Impact of boundary layer flow velocity on oxygen utilisation in coastal sediments

Small pressure gradients generated by boundary flow-topography interactions cause advective pore water flows in permeable sediments. Advective pore water exchange enhances the flux of solutes between the sediment and the overlying water, thus generating conditions for an increased utilisation of oxygen. We compared a less permeable (k = 5 x 10(-12) m(2)) with a permeable sediment (k = 5 x 10(-11) m(2)) typical for coastal and shelf sediments. Total oxygen utilisation (TOU) in incubated sediment cores was measured in 10 laboratory experiments using recirculating flow tanks (33 runs). TOU was a function of now velocity in permeable sediment where advective pore water now occurred. TOU increased with the increasing volume of sediment flushed with oxygenated water. We found that TOU increased by 91 +/- 23% in coarse sand when now increased from 3 to 14 cm s(-1) (38 mounds m(-2) height 10 to 30 mm, now measured 8 cm above the sediment). Addition of fresh algal material caused a stronger stimulation of TOU in the coarse sand than in the fine sand (4 additional flume runs). After the addition, intensive oxygen consumption reduced the oxygen penetration depth in the advectively flushed zone of the coarse sediment. However, counteracting this process, advective flow maintained an oxic sediment volume still larger than that in the less permeable sediment. Flow-enhanced oxygen utilisation is potentially effective in permeable beds of coastal and shelf regions, in contrast to the situation in cohesive sediments limited by predominantly diffusive oxygen supply

Sedimentary pyrite sulfur isotope compositions preserve signatures of the surface microbial mat environment in sediments underlying low-oxygen cyanobacterial mats

The sedimentary pyrite sulfur isotope (delta S-34) record is an archive of ancient microbial sulfur cycling and environmental conditions. Interpretations of pyrite delta S-34 signatures in sediments deposited in microbial mat ecosystems are based on studies of modern microbial mat porewater sulfide delta S-34 geochemistry. Pyrite delta S-34 values often capture delta S-34 signatures of porewater sulfide at the location of pyrite formation. However, microbial mats are dynamic environments in which biogeochemical cycling shifts vertically on diurnal cycles. Therefore, there is a need to study how the location of pyrite formation impacts pyrite delta S-34 patterns in these dynamic systems. Here, we present diurnal porewater sulfide delta S-34 trends and delta S-34 values of pyrite and iron monosulfides from Middle Island Sinkhole, Lake Huron. The sediment-water interface of this sinkhole hosts a low-oxygen cyanobacterial mat ecosystem, which serves as a useful location to explore preservation of sedimentary pyrite delta S-34 signatures in early Earth environments. Porewater sulfide delta S-34 values vary by up to similar to 25 parts per thousand throughout the day due to light-driven changes in surface microbial community activity that propagate downwards, affecting porewater geochemistry as deep as 7.5 cm in the sediment. Progressive consumption of the sulfate reservoir drives delta S-34 variability, instead of variations in average cell-specific sulfate reduction rates and/or sulfide oxidation at different depths in the sediment. The delta S-34 values of pyrite are similar to porewater sulfide delta S-34 values near the mat surface. We suggest that oxidative sulfur cycling and other microbial activity promote pyrite formation in and immediately adjacent to the microbial mat and that iron geochemistry limits further pyrite formation with depth in the sediment. These results imply that primary delta S-34 signatures of pyrite deposited in organic-rich, iron-poor microbial mat environments capture information about microbial sulfur cycling and environmental conditions at the mat surface and are only minimally affected by deeper sedimentary processes during early diagenesis

In situ measurement of fluid flow from cold seeps at active continental margins

In situ measurement of fluid flow rates from active margins is an important parameter in evaluating dissolved mass fluxes and global geochemical balances as well as tectonic dewatering during developments of accretionary prisms. We have constructed and deployed various devices that allow for the direct measurement of this parameter. An open bottom barrel with an exhaust port at the top and equipped with a mechanical flowmeter was initially used to measure flow rates in the Cascadia accretionary margin during an Alvin dive program in 1988. Sequentially activated water bottles inside the barrel sampled the increase of venting methane in the enclosed body of water. Subsequently, a thermistor flowmeter was developed to measure flow velocities from cold seeps. It can be used to measure velocities between 0.01 and 50 cm s−1, with a response time of 200 ms. It was deployed again by the submersible Alvin in visits to the Cascadia margin seeps (1990) and in conjunction with sequentially activated water bottles inside the barrel. We report the values for the flow rates based on the thermistor flowmeter and estimated from methane flux calculations. These results are then compared with the first measurement at Cascadia margin employing the mechanical flowmeter. The similarity between water flow and methane expulsion rates over more than one order of magnitude at these sites suggests that the mass fluxes obtained by our in situ devices may be reasonably realistic values for accretionary margins. These values also indicate an enormous variability in the rates of fluid expulsion within the same accretionary prism. Finally, during a cruise to the active margin off Peru, another version of the same instrument was deployed via a TV-controlled frame within an acoustic transponder net from a surface ship, the R.V. Sonne. The venting rates obtained with the thermistor flowmeter used in this configuration yielded a value of 4411 m−2 day−1 at an active seep on the Peru slope. The ability for deployment of deep-sea instruments capable of measuring fluid flow rates and dissolved mass fluxes from conventional research vessels will allow easier access to these seep sites and a more widespread collection of the data needed to evaluate geochemical processes resulting from venting at cold seeps on a global basis. Comparison of the in situ flow rates from steady-state compactive dewatering models differ by more than 4 orders of magnitude. This implies that only a small area of the margin is venting and that there must be recharge zones associated with venting at convergent margin

