Article

Quantifying bioirrigation in aquatic sediments: An inverse modeling approach

Limnology and Oceanography

January 2001
46(1):164-177

DOI:10.4319/lo.2001.46.1.0164

Authors:

Carla M. Koretsky

Western Michigan University

Philippe Van Cappellen

University of Waterloo

An inverse model was developed to quantify the depth distributions of bioirrigation intensities in sediments based on measured solute concentration and reaction rate profiles. The model computes statistically optimal bioirrigation coefficient profiles; that is, profiles that best represent measured data with the least number of adjustable parameters. A parameter reduction routine weighs the goodness-of-fit of calculated concentration profiles against the number of adjustable parameters by performing statistical F-tests, whereas Monte Carlo simulations reduce the effects of spatial correlation and help avoid local minima encountered by the downhill simplex optimization algorithm. A quality function allows identification of depth intervals where bioirrigation coefficients are not well constrained. The inverse model was applied to four different depositional environments (Sapelo Island, Georgia; Buzzards Bay, Massachu- setts; Washington Shelf; Svalbard, Norway) using total CO2 production, sulfate reduction, and 222 Rn/ 226 Ra disequi- librium data. Calculated bioirrigation coefficients generally decreased rapidly as a function of depth, but distinct subsurface maxima were observed for sites in Buzzards Bay and along the Washington Shelf. Irrigation fluxes of O2 computed with the model-derived bioirrigation coefficients were in good agreement with those obtained by difference between total benthic O2 fluxes measured with benthic chambers and diffusive fluxes calculated from O 2 microprofiles.

Increased Capacity for Polycyclic Aromatic Hydrocarbon Mineralization in Bioirrigated Coastal Marine Sediments

Article

Full-text available

May 2008

Bioirrigation of marine sediments by benthic infauna has the potential to increase both the rate and depth of bacterial mineralization of polycyclic aromatic hydrocarbons (PAHs) by recirculating oxygenated bottom water into sediment burrows. Rates of heterotrophic bacterial production and mineralization of PAHs (naphthalene, phenanthrene, and fluoranthene) were measured in sections of sediment cores sampled from stations in San Diego Bay. Data suggest that rates of PAH biodegradation and bacterial heterotrophy were influenced by bioirrigation by benthic infauna. PAH mineralization and heterotrophic production were higher in core sections where sulfide was not detected relative to core sections containing sulfide. Depth-integrated capacity of the upper 17 cm of sediment to mineralize PAHs was 4 to 10 times higher at the station with bioirrigation coefficients that increased with depth. Remedial dredging of sediments to remove contaminant mass (and presumable lower ecological risk) will also remove benthic infauna. Removal of infauna and the subsequent lowering of bioirrigation in surface sediments would be expected to lower the capacity of intrinsic PAH bioremediation. This could cause local increases in ambient PAH concentration and consequently increase the ecological risk at the site and potentially degrade the health of the ecosystem by removing a sink for PAHs.

Ecologie des foraminifères benthiques, interactions biologiques et géochimiques : approche pluridisciplinaire à différentes échelles

Thesis

Jul 2021

Constance Choquel

The overall aim of this PhD thesis was to investigate sedimentary micro-environments and ecosystem functioning of two coastal areas. We combined different high spatial resolution methods and multivariate analyses at different spatio-temporal scales to reveal interactions between benthic faunal and geochemical compartments. Firstly, we investigated two stations with contrasted oxygen, nitrate and manganese conditions in the Gullmar Fjord (Sweden). We revealed the high contribution (50–100 %) of denitrifying benthic foraminifera to the nitrogen cycle in oxygenated and nitrate-rich micro–environments. Nitrogen and manganese cycles are closely related to oxygenation conditions of the ecosystem. Our results highlighted the high contribution (87 %) of macrofaunal bioirrigation to Mn release to the water column under hypoxic conditions. Secondly, we focused on a monthly monitoring of two ecological bioindicators groups; microphytobenthos (MPB) and foraminifera in the Bourgneuf Bay mudflat (France). We showed that foraminiferal reproduction events were modulated by unfavorable conditions (high hydrodynamic and winter conditions) versus favorable conditions (low hydrodynamic and summer conditions). We also demonstrated that foraminiferal species fed preferentially on diatom species based on their shape, size and life-forms. We further compared, with high spatial resolution methods, geochemical conditions at two contrasted months, which allowed to clarify the behavior of redox species and nutrients. Then, foraminiferal micro-distributions indicated the state of sediment instability versus stability. Finally, this doctoral research opens new perspectives in the use of high spatial resolution in 2D/3D to solve complex benthic ecology problems

Modelling biogeochemical processes in sediments from the north western Adriatic Sea: response to enhanced POC fluxes

Preprint

Full-text available

Jun 2017

This work presents the result of a study carried out in the north-western Adriatic Sea, by combining two different types of biogeochemical models with field sampling efforts. A longline mussel farm was taken as a local source of perturbation to the natural POC downward flux. This flux was first quantified by means of a pelagic model of POC deposition coupled to sediment traps data, and its effects on sediment bioirrigation capacity and OM degradation pathways were investigated by constraining an early diagenesis model, linked to new data in sediment porewaters. The measurements were performed at stations located inside and outside the area affected by mussel farm deposition. Model-predicted POC fluxes showed marked spatial and temporal variability, which were mostly associated with the dynamics of the farming cycle. Sediment traps data at the two sampled stations (in and out of the mussel farm) showed average POC background flux of 20.0–24.2 mmol C m−2 d−1. The difference of OC fluxes between the two stations was in agreement with model results, ranging between 3.3 and 14.2 mmol C m−2 d−1, and primarily associated with mussel physiological conditions. Although restricted, these changes in POC fluxes induced visible effects on sediment biogeochemistry. Observed oxygen microprofiles presented a 50 % decrease in oxygen penetration depth (from 2.3 to 1.4 mm), accompanied by an increase in the O2 influx at the station below the mussel farm (19–31 versus 10–12 mmol O2 m−2 d−1) characterized by higher POC flux. DIC and NH4+ concentrations had similar behavior, with a more evident effect of bioirrigation underneath the farm. This was confirmed through constraining the early diagenesis model, which calibration leads to an estimation of enhanced and shallower bioirrigation underneath the farm: bioirrigation rates of 40 y−1 and irrigation depth of 15 cm were estimated inside the shellfish deposition footprint versus 20 y−1 and 20 cm outside. These findings were confirmed by independent data on macrofauna composition collected at the study site. Early diagenesis model results indicated a larger organic matter mineralization below the mussel farm (11.1 versus 18.7 mmol m−2 d−1), characterized by similar proportions between oxic and anoxic degradation pathways at the two stations, with an increase in the absolute values of oxygen consumed by OM degradation and reduced substances re-oxidation underneath the mussel farm.

Modelling biogeochemical processes in sediments from the north-western Adriatic Sea: Response to enhanced particulate organic carbon fluxes

Article

Full-text available

Mar 2018
BG

This work presents the result of a study carried out in the north-western Adriatic Sea, by combining two different types of biogeochemical models with field sampling efforts. A longline mussel farm was taken as a local source of perturbation to the natural particulate organic carbon (POC) downward flux. This flux was first quantified by means of a pelagic model of POC deposition coupled to sediment trap data, and its effects on sediment bioirrigation capacity and organic matter (OM) degradation pathways were investigated constraining an early diagenesis model by using original data collected in sediment porewater. The measurements were performed at stations located inside and outside the area affected by mussel farm deposition. Model-predicted POC fluxes showed marked spatial and temporal variability, which was mostly associated with the dynamics of the farming cycle. Sediment trap data at the two sampled stations (inside and outside of the mussel farm) showed average POC background flux of 20.0–24.2 mmol C m−2 d−1. The difference of organic carbon (OC) fluxes between the two stations was in agreement with model results, ranging between 3.3 and 14.2 mmol C m−2 d−1, and was primarily associated with mussel physiological conditions. Although restricted, these changes in POC fluxes induced visible effects on sediment biogeochemistry. Observed oxygen microprofiles presented a 50 % decrease in oxygen penetration depth (from 2.3 to 1.4 mm), accompanied by an increase in the O2 influx at the station below the mussel farm (19–31 versus 10–12 mmol O2 m−2 d−1) characterised by higher POC flux. Dissolved inorganic carbon (DIC) and NH4+ concentrations showed similar behaviour, with a more evident effect of bioirrigation underneath the farm. This was confirmed through constraining the early diagenesis model, of which calibration leads to an estimation of enhanced and shallower bioirrigation underneath the farm: bioirrigation rates of 40 yr−1 and irrigation depth of 15 cm were estimated inside the shellfish deposition footprint versus 20 yr−1 and 20 cm outside. These findings were confirmed by independent data on macrofauna composition collected at the study site. Early diagenesis model results indicated a larger organic matter mineralisation below the mussel farm (11.1 versus 18.7 mmol m−2 d−1), characterised by similar proportions between oxic and anoxic degradation rates at the two stations, with an increase in the absolute values of oxygen consumed by OM degradation and reduced substances re-oxidation underneath the mussel farm.

Numerical modeling of early diagenetic processes in Haiyang 4 Area in the northern slope of the South China Sea

Article

Full-text available

Jun 2017
ENVIRON EARTH SCI

Early diagenesis affects the distribution of solutes and minerals in unconsolidated sediments. The investigation of diagenesis is critical to understanding the geochemical transformation and benthic fluxes of elements. During the cruise mission SO-177 in 2004, gravity coring samples were recovered in the Haiyang 4 Area of the northern slope of the South China Sea (SCS). The geochemical concentrations in interstitial water were determined onboard. The 1D C.CANDI reactive transport software was used to model the early diagenesis processes at four sites: 56-GC-3, 70-GC-9, 94-GC-11, and 118-GC-13. All of the simulations reproduced concentration profiles that matched the measurements with the implemented geochemical reactions. The degradation of organic carbon and anaerobic oxidation of methane (AOM) primarily determine the distribution of solutes in the working area. The degradation is active in the top 150 cm, and AOM is vigorous at depths below 200 cm. The local advective flux, sediment rate, and kinetic reaction constants of organic matter, methane and sulfate were calibrated based on the existing concentrations of pore water solutes. Geochemical reactions in this area occur in considerably deeper layers compared to depths cited in the literature. The model results provide evidence for the existence of deep hydrocarbon reservoirs that provide methane to the upper sediments.

