Coupled Nitrification Denitrification Research Articles

Spatial variation in rates of benthic denitrification and environmental controls in four New Zealand estuaries

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 556:59-77 (2016) - DOI: https://doi.org/10.3354/meps11865 Spatial variation in rates of benthic denitrification and environmental controls in four New Zealand estuaries Catherine Gongol1, Candida Savage1,2,* 1Department of Marine Science, University of Otago, PO Box 56, Dunedin, New Zealand 2Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa *Corresponding author: candida.savage@otago.ac.nz ABSTRACT: Denitrification plays a key role in global biogeochemical cycles as the main nitrogen (N) loss process that limits availability of N to primary producers. This study presents the first measurements of sediment denitrification rates for New Zealand estuaries. Spatially explicit rates of direct denitrification (Dw) and coupled nitrification-denitrification (Dn) were quantified using the isotope pairing method in 4 oligotrophic to moderately nutrient-enriched estuaries on the South Island, New Zealand (Avon-Heathcote, Waikouaiti, Tokomairiro, Tautuku). Coupled nitrification-denitrification dominated (>86%), with most sites having low dissolved inorganic nitrogen (DIN) concentrations (<30 µmol l-1). Rates of total denitrification (Dtot) and Dn were negatively correlated with percent sand and positively related to oxygen penetration depth (OPD). Surface sediment chlorophyll a concentrations and percent carbon (%C) were also identified as significant predictors of Dtot and Dn in the single-factor models. By contrast, Dw was the main nitrogen removal process at moderately nutrient-enriched sites and was positively related to DIN concentrations in the water column and negatively correlated with percent sand. OPD and %C were also identified as significant predictors of Dw. While Dw was positively related to DIN concentrations, overall rates of denitrification were not, demonstrating that predictive relationships between N loading and removal are not always possible in oligotrophic estuaries. Our findings demonstrate the importance of grain size as a driver of denitrification rates in estuaries and imply that an increase in fine-grained sediments from land-use intensification may alter rates of N removal in estuaries through complex direct and indirect processes. KEY WORDS: Denitrification · Estuaries · New Zealand · Nitrogen · Benthic · Sediment grain size · Isotope pairing method · Oxygen flux Full text in pdf format PreviousNextCite this article as: Gongol C, Savage C, (2016) Spatial variation in rates of benthic denitrification and environmental controls in four New Zealand estuaries. Mar Ecol Prog Ser 556:59-77. https://doi.org/10.3354/meps11865 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 556. Online publication date: September 08, 2016 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2016 Inter-Research.

Quantifying N2O emissions and production pathways from fresh waste during the initial stage of disposal to a landfill

Intensive nitrous oxide (N2O) emissions usually occur at the working face of landfills. However, the specific amounts and contributions of the multiple pathways to N2O emissions are poorly understood. N2O emissions and the mutual conversions of N-species in both open and sealed simulated landfill reactors filled with fresh refuse were examined during a 100-h incubation period, and N2O sources were calculated using 15N isotope labelling. N2O peak fluxes were above 70μgNkg−1 waste h−1 for both treatments. The sealed incubation reactors became a N2O sink when N2O in the ambient environment was sufficient. The total amount of N2O emissions under sealed conditions was 2.15±0.56mgNkg−1 waste, which was higher than that under open conditions (1.91±0.34mgNkg−1 waste). The NO2− peak appeared prior to the peak in N2O flux. The degree and duration of total nitrogen reduction in open incubations were larger and longer than those of sealed incubations and could possibly be due to oxygen supplementation. Denitrification (DF) was a major source of N2O generation during these incubations. The contribution of the DF pathway decreased from 89.2% to 61.3% during the open incubations. The effects of nitrification (NF) and nitrification-coupled denitrification (NCD) increased during the increasing phase and the decreasing phase of N2O flux, contributing 24.1–37.4% and 31.7–34.4% of total N2O emissions, respectively. In sealed treatments, the DF pathway accounted for more than 90% of the total N2O emission during the entire incubation.

