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Environmental controls of anammox and denitrification in Southern New England estuarine and shelf sediments
Limnology and Oceanography
Abstract
We measured denitrification and anammox potential rates in homogenized sediments over two annual cycles from two estuarine sites (Providence River estuary and Narragansett Bay) and two continental shelf sites (Block Island and Rhode Island sounds). Denitrification varied both spatially and seasonally, but anammox only varied spatially. Denitrification ranged from 2.5 to 112 nmol N h21 mL21 sediment, and anammox from 0 to 8.7 nmol N h21 mL21 sediment, with the contribution of anammox to N2 fluxes (ra) ranging from undetectable to 4% in estuarine sites and 8–42% on the shelf. Oxygen microprofiles were analyzed in intact cores and concentrations of nitrate, nitrite, and ammonium were measured in the sediment slice corresponding to the depth layer in which potential rates were measured. Denitrification rates correlated positively with diffusive O2 consumption and temperature and potential anammox rates correlated positively with pore-water NO{3 concentrations. Anammox was positively correlated with denitrification in shelf sediments where anammox was regularly detected, but not in estuarine sediments. ra was negatively correlated with diffusive O2 consumption and positively correlated with pore-water nitrate. Both organic matter and nitrate were important factors regulating the contribution of anammox to N2 production. As a whole, our results demonstrate that incorporating processes that control these two factors into models of N cycling, rather than focusing on organic matter availability alone, may improve predictions of the relative importance of anammox to N2 production in marine sediments.
... These two processes and their partitioning largely determine the size of the global Nr sink and N 2 O source. Previous studies have shown that anammox could be crucial in some deepsea sediments 17,18 , although Nr removal by benthic denitrification generally exceeds removal by anammox [19][20][21] in such environments. Devol concluded that the fraction of total N 2 production by anammox (ra%) ranged from 0-79% in marine sediments and typically constitutes approximately 10-40% of the total Nr removal 16 . ...
... Devol concluded that the fraction of total N 2 production by anammox (ra%) ranged from 0-79% in marine sediments and typically constitutes approximately 10-40% of the total Nr removal 16 . The variance in ra% has been attributed to a number of environmental factors such as temperature, the quantity and quality of organic matter, and nitrate concentration 19,[22][23][24] . Among these potential environmental variables, temperature is one of the most fundamental factors governing microbial metabolism of denitrification and anammox, but the temperature effect has not been sufficiently resolved. ...
... Global ra% and temperature data 25 show that ra% has an inverse relationship with the temperature at which samples were collected or incubated. Despite decades of study, the factors that control the partitioning between sedimentary denitrification and anammox remain underexplored 16 , specifically, the knowledge of how the two Nr-removal processes respond to future warming remains limited due to lack of field measurements 19,[26][27][28][29] . Understanding the environmental factors of Nr-removal pathways and associated N 2 O production, particularly temperature, will be essential for Earth system models 11 to accurately quantify the Nr-removal flux and to predict future biogeochemical cycles and associated climate feedbacks driven by reactive nitrogen. ...
Temperature is one of the fundamental environmental variables governing microbially mediated denitrification and anaerobic ammonium oxidation (anammox) in sediments. The GHG nitrous oxide (N2O) is produced during denitrification, but not by anammox, and knowledge of how these pathways respond to global warming remains limited. Here, we show that warming directly stimulates denitrification-derived N2O production and that the warming response for N2O production is slightly higher than the response for denitrification in subtropical sediments. Moreover, denitrification had a higher optimal temperature than anammox. Integrating our data into a global compilation indicates that denitrifiers are more thermotolerant, whereas anammox bacteria are relatively psychrotolerant. Crucially, recent summer temperatures in low-latitude sediments have exceeded the optimal temperature of anammox, implying that further warming may suppress anammox and direct more of the nitrogen flow towards denitrification and associated N2O production, leading to a positive climate feedback at low latitudes.
... In sediments in shallow coastal areas, the relative importance of anammox is usually low compared with denitrification, whereas anammox has a higher relative importance for N 2 production in deeper marine sediments (Dalsgaard et al. 2005;Thamdrup and Dalsgaard 2002;Koop-Jakobsen and Giblin 2009;Amano et al. 2011;Brin et al. 2014). The factors controlling anammox are not well understood, but increased anammox activity with available organic matter and increased NO 3 − have been reported (Thamdrup and Dalsgaard 2002;Trimmer et al. 2003;Risgaard-Petersen et al. 2004;Brin et al. 2014). ...
... In sediments in shallow coastal areas, the relative importance of anammox is usually low compared with denitrification, whereas anammox has a higher relative importance for N 2 production in deeper marine sediments (Dalsgaard et al. 2005;Thamdrup and Dalsgaard 2002;Koop-Jakobsen and Giblin 2009;Amano et al. 2011;Brin et al. 2014). The factors controlling anammox are not well understood, but increased anammox activity with available organic matter and increased NO 3 − have been reported (Thamdrup and Dalsgaard 2002;Trimmer et al. 2003;Risgaard-Petersen et al. 2004;Brin et al. 2014). In a hypereutrophic intertidal ecosystem, there are excessive loadings of available N. In addition, macroalgae blooms, as primary producers in these ecosystems, are a source of autochthonous organic matter (Corzo et al. 2009;Bartoli et al. 2012). ...
... In general, autochthonous organic matter is labile for heterotrophic bacteria (Wetzel 2001). Anammox bacteria are reliant on the in situ formation of NO 2 − via NO 3 − reduction by heterotrophic bacteria (Thamdrup and Dalsgaard 2002;Trimmer et al. 2003;Risgaard-Petersen et al. 2004;Brin et al. 2014). Moreover, the tight link between the anammox and denitrification processes found in the coastal sediment suggested that denitrifying bacteria are a primary source of NO 2 − for the anammox bacteria (Meyer et al. 2005;Koop-Jakobsen and Giblin 2009;Hou et al. 2013). ...
An increase in available nitrogen loading in intertidal ecosystems causes eutrophication and macroalgae blooms. Denitrification and anaerobic ammonium oxidation (anammox) lead to the removal of bioavailable nitrogen, but few studies have examined this in intertidal sediments. The sediment anammox and denitrification rates in September 2015 and November 2016 were measured using a ¹⁵N tracer technique at two sites, with and without macroalgae, in the hypereutrophic Yatsu tidal flat, eastern Japan. At both sites, the rate of N2 production via anammox was consistently low compared with that via denitrification, accounting for < 7% of the total N2 production. In a fed-batch incubation experiment, the anammox rate increased in the surface sediment after 3 months. However, the contribution of anammox to nitrogen removal did not exceed that of denitrification, suggesting that denitrification is the major pathway for conversion of inorganic nitrogen to N2, and that anammox plays a limited role in nitrogen removal in the Yatsu tidal flat. Denitrification activity measured from August 2012 to January 2017 using the acetylene block method was higher in the sediment with macroalgae than that without. Multiple linear regression analysis revealed that denitrification in the sediment with macroalgae was limited by the nitrogen substrate, likely due to competition with macroalgae for nitrogen. Temperature and H2S production under macroalgae cover might also affect denitrification. In comparison, the organic carbon content was a key factor regulating heterotrophic denitrification in the sediment without macroalgae. These findings suggest that the occurrence of macroalgae changes the progress of denitrification in intertidal ecosystems.
... The range of average denitrification potential rates (2.1-80.4 nmol N cm −3 h −1 ) across stations that we measured is typical for studies employing similar techniques at different locations in shelf or deep-sea sediments (Trimmer and Engström, 2011;Brin et al., 2014). Higher denitrification potential rates have been reported in samples from coastal bays or estuaries but in general the denitrification potential rates that we measured in shelf sediments are still in the range typically measured in shallower sub-tropical, temperate, or arctic sediments. ...
... Measurements of denitrification and anammox potential rates in sediments within ODZs are relatively rare, with one example from the Arabian Sea (Sokoll et al., 2012). Surprisingly, the average anammox potential rates that we measured at two of our shelf stations in the ODZ of 25.1 and 44.2 nmol N cm −3 h −1 (120 m and 325 m stations, respectively) are higher compared to the range of rates measured in different estuarine, shelf, or deep-sea sediments, including the Arabian Sea (Trimmer and Engström, 2011;Sokoll et al., 2012;Brin et al., 2014). The factors contributing to the high anammox potential rates that we measured are not clear but could be related to a combination of factors, including undetectable O 2 and relatively high NO 3 − and NO 2 − concentrations in the overlying water and lack of dense Thioploca at these two sites. ...
... Another factor controlling ra is likely to be NO 3 − availability. In sediments at different locations with similar labile organic C, greater NO 3 − concentrations in the overlying water or sediment porewater are related to greater ra, perhaps because of relieved competition for NO 2 − between denitrifying and anammox bacteria (Rich et al., 2008;Brin et al., 2014;Algar and Vallino, 2014). The visual presence of Thioploca at two stations in our study may have been a factor contributing to differences in NO 3 − availability in the sediments at these two stations due to the ability of Thioploca to transport NO 3 − down into sediments (Huettel et al., 1996). ...
The upwelling system of coastal Peru supports very high primary production, contributing to an oxygen deficient zone (ODZ) in subsurface waters and high organic matter deposition rates to underlying sediments. Although anammox and denitrification have been relatively well studied in ODZ waters, few studies have investigated these processes in the underlying sediments. We sampled seven stations over a large geographic area along the Peru margin, spanning a water depth of 100–3240 m. At two of the central shelf stations (100 m and 325 m), we observed Thioploca, with a well-developed mat at the shallowest station (100 m). We measured sediment properties and conducted shipboard ¹⁵N-incubations of homogenized sediments to determine potential rates of anammox and denitrification and potential controlling factors at each station. Diversity of anammox bacteria based on 16S rRNA and hydrazine oxidoreductase (hzo) sequences and hzo gene abundances were measured at each station. Overall, organic C content was high across the stations (3–12%), except for two of the deepest stations (~1.5%). Porewater ammonium fluxes and ammonium production rates in shipboard incubations, reflecting sediment organic carbon decomposition rates, were higher at the two central shelf stations compared to the other stations. The range in average potential rates was 2.1–80.4 nmol N cm⁻³ h⁻¹ for denitrification and 1.8–44.2 nmol N cm⁻³ h⁻¹ for anammox. The range in relative anammox (ra) across stations was 2.6–47.4%, with an average of 34.2%. The lowest ra was found at the shallowest shelf station with Thioploca mats and highest ammonium production rates. The ra jumped up to 45.9% at the station with the next highest ammonium production rates, corresponding to the deeper shelf station (325 m). At the other stations, ra was relatively high (39.6–47.4%), except at one station (16.3%), reflecting similar ammonium production rates due to decomposition across these stations. Anammox bacteria in the Candidatus Scalindua genus were the only anammox bacteria detected in Peru margin sediments based on 16S rRNA or hzo sequences. Copy number of hzo indicated abundant populations of anammox bacteria across the stations. However, hzo copy number did not correlate with anammox rates or ra. Overall, our results suggest that anammox contributes significantly to N2 production in Peru margin sediments, except in shelf sediments with high decomposition rates and dense Thioploca mats.
... Macrofaunal activities can also alter NO 3 À reducing processes in sediment via two mechanisms: (1) bioturbation (particle mixing) and (2) bioirrigation (solute transport), both of which can induce changes in redox chemistry and microbial composition (Kristensen et al. 2013;Yazdani Foshtomi et al. 2015;Deng et al. 2020). Organic matter supply and NO 3 À concentrations have also been suggested as key factors that can influence partitioning between sediment denitrification and anammox in the Atlantic shelf (Brin et al. 2014). However, it is unclear what the specific biotic and abiotic factors controlling NO 3 À reduction in shelf sediments with oligotrophic waters are. ...
... Considering the limited substrate availability for anammox in the sediments, rates of anammox on the NE New Zealand shelf are outcompeted by NO x À -consuming denitrification. Anammox remains low and consistent in shallow-shelf sediments (Brin et al. 2014). No significant DNRA rates were detected in the NE New Zealand shelf sediments. ...
Continental shelf sediments are considered hotspots for nitrogen (N) removal. While most investigations have quantified denitrification in shelves receiving large amounts of anthropogenic nutrient supply, we lack insight into the key drivers of N removal on oligotrophic shelves. Here, we measured rates of N removal through denitrification and anammox by the revised‐isotope pairing technique (r‐IPT) along the Northeastern New Zealand shelf. Denitrification dominated total N 2 production at depths between 30 and 128 m with average rates (± SE) ranging from 65 ± 28 to 284 ± 72 μ mol N m ⁻² d ⁻¹ . N 2 production by anammox ranged from 3 ± 1 to 28 ± 11 μ mol N m ⁻² d ⁻¹ and accounted for 2–19% of total N 2 production. DNRA was negligible in these oligotrophic settings. Parallel microbial community analysis showed that both Proteobacteria and Planctomycetota were key taxa driving denitrification. Denitrification displayed a negative correlation with oxygen penetration depth, and a positive correlation with macrofauna abundance. Our denitrification rates were comparable to oligotrophic shelves from the Arctic, but were lower than those from nutrient‐rich Pacific and Atlantic shelves. Based on our results and existing IPT measurements, the global shelf denitrification rate was reassessed to be 53.5 ± 8.1 Tg N yr ⁻¹ , equivalent to 20 ± 2% of marine N removal. We suggest that previous estimates of global shelf N loss might have been overestimated due to sampling bias toward areas with high N loads in the Northern Hemisphere.
... Additions of 1 4NH 4 + + 1 5NO 3 − were used to measure the denitrification and anammox rates. The incubation of slurries for the 1 4NH 4 + + 1 5NO 3 − treatment was stopped at time points of 0, 1, 2, 4, and 8 hr by injecting 200 μL of 7 M ZnCl 2 solution into vials, whereas only beginning and end points were measured for the other two treatments (Brin et al., 2014). After centrifugation, 2 mL of the supernatant for N 2 analysis was transferred through a butyl rubber septum to a 12 mL glass vial which had previously been flushed with high-purity helium. ...
... By convention, the relative contribution of anammox to total N 2 production was calculated as anammox/(anammox + denitrification) × 100 (Brin et al., 2014). ...
The importance of denitrification and anaerobic ammonium oxidation (anammox) in removing nitrogen (N) from upland runoff has been well documented in riparian wetlands. However, the relative contributions of denitrification and anammox to N removal in the rhizosphere and non‐rhizosphere soils of riparian zones remain unclear. Here, we explored the denitrification and anammox rates in the rhizosphere and bulk soils (0–5 and 10–15 cm) of 39 riparian wetlands along the Yangtze River using the ¹⁵N isotope pairing technique. Additionally, we used a quantitative polymerase chain reaction assay to determine the abundance of soil denitrifying and anammox bacteria using nosZ and hzsB genes, respectively. The results showed that both denitrification and anammox rates were significantly higher in rhizosphere soils than in bulk soils, suggesting that the rhizosphere environment is favorable for N removal. The contribution of anammox constituted over half (62.53% ± 1.49%) of the N loss and was greater in bulk soils (68.57% ± 1.42%) than in rhizosphere soils (55.64% ± 2.42%). Higher nosZ and hzsB gene abundances were also observed in rhizosphere soils than in bulk soils. Denitrification and anammox rates were significantly regulated by edaphic properties, microbial abundance, and plant biomass. The structural equation model further revealed that soil pH and N availability could affect denitrification and anammox rates both directly and indirectly by altering nosZ and hzsB gene abundance. Overall, this study highlights that the rhizosphere is a control point for N removal and harbors more functional microbes than bulk soils. Therefore, revegetation may effectively enhance the N removal function of riparian wetlands along the Yangtze River.
... Temperature affecting microbial enzyme activity is critical for dissimilatory nitrate reduction processes Brin et al., 2014). In the deep ocean with consistently low temperatures, present studies paid more attention to the effects of substrates like nitrate and organic carbon (Na et al., 2018;Rich et al., 2020), while the temperature responses were always selectively ignored. ...
... While ammonium accumulates with depth, its concentration in the anoxic layer is generally much higher than K m_NH 4 for anammox reported (<5 mmol L −1 , Strous et al., 1999). Thus, anammox is mainly limited by nitrate as the electron acceptor of the reaction in continental margin sediment (Gihring et al., 2010;Song et al., 2013;Brin et al., 2014). However, in our results, the low concentration of ammonium in pore-water (<10 mmol L −1 ) and the discrepant anammox rates determined by anoxic incubation amended with 15 NO 3 − and 15 NH 4 + + 14 NO 3 − (A P1 and A P2 ) both suggest that ammonium is the limiting substrate instead of nitrate for benthic anammox in the deep-ocean of KE ( Figures 2B, 4B). ...
