Sulfate reduction and sediment metabolism in Tomales Bay,California

Sulfate reduction rates (SRR) in subtidal sediments of Tomales Bay, California, were variable by sediment type, season and depth. Higher rates were measured in near-surface muds during summer (up to 45 nmol cm^-3 h^-1), with lower rates in sandy sediments, in winter and deeper in the sediment. Calculations of annual, average SRR throughout the upper 20 cm of muddy subtidal sediments (about 30 mmol S m^-2 d^-1) were much larger than previously reported net estimates of SRR derived from both benthic alkalinity flux measurements and bay wide, budget stoichiometry (3.5 and 2.6 mmol m^-2 d^-1, respectively), indicating that most reduced sulfur in these upper, well-mixed sediments is re-oxidized. A portion of the net alkalinity flux across the sediment surface may be derived from sulfate reduction in deeper sediments, estimated from sulfate depletion profiles at 1.5 mmol m^-2 d^-1. A small net flux of CO₂ measured in benthic chambers despite a large SRR suggests that sediment sinks for CO₂ must also exist (e.g., benthic microalgae).     

Stable sulfur isotopic distributions and sulfate reduction in lake sediments of the Adirondack Mountains,New York

Cores from five lakes of the Adirondack Mountains, New York, were analyzed for sedimentary sulfur concentrations and stable sulfur isotopic compositions. Isotopic values of total sedimentary sulfur were as much as 6 to 8 lower than isotopic values of sulfur sources (soils, tree leaves and lake water sulfate) which showed little isotopic variation in the Adirondacks. The low isotopic values of recent sediments indicate increased sulfate reduction, probably in response to increased sulfate loading and acid deposition. Detailed historical reconstruction of sulfate loading histories from sedimentary sulfur profiles is premature, however, since model calculations indicate that sulfur can be added to deeper older sediments by ongoing, contemporary sulfate reduction.     

Sulfate reduction by a syntrophic propionate-oxidizing bacterium

The syntrophic propionate-oxidizing bacterium MPOB was able to grow in the absence of methanogens by coupling the oxidation of propionate to the reduction of sulfate. Growth on propionate plus sulfate was very slow (=0.024 day^–1). An average growth yield was found of 1.5 g (dry weight) per mol of propionate. MPOB grew even slower than other sulfate-reducing syntrophic propionate-oxidizing bacteria. The growth rates and yields of strict sulfate-reducing bacteria (Desulfobulbus sp.) grown on propionate plus sulfate are considerably higher.     

The effect of sulfate and nitrate on methane formation in a freshwater sediment

A freshwater sediment from a ditch of a peat grassland near Zegveld (Province of Utrecht, The Netherlands) was investigated for its potential methanogenic and syntrophic activity and the influence of sulfate and nitrate on these potential activities. Methanogenesis started after a 10 days lagphase. After 35–40 days aceticlastic methanogens were sufficiently enriched to cause a net decrease of acetate. In the presence of sulfate methane formation was only slightly affected. The addition of nitrate led to an outcompetion of aceticlastic methanogens by nitrate reducers. When inorganic electron acceptors were absent, substrates like propionate and butyrate were converted by syntrophic methanogenic consortia. Addition of inorganic electron acceptors resulted in an outcompetition of the syntrophic propionate and butyrate degrading consortia by the sulfate and nitrate reducers.     

Dimethylsulfide and methane thiol in sediment porewater of a Danish estuary

Seasonal variation of dimethylsulfide (DMS) and methane thiol (MSH) concentrations in sediment porewater was determined in a Danish estuary. Dimethylsulfide (DMDS) was never found. Detectable DMS levels of up to 0.1 M were found only in the summer and only within the upper 5 cm of the sediment. The DMS accumulation was probably associated with decomposing fragments of macro-algae in the surface layer. Significant MSH accumulation of up to 1 M was found only in the deep, CH₄-rich sediment below the SO₄ ^2- zone. With depth, a detectable MSH level could thus be observed below the 1 mM SO₄ ^2--isopleth which also marked the SO₄ ^2--CH₄ transition. The transition zone was located deeper in the sediment in winter (20–25 cm depth) than in summer (5–10 cm depth). The absence of MSH in the SO₄ ^2- zone could be due to rapid utilization of the compound by SO₄ ^2--reducing bacteria. A possible involvement of MSH in anaerobic CH₄ oxidation at the transition zone is discussed; CH₄ and sulfide (HS^- form, pH 7) are proposed to form MSH and H₂ which in turn may be metabolized by, e.g. SO₄ ^2--reducing bacteria.     

