Description: The fluids emanating from active submarine hydrothermal vent chimneys provide a window into subseafloor processes and, through mixing with seawater, are responsible for steep thermal and compositional gradients that provide the energetic basis for diverse biological communities. Although several models have been developed to better understand the dynamic interplay of seawater, hydrothermal fluid, minerals and microorganisms inside chimney walls, none provide a fully integrated approach to quantifying the biogeochemistry of these hydrothermal systems. In an effort to remedy this, a fully coupled biogeochemical reaction-transport model of a hydrothermal vent chimney has been developed that explicitly quantifies the rates of microbial catalysis while taking into account geochemical processes such as fluid flow, solute transport and oxidation–reduction reactions associated with fluid mixing as a function of temperature. The metabolisms included in the reaction network are methanogenesis, aerobic oxidation of hydrogen, sulfide and methane and sulfate reduction by hydrogen and methane. Model results indicate that microbial catalysis is generally fastest in the hottest habitable portion of the vent chimney (77–102 °C), and methane and sulfide oxidation peak near the seawater-side of the chimney. The fastest metabolisms are aerobic oxidation of H2 and sulfide and reduction of sulfate by H2 with maximum rates of 140, 900 and 800 pmol cm−3 d−1, respectively. The maximum rate of hydrogenotrophic methanogenesis is just under 0.03 pmol cm−3 d−1, the slowest of the metabolisms considered. Due to thermodynamic inhibition, there is no anaerobic oxidation of methane by sulfate (AOM). These simulations are consistent with vent chimney metabolic activity inferred from phylogenetic data reported in the literature. The model developed here provides a quantitative approach to describing the rates of biogeochemical transformations in hydrothermal systems and can be used to constrain the role of microbial activity in the deep subsurface.

Description: This study investigates the controls on organic carbon and molybdenum (Mo) accumulation in sediments deposited within the Western Interior Seaway across the Cenomanian–Turonian boundary interval (94.34–93.04 Ma) including Oceanic Anoxic Event 2 (OAE2). Carbon fluxes to the sediment–water interface (reflecting changes in primary productivity) and bottom-water oxygen concentrations (reflecting preservation effects) are reconstructed from field data and used to constrain a benthic model that simulates the geochemistry of unconsolidated sediments as they were deposited. The results show that increased availability of reactive iron prevents Mo sequestration as thiomolybdate (MoS42 −) during OAE2 (O2 ~ 105 μM) by (i) inhibiting sulfate reduction, and (ii) buffering any free sulfide that becomes available. In the post-OAE2 period (O2 ~ 50 μM), Mo accumulation is favored by a large reduction in iron flux. Importantly, this occurs in parallel with oxygenated bottom waters and high rates of aerobic carbon degradation in the surface sediments, implying that elevated Mo burial fluxes in ancient marine facies do not necessarily reflect euxinic or even anoxic conditions within the water column. Our findings suggest that both an increase in production and preservation lead to enrichment in organic carbon in the Western Interior Seaway. More generally, the results demonstrate that a careful consideration of the coupling between iron, carbon and oxygen cycles during the early stages of diagenesis is critical for interpreting geochemical proxies in modern and ancient settings.