Benthic nitrogen cycling, including nitrification, N-loss, and other nitrogen transformations, plays a crucial role in the marine nitrogen budget. However, studies on benthic nitrogen cycling mainly focus on marginal seas, while attention to the deep ocean, which occupies the largest area of the seafloor, is severely lacking. In this study, we investigate the benthic nitrogen cycling in the Kuroshio Extension region (KE) of the northwest Pacific Ocean at water depths greater than 5,000 m through ¹⁵N enrichment slurry incubation and pore-water dissolved oxygen and inorganic nitrogen profiles. The slurry incubation indicates nitrification is the predominant process in benthic nitrogen cycling. The potential nitrification rates are nearly an order of magnitude higher than dissimilatory nitrate reduction. Nitrification and total N-loss flux estimated from pore-water nitrate and ammonium profiles are 6–42 and 5–30 μmol N m⁻² d⁻¹, respectively. Generally, anammox is the predominant N-loss process in KE sediment. The temperature gradient experiment indicates that the optimum temperature for anammox and denitrification is 13 and 41°C, respectively, partially explaining anammox as the dominant process for deep-ocean benthic N-loss. Both the low concentration of ammonium in pore-water and the discrepant results between anoxic incubation amended with ¹⁵ NO 3 ⁻ and ¹⁵ NH 4 ⁺+¹⁴ NO 3 ⁻ suggest that ammonium is another limiting factor for benthic anammox. N-loss activity gradually declines with the distance from the Oyashio–Kuroshio transition zone. However, nitrification has the opposite trend roughly. This reveals that the sediment in KE transfers from nitrate sink to source from north to south. This trend is mainly caused by the variation of primary production and the supplement of active organic matter, which is the energy source for microbes and the potential source for ammonium through remineralization. Overall, our results highlight temperature and ammonium as two limiting factors for deep-ocean benthic N-loss and also exhibit a tight coupling relationship between pelagic primary production and the benthic nitrogen cycle in KE.
... However, anammox rates tend to decrease in deeper sediments because is limited by the NH 4 + availability (Thamdrup, 2012, and references therein). Conversely, high organic C concentrations in shallow sediments usually stimulate denitrification while suppressing anammox because of the competition for NO 2 − (Nicholls and Trimmer, 2009;Brin et al., 2014). Nevertheless, a number of studies have found positive correlations between organic C content and anammox rates in marine sediments caused by high production of NH 4 + or NO 2 − from remineralization and nitrification (Trimmer et al., 2003;Hou et al., 2013;Lisa et al., 2015). ...
... Estuaries and coastal environments. Anammox has been reported mainly in eutrophic estuaries (e. g., Trimmer et al., 2003;Risgaard-Petersen et al., 2004;Lisa et al., 2015) and coastal sediments (e.g., Engström et al., 2005;Tal et al., 2005;Dang et al., 2013), where the distribution of anammox bacterial diversity and activity is mostly affected by temperature, salinity, NO 3 − and organic N substrates (Hou et al., 2013;Brin et al., 2014;Sonthiphand et al., 2014). Ca. ...
Nitrogen (N) is a key element for life in the oceans. It controls primary productivity in many parts of the global ocean, consequently playing a crucial role in the uptake of atmospheric carbon dioxide. The marine N cycle is driven by multiple biogeochemical transformations mediated by microorganisms, including processes contributing to the marine fixed N pool (N2 fixation) and retained N pool (nitrification, assimilation, and dissimilatory nitrate reduction to ammonia), as well as processes contributing to the fixed N loss (denitrification, anaerobic ammonium oxidation and nitrite-dependent anaerobic methane oxidation). The N cycle maintains the functioning of marine ecosystems and will be a crucial component in how the ocean responds to global environmental change. In this review, we summarize the current understanding of the marine microbial N cycle, the ecology and distribution of the main functional players involved, and the main impacts of anthropogenic activities on the marine N cycle.
... In fact, an annual 5.8 Â 10 4 t of nitrogen removal was estimated to be linked to anammox bacteria in the urban river network of Shanghai, which accounted for approximately 9.9% of the total N delivered annually to the study area ( Cheng et al., 2016;Gu et al., 2012;Yu et al., 2013). The contributions of anammox to overall N 2 emissions in the Shanghai river network were relatively higher than those detected in other estuarine and coastal areas (0e54%) ( Brin et al., 2014;Tan et al., 2019;Teixeira et al., 2014;Wang et al., 2012). However, in the North Atlantic Basin and the OJ estuary in Zhejiang, anammox was found to contribute as high as 68% and 83% to the sedimentary nitrogen removal, respectively (Trimmer and Nicholls, 2009;Yang et al., 2017). ...
... However, in the present study, the role of anammox bacteria in nitrogen removal was not significantly related to organic compounds (P > 0.05). In addition, the organic carbon contents (1.0e5.6%) in the urban river network of Shanghai were comparable to those (0.2e12%) in the habitats where the contribution of anammox to N 2 emission was relatively lower (0e46%) ( Brin et al., 2014;Hou et al., 2013Hou et al., , 2015Teixeira et al., 2014;Wang et al., 2012;Zhu et al., 2015). Whereas, the organic carbon contents in phreatic aquifer and the Yangtze Estuary, where the anammox bacteria were reported to make even higher contributions (67.6% and 77%, respectively), were much lower (<0.05%) ( Wang et al., 2017;Zheng et al., 2016a). ...
Anaerobic ammonium oxidation (anammox) is recognized as an important bioprocess for nitrogen removal, yet little is known about the associated microbial communities in urban river networks which are intensively disturbed by human activity. In the present study, we investigated the community composition and abundance of anammox bacteria in the urban river network of Shanghai, and explored their potential correlations with nitrogen removal activities and the environmental parameters. High biodiversity of anammox bacteria was detected in the sediment of urban river networks, including Candidatus Brocadia, Scalindua, Jettenia, and Kuenenia. Anammox bacterial abundance ranged from 3.7 × 106 to 3.9 × 107 copies g-1 dry sediment based on 16S rRNA gene, which was strongly correlated to the metabolic activity of anammox bacteria (P < 0.01). A strong linkage between anammox bacteria and denitrifiers was detected (P < 0.05), implying a potential metabolic interdependence between these two nitrogen-removing microbes was existed in urban river networks. Sediment ammonium (NH4+) made a significant contribution to the anammox bacterial community-environment relationship, while anammox bacterial abundance related significantly with sediment total organic carbon (TOC) and silt contents (P < 0.05). However, no statistically significant correlation was observed between cell-specific anammox rate and the measured environmental factors (P > 0.05). In general, the community composition and abundance of anammox bacteria in different hierarchies of the river network was homogeneous, without significant spatial variations (P > 0.05). These results provided an opportunity to further understand the microbial mechanism of nitrogen removal bioprocesses in urban river networks.
... Denitrification and anammox processes have been confirmed for removing nitrogen in OMZs of oceans, and their relative contributions are impacted by their responses to immediate or longterm environmental changes, such as pH, salinity or organic matter (C/N ratio in particular) (Babbin et al., 2014;Ward, 2013). In nontypical OMZs, N 2 release by these two groups of microorganisms also has been widely evaluated, including estuaries Brin et al., 2014), marginal sea (Na et al., 2018) and open oceans (Ward et al., 2009). Nitrogen removal from different environments is dominated by either denitrification or anammox, but not both simultaneously. ...
... However, the niche partitioning for denitrifiers and anammox communities in sediments remains unclear so far (Devol, 2015). A few studies have concluded that factors that controlling the dominance of anammox over denitrification may correlate with nitrate concentration (Rich et al., 2018;Teixeira et al., 2012), while others showed equal impact from organic matter (Brin et al., 2014). Similarly, in this study, highly diverted denitrifying bacteria with trends of gene abundance of both denitrifiers and anammox bacteria showed distinct spatial heterogeneity along both latitudinal and longitudinal transects. ...
The Yangtze River, which is the largest in Euro-Asian, receives tremendous anthropogenic nitrogen input and is typically characterized by severe eutrophication and hypoxia. Two major processes, denitrification and anaerobic ammonium oxidation (anammox), play vital roles for removing nitrogen global in nitrogen cycling. In the current study, sediment samples were collected from both latitudinal and longitudinal transects along the coastal Yangtze River and the East China Sea (ECS). We investigated community composition and distributions of nosZ gene-encoded denitrifiers by high throughput sequencing, and also quantified the relative abundances of both denitrifying and anammox bacteria by q-PCR analysis. Denitrifying communities showed distinct spatial distribution patterns that were impacted by physical (water current and river runoffs) and chemical (nutrient availability and organic content) processes. Both denitrifying and anammox bacteria contributed to the nitrogen removal in Yangtze Estuary and the adjacent ECS, and these two processes shifted from coastal to open ocean with reverse trends: the abundance of nosZ gene decreased from coastal to open ocean while anammox exhibited an increasing trend based on quantifications of hzsB and 16S rRNA genes. Further correspondence correlation analysis revealed that salinity and nutrients were the main factors in structuring composition and distribution of denitrifying and anammox bacteria. This study improved our understanding of dynamic processes in nitrogen removal from estuarine to open ocean. We hypothesize that denitrification is the major nitrogen removal pathway in estuaries, but in open oceans, low nutrient and organic matter concentrations restrict denitrification, thus increasing the importance of anammox as a nitrogen removal process.
... In general, temperature directly affects the microbial metabolism, and thus denitrification and anammox rates change as temperature changes (Brin et al., 2017;Tan et al., 2020). The majority of local field observations reported in the literature revealed that temperature plays a crucial role in shaping the biogeographical distribution of the nitrogen removal processes in sediments (Brin et al., 2014;Tan et al., 2017). In addition, site-specific temperature manipulation experiments have shown that rising temperature facilitates the activities of denitrifying and anammox bacteria though with different optimal temperatures Tan et al., 2020). ...
Plain Language Summary
Sediment denitrification plays a critical role in maintaining Nr balance in aquatic ecosystems, but it can also produce a negative climate feedback via organic matter decomposition and N2O release. However, the environmental and climatic effects of sediment denitrification, particularly at a continental shelf scale, are still unclear. According to our field investigation in China's marginal seas, we find that sediment denitrification and associated N2O production are co‐regulated by temperature and organic matter. Extrapolation results based on empirical equations indicate that sediment denitrification removes 2.8 ± 0.4 Tg N yr⁻¹ in China's marginal seas, accounting for 26.5% of riverine input. Meanwhile, approximately 2.2 ± 0.2 Tg C yr⁻¹ of organic carbon is consumed and 15.0 ± 3.5 Gg N yr⁻¹ of N2O is produced along with sediment denitrification, collectively counter‐balancing 15.1 ± 8.1% of the air‐sea CO2 influx. These findings reveal that sedimentary nitrogen removal potentially offsets the climatic benefits of carbon uptake in marginal seas.
... Potential denitrification and anammox rates were measured using the N-isotope tracing technique based on previous studies with some modifications 48,75,77 . Briefly, slurries were prepared using collected sediments and artificial seawater matching in situ salinity, at a sediment/water volume ratio of 1:7. ...
Nitrogen bioavailability, governed by fixation and loss processes, is crucial for oceanic productivity and global biogeochemical cycles. The key nitrogen loss organisms—denitrifiers and anaerobic ammonium-oxidizing (anammox) bacteria—remain poorly understood in deep-sea cold seeps. This study combined geochemical measurements, ¹⁵N stable isotope tracer analysis, metagenomics, metatranscriptomics, and three-dimensional protein structural simulations to explore cold-seeps nitrogen loss processes. Geochemical evidence from 359 sediment samples shows significantly higher nitrogen loss rates in cold seeps compared to typical deep-sea sediments, with nitrogen loss flux from surface sediments estimated at 4.96–7.63 Tg N yr⁻¹ (1.65–2.54% of global marine sediment). Examination of 147 million non-redundant genes indicates a high prevalence of nitrogen loss genes, including nitrous-oxide reductase (NosZ; 6.88 genes per million reads, GPM), nitric oxide dismutase (Nod; 1.29 GPM), and hydrazine synthase (HzsA; 3.35 GPM) in surface sediments. Analysis of 3,164 metagenome-assembled genomes expands the nitrous-oxide reducers by three phyla, nitric oxide-dismutating organisms by one phylum and two orders, and anammox bacteria by ten phyla going beyond Planctomycetota. These microbes exhibit structural adaptations and complex gene cluster enabling survival in cold seeps. Cold seeps likely are previously underestimated nitrogen loss hotspots, potentially contributing notably to the global nitrogen cycle.
... The results consistently revealed a significant positive correlation between anammox and denitrification rates across various aquatic ecosystems on a global scale (p < 0.001) (Fig. 2). Although this positive relationship has been reported in specific ecosystems 27,28 , this study provides a comprehensive description of this interrelationship in inland aquatic ecosystems on a global scale. Notably, distinct response slopes for anammox for denitrification have been reported across different ecosystems. ...
Denitrification and anammox collectively drive nitrogen loss from aquatic ecosystems, yet their global patterns and interactions remain unclear. To fill this gap in knowledge, we compiled a global dataset on anammox and denitrification, encompassing river, lake, wetland, and estuary ecosystems and comprising 2539 observations from 136 peer-reviewed papers. Here, we show that aquatic ecosystems with abundant denitrifying bacteria tend to have abundant anammox bacteria, but the abundance of anammox bacteria is lower than that of denitrifying bacteria. Importantly, we observed that hotspots for denitrification in aquatic ecosystems were also hotspots for anammox, and we explained the variation in anammox (21.55 (95% CI: 8.21–58.90) nmol-N g⁻¹ day⁻¹) and denitrification rates (171.76 (95% CI: 65.40–519.25) nmol-N g⁻¹ day⁻¹) across aquatic ecosystems. These results highlight that anammox should be included in models for accurate nitrogen budget assessment in aquatic ecosystems on a global scale, especially in the context of future climate warming.
... However, anammox rates tend to decrease in marine environments owing to the limited availability of NH 4 + [2]. In contrast, a high concentration of organic carbon in peat soils usually causes denitrification, whereas anammox is suppressed due to NO 2 − competition [87]. However, previous studies demonstrated a positive association between anammox and organic carbon content as a result of remineralization and nitrification [88,89]. ...
Nitrogen is an essential nutrient for living organisms in peat and marine soils, and its transformation within the soil matrix is a complex process mediated by various microbes that inhabit these ecological niches. The metabolism of nitrogen is governed by microbially mediated biogeochemical transformations, such as nitrification, anammox, and denitrification, which contribute to the assimilated pool of nitrogen and fixed nitrogen loss. One of the major challenges facing the field of peat and marine microbiology is the lack of understanding of the correlation between ecosystem-driven nitrogen transformation and microbial diversity. This is crucial because of growing concerns regarding the impacts of human-induced activities and global climate change on microbial nitrogen-cycling processes in peat and marine soils. Thus, this review aimed to provide a comprehensive overview of the current understanding of the microbial communities involved in peat and marine nitrification, anammox, and denitrification; the factors influencing the niche differentiation and distribution of the main functional components; the genes involved; and the main effects of human-induced activities and global climate change on the peat and marine nitrogen cycle. The implications of this review will facilitate an understanding of the complex mechanisms associated with ecosystem function in relation to nitrogen cycling, the role of peat and marine soils as carbon sinks, pollution remediation using naturally occurring populations of diverse microbes, and the development of policies to mitigate the effects of anthropogenic influences in peat and marine soils.
... For instance, in the Thames Estuary (UK) the occurrence of anammox was observed to be much lower contributing to < 10 % of the N 2 production (Trimmer et al., 2003). Similar low values were observed during summer in the Randers Fjord in Denmark (Risgaard- Petersen et al., 2004), in estuarine and coastal sites in Rhode Island in the USA (Brin et al., 2014), and in the subtropical Logan River in Australia (Meyer et al., 2005). While in Chesapeake Bay (USA) a 2 times higher maximum contribution of anammox to N 2 production (22 %) was observed by Rich et al. (2008). ...
Total alkalinity (TA) regulates the oceanic storage capacity of atmospheric CO2. In heterotrophic temperate estuaries, anaerobic respiration of organic matter, e.g., by denitrification, can be an important source of TA. Denitrification is the anaerobic reduction of nitrate (NO3-) to elemental nitrogen (N2). By contrast, anammox yields N2 as its terminal product via comproportionation of ammonium (NH4+) and nitrite (NO2-); however, this occurs without release of TA as a byproduct. In order to investigate these two nitrate and nitrite respiration pathways and their resulting impact on TA generation, we sampled the highly turbid estuary of the Ems River, discharging into the North Sea in June 2020. During ebb tide, a transect was sampled from the Wadden Sea to the upper tidal estuary, where we additionally sampled fluid mud for incubation experiments and five vertical profiles in the hyper-turbid tidal river. The data reveal a strong increase of TA and dissolved inorganic carbon (DIC) in the tidal river, where stable nitrate isotopes indicate water column denitrification as the dominant pathway. However, in the fluid mud of the tidal river, the measured TA and the N2 incubation experiments imply only low denitrification rates, with the majority of the N2 being produced by anammox (>90 %). The relative abundances of anammox and denitrification, respectively, thus exert a major control on the CO2 storage capacity of adjacent coastal waters.