Sulfate reduction and thiosulfate transformations in a cyanobacterial mat during a diel oxygen cycle

Abstract Bacterial sulfate reduction and transformations of thiosulfate were studied with radiotracers in a Microcoleus chthonoplastes -dominated microbial mat growing in a hypersaline pond at the Red Sea. The study showed how a diel cycle of oxygen evolution affected respiration by sulfate-reducing bacteria and the metabolism of thiosulfate through oxidative and reductive pathways. Sulfate reduction occurred in both oxic and anoxic layers of the mat and varied diurnally, apparently according to temperature rather than to oxygen. Time course experiments showed that the radiotracer method underestimated sulfate reduction in the oxic zone due to rapid reoxidation of the produced sulfide. Extremely high reduction rates of up to 10 μmol cm⁻³ d⁻¹ were measured just below the euphotic zone. Although thiosulfate was simultaneously oxidized, reduced and disproportionated by bacteria in all layers of the mat, there was a shift from predominant oxidation in the oxic zone to predominant reduction below. Concurrent disproportionation of thiosulfate to sulfate and sulfide occurred in all zones and was an important pathway of the sulfur cycle in the mat.     

Survival of sulfate-reducing bacteria after oxygen stress, and growth in sulfate-free oxygen-sulfide gradients

Abstract The survival after oxygen stress was studied with eight species of sulfate-reducing bacteria. In the absence of sulfide all species tolerated 6 min of aeration without loss of viability. Even after 3 h of aeration the viability of four species ( Desulfovibrio vulgaris, D. desulfuricans, D. salexigens and Desulfobacter postgatei ) was not impaired. Four other species were sensitive to 3 h of aeration: the surviving fractions of Desulfotomaculum ruminis, D. nigrificans and Desulfococcus multivorans were about 1%, that of Desulfotomaculum orientis about 0.01%. Formation of spores resulted in oxygen resistance of D. orientis . Reducing agents did not protect the vegetative cells of this strain against oxygen toxicity. In contrast, sulfhydryl group-containing agents increased the oxygen sensitivity considerably.
Growth of sulfate- and sulfur-reducing bacteria in oxygen-sulfide gradients in agar tubes was studied. In the gradients these strictly anaerobic bacteria revealed oxygen-dependent growth in sulfate- and sulfur-free medium. Three sulfate-reducing bacteria that could not use thiosulfate or sulfur as electron acceptor failed to grow in oxygen-sulfide gradients. Obviously, not directly molecular oxygen, but oxidation products of sulfide, such as thiosulfate or sulfur, were used as electron acceptors and were continuously regenerated in a cycling process from sulfide by autoxidation. The conceivable ecological significance of a short sulfur cycle driven by autoxidation of sulfide is discussed.     

Sulfate reduction in fine-grained sediments in the Eastern Scheldt,southwest Netherlands

Sulfate reduction and sulfide accumulation were examined in fine-grained sediments from rapidly accreting abandoned channels and mussel culture areas in the Eastern Scheldt, which covered 4 and 5% of the total surface area, respectively.Reduction rates were measured in batch experiments in which the SO₄ ^2– depletion was measured during anoxic incubation. The reduction rates in summer varied between 14–68 mmol SO₄ ^2– m^–2 day^–1 and were related to the sedimentation rate. In the most rapidly accreting channels, SO₄ ^2– was exhausted below 15–50 cm and methanogenesis became the terminal process of organic carbon oxidationOne-dimensional modelling of sulfate profiles in mussel banks indicated that the subsurface influx of SO₄ ^2– was almost of the same order as the diffusive flux at the sediment-seawater interface, during the initial stages of the mussel bank accretion. The energy dissipation of waves and tidal currents on the mussel bank surface increased the apparent sediment diffusivity up to 3-fold, especially in the winterThe results indicate that acid volatile sulfide (AVS) was the major, in-situ reduced, sulfur compound in the sediment. The sulfidation of easily extractable iron was nearly complete. Pyrite concentrations (40–80 M S cm^–3) were as high as the AVS concentrations, but there was apparently no in-situ transformation of AVS into pyrite. The detrital pyrite originated from eroding marine sediments elsewhere     