Rare Earth Element Cycling in a Sandy Subterranean Estuary in Florida, USA

Article

Jul 2015
MAR CHEM

Porewater Redox Species, pH and p CO 2 in Aquatic Sediments: Electrochemical Sensor Studies in Lake Champlain and Sapelo Island

Chapter

Feb 2002

This paper reports millimeter depth resolution microelectrode-based porewater profiles of O2, Mn2+, Fe2+, pH and pCO2 in sediments from Lake Champlain in the northeastern US and from a creek bank in Sapelo Island in the southeastern US. Such fine scale profiles of multiple redox species measured together with pH and pCO2 have not been reported previously for lake or salt marsh creek bank sediments. This paper discusses the relationship between redox reactions and the porewater pH values based on micro-profiles and diagenetic mechanisms from both fresh and salt water systems. The microelectrode data clearly show that the very sharp pH minimum is a result of Mn2+, Fe2+ and NH4+ oxidation at the zone near the O2 penetration depth as well as CO2 release during organic matter decomposition. In the freshwater sediment, an overlapping of O2 and Mn2+ profiles is observed indicating a close coupling between O2 usage and Mn2+ oxidation. This is not the case in the marine system except when biological disturbance is serious. A laboratory experiment supports an earlier hypothesis that an alternative Mn2+ oxidation mechanism such as via NO3- reduction may be important in marine systems unless biological irrigation and/or resuspension bring Mn2+ in direct contact with O2.

Benthic Bulldozers and Pumps: Laboratory and Modelling Studies of Bioturbation and Bioirrigation

Article

Feb 2003

Nicola Jane Grigg

Aquatic sediments are the recipients of a continual rain of organic debris from the water column. The decomposition reactions within the sediment and the rates of material exchange between the sediment and water column are critically moderated by the transport processes within the sediment. The sediment and solute movement induced by burrowing animals – bioturbation and bioirrigation – far exceed abiotic transport processes such as sedimentation burial and molecular diffusion. Thalassinidean shrimp are particularly abundant burrowing animals. Living in high density populations along coastlines around the world, these shrimp build complex burrow networks which they actively maintain and irrigate.¶ I used a laser scanner to map thalassinidean shrimp mound formation. These experiments measured rapid two-way exchange between the sediment and depth. Subduction from the sediment surface proved to be just as important as sediment expulsion from depth, yet this is not detected by conventional direct entrapment techniques. The experiments demonstrated that a daily sampling frequency was needed to capture the extent of the two-way exchange.¶ ...

Bioirrigation in permeable sediments: Advective pore water transport induced by burrow ventilation

Article

Jan 2006

The physical mechanism that drives bioirrigation is strongly dependent on the permeability of the sediment. We advance two mechanisms, each described by a corresponding microenvironment model. In muds, burrow water cannot penetrate the sediment, so bioirrigation is intrinsically driven by diffusional transfer across the burrow wall. This ‘‘diffusive’’ mode of bioirrigation is accurately described by the classical tube irrigation model. In sands, ventilation flows can penetrate the surrounding sediment via dead end burrows. To quantify this ‘‘advective’’ mode of bioirrigation, we propose a novel two-dimensional pocket injection model. This model’s principal features are that (1) organisms indent the sediment–water interface with burrow structures, (2) the specific structure of the burrow can be neglected except for the location of a feeding pocket, and (3) burrow water is injected from this feeding pocket into the surrounding sediment. We tested the adequacy of the pocket injection model in a detailed case study of the lugworm Arenicola marina, comparing model simulations and experimental data from core incubations. Simulation of two different sets of inert tracer experiments shows good agreement between model and data, indicating that our model captures the relevant aspects of lugworm bioirrigation in permeable sediments.

Influence of Spartina and Juncus on Saltmarsh Sediments. I. Pore Water Geochemistry

Article

Sep 2008
CHEM GEOL

The influence of Spartina alterniflora and Juncus roemarianus on saltmarsh sediment pore water geochemistry was investigated during summer at four sites in a saltmarsh on Sapelo Island, GA, USA. Pore waters were collected from each site at 1–2 cm intervals, to a depth of 50 cm, and analyzed for pH, alkalinity, dissolved manganese, ferric iron, ferrous iron, total sulfide, sulfate, phosphate, ammonium, calcium, magnesium and potassium. The most compressed vertical redox stratification occurs at a short Spartina site, followed closely by an adjacent Juncus site. Both sites have shallow oxic and suboxic zones, with sulfidic conditions only a few centimeters or less from the sediment water interface. The densely vegetated Juncus site is inferred to have greater primary productivity and organic matter turnover compared to the short Spartina site. More radial oxygen loss is postulated to occur in the subsurface of the Juncus site, leading to reoxidation of reduced species, more acidic conditions and less accumulation of dissolved sulfide, ammonium and oxidizable-Fe in the solid phase compared to the adjacent short Spartina site. A creekside site vegetated by tall Spartina has the most oxidized sediments, followed by an adjacent unvegetated site. Both of these sites are dominated by suboxic pore waters in most of the upper 50 cm. Subsurface injection of oxygen via roots at the densely vegetated tall Spartina site is inferred to create more acidic pore waters with significantly less accumulation of reduced solutes, including ammonium and alkalinity, compared to the adjacent unvegetated creekside site. Fe and Mn reduction are expected to be significant processes in the bulk near-surface sediments of the tall Spartina and unvegetated sites and within rhizosphere sediments at the tall Spartina and Juncus sites. This study demonstrates the significant influence of Juncus roemarianus and Spartina alterniflora on saltmarsh sediment pore water geochemistry, with important implications for nutrient and trace metal mobility and bioavailability. Future work is needed to explore differences in organic matter concentration and especially lability in the subsurface of saltmarsh sites with varying types and densities of vegetation.

Parametric approach to promote a divergence-free flow in the image-based motion estimation with application to bioirrigation

Article

Full-text available

Jun 2022

Flow fields are determined from image sequences obtained in an experiment in which benthic macrofauna, Arenicola marina , causes water flow and the images depict the distribution of a tracer that is carried with the flow. The experimental setup is such that flow is largely two-dimensional, with a localised region where the Arenicola resides, from which flow originates. Here, we propose a novel parametric framework that quantifies such flow that is dominant along the image plane. We adopt a Bayesian framework so that we can impart certain physical constraints on parameters into the estimation process via prior distribution. The primary aim is to approximate the mean of the posterior distribution to present the parameter estimate via Markov Chain Monte Carlo. We demonstrate that the results obtained from the proposed method provide more realistic flows (in terms of divergence magnitude) than those computed from classical approaches such as the multi-resolution Horn–Schunk method. This highlights the usefulness of our approach if motion is largely constrained to the image plane with localised fluid sources.

Rapid and precise measurements of radon in water using a pulsed ionization chamber

Article

Full-text available

Feb 2021
LIMNOL OCEANOGR-METH

Radon‐in‐air monitor (RAD7, Durridge Co.) has been widely used to measure 222Rn in water samples. RAD7 measures 222Rn via 218Po+ (t1/2 = 3.1 min), which is electrically attracted to a silicon alpha detector. In this study, a new method was developed for measuring 222Rn in water samples by modifying a commercially available pulsed ionization chamber (PIC, FT‐Lab Co.). The PIC detects and amplifies the electric pulses generated by microspace charges produced by 222Rn decay. Two passive PICs (volume: 2 × 400 mL) were combined and modified to form an active system (named Rn‐SNU) that continuously circulates air (~ 1 L min−1). Rn‐SNU is approximately seven to nine times more efficient than RAD7 and does not necessitate a delay of ~ 15 min to reach radioactive equilibrium between 222Rn and 218Po+. However, RAD7 is more accurate in discriminating 222Rn daughters, 218Po+ and 214Po+. In this study, 222Rn was successfully measured in coastal seawater samples using Rn‐SNU connected to a grab bottle. Our results suggest that 222Rn measurements in water samples can be conducted more efficiently and rapidly with an Rn‐SNU than with other widely used instruments and methods.

Methane Source and Turnover in the Shallow Sediments to the West of Haima Cold Seeps on the Northwestern Slope of the South China Sea

Article

Full-text available

Aug 2019
GEOFLUIDS

The Haima cold seeps are active cold seep areas that were recently discovered on the northwestern slope of the South China Sea (SCS). Three piston cores (CL30, CL44, and CL47) were collected within an area characterized by bottom simulating reflectors to the west of Haima cold seeps. Porewater profiles of the three cores exhibit typical kink-type feature, which is attributed to elevated methane flux (CL30) and bubble irrigation (CL44 and CL47). By simulating the porewater profiles of SO 4²⁻ , CH 4 , PO 4³⁻ , Ca ²⁺ , Mg ²⁺, and dissolved inorganic carbon (DIC) in CL44 and CL47 using a steady-state reaction-transport model, we estimated that the dissolved SO 4²⁻ was predominantly consumed by anaerobic oxidation of methane (AOM) at rates of 74.3 mmol m ⁻² yr ⁻¹ in CL44 and 85.0 mmol m ⁻² yr ⁻¹ in CL47. The relatively high AOM rates were sustained by free gas dissolution rather than local methanogenesis. Based on the diffusive Ba ²⁺ fluxes and the excess barium contents in the sediments slightly above the current SMTZ, we estimated that methane fluxes at core CL44 and CL47 have persisted for ca. 3 kyr and 0.8-1.6 kyr, respectively. The non-steady-state modeling for CL30 predicted that a recent increase in upward dissolved methane flux was initiated ca. 85 yr ago. However, the required time for the formation of the barium front above the SMTZ at this core is much longer (ca. 2.2-4.2 kyr), which suggests that the depth of SMTZ possibly has fluctuated due to episodic changes in methane flux. Furthermore, using the model-derived fractions of different DIC sources and the δ¹³ C DIC mass balance calculation, we estimated that the δ¹³ C values of the external methane in cores CL30, CL44, and CL47 are -74.1‰, -75.4‰, and -66.7‰, respectively, indicating the microbial origin of methane. Our results suggest that methane seepage in the broader area surrounding the Haima cold seeps probably has persisted at least hundreds to thousands of years with changing methane fluxes.

