × 10⁵ ton N was annually removed from the TMZ water column, accounting for approximately 18.5% of the total inorganic N (TIN) discharged from the Yangtze River. Overall, this study implies the importance of estuarine turbid water column in controlling N budget, and also improves the understanding of N loss mechanisms in estuarine TMZ systems.

Characteristics of denitrification in a vertical baffled bioreactor

A vertical baffled bioreactor (VBBR) was employed for tertiary denitrification. Its features were designed to minimize the demand for externally supplied electron donor by minimizing net biomass synthesis and oxygen respiration. Over a two-year period, complete denitrification was realized routinely in the VBBR. The nitrate-removal rate was proportion to the influent COD/N ratio, with complete denitrification possible for COD/N ratios >3 gCOD/gN. Batch kinetic tests carried out at the end of years 1 and 2 documented that supplied electron donor was oxidized in the first 1-2 h, but nitrate and nitrite reductions occurred predominantly after 2 h and were driven by internally stored electron donor. Measurements confirmed that the VBBR minimized the demand of added electron donor: The observed yield was only 0.05 mgVSS/mgCOD, and the COD demand for O₂ respiration was only 1-6.7% of the COD demand for N reductions. Biofilm samples taken from the upper and lower ports in cylinder of VBBR had similarly high alpha diversity and dominant genera, but the upper biofilm had a denitrification rate about 70% greater than the lower biofilm. The higher denitrification rate in the upper biofilm correlated its higher content of active biomass.

Effects of Potamogeton crispus decline in the rhizosphere on the abundance of anammox bacteria and nirS denitrifying bacteria☆

Bacteria involved with ecosystem N cycling in the rhizosphere of submerged macrophytes are abundant and diverse. Any declines of submerged macrophytes can have a great influence on the abundance and diversity of denitrifying bacteria and anammox bacteria. Natural decline, tardy decline, and sudden decline methods were applied to cultivated Potamogeton crispus. The abundance of anammox bacteria and nirS denitrifying bacteria in rhizosphere sediment were detected using real-time fluorescent quantitative PCR of 16S rRNA, and phylogenetic trees were constructed to analyze the diversities of these two microbes. The results indicated that the concentration of NH₄⁺ in pore water gradually increased with increasing distances from the roots, whereas, the concentration of NO₃^- showed a reverse trend. The abundance of anammox bacteria and nirS denitrifying bacteria in sediment of declined P. crispus populations decreased significantly over time. The abundance of these two microbes in the sudden decline group were significantly higher (P > 0.05) than the other decline treatment groups. Furthermore, the abundances of these two microbes were positively correlated, with RDA analyses finding the mole ratio of NH₄⁺/NO₃^- being the most important positive factor affecting microbe abundance. Phylogenetic analysis indicated that the anammox bacteria Brocadia fuigida and Scalindua wagneri, and nirS denitrifying bacteria Herbaspirillum and Pseudomonas, were the dominant species in declined P. crispus sediment. We suggest the sudden decline of submerged macrophytes would increase the abundance of anammox bacteria and denitrifying bacteria in a relatively short time.

Spatial and Seasonal Variations in the Abundance of Nitrogen-Transforming Genes and the Microbial Community Structure in Freshwater Lakes with Different Trophic Statuses

Identifying nitrogen-transforming genes and the microbial community in the lacustrine sedimentary environment is critical for revealing nitrogen cycle processes in eutrophic lakes. In this study, we examined the diversity and abundance of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying bacteria (DNB), and anammox bacteria (AAOB) in different trophic status regions of Lake Taihu using the amoA, Arch-amoA, nirS, and hzo genes as functional markers. Quantitative Polymerase Chain Reaction (qPCR) results indicated that the abundance of the nirS gene was the highest, while the amoA gene had the lowest abundance in all regions. Except for the primary inflow area of Lake Taihu, Arch-amoA gene abundance was higher than the hzo gene in three lake bays, and the abundance of the nirS gene increased with decreasing trophic status. The opposite pattern was observed for the amoA, Arch-amoA, and hzo genes. Phylogenetic analyses showed that the predominant AOB and AOA were Nitrosomonas and Nitrosopumilus maritimus, respectively, and the proportion of Nitrosomonas in the eutrophic region (87.9%) was higher than that in the mesotrophic region (71.1%). Brocadia and Anammoxoglobus were the two predominant AAOB in Lake Taihu. Five novel unknown phylotypes of AAOB were observed, and Cluster AAOB-B was only observed in the inflow area with a proportion of 32%. In the DNB community, Flavobacterium occurred at a higher proportion (22.6–38.2%) in all regions, the proportion of Arthrobacter in the mesotrophic region (3.6%) was significantly lower than that in the eutrophic region (15.6%), and the proportions of Cluster DNB-E in the inflow area (24.5%) was significantly higher than that in the lake bay (7.3%). The canonical correspondence analysis demonstrated that the substrate concentration in sedimentary environments, such as NO_x^--N in the sediment, NH₄⁺-N in the pore water, and the total organic matter, were the key factors that determined the nitrogen-transforming microbial community. However, the temperature was also a predominant factor affecting the AOA and AAOB communities.