Coupled nitrification–denitrification leads to extensive N loss in subtidal permeable sediments

AbstractWe investigated microbial pathways of nitrogen transformation in highly permeable sediments from the German Bight (South‐East North Sea) by incubating sediment cores percolated with 15N‐labeled substrates under near in situ conditions. In incubations with added , production of occurred while the sediment was oxic, indicating ammonia oxidation. Similarly, production during incubations indicated nitrite oxidation. Taken together these findings provide direct evidence of high nitrification rates within German Bight sands. The production of 15N‐N2 on addition of revealed high denitrification rates within the sediment under oxic and anoxic conditions. Denitrification rates were strongly and positively correlated with oxygen consumption rates, suggesting that denitrification is controlled by organic matter availability. Nitrification and denitrification rates were of the same magnitude and the rapid production of 15N‐N2 in incubations with added confirmed close coupling of the two processes. Areal rates of N‐transformation were estimated taking advective transport of substrates into account and integrating volumetric rates over modeled oxygen and nitrate penetration depths, these ranged between 22 μmol N m−2 h−1 and 94 μmol N m−2 h−1. Furthermore, results from the 15N‐labeling experiments show that these subtidal permeable sediments are, in sharp contrast to common belief, a substantial source of N2O. Our combined results show that nitrification fuels denitrification by providing an additional source of nitrate, and as such masks true N‐losses from these highly eutrophic sediments. Given the widespread occurrence of anthropogenically influenced permeable sediments, coupled benthic nitrification–denitrification might have an important but so far neglected role in N‐loss from shelf sediments.

Massive nitrous oxide emissions from the tropical South Pacific Ocean

Nitrous oxide is a potent greenhouse gas and a key compound in stratospheric ozone depletion. In the ocean, nitrous oxide is produced at intermediate depths through nitrification and denitrification, in particular at low oxygen concentrations. Although a third of natural emissions of nitrous oxide to the atmosphere originate from the ocean, considerable uncertainties in the distribution and magnitude of the emissions still exist. Here we present high-resolution surface measurements and vertical profiles of nitrous oxide that include the highest reported nitrous oxide concentrations in marine surface waters, suggesting that there is a hotspot of nitrous oxide emissions in high-productivity upwelling ecosystems along the Peruvian coast. We estimate that off Peru, the extremely high nitrous oxide supersaturations we observed drive a massive efflux of 0.2–0.9 Tg of nitrogen emitted as nitrous oxide per year, equivalent to 5–22% of previous estimates of global marine nitrous oxide emissions. Nutrient and gene abundance data suggest that coupled nitrification–denitrification in the upper oxygen minimum zone and transport of resulting nitrous oxide to the surface by upwelling lead to the high nitrous oxide concentrations. Our estimate of nitrous oxide emissions from the Peruvian coast surpasses values from similar, highly productive areas.

Aridland constructed treatment wetlands I: Macrophyte productivity, community composition, and nitrogen uptake

Urbanized areas increasingly rely on constructed treatment wetlands (CTW) for cost effective and environmentally-based wastewater treatment. Constructed treatment wetlands are particularly attractive treatment options in arid urban environments where water reuse is important for dealing with scarce water resources. Emergent macrophytes play an important role in nutrient removal, particularly nitrogen (N) removal, in CTW. However, the role of plant community composition in nutrient removal is less clear. Numerous studies have shown that macrophyte species differentially affect N uptake processes (e.g., direct plant uptake, coupled nitrification–denitrification, soil accretion). However, many of these studies have been based on small-scale experiments and have been carried out in mesic environments, which means that their findings are difficult to extrapolate to aridland CTW systems. Our study sought to examine the relationships among emergent macrophyte productivity, plant community composition, and N uptake [by both the plants and the entire ecosystem] at a 42ha CTW in arid Phoenix, Arizona, USA. We quantified above- and belowground biomass bimonthly and foliar N content annually for four species groups (Typha latifolia+Typha domingensis, Schoenoplectus californicus+Schoenoplectus tabernaemontani, Schoenoplectus acutus, and Schoenoplectus americanus) from July 2011 to September 2013. We quantified dissolved inorganic N fluxes into and out of the system and compared plant N removal to total system fluxes. Additionally, we estimated monotypic N content for each to compare the system’s current community composition and plant N removal to hypothetical scenarios in which the system was dominated by only one species.Peak aboveground biomass ranged from 1586±179 (SE) to 2666±164 (SE) gdwm−2 of which Typha spp. accounted for an increasing portion (>66%). We observed widespread ‘thatching’ – the toppling of large stands of macrophytes – that was likely related to a decline in peak biomass from July 2011 to July 2012. The foliar N content was similar among the species groups and N content for all species combined, at peak biomass, was 31±8Ngm−2. This measured foliar N content was higher than our estimates of the foliar N content in hypothetical monotypic stands, suggesting that the system’s actual community composition performed better, in terms of direct plant N uptake, than if the system had been planted with only one species group. Overall, direct plant N uptake accounted for 7% of inorganic N inputs and 19% of whole-system inorganic N removal. Our findings suggest that managers and designers should consider diverse plant communities rather than monotypic stands when designing, constructing, and managing CWT wetland systems. Future research is needed to elucidate those management strategies that might best promote or preserve diverse plant communities in these systems in a cost effective manner.