Sulfur isotope values in a forested catchment over four years: Evidence for oxidation and reduction processes

A small catchment on the Swedish West Coast has been studied over four years to determine S dynamics by using S isotope ratios. A Norway spruce dominated forest covers the catchment, and small peat areas occur in the lower parts of the catchment. The runoff values varied both during the year, and from year to year. Over the period from February 1990 to December 1993, the values ranged from — 1%. to +11%. Over the same period, the throughfall values ranged from +1%. to +15%. There was no correlation (r ²= 0.01; Pr(F)=0.57) between values in throughfall and runoff. Since the only input of S to the catchment is atmospheric deposition, the long-term runoff S mass flux is controlled by the deposition. Therefore, processes in the catchment are responsible for the variation in the runoff values. During periods with enriched runoff, bacterial dissimilatory SO ₄ ^2– reduction occurs in the catchment. After very dry periods, oxidation of this reduced S, which is³²S-enriched, can be traced in runoff. Previous studies of the catchment have not been able to distinguish between: 1) oxidation of reduced S and dry deposition, and 2) reduction and adsorption. From the current study, it can be concluded that adsorption and dry deposition cannot cause the observed variation in runoff .     

Sulfate reduction at pH 4.0 for treatment of process and wastewaters

Acidic industrial process and wastewaters often contain high sulfate and metal concentrations and their direct biological treatment is thus far not possible as biological processes at pH < 5 have been neglected. Sulfate‐reducing bacteria convert sulfate to sulfide that can subsequently be used to recover metals as metal‐sulfides precipitate. This study reports on high‐rate sulfate reduction with a mixed microbial community at pH 4.0 and 4.5 with hydrogen and/or formate as electron donors. The maximum sulfate reducing activity at pH 4.0 was sustained for over 40 days with a specific activity 500‐fold greater than previously reported values: 151 mmol sulfate reduced/L reactor liquid per day with a maximum specific activity of 84 mmol sulfate per gram of volatile suspended solids per day. The biomass yield gradually decreased from 38 to 0.4 g volatile suspended solids per kilogram of sulfate when decreasing the reactor pH from pH 6 to 4. The microorganisms had a high maintenance requirement probably due maintaining pH homeostasis and the toxicity of sulfide at low pH. The microbial community diversity in the pH 4.0 membrane bioreactor decreased over time, while the diversity of the sulfate reducing community increased. Thus, a specialized microbial community containing a lower proportion of microorganisms capable of activity at pH 4 developed in the reactor compared with those present at the start of the experiment. The 16S rRNA genes identified from the pH 4.0 grown mixed culture were most similar to those of Desulfovibrio species and Desulfosporosinus sp. M1. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

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.     

Demonstration of HOQNO and antimycin A sensitive coupling of NADH oxidation and APS and sulfite reduction in a marine Desulfovibrio strain

Abstract In cell suspensions of the marine sulfate-reducing bacterium Desulfovibrio 20020 (DSM 3099) permeabilized with formaldehyde or Triton X-100, sulfite-dependent NADH oxidation activities of 0.05 μmol · min⁻¹· mg⁻¹ protein were detected. NADH oxidation coupled to APS, thiosulfate and fumarate reduction was also demonstrated. All the activities were subject to inhibition by HOQNO and antimycin A. The rate of NADH oxidation coupled to the reduction of sulfite was extremely low in cell-free extracts. The physiological function and possible mechanism of the NADH oxidation coupled to the reduction of various electron acceptors are discussed.     