Evaluation and application of molecular denitrification monitoring methods in the northern Lake Tai, China

Worldwide, excessive reactive nitrogen in groundwater and surface waters is a growing problem, especially in areas that face rapid urbanization and industrialization. One example for environmental nitrogen pollution is the Lake Tai, China's third largest freshwater Lake, located in the Yangtze River basin. Due to the rapid development of the surrounding area, nitrogen compounds like nitrate are discharged into the Lake. Consequently, eutrophication and harmful algae blooms increased and led to the production of toxins directly affecting water consumers through the water supply chain. Denitrification is the main process that attenuates nitrate by converting it into atmospheric nitrogen and represents an intrinsic natural process to compensate the excess reactive nitrogen. In this study, the methodology to detect nitrate reducing bacteria on a functional gene and transcriptional level was optimized and verified in laboratory experiments with a pure culture of Pseudomonas veronii, isolated from Lake Tai. We demonstrated that transcripts analysis (mRNA) did correspond with nitrate reduction activity. Subsequently, the abundance and the activity of nitrate reducing bacteria in Lake Tai were assessed using the developed methods. We demonstrated that nitrate reducing bacteria can be found throughout all sediment and water samples taken from the northern Lake Tai in September 2017. Measurements of narG transcripts also indicated the activity of the membrane-bound nitrate reductase in the water samples. However, the bioinformatic analysis of narG sequences showed varying binding efficiency of primer and gene sites in dependence of phylogenetic groups, which may lead to an underestimation in the qPCR method. Thus, it is important to point out the precautions and limitations of primer systems to monitor nitrogen transformation by qPCR in the environment. Based on this study, mRNA detection methods are suitable for improved microbiological monitoring of denitrification, as an intrinsic process in Lake Tai to mitigate the inflowing reactive nitrogen compounds.

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.

Clay beads as artificial trapping matrices for monitoring bacterial distribution among urban stormwater infiltration systems and their connected aquifers

Stormwater infiltration systems (SIS) have been developed to limit surface runoff and flooding in urban areas. The impacts of such practices on the ecological and biological quality of groundwater ecosystems remain poorly studied due to the lack of efficient methodologies to assess microbiological quality of aquifers. In the present study, a monitoring method based on the incubation of artificial matrices (clay beads) is presented to evaluate microbial biomass, microbial activities, and bacterial community structure. Four microbial variables (biomass, dehydrogenase and hydrolytic activities, bacterial community structures) were measured on clay beads incubated in three urban water types (stormwater surface runoffs, SIS-impacted and non-impacted groundwaters) for six SIS. Analyses based on next-generation sequencing (NGS) of partial rrs (16S rRNA) PCR products (V5-V6) were used to compare bacterial community structures of biofilms on clay beads after 10 days of incubation with those of waters collected from the same sampling points at three occasions. Biofilm biomass and activities on clay beads were indicative of nutrient transfers from surface to SIS-impacted groundwaters. Biofilms allowed impacts of SIS on groundwater bacterial community structures to be determined. Although bacterial communities on clay beads did not perfectly match those of waters, clay beads captured the most abundant bacterial taxa. They also captured bacterial taxa that were not detected in waters collected at three occasions during the incubation, demonstrating the integrative character of this approach. Monitoring biofilms on clay beads also allowed the tracking of bacterial genera containing species representing health concerns.

Insight into a direct carbon dioxide effect on denitrification and denitrifying bacterial communities in estuarine sediment

With the elevation of atmospheric CO₂ content, the potential effects of CO₂ on organisms and various environmental processes have gained increasing concern. Most previous studies on denitrification have been conducted on ecosystems comprising plants, soils and microbes, but they have ignored the direct effect of CO₂ on denitrification and denitrifying bacterial communities. Here, by excluding the effects of plants, we found that both short- and long-term exposure to CO₂ directly inhibited the denitrification process, and caused the total nitrogen removal efficiency to decrease by up to 37%. Compared with the control, long-term exposure to CO₂ (30,000 ppm) also caused >276-fold increase in N₂O emissions, and significantly inhibited the decomposition process. Enzymatic and qPCR assays showed that CO₂ decreased the denitrifying enzymes activity (DEA) and the copy numbers of denitrifying genes, which directly resulted in the inhibitory effect of CO₂ on denitrification process. Further study indicated that adverse effect of CO₂ on DEA and denitrifying genes were caused by reducing the relative abundance of denitrifying bacteria. Moreover, the relative abundance of fermenting bacteria also decreased as CO₂ concentration increased, which might result in insufficient liable carbon for the activity of denitrifying bacteria, and ultimately exacerbate the negative denitrification performance. Overall, this study suggests that, in the absence of plants, CO₂ could directly affect the denitrifying and fermenting bacterial community, and inhibit denitrification and decomposition processes, which is detrimental to sediment nitrogen and carbon cycles.

nirS-type denitrifying bacterial assemblages respond to environmental conditions of a shallow estuary

Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered 'generalist' and 'specialist' archetypes based on the distribution of archetypes within these assemblages. Generalists, archetypes detected in all samples during at least one season, were commonly world-wide found in estuarine and marine ecosystems, comprised 8%-29% of the abundant NRE archetypes. Archetypes found in a particular site, 'specialists', were found to co-vary based on site specific conditions. Archetypes specific to the lower estuary in winter were designated Cluster I and significantly correlated by sediment Chl a and porewater Fe²⁺ . A combination of specialist and more widely distributed archetypes formed Clusters II and III, which separated based on salinity and porewater H₂ S respectively. The co-occurrence of archetypes correlated with different environmental conditions highlights the importance of habitat type and niche differentiation among nirS-type denitrifying communities and supports the essential role of individual community members in overall ecosystem function.

