| 1. |
- Ahmed, Engy, et al.
(författare)
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Mineral Type Structures Soil Microbial Communities
- 2017
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Ingår i: Geomicrobiology Journal. - : Taylor & Francis. - 0149-0451 .- 1521-0529. ; 34:6, s. 538-545
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Tidskriftsartikel (refereegranskat)abstract
- Soil microorganisms living in close contact with minerals play key roles in the biogeochemical cycling of elements, soil formation, and plant nutrition. Yet, the composition of microbial communities inhabiting the mineralosphere (i.e., the soil surrounding minerals) is poorly understood. Here, we explored the composition of soil microbial communities associated with different types of minerals in various soil horizons. To this effect, a field experiment was set up in which mineral specimens of apatite, biotite, and oligoclase were buried in the organic, eluvial, and upper illuvial horizons of a podzol soil. After an incubation period of two years, the soil attached to the mineral surfaces was collected, and microbial communities were analyzed by means of Illumina MiSeq sequencing of the 16S (prokaryotic) and 18S (eukaryotic) ribosomal RNA genes. We found that both composition and diversity of bacterial, archaeal, and fungal communities varied across the different mineral surfaces, and that mineral type had a greater influence on structuring microbial assemblages than soil horizon. Thus, our findings emphasize the importance of mineral surfaces as ecological niches in soils.
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| 2. |
- Bergkvist, Johanna, 1980, et al.
(författare)
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Turbulence simultaneously stimulates small- and large-scale CO2 sequestration by chain-forming diatoms in the sea
- 2018
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Chain-forming diatoms are key CO2-fixing organisms in the ocean. Under turbulent conditions they form fast-sinking aggregates that are exported from the upper sunlit ocean to the ocean interior. A decade-old paradigm states that primary production in chain-forming diatoms is stimulated by turbulence. Yet, direct measurements of cell-specific primary production in individual field populations of chain-forming diatoms are poorly documented. Here we measured cell-specific carbon, nitrate and ammonium assimilation in two field populations of chain-forming diatoms (Skeletonema and Chaetoceros) at low-nutrient concentrations under still conditions and turbulent shear using secondary ion mass spectrometry combined with stable isotopic tracers and compared our data with those predicted by mass transfer theory. Turbulent shear significantly increases cell-specific C assimilation compared to still conditions in the cells/chains that also form fast-sinking, aggregates rich in carbon and ammonium. Thus, turbulence simultaneously stimulates small-scale biological CO2 assimilation and large-scale biogeochemical C and N cycles in the ocean.
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| 3. |
- Bonaglia, Stefano, 1983-
(författare)
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Control factors of the marine nitrogen cycle : The role of meiofauna, macrofauna, oxygen and aggregates
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The ocean is the most extended biome present on our planet. Recent decades have seen a dramatic increase in the number and gravity of threats impacting the ocean, including discharge of pollutants, cultural eutrophication and spread of alien species. It is essential therefore to understand how different impacts may affect the marine realm, its life forms and biogeochemical cycles. The marine nitrogen cycle is of particular importance because nitrogen is the limiting factor in the ocean and a better understanding of its reaction mechanisms and regulation is indispensable. Furthermore, new nitrogen pathways have continuously been described. The scope of this project was to better constrain cause-effect mechanisms of microbially mediated nitrogen pathways, and how these can be affected by biotic and abiotic factors.This thesis demonstrates that meiofauna, the most abundant animal group inhabiting the world’s seafloors, considerably alters nitrogen cycling by enhancing nitrogen loss from the system. In contrast, larger fauna such as the polychaete Marenzelleria spp. enhance nitrogen retention, when they invade eutrophic Baltic Sea sediments. Sediment anoxia, caused by nutrient excess, has negative consequences for ecosystem processes such as nitrogen removal because it stops nitrification, which in turn limits both denitrification and anammox. This was the case of Himmerfjärden and Byfjord, two estuarine systems affected by anthropogenic activities, such as treated sewage discharges. When Byfjord was artificially oxygenated, nitrate reduction mechanisms started just one month after pumping. However, the balance between denitrification and nitrate ammonification did not favor either nitrogen removal or its retention.Anoxia is also present in aggregates of the filamentous cyanobacteria Nodularia spumigena. This thesis shows that even in fully oxic waters, millimetric aggregates can host anaerobic nitrogen processes, with clear implications for the pelagic compartment. While the thesis contributed to our knowledge on marine nitrogen cycling, more data need to be collected and experiments performed in order to understand key processes and regulation mechanisms of element cycles in the ocean. In this way, stakeholders may follow and take decisions in order to limit the continuous flow of human metabolites and impacts on the marine environment.