The invasive Asian clam (Corbicula fluminea) increases sediment denitrification and ammonium flux in 2 streams in the midwestern USA

The invasive Asian clam, Corbicula fluminea, can enhance conditions needed for denitrification, but the effects of C. fluminea on denitrification in streams have not been measured. In summer 2012, we incubated sand- and gravel-filled boxes in the North Branch of the Chicago River, Illinois (high nutrient), and Eagle Creek, Michigan, USA (low nutrient). One side of the box contained no clams (control), and the other contained C. fluminea. After 6 wk in situ, we measured inorganic N and dissolved-gas fluxes using a continuous-flow approach. At both sites, live C. fluminea significantly increased NH4+ and N2 flux out of sediments and O2 consumption (i.e., respiration) relative to control sediment. Clams did not affect NO3− flux. Clams probably increased NH4+ flux via direct NH4+ excretion or mineralization of clam wastes and increased N2 flux through either increased coupled nitrification–denitrification or enhanced exchange of nutrients between water column and sediment via bioturbation (i.e., burrowing). We used benthic clam density in each stream to scale up effects of live C. fluminea on in situ N fluxes. In the low-nutrient stream, live clams increased NH4+ flux more than N2 production. However, in the high-nutrient stream, live clams enhanced N2 production more than NH4+ flux. The influence of dense assemblages of burrowing bivalves on denitrification may be an overlooked and potentially significant component of lotic N uptake in low- and high-N streams.

Conditioning the alternating aerobic–anoxic process to enhance the removal of inorganic nitrogen pollution from a municipal wastewater in France

Inorganic nitrogen pollution from surface waters can adversely affect human health and the environment. Coupled nitrification–denitrification can significantly remove the total inorganic nitrogen pollution amount from municipal wastewater; however, researchers only have a limited understanding of the alternating aerobic–anoxic process in a single reactor. This study performed a typical treatment using a completely mixed alternating aerobic–anoxic extended aeration treatment process in a single reactor, biological fluidised bed reactor to remove inorganic nitrogen pollution from a municipal wastewater in France. Comparative analysis of the coupled nitrification–denitrification reactions was carried out to investigate the two different alternating aerobic–anoxic processes of 3-h aerobic digestion and 6-h anoxic time and 3-h aerobic digestion and 3-h anoxic time. The results indicate that the change in anoxic time, specifically, from 6 to 3 h, can increase the alternating aerobic–anoxic process performance by approximately 53.4%. The average effluent inorganic nitrogen concentration decreased from 10.3 to 4.8 mg N/L, achieving the desired inorganic nitrogen concentration of less than 10 mg N/L in the outflow to meet the stringent effluent standards. The study offers a proper treatment that can be used to help reduce inorganic nitrogen pollution from municipal wastewater processed in a single-sludge reactor. The study's results advance the understanding of this simple technique that effectively removes inorganic nitrogen pollution from municipal wastewater.