Burrowing Invasive Species: An Unquantified Erosion Risk at the Aquatic‐Terrestrial Interface

Article

Full-text available

Aug 2019
REV GEOPHYS

Invasive nonnative species acting as “ecosystem engineers” or “geomorphic agents” can represent a major landscape disturbance. Quantification of their biogeomorphic impacts remains a key knowledge gap, and aquatic‐terrestrial transition zones may be particularly exposed to impacts. We demonstrate how burrowing invasive species represent a potentially significant but unquantified erosion risk at aquatic margins. We reveal a lack of quantitative research on geophysical impacts, despite increasing concerns over threats to waterways and flood defense infrastructure. We explore example animals of global interest, comprising crustaceans, fish, reptiles, and mammals and reveal the global nature of the issue: over 100 countries, states, or territories where at least one example species is established, and over 20 with 3‐6 species present. We present a conceptual model for the impacts of burrows on stability and erosion at aquatic margins using established models of geotechnical, hydrological, and hydraulic drivers. Burrows are hypothesized to (i) alter failure plane position, decrease failure plane length, and increase failure plane angle (thereby decreasing bank shear strength); (ii) modify the spatial distribution of porewater pressure, thereby increasing subsurface flow (seepage), reducing cohesion, and increasing the likelihood of slip failures at the bank face; (iii) increase turbulence and sediment entrainment at burrow entrances; and (iv) alter flow resistance at the bank face. Most effects are expected to increase bank instability/erosion with the exception of (iv) which has the potential to offer protection from fluvial action. We call for further research in these areas to quantify impacts for different environments and different invasive species.

Author's personal copy Review Erodibility of cohesive sediment: The importance of sediment properties

Article

Feb 2011

Pore fluid compositions and inferred fluid flow patterns at the Haima cold seeps of the South China Sea

Article

May 2019
MAR PETROL GEOL

Porewater salinity in a southeastern United States salt marsh: Controls and interannual variation

Article

Full-text available

Nov 2018

In coastal marsh ecosystems, porewater salinity strongly affects vegetation distribution and productivity. To simulate marsh porewater salinity, an integrated, spatially explicit model was developed, accounting for tidal inundation, evaporation, and precipitation, as well as lateral and vertical exchanges in both surface waters and the subsurface. It was applied to the Duplin River marsh, Sapelo Island, USA, over a 3-year period, which covered both drought and wet conditions. Simulated porewater salinity in the low and high marsh correlated with Duplin River salinity, with evapotranspiration and precipitation leading to substantial variations in porewater salinities across seasons, in particular in the high marsh. The model revealed substantial interannual variability in marsh soil conditions, and—due to its process-based approach linked to external forcings—can be used to explore effects of sea level rise and changes in hydrological forcings on marsh soil conditions.

Carbon oxidation and bioirrigation in sediments along a Skagerrak-Kattegat-Belt Sea depth transect

Article

Oct 2018

Partitioning of electron acceptors and macrofaunal bioirrigation were assessed in sediments from 4 stations along a Skagerrak−Kattegat−Belt Sea depth transect. Sediment was examined for benthic fauna composition and abundance, sediment−water fluxes (O2, dissolved inorganic carbon [DIC], NH4⁺, and NO3⁻), anaerobic reactions (carbon oxidation [Cox], sulfate reduction [SR], manganese reduction [MnR], iron reduction [FeR], and ammonification [Nmin]), porewater profiles (O2, DIC, SO4²⁻ and NH4⁺), and solid phase profiles (organic content, Fe and Mn). Deep stations had less than half the abundance of benthic fauna than shallow stations, while the Belt Sea station was azoic due to bottom-water hypoxia. Solute fluxes and anaerobic reactions showed order-of-magnitude lower rates in sediment from deep than from shallow water. In general, anaerobic Cox in sediments along the Skagerrak−Kattegat−Belt Sea transect is dominated by SR (>50%) in shallow water and decreases gradually when moving into deeper water and reaches 0 at ~700 m depth. FeR increases from 0 in shallow water to ~50% at ~600 m, but rapidly reaches 0 again at 700 m. MnR is close to 0 down to at least 500 m and increases to complete dominance at 700 m. The contribution of denitrification is generally below 10% at all depths. Bioirrigation-quantified as non-local exchange through diagenetic modelling-is proportional to fauna biomass and functional traits. The Br⁻ tracer approach to determine bioirrigation on newly extracted sediment onboard a ship is not recommended. It is concluded that enhanced downward translocation of O2 into anoxic sediment through bioirrigation is the major mechanism reoxidizing subsurface metals in the deep Skagerrak and Kattegat.

Importance of nitrate reduction in benthic carbon mineralization in two eutrophic estuaries: Modeling, observations and laboratory experiments

Article

Jan 2018
MAR CHEM

Modelling of organic matter mineralization in temperate estuarine sediments

Presentation

Jul 2013

Organic matter recycling in estuarine sediments: experiment and modelling

Coupled carbon and sulfur isotope behaviors and other geochemical perspectives into marine methane seepage

Article

Full-text available

Apr 2017

Methane seepage is the signal of the deep hydrocarbon reservoir. The determination of seepage is significant to the exploration of petroleum, gas and gas hydrate. The seepage habits microbial and macrofaunal life which is fueled by the hydrocarbons, the metabolic byproducts facilitate the precipitation of authigenic minerals. The study of methane seepage is also important to understand the oceanographic condition and local ecosystem. The seepage could be active or quiescent at different times. The geophysical surveys and the geochemical determinations reveal the existence of seepage. Among these methods, only geochemical determination could expose message of the dormant seepages. The active seepage demonstrates high porewater methane concentration with rapid SO42– depleted, low H2S and dissolved inorganic carbon (DIC), higher rates of sulfate reduction (SR) and anaerobic oxidation of methane (AOM). The quiescent seepage typically develops authigenic carbonates with specific biomarkers, with extremely depleted ¹³C in gas, DIC and carbonates and with enriched ³⁴S sulfate and depleted ³⁴S pyrite. The origin of methane, minerals precipitation, the scenario of seepage and the possible method of immigration could be determined by the integration of solutes concentration, mineral composition and isotopic fractionation of carbon, sulfur. Numerical models with the integrated results provide useful insight into the nature and intensity of methane seepage occurring in the sediment and paleooceanographic conditions. Unfortunately, the intensive investigation of a specific area with dormant seep is still limit. Most seepage and modeling studies are site-specific and little attempt has been made to extrapolate the results to larger scales. Further research is thus needed to foster our understanding of the methane seepage.

Bottom RedOx Model (BROM v.1.1): A coupled benthic-pelagic model for simulation of water and sediment biogeochemistry

Article

Full-text available

Feb 2017

Interactions between seawater and benthic systems play an important role in global biogeochemical cycling. Benthic fluxes of some chemical elements (e.g., C, N, P, O, Si, Fe, Mn, S) alter the redox state and marine carbonate system (i.e., pH and carbonate saturation state), which in turn modulate the functioning of benthic and pelagic ecosystems. The redox state of the near-bottom layer in many regions can change with time, responding to the supply of organic matter , physical regime, and coastal discharge. We developed a model (BROM) to represent key biogeochemical processes in the water and sediments and to simulate changes occurring in the bottom boundary layer. BROM consists of a transport module (BROM-transport) and several biogeochemical modules that are fully compatible with the Framework for the Aquatic Biogeochemical Models, allowing independent coupling to hydrophysical models in 1-D, 2-D, or 3-D. We demonstrate that BROM is capable of simulating the seasonality in production and mineralization of organic matter as well as the mixing that leads to variations in redox conditions. BROM can be used for analyzing and interpreting data on sediment–water exchange, and for simulating the consequences of forcings such as climate change, external nutrient loading, ocean acidification, carbon storage leakage, and point-source metal pollution.

Production of Reactive Oxygen Species in the Rhizosphere of a Spartina-Dominated Salt Marsh Systems

Article

Full-text available

Dec 2016
AQUAT GEOCHEM

This paper reports the presence of a metastable mixture of Fe(II), O2, superoxide and hydrogen peroxide in sediment pore water in organic carbon-rich sediments in Spartina alterniflora-dominated salt marsh systems. Field measurements at two different estuarine sites in South Carolina (one heavily urbanized and a protected research reserve) showed a broad region of reactive oxygen species (ROS) production more than 15 cm below the sediment surface within and immediately adjacent to the rhizospheres of S. alterniflora. Dissolved Fe(II) was positively correlated with hydrogen peroxide indicating a possible abiotic pathway to ROS production (r² = 0.94). The null hypothesis was tested that Fe(II) inventories were maintained by protective ligands and thus unreactive with respect to O2 consumption and ROS production. The addition of an Fe-binding ligand, DTPA, resulted in rapid decline of ROS in pore water, indicating that Fe(II) was labile. The half-life of superoxide under the measured solution conditions was calculated and found to be less than a second. The combination of high lability and persistent ROS was interpreted to indicate a high rate of Fe(II) and O2 supply to the pore water. The ²²⁴Ra/²²⁸Th disequilibrium was measured to determine the potential for advective mass transfer of dissolved oxygen via pore water exchange. The estimated pore water exchange of 54 L m⁻² day⁻¹ was significant but could not support the measured production of ROS alone, the direct exchange of O2 from the S. alterniflora root system may have contributed significantly to ROS production in the sediments.