Description: We present sedimentary geochemical data and in situ benthic flux measurements of dissolved inorganic nitrogen (DIN: NO3−, NO2−, NH4+) and oxygen (O2) from 7 sites with variable sand content along 18°N offshore Mauritania (NW Africa). Bottom water O2 concentrations at the shallowest station were hypoxic (42 μM) and increased to 125 μM at the deepest site (1113 m). Total oxygen uptake rates were highest on the shelf (−10.3 mmol O2 m−2 d−1) and decreased quasi-exponentially with water depth to −3.2 mmol O2 m−2 d−1. Average denitrification rates estimated from a flux balance decreased with water depth from 2.2 to 0.2 mmol N m−2 d−1. Overall, the sediments acted as net sink for DIN. Observed increases in δ15NNO3 and δ18ONO3 in the benthic chamber deployed on the shelf, characterized by muddy sand, were used to calculate apparent benthic nitrate fractionation factors of 8.0‰ (15εapp) and 14.1‰ (18εapp). Measurements of δ15NNO2 further demonstrated that the sediments acted as a source of 15N depleted NO2−. These observations were analyzed using an isotope box model that considered denitrification and nitrification of NH4+ and NO2−. The principal findings were that (i) net benthic 14N/15N fractionation (εDEN) was 12.9 ± 1.7‰, (ii) inverse fractionation during nitrite oxidation leads to an efflux of isotopically light NO2− (−22 ± 1.9‰), and (iii) direct coupling between nitrification and denitrification in the sediment is negligible. Previously reported εDEN for fine-grained sediments are much lower (4–8‰). We speculate that high benthic nitrate fractionation is driven by a combination of enhanced porewater–seawater exchange in permeable sediments and the hypoxic, high productivity environment. Although not without uncertainties, the results presented could have important implications for understanding the current state of the marine N cycle.

Description: Two ∼6 m long sediment cores were collected along the ∼300 m isobath on the Alaskan Beaufort Sea continental margin. Both cores showed distinct sulfate-methane transition zones (SMTZ) at 105 and 120 cm below seafloor (cmbsf). Sulfate was not completely depleted below the SMTZ but remained between 30 and 500 μM. Sulfate reduction and anaerobic oxidation of methane (AOM) determined by radiotracer incubations were active throughout the methanogenic zone. Although a mass balance could not explain the source of sulfate below the SMTZ, geochemical profiles and correlation network analyses of biotic and abiotic data suggest a cryptic sulfur cycle involving iron, manganese and barite. Inhibition experiments with molybdate and 2-bromoethanesulfonate (BES) indicated decoupling of sulfate reduction and AOM and competition between sulfate reducers and methanogens for substrates. While correlation network analyses predicted coupling of AOM to iron reduction, the addition of manganese or iron did not stimulate AOM. Since none of the classical archaeal anaerobic methanotrophs (ANME) were abundant, the involvement of unknown or unconventional phylotypes in AOM is conceivable. The resistance of AOM activity to inhibitors implies deviation from conventional enzymatic pathways. This work suggests that the classical redox cascade of electron acceptor utilization based on Gibbs energy yields does not always hold in diffusion-dominated systems, and instead biotic processes may be more strongly coupled to mineralogy.

Description: Quantification of global biogeochemical cycles requires knowledge of the rates at which microorganisms catalyze chemical reactions. In order for models that describe these processes to capture global patterns of change, the underlying formulations in them must account for biogeochemical transformations over seasonal and millennial time scales in environments characterized by different energy levels. Building on existing models, a new thermodynamic limiting function is introduced. With only one adjustable parameter, this function that can be used to model microbial metabolism throughout the range of conditions in which organisms are known to be active. The formulation is based on a comparison of the amount of energy available from any redox reaction to the energy required to maintain a membrane potential, a proxy for the minimum amount of energy required by an active microorganism. This function does not require species- or metabolism-specific parameters, and can be used to model metabolisms that capture any amount of energy. The utility of this new thermodynamic rate limiting term is illustrated by applying it to three low-energy processes: fermentation, methanogenesis and sulfate reduction. The model predicts that the rate of fermentation will be reduced by half once the Gibbs energy of the catalyzed reaction reaches −12 kJ (mol e−)−1, and then slowing exponentially until the energy yield approaches zero. Similarly, the new model predicts that the low energy yield of methanogenesis, −4 to −0.5 kJ (mol e−)−1, for a partial pressure of H2 between 11 and 0.6 Pa decreases the reaction rate by 95–99%. Finally, the new function’s utility is illustrated through its ability to accurately model sulfate concentration data in an anoxic marine sediment.

