Genera-specific immunofluorescence labeling of ammonia oxidizers with polyclonal antibodies recognizing both subunits of the ammonia monooxygenase

Polyclonal antibodies that recognize the two subunits AmoA and AmoB of the ammonia monooxygenase (AMO) were applied to identify ammonia-oxidizing bacteria by immunofluorescence (IF) labeling in pure, mixed, and enriched cultures. The antibodies against the AmoA were produced using a synthetic peptide of the AmoA of Nitrosomonas eutropha, whereas the antibodies against the AmoB had been developed previously is against the whole B-subunit of the AMO [Pinck et al. (2001) Appl Environ Microbiol 67:118–124]. Using IF labeling, the AmoA antibodies were specific for the detection of all species of the genus Nitrosomonas. In contrast, the antiserum against AmoB labeled all genera of ammonia oxidizers of the β-subclass of Proteobacteria (Nitrosomonas, Nitrosospira, Nitrosolobus, and Nitrosovibrio). The fluorescence signals of the AmoA antibodies were spread all over the cells, whereas the signals of the AmoB antibodies were associated with the cytoplasmic membranes. The specificity of the reactions of the antisera with ammonia oxidizers were proven in pure and mixed cultures, and the characteristic IF labeling and the morphology of the cells enabled their identification at the genus level. The genus-specific IF labeling could be used to identify ammonia oxidizers enriched from various habitats. In enrichment cultures of natural sandstone, cells of the genera Nitrosomonas, Nitrosovibrio, and Nitrosospira were detected. Members of the genus Nitrosovibrio and Nitrosolobus were most prominent in enriched garden soil samples, whereas members of the genus Nitrosomonas dominated in enriched activated sludge. The antibodies caused only slight background fluorescence on sandstone and soil particles compared to oligonucleotide probes, which could not be used to detect ammonia oxidizers on these materials because of strong nonspecific fluorescence

Optimisation of bioscrubber systems to simultaneously remove methane and purify wastewater from intensive pig farms

The use of bioscrubber is attracting increasing attention for exhaust gas treatment in intensive pig farming. However, the challenge is to improve the methane (CH4) removal efficiency as well as the possibility of pig house wastewater treatment. Three laboratory-scale bioscrubbers, each equipped with different recirculation water types, livestock wastewater (10-times-diluted pig house wastewater supernatant), a methanotroph growth medium (10-times-diluted), and tap water, were established to evaluate the performance of CH4 removal and wastewater treatment. The results showed that enhanced CH4 removal efficiency (25%) can be rapidly achieved with improved methanotrophic activity due to extra nutrient support from the wastewater. The majority of the CH4 was removed in the middle to end part of the bioscrubbers, which indicated that CH4 removal could be potentially optimised by extending the length of the reactor. Moreover, 52–86% of the ammonium (NH4+-N), total organic carbon (TOC), and phosphate (PO43−-P) removal were simultaneously achieved with CH4 removal in the present study. Based on these results, this study introduces a low-cost and simple-to-operate method to improve CH4 removal and simultaneously treat pig farm wastewater in bioscrubbers

Nitrogen isotopic inventory of the Lena River Delta

Permafrost-affected soils around the Arctic Ocean contain a large reservoir of organic matter including nitrogen, which partly reach the river after thawing, degradation and erosion of permafrost. After mobilization, reactive remineralised nitrogen is either used for primary production, microbial processing or is simply transported to coastal waters. We have analyzed soil, suspended matter and dissolved inorganic and organic nitrogen for their contents and 15N stable isotope composition to create a baseline for a nitrogen inventory of the Lena River Delta in 2019/2020. We used samples from two transect cruises through the delta in March and August 2019, a monitoring program at Samoylov Island in the central delta (2019/2020), and different soil type samples from Samoylov Island. Our data shows that the nitrogen transported from the delta to the Laptev Sea were dominated by dissolved organic nitrogen (DON) and nitrate, which occur in similar amounts of approx. 10 μmol/L. DON was available during the whole year. Nitrate showed a clear seasonal pattern: increase from late summer until the spring flood, during summer the nitrate concentration are close to zero. During the spring flood the nitrogen concentration are higher with up to 100 μmol/L. The nitrogen stable isotope values of the different nitrogen components ranges mainly between 0.5 and 4.5‰, and were subsequently enriched from the soils via suspended particulate matter (SPM)/sediment and DON to nitrate. During the spring flood, the stable isotope signature of nitrate suggested a strong source of atmospheric deposition. The 15N values are depleted with appox. -8‰ and the 18O values are enriched up to 60‰. Our data provides a baseline for isoscape analysis and can be used as an endmember signal for modeling approaches

