Modeling effects of patchiness and biological variability on transport rates within bioturbated sediments

Bioturbation models are typically one-dimensional, with the underlying assumption that tracer gradients are predominantly vertical, and that sediment reworking is laterally homogeneous. These models implicitly assume that bioturbation activity does not vary with horizontal location on the sediment surface. Benthic organisms, however, are often patchily distributed. Moreover, due to natural variability, bioturbation activity varies among individuals within a population, and hence, among bioturbated patches. Here we analyze a 1D model formulation that explicitly includes patchiness, exemplified by conveyor-belt transport. The patchiness is represented with one coefficient αb, as the fraction of bioturbated areas of the total area. First, all the mixed patches are considered to feature the same bioturbation rates. Then variability of these rates among patches is introduced in the model. The model is analyzed through different scenarios to assess the influence of patchiness and biological variability on the resulting tracer profiles (luminophores, 234Th and 210Pb). With patchiness, the principal feature of the resulting profiles is exponential decrease of tracer concentrations near the SWI, due to the accumulation of particles in the nonbioturbated patches, and the presence of subsurface peaks or anomalous concentrations at depth, as the result of particle transport in the bioturbated patches. This pattern is unusual compared to published patterns for conveyor-belt transport. Adding intra-population variability in bioturbation rates induces biodiffusive-like transport, especially with luminophores. This theoretical work provides new insights about the influence of patch structure on particle dispersion within sediments and proposes a new applicable approach to model various bioturbation processes (type and rates of transport) that can be horizontally distributed in sediments

Influence of advective bio-irrigation on carbon and nitrogen cycling in sandy sediments

In sandy sediments, the burrow ventilation activity of benthic macrofauna can generate substantial advective flows within the sediment surrounding their burrows. Here we investigated the effects of such advective bio-irrigation on carbon and nitrogen cycling in sandy sediments. To this end, we combined a range of complementary experimental and modelling approaches in a microcosm study of the lugworm Arenicola marina (Polychaeta: Annelida). Bio-irrigation rates were determined using uranine as a tracer, while benthic fluxes of oxygen (O2), total carbon dioxide (TCO2), dissolved inorganic nitrogen (NH4+, ΣNO2− + NO3−) and dinitrogen (N2) were measured in closed-core incubations containing lugworms acclimatized for a relatively short (2 d) and long (3 wk) duration. The fluxes induced by A. marina were compared to those induced by mechanical mimics that simulate the flow pattern induced by the lugworm. These mechanical mimics proved a useful tool to simulate the effect of lugworm irrigation on sediment biogeochemistry. Subsequently, reactive transport model simulations were performed to check the consistency of the measured fluxes and rates, and to construct closed mass balances for sedimentary nitrogen. This reactive transport model successfully captured the essential features of the nitrogen cycling within the sediment. Advective irrigation by both lugworm and mechanical mimics significantly stimulated the sediments O2 consumption, organic matter mineralization rate (TCO2 release), and denitrification rate (N2 production). While sedimentary O2 consumption was directly correlated to advective input of O2, increasing irrigation rates increased the importance of coupled nitrification-denitrification over the external input of nitrate from the overlying water

Rheological and Microstructural Changes of Oat and Barley Starches During Heating and Cooling

Microstructural and rheological changes in barley and oat starch dispersions during heating and cooling were studied by light microscopy and dynamic viscoelastic measurements. The two starch pastes showed similar viscoelastic properties after gelatinization, but during cooling the 20% barley starch pastes heated at 95°C underwent a sharp transition in viscoelastic behaviour probably due to the gelation of amylose. This transition was shifted to lower temperatures at 10% starch concentration. Microstructural studies of an 8% barley starch dispersion heated to 90°C using the smear technique showed amylose to form a network structure around the granules. The granules in starch paste heated to 95°C were poorly stained and amylopectin was fragmented. Microscopic examination of an embedded section of the cooled barley starch gel showed amylose to form a continuous phase in which starch granules were dispersed. G\u27 increased below 80°C during cooling of 10% oat starch dispersions preheated at 95 °C. No rheological changes occurred when they were preheated at only 90°C. Microstructural studies of an 8% oat starch dispersion heated to 90°C using the smear technique showed amylose to form a network structure around the granules. Part of the granule structure had already broken down. Heating to 95°C induced considerable changes in the granule structure of oat starch gels. Amylopectin formed a very fine network. Microscopic examination of embedded sections of the cooled, stored gel showed a much coarser structure compared with that of the smear