Description: The impact of oxygen on the preservation of organic matter in marine surface sediments is still controversial. We revisited this long-standing debate by determining the burial efficiency of sedimentary organic matter in the Black Sea, the largest anoxic and euxinic basin in the modern ocean. Surface sediments were sampled in the Danube paleodelta on the northwestern margin of the Black Sea at 420–1550 m water depth. Steady-state modeling of solid species (particulate organic carbon and nitrogen) and solutes (ammonium, sulfate, and total alkalinity) in sediments was performed to quantify rates of mass accumulation, particulate organic matter (POM) degradation, and POM burial. We develop a novel analytical model to quantify these rates applying an inverse modelling approach to down core data accounting for molecular diffusion, sediment burial and compaction. Our model results indicate that 56.7 ± 6.6 % of the particulate organic matter deposited in the study area is not degraded in surface sediments but accumulates below 10 cm sediment depth. This burial efficiency is substantially higher than those previously derived for seafloor areas underlying oxygenated bottom waters. Hence, our study confirms previous studies showing that euxinic bottom water conditions promote the preservation of particulate organic matter in marine sediments.

Description: Phosphorus is essential for all living organisms, being a component of DNA and RNA and the energy carrier ATP. Phosphogenesis is a main sink of reactive phosphorus in the oceans. The present study reports the presence of intracellular dissolved inorganic phosphate (DIP) in benthic foraminifera from the Peruvian oxygen minimum zone (OMZ). The mean intracellular DIP concentration was 28 ± 3 mM; two to three orders-of-magnitude higher than in the ambient pore waters. The biological implications of the high intracellular phosphate enrichment may be related to the synthesis of polyphosphates or phospholipids for cell-membranes. The comparative genomics analysis of multiple species of foraminifera from different environments reveals that foraminifers encode the genes required for both phospholipid and polyphosphate metabolism. Rapid phosphogenesis and phosphorite formation associated with foraminiferal tests is hypothesized due to the pre-concentration of intracellular phosphate in these organisms. The results indicate that foraminifera may play a key and previously overlooked role in the global phosphorus cycle.

Description: Microbial degradation of organic carbon in marine sediments is a key driver of global element cycles on multiple time scales. However, it is not known to what depth microorganisms alter organic carbon in marine sediments or how microbial rates of organic carbon processing change with depth, and thus time since burial, on a global scale. To better understand the connection between the dynamic carbon cycle and life’s limits in the deep subsurface, we have combined a number of global data sets with a reaction transport model (RTM) describing first, organic carbon degradation in marine sediments deposited throughout the Quaternary Period and second, a bioenergetic model for microbial activity. The RTM is applied globally, recognizing three distinct depositional environments – continental shelf, margin and abyssal zones. The results include the masses of particulate organic carbon, POC, stored in three sediment-depth layers: bioturbated Holocene (1.7 × 10^17 g C), non-bioturbated Holocene (2.6 × 10^18 g C) and Pleistocene (1.4 × 1020 g C) sediments. The global depth-integrated rates of POC degradation have been determined to be 6.8 × 10^13, 1.2 × 10^14 and 1.2 × 10^14 g C yr-1 for the same three layers, respectively. A number of maps depicting the distribution of POC, as well as the fraction that has been degraded have also been generated. Using POC degradation as a proxy for microbial catabolic activity, total heterotrophic processing of POC throughout the Quaternary is estimated to be between 10^-11 – 10^-6 g C cm-3 yr-1, depending on the time since deposition and location. Bioenergetic modeling reveals that laboratory-determined microbial maintenance powers are poor predictors of sediment biomass concentration, but that cell concentrations in marine sediments can be accurately predicted by combining bioenergetic models with the rates of POC degradation determined in this study. Our model can be used to quantitatively describe both the carbon cycle and microbial activity on a global scale for marine sediments less than 2.59 million years old.