Seagrasses and Protective Criteria: A Review and Assessment of Research Status

Technical Report

Full-text available

Jun 2009

Walter G. Nelson

This report is a review and summary of the current status of scientific information relevant to the establishment of protective criteria for the most widely distributed seagrass species of the United States, eelgrass Zostera marina, and turtlegrass Thalassia testudinum. The report focuses on scientific information related to major limiting factors for seagrass survival, and assesses the degree to which environmental factors may need to be included in the development of adequately protective criteria. The review confirmed that there is a great deal of scientific information currently available concerning the responses of Zostera marina and Thalassia testudinum to a wide range of environmental factors. However, interactive effects among factors influencing seagrass survival remain relatively poorly known, especially across broader regional scales. This appears true even for such fundamental environmental characteristics as salinity and temperature and their interactions in the expression of nutrient or sediment impacts on SAV, although research is beginning to fill this gap. The question remains as to whether current modeling approaches, whether empirical or mechanistic, are adequate to predict the response of seagrasses to even single stressors. A key concern is that there is a high level of uncertainty in being able to predict the trophic pathway for expression of nutrient impacts on seagrasses. Thus, water quality criteria based on nutrient concentrations may not be adequately protective of seagrass resources. Alternate standards based on water clarity or water column chlorophyll a criteria may not be adequately protective if the principle expression of nutrient impacts occur through the epiphyte or macroalgal pathways. There are also important influences on seagrass survival through sediment associated mechanisms that may not be adequately captured by water quality criteria alone. There may be advantages to looking for integrative, plant based seagrass condition indicators, such as sucrose content, that relate to the ability of seagrasses to survive within a temporally varying environment. Such measures may be an appropriate method to integrate water column and sediment impacts into single protective criteria.

Sedimentary Diagenesis, Depositional Environments, and Benthic Fluxes

Chapter

Dec 2014

Robert Curwood Aller

Sediment diagenesis is a critical component of the global sedimentary rock cycle. Sedimentary deposits behave as open systems, and sediment-water exchange has major influences on biogeochemical processes in the ocean and on elemental balances in seawater. Diagenetic transport-reaction conditions, sediment-water fluxes, and the eventual storage of material are determined by properties of the depositional environment, including water column oxygenation, particle size distributions, bulk geotechnical properties, sedimentation rates, sedimentary transport dynamics, and benthic biological communities. Reactions associated with thermodynamically unstable biogenic debris dominate early diagenetic processes. These include redox reactions coupled to organic matter decomposition and preservation, carbonate dissolution, opaline silica dissolution and alteration, and authigenic mineral formation (carbonates, sulfides, and silicates). This chapter reviews diagenetic processes and is patterned after the earlier contribution by Emerson and Hedges in the first edition of the Treatise, which stands on its own. It has been extended in some alternative directions, however, as it places greater emphasis on deltaic and shallow water depositional systems and unsteady diagenesis, and it incorporates more recent data obtained through technical advances, such as planar optodes and eddy correlation. It does this in part at the expense of more detailed coverage of deep-sea processes and organic geochemistry.

Rapid transport and high accumulation of amorphous silica in the Congo deep-sea fan: A preliminary budget

Article

Jul 2014

Quantifying porewater exchange across the sediment-water interface in the deep sea with in situ tracer studies

Article

Mar 2004
LIMNOL OCEANOGR-METH

A numerical model of NaBr tracer transport in benthic flux chamber incubations has been developed to simulate temporal changes in chamber water tracer concentrations and applied to four deep sea locations: the California and North Carolina margins, the Ceara rise, and the Cape Verde plateau. Model variables include the chamber volume (which determines the initial tracer concentration), and rates of diffusive and nonlocal exchange across the sediment-water interface. Chamber volume and solute exchange rate estimates were obtained by optimizing the fit between observations and model results using a χ2 statistical scheme. We observe enhanced solute exchange in regions with high organic carbon rain rates, over a wide range of bottom water oxygen concentrations. Furthermore, our results demonstrate that solute exchange rates cannot be assumed constant, even within relatively short deployments. In six of 22 cases, chamber volumes and corresponding benthic solute fluxes derived from model fits were more than 20% greater than values calculated using linear extrapolations of chamber tracer concentration-time relationships. To avoid this discrepancy, future benthic chamber studies should seek to minimize the time interval between tracer injection and sampling while maintaining sufficient time to achieve complete homogenization of the tracer in the chamber waters.

A non-steady state diagenetic model for changes in sediment biogeochemistry in response to seasonally hypoxic/anoxic conditions in the “dead zone” of the Louisiana shelf

Article

Jul 2007
MAR CHEM

Biogeochemical processes occurring near the sediment–water interface can play an important role in the establishment and persistence of hypoxic-to-anoxic conditions in areas of moderate-to-shallow water depth. Results are given in this paper for diagenetic modeling of two sites from the area on the Louisiana shelf west of the Mississippi River Delta known as the “dead zone”. This is one of the largest and most studied regions where seasonal coastal hypoxia occurs. The diagenetic model was capable of generating good matches with depth profiles at both sites in the upper 8 cm. Moderate differences between predicted and observed concentrations below this depth are most likely due to the highly non-steady state conditions in this region. The model was also able to predict extremely low dissolved sulfide concentrations and bacterial sulfate reduction rates that were in good agreement with independent direct observations. A sensitivity analysis of the model to input parameters showed that the model was much more sensitive to changes in values under hypoxic conditions than norm-oxic or anoxic conditions in the overlying water.Simulations were carried out to first determine how the profiles of sediment porewater parameters and interfacial fluxes would change under differing quasi-steady state conditions where overlying dissolved oxygen concentrations and the rate of bioirrigation were varied. Next a non-steady state simulation was run to investigate how sediment biogeochemistry would change between these conditions during a hypothetical annual cycle. Results demonstrated a clear need to better understand the dynamic relationship among overlying water oxygen concentrations, the behavior of the benthic faunal community responsible for bioirrigation and sediment biogeochemistry.

Reactive-transport modeling of iron diagenesis and associated organic carbon remineralization in a Florida (USA) subterranean estuary

Article

Apr 2011
EARTH PLANET SC LETT

Iron oxides are important terminal electron acceptors for organic carbon (OC) remineralization in subterranean estuaries, particularly where oxygen and nitrate concentrations are low. In Indian River Lagoon, Florida, USA, terrestrial Fe-oxides dissolve at the seaward edge of the seepage face and flow upward into overlying marine sediments where they precipitate as Fe-sulfides. The dissolved Fe concentrations vary by over three orders of magnitude, but Fe-oxide dissolution rates are similar across the 25-m wide seepage face, averaging around 0.21 mg/cm2/yr. The constant dissolution rate, but differing concentrations, indicate Fe dissolution is controlled by a combination of increasing lability of dissolved organic carbon (DOC) and slower porewater flow velocities with distance offshore. In contrast, the average rate constants of Fe-sulfide precipitation decrease from 21.9 × 10- 8 s- 1 to 0.64 × 10- 8 s- 1 from the shoreline to the seaward edge of the seepage face as more oxygenated surface water circulates through the sediment. The amount of OC remineralized by Fe-oxides varies little across the seepage face, averaging 5.34 × 10- 2 mg/cm2/yr. These rates suggest about 3.4 kg of marine DOC was remineralized in a 1-m wide, shore-perpendicular strip of the seepage face as the terrestrial sediments were transgressed over the past 280 years. During this time, about 10 times more marine solid organic carbon (SOC) accumulated in marine sediments than were removed from the underlying terrestrial sediments. Indian River Lagoon thus appears to be a net sink for marine OC.

Patterns and variability of groundwater flow and radium activity at the coast: A case study from Waquoit Bay, Massachusetts

Article

Dec 2011
MAR CHEM

Spatial and seasonal variations in depth profile of trace metals in saltmarsh sediments from Sapelo Island, Georgia, USA

Article

May 2007

Alakendra Roychoudhury

This study was undertaken to elucidate the impact of early diagenetic processes on the accumulation of trace metals in Sapelo Island saltmarsh sediments as a function of time, space and sediment properties. Samples were collected from three sites in summer (May 1997) and winter (January 1998) along a transect from an unvegetated Creek Bank through a vegetated Tidal Levee to the vegetated midmarsh with evident lateral heterogeneity caused by hydrologic regime, macrophytes and microbial and macrofaunal activities. A suite of trace metals (As, Ba, Cr, Co, Cu, Cd, Mo, Ni, Pb, Th, Ti, U, V, Zn and Zr) was analyzed to obtain their depth-distribution at the three sites. Spatially marked differences were observed, that were primarily related to hydraulic flushing of trace metals away from the sites in high-energy regimes, rapid downward mixing and reworking of sediment via bioturbation, and below-ground degradation and production of Spartina biomass. Although sulfate reduction and the formation of acid volatile sulfide and pyrite were dominant processes throughout the marsh, the trace metal scavenging role of sulfides was not apparent. However, possible sulfurization of organic matter, leading to enhanced trapping of trace metals with organic carbon, may have played an important role in sequestration of trace metals.No similarity was observed visually between the depth trends of trace metals and sediment properties (grain size, iron-oxyhydroxide content, acid volatile sulfides and pyrite content) that are known to play a major role in trace metal partitioning. Only organic carbon content closely followed the trace metal profiles at all the three sites. Minor variation in depth-integrated sediment trace metal content was observed seasonally at each of the three sites. Furthermore, the depth trend of profiles of individual trace metals also did not vary significantly over the seasons either.