Experimental assessment of particle mixing fingerprints in the deposit-feeding bivalve Abra alba (Wood)

Particle mixing induced by the deposit-feeding bivalve Abra alba was assessed using a new experimental approach allowing for the tracking of individual particle displacements. This approach combines the adaptation of existing image acquisition techniques with new image analysis software that tracks the position of individual particles. This led to measurements of particle mixing fingerprints, namely the frequency distributions of particle waiting times, and of the characteristics (i.e. direction and length) of their jumps. The validity of this new approach was assessed by comparing the so-measured frequency distributions of jump characteristics with the current qualitative knowledge regarding particle mixing in the genus Abra. Frequency distributions were complex due to the coexistence of several types of particle displacements and cannot be fitted with the most commonly used procedures when using the Continuous Time Random Walk (CTRW) model. Our approach allowed for the spatial analysis of particle mixing, which showed: 1) longer waiting times; 2) more frequent vertical jumps; and 3) shorter jump lengths deep in the sediment column than close to the sediment-water interface. This resulted in lower DbX and DbY (vertical and horizontal particle mixing bioffusion coefficients) deep in the sediment column. Our results underline the needs for: 1) preliminary checks of the adequacy of selected distributions to the species/communities studied; and 2) an assessment of vertical changes in particle mixing fingerprints when using CTRW

Cable bacteria generate a firewall against euxinia in seasonally hypoxic basins

Seasonal oxygen depletion (hypoxia) in coastal bottom waters can lead to the release and persistence of free sulfide (euxinia), which is highly detrimental to marine life. Although coastal hypoxia is relatively common, reports of euxinia are less frequent, which suggests that certain environmental controls can delay the onset of euxinia. However, these controls and their prevalence are poorly understood. Here we present field observations from a seasonally hypoxic marine basin (Grevelingen, The Netherlands), which suggest that the activity of cable bacteria, a recently discovered group of sulfur-oxidizing microorganisms inducing long-distance electron transport, can delay the onset of euxinia in coastal waters. Our results reveal a remarkable seasonal succession of sulfur cycling pathways, which was observed over multiple years. Cable bacteria dominate the sediment geochemistry in winter, whereas, after the summer hypoxia, Beggiatoaceae mats colonize the sediment. The specific electrogenic metabolism of cable bacteria generates a large buffer of sedimentary iron oxides before the onset of summer hypoxia, which captures free sulfide in the surface sediment, thus likely preventing the development of bottom water euxinia. As cable bacteria are present in many seasonally hypoxic systems, this euxinia-preventing firewall mechanism could be widely active, and may explain why euxinia is relatively infrequently observed in the coastal ocean

Biogeochemical impacts of fish farming on coastal sediments: Insights into the functional role of cable bacteria

Fish farming in sea cages is a growing component of the global food industry. A prominent ecosystem impact of this industry is the increase in the downward flux of organic matter, which stimulates anaerobic mineralization and sulfide production in underlying sediments. When free sulfide is released to the overlying water, this can have a toxic effect on local marine ecosystems. The microbially-mediated process of sulfide oxidation has the potential to be an important natural mitigation and prevention strategy that has not been studied in fish farm sediments. We examined the microbial community composition (DNA-based 16S rRNA gene) underneath two active fish farms on the Southwestern coast of Iceland and performed laboratory incubations of resident sediment. Field observations confirmed the strong geochemical impact of fish farming on the sediment (up to 150 m away from cages). Sulfide accumulation was evidenced under the cages congruent with a higher supply of degradable organic matter from the cages. Phylogenetically diverse microbes capable of sulfide detoxification were present in the field sediment as well as in lab incubations, including cable bacteria (Candidatus Electrothrix), which display a unique metabolism based on long-distance electron transport. Microsensor profiling revealed that the activity of cable bacteria did not exert a dominant impact on the geochemistry of fish farm sediment at the time of sampling. However, laboratory incubations that mimic the recovery process during fallowing, revealed successful enrichment of cable bacteria within weeks, with concomitant high sulfur-oxidizing activity. Overall our results give insight into the role of microbially-mediated sulfide detoxification in aquaculture impacted sediments.publishedVersio