Nitrogen dynamics at the sediment–water interface in a tropical reservoir

Nitrogen dynamics at the sediment–water interface were examined in a tropical reservoir, Upper Peirce Reservoir, Singapore to provide information on the relative importance of each process and evaluated the spatial differences of nitrogen dynamics. The intact sediment cores were collected from three locations with different depths and distances to the artificial aeration system. The flow-through system combined with the isotope pairing technique was applied to estimate the nitrogen fluxes, potential denitrification rates and anammox rates. A mass balance model was developed and calibrated with the experimental results, and calculated mineralization, nitrification and dissimilatory nitrate reduction process rates. The sediment had a strong mineralization rate (13.39 mmol m−2 d−1) at shallow section, thus, had obvious NH4-N fluxes (17.61 mmol m−2 d−1). The total N2 removal rates through denitrification and anammox processes ranged from 0.08 to 0.28 mmol m−2 d−1, relatively lower than that in estuaries and coastal systems. Denitrification was performed as the main loss pathway, dominating up to 98% of total N2 removal rates. The coupled nitrification–denitrification (Dn) was dominant as compared to denitrification that happened from water column nitrate (Dw). Nitrification and N2 removal rates increased with water column depth. The artificial aeration around the deeper section might have contributed to the bacteria activities, and thus might stimulate high microbial processes converting NH4-N to NO3-N and bioactive nitrogen to N2 gas. The discovery of nitrogen transformation pathways in tropical freshwater systems are proposed to be incorporated into future conceptual models of global nitrogen cycles.

Enhancement of denitrification in permeable carbonate sediment due to intra-granular porosity: A multi-scale modelling analysis

It has recently been hypothesized that bulk denitrification rates in carbonate sands may be enhanced by reactions occurring in the intra-granular pores, cracks and crevices. We tested this hypothesis using a series of flow and reactive transport models spanning from the pore-scale (∼mm) to the continuum scales (∼10cm bedforms). Pore-scale simulations solved the coupled Navier–Stokes and Brinkman equations and represented flow-through reactor experiments previously performed on coral reef sands. The results revealed that intra-granular transport and reactions can explain over-all denitrification enhancement. A sensitivity study with a single grain diffusive transport model showed that in the majority of cases, the resultant increase in denitrification was not coupled to nitrification within a single grain. Only for large grain diameters of 2 and 4mm was coupled nitrification–denitrification important. In most cases, coupled nitrification–denitrification instead arose as conditions became more reducing along a flow path, as is the case in quartz sands without intragranular pores. An intra-granular reaction rate based on a single grain model was incorporated into a continuum-scale Darcy flow and reactive transport model for a rippled sand bed, where porewater flow is driven by the turbulent current over the ripple. The results of the Darcy-scale model suggest that intra-granular pores increase the amount of slow-flowing areas within which coupled nitrification–denitrification can occur. We conclude that the complex advective flow field does not strongly inhibit denitrification enhancement by carbonate sand grains, as it does in silica sands. Thus, intra-granular reactions may enhance bulk denitrification in carbonate sediment with porous grains under natural advective conditions.

Benthic mineralization and nutrient exchange over the inner continental shelf of western India

