Henrik Fossing

Measurement of bacterial sulfate reduction in sediments: Evaluation of a single-step chromium reduction method

A procedure which includes the Total Reduced Inorganic Sulfur (TRIS) in a single distillation step is described for the radiotracer measurement of sulfate reduction in sediments. The TRIS includes both Acid Volatile Sulfide (AVS: H2S + FeS) and the remaining Chromium Reducible Sulfur (CRS: S0, FeS2). The single-step distillation was simpler and faster than the consecutive distillations of AVS and CRS. It also resulted in higher (4–50%) sulfate reduction rates than those obtained from the sum of35S in AVS and CRS. The difference was largest when the sediment had been dried after AVS but before CRS distillation. Relative to the35S-AVS distillation alone, the35S-TRIS single-step distallation yielded 8–87% higher reduction rates. The separation and recovery of FeS, S0 and FeS2 was studied under three distillation conditions: 1) cold acid, 2) cold acid with Cr2+, and 3) hot acid with Cr2+. The FeS was recovered by cold acid alone while pyrite was recovered by cold acid with Cr2+. A smaller S0 fraction, presumably of the finer crystal sizes, was recovered also in the cold acid with Cr2+ while most of the S0 required hot acid with Cr2+ for reduction to H2S.

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.

Electric currents couple spatially separated biogeochemical processes in marine sediment

Some bacteria are capable of extracellular electron transfer, thereby enabling them to use electron acceptors and donors without direct cell contact. Beyond the micrometre scale, however, no firm evidence has previously existed that spatially segregated biogeochemical processes can be coupled by electric currents in nature. Here we provide evidence that electric currents running through defaunated sediment couple oxygen consumption at the sediment surface to oxidation of hydrogen sulphide and organic carbon deep within the sediment. Altering the oxygen concentration in the sea water overlying the sediment resulted in a rapid (<1-h) change in the hydrogen sulphide concentration within the sediment more than 12 mm below the oxic zone, a change explicable by transmission of electrons but not by diffusion of molecules. Mass balances indicated that more than 40% of total oxygen consumption in the sediment was driven by electrons conducted from the anoxic zone. A distinct pH peak in the oxic zone could be explained by electrochemical oxygen reduction, but not by any conventional sets of aerobic sediment processes. We suggest that the electric current was conducted by bacterial nanowires combined with pyrite, soluble electron shuttles and outer-membrane cytochromes. Electrical communication between distant chemical and biological processes in nature adds a new dimension to our understanding of biogeochemistry and microbial ecology.

Sulfide oxidation in the anoxic Black Sea chemocline

The depth distributions of O2 and H2S and of the activity of chemical or bacterial sulfide oxidation were studied in the chemocline of the central Black Sea. Relative to measurements from earlier studies, the sulfide zone had moved upwards by 20–50 m and was now (May 1988) situated at a depth of 81–99 m. Oxygen in the water column immediately overlying the sulfide zone was depleted to undetectable levels resulting in a 20–30-m deep intermediate layer of O2 - and H2S-free water. Radiotracer studies with 35S-labelled H2S showed that high rates of sulfide oxidation, up to a few micromoles per liter per day, occurred in anoxic water at the top of the sulfide zone concurrent with the highest rates of dark CO2 assimilation. The main soluble oxidized products of sulfide were thiosulfate (68–82%) and sulfate. Indirect evidence was presented for the formation of elemental sulfur which accumulated to a maximum of 200 nmol l−1 at the top of the sulfide zone. Sulfide oxidation was stimulated by particles suspended at the chemocline, probably by bacteria. Green phototrophic sulfur bacteria were abundant in the chemocline, suggesting that photosynthetic H2S oxidation took place. Flux calculations showed that the measured H2S oxidation rates were 4-fold higher than could be explained by the downward flux of organic carbon and too high to balance the availability of electron acceptors such as oxidized iron or manganese. A nitrate maximum at the lower boundary of the O2 zone did not extend down to the sulfide zone.

