ALBERT

Description: Permafrost-affected landscape soils are rich in organic matter and contain a high fraction of organic nitrogen, but much of this organic matter remains inaccessible due to nitrogen limitation. Microbial nitrification is a key process in the nitrogen cycle, controlling the availability of dissolved inorganic nitrogen (DIN) such as ammonium and nitrate. In this study, we investigate the microbial diversity of canonical nitrifiers and their potential nitrifying activity in the active layer of different Arctic cryosols in the Lena River Delta in North-East Siberia. These cryosols are located on Samoylov Island, which has two geomorphological landscapes with mineral soils in the modern floodplain and organic-rich soils in the low-centered polygonal tundra of the Holocene river terrace. Microcosm incubations show that the highest potential ammonia oxidation rates are found in low organic soils, and the rates depend on organic matter content and quality, vegetation cover, and water content. As shown by 16S rRNA amplicon sequencing, nitrifiers represented 0.6% to 6.2% of the total microbial community. More than 50% of the nitrifiers belonged to the genus Nitrosospira. Based on PCR amoA analysis, ammonia-oxidizing bacteria (AOB) were found in nearly all soil types, whereas ammonia-oxidizing archaea (AOA) were only detected in low-organic soils. In cultivation-based approaches, mainly Nitrosospira-like AOB were enriched and characterized as psychrotolerant, with temperature optima slightly above 20 °C. This study suggests a ubiquitous distribution of ammonia-oxidizing microorganisms (bacteria and archaea) in permafrost-affected landscapes of Siberia with cold-adapted AOB, especially of the genus Nitrosospira, as potentially crucial ammonia oxidizers in the cryosols.

Description: In this study, we investigate the role of sedimentary N cycling in the Southern North Sea. We present a budget of ammonification, nitrification and sedimentary NO3− consumption/denitrification in contrasting sediment types of the German Bight (Southern North Sea), including novel net ammonification rates. Dissolved inorganic nitrogen concentration (nitrate, nitrite and ammonium) in the water column showed low levels between 0.2 to 3.2 µmol L−1. We incubated sediment cores with labeled nitrate and ammonium to calculate net and gross N transformation rates. The results show that impermeable sediments are the main site of ammonification (on average 10.2 ± 1.2 mmol m−2 d−1) and that they are an important source for primary producers in the water column, contributing ~ 17 to 61 % of reactive nitrogen in the water column. Ammonification and oxygen penetration depth are the main drivers of sedimentary nitrification. One third of freshly produced nitrate in impermeable sediment and two-thirds in permeable sediment were reduced to N2. The semi-permeable and permeable sediments are responsible for ~ 80 % of the total benthic N2 production rates (~ 890 t N d−1) in the southern North Sea. We conclude that impermeable sediments are important sources of reactive N and that semi-permeable and permeable sediments are the main sinks of reactive N, counteracting eutrophication in the southern North Sea (German Bight).

Description: In oceans, estuaries, and rivers, nitrification is an important nitrate source, and stable isotopes of nitrate are often used to investigate recycling processes in the water column. The bulk isotope effect of nitrification is hard to predict: It is a two-step-process, where ammonia is oxidized via nitrite to nitrate. Nitrite usually does not accumulate in natural environments, which makes it even more difficult to unravel the divergent isotope effects of both processes. However, during an exceptional flood in the Elbe River in June 2013, ammonium and nitrite accumulated in the water column for a short period, returning towards normal summer conditions within one week. Concentrations were sufficient for the analysis of δ15N-NH4+ and δ15N-NO2− evolution, which has not been studied before in a major European river like the Elbe River. In the concert with changes in SPM and δ15N-SPM, as well as nitrate concentration, δ15N-NO3− and δ18O-NO3−, we calculated the isotope fractionation effect during nitrification. We found that in the water column, ammonium and nitrite derived from internal recycling processes, whereas nitrate mainly leached from catchment area. Ammonium and nitrite concentrations increased to 3.4 µmol L−1 and 4.5 µmol L−1, respectively, due to remineralization and ammonium oxidation in the water column. δ15N-NH4+ values increased up to 12 ‰, and δ15N-NO2− ranged from −8.0 ‰ to −14.2 ‰. As water column nitrite concentration decreased, we calculated an isotope effect 15ε of −9.3 ‰ for nitrite oxidation. This isotope effect does not correspond to the inverse isotope fractionation with a positive 15ε proposed by pure culture studies. We hypothesize that the molecular mechanisms that lead to inverse fractionation also apply in natural environments, but that the resulting trend in δ15N-NO2− in this natural environment is masked by dilution with fresh nitrite stemming from ammonium oxidation. Our data are a first approximation of the isotope effect of nitrite oxidation in natural environments and highlight that pure culture results cannot readily be extrapolated to natural microbial assemblages or water bodies.