Organic carbon deposition on the North Carolina continental slope off Cape Hatteras (USA)

Article

Dec 2002
DEEP-SEA RES PT II

The continental slope off Cape Hatteras, NC is a region of high sediment accumulation and organic matter deposition. Sediment accumulation rates range from 3 to 151cmkyr−1. Organic carbon deposition rates are 5–13moles Cm−2yr−1, the highest reported for the slope off the eastern US. Burial efficiencies are 3–40%. The organic matter deposited is marine in origin and a mix of old and young particles. High organic carbon deposition rates support remineralization throughout the upper 2–3m of sediment. Deep bioirrigation to depths of 60–100cm within the seabed affects the biogeochemistry of the sediments by extending the zone of sulfate reduction and by steepening DIC porewater gradients through the non-local exchange of porewater. Stable and radiocarbon isotope mixing curves for porewater dissolved inorganic carbon (DIC) indicate that the dominant source of DIC accumulating in the upper 2–3m of the seabed is of nearly uniform δ13C (−21.10‰) and Δ14C (−546‰).

Quantification of macrobenthic effects on diagenesis using a multicomponent inverse model in salt marsh sediments

Article

Nov 2004

Using a multicomponent inverse model, we quantified the rates of organic matter (OM) remineralization and the relative importance of major terminal electron acceptors (Fe(III)-(oxy)hydroxides and SO ) in salt marsh sediments 22 4 with varying degrees of bioturbation and vegetation at Skidaway Island, Georgia. The model determined the rates of OM diagenesis by seeking simultaneous agreement between measured and model-calculated depth-concentration profiles of multiple major redox species while using the biological transport parameters determined from direct field observations. The OM degradation rates are found to be greater and penetrate deeper in sediments with vegetation or bioturbation than in sediments with limited macrobenthic components, in which organic matter degradation is restricted to the immediate vicinity of water-sediment interface. The results also confirmed previous observations that Fe(III)-(oxy)hydroxides are much more important than sulfate as terminal electron acceptors in the heavily bioturbated station and provided the numerical values to the depth-dependent relative importance. Solid-phase Fe is recycled as a terminal electron acceptor $30 times in the bioturbated station, because biological mixing repeatedly moves reduced Fe(II) back into the aerobic environment, where it is reoxidized to form Fe(III)-(oxy)hydroxides and is reused as a terminal electron acceptor. Vegetation appears to have little influence on net solute transport, but it stimulates microbial activities and significantly enhances the remineralization of OM at depths.

Salt marsh biogeochemistry - An overview

Chapter

Full-text available

Jan 2009

Interaction between hydrocarbon seepage, chemosynthetic communities, and bottom water redox at cold seeps of the Makran accretionary prism: Insights from habitat-specific pore water sampling and modeling

Article

Full-text available

Jun 2012
BG

Mercury Dynamics in Sulfide-Rich Sediments: Geochemical Influence on Contaminant Mobilization Within the Penobscot River Estuary, Maine, USA

Article

Nov 2006
GEOCHIM COSMOCHIM AC

Research concerning the fate and biogeochemical cycling of mercury (Hg) within coastal ecosystems has suggested that microbially-mediated diagenetic processes control Hg mobilization and that ligands with strong affinity for Hg, such as dissolved inorganic sulfide (S(-II)) and dissolved organic matter (DOM) control Hg partitioning between the dissolved and particulate phases. We have studied total Hg cycling in the sediments of the Penobscot River estuary using a combination of equilibrium porewater samplers and kinetic modeling. Mercury contamination within the estuary surface sediments ranges from 1.25-27.5 nmol Hg g-1. Porewater Hg profiles for the Penobscot estuary are divisible into three kinetically-discrete intervals with respect to Hg dynamics. Beginning at depth in the sediment and moving upward toward the SWI we have defined: 1) a zone of net Hg solubilization at depth, 2) a zone of net Hg consumption within the zone dominated by FeS(s) precipitation, and 3) a zone of net diffusive transfer within the vicinity of the SWI. Equilibrium and kinetic modeling in Zone 1 suggest that inorganic S(-II) plays the dominant role in both mobilization of sediment-bound Hg and complexation of dissolved Hg. In Zone 2, FeS(s) precipitation occurs concomitant with Hg consumption. Calculated vertical Hg flux from this zone suggests that precipitation does not wholly prevent upward diffusive transfer of porewater Hg. Net transfer within Zone 3 is consistent with the potential for microbially-generated, ligand-mediated Hg efflux across the SWI. S(-II)-mediated Hg mobilization at depth in Penobscot estuary sediments suggests both a broadening of the depth interval over which biogeochemical Hg cycling must be examined and a recognition that while estuary sediments act as a net sink for particulate Hg inputs they also function as a source of dissolved Hg over a considerable time interval.

Bioirrigation modeling in experimental benthic mesocosms

Article

Full-text available

May 2001

Burrow irrigation by benthic infauna affects chemical mass transfer regimes in marine and estuarine sediments. The bioirrigation facilitates rapid exchange of solutes between oxygenated overlying water and anoxic pore water, and thus promotes biogeochemical reactions that include degradation of sedimentary organic matter and reoxidation of reduced species. A comprehensive understanding of chemical mass transfer processes in aquatic sediments thus requires a proper treatment of bioirrigation. We investigated bioirrigation processes during early diagenesis using laboratory benthic mesocosms. Bioirrigation was carried out in the mesocosms by Schizocardium sp., a funnel-feeding enteropneust hemichordate that builds and ventilates a U-shaped burrow. Interpretation of the laboratory results was aided by a two-dimensional multicomponent model for transport and reactions that explicitly accounts for the depth-dependent distribution of burrows as well as the chemical mass transfers in the immediate vicinity of burrow walls. Our study shows that bioirrigation significantly affects the spatial distributions of pore water solutes. Moreover, bioirrigation promotes burrow walls to be the site of steep geochemical gradients and rapid chemical mass transfer. Our results also indicate that the exchange function, , widely used in one-dimensional bioirrigation modeling, can accurately describe the bioirrigation regimes if its depth attenuation is coupled to the depth-dependent distribution of burrows. In addition, this study shows that the multicomponent 2D reaction-transport model is a useful research tool that can be used to critically evaluate common biogeochemical assumptions such as the prescribed depth dependencies of organic matter degradation rate and C/N ratio, as well as the lack of macrofaunal contribution of metabolites to the pore water.

Variation of nonlocal irrigation in a subtidal benthic community

Article

Full-text available

May 2003

Irrigation, the effect of the pumping activity by benthic infauna on pore water solute distribution and fluxes, may be represented by a nonlocal irrigation function, (units: 1/time) in the general diagenetic equation. We derived from the distribution of a solute tracer, bromide, during laboratory incubations of sediment cores containing their natural faunal community. Sediments were sampled on 4 occasions over a period of one year from a site at 30 m depth in the southern North Sea. Fitting an irrigation function exponentially decaying with depth, we arrived at -values ranging from 25 to >200 yr-1 at the sediment water interface and < 10 at 16 cm depth. The importance of meaningful horizontal averaging was shown by contrasting our values with unreasonable high based on inappropriate sampling. Variability of between adjacent samples (n = 3-6) was as large as seasonal differences, and this fact underlines the necessity for cautious interpretation of data from single cores. No temperature effect on was observed in the temperature range of 5-16°C since abundance of fauna and their behavior completely dominated the magnitude of . Nutrient fluxes associated with this nonlocal irrigation are highly variable on a spatial scale reflecting macrofauna heterogeneity. The irrigation flux reduces the relative importance of temperature as a factor on benthic-pelagic solute fluxes.

A fast numerical solution to the general mass-conservation equation for solutes and solids in aquatic sediments

Article

Full-text available

May 2007

Mathematical modeling of species transformations in aquatic sediments is usually based on numerical solutions to the same general one-dimensional mass-conservation equation and is likely to require substantial computation time. In this paper we present a fast numerical solution to this equation. The solution is suited for both single and multi-component models and it is based on an implicit control volume discretization of the general mass-conservation equation. The solution consists of two algorithms, one that decomposes the discretization matrix once and one that subsequently produces multiple solutions with minimal computational effort. A unique feature of these algorithms is that values of boundary conditions can vary as a simulation progresses without requiring new decompositions of the discretization matrix. This feature can reduce computation time significantly relative to commonly used procedures for modeling dynamic systems. Finally, we present four examples in which the numerical solution is applied to specific problems. From these examples guidelines are derived for the discretization in space and time required to obtain precise solutions of the general mass-conservation equation.

Bio-irrigation in permeable sediments: An assessment of model complexity

Article

Full-text available

Jul 2006

Burrowing benthic animals ventilate their burrow networks, and this enhances the transport of solutes in the sediment and exchange with the overlying water column, a process referred to as bio-irrigation. Various models have been proposed to model bio-irrigation, with different levels of sophistication related to model dimensionality and parameter numbers. Here we address the issue of model complexity for bio-irrigation in permeable sediments. To this end, we simulated flowline patterns and tracer signals using (1) a full 3D model that explicitly models the J-shaped geometry of the burrow in a suitable microenvironment surrounding the burrow, (2) a simplified 2D axi-symmetric analogue, which neglects the burrow shaft and only models the location of burrow water injection, (3) a highly simplified 1D model obtained by laterally averaging the microenvironment. Simulation of two separate inert tracer experiments shows that the 2D pocket injection model includes essential features (downward advective transport, spatial heterogeneity of pore water velocity, mechanistic specification of the seepage area) that are lost upon averaging to the corresponding 1D model. This loss of model detail must be compensated for by the introduction of additional, non-mechanistic fitting parameters in the 1D description. Similarly, the extension of the 2D model to a full sophisticated 3D description requires a major increase in computational resources, but only leads to a marginal improvement in the data simulation. Accordingly, we conclude that the 2D description provides an optimal balance between model simplicity and predictive capacity.