Sulfate reduction and methanogenesis in a Thioploca-dominated sediment off the coast of Chile

Continental shelf sediments of the central Chile upwelling area are dominated by the presence of dense mats of the filamentous, sulfur-depositing bacterium Thioploca spp. We examined rates and pathways of S and methane cycling in these sediments along a transect from the Bay of Concepcion to the continental slope. Sulfate reduction rates (170–4670 nmol cm−3 d−1) were equal to or exceeded rates reported for other subtidal marine sediments. Elemental S and pyrite were the dominant end-products of sulfate reduction in Thioploca mats on the continental shelf, whereas, in the highly-reducing, Beggiatoa-dominated sediments of the nearby Bay of Concepcion, acid-volatile S was the principal end-product. Dissolved organic C values were lowest at the stations with the highest sulfate reduction rates and increased offshore. Sediment porewater methane concentrations in all surface sediments were low (<12 nmol cm−3), and methane production rates at the station most dominated by Thioploca were extremely low ( <0.5 nmol cm−3 d−1). Low methane production rates and concentrations were matched by low methane oxidation rates (<0.1 nmol cm−3 d−1). Radio-tracer studies showed that methane production was almost exclusively from methylamines, substrates which are noncompetitive with sulfate reduction, rather than from acetate or CO2/H2. Bacterial MPN (most probable number) counts also indicated the presence of a methylotrophic population of methanogens. Surprisingly, high numbers of autotrophic acetogenic bacteria were found, suggesting that the bacterial population involved in anaerobic DOC degradation is more complex than expected. In spite of the high sulfate reduction rates, sulfide concentrations in the shelf and slope were low or undetectable (<0.5 μM), and sulfate concentrations were never depleted below bottom water levels down to depths of 25–30 cm. Calculations suggest that Thioploca were oxidizing a maximum of 35% of sulfide production—not enough to prevent sulfate depletion. Either other sulfide oxidizers were also present or transient hydrodynamic conditions coupled with bioturbation resulted in oxidation of the sediments.

Sulfate reduction and methane oxidation in continental margin sediments influenced by irrigation (South-East Atlantic off Namibia)

Abstract Sulfate reduction rates (SRR) and concentrations of SO 4 2− , H 2 S, pyrite sulfur, total sulfur, CH 4 , and organic carbon were measured with high depth resolution through the entire length of the SO 4 2− -zone and well into the CH 4 -zone at two continental slope stations in the eastern South Atlantic (Benguela upwelling area). The sediments were characterized by a high organic carbon content of approx. 7.5% at GeoB 3703 and 3.7% at GeoB 3714. At GeoB 3703 SO 4 2− concentrations decreased linearly with depth to about 40 μM at the sulfate-methane transition zone (SMT) at 3.5 m, while at GeoB 3714, SO 4 2− remained at sea water concentration in the top 2 m of the sediment and then decreased linearly to about 70 μM at the SMT at 6 m. Direct rate measurements of SRR ( 35 SO 4 2− ) showed that the highest SRR occurred within the surface 3–5 cm with peak rates of up to 20 and 7 nmol SO 4 2− cm −3 day −1 at GeoB 3703 and GeoB 3714, respectively. SRR decreased quasi-exponentially with depth at GeoB 3703 and the cumulative SRR over the length of the SO 4 2− zone resulted in an areal SRR (SRR area ) of 1114–3493 μmol m −2 day −1 (median value: 2221 μmol m −2 day −1 ) at GeoB 3703 with more than 80% of the total sulfate reduction proceeding in the top 30 cm sediment. At GeoB 3714 SRR exhibited more scatter with a cumulative SRR area of 398–1983 μmol m −2 day −1 (median value: 1251 μmol m −2 day −1 ) and with >60% of the total sulfate reduction occurring below a depth of 30 cm due partially to a deeply buried zone of sulfate reduction located between 3 and 5 m depths. SRR peaks were also observed in SMT of both cores, ostensibly associated with methane oxidation, but with rates about 10 times lower than at the surface. Modeled SRR balanced both methane oxidation rates and measured SRR within the SMT, but severely underestimated by up to 89% the total SRR area that were obtained from direct measurements. Modeled and measured SRR were reconciled by including solute transport by irrigation described by a non-local pore water exchange function (α) which had values of up to 0.3 year −1 in the top sediment, and decreased exponentially to zero (i.e., no irrigation) at 2–3 meters (i.e., above SMT). These results suggested that co-existing sulfate reduction processes and linear SO 4 2− -gradients can be maintained by a non-local transport mechanism such as irrigation, by which pore water in tubes or burrows is exchanged with bottom waters by activities of tube-dwelling animals, or some similar physical transport phenomenon (i.e., bubble ebullition). Further support for an irrigation mechanism was found in the observations of open tubes of up to 8 mm (ID) at depths down to 6 m, which also contained fecal pellets, indicating that these tubes were or had been inhabited.

Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation

In order to better understand the main factors that influence the distribution of sulfate-reducing bacteria (SRB), their population size and their metabolic activity in high- and low-sulfate zones, we studied the SRB diversity in 3- to 5-m-deep sediment cores, which comprised the entire sulfate reduction zone and the upper methanogenic zone. By combining EMA (ethidium monoazide that can only enter damaged/dead cells and may also bind to free DNA) treatment with real-time PCR, we determined the distributions of total intact bacteria (16S rDNA genes) and intact SRB (dsrAB gene), their relative population sizes, and the proportion of dead cells or free DNA with depth. The abundance of SRB corresponded in average to 13% of the total bacterial community in the sulfate zone, 22% in the sulfate-methane transition zone and 8% in the methane zone. Compared with the total bacterial community, there were relatively less dead/damaged cells and free DNA present than among the SRB and this fraction did not change systematically with depth. By DGGE analysis, based on the amplification of the dsrA gene (400 bp), we found that the richness of SRB did not change with depth through the geochemical zones; but the clustering was related to the chemical zonation. A full-length clone library of the dsrAB gene (1900 bp) was constructed from four different depths (20, 110, 280 and 500 cm), and showed that the dsrAB genes in the near-surface sediment (20 cm) was mainly composed of sequences close to the Desulfobacteraceae, including marine complete and incomplete oxidizers such as Desulfosarcina, Desulfobacterium and Desulfococcus. The three other libraries were predominantly composed of Gram-positive SRB.

Oxidation and reduction of radiolabeled inorganic sulfur compounds in an estuarine sediment, Kysing Fjord, Denmark

35S-labeled SO42−, S2O32−, S0, ΣHS− (=H2S + HS− + S2−), and FeS2 were used to trace the oxidative and reductive pathways of the sulfur cycle. We studied the transformation of 35SO42−, 35S2O3−, 35S0, AV35S ( =ΣH35S− + Fe35S), and Fe35S2 in 8-cm long undisturbed estuarine sediment cores in time course experiments of up to 24 h. All the tracers, except for pyrite, were oxidized and/or reduced at all depths. More than 60% of the 35S from 35SO22− reduction was recovered as 35S0g in the top two cm of the sediment. At >2 cm, nearly all of the reduced 35SO42− was recovered as AV35S plus Fe35S2. Thiosulfate was not detected in the sediment. From the combined data of outer- and inner-labeled 35S2O32− injections, concurrent oxidation, reduction, and disproportionation of S2O32− were demonstrated. In oxidized surface sediment the three processes comprised 10, 24, and 66%, respectively, of the metabolized 35S2O32−. In reduced sediment these percentages were 16, 45, and 39%. Injections of SH35S− into S2O32− spiked sediment cores produced 71% 35SO42− and 29%35S2O32− (% of the total 35SO42− + 35S2O32− in the oxidized zone and 8% 35SO42− and 92% 35S2O32− in the reduced zone. A similar experiment with 35S0 produced 62% 35SO42− and 38% 35S2O32− in the oxidized zone and 22 and 78% in the reduced zone. We calculated that more than half of the 35S0 and ΣH35S− oxidation to SO42− proceeded through S2O32− in the reduced sediment. In the oxidized sediment these percentages were 15 and 21% for SH35S− and 35S0, respectively. Thiosulfate was thus a key intermediate in the S cycle.

Impact of Bacterial NO3− Transport on Sediment Biogeochemistry

ABSTRACT Experiments demonstrated that Beggiatoa could induce a H2S-depleted suboxic zone of more than 10 mm in marine sediments and cause a divergence in sediment NO3− reduction from denitrification to dissimilatory NO3− reduction to ammonium. pH, O2, and H2S profiles indicated that the bacteria oxidized H2S with NO3− and transported S0 to the sediment surface for aerobic oxidation.