Abstract. The western Indian continental shelf is one of the most productive coastal systems of the world ocean. This system experiences extreme changes in its oxygen regime, being normoxic from November to May and suboxic (denitrifying)/anoxic from June to October, owing to the biogeochemical response to cyclical monsoonal influence. In order to understand the impact of the seasonally varying oxygen regime on benthic mineralization, nutrient exchange and, in turn, on the shelf ecosystem, we carried out the first ever intact-core incubations during two contrasting seasons – spring intermonsoon and fall intermonsoon (late southwest monsoon) at a 28 m-deep fixed site on the inner shelf off Goa, dominated by fine-grained cohesive sediments. The results showed that incomplete sediment oxygen consumption (SOC) occurred during April as opposed to the complete SOC and subsequent sulfide flux observed in the fall intermonsoon incubations. The sediments acted as a perennial net source of DIN (dissolved inorganic nitrogen i.e. NO3− + NO2− + NH4+), PO43− and SiO44− to the overlying water column. The efflux of DIN increased from 1.4 to 3.74 mmol m−2 d−1 from April to October, of which NH4+ flux comprised 59–100%. During the oxic regime, ∼75% of diffusing NH4+ appeared to be nitrified (2.55 mmol m−2 d−1), of which ∼77% remained coupled to benthic denitrification. Consequently, 58% of NH4+ flux was lost in active coupled nitrification–denitrification, resulting in substantial N loss (1.98 mmol m−2 d−1) in the sediments. The continental shelf sediments switched over from being a NO3− source during the oxic regime to a NO3− sink during the anoxic regime. During suboxia, benthic denitrification that is fed by NO3- from the overlying water caused N loss at the rate of 1.04 mmol m−2 d−1. Nitrogen loss continued even under sulfidic conditions during October, possibly through the chemolithoautotrophic denitrification, at a potential rate of 3.21 mmol m−2 d−1. Phosphate flux increased more than 4-fold during October as compared to April, due to reductive dissolution of Fe- and Mn oxides. The SiO44− flux increased during October apparently due to the higher availability of siliceous ooze from diatom blooms commonly occurring in the monsoon season. Slow oxidation of organic carbon (Corg) under anoxia, lower temperature and reduced benthic faunal activity appeared to decrease benthic mineralization by 25% as suggested by the drop in the Corg oxidation rate from 63.8 mmol C m−2 d−1 in April to 47.8 mmol C m−2 d−1 in October. This indicated a higher preservation of Corg during the late southwest monsoon. Sediment porosity, Corg content and nutrients did not show significant variations from April to October. Porewaters were found to be enriched with NH4+, PO43− and SiO44− but depleted in NO3− and NO2− in these organic-rich sediments. Significant DIN, PO43− and SiO44− effluxes indicate the potential of benthic input in meeting nutrient demand of the phytoplankton community in this seasonally N-limited shelf system.

Correction to Transport Zonation Limits Coupled Nitrification-Denitrification in Permeable Sediments

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionORIGINAL ARTICLEThis notice is a correctionCorrection to Transport Zonation Limits Coupled Nitrification-Denitrification in Permeable SedimentsAdam J. Kessler*, Ronnie N. Glud, M. Bayani Cardenas, and Perran L. M. CookCite this: Environ. Sci. Technol. 2014, 48, 11, 6522Publication Date (Web):May 22, 2014Publication History Published online22 May 2014Published inissue 3 June 2014https://doi.org/10.1021/es502359aCopyright © 2014 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views353Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (756 KB) Get e-Alerts Get e-Alerts

Influence of bioturbation on denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in freshwater sediments

Intensive agriculture leads to increased nitrogen fluxes (mostly as nitrate, NO3 −) to aquatic ecosystems, which in turn creates ecological problems, including eutrophication and associated harmful algal blooms. These problems have focused scientific attention on understanding the controls on nitrate reduction processes such as denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Our objective was to determine the effects of nutrient-tolerant bioturbating invertebrates (tubificid oligochaetes) on nitrogen cycling processes, specifically coupled nitrification–denitrification, net denitrification, DNRA, and biogeochemical fluxes (O2, NO3 −, NH4 +, CO2, N2O, and CH4) in freshwater sediments. A mesocosm experiment determined how tubificid density and increasing NO3 − concentrations (using N15 isotope tracing) interact to affect N cycling processes. At the lowest NO3 − concentration and in the absence of bioturbation, the relative importance of denitrification to DNRA was similar (i.e., 49.6 and 50.4 ± 8.1 %, respectively). Increasing NO3 − concentrations in the control cores (without fauna) stimulated denitrification, but did not enhance DNRA, which significantly altered the relative importance of denitrification compared to DNRA (94.6 vs. 5.4 ± 0.9 %, respectively). The presence of tubificid oligochaetes enhanced O2, NO3 −, NH4 + fluxes, greenhouse gas production, and N cycling processes. The relative importance of denitrification to DNRA shifted towards favoring denitrification with both the increase in NO3 − concentrations and the increase of bioturbation activity. Our study highlights that understanding the interactions between nutrient-tolerant bioturbating species and nitrate contamination is important for determining the nitrogen removal capacity of eutrophic freshwater ecosystems.

