Description: Dissolved silicon isotope compositions have been analysed for the first time in pore waters (δ30SiPW) of three short sediment cores from the Peruvian margin upwelling region with distinctly different biogenic opal content in order to investigate silicon isotope fractionation behaviour during early diagenetic turnover of biogenic opal in marine sediments. The δ30SiPW varies between +1.1‰ and +1.9‰ with the highest values occurring in the uppermost part close to the sediment–water interface. These values are of the same order or higher than the δ30Si of the biogenic opal extracted from the same sediments (+0.3‰ to +1.2‰) and of the overlying bottom waters (+1.1‰ to +1.5‰). Together with dissolved silicic acid concentrations well below biogenic opal saturation, our collective observations are consistent with the formation of authigenic alumino-silicates from the dissolving biogenic opal. Using a numerical transport-reaction model we find that approximately 24% of the dissolving biogenic opal is re-precipitated in the sediments in the form of these authigenic phases at a relatively low precipitation rate of 56 μmol Si cm−2 yr−1. The fractionation factor between the precipitates and the pore waters is estimated at −2.0‰. Dissolved and solid cation concentrations further indicate that off Peru, where biogenic opal concentrations in the sediments are high, the availability of reactive terrigenous material is the limiting factor for the formation of authigenic alumino-silicate phases.

Description: During the discovery and description of seven New Zealand methane seep sites, an infaunal assemblage dominated by ampharetid polychaetes was found in association with high seabed methane emission. This ampharetid-bed assemblage had a mean density of 57,000 ± 7800 macrofaunal individuals m−2 and a maximum wet biomass of 274 g m−2, both being among the greatest recorded from deep-sea methane seeps. We investigated these questions: Does the species assemblage present within these ampharetid beds form a distinct seep community on the New Zealand margin? and What type of chemoautotrophic microbes fuel this heterotrophic community? Unlike the other macro-infaunal assemblages, the ampharetid-bed assemblage composition was homogeneous, independent of location. Based on a mixing model of species-specific mass and isotopic composition, combined with published respiration measurements, we estimated that this community consumes 29–90 mmol C m−2 d−1 of methane-fueled biomass; this is 〉 290 times the carbon fixed by anaerobic methane oxidizers in these ampharetid beds. A fatty acid biomarker approach supported the finding that this community, unlike those previously known, consumes primarily aerobic methanotrophic bacteria. Due to the novel microbial fueling and high methane flux rates, New Zealand's ampharetid beds provide a model system to study the influence of metazoan grazing on microbially mediated biogeochemical cycles, including those that involve greenhouse gas emissions

Description: The discovery that foraminifera are able to use nitrate instead of oxygen as energy source for their metabolism has challenged our understanding of nitrogen cycling in the ocean. It was evident before that only prokaryotes and fungi are able to denitrify. Rate 5 estimates of foraminiferal denitrification were very sparse on a regional scale. Here, we present estimates of benthic foraminiferal denitrification rates from six stations at intermediate water depths in and below the Peruvian oxygen minimum zone (OMZ). Foraminiferal denitrification rates were calculated from abundance and assemblage composition of the total living fauna in both, surface and subsurface sediments, 10 as well as from individual species specific denitrification rates. A comparison with total benthic denitrification rates as inferred by biogeochemical models revealed that benthic foraminifera account for the total denitrification on the shelf between 80 and 250m water depth. They are still important denitrifiers in the centre of the OMZ around 320m (29–56% of the benthic denitrification) but play only a minor role at the lower OMZ 15 boundary and below the OMZ between 465 and 700m (3–7% of total benthic denitrification). Furthermore, foraminiferal denitrification was compared to the total benthic nitrate loss measured during benthic chamber experiments. Foraminiferal denitrification contributes 1 to 50% to the total nitrate loss across a depth transect from 80 to 700 m, respectively. Flux rate estimates ranged from 0.01 to 1.3 mmolm−2 d−1. Fur20 thermore we show that the amount of nitrate stored in living benthic foraminifera (3 to 705 μmolL−1) can be higher by three orders of magnitude as compared to the ambient pore waters in near surface sediments sustaining an important nitrate reservoir in Peruvian OMZ sediments. The substantial contribution of foraminiferal nitrate respiration to total benthic nitrate loss at the Peruvian margin, which is one of the main nitrate sink 25 regions in the world oceans, underpins the importance of previously underestimated role of benthic foraminifera in global biochemical cycles.

