1,721,094 research outputs found
Cadmium transport in sediments by tubificid bioturbation: An assessment of model complexity
Full text linkBiogeochemistry of metals in aquatic sediments is strongly influenced by bioturbation. To determine the effects of biological transport on cadmium distribution in freshwater sediments, a bioturbation model is explored that describes the conveyor-belt feeding of tubificid oligochaetes. A stepwise modelling strategy was adopted to constrain the many parameters of the model: (i) the tubificid transport model was first calibrated on four sets of microspheres (inert solid tracer) profiles to constrain tubificid transport; (ii) the resulting transport coefficients were subsequently applied to simulate the distribution of both particulate and dissolved cadmium. Firstly, these simulations provide quantitative insight into the mechanism of tubificid bioturbation. Values of transport coefficients compare very well with the literature, and based on this, a generic model of tubificid bioturbation is proposed. Secondly, the application of the model to cadmium dataset sheds a light on the behaviour of cadmium under tubificid bioturbation. Cadmium enters the sediment in two ways. In one pathway, cadmium enters the sediment in the dissolved phase, is rapidly absorbed onto solid particles, which are then rapidly transported to depth by the tubificids. In the other pathway, cadmium is adsorbed to particles in suspension in the overlying water, which then settle on the sediment surface, and are transported downwards by bioturbation. In a final step, we assessed the optimal model complexity for the present dataset. To this end, the two-phase conveyor-belt model was compared to two simplified versions. A solid phase-only conveyorbelt model also provides good results: the dissolved phase should not be explicitly incorporated because cadmium adsorption is fast and bioirrigation is weak. Yet, a solid phase-only biodiffusive model does not perform adequately, as it does not mechanistically capture the conveyor-belt transport at short time-scales
Oxidation and origin of organic matter in surficial eastern Mediterranean hemipelagic sediments
No full textAerobic mineralisation of Corg in surface sediments of the deep (>2000 m water depth) eastern Mediterranean Sea has been quantified by analysis of detailed box core Corg concentration versus depth profiles and the modelling environment for early diagenetic problems MEDIA. The reactive fraction comprises 60–80% of the total Corg reaching the sediments and is largely oxidised within the surficial 10 cm. A non-reactive Corg fraction (GNR) dominates at depths >10 cm, and makes up 20–40% of the total Corg flux to the sediments. First-order rate constants for decomposition of the reactive fraction calculated from the Corg profiles range from 5.4 × 10-3 to 8.0 × 10-3 y-1 to 8.0 × 10-3 y-1. Total mineralization rates in the surface sediment are between 1.7 and 2.6 µmol C cm-2 y-1 and thus are typical for oligotrophic, deep-sea environments. The low fluxes and rapid remineralisation of Corg are accompanied by 210Pbexcess surface mixed layers which are only 2 cm deep, among the thinnest reported for oxygenated marine sediments. Model results indicate a mismatch between the Corg profiles and O2 microprofiles which were measured onboard ship. This can be attributed to a combination of decompression artefacts affecting onboard measurement of the O2 profiles or the leakage of oxygen into the core during handling on deck. Furthermore, the used Db values, based on 210Pb, may not be fully appropriate; calculations with higher Db values improve the O2 fits. The surficial sediment δ13Corg values of -22 become less negative with increasing depth and decreasing Corg concentrations. The major 13C change occurs in the top 3 to 4 cm and coincides with the interval where most of the organic carbon oxidation takes place. This indicates that the reactive fraction of organic matter, commonly assumed to be marine, has a more negative δ13Corg than the refractory fraction, usually held to be terrestrial. Palaeoproductivity estimates calculated from the sediment data by means of literature algorithms yield low surface productivities (12–88 gC m-2 y-1), which are in good agreement with field measurements of primary productivity in other studies. Such values are, however, significantly lower than those indicated by recent productivity maps of the area derived from satellite imagery (>100 gC m-2 y-1)
The charge transport mechanism in cable bacteria
No full textIn this dissertation, the charge transport mechanism in the conductive fibres of cable bacteria is investigated. In Chapter 1, the research field of bacterial electricity is introduced. Three kinds of bacterial nanowires are discussed: Shewenella nanowires, Geobacter nanowires and the conductive fibres fromcable bacteria. Even though the three types of protein wires are all conductive, the cable bacteria’s protein wires stand out because their activation energy of conductance is much lower than that of the other nanowires and because they transport electrons over centimeter instead of micrometer distances. These differences suggest they have a distinct charge transport mechanism. To put different transport mechanisms in more context, metallic conduction, semiconduction, and hopping conduction are treated side by side and emphasis is placed on the temperature dependence of conductivity....BT/Environmental Biotechnolog