Diversity and distribution of &amp;lt;i&amp;gt;amoA&amp;lt;/i&amp;gt;-type nitrifying and &amp;lt;i&amp;gt;nirS&amp;lt;/i&amp;gt;-type denitrifying microbial communities in the Yangtze River estuary

Abstract. Coupled nitrification–denitrification plays a critical role in the removal of excess nitrogen, which is chiefly caused by humans, to mitigate estuary and coastal eutrophication. Despite its obvious importance, limited information about the relationships between nitrifying and denitrifying microbial communities in estuaries, and their controlling factors have been documented. We investigated the nitrifying and denitrifying microbial communities in the estuary of turbid subtropical Yangtze River (YRE), the largest river in Asia, by analyzing the ammonia monooxygenase gene amoA, including archaeal and bacterial amoA, and the dissimilatory nitrite reductase gene nirS using clone libraries and quantitative PCR (qPCR). The diversity indices and rarefaction analysis revealed a quite low diversity for both β-proteobacterial and archaeal amoA genes, but qPCR data showed significantly higher amoA gene copy numbers for archaea than β-proteobacteria. Compared with the amoA gene, a significantly higher level of diversity but lower gene copy numbers were found for the nirS gene. Nitrification and denitrification rates based on 15N incubation experiments supported gene abundance data as denitrification rates were below detection limit, suggesting lower denitrification than nitrification potential. In general, the abundances of the amoA and nirS genes were significantly higher in the bottom samples than the surface ones, and in the high-turbidity river mouth, were significantly higher in the particle-associated (&gt; 3 μm) than the free-living (0.2 ~ 3 μm) communities. Notably, positive correlations between the amoA and nirS gene abundances suggested potential gene-based coupling between nitrification and denitrification, especially for the particle-associated assemblages. Statistical analysis of correlations between the community structure, gene abundances and environmental variables further revealed that dissolved oxygen and total suspended material might be the key factors controlling community spatial structure and regulating nitrification and denitrification potentials in the YRE ecosystem.

Niche Differentiation of Ammonia-Oxidising Archaea (AOA) and Bacteria (AOB) in Response to Paper and Pulp Mill Effluent

Sediment organic loading has been shown to affect estuarine nitrification and denitrification, resulting in changes to sediment biogeochemistry and nutrient fluxes detrimental to estuarine health. This study examined the effects of organic loading on nutrient fluxes and microbial communities in sediments receiving effluent from a paper and pulp mill (PPM) by applying microcosm studies and molecular microbial ecology techniques. Three sites near the PPM outfall were compared to three control sites, one upstream and two downstream of the outfall. The control sites showed coupled nitrification-denitrification with minimal ammonia release from the sediment. In contrast, the impacted sites were characterised by nitrate uptake and substantial ammonia efflux from the sediments, consistent with a decoupling of nitrification and denitrification. Analysis of gene diversity demonstrated that the composition of nitrifier communities was not significantly different at the impacted sites compared to the control sites; however, analysis of gene abundance indicated that whilst there was no difference in total bacteria, total archaea or ammonia-oxidising archaea (AOA) abundance between the control and impacted sites, there was a significant reduction in ammonia-oxidising bacteria (AOB) at the impacted sites. The results of this study demonstrate an effect of organic loading on estuarine sediment biogeochemistry and highlight an apparent niche differentiation between AOA and AOB.

Seasonal oxygen, nitrogen and phosphorus benthic cycling along an impacted Baltic Sea estuary: regulation and spatial patterns