Permafrost land-ocean interactions: fluxes, transport processes and degradation pathways

Permafrost-affected soils around the Arctic Ocean contain a large reservoir of organic matter including nitrogen, which partly reaches the riverine system after thawing, degradation and erosion of permafrost. After mobilization, reactive nitrogen in form of dissolved organic nitrogen (DON) ordissolved inorganic nitrogen (DIN: ammonium and nitrate) is either used for primary production, microbial turnover and/or is transported to coastal waters where it serves as a key source of nutrition for the marine food web. In this study, we have followed the nitrogen released from permafrost soil via the Lena River into the Laptev Sea and used the natural abundance of 15N stable isotopes to identify sources, sinks and processes. Therefore, we have investigated different soil. We present a comprehensive data set from two transect cruises (03/08 2019) through the delta, and the outcome of a monitoring program (2018 - 2021) at Samoylov Island in the central delta. High-frequency monitoring and cruise data shows that the nitrogen transported from the river to the Laptev Sea was dominated by DON and nitrate, which occurred in similar amounts of approx. 10 μmol L–1 in the river water. The nitrate concentration decreased during the early summer and increased from late summer throughout the winter until the spring flood. During the spring flood, the nitrogen concentration was up to ten times higher. Thus, spring floods transport approx. 20 % of the annual load of reactive nitrogen into the Laptev Sea just at the onset of the growing season. The nitrogen stable isotope values of the different nitrogen components ranged mainly between 0.5 and 4.5‰, and were subsequently enriched from the permafrost soils via suspended particulate matter/sediment and DON to nitrate, which indicate an oligotrophic ecosystem. Using a Bayesian mixing model, the stable isotope signature of nitrate suggested a strong source of atmospheric deposition during the spring flood. During the rest of the year, soils are the main source of the reactive nitrogen, which is transported to the marine realm

Permafrost Thaw and Liberation of Inorganic Nitrogen in Eastern Siberia

The currently observed climate warming will lead to widespread degradation of near-surface permafrost, which may release substantial amounts of inorganic nitrogen (N) into arctic ecosystems. We studied 11 soil profiles at three different sites in arctic eastern Siberia to assess the amount of inorganic N stored in arctic permafrost soils. We modelled the potential thickening of the active layer for these sites using the CryoGrid2 permafrost model and representative concentration pathways (RCPs) 4.5 (a stabilisation scenario) and 8.5 (a business as usual emission scenario, with increasing carbon emissions). The modelled increases in active-layer thickness (ALT) were used to estimate potential annual liberation of inorganic N from permafrost soils during the course of climate change. We observed significant stores of inorganic ammonium in permafrost, up to 40-fold higher than in the active layer. The modelled increase in ALT under the RCP8.5 scenario can result in substantial liberation of N, reaching values up to the order of magnitude of annual fixation of atmospheric N in arctic soils. However, the thaw-induced liberation of N represents only a small flux in comparison with the overall ecosystem N cycling

Permafrost thaw and release of inorganic nitrogen from polygonal tundra soils in eastern Siberia

