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- De Brabandere, L., et al.
(författare)
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Oxygenation of an anoxic fjord basin strongly stimulates benthic denitrification and DNRA
- 2015
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Ingår i: Biogeochemistry. - : Springer Science and Business Media LLC. - 0168-2563 .- 1573-515X. ; 126:1, s. 131-152
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Tidskriftsartikel (refereegranskat)abstract
- © 2015 Springer International Publishing Switzerland Hypoxia hampers eutrophication reduction efforts by enabling high nutrient fluxes from sediment to bottom waters. Oxygenation of hypoxic water bodies is often proposed to reduce benthic ammonium and phosphate release. This study investigates the functional response of benthic nitrate-reducing processes to a long-term engineered oxygenation effort in a density-stratified fjord with euxinic bottom waters. Oxygenation was achieved by mixing surface water with deep, euxinic water, which increased oxygen and nitrate concentrations in the deep water column. The presence of nitrate instigated benthic nitrate reduction in the newly oxidized sediments by equally stimulating denitrification and dissimilatory nitrate reduction to ammonium (DNRA). DNRA and total nitrate reduction rates, as well as the contribution of DNRA to total nitrate reduction, decreased with increasing exposure time of the sediments to oxygen. The relative importance of DNRA as a nitrate sink was correlated to nitrate concentrations, with more nitrate being reduced to ammonium at higher bottom water nitrate concentrations. Overall, engineered oxygenation decreased the net efflux of dissolved inorganic nitrogen from the sediments by stimulating net nitrate removal through denitrification.
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- Hulth, Stefan, 1965, et al.
(författare)
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Nitrogen removal in marine environments: recent findings and future research challenges
- 2005
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Ingår i: Marine Chemistry. - : Elsevier BV. - 0304-4203. ; 94:1-4, s. 125-145
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Tidskriftsartikel (refereegranskat)abstract
- Respiratory reduction of nitrate (denitrification) is recognized as the most important process converting biologically available (fixed) nitrogen to N-2. In current N cycle models, a major proportion of global marine denitrification (50-70%) is assumed to take place on the sea floor, particularly in organic rich continental margin sediments. Recent observations indicate that present conceptual views of denitrification and pathways of nitrate reduction and N, formation are incomplete. Alternative N cycle pathways, particularly in sediments. include anaerobic ammonium oxidation to nitrite, nitrate and N-2 by Mn-oxides, and anaerobic ammonium oxidation coupled to nitrite reduction and subsequent N, mobilization. The discovery of new links and feedback mechanisms between the redox cycles of, e.g., C, N, S, Mn and Fe casts doubt on the present general understanding of the global N cycle. Recent models of the oceanic N budget indicate that total inputs are significantly smaller than estimated fixed N removal. The occurrence of alternative N reaction pathways further exacerbates the apparent imbalance as they introduce additional routes of N removal. In this contribution, we give a brief historical background of the conceptual understanding of N cycling in marine ecosystems, emphasizing pathways of aerobic and anaerobic N mineralization in marine sediments, and the implications of recently recognized metabolic pathways for N removal in marine environments. (c) 2004 Elsevier B.V. All rights reserved.
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- Kruger, M., et al.
(författare)
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Differential contribution of nitrifying prokaryotes to groundwater nitrification
- 2023
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Ingår i: ISME Journal. - 1751-7362. ; 17, s. 1601-1611
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Tidskriftsartikel (refereegranskat)abstract
- The ecophysiology of complete ammonia-oxidizing bacteria (CMX) of the genus Nitrospira and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the specific contribution of their activity to nitrification processes has remained unclear. We aimed to disentangle the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen in oligotrophic carbonate rock aquifers. CMX ammonia monooxygenase sub-unit A (amoA) genes accounted on average for 16 to 75% of the total groundwater amoA genes detected. Nitrification rates were positively correlated to CMX clade A associated phylotypes and AOB affiliated with Nitrosomonas ureae. Short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed a large fraction to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOB and AOA was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater appears to be primarily governed by AOB. Higher growth yields at lower ammonia turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations.
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- Muratore, D., et al.