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| 4. |
- Bonaglia, Stefano, et al.
(författare)
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Denitrification and DNRA at the Baltic Sea oxic-anoxic interface : Substrate spectrum and kinetics
- 2016
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Ingår i: Limnology and Oceanography. - : Wiley. - 0024-3590 .- 1939-5590. ; 61:5, s. 1900-1915
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Tidskriftsartikel (refereegranskat)abstract
- The dependence of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) on different electron donors was tested in the nitrate-containing layer immediately below the oxic-anoxic interface (OAI) at three stations in the central anoxic basins of the Baltic Sea. Additionally, pathways and rates of fixed nitrogen transformation were investigated with N-15 incubation techniques without addition of donors. Denitrification and anammox were always detected, but denitrification rates were higher than anammox rates. DNRA occurred at two sites and rates were two orders of magnitude lower than denitrification rates. Separate additions of dissolved organic carbon and sulfide stimulated rates without time lag indicating that both organotrophic and lithotrophic bacterial populations were simultaneously active and that they could carry out denitrification or DNRA. Manganese addition stimulated denitrification and DNRA at one station, but it is not clear whether this was due to a direct or indirect effect. Ammonium oxidation to nitrite was detected on one occasion. During denitrification, the production of nitrous oxide (N2O) was as important as dinitrogen (N-2) production. A high ratio of N2O to N-2 production at one site may be due to copper limitation, which inhibits the last denitrification step. These data demonstrate the coexistence of a range of oxidative and reductive nitrogen cycling processes at the Baltic OAI and suggest that the dominant electron donor supporting denitrification and DNRA is organic matter. Organotrophic denitrification is more important for nitrogen budgets than previously thought, but the large temporal variability in rates calls for long-term seasonal studies.
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| 5. |
- Bonaglia, Stefano, et al.
(författare)
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Methane fluxes from coastal sediments are enhanced by macrofauna
- 2017
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Methane and nitrous oxide are potent greenhouse gases (GHGs) that contribute to climate change. Coastal sediments are important GHG producers, but the contribution of macrofauna (benthic invertebrates larger than 1 mm) inhabiting them is currently unknown. Through a combination of trace gas, isotope, and molecular analyses, we studied the direct and indirect contribution of two macrofaunal groups, polychaetes and bivalves, to methane and nitrous oxide fluxes from coastal sediments. Our results indicate that macrofauna increases benthic methane efflux by a factor of up to eight, potentially accounting for an estimated 9.5% of total emissions from the Baltic Sea. Polychaetes indirectly enhance methane efflux through bioturbation, while bivalves have a direct effect on methane release. Bivalves host archaeal methanogenic symbionts carrying out preferentially hydrogenotrophic methanogenesis, as suggested by analysis of methane isotopes. Low temperatures (8 °C) also stimulate production of nitrous oxide, which is consumed by benthic denitrifying bacteria before it reaches the water column. We show that macrofauna contributes to GHG production and that the extent is dependent on lineage. Thus, macrofauna may play an important, but overlooked role in regulating GHG production and exchange in coastal sediment ecosystems.
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| 6. |
- Bonaglia, Stefano, et al.
(författare)
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Sulfide oxidation in deep Baltic Sea sediments upon oxygenation and colonization by macrofauna
- 2019
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Ingår i: Marine Biology. - : Springer Science and Business Media LLC. - 0025-3162 .- 1432-1793. ; 166
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Tidskriftsartikel (refereegranskat)abstract
- Coastal and shelf sediments affected by transient or long-term bottom water anoxia and sulfidic conditions undergo drastic changes in macrofauna communities and abundances. This study investigates how early colonization by two macrofaunal functional traits (epifauna vs. infauna) affects oxygen, sulfide, and pH dynamics in anoxic sediment upon recent bottom water oxygenation. Large mesocosms (area 900 cm(2)) with 150-m-deep Baltic Sea soft sediments were exposed to three treatments: (1) no animals; (2) addition of 170 polychaetes (Marenzelleria arctia); (3) addition of 181 amphipods (Monoporeia affinis). Porewater chemistry was investigated repeatedly by microsensor profiling over a period of 65 days. Colonization by macrofauna did not significantly deepen penetration of oxygen compared to the animal-free sediment. Bioturbation by M. affinis increased the volume of the oxidized, sulfide-free sediment by 66% compared to the animal-free control already after 13 days of incubation. By the end of the experiment M. affinis and M. arctia increased the oxidized sediment volume by 87 and 35%, respectively. Higher efficiency of epifaunal amphipods in removing hydrogen sulfide than deep-burrowing polychaetes is likely due to more substantial re-oxidation of manganese and/or nitrogen compounds associated with amphipod mixing activity. Our results thus indicate that early colonization of different functional groups might have important implications for the later colonization by benthic macrofauna, meiofauna and microbial communities that benefit from oxidized and sulfide-free sediments.