... The contributions of anammox to nitrogen loss in sediments have been well studied, e.g., up to 19% in the Jiaozhou Bay of the Yellow Sea , 22% in the Bohai Sea and 42% in southern New England Estuary and its shelf area (Brin et al., 2014). However, due to the difficulties of bacteria culture, studies of anammox were hardly carried out in particulates of the water column using isotope labelling or sequencing techniques. ...
Anaerobic ammonium oxidation (anammox) plays an important role in nitrogen removal in coastal seas, and ladderanes, as specific biomarkers of anammox bacteria, can be used to indicate the anammox activity. However, the origins of ladderanes and their controlling factors in the coastal seas influenced by anthropogenic activities are still not well constrained. To address this, we reported ladderanes, long-chain n-alkanols (terrestrial biomarker) and sterols (marine biomarker) in suspended particulates from the estuaries and inner area of Laizhou Bay in North China, to study ladderane sources and its distribution patterns. This study proposed a novel index, Rlad, using ladderane ratio of ladderane III to ladderane IV, and by correlating this index with other biomarker distributions to evaluate the source of ladderanes. High Rlad values (> 0.9) indicated biosynthesis by terrestrial anammox bacteria Ca. Brocadia and Ca. Kuenenia, while low Rlad values (< 0.9) indicated biosynthesis by marine anammox bacteria Ca. Scalindua. High Rlad values and high ladderane concentrations in particulates from the estuaries and nearshore area of Laizhou Bay revealed sources from the terrestrial input via riverine inflow as well as in situ production in oxygen-depleted estuaries, supported by high concentrations of terrestrial biomarkers; Low Rlad values and low ladderane concentrations in particulates from offshore area indicated sources from marine environment via the cold hypoxia water input by the Bohai circulation. Comparison of ladderane concentrations of our study with previously published results from a wide range of environments with human influences from Chinese coastal area revealed that high ladderane concentrations synthesized by terrestrial anammox bacteria could contribute significantly to coastal seas, and the anammox process in river-estuary-bay system might be underestimated. This study provides new understandings about the evaluation of the source and distribution of ladderanes under anthropogenic influences in coastal seas.
... High temperature and availability of labile organic carbon have been shown to favor heterotrophic denitrification over autotrophic anammox (Babbin et al., 2014;Canion et al., 2014;Rysgaard et al., 2004;Tan et al., 2020). Similarly, high and stable nitrate loading might favor anammox over denitrification (Brin et al., 2014;Rysgaard et al., 2004). Alternatively, high carbon availability might indicate high decomposition and O 2 consumption that could reduce O 2 penetration depth, and change N 2 O fluxes by altering the balance between various N 2 O-producing and -consuming processes. ...
Nitrous oxide (N2O) is a strong greenhouse gas and stratospheric ozone‐depleting substance. Around 20% of global emissions stem from the ocean, but current estimates and future projections are uncertain due to poor spatial coverage over large areas and limited understanding of drivers of N2O dynamics. Here, we focus on the extensive and particularly data‐lean Arctic Ocean shelves north of Siberia that experience rapid warming and increasing input of land‐derived nitrogen with permafrost thaw. We combine water column N2O measurements from two expeditions with on‐board incubation of intact sediment cores to assess N2O dynamics and the impact of land‐derived nitrogen. Elevated nitrogen concentrations in water column and sediments were observed near large river mouths. Concentrations of N2O were only weakly correlated with dissolved nitrogen and turbidity, reflecting particulate matter from rivers and coastal erosion, and correlations varied between river plumes. Surface water N2O concentrations were on average close to equilibrium with the atmosphere, but varied widely (N2O saturation 38%–180%), indicating strong local N2O sources and sinks. Water column N2O profiles and low sediment‐water N2O fluxes do not support strong sedimentary sources or sinks. We suggest that N2O dynamics in the region are influenced by water column N2O consumption under aerobic conditions or in anoxic microsites of particles, and possibly also by water column N2O production. Changes in biogeochemical and physical conditions will likely alter N2O dynamics in the Siberian Arctic Ocean over the coming decades, in addition to reduced N2O solubility in a warmer ocean.
... However, there also studies showing that anammox coupled with nitrification rather than denitrification in estuarine sediments in winter Lin et al., 2017). The uncertainties in the relationships between anammox and denitrification might be attributed to organic acids, and anammox bacteria can convert NO 3 − to NO 2 − in the presence of organic acids (Brin et al., 2014). Thus, coupled anammox and nitrification or denitrification play a vital role in N removal processes from the surface of marine sediments. ...
Introduction
Denitrification and anammox play the crucial role for N removal processes in coastal ecosystems, but the ecological distribution of denitrifying and anammox microorganisms and their N removal rates in the Yangtze Estuary and its adjacent sea are required in-depth analysis.
Methods
Here, we utilized high-throughput sequencing, qPCR, and ¹⁵N isotope to reveal the community structure and function of denitrifying and anammox microorganisms in the surface sediments from Yangtze Estuary and adjacent sea.
Results
The results suggested that the gene abundances of nirS and nirK for denitrifiers were higher than AMX 16S rRNA for anammox bacteria. The genera composition of nirS- and nirK-encoding denitrifiers communities showed different distribution patterns. Furthermore, Candidatus Anammoximicrobium dominated the anammox community, implying the anammox oxidation capacity of the other genera should be noted in marine sediments.
Discussion
Compared to anammox, denitrification was the dominant contributor of nitrogen removal process and contributed 73.5% on average. The sediment Chla was the key factor to regulate denitrification and anammox rates, indicating the fresh organic matter was more labile and easier to be utilized by NOx⁻ removal processes.
... (See S6 of the online supplemental material for further discussion.) This finding confirms expectations based on field studies showing the low relative importance of anammox in near-shore sediments: for example, in Narragansett Bay % ra (i.e., anammox N/total N production × 100) = 0-4 (Brin, Giblin, and Rich 2014); in Long Island Sound % ra = 4-7 (Engström et al. 2005); in eastern English estuaries % ra = 1-11% (Nicholls and Trimmer 2009); in Norsminde Fjord % ra = 0 % (Risgaard- Petersen et al. 2004), and in others (Devol 2015). For this reason and because of the low level of NO 3 observed in GPB seawater (< 2 μM), N 2 production in GPB muds is attributed to coupled sedimentary nitrification-denitrification. ...
To better understand the capacity of sediments to serve as both source and sink of nitrogen (N) and to identify any evidence of evolving changes in sedimentary N cycling, N 2 production, N remineralization, and N 2 fixation were studied over a multi-year period (2010–2015) in bioturbated mud of Great Peconic Bay, a temperate northeastern U. S. estuary. Benthic fluxes and rates of organic matter remineralization were measured using in situ and ex situ incubations. Net annual NH ⁺ 4 , NO– 3 /NO– 2 , and N 2 –N fluxes (μ = 1.1, 0.03, and 1.2 mmol m –2 d –1 ) were close to averages for comparable sedi- mentary environments from surveys of published field studies. Net N 2 fluxes (by membrane inlet mass spectrometry) were influenced in different periods by temperature, oxygenation of sediment, pulsed C org , and the activity of benthic macrofauna and benthic microalgae, although no single physical or biogeochemical variable showed a strong, direct relationship with net N 2 fluxes over all sampling periods. In situ measurements sometimes showed more dynamic and higher amplitude diurnal N flux cycles than did ex situ incubations, suggesting ex situ incubations did not fully capture impacts of bioirrigation or benthic photosynthesis. ¹⁵ N tracer experiments indicated anammox was < 7% of total N 2 production. Acetylene reduction assays demonstrated C 2 H 4 production to depths ≥ 15 cm and suggested N 2 fixation may have approached 25% of gross N 2 production(3:1 C 2 H 4 : N 2 ) . Mass balances incorporating independently measured N remineralization estimates were consistent with measured levels of N 2 fixation. Overall, complex balances of competing processes governed sedimentary N cycling seasonally, and N 2 production dominated N 2 fixation. Measured N 2 fixation was consistent with constraints from N remineralization rates and net N fluxes except in episodic conditions (e. g., algal blooms). There was no indication of progressive changes in N cycling magnitudes or relative N reaction balances over the study period.
... Denitrification will also diminish nitrate, and substantial denitrification may occur on the seafloor (Seitzinger and Giblin, 1996;Fennel, 2010). However, as the dN/dP ratio of 16.96 ± 0.42 is similar to the Redfield ratio of N:P = 16 (Figure 7C), we conclude that the impact of benthic denitrification on water column N is quite limited in winter, probably because of the diminished denitrification under low temperature (Brin et al., 2014) and high oxygen concentration due to a well-mixed condition during wintertime. Finally, the FIGURE 8 | (A) dpH in situ vs. dAOU, (B) d Arag vs. dAOU, (C) dpH in situ vs. dDIC, (D) d Arag vs. dDIC, (E) dpH in situ vs. dP, (F) d Arag vs. dP, (G) dpH in situ vs. dN, and (H) d Arag vs. dN in the MAB. ...
The United States Department of Energy (DOE)’s Ocean Margins Program (OMP) cruise EN279 in March 1996 provides an important baseline for assessing long-term changes in the carbon cycle and biogeochemistry in the Mid-Atlantic Bight (MAB) as climate and anthropogenic changes have been substantial in this region over the past two decades. The distributions of O2, nutrients, and marine inorganic carbon system parameters are influenced by coastal currents, temperature gradients, and biological production and respiration. On the cross-shelf direction, pH decreases seaward, but carbonate saturation state (ΩArag) does not exhibit a clear trend. In contrast, ΩArag increases from north to south, while pH has no clear spatial patterns in the along-shelf direction. In order to distinguish between the effects of physical mixing of various water masses and those of biological activities on the marine inorganic carbon system, we use the potential temperature-salinity diagram to identify water masses, and differences between observations and theoretical mixing concentrations to measure the non-conservative (primarily biological) effects. Our analysis clearly shows the degree to which ocean margin pH and ΩArag are regulated by biological activities in addition to water mass mixing, gas exchange, and temperature. The correlations among anomalies in dissolved inorganic carbon, phosphate, nitrate, and apparent oxygen utilization agree with known biological stoichiometry. Biological uptake is substantial in nearshore waters and in shelf-slope mixing areas. This work provides valuable baseline information to assess the more recent changes in the marine inorganic carbon system and the status of coastal ocean acidification.
... The potential rates of DNF, ANA, and DNRA in Knysna Estuary varied from 3.67 to 16.21 nmol g −1 h −1 , 0.27 to 1.82 nmol g −1 h −1 , and 1.44 to 8.33 nmol g −1 h −1 , respectively, which were comparable to rates reported for most estuarine ecosystems (Teixeira et al. 2012;Decleyre et al. 2015;Cao et al. 2016;Kessler et al. 2018;Fozia et al. 2020). Previous studies reported that NO 3 − reduction process rates increase (Smith et al. 2015) or decrease (Brin et al. 2014) along the estuarine gradient from the downstream to the upstream zones. However, these spatial patterns were not pronounced for the NO 3 − reduction process in this study (Fig. 4). ...
Purpose
The quality of organic matter influencing sediment nitrate (NO3⁻) reduction processes in estuarine zones is not well understood. This study aimed to assess the denitrification (DNF), anaerobic ammonium oxidation (ANA), and dissimilatory reduction of nitrate to ammonium (DNRA) in estuarine zones of South Africa, and to understand the effects of organic matter fractions and degradation states on anaerobic NO3⁻ reduction processes.
Materials and methods
We measured the anaerobic NO3⁻ reduction process rates using ¹⁵N isotope-tracing techniques in Knysna Estuary, South Africa. Total hydrolyzable amino acids and fractions and geochemical parameters were also measured. The correlation analysis and structural equation model were used to evaluate the key environmental factors driving NO3⁻ reduction processes.
Results and discussion
Potential DNF, ANA, and DNRA rates in Knysna Estuary varied from 3.59 to 16.62, 0.28 to 1.16, and 1.52 to 8.38 nmol g⁻¹ h⁻¹, respectively, with a large spatial variation. The variations in NO3⁻ reduction process rates can largely be explained by sediment water content, dissolved organic carbon, and amino acid–based degradation index, while the total organic carbon and inorganic nitrogen contents were not related to the NO3⁻ reduction processes. The DNF process contributed 47.28–79.34% total NO3⁻ reduction, as compared to 17.59–47.58% for DNRA and 2.53–5.76% for ANA. The retention of reactive nitrogen (N) attributed to the DNRA process was approximately 42 t N km⁻² year⁻¹.
Conclusions
This study reported the first simultaneous investigation of the anaerobic NO3⁻ reduction processes in estuarine areas of South Africa, implying that the qualities of substrate were more important in regulating NO3⁻ reduction processes than substrate quantities and highlighting that DNRA played an important role in reactive N retention.
... Anammox tends to be more important in deeper, continental shelf sediments and has been shown to increase in importance with depth, where low organic matter inputs favour autotrophic anammox over heterotrophic DNF (Devol 2015). In estuaries, anammox generally accounts for approximately 0-10% of N 2 produced (Brin et al. 2014;Trimmer et al. 2003), though greater contributions, up to 26 and 79 % have been reported (Risgaard-Petersen et al. 2004;Teixeira et al. 2012, respectively). Anammox has not been found to be correlated with water column or porewater NH 4 + , likely because it is rarely limiting in marine sediments (Dalsgaard et al. 2005). ...
Coastal nutrient pollution is an ever-present threat to estuaries worldwide. Benthic denitrification has been identified as a crucial ecosystem service to help mitigate increasing N loads to the coast. However, the controls on denitrification in low-nutrient systems are not well constrained and are likely different to those in more widely studied eutrophic systems. This study aims to identify the specific controls on denitrification in low-nutrient estuaries, including the contribution of the macrofaunal community to denitrification rates, and to understand how this important service fits into the network of ecogeochemical processes in these systems. Results show that porewater ammonium concentrations and mud content are good predictors of net N2 flux in the dark. Additionally, models predict N2 flux rates much more effectively in the dark than in the light, but the macrofaunal community data, specifically species richness, is a key factor in both increasing the explanatory power of both models by nearly 20%. Additionally, interaction networks reveal that increasing mud content results in a shift in the macrofaunal community and a reduction in the N removal capacity of these intertidal systems.
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... Each measurement was completed within 10 min and produced a vertical DO profile with 250 μm increments (Fig. S1). Diffusive O 2 consumption rates (μmol O 2 m −2 h −1 ) were determined by applying a classical steady-state one-dimension diffusion-reaction model to the DO profiles (Boudreau 1997;Soetaert and Meysman 2009;Brin et al. 2014;Hardison et al. 2017): ...
While organic and inorganic nutrient inputs from land are recognized as a major driver of primary production in estuaries, remarkably little is known about how processes within the tidal freshwater zones (TFZs) of rivers modify these inputs. This study quantifies organic matter (OM) decomposition rates in surface sediment layers in the lower reaches of two south Texas river channels and identifies key parameters that influence sediment decomposition rates. Sediment cores were collected from non-tidal and tidal freshwater sites in the Mission and Aransas rivers during two summers (June 2015 and June 2016) and two winters (February 2016, January 2017). We measured oxygen consumption rates, organic carbon and nitrogen content, stable isotope ratios (δ13C and δ15N of OM), and sediment porosity. O2 consumption rates in TFZ sediments were 385 ± 88 μmol O2 m−2 h−1 (summer) and 349 ± 87 μmol O2 m−2 h−1 (winter) in the Aransas River and 767 ± 153 μmol O2 m−2 h−1 (summer) and 691 ± 95 μmol O2 m−2 h−1 (winter) in the Mission River. These rates in TFZs were similar to rates in estuaries and higher than rates at non-tidal riverine sites. Rates of sediment O2 consumption were primarily controlled by OM content and temperature. Sediment OM was dominated by algal biomass from in situ production in both TFZs. We hypothesize that algal production and sinking within TFZs is a major pathway for translocation of watershed-derived nutrients from the water column to the sediments within TFZs. Further work is needed to quantify linkages between decomposition, nutrient remineralization, and potential removal through processes such as denitrification.
... This conclusion is corroborated by earlier studies in Yangtze River which have reported that the denitrification rates are significantly coupled with the anammox rates with a linear correlation index of 0.803 (Zheng et al. 2016). These findings are also supported by the hypothesis that nitrite as the anammox substrate could be released by the denitrifier owing to the imbalance of the required nitrate and carbon condition (Brin et al. 2014). The relative contribution of anammox in the N 2 production (ra%) ranged between 14 and 74%, with an average value of 43.5%. ...
