Stefano Bonaglia

Stefano Bonaglia


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Arbetar vid Institutionen för ekologi miljö och botanik
Telefon 08-16 12 38
Besöksadress Svante Arrhenius väg 20 A
Rum N 217
Postadress Institutionen för ekologi miljö och botanik 106 91 Stockholm

Om mig

I hold a PhD in Geochemistry from the Department of Geological Sciences at Stockholm University. I work as a researcher (externally funded by the Swedish Research Council FORMAS) between the Department of Ecology, Environment and Plant Sciences (DEEP) at Stockholm University and the Nordic Center for Earth Evolution (NordCEE) at the University of Southern Denmark. My main interest is to understand how ecological factors and human processes influence aquatic biogeochemical cycles.

Among my working tools I constantly use the stable isotope technique, both at natural abundance and in tracer experiments to quantify pathways of microbial metabolism. I enjoy very much activities involving sea expeditions, deployment of in situ benthic landers, mesocosm experiments coupled to a wide range of analytical tecnhiques (GC, GC-IRMS, ICP, HPLC-ESI-MS/MS, SEM and microsensor profiling). Recently, I have started employing molecular techniques such as lipid and DNA analyses in my studies.


I urval från Stockholms universitets publikationsdatabas
  • 2019. Isabell Klawonn (et al.). The ISME Journal

    Ammonium is a central nutrient in aquatic systems. Yet, cell-specific ammonium assimilation among diverse functional plankton is poorly documented in field communities. Combining stable-isotope incubations (15N-ammonium, 15N2 and 13C-bicarbonate) with secondary-ion mass spectrometry, we quantified bulk ammonium dynamics, N2-fixation and carbon (C) fixation, as well as single-cell ammonium assimilation and C-fixation within plankton communities in nitrogen (N)-depleted surface waters during summer in the Baltic Sea. Ammonium production resulted from regenerated (≥91%) and new production (N2-fixation, ≤9%), supporting primary production by 78–97 and 2–16%, respectively. Ammonium was produced and consumed at balanced rates, and rapidly recycled within 1 h, as shown previously, facilitating an efficient ammonium transfer within plankton communities. N2-fixing cyanobacteria poorly assimilated ammonium, whereas heterotrophic bacteria and picocyanobacteria accounted for its highest consumption (~20 and ~20–40%, respectively). Surprisingly, ammonium assimilation and C-fixation were similarly fast for picocyanobacteria (non-N2-fixing Synechococcus) and large diatoms (Chaetoceros). Yet, the population biomass was high for Synechococcus but low for Chaetoceros. Hence, autotrophic picocyanobacteria and heterotrophic bacteria, with their high single-cell assimilation rates and dominating population biomass, competed for the same nutrient source and drove rapid ammonium dynamics in N-depleted marine waters.

  • Jane M. Caffrey, Stefano Bonaglia, Daniel J. Conley. FEMS Microbiology Letters

    Increased organic loading to sediments from eutrophication often results in hypoxia, reduced nitrification and increased production of hydrogen sulfide, altering the balance between nitrogen removal and retention. We examined the effect of short-term exposure to various oxygen and sulfide concentrations on sediment nitrification, denitrification and DNRA from a chronically hypoxic basin in Roskilde Fjord, Denmark. Surprisingly, nitrification rates were highest in the hypoxic and anoxic treatments (about 5 μmol cm−3 d−1) and the high sulfide treatment was not significantly different than the oxic treatment. Denitrification in the hypoxic treatment was highest at 1.4 μmol cm−3 d−1 and significantly higher than the high sulfide treatment. For DNRA, the rate in high sulfide treatment was 2 μmol cm−3 d−1. This was significantly higher than all oxygen treatments which were near zero. In this system, nitrifiers rapidly recovered from conditions typically considered inhibiting, while denitrifiers had a more muted response. DNRA bacteria appear to depend on sulfide for nitrate reduction. Anammox was insignificant. Thus, in estuaries and coastal systems that experience short-term variations in oxygen and sulfide, capabilities of microbial communities are more diverse and tolerant of suboptimal conditions than some paradigms suggest.