Description: In oceans, estuaries, and rivers, nitrification is an important nitrate source, and stable isotopes of nitrate are often used to investigate recycling processes (e.g. remineralisation, nitrification) in the water column. Nitrification is a two-step process, where ammonia is oxidised via nitrite to nitrate. Nitrite usually does not accumulate in natural environments, which makes it difficult to study the single isotope effect of ammonia oxidation or nitrite oxidation in natural systems. However, during an exceptional flood in the Elbe River in June 2013, we found a unique co-occurrence of ammonium, nitrite, and nitrate in the water column, returning towards normal summer conditions within 1 week. Over the course of the flood, we analysed the evolution of δ15N–NH4+ and δ15N–NO2− in the Elbe River. In concert with changes in suspended particulate matter (SPM) and δ15N SPM, as well as nitrate concentration, δ15N–NO3− and δ18O–NO3−, we calculated apparent isotope effects during net nitrite and nitrate consumption. During the flood event, 〉 97 % of total reactive nitrogen was nitrate, which was leached from the catchment area and appeared to be subject to assimilation. Ammonium and nitrite concentrations increased to 3.4 and 4.4 µmol L−1, respectively, likely due to remineralisation, nitrification, and denitrification in the water column. δ15N–NH4+ values increased up to 12 ‰, and δ15N–NO2− ranged from −8.0 to −14.2 ‰. Based on this, we calculated an apparent isotope effect 15ε of −10.0 ± 0.1 ‰ during net nitrite consumption, as well as an isotope effect 15ε of −4.0 ± 0.1 ‰ and 18ε of −5.3 ± 0.1 ‰ during net nitrate consumption. On the basis of the observed nitrite isotope changes, we evaluated different nitrite uptake processes in a simple box model. We found that a regime of combined riparian denitrification and 22 to 36 % nitrification fits best with measured data for the nitrite concentration decrease and isotope increase.

Description: The study addresses the nitrogen cycling in Elbe estuary. Observations of salinity, nutrients and oxygen from moored stations, ship casts and helicopter surveys are presented. Observations are complemented by simulations obtained from a coupled physical-biogeochemical 3D unstructured model, applied for the first time to the estuarine environment. Model simulations reproduce the temporal variability of nutrients and oxygen along the estuarine salinity gradient. Both, observations and model results, demonstrate mostly conservative mixing of nitrate and non-conservative behavior of ammonium. Model hind-casts of the years 2012 and 2013 provide a detailed reconstruction of nitrogen recycling with ammonium appearing as the key species of the remineralisation process. Estuarine turnover processes are fueled by inputs of diatoms and organic nitrogen at the tidal weir with intense primary production manifest in the shallow river section downstream of the weir. The harbor area is the hot spot of heterotrophic decay associated with growth of meso-zooplankton, sedimentation of degradable material, remineralisation, oxygen depletion, denitrification and ammonium production. In the harbor, biochemistry shows strong vertical gradients while hydrodynamics demonstrate connectivity between the main channel and the harbor. At the estuary bed nitrogen is deposited during spring and early summer. Resuspension leads to nearly closed budget by the end of the year. During the Elbe flood in June 2013, estuarine biogeochemistry is significantly disturbed with the harbor being deactivated as hot spot of heterotrophic decay. Plankton and organic matter are flushed towards the outer estuary which in consequence sees high abundance of grazers, oxygen depletion and elevated release of ammonium.

Description: Recent studies on permafrost organic matter (OM) suggest that a portion of previously frozen carbon will enter the active carbon cycle as high latitudes warm. Less is known about the fate of other OM components, including nutrients such as nitrogen (N). The abundance and availability of N following permafrost thaw will regulate the ability of plants to offset carbon losses. Additionally, lateral N losses could alter aquatic food webs. There is growing evidence that some N is lost vertically as N2O, a greenhouse gas 300 times stronger than CO2 over 100 years. Despite broad recognition of its role regulating both carbon and non-carbon aspects of the permafrost climate feedback, estimates of permafrost N remain uncertain. To address this knowledge gap, we quantified N content for different stratigraphic units, including yedoma, Holocene cover deposits, refrozen thermokarst deposits, taberal sediments, and active layer soils. The resulting N estimates from this one permafrost region were similar in magnitude to previous estimates for the entire permafrost zone. We conclude that the permafrost N pool is much larger than currently appreciated and a substantial pool of permafrost N could be mobilized after thaw, with continental-scale consequences for biogeochemical budgets and global-scale consequences.

Description: Fossil organic matter (OM) stored in permafrost is an important subject in climate research. Such OM represents a huge reservoir of carbon (C). Multiple studies suggest its source potential for C release into the active C cycle through permafrost thaw and subsequent microbial turnover in a warming Arctic. However, net ecosystem OM balance in the permafrost region depends on more than just carbon. The abundance and availability of nitrogen (N) following permafrost thaw will influence plant growth, nutrient delivery to aquatic and estuarine ecosystems, and N oxide (N2O) emissions. Despite its central importance to predicting permafrost impacts and feedbacks to climate change, relatively little is known about permafrost N stocks and composition. In this study, we present the most extensive dataset to date of permafrost N in the Siberian and Alaskan Yedoma domain. The Yedoma domain comprises decameter thick ice-rich silts intersected by syngenetic ice wedges, which formed in late Pleistocene tundra-steppe environments, as well as other deposits resulting from permafrost degradation during the Holocene. Together, the deposits in this region constitute a large C inventory storing several hundred Gt C, but are also known to be nutrient-rich due to rapid burial and freezing of plant remains. Hitherto, the total organic C pool of the Yedoma region was quantified, while the total N inventory is lacking so far. Based on the most comprehensive data set of N content in permafrost to date, our study aims to estimate the present pool of N stored in the different stratigraphic units of the Yedoma domain: 1) late Pleistocene Yedoma deposits, 2) in-situ thawed and diagenetically altered Yedoma deposits (taberite), 3) Holocene thermokarst deposits, 4) Holocene cover deposits on top of Yedoma, and 5) the modern active layer of soils. To quantify measurement uncertainty, we estimated nitrogen stocks with bootstrapping techniques. We show that the deposits of the Yedoma region store a substantial pool of N that is expected to get mobilized after thaw and, at least partially, affecting biogeochemical budgets of thawing warming permafrost ecosystems.