Excessive nitrogen (N) loading has had severe consequences in coastal zones around the world. Denitrification and anammox are major microbial pathways for removing N in aquatic environments before it is exported to the coast. To assess two processes in eutrophic riverine systems, the denitrification and anammox and their bacterial participants were investigated in sediments of the Xiaoqing (XQ) River and Jiaolai (JL) River in Northeast China. By combining the evidence from N15 isotope tracing experiment and functional gene-based analysis, it was found that denitrification and anammox are ubiquitous along the investigated riverine sediments. The denitrification varied from 39.38 to 1433.01 nmol N2 m−2 h−1. Moreover, the anammox rates were in the range of 15.91 to 1209.97 nmol N2 m−2 h−1. Quantitative PCR results revealed that the nirK and nirS genes were in the order of 104–106 copies g−1 and 103–105 copies g−1, respectively, in both river sediments, while the hzsA was in the order of 106–105 copies g−1 in XQ at approximately two orders of magnitude compared with JL. The phylogenetic analysis of functional genes revealed the high diversity of the denitrifier and low diversity of anammox bacteria. Variance partitioning analyses verified that the grain particle characteristics were the major factor group determined the N removal efficiency. The denitrification and anammox processes were estimated to have removed 16.1% of the inorganic nitrogen inputs before being exported to Laizhou Bay, which highlights that a more extensive understanding of the regularity of the N removal processes is important in the technical remediation of eutrophication problems.
... ? concentrations in the overlying water, WLD is expected to have much lower rates of anammox compared to denitrification as found in other similar tidal freshwater ecosystems (Trimmer et al. 2003;Koop-Jakobsen and Giblin 2009;Brin et al. 2014). However, N 2 fixation is becoming more evident as a significant process in estuarine and coastal ecosystems (Gardner et al. 2006;Yin et al. 2014;Bentzon-Tilia et al. 2015;Damashek and Francis 2018). ...
We tested the hypothesis that benthic fluxes will increase spatially in a coastal deltaic floodplain as sediment organic matter increases in response to developing hydrogeomorphic zones along a chronosequence of the active Mississippi River Delta. A continuous flow-through core system was used to incubate intact sediment cores from three hydrogeomorphic zones along a chronosequence in the emerging Wax Lake Delta (WLD). Organic matter content increased from younger to older deltaic sediments from subtidal to supratidal hydrogeomorphic zones, which were coupled with increasing benthic oxygen and nitrogen fluxes. Mean net denitrification rate in spring was 100 µmol N2–N m−2 h−1 with significantly lower rates occurring in the younger intertidal zones (T4 transect, − 22 µmol N2–N m−2 h−1) and higher rates occurring in the older supratidal zones (T2 and T1 transects, 330 and 262 µmol N2–N m−2 h−1, respectively). Mean net denitrification rate in summer was 397 µmol N2–N m−2 h−1 without significant site-to-site variability except for the supratidal-T2 site (911 µmol N2–N m−2 h−1) showing higher denitrification rate than the other sites. Based on seasonal temperature and inundation time, annual rates of benthic NO3− removal varied from − 0.5 to − 3.4 mol m−2 y−1 and N2–N production rates varied from 1.0 to 3.2 mol N m−2 y−1 across WLD. The subtidal zone had the lowest fluxes associated with lower organic matter content, but was the hydrogeomorphic zone with the largest area and longest flood duration, and therefore contributed over half of N removal in WLD. The estimated annual NO3− removal of 896 Mg N y−1 in WLD accounts for 10 to 27% of total NO3− load to WLD, most of which is converted to N2 through denitrification. As a small prograding coastal deltaic floodplain under early stages of delta development, WLD is a continuously emerging ecosystem where the capacity of N removal increases by 0.2 to 2% per year prior to riverine NO3− is export to coastal ocean. These results highlight the contribution of the coastal deltaic floodplain in an active coastal basin in processing elevated riverine NO3− at continental margins with coastal ocean. The potential loss of this ecosystem service in N removal may increase in global significance as delta areas decline as result of accelerated relative sea level rise and decreased sediment loading in major river basins around the world.
... Sediment-water and sediment-air flux of N 2 during tidal inundation and exposure was the main biological pathway for MPB-N loss from sediments in the current study (2.6%; Figs. 3 and 4). N 2 production may result from denitrification or anammox, but is typically dominated by denitrification (accounting for~30% of N 2 efflux; Ward 2013), particularly in shallow coastal sediments (≥ 93%; Dalsgaard and Thamdrup 2002;Brin et al. 2014;Senga et al. 2019 Denitrification in intertidal sediments of the Richmond River appears to have been predominantly supported by remineralization of newly assimilated MPB-N, given that there was no apparent shift in MPB-N processing, despite changes in DIN concentrations from < 2 μmol L −1 prior to 9 d to < 20 μmol L −1 post flood (Oakes and Eyre 2014). Denitrification from inundated sediment remained the largest biological pathway for export of 15 N after flooding occurred (9 d). ...
Microphytobenthos (MPB) are an important nitrogen (N) sink in coastal systems, but little is known about the fate of N assimilated by MPB. We used an in situ 15N pulse‐chase experiment in intertidal, nonpermeable, sandy mud to trace the assimilation, transformation, and loss from the sediment of MPB‐N over 31 d. Following assimilation, 15N was tightly retained in surface sediments, with only up to 8.1% transported to 2–10 cm sediments over 31 d. MPB accounted for a considerable portion of the 15N in surface sediments throughout the study (59% ± 13%). Bacteria rapidly assimilated 15N but accounted for only up to 17% of the 15N within surface sediments. Of the assimilated 15N, 78.9% was lost from the sediment over 31 d. Resuspension was the dominant loss pathway (74.4%) and was primarily associated with minor flooding following a rainfall event at 8 d. Biological pathways for N export were far less important. Denitrification, during both sediment exposure and inundation, was the main biological pathway for 15N loss (2.6% total), whereas there was little loss through ammonification and nitrification (NH4+ or NOx efflux; 1.4% combined) and dissolved organic nitrogen efflux (0.5%). It was estimated that the N incorporated by MPB within one emersion period would take ~ 40 d to be entirely removed from the sediment. This study highlights the potential importance of MPB and intertidal sediments for the uptake and longer‐term storage of coastal N, and the need to better quantify the impact of episodic flooding on coastal N budgets.
... N-isotope tracing method was used to measure the spatial and temporal activity of denitrification and anammox in the sediments from PRE, following protocols in previous studies (Brin et al. 2014;Hou et al. 2013;Lin et al. 2017a, b). In short, slurry was made at a sediment/benthic water ratio of 1:7 (w/v) in a 500-mL plastic bottle (Nalgene). ...
Anaerobic ammonium oxidation (anammox) is an important pathway for the removal of fixed nitrogen from aquatic and terrestrial ecosystems. Previous studies on anammox were focused on the surface sediments in estuaries, but the activity and community composition of anammox bacteria in the estuarine subsurface sediments remained unknown. In this study, we used high-throughput sequencing of 16S rRNA gene combined with ¹⁵N isotope tracing method to investigate the activity, diversity, and spatio-temporal distribution of anammox bacteria in sediment cores of the Pearl River Estuary (PRE). Our results indicated that anammox in the subsurface sediments has significant potential activity, contributing to approximately 17.49% of the total microbial nitrogen loss. A variety of anammox bacteria, including Candidatus Scalindua, Ca. Brocadia, Ca. Jettenia, and Ca. Kuenenia, were all detected in the subsurface sediments. Moreover, the anammox bacterial community had a significant specific geographic distribution but no obvious difference along the sediment depth. Multiple environmental factors including salinity, and NH4⁺ and NO3⁻ contents, synergistically shaped the diversity and distribution of anammox bacteria in PRE sediments.
... N-isotope tracing method was used to measure the spatial and temporal activity of denitrification and anammox in the sediments from PRE, following protocols in previous studies (Brin et al. 2014;Hou et al. 2013;Lin et al. 2017a, b). In short, slurry was made at a sediment/benthic water ratio of 1:7 (w/v) in a 500-mL plastic bottle (Nalgene). ...
Anaerobic ammonium-oxidation (anammox) is an important pathway for the removal of fixed nitrogen from aquatic and terrestrial ecosystems. Previous studies on anammox were focused on the surface sediments in estuaries, but the activity and community composition of anammox bacteria in the estuarine subsurface sediments remained unknown. In this study, we used high-throughput sequencing of 16S rRNA gene combined with 15N isotope tracing method to investigate the activity, diversity, and spatio-temporal distribution of anammox bacteria in sediment cores of the Pearl River Estuary (PRE). Our results indicated that anammox in the subsurface sediments have significant potential activity, contributing to approximately 17.49% of the total microbial nitrogen loss. A variety of anammox bacteria, including Candidatus Scalindua, Ca. Brocadia, Ca. Jettenia, and Ca. Kuenenia, were all detected in the subsurface sediments. Moreover, the anammox bacterial community had a significant specific geographic distribution but no obvious difference in vertical direction of sediment cores. Multiple environmental factors including salinity, NH4+ and NO3- contents synergistically shaped the diversity and distribution of anammox bacteria in PRE sediments.
... Denitrification almost occurred in the anoxic environment and low oxygen better accelerated this process. High temperature could promote the activity of denitrifying bacteria and lead to better use of organic matter (Brin et al., 2014). Salinity was considered to affect denitrification by regulating the nitrate level because the higher ammonium adsorption capacity of low salinity sediments allows the bacteria to more effectively nitrify the ammonium (Giblin et al., 2010). ...
Nitrogen biogeochemistry occupies a central role in nitrogen cycles and exerts a significant influence on primary productivity and global carbon cycles. In order to better understand the nitrogen biogeochemistry in coastal regions, spatiotemporal nitrogen fixation, denitrification and anammox were investigated in the coastal regions of northern Beibu Gulf (NBG), South China Sea (SCS). Nitrogen fixation was mainly detected in the water column of outer bays, attributed to the low nitrate concentration and low N/P (N/P < 16). Comparisons of the nitrogen fixation rates between unicellular (<10 mm) and the filamentous diazotrophs (>10 mm) indicated that the contribution of unicellular diazotrophs was more important than filamentous diazotrophs. Besides, field investigation revealed that Richelia was the dominant species in filamentous diazotrophs. On the other hand, both denitrification and anammox were found in the surface sediment and denitrification dominated the nitrogen loss process. Denitrification was mainly related to the nitrate concentration in pore water and organic matter in the sediment, while anammox was mainly regulated by the concentration of nitrate and nitrite in pore water. Additionally, temperature, dissolved oxygen (DO) and salinity also had an impact on denitrification and anammox. The net areal yield of nitrogen biogeochemical processes was estimated to be -1079t/a, as an important pathway of nitrogen removal. This study adds to the knowledge of nitrogen biogeochemistry in the nutrient-replete coastal region and highlights its significance in such an environment.
... However, based on previous work in Waquoit Bay (Newell et al., 2016), sediment anammox rates were not detectable. This is consistent with other shallow (<20 m) estuarine systems where anammox typically accounts for <6% of total N removal (Brin et al., 2014;Dalsgaard et al., 2005). ...
Estuarine ecosystems are considered among the most valuable regions worldwide because of the wealth of ecosystem services they provide. Given their proximity to the land, they are also vulnerable to excessive nutrient inputs, which can lead to eutrophication and hypoxia. Water column hypoxia can dramatically alter sediment biogeochemistry, yet the response of specific processes varies widely. Predicting whether sediments are sources or sinks of ecologically and climatologically relevant nutrients and gases remains elusive, particularly for shallow coastal regions. In this study, we conducted experiments with sediments collected from Waquoit Bay (Massachusetts, United States) and measured dissolved nutrient and gas fluxes across the sediment‐water interface to investigate the impact of water column hypoxia (defined here as dissolved oxygen ≤3 mg/L) on three important ecosystem functions: nutrient regeneration, removal of reactive nitrogen, and the regulation of greenhouse gases. Under hypoxia we observed variable responses in sediment biogeochemical cycling, including little to no change in important nitrogen cycling processes such as ammonium efflux and nitrogen removal through denitrification. As expected, low oxygen conditions stimulated sediment phosphate efflux. This caused nutrient ratios for both nitrogen to phosphorus and silica to phosphorus in the overlying water to decrease by 50%. Such changes can alter both the composition of water column primary producers as well as the rate of primary production. Hypoxia led to an almost 60% decrease in sediment nitrous oxide consumption but had little impact on sediment methane emissions. Taken together, these experimental results suggest sediment biogeochemical cycling has variable and dynamic responses to hypoxia.
... Nitrite oxidation rates here are also lower than values observed in ODZs (~3 μM y À1 ; ), but closer to water column values than other sediment environments. Nitrite oxidation rates are much lower (4 to 5 orders of magnitude) than values measured in coastal sediments (2.2 e 4 to 9.8 e 4 μM y À1 ; (e.g., (Brin et al., 2014)). The values for nitrite oxidation in this study (up to 0.3 μM y À1 ) equate to a residence time for nitrite of 70 years. ...
Little is known about the nature of microbial community activity contributing to the cycling of nitrogen in organic-poor sediments underlying the expansive oligotrophic ocean gyres. Here we use pore water concentrations and stable N and O isotope measurements of nitrate and nitrite to constrain rates of nitrogen cycling processes over a 34-m profile from the deep North Atlantic spanning fully oxic to anoxic conditions. Using a 1-D reaction-diffusion model to predict the distribution of nitrogen cycling rates, results converge on two distinct scenarios: (1) an exceptionally high degree of coupling between nitrite oxidation and nitrate reduction near the top of the anoxic zone or (2) an unusually large N isotope effect (~60‰) for nitrate reduction that is decoupled from the corresponding O isotope effect, which is possibly explained by enzyme-level interconversion between nitrite and nitrate.
... Along with denitrification, many recent studies have investigated the role of anammox in benthic N-cycling and observed wide variation in its average rate and relative importance in urban and eutrophic benthic sediments. While all studies published to date have found that benthic anammox was relatively less important than benthic denitrification in N r -removal; (0-33% of total N 2 production; Rich, Dale, Bongkeun Song, and Ward 2008;Crowe et al. 2012;Teixeira et al. 2014Teixeira et al. , 2012Teixeira et al. , 2016Yin et al. 2015;Deng et al. 2015;Trimmer, Nicholls, and Deflandre 2003;Nicholls and Trimmer 2009;Song et al. 2016;Brin, Giblin, and Rich 2014), it was still a significant contributor to system-wide benthic N r -regulation at several of the sites investigated. Anammox was first observed in a WWTP (Mulder et al. 1995), and it has been hypothesized that WWTP effluent can serve as a source of anammox bacteria in the natural environment (Dale, Tobias, and Song 2009). ...
Dense cities represent biogeochemical hot spots along the shoreline, concentrating fixed nitrogen that is subsequently discharged into adjacent coastal receiving waters. Thus, the ecosystem services provided by natural systems in highly urban environments can play a particularly important role in the global nitrogen cycle. In this paper, we review the recent literature on nitrogen regulation by temperate coastal ecosystems, with a focus on how the distinct physical and biogeochemical features of the urban landscape can affect the provision of this ecosystem service. We use Jamaica Bay, an ultra-urbanized coastal lagoon in the United States of America, as a demonstrative case study. Based on simple areal and tidal-based calculations, the natural systems of Jamaica Bay remove ~ 24% of the reactive nitrogen discharged by wastewater treatment plants. However, this estimate does not represent the dynamic nature of urban nitrogen cycling represented in the recent literature and highlights key research needs and opportunities. Our review reveals that ecosystem-facilitated denitrification may be significant in even the most densely urbanized coastal landscapes, but critical uncertainties currently limit incorporation of this ecosystem service in environmental management.
... In addition to DO, nitrogen species including NO 2 − , NH 4 + , NO 3 − (in sediment) also favored growth and activities of anammox bacteria Zhu et al., 2011Zhu et al., , 2013. For instance, the nitrate concentration has been reported being positively correlated with the anammox rate (Rich et al., 2008;Teixeira et al., 2012;Brin et al., 2014), The EIO is a typical oligotrophic environment, especially during the inter monsoon, with NO 3 − -N concentrations ranging from 1.4 × 10 −3 to 5.2 × 10 −1 mg L −1 . Anammox bacteria had been noted for its ability to adapt to oligotrophic environments Jiang et al., 2015), and also showed good reaction compared to denitrification under nutrient limits (Chen et al., 2017;Sheng et al., 2018). ...
Denitrification and anaerobic ammonium oxidation (anammox) are the major microbial processes responsible for global nitrogen (N) loss. Yet, the relative contributions of denitrification and anammox to N loss across contrasting terrestrial and aquatic ecosystems worldwide remain unclear, hampering capacities to predict the human alterations in the global N cycle. Here, a global synthesis including 3240 observations from 199 published isotope pairing studies is conducted and finds that denitrification governs microbial N loss globally (79.8±0.4%). Significantly, anammox is more important in aquatic than terrestrial ecosystems worldwide and can contribute up to 43.2% of N loss in global seawater. Global maps for N loss associated with denitrification and anammox are further generated and show that the contribution of anammox to N loss decreases with latitude for soils and sediments but generally increases with substrate depth. This work highlights the importance of anammox as well as denitrification in driving ecosystem N losses, which is critical for improving the current global N cycle model and achieving sustainable N management.