  • 2018. Stefano Bonaglia (et al.). Water Research

    Sediment capping with activated carbon (AC) is an effective technique used in remediation of contaminated sediments, but the ecological effects on benthic microbial activity and meiofauna communities have been largely neglected. This study presents results from a 4-week experiment investigating the influence of two powdered AC materials (bituminous coal-based and coconut shell-derived) and one control material (clay) on biogeochemical processes and meiofauna in contaminated sediments. Capping with AC induced a 62‒63% decrease in denitrification and a 66‒87 % decrease in dissimilatory nitrate reduction to ammonium (DNRA). Sediment porewater pH increased from 7.1 to 9.0 and 9.7 after addition of bituminous AC and biomass-derived AC, respectively. High pH (>8) persisted for at least two weeks in the bituminous AC and for at least 24 days in the coconut based AC, while capping with clay had no effect on pH. We observed a strong impact (nitrate fluxes being halved in presence of AC) on nitrification activity as nitrifiers are sensitive to high pH. This partly explains the significant decrease in nitrate reduction rates since denitrification was almost entirely coupled to nitrification. Total benthic metabolism estimated by sediment oxygen uptake was reduced by 30 and 43 % in presence of bituminous coal-based AC and coconut shell-derived AC, respectively. Meiofauna abundances decreased by 60‒62 % in the AC treatments. Taken together, these observations suggest that AC amendments deplete natural organic carbon, intended as food, to heterotrophic benthic communities. Phosphate efflux was 91 % lower in presence of bituminous AC compared to untreated sediment probably due to its content of aluminum (Al) oxides, which have high affinity for phosphate. This study demonstrates that capping with powdered AC produces significant effects on benthic biogeochemical fluxes, microbial processes and meiofauna abundances, which are likely due to an increase in porewater pH and to the sequestration of natural, sedimentary organic matter by AC particles.

  • 2018. Ugo Marzocchi (et al.). Environmental Microbiology

    Cable bacteria have been reported in sediments from marine and freshwater locations, but the environmental factors that regulate their growth in natural settings are not well understood. Most prominently, the physiological limit of cable bacteria in terms of oxygen availability remains poorly constrained. In this study, we investigated the presence, activity, and diversity of cable bacteria in relation to a natural gradient in bottom water oxygenation in a depth transect of the Eastern Gotland Basin (Baltic Sea).

    Cable bacteria were identified by FISH at the oxic and transiently oxic sites, but not at the permanently anoxic site. Three species of the candidate genus Electrothrix i.e., marina, aarhusiensis, and communis were found coexisting within one site. The highest filament density (33 m cm‐2) was associated with a 6.3 mm wide zone depleted in both oxygen and free sulphide, and the presence of an electric field resulting from the electrogenic sulphur oxidizing metabolism of cable bacteria. However, the measured filament densities and metabolic activities remained low overall, suggesting a limited impact of cable bacteria at the basin level. The observed bottom water oxygen levels (<5 μM) are the lowest so far reported for cable bacteria, thus expanding their known environmental distribution.

  • 2018. Cintia O. Quintana (et al.). Estuaries and Coasts

    A 4-week laboratory experiment investigated the behaviour (survival and bioirrigation) and impact of the invasive polychaetes Marenzelleria viridis, M. neglecta and M. arctia on sediment-water solutes exchange, porewater chemistry, and Fe and P interactions in high-salinity sandy sediment (HSS) and low-salinity muddy sediment (LSM) from the Baltic Sea. M. viridis showed deep burrowing with efficient bioirrigation (11 L m−2 day−1) and high survival (71%) in HSS, while M. arctia exhibited shallow burrowing with high bioirrigation (12 L m−2 day−1) and survival (88%) in LSM. M. neglecta behaved poorly in both ecological settings (bioirrigation, 5–6 L m−2 day−1; survival, 21–44%). The deep M. viridis bioirrigation enhanced total microbial CO2 (TCO2) production in HSS by 175% with a net efflux of NH4+ and PO43−, at rates 3- to 27-fold higher than for the other species. Although the shallow and intense bioirrigation of M. arctia in LSM stimulated microbial TCO2 production to some extent (61% enhancement), the nutrient fluxes close to zero indicate that it effectively prevented the P release. Porewater Fe:PO43− ratios revealed that the oxidizing effect of M. arctia bioirrigation increased the PO43− adsorption capacity of LSM twofold relative to defaunated controls while no buffering of PO43− was detected in M. viridis HSS treatment. Therefore, the different behaviour of the three species in various environments and the sharp contrast between M. viridis and M. arctia effects on C, N and P cycling must be considered carefully when the ecological role of Marenzelleria species in the Baltic Sea is evaluated.