Dual sources and consumption of methane in shallow sediments of southern SCS: Insight from porewater composition and numerical modeling

Article

Sep 2023
MAR PETROL GEOL

Quantitative assessment of dissolved inorganic carbon cycling in marine sediments from gas hydrate-bearing areas in the South China Sea

Article

Full-text available

Aug 2022
MAR PETROL GEOL

Quantitatively assessing dissolved inorganic carbon (DIC) cycling in methane-rich marine sediments is essential for understanding the contributions of different carbon sources to the global carbon cycle. Here, the data of δ¹³C-DIC, SO4²⁻, DIC, Ca²⁺, Mg²⁺, PO4³⁻, and a reactive transport model were used to analyze the DIC and methane source and calculate the DIC budget in the shallow sediments at two methane seep sites in the Xisha Trough (CL27A) and to the west of the Haima cold seeps in the Qiongdongnan Basin (CL44). Model results show that methane contributed to 92.75% and 79.95% of DIC sources through anaerobic oxidation of methane (AOM) versus only 7.25% and 12.90% by organic matter via organoclastic sulfate reduction (OSR) and methanogenesis at both sites. However, the methane sources vary between the two sites. External thermogenic methane that is decoupled from contemporaneous organic matter deposition drives the AOM at CL27A. A combination of upwardly diffusing external biogenic methane and internal methane derived from in situ methanogenesis drives the AOM at CL44. Internal methane flux from depth reveals the deep methanogenic zone influences the DIC cycling in the shallow sediments at CL44. It is accompanied by the upward diffusive DIC flux that can be identified by the δ¹³C-DIC data when modeling, which contributes to the remaining 7.15% of the DIC source. Neglecting this DIC source that is set as a fixed value at the lower boundary will misunderstand the DIC cycling in the shallow sediments. This study identified and highlighted the influence of external thermogenic methane and the methanogenic zone on the DIC cycling in marine sediments, and demonstrated assessing DIC cycling accurately in methane-rich marine sediments is important to estimate its contribution to oceanic carbon cycling.

Bioturbation feedbacks on the phosphorus cycle

Article

Jul 2021
EARTH PLANET SC LETT

Bioturbation—sediment mixing and ventilation by burrowing animals—provides one of the most prominent examples of how animals shape their surroundings. A critical but longstanding question is when and how in Earth's history bioturbators began to similarly influence marine biogeochemistry. Recent work has proposed that even though the development of well-mixed sediments was a protracted process, the initial rise of bioturbators led to a decrease in marine phosphate levels, global productivity crises and ultimately deoxygenation events in the early Cambrian oceans. Herein, using a diagenetic model, we provide a new view of how bioturbators impact the global phosphorus cycle. Our work focuses on incorporating more realistic representation of bioturbation with a more complete and mechanistic parameterization of benthic phosphorus cycling than has previously been used to explore the early Paleozoic. We find, in contrast to previous modeling studies, that bioturbation does not uniformly or unidirectionally mediate increased phosphorus burial. Enhanced biodiffusion of sedimentary particles can mediate enhanced phosphorus burial. In contrast, bioirrigation—nonlocal transport of solutes via burrows—enhances phosphorus recycling and may therefore stimulate rather than stymy productivity. Given evidence from the geologic record that bioirrigation rather than biodiffusion was predominant during the ramping up of bioturbation (through the early Paleozoic), the emergence of bioturbation is unlikely to have driven deoxygenation events.

Technical Evaluation of a Total Maximum Daily Load Model for Upper Klamath Lake, Oregon

Technical Report

Full-text available

Mar 2019

We reviewed a mass balance model developed in 2001 that guided establishment of the phosphorus total maximum daily load (TMDL) for Upper Klamath and Agency Lakes, Oregon. The purpose of the review was to evaluate the strengths and weaknesses of the model and to determine whether improvements could be made using information derived from studies since the model was first developed. The new data have contributed to the understanding of processes in the lakes, particularly internal loading of phosphorus from sediment, and include measurements of diffusive fluxes of phosphorus from the bottom sediments, groundwater advection, desorption from iron oxides at high pH in a laboratory setting, and estimates of fluxes of phosphorus bound to iron and aluminum oxides. None of these processes in isolation, however, is large enough to account for the episodically high values of whole-lake internal loading calculated from a mass balance, which can range from 10 to 20 milligrams per square meter per day for short periods. The possible role of benthic invertebrates in lake sediments in the internal loading of phosphorus in the lake has become apparent since the development of the TMDL model. Benthic invertebrates can increase diffusive fluxes several-fold through bioturbation and biodiffusion, and, if the invertebrates are bottom feeders, they can recycle phosphorus to the water column through metabolic excretion. These organisms have high densities (1,822–62,178 individuals per square meter) in Upper Klamath Lake. Conversion of the mean density of tubificid worms (Oligochaeta) and chironomid midges (Diptera), two of the dominant taxa, to an areal flux rate based on laboratory measurements of metabolic excretion of two abundant species suggested that excretion by benthic invertebrates is at least as important as any of the other identified processes for internal loading to the water column. Data from sediment cores collected around Upper Klamath Lake since the development of the TMDL model also contributed to this review. Cores were sequentially extracted to determine the distribution of phosphorus associated with several matrices in the sediment (freely exchangeable, metal-oxides, acid-soluble minerals, and residual). The concentrations of phosphorus in these fractions varied around the lake in patterns that reflect transport processes in the lake and the ultimate deposition of organic and inorganic forms of phosphorus from the water column. Both organic and inorganic phosphorus had higher concentrations in the northern part of the lake, in and just west of Goose Bay. At the time that these cores were collected, prior to restoration of the Williamson River Delta, this area was close to the shoreline of the lake and east of the Williamson River mouth. This contrasts with erosional inputs, which, in addition to being high to the east of the pre-restoration Williamson River mouth, were higher in the middle of the lake than at the northern end. Organic forms of phosphorus had particularly high concentrations in the northern bays. When these cores were used to calculate a new estimate of the whole-lake-averaged concentration of total phosphorus in the top 10 centimeters of the lake sediments, the estimate was about one-third of the best estimate available when the TMDL model was developed.

Interaction between hydrocarbon seepage, chemosynthetic communities and bottom water redox at cold seeps of the Makran accretionary prism: insights from habitat-specific pore water sampling and modeling

Article

Full-text available

Sep 2011
BGD

The interaction between fluid seepage, bottom water redox, and chemosynthetic communities was studied at cold seeps across one of the world's largest oxygen minimum zones (OMZ) located at the Makran convergent continental margin. Push cores were obtained from seeps within and at the lower boundary of the core-OMZ with a remotely operated vehicle. Extracted pore water was analyzed for sulfide and sulfate contents. Depending on oxygen availability, seeps were either colonized by microbial mats or by mats and macrofauna. The latter, including ampharetid polychaetes and vesicomyid clams, occurred in distinct benthic habitats which were arranged in a concentric fashion around gas orifices. At most sites colonized by microbial mats, hydrogen sulfide was exported into the bottom water. Where macrofauna was widely abundant, hydrogen sulfide was consumed within the sediment. Numerical modeling of pore water profiles was performed in order to assess rates of fluid advection and bioirrigation. While the magnitude of upward fluid flow decreased from 11 cm yr−1 to <1 cm yr−1 and the sulfate/methane transition zone (SMTZ) deepened with increasing distance from the central gas orifice, the fluxes of sulfate into the SMTZ did not significantly differ (6.6–9.3 mol m−2 yr−1). Depth-integrated rates of bioirrigation increased from 162 cm yr−1 in central habitats characterized by microbial mats and sparse macrofauna to 348 cm yr−1 in habitats of large and small vesicomyid clams. These results reveal that chemosynthetic macrofauna inhabiting the outer seep habitats at the lower boundary of the OMZ efficiently bioirrigate and thus transport sulfate into the upper 10 to 15 cm of the sediment. In this way bioirrigation compensates for the lower upward flux of methane in outer habitats and stimulates rates of anaerobic oxidation of methane (AOM) with sulfate high enough to provide sulfide for chemosynthesis. Through bioirrigation macrofauna engineer their geochemical environment and fuel upward sulfide flux via AOM. Due to the introduction of oxygenated bottom water into the sediment via bioirrigation the depth of the sulfide sink gradually deepens towards outer habitats. We therefore suggest that – in addition to the oxygen levels in the water column which determine whether macrofaunal communities can develop or not – it is rather the depth of the SMTZ and thus of sulfide production that determines which chemosynthetic communities are able to exploit the sulfide at depth. Moreover, large vesicomyid clams most efficiently expand the sulfate zone in the sediment and cut off smaller or immobile organisms from the sulfide source.

Two dimensional mapping of iron release in marine sediments at submillimetre scale

Article

Apr 2017
MAR CHEM

Coastal and shelf sediments are considered as an important source of dissolved iron to the ocean. Here, we present a new numerical approach to estimate geochemical fluxes and production rates in an estuarine sediment at sub-millimetre resolution. This approach is based on application of Savitsky–Golay filter (SGF) procedure to two-dimensional concentration distributions of dissolved iron. We verified the procedure by applying it to artificial data of known production rates, and analysed the resulting uncertainty on production rates and fluxes across the water–sediment interface. This SGF procedure was applied to data from an intertidal mudflat that is densely inhabited by macrofauna (e.g. 630 ind m− 2 of Hediste diversicolor, I. Métais, pers.com.). Our analysis reveals an apparent recycling rate of 3780 ± 1399 μmol m− 2 d− 1 and a mean residence time of iron in the dissolved phase of 2.3 days. Visual identification of burrows permitted to calculate separately the diffusive flux across the sediment–water interface (104 ± 20 μmol m− 2 d− 1) and the bio-irrigational flux (410 ± 213 μmol m− 2 d− 1). Reactive iron particles will undergo on average 7.4 cycles of dissolution/precipitation before being released to the water column. These results show that estuarine sediments support intensive iron recycling that has probably a large impact on terrigeneous particles before being released into the ocean.