Seasonality of sulfate reduction and pore water solutes in a marine fish farm sediment: the importance of temperature and sedimentary organic matter

Sulfate reduction and pore water solutes related to sulfur cycling and anaerobic processes (short chain fatty acids (SCFA), SO₄ ^2–, TCO₂, NH₄ ⁺, dissolved sulfides (H₂S) and CH₄) were examined during one year at a marine fish farm. Mineralization of fish farm waste products was rapid in this non-bioturbated, organic rich sediment. Stimulation of sulfate reduction rates (SRR) occurred primarily in the surface layers where the organic matter was deposited. Acetate was the most important (<99%) of the measured SCFA attaining high concentrations during summer months (up to 4.7 mM). The acetate profiles exhibited distinct seasonal cycles, where periods with high concentrations in the pore waters were found coincident with a high pool of particulate organic matter in the surface sediments and a low activity of the sulfate reducing bacteria (early spring and late summer). Periods with low acetate pools occurred when sulfate reduction rates were high in early summer and in winter were pools of particulate organic matter were decreasing. Methane production was observed concurrent with sulfate reduction in the microbial active surface layers in late summer. Subsurface peaks of SO₄ ^2–, TCO₂, NH₄ ⁺ and H₂S were evident in July and August due to rapid mineralization in these surface layers. With decreasing autumn water temperatures mineralization rates declined and subsurface peaks of these solutes disappeared. A strong relationship was found between pore water TCO₂, and NH₄ ⁺. Ratios between TCO₂, and NH₄ ⁺ were low compared to a control site, attaining minimum values in mid-summer. This indicated rapid nitrogen mineralization of nitrogen rich labile substrates in the fish farm sediment during the entire season.     

Inorganic sulfur turnover in oligohaline estuarine sediments

Inorganic sulfur turnover was examined in oligohaline (salinity < 2 g kg^-1) Chesapeake Bay sediments during the summer. Cores incubated for < 3 hr exhibited higher sulfate reduction (SR) rates (13–58 mmol m^-2 d^-1) than those incubated for 3–8 hr (3–8 mmol m^-2 d^-1). SR rates (determined with³⁵SO ₄ ^2- ) increased with depth over the top few cm to a maximum at 5 cm, just beneath the boundary between brown and black sediment. SR rates decreased below 5 cm, probably due to sulfate limitation (sulfate < 25 μM). Kinetic experiments yielded an apparent half-saturating sulfate concentration (K_s) of 34 μM, ≈ 20-fold lower than that determined for sediments from the mesohaline region of the estuary. Sulfate loss from water overlying intact cores, predicted on the basis of measured SR rates, was not observed over a 28-hr incubation period. Reduction of³⁵SO ₄ ^2- during diffusion experiments with intact core segments from 0–4 and 5–9 cm horizons was less than predicted by non-steady state diagenetic models based on³⁵SO ₄ ^2- reduction in whole core injection experiments. The results indicate that net sulfate flux into sediments was an order of magnitude lower than the gross sulfur turnover rate. Solid phase reduced inorganic sulfur concentrations were only 2–3 times less than those in sediments from the mesohaline region of the Bay, despite the fact that oligohaline bottom water sulfate concentrations were 10-fold lower. Our results demonstrate the potential for rapid SR in low salinity estuarine sediments, which are inhabited by sulfate-reducing bacteria with a high affinity for sulfate, and in which sulfide oxidation processes replenish the pore water sulfate pool on a time scale of hours.     

Sulfate reduction in coastal ecosystems

The diversity and activity of dissimilatory Fe(III)-reducing bacteria was investigated in acidic, ochre-precipitating springs on Mam Tor, East Midlands, UK. The springs at this acid rock drainage site are located below a 3000 year old landslip, where biooxidation of exposed pyrite-containing minerals has resulted in the production of metal-laden acidic waters. A diverse microbial community was found downstream in the sediments dominated by Fe(III) minerals, and included close relatives to known acidophilic (Acidimicrobium and Acidiphilium) and neutraphilic (Geobacter and Pelobacter) Fe(III)-reducing bacteria. Analysis by XRD and TEM confirmed the presence of both amorphous and well-defined Fe(III) mineral phases in the sediments including lepidocrocite, goethite and schwertmannite. Microcosm-based experiments demonstrated that the bioavailable Fe(III) was reduced under anaerobic conditions, concomitant with sulphate release. XRD analysis suggested that schwertmannite (an iron sulphate hydroxide) was utilized preferentially by the Fe(III)-reducing bacteria, leading to the release of sulphate. Although the microcosms contained sufficient concentrations of naturally occurring electron donor to sustain significant levels of Fe(III) reduction, this process was stimulated by the addition of glycerol and complex electron donors. Thus, the acidic Fe(III)-containing sediments contain a diversity of DIRBs that can be stimulated by the addition of electron donor as a first step in the reversal of acid rock and acid mine drainage contamination.     