Deep sequencing of subseafloor eukaryotic rRNA reveals active fungi across marine subsurface provinces

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e56335, doi:10.1371/journal.pone.0056335.The deep marine subsurface is a vast habitat for microbial life where cells may live on geologic timescales. Because DNA in sediments may be preserved on long timescales, ribosomal RNA (rRNA) is suggested to be a proxy for the active fraction of a microbial community in the subsurface. During an investigation of eukaryotic 18S rRNA by amplicon pyrosequencing, unique profiles of Fungi were found across a range of marine subsurface provinces including ridge flanks, continental margins, and abyssal plains. Subseafloor fungal populations exhibit statistically significant correlations with total organic carbon (TOC), nitrate, sulfide, and dissolved inorganic carbon (DIC). These correlations are supported by terminal restriction length polymorphism (TRFLP) analyses of fungal rRNA. Geochemical correlations with fungal pyrosequencing and TRFLP data from this geographically broad sample set suggests environmental selection of active Fungi in the marine subsurface. Within the same dataset, ancient rRNA signatures were recovered from plants and diatoms in marine sediments ranging from 0.03 to 2.7 million years old, suggesting that rRNA from some eukaryotic taxa may be much more stable than previously considered in the marine subsurface.This work was performed with funding from the Center for Dark Energy Biosphere Investigations (C-DEBI) to William Orsi (OCE-0939564) and The Ocean Life Institute (WHOI) to Virginia Edgcomb (OLI-27071359)

Comparative Composition, Diversity and Trophic Ecology of Sediment Macrofauna at Vents, Seeps and Organic Falls

Sediments associated with hydrothermal venting, methane seepage and large organic falls such as whale, wood and plant detritus create deep-sea networks of soft-sediment habitats fueled, at least in part, by the oxidation of reduced chemicals. Biological studies at deep-sea vents, seeps and organic falls have looked at macrofaunal taxa, but there has yet to be a systematic comparison of the community-level attributes of sediment macrobenthos in various reducing ecosystems. Here we review key similarities and differences in the sediment-dwelling assemblages of each system with the goals of (1) generating a predictive framework for the exploration and study of newly identified reducing habitats, and (2) identifying taxa and communities that overlap across ecosystems. We show that deep-sea seep, vent and organic-fall sediments are highly heterogeneous. They sustain different geochemical and microbial processes that are reflected in a complex mosaic of habitats inhabited by a mixture of specialist (heterotrophic and symbiont-associated) and background fauna. Community-level comparisons reveal that vent, seep and organic-fall macrofauna are very distinct in terms of composition at the family level, although they share many dominant taxa among these highly sulphidic habitats. Stress gradients are good predictors of macrofaunal diversity at some sites, but habitat heterogeneity and facilitation often modify community structure. The biogeochemical differences across ecosystems and within habitats result in wide differences in organic utilization (i.e., food sources) and in the prevalence of chemosynthesis-derived nutrition. In the Pacific, vents, seeps and organic-falls exhibit distinct macrofaunal assemblages at broad-scales contributing to ß diversity. This has important implications for the conservation of reducing ecosystems, which face growing threats from human activities

A diver observatory for in-situ studies in sublittoral sediments

In marine sediments macrofaunal organisms often produce deep reaching tubes or burrows that greatly influence the biogeochemistry of the inhabited sediment (Hylleberg & Henriksen 1980, Aller 1982, Huettel 1990). Among the burrowing organisms thalassinidean shrimps are a group of decapod crustaceans that are often abundant in coastal sediments (Suchanek 1985, Griffis & Suchanek 1993) and build complex burrow systems reaching up to 2.5 m or more into the sediment (Pemberton et at. 1976), Recent studies focused on the species Callianassa truncata that occurs at high densities (120 ind. m(-2)) in shallow-water sediments off the coast of the Italian island Giglio in the Mediterranean sea and constructs elaborate burrows to a sediment depth of 80-100 cm (Ziebis et al. 1996a). Like many burrowing organisms it produces a ventilation current through its burrow system. Many attempts to study this ventilation in laboratory systems were difficult due to the constraints of aquariums and the difficulty of measuring inside burrows without destroying the sediment structure (Witbaard & Duineveld 1989, Forster & Graf 1992, 1995). Our interest was to gain information on the in situ burrowing behaviour and to find out how deep oxygen-rich water is actually pumped into the sediment by bio-irrigation and how this is affecting the sediment chemistry. We report here the construction of a diver observatory and its deployment in the field for in situ investigations of deep-burrowing organisms and their effects on the sedimentary environment. The large, hexagonal container (1.2 m high, 2 m diameter) was built of 6 transparent acrylic walls held by a stainless steel frame, and was covered by a lid made of PVC to avoid light penetration. It was buried in the sediment so that the lid was level with the sediment surface. The sediment from inside was removed to allow divers to enter through a door in the lid in order to perform observations and measurements from inside the observatory into the surrounding sediment, We demonstrate the unique possibilities of observing the behaviour of burrowing animals in their natural habitat down to a sediment depth of Im and show the opportunities of direct sampling of pore and burrow water in intact systems as well as detailed in situ measurements through silicone-filled ports in the walls of the observatory