Description: A 2-Dimensional mathematical reaction-transport model was developed to study the impact of the mud-dwelling frenulate tubeworm Siboglinum sp. on the biogeochemistry of a sediment (MUC15) at the Captain Arutyunov mud volcano (CAMV). By explicitly describing the worm in its surrounding sediment, we are able to make budgets of processes occurring in- or outside of the worm, and to quantify how different worm densities and biomasses affect the anaerobic oxidation of methane (AOM) and sulfide reoxidation (HSox). The model shows that, at the observed densities, the presence of a thin worm body is sufficient to keep the upper 10 cm of sediment well homogenised with respect to dissolved substances, in agreement with observations. By this "bio-ventilation" activity, the worm pushes the sulfate-methane transition (SMT) zone downward to the posterior end of its body, and simultaneously physically separates the sulfide produced during the anaerobic oxidation of methane from oxygen. While there is little scope for AOM to take place in the tubeworm's body, 70% of the sulfide that is produced by sulfate reduction processes or that is advected in the sediment is preferentially shunted via the organism where it is oxidised by endosymbionts providing the energy for the worm's growth. The process of sulfide reoxidation, occurring predominantly in the worm's body is thus very distinct from the anaerobic oxidation of methane, which is a diffuse process that takes place in the sediments in the methane-sulfate transition zone. We show how the sulfide oxidation process is affected by increasing densities and length of the frenulates, and by upward advection velocity. Our biogeochemical model is one of the first to describe tubeworms explicitly. It can be used to directly link biological and biogeochemical observations at seep sites, and to study the impacts of mud-dwelling frenulates on the sediment biogeochemistry under varying environmental conditions. Also, it provides a tool to explore the competition between bacteria and fauna for available energy resources.

Description: Continental shelves are predominately (~70%) covered with permeable, sandy sediments. While identified as critical sites for intense oxygen, carbon, and nutrient turnover, constituent exchange across permeable sediments remains poorly quantified. The central North Sea largely consists of permeable sediments and has been identified as increasingly at risk for developing hypoxia. Therefore, we investigate the benthic O2 exchange across the permeable North Sea sediments using a combination of in situ microprofiles, a benthic chamber, and aquatic eddy correlation. Tidal bottom currents drive the variable sediment O2 penetration depth (from ~3 to 8 mm) and the concurrent turbulence-driven 25-fold variation in the benthic sediment O2 uptake. The O2 flux and variability were reproduced using a simple 1-D model linking the benthic turbulence to the sediment pore water exchange. The high O2 flux variability results from deeper sediment O2 penetration depths and increased O2 storage during high velocities, which is then utilized during low-flow periods. The study reveals that the benthic hydrodynamics, sediment permeability, and pore water redox oscillations are all intimately linked and crucial parameters determining the oxygen availability. These parameters must all be considered when evaluating mineralization pathways of organic matter and nutrients in permeable sediments.

Description: Many biological seep studies focused on the distribution, structure, nutrition and food web architecture of seep communities as well as on their interaction with the seep geochemistry. However, overall respiration at cold seeps received only little attention. We conducted in-situ oxygen flux measurements in combination with ex-situ oxygen micro-profiles, respiration measurements, as well as rate determinations of microbial methane and sulfate turnover to assess respiration pathways as well as carbon turnover at a seep habitat that was recently discovered alongside the Hikurangi Margin offshore northern New Zealand. This habitat is dominated by dense beds of tube-building, heterotrophic ampharetid polychaetes. Average total oxygen uptake (TOU) from this habitat was very high (83.7 mmol m− 2 day− 1). TOU at a non-seep reference site ranged between 2.7 and 5.8 mmol m− 2 day− 1. About 37% (30.8 mmol m− 2 day− 1) of the average TOU was consumed by ampharetids. Considering mean diffusive oxygen uptake (8.5 mmol m− 2 day− 1) the remaining fraction of ~ 53% of the TOU (44.4 mmol m− 2 day− 1) might be explained by respiration of epibenthic organisms as well as aerobic methane and sulfide oxidation at the sediment–water interface. The strongly negative carbon isotopic signatures (− 52.9 ± 5‰ VPDB) of the ampharetid tissues indicate a methane derived diet. However, carbon production via anaerobic oxidation of methane (AOM) was too low (0.1 mmol C m− 2 day− 1) to cover the mean carbon demand of the ampharetid communities (21 mmol C m− 2 day− 1). Likely, organic carbon generated via aerobic methane oxidation represents their major carbon source. This is in contrast to other seep habitats, where energy bound in methane is partly transferred to sulfide via AOM and finally consumed by sulfide-oxidizing chemoautotrophs providing carbon that subsequently enters the benthic food web.