  • 2018. Åsa Danielsson (et al.). Boreal environment research 23, 16-28

    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.

  • 2017. Stefano Bonaglia (et al.). Scientific Reports 7 (1)

    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.

  • 2017. Jennifer R. Griffiths (et al.). Global Change Biology 23 (6), 2179-2196

    Benthic-pelagic coupling is manifested as the exchange of energy, mass, or nutrients between benthic and pelagic habitats. It plays a prominent role in aquatic ecosystems, and it is crucial to functions from nutrient cycling to energy transfer in food webs. Coastal and estuarine ecosystem structure and function are strongly affected by anthropogenic pressures; however, there are large gaps in our understanding of the responses of inorganic nutrient and organic matter fluxes between benthic habitats and the water column. We illustrate the varied nature of physical and biological benthic-pelagic coupling processes and their potential sensitivity to three anthropogenic pressures - climate change, nutrient loading, and fishing - using the Baltic Sea as a case study and summarize current knowledge on the exchange of inorganic nutrients and organic material between habitats. Traditionally measured benthic-pelagic coupling processes (e.g., nutrient exchange and sedimentation of organic material) are to some extent quantifiable, but the magnitude and variability of biological processes are rarely assessed, preventing quantitative comparisons. Changing oxygen conditions will continue to have widespread effects on the processes that govern inorganic and organic matter exchange among habitats while climate change and nutrient load reductions may have large effects on organic matter sedimentation. Many biological processes (predation, bioturbation) are expected to be sensitive to anthropogenic drivers, but the outcomes for ecosystem function are largely unknown. We emphasize how improved empirical and experimental understanding of benthic-pelagic coupling processes and their variability are necessary to inform models that can quantify the feedbacks among processes and ecosystem responses to a changing world.

  • 2017. Per O. J. Hall (et al.). Frontiers in Marine Science 4
  • 2017. Stefano Bonaglia (et al.). Biogeosciences 14 (2), 285-300

    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.

  • 2016. Stefano Bonaglia (et al.). Limnology and Oceanography 61 (5), 1900-1915

    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.

  • 2015. Loreto De Brabandere (et al.). Biogeochemistry 126 (1-2), 131-152

    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.

  • 2015. Elisa Soana (et al.). Biogeochemistry 124 (1-3), 387-404

    Organic enrichment may deeply affect benthic nitrogen (N) cycling in macrophyte meadows, either promoting N loss or its recycling. This depends upon the plasticity of plants and of the associated microbial communities, as those surrounding the rhizosphere. Rates of denitrification, dissolved inorganic N fluxes and N uptake were measured in sediments vegetated by the submerged macrophyte Vallisneria spiralis L. under increasing organic matter loads. The aim was to investigate how the combined N assimilation and denitrification, which subtract N via temporary retention and permanent removal, respectively, do vary along the gradient. Results showed that V. spiralis meadows act as regulators of benthic N cycling even in organic enriched sediments, with negative feedbacks for eutrophication. A moderate organic load stimulates N uptake and denitrification coupled to nitrification in the rhizosphere. This is due to a combination of weakened competition between macrophytes and N cycling bacteria and enhanced radial oxygen loss by roots. An elevated organic enrichment affects N uptake due to hostile conditions in pore water and plant stress and impairs N mineralisation and its removal via denitrification coupled to nitrification. However, the loss of plant performance is almost completely compensated by increased denitrification of water column nitrate, resulting in a shift between the relative relevance of temporary and permanent N removal processes.