Flow-induced uptake of particulate matter in permeable sediments

We demonstrate the fast transfer of suspended particles from the boundary layer into the upper strata (z 2 x 10(-11) m(2)) incubated in a laboratory flume. Increased pressure up- and downstream of small mounds (z = 2.5 cm) drove water 5.5 cm into the core, carrying suspended particles (1 mu m) to 2.2-cm sediment depth within 10 h. Simultaneously, decreased pressure at the downstream slope of the protrusions drew pore fluid from deeper layers (z less than or equal to 10 cm) to the surface. In the sediment, friction reduced the velocity of the particulate tracers, resulting in size fractionation and layers of increased particle concentration. Ripple topography (0.8-2.8 cm high) enhanced interfacial particle (1 mu m) flux by a factor 2.3 when compared to a level control core. The pathways of the particle and solute tracers below a sediment ripple are explained with a source-sink model that describes the pore flow velocity field. Our results suggest that bedform-induced interfacial flows are important for the uptake of particulate organic matter into permeable shelf sediments

Impact of biogenic sediment topography on oxygen fluxes in permeable seabeds

Boundary layer flows, interacting with roughness elements at the sediment surface, alter the small-scale flow regime. Consequently, pressure differences are generated that are the driving forces for advective pore-water flow. We investigated topography-induced transport of oxygen in a permeable coastal sediment from the Mediterranean Sea (Isola del Giglio, Italy). The sediment surface was characterized by a high abundance (120 m(-2)) of sediment mounds (average height: 4 cm) built by the mud shrimp Callianassa truncata (Decapoda, Thalassinidea). Boundary layer flow velocities recorded in situ ranged between 2 and 16 cm s(-1). Detailed experiments were performed in a recirculating laboratory flow channel. A natural sediment core, 20 cm deep with a surface area of 0.3 m(2), was exposed to a unidirectional flow of varying current velocity (3, 6, 10 cm s(-1)). The alteration of the small-scale now regime at a sediment mound was documented by vertical velocity profiles measured in 1 mm resolution with temperature-compensated thermistor probes. Oxygen distribution in the sediment was investigated with Clark-type microelectrodes. At a smooth surface, oxygen penetration depth in the permeable sediment did not exceed 4 mm, independent of flow velocity. In contrast, the topography-induced advective oxygen transport increased significantly with current speed. Oxygen reached down to almost 40 mm at the upstream foot of a 1 cm high sediment mound at a now velocity of 10 cm s(-1). Thus, the oxic sediment volume increased locally by a factor of 4.8 compared to the oxic zone underneath a smooth surface. At a natural abundance of 120 mounds m(-2) the oxic sediment volume per m(2) seabed was calculated to be 3.3-fold higher than in a seabed with a smooth surface. In a parallel experiment, advective solute transport was also demonstrated in a less permeable sediment (k = 5 x 10(-12) m(2)) from the North Sea intertidal flat. Due to the lower permeability the effect on O-2 transport was less than in the Mediterranean sand, but oxygen penetration depth increased locally 2-fold at a sediment mound under a flow velocity of 10 cm s(-1). The experiments showed the high spatial and temporal variability of oxygen distribution in a coastal seabed depending on sediment surface topography, boundary layer now velocities and sediment permeability

Advective transport affecting metal and nutrient distributions and interfacial fluxes in permeable sediments

Our laboratory flume experiments demonstrate that advective porewater flows produce biogeochemical reaction zones in permeable sediments, leading to specific and reproducible complex patterns of Fe, Mn, and nutrients. Oxygenated water, forced into the sediment when boundary flows were deflected by protruding sediment structures, generated distinct zones of nitrification and ferric iron precipitation. This inflow was balanced by ammonium-rich porewater ascending from deeper sediment layers, thereby creating an anoxic channel where dissolved Fe(2+) and Mn(2+) could reach the surface. Between the zones of ferric iron precipitation and Fe(2+) upwelling, a layer with increased manganese oxide and solid phase Fe(II) concentrations formed, indicating redo?( reaction between these components. The establishment of topography on the previously smooth sediment surface reversed the net interfacial flux of solutes. While the smooth control core was found to be a sink for metals and nutrients, the sediment with mounds acted as a source for these substances. Our experiments show that in sandy sediment with an oxidised surface layer, reduced metal species can be released to the water column by flow-topography interactions. We conclude that advective transport processes constitute an important process controlling biogeochemical zonations and fluxes in permeable sea beds. Copyright (C) 1998 Elsevier Science Ltd