Capturing Compositional Variation in Denitrifying Communities: a Multiple-Primer Approach That Includes Epsilonproteobacteria

Denitrifying Epsilonproteobacteria may dominate nitrogen loss processes in marine habitats with intense redox gradients, but assessment of their importance is limited by the currently available primers for nitrite reductase genes. Nine new primers targeting the nirS gene of denitrifying Epsilonproteobacteria were designed and tested for use in sequencing and quantitative PCR on two microbial mat samples (vent 2 and vent 4) from the Calypso hydrothermal vent field, Bay of Plenty, New Zealand. Commonly used nirS and nirK primer sets nirS1F/nirS6R, cd3aF/R3cd, nirK1F/nirK5R, and F1aCu/R3Cu were also tested to determine what may be missed by the common single-primer approach to assessing denitrifier diversity. The relative importance of Epsilonproteobacteria in these samples was evaluated by 16S rRNA gene sequencing. Epsilonproteobacteria represented up to 75.6% of 16S rRNA libraries, but nirS genes from this group were not found with commonly used primers. Pairing of the new primer EPSnirS511F with either EPSnirS1100R or EPSnirS1105R recovered nirS sequences from members of the genera Sulfurimonas, Sulfurovum, and Nitratifractor. The new quantitative PCR primers EPSnirS103F/EPSnirS530R showed dominance of denitrifying Epsilonproteobacteria in vent 4 compared to vent 2, which had greater representation by "standard" denitrifiers measured with the cd3aF/R3cd primers. Limited results from commonly used nirK primers suggest biased amplification between primers. Future application of multiple nirS and nirK primers, including the new epsilonproteobacterial nirS primers, will improve the detection of denitrifier diversity and the capability to identify changes in dominant denitrifying communities.IMPORTANCE Estimating the potential for increasing nitrogen limitation in the changing global ocean is reliant on understanding the microbial community that removes nitrogen through the process of denitrification. This process is favored under oxygen limitation, which is a growing global-ocean phenomenon. Current methods use the nitrite reductase genes nirS and nirK to assess denitrifier diversity and abundance using primers that target only a few known denitrifiers and systematically exclude denitrifying Epsilonproteobacteria, a group known to dominate in reducing environments, such as hydrothermal vents and anoxic basins. As oxygen depletion expands in the oceans, it is important to study denitrifier community dynamics within those areas to predict future global ocean changes. This study explores the design and testing of new primers that target epsilonproteobacterial nirS and reveals the varied success of existing primers, leading to the recommendation of a multiple-primer approach to assessing denitrifier diversity.

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

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

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

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

Microbial Mat Compositional and Functional Sensitivity to Environmental Disturbance

The ability of ecosystems to adapt to environmental perturbations depends on the duration and intensity of change and the overall biological diversity of the system. While studies have indicated that rare microbial taxa may provide a biological reservoir that supports long-term ecosystem stability, how this dynamic population is influenced by environmental parameters remains unclear. In this study, a microbial mat ecosystem located on San Salvador Island, The Bahamas was used as a model to examine how environmental disturbance affects the protein synthesis potential (PSP) of rare and abundant archaeal and bacterial communities and how these changes impact potential biogeochemical processes. This ecosystem experienced a large shift in salinity (230 to 65 g kg-1) during 2011-2012 following the landfall of Hurricane Irene on San Salvador Island. High throughput sequencing and analysis of 16S rRNA and rRNA genes from samples before and after the pulse disturbance showed significant changes in the diversity and PSP of abundant and rare taxa, suggesting overall compositional and functional sensitivity to environmental change. In both archaeal and bacterial communities, while the majority of taxa showed low PSP across conditions, the overall community PSP increased post-disturbance, with significant shifts occurring among abundant and rare taxa across and within phyla. Broadly, following the post-disturbance reduction in salinity, taxa within Halobacteria decreased while those within Crenarchaeota, Thaumarchaeota, Thermoplasmata, Cyanobacteria, and Proteobacteria, increased in abundance and PSP. Quantitative PCR of genes and transcripts involved in nitrogen and sulfur cycling showed concomitant shifts in biogeochemical cycling potential. Post-disturbance conditions increased the expression of genes involved in N-fixation, nitrification, denitrification, and sulfate reduction. Together, our findings show complex community adaptation to environmental change and help elucidate factors connecting disturbance, biodiversity, and ecosystem function that may enhance ecosystem models.

Reduction of the Powerful Greenhouse Gas N2O in the South-Eastern Indian Ocean

Nitrous oxide (N₂O) is a powerful greenhouse gas and a key catalyst of stratospheric ozone depletion. Yet, little data exist about the sink and source terms of the production and reduction of N₂O outside the well-known oxygen minimum zones (OMZ). Here we show the presence of functional marker genes for the reduction of N₂O in the last step of the denitrification process (nitrous oxide reductase genes; nosZ) in oxygenated surface waters (180–250 O₂ μmol.kg^-1) in the south-eastern Indian Ocean. Overall copy numbers indicated that nosZ genes represented a significant proportion of the microbial community, which is unexpected in these oxygenated waters. Our data show strong temperature sensitivity for nosZ genes and reaction rates along a vast latitudinal gradient (32°S-12°S). These data suggest a large N₂O sink in the warmer Tropical waters of the south-eastern Indian Ocean. Clone sequencing from PCR products revealed that most denitrification genes belonged to Rhodobacteraceae. Our work highlights the need to investigate the feedback and tight linkages between nitrification and denitrification (both sources of N₂O, but the latter also a source of bioavailable N losses) in the understudied yet strategic Indian Ocean and other oligotrophic systems.