Benthic fauna bio-irrigation effects on nutrient regeneration in fish farm sediments

Article

Dec 2006
J EXP MAR BIOL ECOL

Impacts of organic enrichment and a modified benthic fauna community (caused by fish farming) on benthic mineralization rates and nutrient cycling were studied in sediments at one Danish and one Cypriote fish farm. Sediment organic matter concentration and macrofauna community composition were manipulated in microcosms and changes in total benthic metabolism (oxygen consumption, TCO2 production), anaerobic metabolism (sulfate reduction rates), nutrient fluxes and sediment parameters were followed for a period of 3 weeks. Mineralization rates were found to be highly correlated with irrigation velocities and largest fauna effects were found in the Danish sediments with the large and active irrigating climax species (Nereis diversicolor and Macoma balthica). Eastern Mediterranean climax species (Glycera rouxii and Naineris laevigata) also stimulated mineralization rates but to a smaller extent due to lower irrigation, whereas the opportunistic species (Capitella in Danish sediment and Hermodice carunculata in Cypriote sediment) showed less effect on mineralization. Ammonium and phosphate release increased with increasing irrigation velocities, but much less in Cyprus indicating higher nutrient retention at the ultra-oligotrophic location compared to eutrophic Danish site. Irrigation velocities, and thus mineralization rates, increased by organic matter loading, indicating larger fauna-induced oxidation in enriched environments. The result implies that a change in fauna structure in fish farm sediment towards smaller opportunistic polychaete species with lower irrigation will result in slower mineralization rates and potentially increase accumulation of organic waste products.

Unusual features of the distribution of Radon222 in the bottom waters of the continental slope of the Mid-Atlantic Bight: Hydrodynamic implications

Article

Aug 2006
PROG OCEANOGR

222Rn was measured in the near-bottom waters of the continental slope of the Mid-Atlantic Bight. Separate measurements of the 222Rn supported by dissolved 226Ra allowed the excess 222Rn that is derived from the underlying sediments to be distinguished. Measurements of production of 222Rn by the sediments were used to calculate fluxes of 222Rn from sediments that would be expected as a result of molecular diffusion. On the upper slope and on the lower slope excess 222Rn standing crops were, respectively, greater than and consistent with fluxes of radon from sediments by molecular diffusion as are typical of most ocean environments. On the middle slope, however, observed excess 222Rn concentrations and standing crops were significantly lower than what would be expected from the calculated fluxes from the underlying sediments. This unusual feature of low radon concentrations on the middle slope is referred to as the low-radon zone (LRZ). This LRZ was always present over several years and seasons, but was variable in intensity (excess-radon concentration and standing crop) and in location on the slope. Low concentrations of suspended particulate matter and low current velocities observed by others in the same region are consistent with low mixing as a possible cause of the LRZ. Radon profile shapes and recent work by others on near bottom mixing due to interactions between topography and internal waves, however, suggest that high mixing due to internal waves is a more likely cause of the LRZ.

Dynamic Modeling of Early Diagenesis and Nutrient Cycling. A Case Study in an Artic Marine Sediment

Article

Dec 2003

P. Berg

In this paper, we present a dynamic diagenetic model of the oxygen consumption pathways and cycling of carbon, nitrogen, manganese, iron, and sulfur in marine sediments. Sixteen dissolved or solid species are included in our model and the vertical transport processes accounted for are molecular diffusion, bioturbation, irrigation, and burial. Adsorption of dissolved species onto solid sediment is assumed to be reversible and to follow a linear equilibrium isotherm. Interactions between species are formulated in 21 biogeochemical reactions that are regulated through simplified Michaelis-Menten kinetics. The key driving input parameter to the model is the transient flux of organic matter supplied to the sediment surface, below which mineralization is described through the well-known 3-G model that includes a fast, a slow, and a non-degradable pool of organic matter. The model was applied to the Arctic sediment of Young Sound in Northeast Greenland using extensive measurements covering a full annual cycle. The model parameterization was performed in a stepwise process, first focusing on parameters describing transport in the sediment and then on parameters related to biogeochemical reactions. The model successfully simulated the measured concentration-depth profiles of O2, ΣCO2, NH4⁺, NO3⁻, Mn²⁺, Fe²⁺, adsorbed Fe²⁺, SO4⁺, H2S, FeS, FeS2, MnO2, FeOOH, and organic matter; sediment-water fluxes of ΣCO2, O2, NH4⁺, and NO3⁻; depth-integrated process rates of denitrification and sulfate reduction; and depth profiles of iron-and sulfate reduction rates. The model application to the Young Sound sediment provided an excellent means to examine whether our perceptions of the most significant transport processes and biogeochemical reactions were correct. The successful simulation of measured data supported their internal consistency and confirmed previously reported interpretations and conclusions. The imposed supply of organic matter to the sediment surface that reproduced the measured data was found to be almost three times higher for the month of July than the average for the rest of the year. The peak in organic matter supply in mid-July coincided with the disappearance of sea ice. A sensitivity analysis performed for the model showed that the rate constants for the two degradable pools of organic matter were among those input variables that most affected the simulated results. As a result, we are confident of the accuracy of these rate constants of 76 y⁻¹ and 0.095 y⁻¹. In comparison with results from temperate sediments, these constants showed no significant correlation to the sub-zero Arctic temperatures. The reproduction of measured data for the sulfur cycle could be obtained only when sulfur disproportionation was included in the model as a sink for S⁰, indicating that this process plays an important role in the Young Sound sediment.

Nitrogen Cycling in Coastal Sediments

Chapter

Dec 2008

This chapter reviews the factors regulating sediment N-cycling, both in the bulk sediment environment and on a process level. N availability is frequently cited as the factor limiting primary production in marine systems over annual time scales though phosphorus (P), silica (Si) limitation or colimitation by N, P, and/or Si sometimes occur on seasonal time scales. In offshore waters, the presence of bioavailable iron can also regulate primary productivity, particularly that by diatoms. Sediment N pools reflect a balance between inputs (external or internal) and outputs (sedimentation, denitrification (DNF), long-term burial, or export), and this balance is affected by a variety of environmental and physiological factors. Within the sediment, N is cycled primarily by microbially mediated redox reactions between more highly oxidized forms (nitrate, NO3-, or nitrite, NO2-) and more reduced forms (ammonium, NH4-, amino acids, or organic nitrogen compounds). Gaseous products of these redox reactions may include dinitrogen, N2, nitric oxide, NO, and nitrous oxide, N2O. One characteristic of the sediment N-cycle is the coupling between aerobic and anaerobic processes. Another characteristic is that for a given species, for example, NO3-, several competing pathways and potential fates may exist.

Interpretation of measured concentration profiles in sediment pore water

Article

Full-text available

Jan 1998

Nitrification potentials of benthic macrofaunal tubes and burrow walls: Effects of sediment NH4+ and animal irrigation behavior

Article

Full-text available

May 1995

We examined the natural variation of nitrification potentials (NPs) of surface sediments and macrofaunal tubes and burrow walls in relation to sediment NH,' level, season, and macrofaunal species. NP (the ability of a unit of sediment to oxidize NH,' when NH,+ and O2 are not limting) is an index of the abundance and activity of nitrifying bacteria which we measured in slurries with the chlorate block technique (nmol NO2--N produced g-' dry weight sediment h -') . The NP of the tubes of the polychaete Loimia medusa was positively related to sediment NI I<+ (KC]-extractable) concentration at 3 sites where tubes were collected in June 1990 (Spearman rank correlation coefficient rs 0.90. p = 0.03), as was the NP of surface (0 to 1 cm) sediment (r2 = 0.92, p = 0.002). The degree to which tube NP exceeded the NP of surface sediment was, however, negatively associated with sediment NH4+ (rS = -0.84, p = 0.05). Tube NP of L. medusa did not vary significantly with date (February, April, and June 1990). Tubes or burrow walls of Macoma balthjca (bivalve), Leptocheirusplumulosus (amphipod), and the polychaetes Macroclymene zonalis, Pectinaria gouldll, L. medusa, and Diopatra cuprea had NPs significantly greater (2 to 20 times) than that of adjacent sediment from the same depth interval, indicating that these species stimulated nitrification. Except for burrows of M. balthjca, the NPs of these structures were significantly (p 2 0.05) greater (1.5 to 61 times) than that of surface sediment. The duration of macrofaunal irrigation activity, but not irrigation rate, was positively associated (rS = 0.72, p = 0.01) with the enhancement of NP in tubes and burrow walls relative to surface sediment. These findings indicate that macrofaunal tubes and burrows tend to be sites of enhanced NP and that this enhancement varies among species due to variations in irrigation behavior. The NP of macrofaunal structures also varies among sites in relation to sediment NH,' concentrations.

Rates and pathways of carbon oxidation in permanently cold Arctic sediments

Article

Full-text available

May 1999

We report her-e a comprehensive study of the rates and pathways of carbon mineralization in Arctic sediments. Four sites were studied at 115 to 329 m water depth in fjords on Svalbard and in coastal Norway. The Svalbard coastal region is characterized by permanently cold bottom water temperatures of -1.7 to 2.6 degrees C. Carbon oxidation (avg = 20 to 400 nmol cm(-3) d(-1)) and sulfate reduction rates (avg = 10 to 350 nmol cm(-3) d(-1)) were measured at high resolution to 10 cm depth in sediment incubations. The distribution of oxidants available for microbial respiration was determined through porewater and solid phase geochemistry. By comparing the distribution of potential oxidants to the depth-integrated mineralization rates, the importance of various respiratory pathways to the oxidation of organic C could be quantified. Integrated C oxidation rates measured in sediment incubations (11 to 24 mmol m(-2) d(-1)) were comparable to within a factor of 2 to dissolved inorganic carbon (DIC) fluxes measured in situ using a benthic lander. Sulfate reduction was the dominant microbial respiration pathway (58 to 92% of total C oxidation) followed by Fe(III) reduction (10 to 26%), oxygen (5 to 14%), and nitrate respiration (2 to 3%). At sediment depths where sulfate reduction was dominant, C oxidation equivalents, calculated from independently measured sulfate reduction rates, matched DIC production rates in incubations. Sediment geochemistry revealed that the same vertical sequence of oxidants is reduced/respired in these Arctic sediments as in temperate continental shelf sediments of equivalent water depths. Microbial communities in permanently cold Arctic sediments exhibited mineralization rates and pathways comparable to temperate nearshore environments. This study completely partitioned C oxidation pathways, showing a predominance of sulfate respiration and a substantial contribution of Fe(III) reduction to organic matter mineralization in Arctic sediments for the first time. Microbial communities in cold sediments exposed to relatively high C deposition appear to respond to the input or availability of organic matter rather than to temperature.

