Bo Thamdrup

The anaerobic degradation of organic matter in Danish coastal sediments: Iron reduction, manganese reduction, and sulfate reduction

We used a combination of porewater and solid phase analysis, as well as a series of sediment incubations, to quantify organic carbon oxidation by dissimilatory Fe reduction, Mn reduction, and sulfate reduction, in sediments from the Skagerrak (located off the northeast coast of Jutland, Denmark). In the deep portion of the basin, surface Mn enrichments reached 3.5 wt%, and Mn reduction was the only important anaerobic carbon oxidation process in the upper 10 cm of the sediment. In the less Mn-rich sediments from intermediate depths in the basin, Fe reduction ranged from somewhat less, to far more important than sulfate reduction. Most of the Mn reduction in these sediments may have been coupled to the oxidation of acid volatile sulfides (AVS), rather than to dissimilatory reduction. High rates of metal oxide reduction at all sites were driven by active recycling of both Fe and Mn, encouraged by bioturbation. Recycling was so rapid that the residence time of Fe and Mn oxides, with respect to reduction, ranged from 70-250 days. These results require that, on average, an atom of Fe or Mn is oxidized and reduced between 100-300 times before ultimate burial into the sediment. We observed that dissolved Mn2+ was completely removed onto fully oxidized Mn oxides until the oxidation level of the oxides was reduced to about 3.8, presumably reflecting the saturation by Mn2+ of highly reactive surface adsorption sites. Fully oxidized Mn oxides in sediments, then, may act as a cap preventing Mn2+ escape. We speculate that in shallow sediments of the Skagerrak, surface Mn oxides are present in a somewhat reduced oxidation level (< 3.8) allowing Mn2+ to escape, and perhaps providing the Mn2+ which enriches sediments of the deep basin.

Pathways of organic carbon oxidation in three continental margin sediments

We have combined several different methodologies to quantify rates of organic carbon mineralization by the various electron acceptors in sediments from the coast of Denmark and Norway. Rates of NH4+ and Sigma CO2 liberation sediment incubations were used with O2 penetration depths to conclude that O2 respiration accounted for only between 3.6-17.4% of the total organic carbon oxidation. Dentrification was limited to a narrow zone just below the depth of O2 penetration, and was not a major carbon oxidation pathway. The processes of Fe reduction, Mn reduction and sulfate reduction dominated organic carbon mineralization, but their relative significance varied depending on the sediment. Where high concentrations of Mn-oxide were found (3-4 wt% Mn), only Mn reduction occurred. With lower Mn oxide concentrations more typical of coastal sediments, Fe reduction and sulfate reduction were most important and of a similar magnitude. Overall, most of the measured O2 flux into the sediment was used to oxidized reduced inorganic species and not organic carbon. We suspect that the importance of O2 respiration in many coastal sediments has been overestimated, whereas metal oxide reduction (both Fe and Mn reduction) has probably been well underestimated.

Manganese, iron and sulfur cycling in a coastal marine sediment, Aarhus bay, Denmark

The seasonal variation in oxidized and reduced pools of Mn, Fe and S, as well as the rates of SO42− reduction, were studied in a fine-grained sediment. Below the 1–5 mm thick oxic zone, a zone of net Mn reduction extended to 1–2 cm depth, while iron reduction was found to 4–6 cm depth. Although the reactive Mn oxide pool was ten times smaller than the reactive Fe(III) pool, the average ratio between depth gradients of Fe and Mn oxides was only 1.7, which implied that rates of Mn and Fe reduction were similar. Sulfate reduction was maximal near the bottom of the suboxic zone, but fine-scale measurements showed that it extended to the upper 0–2.5 mm during summer, when the zones of Mn and Fe reduction were compressed towards the surface. Most of the H2S produced precipitated as iron sulfides and S0 by reaction with Fe. Both Fe(III) and a nonsulfur-bound authigenic Fe(II) pool reacted efficiently with H2S. The authigenic Fe(II) pool was present at one hundredfold higher concentration than dissolved Fe2+. Only 15% of the precipitated sulfide was buried permanently. Most of the reoxidation of reduced S occurred within 1 cm of the sediment-water interface and was supported by upward bioturbation. All of the estimated Mn reduction could be coupled to the reoxidation of reduced S and Fe. Partial oxidation of H2S, forming S0 and pyrite, accounted for 63% of the estimated Fe reduction. The remaining Fe reduction was coupled to complete oxidation of reduced S or to C mineralization. The settling of a diatom spring bloom caused distinct maxima in SRR and Mn2+ at 0.5–1 cm depth within two weeks. In autumn, the reactive Mn oxides were depleted due to a net release of Mn2+ to the water column. Thus, the Mn cycle extended significantly into the water column, while a constant Fe pool over the year suggests that the Fe cycle was restricted to the sediment.