Abundance and distribution of microorganisms involved in denitrification in sediments of a Myriophyllum elatinoides purification system for treating swine wastewater

Environmental pollution from livestock production, particularly swine production, is often managed by the use of constructed wetlands, which incorporate plants such as Myriophyllum elatinoides as a means of treating wastewater. The M. elatinoides purification system has been shown to effectively remove, via nitrification and denitrification, more than 90% of the total nitrogen (TN) and 84% of the NH4 (+)-N produced in swine wastewater. However, the mechanisms of variation in aquatic environmental factors and how the interaction of these factors affects denitrification by microorganisms in sediments remain poorly understood. In this study, the impacts of dissolved oxygen (DO), TN, NH4(+)-N, and NO3(-)-N on the abundance, diversity, and community distribution of denitrifiers in the sediments from different concentrations and types of wastewater including tap water (CK), two strengths of synthetic wastewater: 200 mg NH4(+)-N L(-1) (T1) and 400 mg NH4(+)-N L(-1) (T2), swine wastewater diluted 50% (T3), and swine wastewater (T4) were investigated in a microcosm experiment. A significant improvement was observed in the abundance of denitrification genes (nirK and nirS) in response to increased NO3(-)-N and DO in the swine wastewater sediments. The abundance of these denitrification genes was highest in the T4 sediments compared with other treatments. Terminal restriction fragment length polymorphism (T-RFLP) analysis revealed that the DO, TN, and NH4(+)-N positively impacted the richness index (S) of the nirK denitrifiers in T1, whereas the NO3(-)-N negatively affected the Simpson diversity index (D) of nirK and nirS denitrifiers in T3 and T4. However, the NO3(-)-N positively affected the nirK and nirS denitrifier community distribution, whereas the DO negatively affected the nirK and nirS denitrifier distribution in T3 and T4. These findings will be helpful in that they allow us to recognize the effects of environmental factors on the formation of the denitrifiers in the sediments in a M. elatinoides purification system.

Substrates specialization in lipid compounds and hydrocarbons of Marinobacter genus

The impact of petroleum contamination and of burrowing macrofauna on abundances of Marinobacter and denitrifiers was tested in marine sediment mesocoms after 3 months incubation. Quantification of this genus by qPCR with a new primer set showed that the main factor favoring Marinobacter abundance was hydrocarbon amendment followed by macrofauna presence. In parallel, proportion of nosZ-harboring bacteria increased in the presence of marcrofauna. Quantitative finding were explained by physiological data from a set of 34 strains and by genomic analysis of 16 genomes spanning 15 different Marinobacter-validated species (Marinobacter hydrocarbonoclasticus, Marinobacter daeopensis, Marinobacter santoriniensis, Marinobacter pelagius, Marinobacter flavimaris, Marinobacter adhaerens, Marinobacter xestospongiae, Marinobacter algicola, Marinobacter vinifirmus, Marinobacter maritimus, Marinobacter psychrophilus, Marinobacter lipoliticus, Marinobacter manganoxydans, Marinobacter excellens, Marinobacter nanhaiticus) and 4 potential novel ones. Among the 105 organic electron donors tested in physiological analysis, Marinobacter pattern appeared narrow for almost all kinds of organic compounds except lipid ones. Strains of this set could oxidize a very large spectrum of lipids belonging to glycerolipids, branched, fatty acyls, and aromatic hydrocarbon classes. Physiological data were comforted by genomic analysis, and genes of alkane 1-monooxygenase, haloalkane dehalogenase, and flavin-binding monooxygenase were detected in most genomes. Denitrification was assessed for several strains belonging to M. hydrocarbonoclasticus, M. vinifirmus, Marinobacter maritinus, and M. pelagius species indicating the possibility to use nitrate as alternative electron acceptor. Higher occurrence of Marinobacter in the presence of petroleum appeared to be the result of a broader physiological trait allowing this genus to use lipids including hydrocarbon as principal electron donors.

Marine Oxygen-Deficient Zones Harbor Depauperate Denitrifying Communities Compared to Novel Genetic Diversity in Coastal Sediments

Denitrification is a critically important biogeochemical pathway that removes fixed nitrogen from ecosystems and thus ultimately controls the rate of primary production in nitrogen-limited systems. We examined the community structure of bacteria containing the nirS gene, a signature gene in the denitrification pathway, from estuarine and salt marsh sediments and from the water column of two of the world's largest marine oxygen-deficient zones (ODZs). We generated over 125,000 nirS gene sequences, revealing a large degree of genetic diversity including 1,815 unique taxa, the vast majority of which formed clades that contain no cultured representatives. These results underscore how little we know about the genetic diversity of metabolisms underlying this critical biogeochemical pathway. Marine sediments yielded 1,776 unique taxa when clustered at 95 % sequence identity, and there was no single nirS denitrifier that was a competitive dominant; different samples had different highly abundant taxa. By contrast, there were only 39 unique taxa identified in samples from the two ODZs, and 99 % of the sequences belonged to 5 or fewer taxa. The ODZ samples were often dominated by nirS sequences that shared a 92 % sequence identity to a nirS found in the anaerobic ammonium-oxidizing (anammox) genus Scalindua. This sequence was abundant in both ODZs, accounting for 38 and 59 % of all sequences, but it was virtually absent in marine sediments. Our data indicate that ODZs are remarkably depauperate in nirS genes compared to the remarkable genetic richness found in coastal sediments.