Nitrogen-cycling processes in the deep sea remain understudied. This study investigates the distribution of nitrogen-cycling microbial communities in the deep-sea surface sediments of the western South China Sea, using metagenomic sequencing and real-time fluorescent quantitative PCR techniques to analyze their composition and abundance, and the effects of 11 environmental parameters, including NH4⁺-N, NO3⁻-N, NO2⁻-N, PO4³⁻-P, total nitrogen (TN), total organic carbon (TOC), C/N ratio, pH, electrical conductivity (EC), SO4²⁻, and Cl⁻. The phylum- and species-level microbial community compositions show that five sites can be grouped as a major cluster, with sites S1 and S9 forming a sub-cluster, and sites S13, S19, and S26 forming the other; whereas sites S3 and S5 constitute a separate cluster. This is also evident for nitrogen-cycling functional genes, where their abundance is influenced by distinct environmental conditions, including water depths (shallower at sites S1 and S9 against deeper at sites S13, S19, and S26) and unique geological features (sites S3 and S5), whereas the vertical distribution of nitrogen-cycling gene abundance generally shows a decreasing trend against sediment depth. Redundancy analysis (RDA) exploring the correlation between the 11 environmental parameters and microbial communities revealed that the NO2⁻-N, C/N ratio, and TN significantly affect microbial community composition (p < 0.05). This study assesses the survival strategies of microorganisms within deep-sea surface sediments and their role in the marine nitrogen cycle.
Ammonia oxidising bacteria (AOB) and archaea are ubiquitous microorganisms, but their abundance and diversity vary widely across environments and play a crucial role in many ecosystems and aquatic ecosystems in particular. However, characterization of AOB communities require genomic methods as they are difficult to isolate from samples. Although non-toxic to humans, in the short term, ammonia in water systems are harmful to aquatic life both directly and indirectly through the disruption of the ecosystem by promoting the proliferation of algae (a process called eutrophication). Contamination often occurs due to use of disinfectants with chloramines, fertilizers, waste disposal and from natural processes. Due to their natural presence, utilising AOBs to treat water is viewed as an attractive solution, but greater knowledge of their biochemical processes and measurement of their efficacy is required.
Ideal for postgraduates and researchers in a variety of disciplines, this book covers the ecology, genomics, physiology and biochemistry of AOBs and their presence in wastewater, and the challenges, opportunities and potential applications for nitrification and ammonia removal.
Anammox bacteria can remove ammonium directly, which is different from what was previously believed. This is an important process for the global nitrogen cycle. Anammox bacteria were first identified in sewage treatment systems and were later proven to exist widely in natural ecosystems. To better understand the relationship between the anammox reaction and different systems, and to maintain the stability of the nitrogen cycle, anammox functional microorganisms found in different natural environments were summarized. In addition, anammox nitrogen production rate and the contribution of anammox to nitrogen were discussed under different ecological environments. A literature analysis showed that the contribution rate of nitrogen removal of anammox was the highest in the Terrestrial ecosystem, up to 87.5%. The Terrestrial ecosystem is more likely to form an anoxic or even anaerobic environment conducive to anaerobic ammoxidation. Therefore, the control of DO is an important factor in the activity of anaerobic ammoxidation. Other environmental factors affecting the contribution of anammox to nitrogen removal include temperature, pH, organic matter content, inorganic nitrogen concentration, and salinity. However, the dominant influencing factors of anammox reactions in different ecosystems are evidently different. Therefore, the mechanism of the impact of different environmental factors on the anaerobic ammonia oxidation process is necessary to discuss. This provides a scientific basis for the global nitrogen cycle and is of great significance to improve nitrogen’s biogeochemical cycle in the ecosystem.
Total alkalinity (TA) regulates the oceanic storage capacity of atmospheric CO2. TA is produced along two general pathways, weathering reactions and anaerobic respiration of organic matter, e.g., by denitrification, the anaerobic reduction of nitrate (NO3-) to elemental nitrogen (N2). Anammox, is another anaerobic pathway, yields N2 as its terminal product via comproportionation of ammonium (NH4+) and nitrite (NO2-); this is, however, without release of alkalinity as a byproduct. In order to investigate these two nitrate / nitrite respiration pathways and their resulting impact on TA generation, we sampled the highly turbid estuary of the Ems River, discharging into the North Sea in June 2020. We sampled a transect from the Wadden Sea to the upper tidal estuary, five vertical profiles during ebb tide, and fluid mud for incubation experiments in the hyper-turbid tidal river. The data reveal a strong increase of TA and DIC in the tidal river, where stable nitrate isotopes indicate water column denitrification as the dominant pathway. In the fluid mud of the tidal river, the TA data imply only low denitrification rates, with the majority of the N2 being produced by anammox (> 90 %). The relative abundances of anammox and denitrification, respectively, thus exert a major control on the CO2 storage capacity of adjacent coastal waters.
Organic matter is a critical factor which regulates nitrogen loss pathways of denitrification and anammox for microbes in marine ecosystems. However, only a little attention has been paid to contrasting studies on denitrification and anammox in sandy and muddy sediments, especially in the coastal continental shelf dominated by sandy sediments. This study determined the bulk properties and associated microbial nitrogen transformation processes of surface sediments in the East China Sea coastal shelf, with the aim of gaining insight into the interaction of nitrogen loss with organic matter at the molecular level. The results illustrate that nitrogen loss dominates in organic-rich muddy sediments, and its denitrification rate (14.39 nmol N g⁻¹ h⁻¹) and anammox rate (2.73 nmol N g⁻¹ h⁻¹) are greater than those of sandy sediments (denitrification rate = 5.55 nmol N g⁻¹ h⁻¹, anammox rate = 1.57 nmol N g⁻¹ h⁻¹). Furthermore, determination of the mean summed ladderanes shows higher anammox generated in the muddy sediments with a value of 167.78 ng g⁻¹ dw. Quantitative analysis demonstrated that organic-rich muddy sediments enhanced the copy number of the denitrifying functional gene nosZ and anammox functional gene hzsB. We inferred that the greater rate of nitrogen loss in muddy sediments was due to the coupling relationship between anammox and denitrification. Overall, the community distribution and abundance of denitrifying bacteria and anammox bacteria changed intricately under the influence of organic matter. Moreover, this study further improves the understanding of nitrogen loss pathways and mechanistic factors from sediments.
Degradation of aquatic ecosystems from nutrient pollution is a global issue, and quantifying nutrient removal in coastal ecosystems is a topic of interest for coastal managers worldwide. Analysing relationships between natural nitrogen removal processes, such as denitrification, and environmental variables from an ecological (rather than biogeochemical) perspective may help to identify and predict biogeochemically important habitat patches (hot spots). However, in situ measurements of denitrification that are coupled with ecosystem variables are rare. In this study, we analysed a dataset encompassing 18 estuaries, broad environmental gradients, and two methods of measuring denitrification (denitrification enzyme activity (DEA) and in situ N2 flux quantification) to better understand natural estuarine nitrogen removal processes and to rationalise methods. Generally poor relationships between denitrification measures and environmental variables suggest strong context dependency, with different activation or limiting reactants affecting denitrification rates differentially in space and time. This research illustrates how biogeochemically important habitat patches may develop and demonstrates that single-method studies have the potential to miss hot spots or hot moments of nitrogen removal. A two-method approach that integrates both long-term (DEA) and short-term (in situ N2 flux) conditions is more likely to lead to the identification of biogeochemically important habitat patches. A better understanding of natural nitrogen removal processes in estuaries will clarify assimilative capacity questions and feed into eutrophication mitigation management efforts in these highly valued freshwater–coastal interface areas.
Nitrogen (N) limits primary production over large areas of the earth and has a particularly complex and interesting series of biological transformations in its cycle. Human manipulation of the N cycle is intense, as large amounts of “reactive” N are needed for crop production and are produced as a by-product of fossil fuel combustion. This manipulation leads to an excess of N in the environment that “cascades” through ecosystems, causing air and water pollution. This chapter focuses on the processes and transformations that make up the N “cycle” and how these processes are expressed and regulated in terrestrial and aquatic ecosystems.
Estuaries are depositional environments prone to terrigenous mud sedimentation. While macrofaunal diversity and nitrogen retention are greatly affected by changes in sedimentary mud content, its impact on prokaryotic diversity and nitrogen cycling activity remains understudied. We characterized the composition of estuarine tidal flat prokaryotic communities spanning a habitat range from sandy to muddy sediments, while controlling for salinity and distance. We also determined the diversity, abundance and expression of ammonia oxidizers and N2O‐reducers within these communities by amoA and clade I nosZ gene and transcript analysis. Results show that prokaryotic communities and nitrogen cycling fractions were sensitive to changes in sedimentary mud content, and that changes in the overall community were driven by a small number of phyla. Significant changes occurred in prokaryotic communities and N2O‐reducing fractions with only a 3% increase in mud, while thresholds for ammonia oxidizers were less distinct, suggesting other factors are also important for structuring these guilds. Expression of nitrogen cycling genes was substantially higher in muddier sediments, and results indicate that the potential for coupled nitrification–denitrification became increasingly prevalent as mud content increased. Altogether, results demonstrate that mud content is a strong environmental driver of diversity and N‐cycling dynamics in estuarine microbial communities. This article is protected by copyright. All rights reserved.
The marine N cycle is driven mainly by microorganisms whose distribution can be shaped by mesoscale eddies. Recently, eddies containing oxygen minimum zones (OMZs) have been recognised as N-loss hotspots, complicating even more the calculations of the marine N budgets. As a contribution to this understanding, we investigated the effect of a cyclonic eddy confined in an oxygen-depleted basin on the distribution of the N-cycling communities. We measured hydrographic properties of the water column, nutrient concentrations, and the abundance of key genes involved in the processes of nitrification (archaeal and bacterial amoA), denitrification (nirS and nirK), dissimilatory nitrate reduction to ammonia (DNRA; nrfA) and anammox (hzo) within the eddy. Our results indicated that the cyclonic circulation affected the distribution of nutrients and the abundance of amoA and nirS genes, whereas oxygen influenced the distribution of nirK, nrfA, and hzo genes. Additionally, the aerobic ammonium oxidation by archaea seems to be an important source of nitrite, which might fuel denitrifier, DNRA, and anammox communities in this basin. These findings along with the high N deficit in the OMZ suggest the existence of an active N cycling that might enhance the N-loss in this oxygen-depleted basin.
Nitrate (NO3–) enrichment in rivers over the last four decades has potentially shifted how coastal ecosystems process nitrogen (N). Shifts in N dynamics may be particularly significant in coastal deltaic floodplains when sediments are inundated during river flood stage as this may change the fate of NO3– transported to the coastal ocean. We evaluated the relative importance of denitrification, dissimilative nitrate reduction to ammonium (DNRA), and anaerobic ammonium oxidation (anammox) in intact sediment cores of Wax Lake Delta (WLD) using continuous flow-through system. We manipulated this experimental system with two concentrations of riverine NO3– (lower concentration at 5 μM and ambient concentration at 100 μM) to test how nitrate-enriched waters may modify N cycling in coastal deltaic floodplains. Inundated sediments in a coastal deltaic floodplain removed bio-reactive N as a function of sediment organic matter (SOM) concentrations, indicating how N dynamics vary as a result of deltaic succession. Direct denitrification was the dominant N pathway in inundated sediments in WLD, which was several times greater than coupled nitrification-denitrification, DNRA, and anammox. Gross denitrification (direct denitrification + coupled nitrification-denitrification) rates generally increased with SOM concentrations and ranged from 4 to 12 μmol N m–2 h–1 under lower NO3– enrichment (5 μM) and 68 to 276 μmol N m–2 h–1 under higher NO3– enrichment (100 μM). Most of these changes in N fluxes with SOM and NO3– enrichment resulted from the increase in direct denitrification rates rather than coupled nitrification-denitrification rates. DNRA rates varied from 0 to 65 μmol N m–2 h–1, and the relative significance of DNRA increased as a percentage of total NO3– reduction (%DNRA) with increasing ratio of organic carbon to NO3– concentrations (OC/NO3–). Anammox rates increased among sites as SOM increased, but rates were lower from 0.0 to 38 μmol N m–2 h–1. The dominance of direct denitrification and increased anammox rates with SOM concentrations indicate that dynamic deltaic floodplains can permanently remove bio-reactive N in the proximal zone of river deposition of tidal freshwater wetlands.
Human activities are dramatically increasing estuarine nitrogen (N) loads, further altering N processes. However, relative importance of denitrification and anaerobic ammonium oxidation (anammox) in response to human activities intensity gradient remains poorly understood for estuaries. In this study, we used a ¹⁵N isotope tracer approach to characterize the variations in sediment denitrification and anammox rates and determined the crucial factors controlling the partitioning of N2 production and regulating N2O production across five subtropical estuaries in southeast China. Denitrification rates increased significantly from 8.82 ± 3.89 nmol N g⁻¹ h⁻¹ (low human activity intensity) to 41.2 ± 11.5 nmol N g⁻¹ h⁻¹ (high human activity intensity) across the studied estuaries. Anammox rates not varied significantly between low (2.37 ± 0.66 nmol N g⁻¹ h⁻¹), moderate (3.96 ± 0.91 nmol N g⁻¹ h⁻¹), and high (4.04 ± 1.09 nmol N g⁻¹ h⁻¹) human activity intensity estuaries. Relative contribution of anammox to total N2 production (Ra) decreased toward estuary mouth within each estuary. The Ra was also significantly lower in the estuaries characterized by high N loads and low DO. N2O production rates were in a range of 0.192–1.92 nmol N2O g⁻¹ h⁻¹ across the estuaries and controlled by water NO2–, salinity and TOC. DO, NH4⁺, and NO3– were the best predictors of the partitioning of N2 production between denitrification and anammox. The high human activities intensity increased NH4⁺ and NO3– loads and further enhanced denitrification, leading to the decrease in Ra and increase in N2O production. These findings suggest that low DO and high N loads estuaries can increase denitrification and N2O emissions, whereas not affect anammox substantially under the higher intensity of human activities.
Estuarine sediment denitrification and anammox in response to increased nitrogen (N) loads remain poorly understood. In this study, we used N isotope tracer approach to investigate the spatial distribution of denitrification and anammox and identified the crucial controls on the partitioning of dinitrogen gas (N2) production along the Min River Estuary (MRE), a highly impacted estuary in southeast China. The results indicated that denitrification and anammox rates ranged from 10.5 to 70.7 nmol g–1 h–1 and from 0.44 to 4.31 nmol g–1 h–1, respectively. Relative contribution of anammox to N2 production (Ra) was in a range of 1.04–15.1%, tending to increase toward estuary mouth. Denitrification rates were significantly higher in upper (high N loads) than in lower estuary (low N loads), while anammox rates and Ra showed inverse distributions along the MRE. Wastewater discharge caused the N point pollution triggering denitrification but inhibiting anammox. The best predictor of the variations in denitrification rates was total nitrogen, whereas pH and NH4⁺ could explained the variations in anammox rates across the estuary. The crucial predictors for the partitioning of N2 production between denitrification and anammox were NH4⁺ and NOx–. These results suggest that the increase in human activities intensity can alter the partitioning of N2 production between denitrification and anammox, and the magnitude of this switch can be predicted by N loads in MRE and other highly impacted estuaries.
Depth-dependent distribution patterns of bacterial and archaeal communities in deep sea water column around the Ninetyeast Ridge in the Indian Ocean were investigated using 16S rRNA gene profiling. Sampling was conducted at the northern Ninetyeast Ridge (1°59.89′N–9°59.70′S, 87°58.90′E–88°00.03′E) from September to November 2016 where samples were collected from the bathyal (1 000 m) to bathypelagic depths (>4 000 m) in four different stations. A total of 1 565 405 clean data falling into 6 712 bacterial OTUs and 1 452 727 clean data falling into 806 archaeal OTUs based on 97% similarity level were analyzed. Most of the bacterial 16S rRNA gene sequences were affiliated with Gammaproteobacteria, followed by Alphaproteobacteria and Bacteroidia. The archaeal 16S rRNA gene sequences mostly affiliated to Nitrososphaeria (Thaumarchaeota) dominated with relative abundances ranging from 52.68% to 97.2%, followed by Thermoplasmata (Euryarchaeota). Vertical partitioning of bacterial and archaeal communities among different water layers was observed. Canonical correspondence analysis (CCA) and Spearman’s correlations revealed that depth (P=0.003), dissolved oxygen (P=0.019), and nitrite (P=0.033) were the main environmental factors affecting bacterial community structure at genus level in the Ninetyeast Ridge. On the other hand, the first two CCA axes accounted for 74.4% of the explained total variance, it seems that the archaeal communities at genus level were heavily influenced by the environmental variables including depth, dissolved oxygen (DO), nitrite, salinity, phosphate, ammonia, nitrate, and silicate, but none of them exhibited any significant correlation on the structuring (P>0.1).