Influence of water column dynamics on sulfide oxidation and other major biogeochemical processes in the chemocline of Mariager Fjord (Denmark)

Abstract Major electron donors (H2S, NH4+, Mn2+, Fe2+) and acceptors (O2, NO3−, Mn(IV), Fe(III)), process rates (35SO42− reduction, dark 14CO2 fixation) and vertical fluxes were investigated to quantify the dominant biogeochemical processes at the chemocline of a shallow brackish fjord. Under steady-state conditions, the upward fluxes of reductants and downward fluxes of oxidants in the water column were balanced. However, changes in the hydrographical conditions caused a transient nonsteady-state at the chemocline and had a great impact on process rates and the distribution of chemical species. Maxima of S0 (17.8 μmol l−1), thiosulfate (5.2 μmol l−1) and sulfite (1.1 μmol l−1) occurred at the chemocline, but were hardly detectable in the sulfidic deep water. The distribution of S0 suggested that the high concentration of S0 was (a) more likely due to a low turnover than a high formation rate and (b) was only transient, caused by chemocline perturbations. Kinetic calculations of chemical sulfide oxidation based on actual conditions in the chemocline revealed that under steady-state conditions with a narrow chemocline and low reactant concentrations, biological sulfide oxidation may account for more than 88% of the total sulfide oxidation. Under nonsteady-state conditions, where oxic and sulfidic water masses were recently mixed, resulting in an expanded chemocline, the proportion of chemical sulfide oxidation increased. The sulfide oxidation rate determined by incubation experiments was 0.216 μmol l−1 min−1, one of the highest reported for stratified basins and about 15 times faster than the initial rate for chemical oxidation. The conclusion of primarily biological sulfide oxidation was consistent with the observation of high rates of dark 14CO2 fixation (10.4 mmol m−2 day−1) in the lower part of the chemocline. However, rates of dark 14CO2 fixation were too high to be explained only by lithoautotrophic processes. CO2 fixation by growing populations of heterotrophic microorganisms may have additionally contributed to the observed rates.

The response of the microbial community of marine sediments to organic carbon input under anaerobic conditions.

Cyanobacterial biomass was added to anaerobic sediment to simulate the natural input of complex organic substrate that occurs in nature after algae blooms. Sediments were incubated at 0 degree C, 8 degrees C and 24 degrees C for 13 days. Community dynamics were measured by fluorescence in situ hybridisation (FISH), denaturing gradient gel electrophoresis (DGGE), and sequencing of 16S rDNA PCR products. Metabolic changes were followed by the analysis of total carbon mineralisation, sulfate reduction, and ammonium production rates. The addition of organic material resulted in significant changes in the composition of the microbial community at all temperatures tested. Sulfate reduction was the main mineralisation process detected. However, not sulfate-reducers but rather members of the Cytophaga-Flavobacterium phylogenetic cluster showed the highest increase in the bacterial cells as detected by FISH. We conclude that these organisms play an important role in the anaerobic decomposition of complex organic material perhaps because they are the main catalysts of macromolecule hydrolysis and fermentation. The molecular methods also indicated a stimulation of ribosome synthesis. The detection of a large number of rRNA-rich cells belonging to the Cytophaga-Flavobacterium phylogenetic cluster further supports the importance of their role in the degradation of complex organic material in anaerobic marine sediments. Their detection in high numbers in the field may indicate recent deposition events.

Thiosulfate and sulfite distributions in porewater of marine sediments related to manganese, iron, and sulfur geochemistry

Depth distributions of thiosulfate (S[sub 2]O[sub 3][sup 2[minus]]) and sulfite (SO[sub 3][sup 2[minus]]) were measured in the porewaters of a Danish salt marsh and subtidal marine sediments by HPLC analysis after derivatization with DTNP [2,2[prime]-dithiobis(5-nitropyridine)]. The distributions were compared to the redox zonation as indicated by Eh and Mn[sup 2+], Fe[sup 2+], and H[sub 2]S distributions. Concentrations of S[sub 2]O[sub 3][sup 2[minus]] varied from below detection (<50 nM) to 600 nM while SO[sub 3][sup 2[minus]] concentrations generally were 2-3 times higher, 100-1500 nM. Depth distributions of the two species were roughly similar. Lowest concentrations were found in the oxidized zone, including both the oxic surface layer and the suboxic and into the reduced, sulfidic zone. The similarity of SO[sub 3][sup 2[minus]] and S[sub 2]O[sub 3][sup 2[minus]] profiles suggested a close coupling of the cycling of the two species. Rates of consumption were suggested as the main factor governing their distribution. Rapid turnover times for S[sub 2]O[sub 3][sup 2[minus]] and H[sub 2]S of 4 and 1.1 h, respectively, were estimated for the upper 0-1 cm of a subtidal sediment.

Nitrogen losses in anoxic marine sediments driven by Thioploca-anammox bacterial consortia

Ninety per cent of marine organic matter burial occurs in continental margin sediments, where a substantial fraction of organic carbon escapes oxidation and enters long-term geologic storage within sedimentary rocks. In such environments, microbial metabolism is limited by the diffusive supply of electron acceptors. One strategy to optimize energy yields in a resource-limited habitat is symbiotic metabolite exchange among microbial associations. Thermodynamic and geochemical considerations indicate that microbial co-metabolisms are likely to play a critical part in sedimentary organic carbon cycling. Yet only one association, between methanotrophic archaea and sulphate-reducing bacteria, has been demonstrated in marine sediments in situ, and little is known of the role of microbial symbiotic interactions in other sedimentary biogeochemical cycles. Here we report in situ molecular and incubation-based evidence for a novel symbiotic consortium between two chemolithotrophic bacteria—anaerobic ammonium-oxidizing (anammox) bacteria and the nitrate-sequestering sulphur-oxidizing Thioploca species—in anoxic sediments of the Soledad basin at the Mexican Pacific margin. A mass balance of benthic solute fluxes and the corresponding nitrogen isotope composition of nitrate and ammonium fluxes indicate that anammox bacteria rely on Thioploca species for the supply of metabolic substrates and account for about 57 ± 21 per cent of the total benthic N2 production. We show that Thioploca–anammox symbiosis intensifies benthic fixed nitrogen losses in anoxic sediments, bypassing diffusion-imposed limitations by efficiently coupling the carbon, nitrogen and sulphur cycles.