Diversity, Abundance, and Distribution of nirS-Harboring Denitrifiers in Intertidal Sediments of the Yangtze Estuary

Denitrification plays a critical role in nitrogen removal in estuarine and coastal ecosystems. In this study, the community composition, diversity, abundance, and distribution of cytochrome cd1-type nitrite reductase gene (nirS)-harboring denitrifiers in intertidal sediments of the Yangtze Estuary were analyzed using polymerase chain reaction (PCR)-based clone libraries and quantitative PCR techniques. Clone library analysis showed that the nirS-encoding bacterial biodiversity was significantly higher at the lower salinity sites than at the higher salinity sites. However, there was no significant seasonal difference in the nirS gene diversity between summer and winter. Phylogenetic analysis revealed that the nirS-harboring denitrifier communities at the study area had distinctive spatial heterogeneity along the estuary. At the lower salinity sites, the nirS-harboring bacterial community was co-dominated by clusters III and VII; while at the higher salinity sites, it was dominated by cluster I. Canonical correspondence analysis indicated that the community compositions of nirS-type denitrifiers were significantly correlated with salinity, ammonium, and nitrate. Quantitative PCR results showed that the nirS gene abundance was in the range of 1.01 × 10(6) to 9.00 × 10(7) copies per gram dry sediment, without significant seasonal variation. Among all the environmental factors, the nirS gene abundance was only significantly related to the change of salinity. These results can extend our current knowledge about the composition and dynamics of denitrification microbial community in the estuarine ecosystem.

Seasonal variation in denitrification and dissimilatory nitrate reduction to ammonia process rates and corresponding key functional genes along an estuarine nitrate gradient

This research investigated spatial-temporal variation in benthic bacterial community structure, rates of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) processes and abundances of corresponding genes and transcripts at three sites—the estuary-head, mid-estuary and the estuary mouth (EM) along the nitrate gradient of the Colne estuary over an annual cycle. Denitrification rates declined down the estuary, while DNRA rates were higher at the estuary head and middle than the EM. In four out of the six 2-monthly time-points, rates of DNRA were greater than denitrification at each site. Abundance of gene markers for nitrate-reduction (nitrate reductase narG and napA), denitrification (nitrite reductase nirS) and DNRA (DNRA nitrite reductase nrfA) declined along the estuary with significant relationships between denitrification and nirS abundance, and DNRA and nrfA abundance. Spatially, rates of denitrification, DNRA and corresponding functional gene abundances decreased along the estuary. However, temporal correlations between rate processes and functional gene and transcript abundances were not observed.

A doubling of microphytobenthos biomass coincides with a tenfold increase in denitrifier and total bacterial abundances in intertidal sediments of a temperate estuary

Surface sediments are important systems for the removal of anthropogenically derived inorganic nitrogen in estuaries. They are often characterized by the presence of a microphytobenthos (MPB) biofilm, which can impact bacterial communities in underlying sediments for example by secretion of extracellular polymeric substances (EPS) and competition for nutrients (including nitrogen). Pyrosequencing and qPCR was performed on two intertidal surface sediments of the Westerschelde estuary characterized by a two-fold difference in MPB biomass but no difference in MPB composition. Doubling of MPB biomass was accompanied by a disproportionately (ten-fold) increase in total bacterial abundances while, unexpectedly, no difference in general community structure was observed, despite significantly lower bacterial richness and distinct community membership, mostly for non-abundant taxa. Denitrifier abundances corresponded likewise while community structure, both for nirS and nirK denitrifiers, remained unchanged, suggesting that competition with diatoms for nitrate is negligible at concentrations in the investigated sediments (appr. 1 mg/l NO₃^-). This study indicates that MPB biomass increase has a general, significantly positive effect on total bacterial and denitrifier abundances, with stimulation or inhibition of specific bacterial groups that however do not result in a re-structured community.

Redox gradients in distribution systems influence water quality, corrosion, and microbial ecology

Simulated distribution systems (SDSs) defined the interplay between disinfectant type (free chlorine and chloramines), water age (1-10.2 days), and pipe material (PVC, iron and cement surfaces) on water chemistry, redox zones and infrastructure degradation. Redox gradients developed as a function of water age and pipe material affected the quality of water consumers would receive. Free chlorine was most stable in the presence of PVC while chloramine was most stable in the presence of cement. At a 3.6 day water age the residual in the chlorinated PVC SDS was more than 3.5 times higher than in the chlorinated iron or cement systems. In contrast, the residual in the chloraminated cement SDS was more than 10 times greater than in the chloraminated iron or PVC systems. Near the point of entry to the SDSs where disinfectant residuals were present, free chlorine tended to cause as much as 4 times more iron corrosion when compared to chloramines. Facultative denitrifying bacteria were ubiquitous, and caused complete loss of nitrogen at distal points in systems with iron, and these bacteria co-occurred with very severe pitting attack (1.6-1.9 mm/year) at high water age.

Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments

Archaea are widespread in marine sediments, but their occurrence and relationship with natural salinity gradients in estuarine sediments is not well understood. This study investigated the abundance and diversity of Archaea in sediments at three sites [Brightlingsea (BR), Alresford (AR) and Hythe (HY)] along the Colne Estuary, using quantitative real-time PCR (qPCR) of 16S rRNA genes, DNA hybridization, Archaea 16S rRNA and mcrA gene phylogenetic analyses. Total archaeal 16S rRNA abundance in sediments were higher in the low-salinity brackish sediments from HY (2-8 × 10(7) 16S rRNA gene copies cm(-3)) than the high-salinity marine sites from BR and AR (2 × 10(4)-2 × 10(7) and 4 × 10(6)-2 × 10(7) 16S rRNA gene copies cm(-3), respectively), although as a proportion of the total prokaryotes Archaea were higher at BR than at AR or HY. Phylogenetic analysis showed that members of the 'Bathyarchaeota' (MCG), Thaumarchaeota and methanogenic Euryarchaeota were the dominant groups of Archaea. The composition of Thaumarchaeota varied with salinity, as only 'marine' group I.1a was present in marine sediments (BR). Methanogen 16S rRNA genes from low-salinity sediments at HY were dominated by acetotrophic Methanosaeta and putatively hydrogentrophic Methanomicrobiales, whereas the marine site (BR) was dominated by mcrA genes belonging to methylotrophic Methanococcoides, versatile Methanosarcina and methanotrophic ANME-2a. Overall, the results indicate that salinity and associated factors play a role in controlling diversity and distribution of Archaea in estuarine sediments.

Connecting the dots: linking nitrogen cycle gene expression to nitrogen fluxes in marine sediment mesocosms

Connecting molecular information directly to microbial transformation rates remains a challenge, despite the availability of molecular methods to investigate microbial biogeochemistry. By combining information on gene abundance and expression for key genes with quantitative modeling of nitrogen fluxes, we can begin to understand the scales on which genetic signals vary and how they relate to key functions. We used quantitative PCR of DNA and cDNA, along with biogeochemical modeling to assess how the abundance and expression of microbes responsible for two steps in the nitrogen cycle changed over time in estuarine sediment mesocosms. Sediments and water were collected from coastal Massachusetts and maintained in replicated 20 L mesocosms for 45 days. Concentrations of all major inorganic nitrogen species were measured daily and used to derive rates of nitrification and denitrification from a Monte Carlo-based non-negative least-squares analysis of finite difference equations. The mesocosms followed a classic regeneration sequence in which ammonium released from the decomposition of organic matter was subsequently oxidized to nitrite and then further to nitrate, some portion of which was ultimately denitrified. Normalized abundances of ammonia oxidizing archaeal ammonia monoxoygenase (amoA) transcripts closely tracked rates of ammonia oxidation throughout the experiment. No such relationship, however, was evident between denitrification rates and the normalized abundance of nitrite reductase (nirS and nirK) transcripts. These findings underscore the complexity of directly linking the structure of the microbial community to rates of biogeochemical processes.

Habitat specialization along a wetland moisture gradient differs between ammonia-oxidizing and denitrifying microorganisms

Gradients in abiotic parameters, such as soil moisture,can strongly influence microbial community structure and function. Denitrifying and ammonia-oxidizing microorganisms,in particular, have contrasting physiological responses to abiotic factors such as oxygen concentration and soil moisture. Identifying abiotic factors that govern the composition and activity of denitrifying and ammonia-oxidizing communities is critical for understanding the nitrogen cycle.The objectives of this study were to (i) examine denitrifier andarchaeal ammonia oxidizer community composition and (ii) assess the taxa occurring within each functional group related to soil conditions along an environmental gradient. Soil was sampled across four transects at four locations along a dry to saturated environmental gradient at a restored wetland. Soil pH and soil organic matter content increased from dry to saturated plots. Composition of soil denitrifier and ammonia oxidizer functional groups was assessed by terminal restriction fragment length polymorphism (T-RFLP) community analysis, and local soil factors were also characterized. Microbial community composition of denitrifiers and ammonia oxidizers differed along the moisture gradient (denitrifier:ANOSIM R = 0.739, P < 0.001; ammonia oxidizers: ANOSIMR = 0.760, P < 0.001). Individual denitrifier taxa were observed over a larger range of moisture levels than individual archaeal ammonia oxidizer taxa (Wilcoxon rank sum, W = 2413, P value = 0.0002). Together, our data suggest that variation in environmental tolerance of microbial taxa have potential to influence nitrogen cycling in terrestrial ecosystems.

Nitrate reduction functional genes and nitrate reduction potentials persist in deeper estuarine sediments. Why?

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are processes occurring simultaneously under oxygen-limited or anaerobic conditions, where both compete for nitrate and organic carbon. Despite their ecological importance, there has been little investigation of how denitrification and DNRA potentials and related functional genes vary vertically with sediment depth. Nitrate reduction potentials measured in sediment depth profiles along the Colne estuary were in the upper range of nitrate reduction rates reported from other sediments and showed the existence of strong decreasing trends both with increasing depth and along the estuary. Denitrification potential decreased along the estuary, decreasing more rapidly with depth towards the estuary mouth. In contrast, DNRA potential increased along the estuary. Significant decreases in copy numbers of 16S rRNA and nitrate reducing genes were observed along the estuary and from surface to deeper sediments. Both metabolic potentials and functional genes persisted at sediment depths where porewater nitrate was absent. Transport of nitrate by bioturbation, based on macrofauna distributions, could only account for the upper 10 cm depth of sediment. A several fold higher combined freeze-lysable KCl-extractable nitrate pool compared to porewater nitrate was detected. We hypothesised that his could be attributed to intracellular nitrate pools from nitrate accumulating microorganisms like Thioploca or Beggiatoa. However, pyrosequencing analysis did not detect any such organisms, leaving other bacteria, microbenthic algae, or foraminiferans which have also been shown to accumulate nitrate, as possible candidates. The importance and bioavailability of a KCl-extractable nitrate sediment pool remains to be tested. The significant variation in the vertical pattern and abundance of the various nitrate reducing genes phylotypes reasonably suggests differences in their activity throughout the sediment column. This raises interesting questions as to what the alternative metabolic roles for the various nitrate reductases could be, analogous to the alternative metabolic roles found for nitrite reductases.