Biogeochemistry: Oxygen burrowed away
No full textMulticellular animals probably evolved at the seafloor after a rise in oceanic oxygen levels. Biogeochemical model simulations suggest that as these animals started to rework the seafloor, they triggered a negative feedback that reduced global oxygen
The ecophysiology of multicellular cable bacteria: insights from single cell imaging techniques
No full textCable bacteria form centimeter-long, multicellular filaments than can consist of ten thousands of cells. They evolved a unique energy metabolism that involves co-operation among cells that separately perform oxidation of the electron donor (sulfide, H2S) and reduction of the electron acceptor (oxygen, O2). This division of labor is facilitated via long-range electrical currents that run from cell to cell along a network of conductive fibers. This research provides further insights into the metabolism of these peculiar organisms. It was discovered that only the cells that oxidize sulfide have the capacity for growth whereas the cells that reduce oxygen serve to dispense electrons as quickly as possible without any growth. Thus, these oxygen-reducing cells appear to provide a kind of “community service” to the filament by ensuring an electron current without any capacity for growth. However, access to oxygen is essential for the survival of the filament and it appears to pace the cycles of growth and cell division among a filament where cell division is synchronized among cells within a filament. Cells residing in the oxic zone are believed to (temporarily) rely on storage compounds of which polyphosphate (poly-P) is most ubiquitously found in cable bacteria. Poly-P is an inorganic biopolymer that consists of tens to hundreds of phosphate residues linearly linked together by high-energy phosphoanhydride bonds. We found poly-P activity in almost all cable bacteria cells and it appears to have an essential role in the metabolic regulation of cable bacteria
Bacterial chemoautotrophy in coastal sediments
Full text linkChemoautotrophy is the process by which micro-organisms fix CO2 by obtainingenergy from the oxidation of reduced compounds such sulfide and ammonium (e.g.sulfur oxidation and nitrification). This metabolism is widespread in nature and isvastly studied in extreme environments such as hydrothermal vents and chemoclinesin hypoxic basins where it contributes greatly to primary production. However, chemoautotrophsare easily overlooked in coastal areas where the photoautotrophicorganisms are the main primary producers. Moreover, chemoautotrophs are estimatedto have CO2 fixation efficiencies of less than 10% (i.e., the ratio of chemoautotrophicCO2 fixation over the total CO2 released from the mineralization of organic matter),which results in the exclusion of chemoautotrophic carbon production from coastalcarbon budgets. Nonetheless, the production of sulfide (the main electron donor forchemoautotrophic bacteria in sediments) is much higher in coastal sediments thanin hydrothermal vent systems, which suggests a greater potential for chemoautotrophicsulfur oxidizers in coastal sediments. In fact, chemoautotrophs have been shown tofix up to 22% of the carbon respired in subtidal sediments, and sulfur oxidation bylarge filamentous bacteria (Beggiatoaceae) can account for up to 90% of the oxygenrespiration in sediments with overlapping O2 and H2S. Thus the aim of this thesiswas to assess chemoautotrophic activity in a range of coastal environments by identifyingpotential key players, determining regulatory factors of the process and evaluatingthe importance of chemoautotrophic activity in coastal ocean sediments.The majority of chemoautotrophic bacteria identified through sequencing (16SrRNA gene and 16S rRNA, and carboxylation genes of two carbon fixation pathways:the Calvin Benson-Bassham and the reductive tricarboxylic acid cycles) wasrelated to sulfur oxidizing bacteria, from the Gamma-, Epsilon- and Deltaproteobacteriaclades (Chapters 2, 3, 4). The co-occurrence of these diverse groups ofsulfur-oxidizing chemoautotrophic bacteria may be attributed to a complex nichedifferentiation driven most likely by the availability of different sulfur species (freesulfide, iron sulfide, thiosulfate, elemental sulfur) in the different sediment types. Forexample, filamentous Beggiatoaceae (Gammaproteobacteria) are characteristic forcohesive, sulfur-rich sediments because they have a high affinity for H2S and highuptake rates that allow them to compete with chemical sulfide oxidation at O2-H2S interfaces (Chapter 2). Furthermore, vacuolated Beggiatoaceae can outcompete othersulfur-oxidizers because they are capable of storing nitrate intracellularly and oxidizingsulfide to sulfate in two spatially separated reactions (Chapter 4). Metabolicallyversatile