Description: This study presents benthic data from 12 samplings from February to December 2010 in a 28 m deep channel in the southwest Baltic Sea. In winter, the distribution of solutes in the porewater was strongly modulated by bioirrigation which efficiently flushed the upper 10 cm of sediment, leading to concentrations which varied little from bottom water values. Solute pumping by bioirrigation fell sharply in the summer as the bottom waters became severely hypoxic (〈 2 μM O2). At this point the giant sulfide-oxidizing bacteria Beggiatoa was visible on surface sediments. Despite an increase in O2 following mixing of the water column in November, macrofauna remained absent until the end of the sampling. Contrary to expectations, metabolites such as dissolved inorganic carbon, ammonium and hydrogen sulfide did not accumulate in the upper 10 cm during the hypoxic period when bioirrigation was absent, but instead tended toward bottom water values. This was taken as evidence for episodic bubbling of methane gas out of the sediment acting as an abiogenic irrigation process. Porewater–seawater mixing by escaping bubbles provides a pathway for enhanced nutrient release to the bottom water and may exacerbate the feedback with hypoxia. Subsurface dissolved phosphate (TPO4) peaks in excess of 400 μM developed in autumn, resulting in a very large diffusive TPO4 flux to the water column of 0.7 ± 0.2 mmol m−2 d−1. The model was not able to simulate this TPO4 source as release of iron-bound P (Fe–P) or organic P. As an alternative hypothesis, the TPO4 peak was reproduced using new kinetic expressions that allow Beggiatoa to take up porewater TPO4 and accumulate an intracellular P pool during periods with oxic bottom waters. TPO4 is then released during hypoxia, as previous published results with sulfide-oxidizing bacteria indicate. The TPO4 added to the porewater over the year by organic P and Fe–P is recycled through Beggiatoa, meaning that no additional source of TPO4 is needed to explain the TPO4 peak. Further experimental studies are needed to strengthen this conclusion and rule out Fe–P and organic P as candidate sources of ephemeral TPO4 release. A measured C/P ratio of 〈 20 for the diffusive flux to the water column during hypoxia directly demonstrates preferential release of P relative to C under oxygen-deficient bottom waters. This coincides with a strong decrease in dissolved inorganic N/P ratios in the water column to ~ 1. Our results suggest that sulfide oxidizing bacteria could act as phosphorus capacitors in systems with oscillating redox conditions, releasing massive amounts of TPO4 in a short space of time and dramatically increasing the internal loading of TPO4 to the overlying water.

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: In recent decades, the central North Sea has been experiencing a general trend of decreasing dissolved oxygen (O2) levels during summer. To understand potential causes driving lower O2, we investigated a 3-day period of summertime turbulence and O2 dynamics in the thermocline and bottom boundary layer (BBL). The study focuses on coupling biogeochemical with physical transport processes to identify key drivers of the O2 and organic carbon turnover within the BBL. Combining our flux observations with an analytical process-oriented approach, we resolve drivers that ultimately contribute to determining the BBL O2 levels. We report substantial turbulent O2 fluxes from the thermocline into the otherwise isolated bottom water attributed to the presence of a baroclinic near-inertial wave. This contribution to the local bottom water O2 and carbon budgets has been largely overlooked and is shown to play a role in promoting high carbon turnover in the bottom water while simultaneously maintaining high O2 concentrations. This process may become suppressed with warming climate and stronger stratification, conditions which could promote migrating algal species that potentially shift the O2 production zone higher up within the thermocline.