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| 2. |
- 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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| 3. |
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| 4. |
- Ahmed, Engy, et al.
(författare)
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The Role of Microorganisms in the diversity and distribution of siderophores in Podzolic Forest Soil
- 2013
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Ingår i: Mineralogical magazine. - 0026-461X .- 1471-8022. ; 77:2, s. 161--208(48)
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Iron is a key component of the chemical architecture of the biosphere. Due to the low bioavailability of iron in the environment, microorganisms have developed specific uptake strategies. The most important one is the production of siderophores, which are operationally defined as low-molecular-mass biogenic Fe (III)-binding compounds which may greatly increase bioavailability of Fe [1]. One of the primary biogeochemical functions of siderophores is therefore to increase Fe bioavailability by promoting the dissolution of iron-bearing minerals [2]. This study aims to understand the role of microorganisms in the chemical diversity and distribution of siderophores in podzol soil and how this diversity can contribute to the bioavailability of Fe in forest soil.Soil samples were collected from an experimental site in the area of Bispgården in central Sweden (63°07′N, 16°70′E) from the O (organic), E (eluvial), B1 (upper illuvial), and C (mineral) horizons. Concentration and chemical composition of dissolved and adsorbed siderophores in the soil samples were determined using colorimetric assays and high-performance liquid chromatography.The highest siderophore concentrations were found in the O layer and thereafter decreased by depth. Concentrations of dissolved hydroxamate, catecholate and carboxylate siderophores were up to 84, 17 and 0.2 nmol/ g soil, respectively. In contrast, concentrations of adsorbed hydroxamates, catecholates and carboxylates were only up to 1.8, 3 and 0.2 nmol/ g soil, respectively.Siderophore-producing microorganisms were isolated from the same soil samples. Viable fungi, bacteria and actinomycete counts ranged from 7 to 300, from 300 to 1800, and from 0 to 5 cfu/gm, respectively. The highest counts were found in the O and E layers. Only the E layer contained the three types of siderophore-producing microorganisms investigated in this study. Siderophores were extracted from culture filtrates of the isolated microorganisms when grown under iron-limited conditions. These extracts varied considerably in siderophore composition. Fungal isolates produced up to 183 μM of hydroxamates, especially those isolated from the O layer, whereas bacteria and actinomycete isolated from the O and E layers of the soil produced high amounts of carboxylate, catecholate and hydroxamate siderophores. Actinomycete produced up to 93 μM of hydroxamates and 47 μM of catecholates, while bacteria produced up to 34 μM of carboxylates and up to 14 μM of catecholates.The depth variability in concentration and chemical composition and the good correlation between abundance of siderophore-producing microorganisms and siderophore soil concentrations strongly suggest that these siderophore-producing microorganisms play an important role in the mobilization of iron in the podzol soil that may be important in iron availability to plants in forest environment.[1] Clay et al. (1981) Biochemistry 20, 2432-2436. [2] Duckworth et al. (2009) ChemGeol 260, 149-158.
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| 6. |
- 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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| 7. |
- 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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| 8. |
- 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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| 9. |
- Bonaglia, Stefano, et al.
(författare)
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EFFECT OF MEIOFAUNA ON BENTHIC ELEMENT CYCLING IN A BALTIC SEA COASTAL AREA
- 2013
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Konferensbidrag (refereegranskat)abstract
- We have studied the role of meiofaunal communities for nutrient cycling and organic matter mineralization in coastal sediments of the Baltic Sea. Although meiofauna is orders of magnitude more abundant than macrofauna and has commonly a much more diverse community structure, its importance for sediment biogeochemical pathways is poorly understood because of objective experimental difficulties when manipulating meiofauna communities due to small body sizes (0.04 to 1 mm) and inherent fragility. We used a density extraction method to separate intact and living metazoans from sediment and tested the effect of low meiofauna and high meiofauna abundances in the presence and absence of macrofauna for exchange rates of nutrients, O2, DIC, N2, and CH4. High abundances of meiofauna stimulated O2 uptake and the net N2 efflux by 16% and 34%, respectively, but did not change oxygen penetration depths significantly. By contrast, macrofauna increased oxygen penetration depths by 21% and stimulated methane emissions by a factor of 8. These results demonstrate the importance of meiofauna in the regulation of aerobic and anaerobic microbial processes and benthic fluxes in marine sediments.
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| 10. |
- Bonaglia, Stefano, et al.
(författare)
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Effect of reoxygenation and Marenzelleria spp. bioturbation on Baltic Sea sediment metabolism
- 2013
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Ingår i: Marine Ecology Progress Series. - : Inter Research. - 0171-8630 .- 1616-1599. ; 482, s. 43-55
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Tidskriftsartikel (refereegranskat)abstract
- Nutrient reduction and the improvement of bottom water oxygen concentrations are thought to be key factors in the recovery of eutrophic aquatic ecosystems. The effects of reoxygenation and bioturbation of natural hypoxic sediments in the Baltic Sea were studied using a mesocosm experiment. Anoxic sediment box cores were collected from 100 m depth in Kanholmsfjärden (Stockholm Archipelago) and maintained in flow-through mesocosms with 3 treatments: (1) hypoxic: supplied with hypoxic water; (2) normoxic: supplied with oxic water; and (3) Marenzelleria: supplied with oxic water and the polychaete Marenzelleria spp. (2000 ind. m–2). After a 7 wk long conditioning period, net fluxes of dissolved O2, CH4, Fe2+, Mn2+, NH4+, NO2-, NO3-, PO43- and H4SiO4, and rates of nitrate ammonification (DNRA), denitrification and anammox were determined. Phosphate was taken up by the sediment in all treatments, and the uptake was highest in the normoxic treatment with Marenzelleria. Normoxic conditions stimulated the denitrification rate by a factor of 5. Denitrification efficiency was highest under normoxia (50%), intermediate in bioturbated sediments (16%), and very low in hypoxic sediments (4%). The shift from hypoxic to normoxic conditions resulted in a significantly higher retention of NH4+, H4SiO4 and Mn2+ in the sediment, but the bioturbation by Marenzelleria reversed this effect. Results from our study suggest that bioturbation by Marenzelleria stimulates the exchange of solutes between sediment and bottom water through irrigation and enhances bacterial sulfate reduction in the burrow walls. The latter may have a toxic effect on nitrifying bacteria, which, in turn, suppresses denitrification rates.
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