Profiling gene expression to distinguish the likely active diazotrophs from a sea of genetic potential in marine sediments

Nitrogen (N) cycling microbial communities in marine sediments are extremely diverse, and it is unknown whether this diversity reflects extensive functional redundancy. Sedimentary denitrifiers remove significant amounts of N from the coastal ocean and diazotrophs are typically regarded as inconsequential. Recently, N fixation has been shown to be a potentially important source of N in estuarine and continental shelf sediments. Analysis of expressed genes for nitrite reductase (nirS) and a nitrogenase subunit (nifH) was used to identify the likely active denitrifiers and nitrogen fixers in surface sediments from different seasons in Narragansett Bay (Rhode Island, USA). The overall diversity of diazotrophs expressing nifH decreased along the estuarine gradient from the estuarine head to an offshore continental shelf site. Two groups of sequences related to anaerobic sulphur/iron reducers and sulphate reducers dominated libraries of expressed nifH genes. Quantitative polymerase chain reaction (qPCR) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) data shows the highest abundance of both groups at a mid bay site, and the highest nifH expression at the head of the estuary, regardless of season. Several potential environmental factors, including water temperature, oxygen concentration and metal contamination, may influence the abundance and nifH expression of these two bacterial groups.

Denitrification and N2O:N2 production in temperate grasslands: processes, measurements, modelling and mitigating negative impacts

In this review we explore the biotic transformations of nitrogenous compounds that occur during denitrification, and the factors that influence denitrifier populations and enzyme activities, and hence, affect the production of nitrous oxide (N2O) and dinitrogen (N2) in soils. Characteristics of the genes related to denitrification are also presented. Denitrification is discussed with particular emphasis on nitrogen (N) inputs and dynamics within grasslands, and their impacts on the key soil variables and processes regulating denitrification and related gaseous N2O and N2 emissions. Factors affecting denitrification include soil N, carbon (C), pH, temperature, oxygen supply and water content. We understand that the N2O:N2 production ratio responds to the changes in these factors. Increased soil N supply, decreased soil pH, C availability and water content generally increase N2O:N2 ratio. The review also covers approaches to identify and quantify denitrification, including acetylene inhibition, (15)N tracer and direct N2 quantification techniques. We also outline the importance of emerging molecular techniques to assess gene diversity and reveal enzymes that consume N2O during denitrification and the factors affecting their activities and consider a process-based approach that can be used to quantify the N2O:N2 product ratio and N2O emissions with known levels of uncertainty in soils. Finally, we explore strategies to reduce the N2O:N2 product ratio during denitrification to mitigate N2O emissions. Future research needs to focus on evaluating the N2O-reducing ability of the denitrifiers to accelerate the conversion of N2O to N2 and the reduction of N2O:N2 ratio during denitrification.

Transitions in nirS-type denitrifier diversity, community composition, and biogeochemical activity along the Chesapeake Bay estuary

Chesapeake Bay, the largest estuary in North America, can be characterized as having steep and opposing gradients in salinity and dissolved inorganic nitrogen along the main axis of the Bay. In this study, the diversity of nirS gene fragments (encoding cytochrome cd 1-type nitrite reductase), physical/chemical parameters, and benthic N2-fluxes were analyzed in order to determine how denitrifier communities and biogeochemical activity vary along the estuary salinity gradient. The nirS gene fragments were PCR-amplified, cloned, and sequenced from sediment cores collected at five stations. Sequence analysis of 96-123 nirS clones from each station revealed extensive overall diversity in this estuary, as well as distinct spatial structure in the nirS sequence distributions. Both nirS-based richness and community composition varied among stations, with the most dramatic shifts occurring between low-salinity (oligohaline) and moderate-salinity (mesohaline) sites. For four samples collected in April, the nirS-based richness, nitrate concentrations, and N2-fluxes all decreased in parallel along the salinity gradient from the oligohaline northernmost station to the highest salinity (polyhaline) station near the mouth of the Bay. The vast majority of the 550 nirS sequences were distinct from cultivated denitrifiers, although many were closely related to environmental clones from other coastal and estuarine systems. Interestingly, 8 of the 172 OTUs identified accounted for 42% of the total nirS clones, implying the presence of a few dominant and many rare genotypes, which were distributed in a non-random manner along the salinity gradient of Chesapeake Bay. These data, comprising the largest dataset to investigate nirS clone sequence diversity from an estuarine environment, also provided information that was required for the development of nirS microarrays to investigate the interaction of microbial diversity, environmental gradients, and biogeochemical activity.