Sulfur isotope's signal of nanopyrites enclosed in 2.7 Ga stromatolitic organic remains reveal microbial sulfate reduction

Microbial sulfate reduction (MSR) is thought to have operated very early on Earth and is often invoked to explain the occurrence of sedimentary sulfides in the rock record. Sedimentary sulfides can also form from sulfides produced abiotically during late diagenesis or metamorphism. As both biotic and abiotic processes contribute to the bulk of sedimentary sulfides, tracing back the original microbial signature from the earliest Earth record is challenging. We present in situ sulfur isotope data from nanopyrites occurring in carbonaceous remains lining the domical shape of stromatolite knobs of the 2.7‐Gyr‐old Tumbiana Formation (Western Australia). The analyzed nanopyrites show a large range of δ³⁴S values of about 84‰ (from ?33.7‰ to +50.4‰). The recognition that a large δ³⁴S range of 80‰ is found in individual carbonaceous‐rich layers support the interpretation that the nanopyrites were formed in microbial mats through MSR by a Rayleigh distillation process during early diagenesis. An active microbial cycling of sulfur during formation of the stromatolite may have facilitated the mixing of different sulfur pools (atmospheric and hydrothermal) and explain the weak mass independent signature (MIF‐S) recorded in the Tumbiana Formation. These results confirm that MSR participated actively to the biogeochemical cycling of sulfur during the Neoarchean and support previous models suggesting anaerobic oxidation of methane using sulfate in the Tumbiana environment.     

Establishment of anaerobic,reducing conditions in lake sediment after deposition of acidic,aerobic sediment by a major storm

Hurricane Danny resulted in the rapid deposition of 10cm of oxidized, acidic sediment in the Contrary Creek arm of Lake Anna, Virginia. Several biological and geochemical parameters were monitored with time to ascertain how long it took the newly-deposited lake sediments to attain the anaerobic, circumneutral, actively sulfate-reducing state normally observed in this portion of the lake. The sediment platinum-electrode potential dropped from 350 mV to 100 mV within the first week after the storm. The pH of the pore water increased from 4.5 to 5.8 within three weeks, and titratable alkalinity was detected within two weeks and three weeks at 3 cm and 1 cm depths, respectively. Accumulation of reduced products of sulfate reduction (acid volatile sulfide) began by three to four weeks after the storm event. Both methanogens and sulfate reducers were present in high and approximately equal numbers in the freshly deposited material. The rapid neutralization of the acidity in the fresh sediment prior to the onset of sulfate reduction suggests that reactions other than sulfate reduction caused the initial increase in pH and alkalinity in this system.     

Unprecedented 34S‐enrichment of pyrite formed following microbial sulfate reduction in fractured crystalline rocks

In the deep biosphere, microbial sulfate reduction (MSR) is exploited for energy. Here, we show that, in fractured continental crystalline bedrock in three areas in Sweden, this process produced sulfide that reacted with iron to form pyrite extremely enriched in ³⁴S relative to ³²S. As documented by secondary ion mass spectrometry (SIMS) microanalyses, the δ³⁴S_pyrite values are up to +132‰V‐CDT and with a total range of 186‰. The lightest δ³⁴S_pyrite values (?54‰) suggest very large fractionation during MSR from an initial sulfate with δ³⁴S values (δ³⁴S_sulfate,0) of +14 to +28‰. Fractionation of this magnitude requires a slow MSR rate, a feature we attribute to nutrient and electron donor shortage as well as initial sulfate abundance. The superheavy δ³⁴S_pyrite values were produced by Rayleigh fractionation effects in a diminishing sulfate pool. Large volumes of pyrite with superheavy values (+120 ± 15‰) within single fracture intercepts in the boreholes, associated heavy average values up to +75‰ and heavy minimum δ³⁴S_pyrite values, suggest isolation of significant amounts of isotopically light sulfide in other parts of the fracture system. Large fracture‐specific δ³⁴S_pyrite variability and overall average δ³⁴S_pyrite values (+11 to +16‰) lower than the anticipated δ³⁴S_sulfate,0 support this hypothesis. The superheavy pyrite found locally in the borehole intercepts thus represents a late stage in a much larger fracture system undergoing Rayleigh fractionation. Microscale Rb–Sr dating and U/Th–He dating of cogenetic minerals reveal that most pyrite formed in the early Paleozoic era, but crystal overgrowths may be significantly younger. The δ¹³C values in cogenetic calcite suggest that the superheavy δ³⁴S_pyrite values are related to organotrophic MSR, in contrast to findings from marine sediments where superheavy pyrite has been proposed to be linked to anaerobic oxidation of methane. The findings provide new insights into MSR‐related S‐isotope systematics, particularly regarding formation of large fractions of ³⁴S‐rich pyrite.     