Anaerobic ammonium oxidation (anammox) is an important bioprocess for nitrogen removal and has been studied in estuarine environments. However, knowledge on anammox bacterial community dynamics and related controlling factors remains limited in these ecosystems. In this study, the community compositions, abundance, and activity of anammox bacteria in the surface sediments from the Indus Estuary were investigated along a salinity gradient, considering the links between the anammox bacterial community dynamics and environmental variables. The potential importance of anammox was also estimated for nitrogen removal. High anammox bacterial diversity was detected in the sediments of the Indus Estuary, including Kuenenia, Brocadia, Scalindua, Jettenia, and a novel anammox-like cluster. Kuenenia was identified as the dominant anammox bacteria in most samples. Anammox bacterial diversity was significantly correlated with sediment NO3⁻ , while the distribution of anammox bacterial community was significantly related to temperature and sediment sulfide (P<0.05). The anammox bacterial abundance based on the 16S rRNA gene varied between 1.64 × 10⁶ copies g⁻¹ and 8.21 × 10⁸ copies g⁻¹, and was significantly correlated with sediment Fe(II). Based on an ¹⁵N isotope-tracing technique, potential anammox rates were found in the range 0.01 - 0.32 μmol N kg⁻¹ h⁻¹, and were controlled mainly by salinity, Fe(II), and TOC. It was estimated that the anammox bacteria contributed about 21.9 % to the total nitrogen loss, on average. These results show the importance of anammox bacteria for nitrogen transformation and removal in estuarine and coastal environments.
Climate-driven sea level rise has severe consequences for drained agricultural areas near coasts. The least productive of these can be restored into marine wetlands of high ecological quality by managed realignment. This study assessed the nitrogen (N) and phosphorus (P) balance in a 214 ha coastal lagoon formed after flooding of agricultural land by managed realignment. N and P loss from the soils was monitored over a 5-year period after flooding using three independent approaches: (1) temporal changes in N and P inventories of the soil; (2) flux of dissolved inorganic N and P from the flooded soil; and (3) tidal N and P exchange across the outer boundary in the form of particulate and dissolved nutrients. All three approaches showed similar initial release and tidal export of N and P the first year(s) after flooding followed by decreasing rates. The annual loss ranged from 157 to 299 kg N ha−1 yr−1 and 29 to 63 kg P ha−1 yr−1 during the first year. N loss decreased rapidly after the first 2 years and reached a level of 28–65 kg N ha−1 yr−1, while P loss declined after the first year and remained stable and relatively high at 18–32 kg P ha−1 yr−1 thereafter. High N and P export after implementing managed realignment of agricultural land may deteriorate environmental conditions in the adjacent marine recipients for at least 5 years. Particularly small and stagnant water bodies vulnerable to eutrophication should be avoided as recipients.
Denitrifi cation and anammox processes are major nitrogen removal processes in coastal ecosystems. However, the spatiotemporal dynamics and driving factors of the diversity and community structure of involved functional bacteria have not been well illustrated in coastal environments, especially in human-dominated ecosystems. In this study, we investigated the distributions of denitrifi ers and anammox bacteria in the eutrophic Bohai Sea and the northern Yellow Sea of China in May and November of 2012 by constructing clone libraries employing nosZ and 16S rRNA gene biomarkers. The diversity of nosZ-denitrifi er was much higher at the coastal sites compared with the central sites, but not signifi cant among basins or seasons. Alphaproteobacteria were predominant and prevalent in the sediments, whereas Betaproteobacteria primarily occurred at the site near the Huanghe (Yellow) River estuary. Anammox bacteria Candidatus Scalindua was predominant in the sediments, and besides, Candidatus Brocadia and Candidatus Kuenenia were also detected at the site near the Huanghe River estuary that received strong riverine and anthropogenic impacts. Salinity was the most important in structuring communities of nosZ-denitrifi er and anammox bacteria. Additionally, anthropogenic perturbations (e.g. nitrogen overloading and consequent high primary productivity, and heavy metal discharges) contributed signifi cantly to shaping community structures of denitrifi er and anammox bacteria, suggesting that anthropogenic activities would infl uence and even change the ecological function of coastal ecosystems.
The coupling process of anaerobic ammonia oxidation (anammox) and denitrification plays an important role in natural ecosystems. As a part of the nitrogen cycle, denitrification and anaerobic ammonia oxidation are critical for balance of nitrogen budget, nitrogen pollution improvement and greenhouse gas reduction. The review focuses on the key issues revolved in the coupling process of anammox and denitrification in both aquatic and terrestrial ecosystems, including (1) Reaction medium, rate and the contribution of N2 in different environmental conditions and the interrelationship. It is found that the contribution of anaerobic ammonia oxidation to N2 production in aquatic ecosystem is greater than that in terrestrial ecosystem. (2) Bacterial community and functional genes of anammox and denitrification that may alter their dominant roles in the changing environment, and Candidatus brocadia having its highest frequency of occurrence. (3) The influencing factors in the coupling process, in which the optimum pH of coupling of anammox and denitrification is 6.7-8.3 in environmental factors, and the coupling reaction will be inhibited when the content of dissolved oxygen is too high. In substrate environment, a great organic content or C/N can promote denitrification, while it inhibits anammox. More attention should be paid to the global scale of the coupling reaction of anammox and denitrification, especially in the terrestrial ecosystems, which is relatively limited to be studied at present. It should also deepen the response to the theoretical and practical study on relationships between the rates of anammox and denitrification. Moreover, in practice, on the basis of determining the optimum growth of anammox bacteria and denitrifying bacteria, and determining the optimum growth of anaerobic ammonia-oxidizing bacteria and denitrifying bacteria, a mathematical model of coupling system theory should be established to quantify the coupling effect of two kinds of functional microorganisms. © 2018, Editorial Board, Research of Environmental Sciences. All right reserved.
Phytoplankton pigment samples are routinely collected by filtering water and storing filters at -20°C before extraction and fluorometric analyses. Although pigment loss on frozen filters has been demonstrated for phytoplankton cultures, its effect on taxonomically diverse, natural assemblages is unknown. We examined the effect of freezing filters on pigment measurements from weekly field samples collected for 1 y from Narragansett Bay, RI. Over 1000 filters representing the total and < 20 μm size fractions were collected. One set of filters was treated with MgCO3 and stored at -20°C for ≤ 200 d before extraction. Another set was immediately extracted following filtration and not treated with MgCO3. A third subset was treated without MgCO3 and frozen for δ 70 d. Frozen storage decreased the annual average Chlorophyll a concentration by 51%. Pigment loss was greatest in samples dominated by the > 20 μm size class, such as during the winter-spring bloom peak when 62% of Chl a was lost from frozen samples. Freezing filters reduced analytical precision, increasing the coefficient of variation of Chl a measurements from 3.4% using immediate extraction to 13.1% using frozen filter storage. Correction factors created from regression analyses were applied to the year-long frozen storage dataset and brought the annual average Chl a concentration to within 4% of the value determined using the immediate extraction technique. The application of correction factors to the Narragansett Bay Long-Term Monitoring Program from 1999-2007 resulted in an average Chl a concentration that was 94% greater than the historical average. © 2011, by the American Society of Limnology and Oceanography, Inc.
The occurrence and significance of the anammox (anaerobic ammonium oxidation) process relative to denitrification was studied in photosynthetically active sediment from 2 shallow-water estuaries: Randers Fjord and Norsminde Fjord, Denmark. Anammox accounted for 5 to 24 % of N-2 production in Randers Fjord sediment, whereas no indication was seen of the process in sediment from Norsminde Fjord, It is suggested that the presence of anammox in Randers Fjord and its absence from Norsminde Fjord is associated with differences in the availability of NO3- + NO2- (NOx-) in the suboxic zone of the sediment. In Randers Fjord, NOx- is present in the water column throughout the year and NOx- porewater profiles showed that NOx- penetrates into the suboxic zone of the sediment. In Norsminde Fjord, NOx- is absent from the water column during the summer months and, via assimilation, benthic microalgae may prevent penetration of NOx- into the suboxic zone of the sediment. Volume-specific anammox rates in Randers Fjord were comparable with rates measured previously in Skagerrak sediment by other investigators, but denitrification rates were 10 to 15 times higher. Thus, anammox contributes less to N-2, production in Randers Fjord than in Skagerrak sediment, We propose that the lower contribution of anammox in Randers Fjord is linked to the higher availability of easily accessible carbon, which supports a higher population of denitrifying bacteria. Amplification of DNA extracted from the sediment samples from Randers Fjord using planctomycete-specific primers yielded 16S rRNA gene sequences closely related to candidatus Scalindua sorokinii found in the Black Sea by other investigators. The present study thus confirms the link between the presence of bacteria affiliated with candidatus S. sorokinii and the anammox reaction in marine environments. Anammox rates in sediment with intact chemical gradients were estimated using both N-15 and microsensor techniques. Anammox rates estimated with microsensors were less than 22 % of the rates measured with isotopes. It is suggested that this discrepancy was due to the presence of fauna, because the applied N-15 technique captures total N-2 production while the microsensor technique only captures diffusion-controlled N-2 production at the sediment surface. This hypothesis was verified by consistent agreement between the methods when applied to defaunated sediments.
Seasonal measurements of organic matter mineralisation by oxygen uptake and denitrification were carried out from July 1996 to March 1998 along a similar to 200 km transect of the River Thames estuary, UK. There was a distinct gradient of decreasing rates of organic matter mineralisation seaward, which was related to the concentration of suspended solids and sedimentary organic carbon (C) at each site. There was clear seasonality and highest rates of oxygen uptake (10 056 pmol O-2 m(-2) h(-1)) at the muddy sites, but lower rates and non-temperature-dependent oxygen uptake at the sandier sites. Denitrification, both that driven by nitrate from the overlying water (D-w) and that coupled to nitrification in the sediment (D-n), followed a similar trend to oxygen uptake, from negligible rates of approximately 1 mu mol N m(-2) h(-1) for both D-w and D-n at the furthest offshore site, Site 12, to 11 407 and 8209 mu mol N m(-2) h(-1), respectively, at the inner muddy Site 1. The Thames estuary is heterotrophic and a very efficient organic C filter, trapping and remineralising 77% of its organic C input. Attenuation of fluvial nitrate loads was regulated by freshwater flow. Minimal attenuation (3%) occurred during peak flows (i.e. during periods of shortest freshwater flushing time) and >100% attenuation during periods of lowest freshwater flow (longest flushing times). Including the sewage treatment works (STWs) nitrate load in this calculation reduced the degree of attenuation of the nitrate load to, on average, 11%. Annual rates of D-w and D-n for an inner area of 125 km(2) were 112 and 85 Mmol N yr(-1), respectively, with a total rate of 196 Mmol N yr(-1) (2744 t), which was equivalent to 9% of the total dissolved inorganic nitrogen (DIN) load for 1995-96. A mean denitrification rate (D-w) of 0.64 mol N (m-)2 yr(-1), based on measurements in 4 east coast estuaries, was used to estimate a total rate of denitrification for the entire area of UK east coast estuaries. The total rate of 0.81 Gmol N yr(-1) represented 16% attenuation of the total fluvial discharge of nitrate (similar to 6 Gmol N yr(-1)) to the UK's east coast estuaries (1995-96) and hence a 16% reduction in the UK nitrate load to the North Sea.
Abstract The second largest zone of coastal hypoxia (oxygen-depleted waters) in the world is found on the northern Gulf of Mexico continental shelf adjacent to the outflows of the Mississippi and Atchafalaya Rivers. The combination of high freshwater discharge, wind mixing, regional circulation, and summer warming controls the strength of stratification that goes through a well-defined seasonal cycle. The physical structure of the water column and high nutrient loads that enhance primary production lead to an annual formation of the hypoxic water mass that is dominant from spring through late summer. Paleoindicators in dated sediment cores indicate that hypoxic conditions likely began to appear around the turn of the last century and became more severe since the 1950s as the nitrate flux from the Mississippi River to the Gulf of Mexico tripled. Whereas increased nutrients enhance the production of some organisms, others are eliminated from water masses (they either emigrate from the area or die) where the...
The bioavailability of nutrients represents one of the most important factors controlling the strength of the biological carbon pump and ultimately the impact of ocean biology on atmospheric CO2. Among those nutrients, the macro-nutrients nitrate (NO
2-) and phosphate (PO
4-3) play a particularly important role in limiting biological productivity as evidenced by their often near complete exhaustion in surface waters. As near surface NO
2- concentrations are generally somewhat lower than those of PO
4-3 relative to the demand by phytoplankton, biological oceanographers have argued historically that NO
2- rather than PO
4-3 is the primary macro-nutrient controlling phytoplankton productivity[Smith, 1984; Codispoti, 1989; Tyrrell, 1999] . Geologists, in contrast, regarded PO
4-3 as the primary controlling macronutrient[Codispoti, 1989]. They argued that while NO
2- may indeed be the limiting factor at any given location and time, PO
4-3 is truly the limiting factor on geological time-scales, because the biologically mediated fixation of the much more abundant dinitrogen gas (N2) into organic nitrogen is alleviating the scarcity of bioavailable nitrogen (Figure 1). Phosphate on the other hand, does not have such a biologically mediated source (Figure 1). It is therefore the geologically controlled balance between the riverine (and atmospheric) input of PO
4-3 and its burial on the sea-floor that ultimately controls marine biological productivity. Tyrrell [ 1999] provided a synthesis of these two views by identifying NO
2- as the proximate nutrient, while giving PO
4-3 the role of being the ultimate nutrient.
1] The biogeochemistry of continental shelf systems plays an important role in the global elemental cycling of nitrogen and carbon, but remains poorly quantified. We have developed a high-resolution physical-biological model for the U.S. east coast continental shelf and adjacent deep ocean that is nested within a basin-wide North Atlantic circulation model in order to estimate nitrogen fluxes in the shelf area of the Middle Atlantic Bight (MAB). Our biological model is a relatively simple representation of nitrogen cycling processes in the water column and organic matter remineralization at the water-sediment interface that explicitly accounts for sediment denitrification. Climatological and regionally integrated means of nitrate, ammonium, and surface chlorophyll are compared with its model equivalents and were found to agree within 1 standard deviation. We also present regional means of primary production and denitrification, and statistical measures of chlorophyll pattern variability. A nitrogen budget for the MAB shows that the sediment denitrification flux is quantitatively important in determining the availability of fixed nitrogen and shelf primary production (it was found to remove 90% of all the nitrogen entering the MAB). Extrapolation of nitrogen fluxes estimated for the MAB to the North Atlantic basin suggests that shelf denitrification removes 2.3 Â 10 12 mol N annually; this estimate exceeds estimates of N 2 fixation by up to an order of magnitude. Our results emphasize the importance of representing shelf processes in biogeochemical models.
Benthic O 2 availability regulates many important biogeochemical processes and has crucial implications for the biology and ecology of benthic communities. Further, the benthic O 2 exchange rate represents the most widely used proxy for quantifying mineralization and primary production of marine sediments. Consequently, numerous researchers have investigated the benthic O 2 dynamics in a wide range of environments. On the basis of case studies Á from abyssal sediments to microbial phototrophic communities Á I hereby try to review the current status on what we know about controls that interrelate with the O 2 dynamics of marine sediments. This includes factors like: sedimentation rates, bottom water O 2 concentrations, diffusive boundary layers, fauna activity, light, temperature, and sediment permeability. The investigation of benthic O 2 dynamics represents a challenge in resolving variations on temporal and spatial scales covering several orders of magnitude. Such an effort requires the use of several complementary measuring techniques and modeling approaches. Recent technical developments (improved chamber approaches, O 2 optodes, eddy-correlation, benthic observatories) and advances in diagenetic modeling have facilitated our abilities to resolve and interpret benthic O 2 dynamics. However, all approaches have limitations and caveats that must be carefully evaluated during data interpretation. Much has been learned during the last decades but there are still many unanswered questions that need to be addressed in order to fully understand benthic O 2 dynamics and the role of sediments for marine carbon cycling.
The Baltic Sea is one of the most eutrophic marine areas in the world. The role of nitrogen as a eutrophicating nutrient in the Baltic Sea has remained controversial owing to a lack of understanding of nitrogen cycling in the area. We investigated the seasonal variation in sediment nitrification, denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) at 2 coastal sites in the Gulf of Finland. In addition to the estimation of in situ rates, we assessed the potential for nitrification and denitrification in different seasons. The nitrification and nitrogen removal processes were maximal during the warm summer months, when the sediment organic content was highest. In colder seasons, the rates of nitrification and nitrate reduction measured under in situ conditions decreased, but the potential for nitrification remained equal to, or higher than, that during the warm months. The rates of denitrification and nitrification were usually higher in the accumulation basin, where the organic content of the sediment was higher, but the transportation area, despite lower denitrification rates and potential, typically had a higher potential for nitrification than the accumulation basin. Anammox and DNRA were not important nitrate sinks in any of the seasons sampled. The results also show that the rates of denitrification in the coastal Gulf of Finland sediment have decreased, and that benthic denitrification might be a less important sink for fixed nitrogen than previously assumed.