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| 7. |
- Bonaglia, Stefano, et al.
(författare)
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The fate of fixed nitrogen in marine sediments with low organic loading : an in situ study
- 2017
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 14:2, s. 285-300
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Tidskriftsartikel (refereegranskat)abstract
- Over the last decades, the impact of human activities on the global nitrogen (N) cycle has drastically increased. Consequently, benthic N cycling has mainly been studied in anthropogenically impacted estuaries and coasts, while in oligotrophic systems its understanding is still scarce. Here we report on benthic solute fluxes and on rates of denitrification, anammox, and dissimilatory nitrate reduction to ammonium (DNRA) studied by in situ incubations with benthic chamber landers during two cruises to the Gulf of Bothnia (GOB), a cold, oligotrophic basin located in the northern part of the Baltic Sea. Rates of N burial were also inferred to investigate the fate of fixed N in these sediments. Most of the total dissolved fixed nitrogen (TDN) diffusing to the water column was composed of organic N. Average rates of dinitrogen (N-2) production by denitrification and anammox (range: 53-360 mu mol Nm(-2) day(-1)) were comparable to those from Arctic and subarctic sediments worldwide (range: 34-344 mu mol Nm(-2) day(-1)). Anammox accounted for 18-26% of the total N2 production. Absence of free hydrogen sulfide and low concentrations of dissolved iron in sediment pore water suggested that denitrification and DNRA were driven by organic matter oxidation rather than chemolithotrophy. DNRA was as important as denitrification at a shallow, coastal station situated in the northern Bothnian Bay. At this pristine and fully oxygenated site, ammonium regeneration through DNRA contributed more than one-third to the TDN efflux and accounted, on average, for 45% of total nitrate reduction. At the offshore stations, the proportion of DNRA in relation to denitrification was lower (0-16% of total nitrate reduction). Median value and range of benthic DNRA rates from the GOB were comparable to those from the southern and central eutrophic Baltic Sea and other temperate estuaries and coasts in Europe. Therefore, our results contrast with the view that DNRA is negligible in cold and well-oxygenated sediments with low organic carbon loading. However, the mechanisms behind the variability in DNRA rates between our sites were not resolved. The GOB sediments were a major source (237 kt yr(-1), which corresponds to 184% of the external N load) of fixed N to the water column through recycling mechanisms. To our knowledge, our study is the first to document the simultaneous contribution of denitrification, DNRA, anammox, and TDN recycling combined with in situ measurements.
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| 8. |
- Brüchert, Volker, et al.