The currently observed climate warming will lead to substantial permafrost degradation and mobilization of formerly freeze-locked matter. Based on recent findings, we assume that there are substantial stocks of inorganic nitrogen (N) within the perennially frozen ground of arctic ecosystems. We studied eleven soil profiles down to one meter depth below surface at three different sites in arctic eastern Siberia, covering polygonal tundra and river floodplains, to assess the amount of inorganic N stores in arctic permafrost-affected soils. Furthermore, we modeled the potential thickening of the seasonally unfrozen uppermost soil (active) layer for these sites, using the CryoGrid2 permafrost model and representation concentration pathway (RCP) 4.5 and 8.5 scenarios. The first scenario, RCP4.5, is a stabilization pathway that reaches plateau atmospheric carbon concentrations early in the 21st century; the second, RCP8.5, is a business as usual emission scenario with increasing carbon emissions. The modeled increases in active layer thickness (ALT) were used to estimate potential annual N mobilization from permafrost-affected soils in the course of climate-induced active-layer deepening. We observed significant stores of inorganic ammonium in the perennially frozen ground of all investigated soils, up to 40-fold higher than in the active layer. The modeled ALT increase until 2100 under the RCP8.5 scenario was between 19 ± 3 cm and 35 ± 6 cm, depending on the location. Under the RCP4.5 scenario, the ALT remained stable in all investigated soils. Our estimated mean annual N release under the RCP8.5 scenario is between 8 ± 3 mg m−2 and 81 ± 14 mg m−2 for the different locations, which reaches values up to the order of magnitude of annual fixation of atmospheric N in arctic soils. However, the thawing induced release of N represents only a small flux in comparison with the overall ecosystem N cycling

Seasonal nitrogen fluxes of the Lena River Delta

The Arctic is nutrient limited, particularly by nitrogen, and is impacted by anthropogenic global warming which occurs approximately twice as fast compared to the global average. Arctic warming intensifies thawing of permafrost-affected soils releasing their large organic nitrogen reservoir. This organic nitrogen reaches hydrological systems, is remineralized to reactive inorganic nitrogen, and is transported to the Arctic Ocean via large rivers. We estimate the load of nitrogen supplied from terrestrial sources into the Arctic Ocean by sampling in the Lena River and its Delta. We took water samples along one of the major deltaic channels in winter and summer in 2019 and sampling station in the central delta over a one-year cycle. Additionally, we investigate the potential release of reactive nitrogen, including nitrous oxide from soils in the Delta. We found that the Lena transported nitrogen as dissolved organic nitrogen to the coastal Arctic Ocean and that eroded soils are sources of reactive inorganic nitrogen such as ammonium and nitrate. The Lena and the Deltaic region apparently are considerable sources of nitrogen to nearshore coastal zone. The potential higher availability of inorganic nitrogen might be a source to enhance nitrous oxide emissions from terrestrial and aquatic sources to the atmosphere

Ammonia oxidation: Ecology, physiology, biochemistry and why they must all come together

Ammonia oxidation is a fundamental core process in the global biogeochemical nitrogen cycle. Oxidation of ammonia (NH3) to nitrite (NO2 −) is the first and rate-limiting step in nitrification and is carried out by distinct groups of microorganisms. Ammonia oxidation is essential for nutrient turnover in most terrestrial, aquatic and engineered ecosystems and plays a major role, both directly and indirectly, in greenhouse gas production and environmental damage. Although ammonia oxidation has been studied for over a century, this research field has been galvanised in the past decade by the surprising discoveries of novel ammonia oxidising microorganisms. This review reflects on the ammonia oxidation research to date and discusses the major gaps remaining in our knowledge of the biology of ammonia oxidation

The pH dependency of N-converting enzymatic processes, pathways and microbes: effect on net N₂O production

Nitrous oxide (N2O) is emitted during microbiological nitrogen (N) conversion processes, when N2O production exceeds N2O consumption. The magnitude of N2O production vs. consumption varies with pH and controlling net N2O production might be feasible by choice of system pH. This article reviews how pH affects enzymes, pathways and microorganisms that are involved in N-conversions in water engineering applications. At a molecular level, pH affects activity of cofactors and structural elements of relevant enzymes by protonation or deprotonation of amino acid residues or solvent ligands, thus causing steric changes in catalytic sites or proton/electron transfer routes that alter the enzymes' overall activity. Augmenting molecular information with, e.g., nitritation or denitrification rates yields explanations of changes in net N2O production with pH. Ammonia oxidizing bacteria are of highest relevance for N2O production, while heterotrophic denitrifiers are relevant for N2O consumption at pH > 7.5. Net N2O production in N-cycling water engineering systems is predicted to display a ‘bell-shaped’ curve in the range of pH 6.0–9.0 with a maximum at pH 7.0–7.5. Net N2O production at acidic pH is dominated by N2O production, whereas N2O consumption can outweigh production at alkaline pH. Thus, pH 8.0 may be a favourable pH set-point for water treatment applications regarding net N2O production