The regulatory roles of temperature, eutrophication and oxygen availability on benthic nitrogen (N) cycling and the stoichiometry of regenerated nitrogen and phosphorus (P) were explored along a Baltic Sea estuary affected by treated sewage discharge. Rates of sediment denitrification, anammox, dissimilatory nitrate reduction to ammonium (DNRA), nutrient exchange, oxygen (O2) uptake and penetration were measured seasonally. Sediments not affected by the nutrient plume released by the sewage treatment plant (STP) showed a strong seasonality in rates of O2 uptake and coupled nitrification–denitrification, with anammox never accounting for more than 20 % of the total dinitrogen (N2) production. N cycling in sediments close to the STP was highly dependent on oxygen availability, which masked temperature-related effects. These sediments switched from low N loss and high ammonium (NH4 +) efflux under hypoxic conditions in the fall, to a major N loss system in the winter when the sediment surface was oxidized. In the fall DNRA outcompeted denitrification as the main nitrate (NO3 −) reduction pathway, resulting in N recycling and potential spreading of eutrophication. A comparison with historical records of nutrient discharge and denitrification indicated that the total N loss in the estuary has been tightly coupled to the total amount of nutrient discharge from the STP. Changes in dissolved inorganic nitrogen (DIN) released from the STP agreed well with variations in sedimentary N2 removal. This indicates that denitrification and anammox efficiently counterbalance N loading in the estuary across the range of historical and present-day anthropogenic nutrient discharge. Overall low N/P ratios of the regenerated nutrient fluxes impose strong N limitation for the pelagic system and generate a high potential for nuisance cyanobacterial blooms.

Nutrient Fluxes from Sediments in the San Francisco Bay Delta

In September 2011 and March 2012, benthic nutrient fluxes were measured in the San Francisco Bay Delta, across a gradient from above the confluence of the Sacramento and San Joaquin Rivers to Suisun Bay. Dark and illuminated core incubation techniques were used to measure rates of denitrification, nutrient fluxes (phosphate, ammonium, nitrate), and oxygen fluxes. While benthic nutrient fluxes have been assessed at several sites in northern San Francisco Bay, such data across a Delta–Bay transect have not previously been determined. Average September rates of DIN (nitrate, nitrite, ammonium) flux were net positive across all sites, while March DIN flux indicated net uptake of DIN at some sites. Denitrification rates based on the N2/Ar ratio approach were between 0.6 and 1.0 mmol m−2 day−1, similar to other mesotrophic estuarine sediments. Coupled nitrification–denitrification was the dominant denitrification pathway in September, with higher overlying water nitrate concentrations in March resulting in denitrification driven by nitrate flux into the sediments. Estimated benthic microalgal productivity was variable and surprisingly high in Delta sediments and may represent a major source of labile carbon to this ecosystem. Variable N/P stoichiometry was observed in these sediments, with deviations from Redfield driven by processes such as denitrification, variable light/dark uptake of nutrients by microalgae, and adsorption of soluble reactive phosphorus.

Stimulation of microbial nitrogen cycling in aquatic ecosystems by benthic macrofauna: mechanisms and environmental implications

Abstract. Invertebrate animals that live at the bottom of aquatic ecosystems (i.e., benthic macrofauna) are important mediators between nutrients in the water column and microbes in the benthos. The presence of benthic macrofauna stimulates microbial nutrient dynamics through different types of animal–microbe interactions, which potentially affect the trophic status of aquatic ecosystems. This review contrasts three types of animal–microbe interactions in the benthos of aquatic ecosystems: (i) ecosystem engineering, (ii) grazing, and (iii) symbiosis. Their specific contributions to the turnover of fixed nitrogen (mainly nitrate and ammonium) and the emission of the greenhouse gas nitrous oxide are evaluated. Published data indicate that ecosystem engineering by sediment-burrowing macrofauna stimulates benthic nitrification and denitrification, which together allows fixed nitrogen removal. However, the release of ammonium from sediments is enhanced more strongly than the sedimentary uptake of nitrate. Ecosystem engineering by reef-building macrofauna increases nitrogen retention and ammonium concentrations in shallow aquatic ecosystems, but allows organic nitrogen removal through harvesting. Grazing by macrofauna on benthic microbes apparently has small or neutral effects on nitrogen cycling. Animal–microbe symbioses provide abundant and distinct benthic compartments for a multitude of nitrogen-cycle pathways. Recent studies reveal that ecosystem engineering, grazing, and symbioses of benthic macrofauna significantly enhance nitrous oxide emission from shallow aquatic ecosystems. The beneficial effect of benthic macrofauna on fixed nitrogen removal through coupled nitrification–denitrification can thus be offset by the concurrent release of (i) ammonium that stimulates aquatic primary production and (ii) nitrous oxide that contributes to global warming. Overall, benthic macrofauna intensifies the coupling between benthos, pelagial, and atmosphere through enhanced turnover and transport of nitrogen.