Epsilonproteobacteria were also found in this sediment type where theyprobably oxidize elemental sulfur aerobically or with nitrate. The research describedin this thesis suggests that these Epsilonproteobacteria may depend on the activityof filamentous sulfur oxidizers such as vacuolated-Beggiatoaceae and heterotrophiccable bacteria (Chapter 3, 4). Unicellular, sulfur-oxidizing Gammaproteobacteriaalso appear to be metabolically linked to cable bacteria in cohesive sediments butthe exact mechanism remains elusive (Chapter 3, 4). In contrast, in bioturbated sedimentsunicellular Gammaproteobacteria potentially use iron sulfide as their mainelectron donor (Chapter 2). Lastly, chemoautotrophic Deltaproteobacteria relatedto sulfate reducers that can disproportionate sulfur were prevalent in deeper anoxicsediment layers and during hypoxic bottom water conditions (Chapter 2, 4).Rates of bacterial dark carbon fixation by bacteria were surveyed in a variety ofcoastal sediments covering intertidal flats, a marine lake, nearshore and continentalshelf sediments by means of stable isotope probing (¹³C-DIC) and bacterial biomarkeranalysis (phospholipid derived fatty acids, PLFA-SIP). In total we report 26 newobservations that more than quadruple the existing number (6) of sedimentary chemoautotrophyrates available in the literature. Dark carbon fixation rates rangedfrom 0.07 to 36 mmol C m¯² d¯¹ with highest activity found in cohesive salt marshsediments, while lowest rates were found in advective-driven continental shelf sediments.The majority of the dark carbon fixation rates (n=17) fell within 1 and 10mmol C m¯² d¯¹. A correlation analysis to determine possible environmental factorsthat influence the dark carbon fixation rate resulted in a significant power-law correlationbetween chemoautotrophy rates and the benthic oxygen consumption (Chapter6). This correlation indicates that as benthic oxygen consumption increases, darkcarbon fixation increases more than proportionally with the highest values towardsshallower water depth. Using the sediment oxygen uptake rate as a proxy for sedimentmineralization we were able to estimate the CO2 fixation efficiency for thedifferent sediments. Across the dataset, we found a CO2 fixation efficiency rangingfrom 0.01 to 0.32 with a median of ~0.06, which corresponds well with the CO2fixation efficiency of 0.07 that has been estimated for coastal sediments based onsimplified electron balance calculations. When differentiating between three depthzones in the coastal ocean, we found 3% CO2 fixation efficiency in continental shelfsediments (50-200 m water depth), 9% for nearshore sediments (0-50 m water depth,including intertidal sediments), and 21% for salt marshes (Chapter 6). Thus, chemoautotrophicactivity plays a more prevalent role in the carbon cycling in reactiveintertidal sediments (especially in salt marshes) than in deeper continental shelf sediments. With these mean CO2 fixation efficiencies for the different water depthswe estimated for coastal sediments a global chemoautotrophic production of 0.06Pg C y¯¹ (Chapter 6). This is two-and-a-half times lower than the conservative estimateof 0.15 Pg C y¯¹ indicating that previous studies have severely overestimatedthe contribution of chemoautotrophy in coastal sediments.Furthermore, five distinct depth-distribution patterns of chemoautotrophy aredescribed that could be linked to three sediment types that differ in the main modeof pore water transport: advective, bioturbated, and diffusive, which align well withsediment characteristics such as grain size, porosity, organic matter content and faunaactivity (Chapter 6). In the case of diffusive sediments, the prevalent mode of sulfuroxidation was used to distinguish between three additional categories: electrogenicsulfur oxidation by cable bacteria, sulfide by motile, nitrate accumulating Beggiatoaceaeand canonical sulfide oxidation within an overlapping O2-H2S interface. (1)Sediments with canonical sulfide oxidation had most of the chemoautotrophic activityat the sediment surface where electron donor (H2S) and acceptor (O2 or NO3¯) overlap(Chapters 2, 3, 4). (2) Nitrate-storing Beggiatoaceae create a suboxic zone in thesediment by gliding up and down between the surface and the sulfide horizon depth.In this scenario Beggiatoa is the main contributor to chemoautotrophic activity, whichis found at the surface and throughout the suboxic zone (Chapter 4). (3) Electrogenicsulfur oxidation by cable bacteria also creates a suboxic zone in sediments but has adistinct pH profile, which distinguishes it from that of the nitrate-storing Beggiatoaceae.In this case, dark carbon fixation is evenly distributed from the surface tobelow the sulfide horizon potentially by means of a sulfur-oxidizing consortiumbetween chemoautotrophic bacteria and the heterotrophic cable bacteria (Chapters3, 4). (4) Bioturbating activity results in the intrusion of electron acceptors into deepanoxic sediments via intense bio-irrigation whereas strong particle mixing supportsiron cycling. Thus chemoautotrophic activity is enhanced in deeper sediments andalong the burrow walls, as well