(författare)
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Carbon mineralization in Laptev and East Siberian sea shelf and slope sediment
- 2018
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 15:2, s. 471-490
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Tidskriftsartikel (refereegranskat)abstract
- The Siberian Arctic Sea shelf and slope is a key region for the degradation of terrestrial organic material transported from the organic carbon-rich permafrost regions of Siberia. We report on sediment carbon mineralization rates based on O2 microelectrode profiling, intact sediment core incubations, 35 S-sulfate tracer experiments, porewater dissolved inorganic carbon (DIC), δ13 CDIC, and iron, manganese, and ammonium concentrations from 20 shelf and slope stations. This data set provides a spatial overview of sediment carbon mineralization rates and pathways over large parts of the outer Laptev and East Siberian Arctic shelf and slope, and allowed us to assess degradation rates and efficiency of carbon burial in these sediments. Rates of oxygen uptake and iron and manganese reduction were comparable to temperate shelf and slope environments, but bacterial sulfate reduction rates were comparatively low. In the topmost 20 to 50 cm of sediment, aerobic carbon mineralization dominated degradation and comprised on average 82% of the depthintegrated carbon mineralization. Oxygen uptake rates and 35 S-sulfate reduction rates were higher in the eastern East Siberian Sea shelf compared to the Laptev Sea shelf. DIC/NH4 + ratios in porewaters and the stable carbon isotope composition of remineralized DIC indicated that the degraded organic matter on the Siberian shelf and slope was a mixture of marine and terrestrial organic matter. Based on dual end member calculations, the terrestrial organic carbon contribution varied between 32% and 36%, with a higher contribution in the Laptev Sea than in the East Siberian Sea. Extrapolation of the measured degradation rates using isotope end member apportionment over the outer shelf of the Laptev and East Siberian Sea suggests that about 16 Tg C per year are respired in the outer shelf sea floor sediment. Of the organic matter buried below the oxygen penetration depth, between 0.6 and 1.3 Tg C per year are degraded by anaerobic processes, with a terrestrial organic carbon contribution ranging between 0.3 and 0.5 Tg per year.
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| 9. |
- Danielsson, Åsa, et al.
(författare)
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Effects of re-oxygenation and bioturbation by the polychaete Marenzelleria arctia on phosphorus, iron and manganese dynamics in Baltic Sea sediments
- 2018
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Ingår i: Boreal environment research. - : FINNISH ENVIRONMENT INST. - 1239-6095 .- 1797-2469. ; 23, s. 15-28
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Tidskriftsartikel (refereegranskat)abstract
- Sediments underlying hypoxic or anoxic water bodies constitute a net source of phosphorus to the bottom water. This source has the potential to enhance eutrophication. Benthic fluxes of dissolved phosphorus, iron and manganese were measured from hypoxic, normoxic, and normoxic bioturbated by the invasive polychaete Marenzelleria arctia sediment in a mesocosm experiment. The highest benthic phosphorus efflux was detected in mesocosms with the hypoxic treatment. Normoxic, bioturbated sediments led to weaker retention of phosphorus compared to oxic, defaunated sediments. Both iron and manganese fluxes increased under bioturbated conditions compared to defaunated sediments. This study shows that re-oxygenation of previously anoxic coastal sediments enhance phosphorus retention in the sediments. Colonisation by M. arctia induce strong mobilisation of iron and manganese due to its intense bioirrigation, which facilitates organic matter degradation and decreases the phosphorus retention by metal oxides in sediment.
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| 10. |
- Fripiat, F., et al.
(författare)
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Influence of the bordering shelves on nutrient distribution in the Arctic halocline inferred from water column nitrate isotopes
- 2018
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Ingår i: Limnology and Oceanography. - : Wiley. - 0024-3590 .- 1939-5590. ; 63:5, s. 2154-2170
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Tidskriftsartikel (refereegranskat)abstract
- The East Siberian Sea and contiguous western Arctic Ocean basin are characterized by a subsurface nutrient maximum in the halocline, generally attributed to both Pacific inflow and intensive remineralization in shelf bottom waters that are advected into the central basin. We report nitrogen and oxygen isotopic measurement of nitrate from the East Siberian Sea and western Eurasian Basin, in order to gain insight into how nitrate is processed by the microbial community and redistributed in the Arctic Ocean. A large decoupling between nitrate delta N-15 and delta O-18 is reported, increasing and decreasing upward from the Atlantic temperature maximum layer toward the surface, respectively. A correlation between water and nitrate delta O-18 indicates that most of the nitrate (> 60%) at the halocline has been regenerated within the Arctic Ocean. The increase in nitrate delta N-15 correlates with the fixed N deficit, indicating a causal link between the loss of fixed N and the delta N-15 enrichment. This suggests that a significant share of benthic denitrification is driven by nitrate supplied by remineralization and partial nitrification, allowing residual delta N-15-enriched ammonium to diffuse out of the sediments. By increasing nutrient concentrations and fixed N deficit in shelf bottom waters, this imprint is attenuated offshore following advection into the halocline by nitrate regeneration and mixing. Estimation of the sedimentary isotope effect related to benthic denitrification yields values in the range of 2.4-3.8 parts per thousand, with its magnitude driven by both the degree of coupling between remineralization and nitrification, and fixed N concentrations in shelf bottom waters.
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