Sediment-water oxygen and nutrient (NH4
+, NO3
−+NO2
−, DON, PO4
3−, and DSi) fluxes were measured in three distinct regions of Chesapeake Bay at monthly intervals during 1 yr and for portions
of several additional years. Examination of these data revealed strong spatial and temporal patterns. Most fluxes were greatest
in the central bay (station MB), moderate in the high salinity lower bay (station SB) and reduced in the oligohaline upper
bay (station NB). Sediment oxygen consumption (SOC) rates generally increased with increasing temperature until bottom water
concentrations of dissolved oxygen (DO) fell below 2.5 mg l−1, apparently limiting SOC rates. Fluxes of NH4
+ were elevated at temperatures >15°C and, when coupled with low bottom water DO concentrations (<5 mg l−1), very large releases (>500 μmol N m−2 h−1) were observed. Nitrate + nitrite (NO3
−+NO2
−) exchanges were directed into sediments in areas where bottom water NO3
−+NO2
− concentrations were high (>18 μM N); sediment efflux of NO3
−+NO2
− occurred only in areas where bottom water NO3
−+NO2
− concentrations were relatively low (<11 μM N) and bottom waters well oxygenated. Phosphate fluxes were small except in areas
of hypoxic and anoxic bottom waters; in those cases releases were high (50–150 μmol P m−2 h−1) but of short duration (2 mo). Dissolved silicate (DSi) fluxes were directed out of the sediments at all stations and appeared
to be proportional to primary production in overlying waters. Dissolved organic nitrogen (DON) was released from the sediments
at stations NB and SB and taken up by the sediments at station MB in summer months; DON fluxes were either small or noninterpretable
during cooler months of the year. It appears that the amount and quality of organic matter reaching the sediments is of primary
importance in determining the spatial variability and interannual differences in sediment nutrient fluxes along the axis of
the bay. Surficial sediment chlorophyll-a, used as an indicator of labile sediment organic matter, was highly correlated with NH4
−, PO4
3−, and DSi fluxes but only after a temporal lag of about 1 mo was added between deposition events and sediment nutrient releases.
Sediment O:N flux ratios indicated that substantial sediment nitrification-denitrification probably occurred at all sites
during winter-spring but not summer-fall; N:P flux ratios were high in spring but much less than expected during summer, particularly
at hypoxic and anoxic sites. Finally, a comparison of seasonal N and P demand by phytoplankton with sediment nutrient releases
indicated that the sediments provide a substantial fraction of nutrients required by phytoplankton in summer, but not winter,
especially in the mid bay region.
The importance of anaerobic ammonium oxidation (anammox)-a metabolic pathway that can generate dinitrogen-remains poorly described in temperate estuarine systems. We evaluated the relative importance of anammox and denitrification along the salinity gradient of the Cavado River estuary (NW Portugal) during a seasonal survey. Potential rates of anammox and denitrification were measured in anaerobic sediment slurries using N-15-labeled NO3- and NH4+ amendments. Production of N-29(2) and N-30(2) in the slurries was quantified using membrane inlet mass spectrometry (MIMS). Environmental parameters such as salinity, temperature and inorganic nitrogen were also monitored. Anammox and denitrification potentials in Cavado estuarine sediments varied from 0 to 3.3 and from 1.1 to 10.8 nmol N cm(-3) wet sediment h(-1), respectively. During 1 sampling occasion, anammox activity accounted for as much as 72% of the measured production of dinitrogen, while annual averages varied from 17 to 33% depending on location. Nitrate availability and temperature appeared to be the primary environmental controls of anammox. Higher concentrations of NO3- and intermediate temperatures in the estuarine water (14 to 16 degrees C) supported higher anammox activities. Using 16S rRNA gene-specific primers, anammox-like bacterial sequences were recovered from Cavado sediments-corroborating the measured anammox activities. Our results support the environmental importance of anammox for removal of nitrogen in estuarine sediments, and suggest that this process is apparently regulated by few variables.
Estuarine sediments are the location for significant bacterial removal of anthropogenically derived inorganic nitrogen, in
particular nitrate, from the aquatic environment. In this study, rates of benthic denitrification (DN), dissimilatory nitrate
reduction to ammonium (DNRA), and anammox (AN) at three sites along a nitrate concentration gradient in the Colne estuary,
United Kingdom, were determined, and the numbers of functional genes (narG, napA, nirS, and nrfA) and corresponding transcripts encoding enzymes mediating nitrate reduction were determined by reverse transcription-quantitative
PCR. In situ rates of DN and DNRA decreased toward the estuary mouth, with the findings from slurry experiments suggesting
that the potential for DNRA increased while the DN potential decreased as nitrate concentrations declined. AN was detected
only at the estuary head, accounting for ∼30% of N2 formation, with 16S rRNA genes from anammox-related bacteria also detected only at this site. Numbers of narG genes declined along the estuary, while napA gene numbers were stable, suggesting that NAP-mediated nitrate reduction remained important at low nitrate concentrations.
nirS gene numbers (as indicators of DN) also decreased along the estuary, whereas nrfA (an indicator for DNRA) was detected only at the two uppermost sites. Similarly, nitrate and nitrite reductase gene transcripts
were detected only at the top two sites. A regression analysis of log(n + 1) process rate data and log(n + 1) mean gene abundances showed significant relationships between DN and nirS and between DNRA and nrfA. Although these log-log relationships indicate an underlying relationship between the genetic potential for nitrate reduction
and the corresponding process activity, fine-scale environmentally induced changes in rates of nitrate reduction are likely
to be controlled at cellular and protein levels.
Dead zones in the coastal oceans have spread exponentially since the 1960s and have serious consequences for ecosystem functioning.
The formation of dead zones has been exacerbated by the increase in primary production and consequent worldwide coastal eutrophication
fueled by riverine runoff of fertilizers and the burning of fossil fuels. Enhanced primary production results in an accumulation
of particulate organic matter, which encourages microbial activity and the consumption of dissolved oxygen in bottom waters.
Dead zones have now been reported from more than 400 systems, affecting a total area of more than 245,000 square kilometers,
and are probably a key stressor on marine ecosystems.
After shifting an oxygen-respiring culture of Pseudomonas stutzeri to nitrate or nitrite respiration, we directly monitored the expression of the nirS gene by mRNA analysis. nirS encodes the 62-kDa subunit of the homodimeric cytochrome cd1 nitrite reductase involved in denitrification. Information was sought about the requirements for gene activation, potential regulators of such activation, and signal transduction pathways triggered by the alternative respiratory substrates. We found that nirS, together with nirT and nirB (which encode tetra- and diheme cytochromes, respectively), is part of a 3.4-kb operon. In addition, we found a 2-kb monocistronic transcript. The half-life of each of these messages was approximately 13 min in denitrifying cells with a doubling time of around 2.5 h. When the culture was subjected to a low oxygen tension, we observed a transient expression of nirS lasting for about 30 min. The continued transcription of the nirS operon required the presence of nitrate or nitrite. This anaerobically manifested N-oxide response was maintained in nitrate sensor (NarX) and response regulator (NarL) knockout strains. Similar mRNA stability and transition kinetics were observed for the norCB operon, encoding the NO reductase complex, and the nosZ gene, encoding nitrous oxide reductase. Our results suggest that a nitrate- and nitrite-responsive regulatory circuit independent of NarXL is necessary for the activation of denitrification genes.
In the global nitrogen cycle, bacterial denitrification is recognized as the only quantitatively important process that converts
fixed nitrogen to atmospheric nitrogen gas, N2, thereby influencing many aspects of ecosystem function and global biogeochemistry. However, we have found that a process
novel to the marine nitrogen cycle, anaerobic oxidation of ammonium coupled to nitrate reduction, contributes substantially
to N2 production in marine sediments. Incubations with 15N-labeled nitrate or ammonium demonstrated that during this process, N2 is formed through one-to-one pairing of nitrogen from nitrate and ammonium, which clearly separates the process from denitrification.
Nitrite, which accumulated transiently, was likely the oxidant for ammonium, and the process is thus similar to the anammox
process known from wastewater bioreactors. Anaerobic ammonium oxidation accounted for 24 and 67% of the total N2 production at two typical continental shelf sites, whereas it was detectable but insignificant relative to denitrification
in a eutrophic coastal bay. However, rates of anaerobic ammonium oxidation were higher in the coastal sediment than at the
deepest site and the variability in the relative contribution to N2 production between sites was related to large differences in rates of denitrification. Thus, the relative importance of anaerobic
ammonium oxidation and denitrification in N2 production appears to be regulated by the availability of their reduced substrates. By shunting nitrogen directly from ammonium
to N2, anaerobic ammonium oxidation promotes the removal of fixed nitrogen in the oceans. The process can explain ammonium deficiencies
in anoxic waters and sediments, and it may contribute significantly to oceanic nitrogen budgets.
Factors controlling the anaerobic oxidation of ammonium with nitrate and nitrite were explored in a marine sediment from the Skagerrak in the Baltic-North Sea transition. In anoxic incubations with the addition of nitrite, approximately 65% of the nitrogen gas formation was due to anaerobic ammonium oxidation with nitrite, with the remainder being produced by denitrification. Anaerobic ammonium oxidation with nitrite exhibited a biological temperature response, with a rate optimum at 15 degrees C and a maximum temperature of 37 degrees C. The biological nature of the process and a 1:1 stoichiometry for the reaction between nitrite and ammonium indicated that the transformations might be attributed to the anammox process. Attempts to find other anaerobic ammonium-oxidizing processes in this sediment failed. The apparent K(m) of nitrite consumption was less than 3 microM, and the relative importance of ammonium oxidation with nitrite and denitrification for the production of nitrogen gas was independent of nitrite concentration. Thus, the quantitative importance of ammonium oxidation with nitrite in the jar incubations at elevated nitrite concentrations probably represents the in situ situation. With the addition of nitrate, the production of nitrite from nitrate was four times faster than its consumption and therefore did not limit the rate of ammonium oxidation. Accordingly, the rate of this process was the same whether nitrate or nitrite was added as electron acceptor. The addition of organic matter did not stimulate denitrification, possibly because it was outcompeted by manganese reduction or because transport limitation was removed due to homogenization of the sediment.
In many oceanic regions, growth of phytoplankton is nitrogen-limited because fixation of N2 cannot make up for the removal of fixed inorganic nitrogen (NH⁺4, NO⁻2, and NO⁻3) by anaerobic microbial processes. Globally, 30-50% of the total nitrogen loss occurs in oxygen-minimum zones (OMZs) and is commonly attributed to denitrification (reduction of nitrate to N2 by heterotrophic bacteria). Here, we show that instead, the anammox process (the anaerobic oxidation of ammonium by nitrite to yield N2) is mainly responsible for nitrogen loss in the OMZ waters of one of the most productive regions of the world ocean, the Benguela upwelling system. Our in situ experiments indicate that nitrate is not directly converted to N2 by heterotrophic denitrification in the suboxic zone. In the Benguela system, nutrient profiles, anammox rates, abundances of anammox cells, and specific biomarker lipids indicate that anammox bacteria are responsible for massive losses of fixed nitrogen. We have identified and directly linked anammox bacteria to the removal of fixed inorganic nitrogen in the OMZ waters of an open-ocean setting. We hypothesize that anammox could also be responsible for substantial nitrogen loss from other OMZ waters of the ocean.
• anammox
• denitrification
• oceanic nitrogen cycle
• oxygen-minimum zone
The distribution of anaerobic ammonium oxidation (anammox) in nature has been addressed by only a few environmental studies,
and our understanding of how anammox bacteria compete for substrates in natural environments is therefore limited. In this
study, we measure the potential anammox rates in sediment from four locations in a subtropical tidal river system. Porewater
profiles of NOx− (NO2− plus NO3−) and NO2− were measured with microscale biosensors, and the availability of NO2− was compared with the potential for anammox activity. The potential rate of anammox increased with increasing distance from
the mouth of the river and correlated strongly with the production of nitrite in the sediment and with the average concentration
or total pool of nitrite in the suboxic sediment layer. Nitrite accumulated both from nitrification and from NOx− reduction, though NOx− reduction was shown to have the greatest impact on the availability of nitrite in the suboxic sediment layer. This finding
suggests that denitrification, though using NO2− as a substrate, also provides a substrate for the anammox process, which has been suggested in previous studies where microscale
NO2− profiles were not measured.
The kinetics of denitrification and the causes of nitrite and nitrous oxide accumulation were examined in resting cell suspensions of three denitrifiers. An Alcaligenes species and a Pseudomonas fluorescens isolate characteristically accumulated nitrite when reducing nitrate; a Flavobacterium isolate did not. Nitrate did not inhibit nitrite reduction in cultures grown with tungstate to prevent formation of an active nitrate reductase; rather, accumulation of nitrite seemed to depend on the relative rates of nitrate and nitrite reduction. Each isolate rapidly reduced nitrous oxide even when nitrate or nitrite had been included in the incubation mixture. Nitrate also did not inhibit nitrous oxide reduction in Alcaligenes odorans, an organism incapable of nitrate reduction. Thus, added nitrate or nitrite does not always cause nitrous oxide accumulation, as has often been reported for denitrifying soils. All strains produced small amounts of nitric oxide during denitrification in a pattern suggesting that nitric oxide was also under kinetic control similar to that of nitrite and nitrous oxide. Apparent K(m) values for nitrate and nitrite reduction were 15 muM or less for each isolate. The K(m) value for nitrous oxide reduction by Flavobacterium sp. was 0.5 muM. Numerical solutions to a mathematical model of denitrification based on Michaelis-Menten kinetics showed that differences in reduction rates of the nitrogenous compounds were sufficient to account for the observed patterns of nitrite, nitric oxide, and nitrous oxide accumulation. Addition of oxygen inhibited gas production from NO(3) by Alcaligenes sp. and P. fluorescens, but it did not reduce gas production by Flavobacterium sp. However, all three isolates produced higher ratios of nitrous oxide to dinitrogen as the oxygen tension increased. Inclusion of oxygen in the model as a nonspecific inhibitor of each step in denitrification resulted in decreased gas production but increased ratios of nitrous oxide to dinitrogen, as observed experimentally. The simplicity of this kinetic model of denitrification and its ability to unify disparate observations should make the model a useful guide in research on the physiology of denitrifier response to environmental effectors.
Anaerobic ammonium oxidation (anammox) has recently been recognized as a pathway for the removal of fixed N from aquatic ecosystems. However, the quantitative significance of anammox in estuarine sediments is variable, and measurements have been limited to a few estuaries. We measured anammox and conventional denitrification activities in sediments along salinity gradients in the Chesapeake Bay and two of its sub-estuaries, the Choptank River and Patuxent River. Homogenized sediments were incubated with (14/15)N amendments of NH4+, NO3-, and NO2- to determine relative activities of anammox and denitrification. The percent of N2 production due to anammox (ra%) ranged from 0 to 22% in the Chesapeake system, with the highest ra% in the freshwater portion of the main stem of upper Chesapeake Bay, where water column NO3- concentrations are consistently high. Intermediate levels of relative anammox (10%) were detected at locations corresponding to tidal freshwater and mesohaline locations in the Choptank River, whereas anammox was not detected in the tidal freshwater location in the Patuxent River. Anammox activity was also not detected in the seaward end of Chesapeake Bay, where water column No3- concentrations are consistently low. The ra% did not correlate with NH4+ accumulation rate in anoxic sediment incubations, but ra% was related to water column NO3- concentrations and salinity. Anammox bacterial communities were also examined by amplifying DNA extracted from the upper Chesapeake Bay sediment with polymerase chain reaction (PCR) primers that are specific for 16S rRNA genes of anammox organisms. A total of 35 anammox-like sequences were detected, and phylogenetic analysis grouped the sequences in two distinct clusters belonging to the Candidatus "Scalindua" genus.
The flux of nitrogen from land and atmosphere to estuaries and the coastal ocean has increased substantially in recent decades. The observed increase in nitrogen loading is caused by population growth, urbanization, expanding water and sewer infrastructure, fossil fuel combustion and synthetic fertilizer consumption. Most of the nitrogen is removed by denitrification in the sediments of estuaries and the continental shelf, leading to a reduction in both cultural eutrophication and nitrogen pollution of the open ocean. Nitrogen fixation, however, is thought to be a negligible process in sub-tidal heterotrophic marine systems. Here we report sediment core data from Narragansett Bay, USA, which demonstrate that heterotrophic marine sediments can switch from being a net sink to being a net source of nitrogen. Mesocosm and core incubation experiments, together with a historic data set of mean annual chlorophyll production, support the idea that a climate-induced decrease in primary production has led to a decrease in organic matter deposition to the benthos and the observed reversal of the net sediment nitrogen flux. Our results suggest that some estuaries may no longer remove nitrogen from the water column. Instead, nitrogen could be exported to the continental shelf and the open ocean and could shift the effect of anthropogenic nitrogen loading beyond the immediate coastal zone.