  • 2015. Klawonn Isabell (et al.). The ISME Journal 9 (1), 1456-1466

    Colonies of N2-fixing cyanobacteria are key players in supplying new nitrogen to the ocean, but the biological fate of this fixed nitrogen remains poorly constrained. Here, we report on aerobic and anaerobic microbial nitrogen transformation processes that co-occur within millimetre-sized cyanobacterial aggregates (Nodularia spumigena) collected in aerated surface waters in the Baltic Sea. Microelectrode profiles showed steep oxygen gradients inside the aggregates and the potential for nitrous oxide production in the aggregates’ anoxic centres. 15N-isotope labelling experiments and nutrient analyses revealed that N2 fixation, ammonification, nitrification, nitrate reduction to ammonium, denitrification and possibly anaerobic ammonium oxidation (anammox) can co-occur within these consortia. Thus, N. spumigena aggregates are potential sites of nitrogen gain, recycling and loss. Rates of nitrate reduction to ammonium and N2 were limited by low internal nitrification rates and low concentrations of nitrate in the ambient water. Presumably, patterns of N-transformation processes similar to those observed in this study arise also in other phytoplankton colonies, marine snow and fecal pellets. Anoxic microniches, as a pre-condition for anaerobic nitrogen transformations, may occur within large aggregates (1 mm) even when suspended in fully oxygenated waters, whereas anoxia in small aggregates (<1 to 0.1 mm) may only arise in low-oxygenated waters (25 μM). We propose that the net effect of aggregates on nitrogen loss is negligible in NO3-depleted, fully oxygenated (surface) waters. In NO3-enriched (>1.5 μM), O2-depleted water layers, for example, in the chemocline of the Baltic Sea or the oceanic mesopelagic zone, aggregates may promote N-recycling and -loss processes.

  • 2014. Stefano Bonaglia (et al.). Nature Communications 5, 5133

    Denitrification is a critical process that can alleviate the effects of excessive nitrogen availability in aquatic ecosystems subject to eutrophication. An important part of denitrification occurs in benthic systems where bioturbation by meiofauna (invertebrates <1mm) and its effect on element cycling are still not well understood. Here we study the quantitative impact of meiofauna populations of different abundance and diversity, in the presence and absence of macrofauna, on nitrate reduction, carbon mineralization and methane fluxes. In sediments with abundant and diverse meiofauna, denitrification is double that in sediments with low meiofauna, suggesting that meiofauna bioturbation has a stimulating effect on nitrifying and denitrifying bacteria. However, high meiofauna densities in the presence of bivalves do not stimulate denitrification, while dissimilatory nitrate reduction to ammonium rate and methane efflux are significantly enhanced. We demonstrate that the ecological interactions between meio-, macrofauna and bacteria are important in regulating nitrogen cycling in soft-sediment ecosystems.

  • 2014. Stefano Bonaglia (et al.). Biogeochemistry 119 (1-3), 139-160

    The regulatory roles of temperature, eutrophication and oxygen availability on benthic nitrogen (N) cycling and the stoichiometry of regenerated nitrogen and phosphorus (P) were explored along a Baltic Sea estuary affected by treated sewage discharge. Rates of sediment denitrification, anammox, dissimilatory nitrate reduction to ammonium (DNRA), nutrient exchange, oxygen (O2) uptake and penetration were measured seasonally. Sediments not affected by the nutrient plume released by the sewage treatment plant (STP) showed a strong seasonality in rates of O2 uptake and coupled nitrification-denitrification, with anammox never accounting for more than 20% of the total dinitrogen (N2) production. N cycling in sediments close to the STP was highly dependent on oxygen availability, which masked temperature-related effects. These sediments switched from low N loss and high ammonium (NH4+) efflux under hypoxic conditions in the fall, to a major N loss system in the winter when the sediment surface was oxidized. In the fall DNRA outcompeted denitrification as the main nitrate (NO3-) reduction pathway, resulting in N recycling and potential spreading of eutrophication. A comparison with historical records of nutrient discharge and denitrification indicated that the total N loss in the estuary has been tightly coupled to the total amount of nutrient discharge from the STP. Changes in dissolved inorganic nitrogen (DIN) released from the STP agreed well with variations in sedimentary N2 removal. This indicates that denitrification and anammox efficiently counterbalance N loading in the estuary across the range of historical and present-day anthropogenic nutrient discharge. Overall low N/P ratios of the regenerated nutrient fluxes impose strong N limitation for the pelagic system and generate a high potential for nuisance cyanobacterial blooms.

  • 2013. Stefano Bonaglia (et al.). Marine Ecology Progress Series 482, 43-55

    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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Senast uppdaterad: 11 april 2019

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