Microbial community in packed bed bioreactor involved in nitrate remediation from low level radioactive waste

Nitrate is the second largest contaminant of agriculture soil after pesticides. It also is a major pollutant from nuclear and metallurgical operations. Conventional methods for nitrate removal suffers from high cost and complexity leaving bioremediation as a viable alternative strategy. A pilot plant of 2.5 m(3)/day capacity has been functioning since 2005 based on microbial consortia treating actual effluent from nuclear power plant having pH of 7-8.5 (optimum) with N:C ratio of 1:1.7. The maximum biodegradable nitrate concentration of 3000 ppm could be reduced to below permissible limit (44.2 ppm) within 24 h in presence of sodium acetate as carbon source. Culture independent analysis (16S rDNA based) revealed clones having closest identity with uncultured bacterium, Pseudomonas stutzeri and Azoarcus sp. The existence of dissimilatory pathway of nitrate reduction in the community DNA is indicated by presence of nirS and nirK gene. Though the microbial mass was developed using municipal sewage, absence of Mycobacterium sp was confirmed using PCR. The understanding of the molecular identification of the consortium would help in developing the preservation strategy of the microbial mass for replication and perpetuation of the system.

Proteomic analysis of Herbaspirillum seropedicae cultivated in the presence of sugar cane extract

Bacterial endophytes of the genus Herbaspirillum colonize sugar cane and can promote plant growth. The molecular mechanisms that mediate plant- H. seropedicae interaction are poorly understood. In this work, we used 2D-PAGE electrophoresis to identify H. seropedicae proteins differentially expressed at the log growth phase in the presence of sugar cane extract. The differentially expressed proteins were validated by RT qPCR. A total of 16 differential spots (1 exclusively expressed, 7 absent, 5 up- and 3 down-regulated) in the presence of 5% sugar cane extract were identified; thus the host extract is able to induce and repress specific genes of H. seropedicae. The differentially expressed proteins suggest that exposure to sugar cane extract induced metabolic changes and adaptations in H. seropedicae presumably in preparation to establish interaction with the plant.

Primers for amplification of nitrous oxide reductase genes associated with Firmicutes and Bacteroidetes in organic-compound-rich soils

The nosZ gene encodes nitrous oxide reductase, a key enzyme in the nitrous oxide reduction that occurs during complete denitrification. Many conventional approaches have used Proteobacteria-based primers to detect nosZ in environmental samples. However, these primers often fail to detect nosZ in non-Proteobacteria strains, including Firmicutes (Gram-positive) and Bacteroidetes. In this study, newly designed nosZ primers successfully amplified this gene from five Geobacillus species (Firmicutes). The primers were used to construct nosZ clone libraries from DNA extracted from sludge and domestic animal feedlot soils, all with high organic carbon contents. After DNA sequencing, phylogenetic analysis identified many new nosZ sequences with high levels of homology to nosZ from Bacteroidetes, probably because of the high sequence similarity of nosZ from Firmicutes and Bacteroidetes, and a predominance of Bacteroidetes in feedlot environments. Three sets of new quantitative real-time PCR (qPCR) primers based on our clone library sequences were designed and tested for their specificities. Our data showed that only Bacteroidetes-related nosZ sequences were amplified, whereas conventional Proteobacteria-based primers amplified only Proteobacteria-related nosZ. Quantitative analysis of nosZ with the new qPCR primers recovered ~10(4) copies per 100 ng DNA. Thus, it appears that amplification with conventional primers is insufficient for developing an understanding of the diversity and abundance of nosZ genes in the environment.

Relationships between nitrogen transformation rates and gene abundance in a riparian buffer soil

Denitrification is a critical biogeochemical process that results in the conversion of nitrate to volatile products, and thus is a major route of nitrogen loss from terrestrial environments. Riparian buffers are an important management tool that is widely utilized to protect water from non-point source pollution. However, riparian buffers vary in their nitrate removal effectiveness, and thus there is a need for mechanistic studies to explore nitrate dynamics in buffer soils. The objectives of this study were to examine the influence of specific types of soluble organic matter on nitrate loss and nitrous oxide production rates, and to elucidate the relationships between these rates and the abundances of functional genes in a riparian buffer soil. Continuous-flow soil column experiments were performed to investigate the effect of three types of soluble organic matter (citric acid, alginic acid, and Suwannee River dissolved organic carbon) on rates of nitrate loss and nitrous oxide production. We found that nitrate loss rates increased as citric acid concentrations increased; however, rates of nitrate loss were weakly affected or not affected by the addition of the other types of organic matter. In all experiments, rates of nitrous oxide production mirrored nitrate loss rates. In addition, quantitative polymerase chain reaction (qPCR) was utilized to quantify the number of genes known to encode enzymes that catalyze nitrite reduction (i.e., nirS and nirK) in soil that was collected at the conclusion of column experiments. Nitrate loss and nitrous oxide production rates trended with copy numbers of both nir and 16s rDNA genes. The results suggest that low-molecular mass organic species are more effective at promoting nitrogen transformations than large biopolymers or humic substances, and also help to link genetic potential to chemical reactivity.

Identification of active denitrifiers in rice paddy soil by DNA- and RNA-based analyses

Denitrification occurs markedly in rice paddy fields; however, few microbes that are actively involved in denitrification in these environments have been identified. In this study, we used a laboratory soil microcosm system in which denitrification activity was enhanced. DNA and RNA were extracted from soil at six time points after enhancing denitrification activity, and quantitative PCR and clone library analyses were performed targeting the 16S rRNA gene and denitrification functional genes (nirS, nirK and nosZ) to clarify which microbes are actively involved in denitrification in rice paddy soil. Based on the quantitative PCR results, transcription levels of the functional genes agreed with the denitrification activity, although gene abundance did not change at the DNA level. Diverse denitrifiers were detected in clone library analysis, but comparative analysis suggested that only some of the putative denitrifiers, especially those belonging to the orders Neisseriales, Rhodocyclales and Burkholderiales, were actively involved in denitrification in rice paddy soil.