We measured the production of N2 gas from anammox and denitrification simultaneously in intact sediment cores at six sites along a transect of the continental shelf (50 m) and deeper slope (2000 m) in the North Atlantic. Maximum rates of total N2 production were measured on the shelf and were largely due to denitrification, with anammox contributing, on average, 33% of this production. On the continental slope, the production of N2 gas decreased but the proportion due to anammox reached a maximum of 65%. This change in both amount and dominant pathway of N2 production could be explained largely by the concentration of organic carbon at each site. With increasing carbon the total production of N2 increased rapidly while the response of anammox was not significant. On the continental slope, total N2 production fell below 2 μmol N m22 h21 and anammox was strongly related (r = 0.95) to denitrification but the relative magnitude of anammox to denitrification (1.65 : 1) suggested that anammox could not be fuelled by NO-2 from denitrification alone. On the shelf, however, where total N2 production was predominantly greater than 2 μmol N m-2 h-1, no relationship between anammox and denitrification was found and anammox remained constant at 1.4 mmol N m22 h21. Despite the constancy and greater availability of NO-3 and lower temperatures on the continental slope, the significance of anammox to the total production of N2 appears primarily controlled by the overall rate of N2 production. © 2009, by the American Society of Limnology and Oceanography, Inc.
We measured denitrification, anaerobic ammonium oxidation (anammox), oxygen uptake, nutrient exchange, and pore-water profiles of oxygen in intact sediments at three sites in the southern North Sea, which we experimentally exposed to different oxygen saturations (ambient and ∼ 33% of air-saturation for oxygen [i.e., our hypoxic treatment]) over 14 months. Denitrification ranged from 1 μmol N m−2 h−1 to 21 μmol N m−2 h−1, anammox 0.2 μmol N m−2 h−1 to 5.7 μmol N m−2 h−1, and oxygen uptake 47 μmol O2 m−2 h−1 to 631 μmol O2 m−2 h−1. The seasonal patterns under ambient oxygen were correlated with those in the hypoxic treatment; though, on the whole, the magnitude of flux was different. On average, under hypoxia, both the penetration and consumption of oxygen decreased by ∼ 50%, denitrification increased by 32%, and anammox remained constant. Anammox accounted for between 10% and 20% of the total N2 production, which agrees with expectations for waters of these depths (30-80 m). Under ambient oxygen the sediments were strong sources of nitrate to the overlying water, 12 μmol NO−3 m−2 h−1 on average, but under hypoxia total N mineralization decreased by 46% and nitrate exchanged ceased. Short-term hypoxia alters the balance between available N returned to the overlying water, primarily as NO−3, and that removed from the ecosystem as N2 gas.
The supply and composition of organic matter control the processes by which fixed nitrogen is lost from the ocean.
A chemiluminescent analysis technique for the determination of nanomolar quantities of nitrate, nitrate plus nitrite or nitrite alone in seawater is described. The method depends on the selective reduction of these species to nitric oxide which is then determined by its chemiluminescent reaction with ozone, using a commercial nitrogen oxides analyzer. The necessary equipment is compact and sufficiently sturdy to allow shipboard use. A precision of ±2 nM is claimed with analytical rates of 10–12 samples h−1, and modifications are discussed to allow doubling the analytical rate.
Analysis suggests that feedbacks between carbon (C), nitrogen (N), and oxygen (O) cycles helped prevent the oxidation of Earth in the Paleoproterozic. This stabilizing feedback, which was ultimately overridden, led to the contemporary nitrogen cycle where nitrate, rather than ammonium, was the stable form of fixed inorganic nitrogen in the oceans. Barring some minor changes in the trace element composition in nitrogenases, the core proteins remained essentially unchanged following the transition to an oxidized atmosphere. In the contemporary ocean, approximately 20%-30% of nitrogenase activity is inhibited at any moment in time by O2. This inhibition results in a negative feedback which constrains the upper level of O2 on Earth. Three central aspects of cyanobacterial nitrogen fixation remain curious. First, although some trace elements have been altered in the evolution of nitrogenases, the core proteins have remained virtually unchanged. Second, while there is abundant evidence of lateral transfer of nitrogenase genes between prokaryotes, in the endosymbiotic appropriation of cyanobacteria into heterotrophic hosts to photosynthetic eukaryotes, nitrogenases were lost. Third, although free-living heterocystous cyanobacteria are abundant in lakes and brackish water ecosystems, they appear to be rare in the open ocean.
We quantified the removal of fixed nitrogen as N 2 production by anammox and N 2 and N 2 O production by denitrification over a distance of 1900 km along the coasts of Chile and Peru, using short-term incubations with 15 N-labeled substrates. The eastern South Pacific contains an oxygen minimum zone (OMZ) characterized by an anoxic, nitrate- and nitrite-rich layer of , 200-m thickness below 30–90 m of oxic water. Anammox and denitrification were almost exclusively recorded when the in situ O 2 concentration was below detection, indicating that the induction of these processes is highly oxygen sensitive. Anammox was detected in 70% of the samples from anoxic depths. Denitrification was detected in fewer samples, but maximum rates were an order of magnitude higher than those of anammox. In our incubations denitrification was responsible for 72% of the total N 2 production and 77% of the total removal of fixed nitrogen including N 2 O production. However, at the individual depths it could be one or the other process that was responsible for all of the nitrogen removal. Anammox activity was highest just below the oxic–anoxic interface and declined exponentially with depth, whereas no depth dependence was discerned for denitrification. Denitrification resulted in net production of N 2 O in some of the samples and consumption of added 15 N 2 O in others. Together with the accumulation of NO 2 - this indicates that denitrification must be seen as a sequence of individually regulated reactions, each of which may start and stop depending on the electron donor input, while anammox is much less variable. The highly patchy distribution of denitrification contributes to explain the apparent imbalances between ammonium sources and sinks suggested by previous 15 N-based studies in OMZs
We measured rates of N-2 production through anaerobic NH4+ oxidation with NO2- (anammox) and denitrification in permanently cold (from - 1.7degreesC to 4degreesC) sediments off the east and west coasts of Greenland. The investigated sites (36- to 100-m water depth) covered sediments in which carbon contents ranged from 0.3 to 3.2 dry weight O-2 uptake rates ranged from 3.4 to 8.3 mmol m(-1) d(-1), O-2 penetration depths ranged from 0.25 to 1.70 cm, and bottom-water NO3- concentrations ranged from 0.3 to 15.3 mumol L-1. Total N-2 production was 34-344 mumol N m(-2) d(-1), of which anammox accounted for 1-92 mumol N m(-1) d(-1) (1-35% of total) and denitrification for 33-265 mumol N m(-2) d(-1). At one of the high-Arctic sites, anammox activity had an optimum temperature (T-opt) of 12degreesC, while that of bacterial denitrification was 24degreesC. According to the classical temperature scheme for metabolic growth, the anammox response was psychrophilic, while denitrification was psychrotrophic. Although T-opt was considerably higher than in situ temperatures, rates of denitrification and anammox were still high at - 1.3degreesC, reaching 17% and 40%, respectively, of those found at T-opt. The activation energies, E-a, of anammox and denitrification were 51.0 and 60.6 kJ mo(-1), respectively, and the corresponding Q(10) values were 2.2 and 2.4. Rates of anammox were linearly correlated with bottom-water NO3- concentrations W = 0.96, p < 0.0001, n = 11) at the investigated sites. We suggest that the slow-growing anammox bacteria are favored in sediments with high and stable NO3- conditions. This may be a general pattern in deeper waters at other latitudes as well.
The significance of anaerobic ammonium oxidation (anammox) for nitrogen removal in deep continental margin sediments was studied with 15N amendments to suboxic sediments collected from 2800–3100-m water depth at eight sites in the Cascadia Basin (eastern North Pacific Ocean). Consistent with earlier data from deep continental margin sediments, pore-water distributions of inorganic N indicated NH4 removal from suboxic zone sediments, likely due to reaction with nitrate. Anammox rates estimated from suboxic sediment incubations with 15N-labled substrates ranged between 0.065 and 1.7 nmol N mL21 h21 (wet sediment), which suggested that anammox was responsible for the observed NH4 removal. Anammox and denitrification rates derived from NH4 and NO3 pore-water profiles were 32–82 mmol N m22 d21 and 50–110 mmol N m22 d21, respectively. The average contribution of anammox to total N2 production was 40% (15N-amended sediment incubations) to 42% (flux from pore-water inorganic N), which does not support earlier reports that suggested that the relative importance of anammox increased with water depth and thereby should dominate over denitrification at depths greater than 1000 m.
The respiratory reduction of nitrate (denitrification) is acknowledged as the most important process that converts biologically available nitrogen to gaseous dinitrogen (N2) in marine ecosystems. Recent findings, however, indicate that anaerobic ammonium oxidation by nitrite (anammox) may be an important pathway for N2 formation and N removal in coastal marine sediments and in anoxic water columns of the oceans. In the present study, we explored this novel mechanism during N mineralization by 15N amendments (single and coupled additions of 15NH4+, 14NO3− and 15NO3−) to surface sediments with a wide range of characteristics and overall reactivity. Patterns of 29/30N2 production in the pore water during closed sediment incubations demonstrated anammox at all 7 of the investigated sites. Stoichiometric calculations revealed that 4% to 79% of total N2 production was due to this novel route. The relative importance of anammox for N2 release was inversely correlated with remineralized solute production, benthic O2 consumption, and surface sediment Chl a. The observed correlations indicate competition between reductants for pore water nitrite during early diagenesis and that additional factors (e.g. availability of Mn-oxides), superimposed on overall patterns of diagenetic activity, are important for determining absolute and relative rates of anammox in coastal marine sediments.
A manual method for nitrate analysis that meets the objectives of accuracy, efficiency, and small sample volume is presented. Samples buffered at pH 8.5 are shaken for about 90 min with spongy cadmium. Nitrate is reduced to nitrite, which is analyzed colorimetrically. Sample-cadmium contact time is more consistently controlled for a large series of samples simultaneously than with a column method. Problems with progressive deterioration in reduction capacity encountered in column methods are avoided. Analyses of nitrate-spiked natural water samples (salinity 0–12%) yielded recoveries of 94–106%. The 95% confidence interval of the mean of 10 observations was 0.254 ± 0.011 μM NO3−, using a 10-cm optical path.
This paper presents the results of a study of benthic organic matter decomposition on the continental margin in the northwest Atlantic Ocean at 70°W, the same region that was studied as part of the SEEP-I project (Cont. Shelf Res. 8(5–7) (1988) 925). We collected all of our samples via submersible during July, 1996, and September, 1997. An extensive set of in situ microelectrode O2 profiles indicate that sedimentary O2 consumption was essentially constant at 50–55 μmol/cm2/yr from 460 to 1467 m water depth, with a lower rate in the coarser-grained sediments at 260 m. The O2 penetration depth increased steadily over the depth transect, from 1.0±0.1 cm at 260 m to 2.7±0.3 cm at 1467 m. The organic matter oxidation rate increased from ∼30 μmol/cm2/yr at 260 m to ∼42 μmol/cm2/yr over the 460–1035 m depth range, and decreased gradually below that to 32 μmol/cm2/yr at 2500 m. O2 was quantitatively the most important electron acceptor, accounting for 75–91% of organic matter oxidation, while denitrification accounted for 2–5% and iron and sulfate reduction 8–20%. A comparison with organic matter oxidation rates measured at the site of the mid-slope depocenter in the southern Mid-Atlantic Bight showed a north/south difference in benthic organic matter oxidation rates similar to that found in particle fluxes to the sea floor. Benthic organic carbon oxidation rates measured in the southern depocenter were 3–6 times the rates we measured at 70°W, while fluxes of total mass, organic carbon, and excess 210Pb were 3.4–4.6 times larger in the southern depocenter (Cont. Shelf Res. 8(5–7) (1988) 855; Deep-Sea Res. II 41 (1994) 459). Measurements of the enhancement of solute transport between sediments and bottom water, using Br− and the 222Rn deficit as tracers, indicated that sediment irrigation may enhance O2 exchange by 50–100% at 460 and 260 m, but is likely to be of limited significance at deeper water depths. In addition, enhanced solute exchange by irrigation may reduce net bottom water/sediment exchange of NO3− by as much as 50%, and may increase the denitrification rate by a similar amount at our 460 m site.
(USA) over the last half century. The traditional winter-spring bloom has decreased or, in many years, disappeared. Relatively short, often intense, diatom blooms have become common in spring, summer, and fall replacing the summer flagellate blooms of the past. The annual and summer mean abundance (cell counts) and biomass (chl a) of phytoplankton appear to have decreased based on almost 50 years of biweekly monitoring by others at a mid bay station. These changes have been related to warming of the water, especially during winter, and to increased cloudiness. A significant decline in the winter wind speed may also have played a role. The changes in the phenology of the phytoplankton and the oligotrophication of the bay appear to have decreased greatly the quantity and (perhaps) quality of the organic matter being deposited on the bottom of the bay. This decline has resulted in a very much reduced benthic metabolism as reflected in oxygen uptake, nutrient regeneration, and the magnitude and direction of the net flux of N(2) gas. Based an many decades of standard weekly trawls carried out by the Graduate School of Oceanography, the winter biomass of bottom feeding epibenthic animals has also declined sharply at the mid bay station. After decades of relatively constant anthropogenic nitrogen loading (and declining phosphorus loading), the fertilization of the bay will soon be reduced during May-October due to implementation of advanced wastewater treatment. This is intended to produce an oligotrophication of the urban Providence River estuary and the Upper Bay. The anticipated decline in the productivity of the upper bay region will probably decrease summer hypoxia in that area. However, it may have unanticipated consequences for secondary production in the mid and lower bay where climate-induced oligotrophication has already much weakened the historically strong benthic pelagic coupling.
For rate determinations of anaerobic metabolism it is essential to maintain strictly anoxic conditions throughout the experiment. However, even if oxygen contamination can be avoided while preparing the incubation containers, it is still possible that the incubation containers themselves contaminate the samples by oxygen diffusing from or through their plastic or rubber components. In this study, we investigated the sources and extent of oxygen contamination during anoxic incubations, and present solutions to minimize oxygen contamination. In particular, we investigated oxygen contamination in Labco® Exetainers, glass vials with a butyl rubber septum in the screw cap, which are frequently used in microbiological experiments. Our results show that significant oxygen contamination occurred at different stages during the incubation. Contamination occurred when Exetainers were either filled or incubated for more than 16h under oxic atmosphere, but also under an oxygen-free atmosphere due to diffusion of oxygen out of the butyl rubber septum. Therefore, to avoid oxygen contamination during incubations, we suggest (1) filling and incubating the incubation containers under anoxic atmosphere (glove bag) and (2) deoxygenating all elastomers in sample processing and incubation equipment. If initial oxygen contamination cannot be avoided, introduction of an anoxic headspace might help extract oxygen from the incubated sample and present a buffer against oxygen diffusing out of the septum. We modeled the amount of oxygen diffusing out of butyl rubber septa under different conditions, and results fitted well with the observed oxygen contamination. Thus, the model can be used to predict oxygen contamination under varying conditions and for differently sized septa.
Anammox, anaerobic ammonium oxidation with nitrite, is now recognized as an important process in the marine nitrogen cycle. The bacteria conducting anammox are highly specialized and appear to belong to the Planctomycetales. The process has now been found in a range of environments including marine sediments, sea ice and anoxic water columns, and it may be responsible for up to 50% of the global removal of fixed nitrogen from the oceans.
Anaerobic ammonium-oxidizing (anammox) bacteria oxidize ammonium with nitrite and produce N(2). They reside in many natural ecosystems and contribute significantly to the cycling of marine nitrogen. Anammox bacteria generally live under ammonium limitation, and it was assumed that in nature anammox bacteria depend on other biochemical processes for ammonium. In this study we investigated the possibility of dissimilatory nitrate reduction to ammonium by anammox bacteria. Physically purified Kuenenia stuttgartiensis cells reduced (15)NO(3) (-) to (15)NH(4) (+) via (15)NO(2) (-) as the intermediate. This was followed by the anaerobic oxidation of the produced ammonium and nitrite. The overall end-product of this metabolism of anammox bacteria was (15)N(15)N dinitrogen gas. The nitrate reduction to nitrite proceeds at a rate of 0.3 +/- 0.02 fmol cell(-1) day(-1) (10% of the 'normal' anammox rate). A calcium-dependent cytochrome c protein with a high (305 mumol min(-1) mg protein(-1)) rate of nitrite reduction to ammonium was partially purified. We present evidence that dissimilatory nitrate reduction to ammonium occurs in Benguela upwelling system at the same site where anammox bacteria were previously detected. This indicates that anammox bacteria could be mediating dissimilatory nitrate reduction to ammonium in natural ecosystems.
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