as at the surface compared to non-bioturbating sediments(Chapter 5, 6). Moreover, the effects of bioturbation on chemoautotrophicbacteria are species-specific and thus vary between sites with differing macrofaunalcommunities (Chapter 5). (5) In advective-driven permeable sediments, the constantflushing of the sediment produces deep oxygen penetration which enhances aerobicrespiration that favors nitrifying bacteria with low growth yields (0.10), but diminishesanaerobic sulfate reduction and thus sulfide oxidation. This results in a minimumchemoautotrophic activity throughout the sediment matrix (Chapter 6).In accordance with the three main objectives of this thesis it is concluded that 1)chemoautotrophy in coastal sediments is conducted by a diverse group of sulfur-oxidizingbacteria which co-occur either through complex sulfur-niche differentiation inbioturbated sediments or by way of a bacterial consortium when filamentous sulfuroxidizers are present in diffusive sediments, but the exact mechanisms involved remainto be determined. 2) Chemoautotrophy rates vary depending on the main mode ofpore water transport, which affects the sediment mineralization rate and the availabilityof electron donors and acceptors. Five distinct depth-distribution patterns of the darkcarbon fixation are described that are linked to the main mode of sulfur oxidation. 3)Globally, chemoautotrophic production is one order of magnitude higher than thatfound in hydrothermal vents where chemoautotrophic bacteria are responsible for mostof the primary production. Coastal benthic chemoautotrophy may therefore be animportant source of renewed labile organic matter, especially in intertidal sediments,which should not be overlooked in future food web and biogeochemical studies
A Cross-System Comparison of Dark Carbon Fixation in Coastal Sediments
No full textDark carbon fixation (DCF) by chemoautotrophic microorganisms can sustain food webs in the seafloor by local production of organic matter independent of photosynthesis. The process has received considerable attention in deep sea systems, such as hydrothermal vents, but the regulation, depth distribution, and global importance of coastal sedimentary DCF have not been systematically investigated. Here we surveyed eight coastal sediments by means of stable isotope probing (13C-DIC) combined with bacterial biomarkers (phospholipid-derived fatty acids) and compiled additional rates from literature into a global database. DCF rates in coastal sediments range from 0.07 to 36.30 mmol C m−2 day−1, and there is a linear relation between DCF and water depth. The CO2 fixation ratio (DCF/CO2 respired) also shows a trend with water depth, decreasing from 0.09 in nearshore environments to 0.04 in continental shelf sediments. Five types of depth distributions of chemoautotrophic activity are identified based on the mode of pore water transport (advective, bioturbated, and diffusive) and the dominant pathway of microbial sulfur oxidation. Extrapolated to the global coastal ocean, we estimate a DCF rate of 0.04 to 0.06 Pg C year−1, which is less than previous estimates based on indirect measurements (0.15 Pg C year−1), but remains substantially higher than the global DCF rate at deep sea hydrothermal vents (0.001–0.002 Pg C year−1).BT/Environmental Biotechnolog
Rapid redox signal transmission by "Cable Bacteria" beneath a photosynthetic biofilm
No full textRecently, long filamentous bacteria, belonging to the family Desulfobulbaceae, were shown to induce electrical currents over long distances in the surface layer of marine sediments. These “cable bacteria” are capable of harvesting electrons from free sulfide in deeper sediment horizons and transferring these electrons along their longitudinal axes to oxygen present near the sediment-water interface. In the present work, we investigated the relationship between cable bacteria and a photosynthetic algal biofilm. In a first experiment, we investigated sediment that hosted both cable bacteria and a photosynthetic biofilm and tested the effect of an imposed diel light-dark cycle by continuously monitoring sulfide at depth. Changes in photosynthesis at the sediment surface had an immediate and repeatable effect on sulfide concentrations at depth, indicating that cable bacteria can rapidly transmit a geochemical effect to centimeters of depth in response to changing conditions at the sediment surface. We also observed a secondary response of the free sulfide at depth manifest on the time scale of hours, suggesting that cable bacteria adjust to a moving oxygen front with a regulatory or a behavioral response, such as motility. Finally, we show that on the time scale of days, the presence of an oxygenic biofilm results in a deeper and more acidic suboxic zone, indicating that a greater oxygen supply can enable cable bacteria to harvest a greater quantity of electrons from marine sediments. Rapid acclimation strategies and highly efficient electron harvesting are likely key advantages of cable bacteria, enabling their success in high sulfide generating coastal sediments
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