Ongoing transients in carbonate compensation

Uptake of anthropogenic CO2 is acidifying the oceans. Over the next 2000 years, this will modify the dissolution and preservation of sedimentary carbonate. By coupling new formulas for the positions of the calcite saturation horizon, zsat, the compensation depth, zcc, and the snowline, zsnow, to a biogeochemical model of the oceanic carbonate system, we evaluate how these horizons will change with ongoing ocean acidification. Our model is an extended Havardton-Bear-type box model, which includes novel kinetic descriptions for carbonate dissolution above, between, and below these critical depths. In the preindustrial ocean, zsat and zcc are at 3939 and 4750 m, respectively. When forced with the IS92a CO2 emission scenario, the model forecasts (1) that zsat will rise rapidly (“runaway” conditions) so that all deep water becomes undersaturated, (2) that zcc will also rise and over 1000 years will pass before it will be stabilized by the dissolution of previously deposited CaCO3, and (3) that zsnow will respond slowly to acidification, rising by ∼1150 m during a 2000 year timeframe. A further simplified model that equates the compensation and saturation depths produces quantitatively different results. Finally, additional feedbacks due to acidification on calcification and increased atmospheric CO2 on organic matter productivity strongly affect the positions of the compensation horizons and their dynamics.

The cell envelope structure of cable bacteria

Cable bacteria are long, multicellular micro-organisms that are capable of transporting electrons from cell to cell along the longitudinal axis of their centimeter-long filaments. The conductive structures that mediate this long-distance electron transport are thought to be located in the cell envelope. Therefore, this study examines in detail the architecture of the cell envelope of cable bacterium filaments by combining different sample preparation methods (chemical fixation, resin-embedding, and cryo-fixation) with a portfolio of imaging techniques (scanning electron microscopy, transmission electron microscopy and tomography, focused ion beam scanning electron microscopy, and atomic force microscopy). We systematically imaged intact filaments with varying diameters. In addition, we investigated the periplasmic fiber sheath that remains after the cytoplasm and membranes were removed by chemical extraction. Based on these investigations, we present a quantitative structural model of a cable bacterium. Cable bacteria build their cell envelope by a parallel concatenation of ridge compartments that have a standard size. Larger diameter filaments simply incorporate more parallel ridge compartments. Each ridge compartment contains a similar to 50 nm diameter fiber in the periplasmic space. These fibers are continuous across cell-to-cell junctions, which display a conspicuous cartwheel structure that is likely made by invaginations of the outer cell membrane around the periplasmic fibers. The continuity of the periplasmic fibers across cells makes them a prime candidate for the sought-after electron conducting structure in cable bacteria

The Cell Envelope Structure of Cable Bacteria

Cable bacteria are long, multicellular micro-organisms that are capable of transporting electrons from cell to cell along the longitudinal axis of their centimeter-long filaments. The conductive structures that mediate this long-distance electron transport are thought to be located in the cell envelope. Therefore, this study examines in detail the architecture of the cell envelope of cable bacterium filaments by combining different sample preparation methods (chemical fixation, resin-embedding, and cryo-fixation) with a portfolio of imaging techniques (scanning electron microscopy, transmission electron microscopy and tomography, focused ion beam scanning electron microscopy, and atomic force microscopy). We systematically imaged intact filaments with varying diameters. In addition, we investigated the periplasmic fiber sheath that remains after the cytoplasm and membranes were removed by chemical extraction. Based on these investigations, we present a quantitative structural model of a cable bacterium. Cable bacteria build their cell envelope by a parallel concatenation of ridge compartments that have a standard size. Larger diameter filaments simply incorporate more parallel ridge compartments. Each ridge compartment contains a ~50 nm diameter fiber in the periplasmic space. These fibers are continuous across cell-to-cell junctions, which display a conspicuous cartwheel structure that is likely made by invaginations of the outer cell membrane around the periplasmic fibers. The continuity of the periplasmic fibers across cells makes them a prime candidate for the sought-after electron conducting structure in cable bacteria