Biogeochemical cycling of sulfur and iron in sediments of a south-east Asian mangrove,Phuket Island,Thailand

Benthic sulfate reduction and sediment pools of sulfur and iron were examined during January 1992 at 3 stations in the Ao Nam Bor mangrove, Phuket, Thailand. Patterns of sulfate reduction rates (0–53 cm) reflected differences in physical and biological conditions at the 3 stations, and highest rates were found at the vegetated site within the mangrove (Rhizophora apiculata) forest. Due to extended oxidation of mangrove sediments, a large portion of the added³⁵S-label was recovered in the chromium reducible pools (FeS₂ and S⁰) (41–91% of the reduced sulfur). Pyrite was the most important inorganic sulfur component, attaining pool sizes 50–100 times higher than acid volatile pools (FeS). HCl-extractable (0.5 M HCl) iron pools, including Fe(II)_HCl and Fe(III)_HCl, were generally low and Fe(III)_HCl was only present in the upper surface layers (0–5 cm). Maximum concentrations of dissolved Fe²⁺ (35–285 M) occurred just about the depth where dissolved H₂S accumulated. Furthermore Fe²⁺ and H₂S coexisted only where concentrations of both were low. There was an accumulation of organic sulfur in the deep sediment at 2 stations in the inner part of the mangrove. The reoxidation of reduced sulfides was rapid, and storage of sulfur was minor in the upper sediment layers, where factors like bioturbation, the presence of roots, or tidal mixing enhance oxidation processes.Author of correspondence.     

Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara

To extend comparative metagenomic analyses of the deep-sea, we produced metagenomic data by direct 454 pyrosequencing from bathypelagic plankton (1000 m depth) and bottom sediment of the Sea of Marmara, the gateway between the Eastern Mediterranean and the Black Seas. Data from small subunit ribosomal RNA (SSU rRNA) gene libraries and direct pyrosequencing of the same samples indicated that Gamma- and Alpha-proteobacteria, followed by Bacteroidetes, dominated the bacterial fraction in Marmara deep-sea plankton, whereas Planctomycetes, Delta- and Gamma-proteobacteria were the most abundant groups in high bacterial-diversity sediment. Group I Crenarchaeota/Thaumarchaeota dominated the archaeal plankton fraction, although group II and III Euryarchaeota were also present. Eukaryotes were highly diverse in SSU rRNA gene libraries, with group I (Duboscquellida) and II (Syndiniales) alveolates and Radiozoa dominating plankton, and Opisthokonta and Alveolates, sediment. However, eukaryotic sequences were scarce in pyrosequence data. Archaeal amo genes were abundant in plankton, suggesting that Marmara planktonic Thaumarchaeota are ammonia oxidizers. Genes involved in sulfate reduction, carbon monoxide oxidation, anammox and sulfatases were over-represented in sediment. Genome recruitment analyses showed that Alteromonas macleodii ‘surface ecotype'', Pelagibacter ubique and Nitrosopumilus maritimus were highly represented in 1000 m-deep plankton. A comparative analysis of Marmara metagenomes with ALOHA deep-sea and surface plankton, whale carcasses, Peru subsurface sediment and soil metagenomes clustered deep-sea Marmara plankton with deep-ALOHA plankton and whale carcasses, likely because of the suboxic conditions in the deep Marmara water column. The Marmara sediment clustered with the soil metagenome, highlighting the common ecological role of both types of microbial communities in the degradation of organic matter and the completion of biogeochemical cycles.