(författare)
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Microbial and Viral Genome and Proteome Nitrogen Demand Varies across Multiple Spatial Scales within a Marine Oxygen Minimum Zone
- 2023
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Ingår i: Msystems. - : American Society for Microbiology. - 2379-5077. ; 8:2
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Tidskriftsartikel (refereegranskat)abstract
- The genomes of marine microbes can be shaped by nutrient cycles, with ocean-scale gradients in nitrogen availability being known to influence microbial amino acid usage. It is unclear, however, how genomic properties are shaped by nutrient changes over much smaller spatial scales, for example, along the vertical transition into oxygen minimum zones (OMZs) or from the exterior to the interior of detrital particles. Nutrient availability can significantly influence microbial genomic and proteomic streamlining, for example, by selecting for lower nitrogen to carbon ratios. Oligotrophic open ocean microbes have streamlined genomic nitrogen requirements relative to those of their counterparts in nutrient-rich coastal waters. However, steep gradients in nutrient availability occur at meter-level, and even micron-level, spatial scales. It is unclear whether such gradients also structure genomic and proteomic stoichiometry. Focusing on the eastern tropical North Pacific oxygen minimum zone (OMZ), we use comparative metagenomics to examine how nitrogen availability shapes microbial and viral genome properties along the vertical gradient across the OMZ and between two size fractions, distinguishing free-living microbes versus particle-associated microbes. We find a substantial increase in the nitrogen content of encoded proteins in particle-associated over free-living bacteria and archaea across nitrogen availability regimes over depth. Within each size fraction, we find that bacterial and viral genomic nitrogen tends to increase with increasing nitrate concentrations with depth. In contrast to cellular genes, the nitrogen content of virus proteins does not differ between size fractions. We identified arginine as a key amino acid in the modulation of the C:N ratios of core genes for bacteria, archaea, and viruses. Functional analysis reveals that particle-associated bacterial metagenomes are enriched for genes that are involved in arginine metabolism and organic nitrogen compound catabolism. Our results are consistent with nitrogen streamlining in both cellular and viral genomes on spatial scales of meters to microns. These effects are similar in magnitude to those previously reported across scales of thousands of kilometers.IMPORTANCE The genomes of marine microbes can be shaped by nutrient cycles, with ocean-scale gradients in nitrogen availability being known to influence microbial amino acid usage. It is unclear, however, how genomic properties are shaped by nutrient changes over much smaller spatial scales, for example, along the vertical transition into oxygen minimum zones (OMZs) or from the exterior to the interior of detrital particles. Here, we measure protein nitrogen usage by marine bacteria, archaea, and viruses by using metagenomes from the nitracline of the eastern tropical North Pacific OMZ, including both particle-associated and nonassociated biomass. Our results show higher genomic and proteomic nitrogen content in particle-associated microbes and at depths with higher nitrogen availability for cellular and viral genomes. This discovery suggests that stoichiometry influences microbial and viral evolution across multiple scales, including the micrometer to millimeter scale associated with particle-associated versus free-living lifestyles.
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- Schmid, M. C., et al.
(författare)
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Anaerobic ammonium-oxidizing bacteria in marine environments: widespread occurrence but low diversity
- 2007
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 9:6, s. 1476-1484
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Tidskriftsartikel (refereegranskat)abstract
- Laboratory and field studies have indicated that anaerobic ammonium oxidation (anammox) is an important process in the marine nitrogen cycle. In this study 11 additional anoxic marine sediment and water column samples were studied to substantiate this claim. In a combined approach using the molecular methods, polymerase chain reaction (PCR), qualitative and quantitative fluorescence in situ hybridization (FISH), as well as N-15 stable isotope activity measurements, it was shown that anammox bacteria were present and active in all samples investigated. The anammox activity measured in the sediment samples ranged from 0.08 fmol cell(-1) day(-1) N-2 in the Golfo Dulce (Pacific Ocean, Costa Rica) sediment to 0.98 fmol cell(-1) day(-1) N-2 in the Gullmarsfjorden (North Sea, Sweden) sediment. The percentage of anammox cell of the total population (stained with DAPI) as assessed by quantitative FISH was highest in the Barents Sea (9% +/- 4%) and in most of the samples well over 2%. Fluorescence in situ hybridization and phylogenetic analysis of the PCR products derived from the marine samples indicated the exclusive presence of members of the Candidatus 'Scalindua' genus. This study showed the ubiquitous presence of anammox bacteria in anoxic marine ecosystems, supporting previous observations on the importance of anammox for N cycling in marine environments.
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- Trimmer, M., et al.
(författare)
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Stark Contrast in Denitrification and Anammox across the Deep Norwegian Trench in the Skagerrak
- 2013
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Ingår i: Applied and Environmental Microbiology. - : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 79:23, s. 7381-7389
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Tidskriftsartikel (refereegranskat)abstract
- Environmental anaerobic ammonium oxidation (anammox) was demonstrated for the first time in 2002, using N-15 labeling, in homogenized sediment from the Skagerrak, where it accounted for up to 67% of N-2 production. We returned to some of these original sites in 2010 to make measurements of nitrogen and carbon cycling under conditions more representative of those in situ, quantifying anammox and denitrification, together with oxygen penetration and consumption, in intact sediment cores. Overall, oxygen consumption and N-2 production decayed with water depth, as expected, but the drop in N-2 production was relatively more pronounced. Whereas we confirmed the dominance of N-2 production by anammox (72% and 77%) at the two deepest sites (similar to 700 m of water), anammox was conspicuously absent from two shallower sites (similar to 200 m and 400 m). At the shallower sites, we could measure no anammox activity with either intact or homogeneous sediment, and quantitative PCR (16S rRNA) gave a negligible abundance of anammox bacteria in the anoxic layers. Such an absence of anammox, especially at one locale where it was originally demonstrated, is hard to reconcile. Despite the dominance of anammox at the deepest sites, anammox activity could not make up for the drop in denitrification, and assuming Redfield ratios for the organic matter being mineralized, the estimated retention of fixed N actually increased to 90% to 97% of that mineralized, whereas it was 80% to 86% at the shallower sites.
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