Description: Marine sediments are an important source and sink of bio-essential trace metals to the ocean. However, the different mechanisms leading to trace metal release or burial are not fully understood and the associated fluxes are not well quantified. Here, we present sediment, pore water, sequential extraction and benthic flux data of Mn, Co, Ni, Cu, Zn and Cd along a latitudinal depth transect across the Peruvian oxygen minimum zone at 12°S. Sediments are depleted in Mn and Co compared to the lithogenic background. Diffusive Mn fluxes from the sediments into the bottom water (−26 to −550 μmol m−2 y−1) are largely consistent with the rate of Mn loss from the solid phase (−100 to −1160 μmol m−2 yr−1) suggesting that 50% or more of the sedimentary Mn depletion is attributed to benthic efflux. In contrast, benthic Co fluxes (~ −3 μmol m−2 yr−1) are lower than the rate of Co loss from the solid phase (up to −120 μmol m−2 yr−1), implying Co dissolution in the water column. The trace metals Ni, Cu, Zn and Cd are enriched within the sediments with respect to the lithogenic background. Uptake of Ni by phytoplankton in the photic zone and delivery with organic matter to the sediment surface can account for up to 100% of the excess Ni accumulation (87 to 180 μmol m−2 y−1) in shelf sediments near the coast, whereas at greater water depth additional scavenging by Mn- and Fe-oxides may contribute to Ni accumulation. Up to 20% of excess Cu (33 to 590 μmol m−2 y−1) and generally less than 20% of excess Zn (58 to 2170 μmol m−2 y−1) and Cd (6 to 260 μmol m−2 y−1) can be explained by delivery with fresh organic matter. Sequential extraction data suggest that the discrepancies between the known sources of Cd (and Cu) and their excess accumulation may be driven by the delivery of allochthonous sulphide minerals precipitated from the water column. Additionally, Cu may be scavenged by downward sinking organic material. In contrast, precipitation of Zn sulphide chiefly takes place in the sediment. Diffusive Zn fluxes into the sediment (21 to 1990 μmol m−2 y−1) match the excess Zn accumulation suggesting that Zn delivery is mediated by molecular diffusion from bottom waters. Considering the diverse behavioural pattern of trace metals observed in this study, we argue that declining oxygen and increasing hydrogen sulphide concentrations in a future ocean will modify trace metal fluxes at the seafloor and the trace metal stoichiometry of seawater.

Description: An understanding of how the coupled cycles of carbon, iron and sulfur in sediments respond to environmental change throughout Earth history requires the reconstruction of biogeochemical processes over a range of spatial and temporal scales. In this study, sediment cores from the southwestern Black Sea were analyzed to gain insight into past changes in biogeochemical processes with particular focus on the cycling of dissolved organic carbon (DOC). The sediment consists of Late Pleistocene deposits of iron oxide-rich and organic-poor lacustrine sediments, a Holocene sapropel layer deposited after the inflow of saline Mediterranean seawater about 9300 yr BP, and overlying recent marine sediments. The porewaters displayed high concentrations of DOC, acetate, dissolved iron and an extended depth interval over which sulfate and methane were both present. The historical fluctuations of the fluxes of carbon, sulfur and iron species at the seafloor that led to these present-day geochemical profiles, and which cannot be easily interpreted from the measured data alone, were hindcasted with a reaction-transport model. The model suggests that the inflow of Mediterranean seawater impacted the rain rate and reactivity of organic matter reaching the sediments, which shifted the sedimentary redox regimes throughout the Holocene that now are reflected on different lithology units. Organic matter in the sapropel layer is apparently the main source of modern-day accumulations of DOC and acetate, both of which probably sustained subsurface microbial activity throughout the post-glacial period. The ratio between DOC and dissolved inorganic carbon (DIC) flux to the bottom water decreased from ∼40% before the inflow of Mediterranean water to ∼2% at the present day. We suggest that the coexistence of methanogenesis and sulfate reduction was associated with sulfate-reducing bacteria and methanogens sharing common substrates of acetate and lactate and utilizing non-competitive substrates such as methylated compounds in the sapropel layer and in the bottom of modern marine deposits. Intense sulfur and iron cycling mainly took place in the organic-poor freshwater deposits, today characterized by high concentrations of dissolved iron and methane. In contrast to previous studies in similar environments, anaerobic oxidation of methane coupled to the reduction of ferric iron was negligible. The results have broad implications for coastal environments that are currently experiencing deoxygenation and seawater intrusion and also for understanding the role of DOC in the sedimentary carbon cycle.