Transport Zonation Limits Coupled Nitrification-Denitrification in Permeable Sediments

Measurement of biogeochemical processes in permeable sediments (including the hyporheic zone) is difficult because of complex multidimensional advective transport. This is especially the case for nitrogen cycling, which involves several coupled redox-sensitive reactions. To provide detailed insight into the coupling between ammonification, nitrification and denitrification in stationary sand ripples, we combined the diffusion equilibrium thin layer (DET) gel technique with a computational reactive transport biogeochemical model. The former approach provided high-resolution two-dimensional distributions of NO3(-) and (15)N-N2 gas. The measured two-dimensional profiles correlate with computational model simulations, showing a deep pool of N2 gas forming, and being advected to the surface below ripple peaks. Further isotope pairing calculations on these data indicate that coupled nitrification-denitrification is severely limited in permeable sediments because the flow and transport field limits interaction between oxic and anoxic pore water. The approach allowed for new detailed insight into subsurface denitrification zones in complex permeable sediments.

Flood pulses control soil nitrogen cycling in a dynamic river floodplain

Flood pulses are major drivers of river–floodplain processes. We investigated their effects on soil nitrogen (N) transformations along a lateral gradient from the river to a mature alluvial forest in the Thur River floodplain (NE Switzerland). Selected N pools (ammonium and nitrate) and N transformations (mineralization, nitrification and denitrification) in the topsoils were repeatedly quantified over a period of six months. During this period, the floodplain was affected by two flood events of different magnitude.Our results showed a distinct difference in size and temporal changes of N pools and transformation rates among functional process zones (FPZs) differing in flooding disturbance. A strong temporary increase in N mineralization in a FPZ with young soil on the frequently flooded gravel bars was the most prominent flood-related effect. This was most likely related to the fast-flowing water during inundation that deposited fresh dispersed sediments with a coarse sandy texture containing highly bioavailable organic N, and/or stimulated the turnover of existing N by destroying sediment aggregates already present before the flood. Increased N mineralization appeared to stimulate coupled nitrification–denitrification in this FPZ during the drying phase. In the more stable FPZs, N mineralization was not strongly enhanced by flooding, whereas nitrification and denitrification were also increased during the drying phase, however to a lesser degree than in the gravel bar soils. Based on our results we propose that floodplain zones characterized by short intensive floods with fast over-flowing water are “hot spots” and the drying phases after the floods are “hot moments” of N transformations.

Activity, Abundance, and Diversity of Nitrifying Archaea and Denitrifying Bacteria in Sediments of a Subtropical Estuary: Bahía del Tóbari, Mexico

Fixed nitrogen (N) removal from estuaries via coupled nitrification–denitrification plays a significant role in the global N cycle and the biogeochemistry of individual estuaries. Much of our understanding of these processes is drawn from temperate estuaries, yet tropical and subtropical estuaries may respond differently to N inputs. I tested the hypothesis that nitrification is limited within subtropical estuaries by comparing nitrification and denitrification potentials, and the abundance of archaeal ammonia monooxygenase (amoA) and bacterial nitrite reductase (nirS) genes, across five sites in Bahia del Tobari, Mexico. Sampling was conducted when agricultural runoff supplied substantial quantities of N (ca. 20–80 μM ammonium), yet nitrification was detected at a single site. Denitrification was measured at four sites, and three displayed nitrate uptake rather than net nitrification—indicating a N sink within these sediments. Bacterial nirS genes uniformly outnumbered archaeal amoA genes (3- to 49-fold) and were more abundant in the northern part of the estuary. Patterns of community similarity among different sites were also different for nirS and archaeal amoA: similarities between sites based on nirS were often greater than for amoA, and sites were more rarely statistically different from each other. While amoA abundance was inversely related to temperature, neither amoA nor nirS was correlated with nitrification or denitrification potentials. My results are broadly consistent with known and proposed patterns of nitrification and denitrification in subtropical estuarine sediments, including the idea that nitrification is limited within subtropical estuarine sediments.