Mathematics of Tracer Mixing in Sediments: III. The Theory of Nonlocal Mixing within Sediments

Article

Full-text available

Sep 1987

The general integro-differential model for deterministic bioturbation, developed in part II, is analyzed for its properties, and its solution is discussed for two special cases of nonlocal mixing within sediments. Integral mixing accounts for exchanges on all scales, including small mixing lengths normally associated with diffusion. If the exchange function is symmetric, the limiting form of the integral mixing model for short mixing lengths of high intensity is a diffusion equation with spatially-dependent diffusivity. (more follows)

Benthic nutrient regeneration and its coupling to primary productivity in coastal waters

Article

Full-text available

Apr 1975

SHALLOW near-shore ocean waters support high primary production because of the availability of inorganic nutrients. The availability is usually attributed to the proximity of fresh-water runoff or to coastal upwelling and deep water advection1,2.

Benthic mineralization and exchange in Arctic sediments (Svalbard, Norway)

Article

Full-text available

Nov 1998
MAR ECOL-PROG SER

By means of benthic landers, sediment core incubations and the whole core squeezing (WCS) technique, benthic exchange and mineralization rates were investigated in 4 different fjords of Arctic Norway (Svalbard). These coastal sediments experience constant low temperatures close td 0 degrees C. The sediments were dominated by large densities of bioirrigating macrofauna, which enhanced the benthic in situ Oz uptake by a factor of 1.8 to 2.9 over the diffusive mediated uptake. Recovered sediment cores significantly underestimated the in situ solute exchange rate, presumably due to exclusion of fauna. Faunal activity in situ additionally resulted in a complex sediment structure, which created a smearing of chemical profiles when applying the WCS technique. The benthic exchange rates of dissolved inorganic carbon determined in situ varied between 9 and 20 mmol m(-2) d(-1) at the different stations. Denitrification was of minor importance for benthic mineralization, and the C/N ratio of the effluxing inorganic solutes was close to 10, indicating that relatively fresh organic material was mineralized. The sediment accumulation rate was estimated from Pb-210 profiles to be in the range of 1.3 to 5.9 mm yr(-1). Assuming that our estimated mineralization rates approach the yearly average, it was calculated that 31 to 47 % of the organic carbon reaching the sediment surface was permanently buried. Benthic mineralization rates and carbon burial rates were similar to those obtained in coastal sediments of temperate and tropical regions. This indicates that benthic communities in Arctic sediments rather than being limited by low temperatures are Limited by carbon availability.

An experimental and modeling study of pH and related solutes in an irrigated anoxic coastal sediment

Article

Full-text available

Sep 1996

Macrofaunal irrigation is an important process in nearshore sediments, facilitating greater exchange between sediments and seawater and imparting significant lateral heterogeneity to the porewater profiles of many constituents. Like many macrofaunal activities, irrigation is a transient behavior, i.e. tubes and burrows are flushed periodically, at frequencies that generally are species-specific. As a result, transient concentrations within the dwelling arise, potentially impacting gradients, fluxes and reaction rates in the vicinity of the dwelling. We investigated the impact of periodic burrow irrigation on the distribution of several diagenetically important porewater constituents. Laboratory experiments evaluated irrigation periodicity using artificially irrigated tubes embedded in nearshore organic-rich sediments, and microdistributions of oxygen and pH in laboratory experiments were measured with microelectrodes. To help interpret our results, we also constructed a simplified time and space-dependent transport-reaction model for oxygen, pH and sulfide in irrigated sediments. Laboratory results show substantial differences in the pH field of sediments surrounding an irrigated tube as a function of irrigation frequency. Higher pH values, indicative of an overlying water signature, were observed in the vicinity of the tube wall with increasing duration of irrigation. Conversely, oxygen concentrations did not vary significantly with the amount of irrigation, most likely a result of extremely high sediment oxygen demand. Model results are consistent with laboratory findings in predicting differences in the measured variables as a function of irrigation frequency. However, the nature and extent of the model-predicted differences are often at variance with the experimental data. Overall, experimental and modeling results both suggest irrigation periodicity can substantially influence porewater distributions and diagenetic processes in sediments. Future studies should examine the influence of irrigation periodicity on the types and rates of reactions, and the attendant biological features, in the environment encompassing the tube or burrow wall.

The measurement of sediment irrigation rates: a comparison of the BR- tracer and 222RN/226RA disequilibrium techniques

Article

Full-text available

Feb 1992

We have carried out a series of experiments designed to allow comparison of sediment irrigation rates determined simultaneously using two methods: the measurement of 222Rn/226Ra disequilibrium in pore waters, and the measurement of distributions of a tracer, Br−, which was added to the water overlying sediments at the start of incubation experiments. The experiments were carried out on fine-grained sediments from Buzzards Bay, MA. We made irrigation rate measurements on sediments in their natural state, as well as on sediments that had been treated to alter macrofaunal abundance and diversity. The range of irrigation rates measured was similar for both tracers, and was similar to rates measured at the study site previously by Martin and Sayles (1987). Furthermore, the two tracers gave similar patterns of irrigation rate variability between cores and with depth below the sediment-water interface. On the other hand, comparisons of individual cores showed significant differences in the absolute rates measured using the different tracers; in particular, the 222Rn/226Ra disequilibrium method yielded more rapid irrigation rate estimates at depths exceeding 10 cm below the sediment-water interface. These differences could be due to the inherent limitations on the sensitivity of the methods, to artifacts in measurement procedures, to differences in the permeability of burrow walls to the two tracers (Rn and Br−), or to differences in the time-scales on which the two tracers record irrigation events. Irrigation rates determined by the Br− tracer method were roughly correlated with the abundance of Nephtys incisa in the sediments, but were not related to abundances of the other numerically important deposit feeders, Nucula annulata and Mediomastus ambiseta.

Comparative biogeochemistry of water in intertidal Onuphis (Polychaeta) and Upogebia (Crustacea) burrows: temporal patterns and causes

Article

Full-text available

Aug 1983

The burrows of macrobenthos represent an important class of sedimentary microenvironments which significantly influence chemical, biological, and physical characteristics of a deposit. In intertidal regions, the time-dependent changes in composition during ebb-tide of water contained in burrows is a sensitive indicator of biogenic and abiogenic chemical reactions in burrow walls and adjacent sediment. Comparison of time series water samples taken from Onuphis jenneri (polychaete) and Upogebia affinis (crustacean) burrows in the same tidal flat demonstrate substantial differences in biogeochemical microenvironments despite the spatial proximity of the two species. Both types of burrows are influenced by the same general kinds of biogeochemical reactions but the relative intensity of these reactions differs in each case. Evidence for both heterotrophic and chemoautotrophic metabolic activity in each burrow type comes from the build-up or consumption patterns in burrow water of solutes such as NH4+, NO3−, Mn++, l−, HPO4−, and HCO3−. Burrow irrigation models and the stoichiometry of solute build-up imply that Upogebia burrows are sites of more intense nitrification-denitrification and microbial activity generally than are Onuphis tubes. Upogebia burrow water is also distinctly undersaturated with respect to carbonate minerals and has high numbers of bacteria relative to Onuphis. In addition to reaction rates, burrow geometry and the adsorption-diffusive permeability properties of the burrow wall also affect transient behavior of solutes. The organic burrow lining of Onuphis shows linear adsorption isotherms for positive, negative, and neutrally charged solutes represented by NH4−, HP04−, and Si(OH)4. Diffusion-reaction modeling demonstrates that adsorption, in particular, can significantly lower the transient state concentrations of burrow water trace solutes even for tube wall thicknesses of only 200 μm. The observed differences between burrow microenvironments of the two species living in close proximity suggest distinct biogeochemical associations between microbes and species specific biogenic structures.

The effect of biogenic irrigation intensity and solute exchange on diagenetic reaction rates in marine sediments

Article

Full-text available

Jul 1998

The activities of infaunal macrobenthos strongly influence the pathways, rates, and extent of organic matter remineralization and associated reactions in marine sediments. Solute transport during irrigation is a particularly important process that stimulates microbial activity and net remineralization, both within and adjacent to the bioturbated zone. Part of the stimulation proximal to the bioturbated zone is due to redox oscillation and oxidant supply during transport, but part of both the near and far-field effects are a result of other factors. Experiments designed to simulate different degrees of diffusive exchange, and thus infaunal abundances or activity, demonstrate a regular and strong dependence of anaerobic remineralization on diffusive transport. For example, net production of NH4+, HPO4=, I-, and Mn++ increases as the effective distance between burrows becomes 2 cm (burrow abundance 800 m-2) in otherwise identical anoxic sediment. Corresponding changes in sedimentary bacterial numbers, exoenzyme activity, per cell growth rate (RNA), and solid phase properties (N, C/N, P) indicate that the increases in net rates are due in part to an absolute increase in total production. Transport-reaction models and experimental results demonstrate that relative decreases in the uptake of solutes into biomass, abiogenic precipitation reactions, and increased removal of inhibiting metabolites all occur simultaneously, enhancing both total and net remineralization. The phenonomenological first-order rate constant for organic matter decomposition is therefore a function not only of the reductant and oxidant pool properties, but also the environmental transport regime. Solid phase reaction products can differ substantially as a function of diffusive openness. For example, both organic P and the organic P/inorganic P ratio increase in more diffusively-open (irrigated) compared to diffusively-closed, anoxic sediment. The sensitivity of solute concentrations, microbial activity and diagenetic reaction balances to diffusive transport regime, indicates that macrofauna can functionally manipulate these properties through relatively small changes in burrow spacing patterns and individual burrow geometries.

The role of biologically-enhanced pore water transport in early diagenesis: An example from carbonate sediments in the vicinity of North Key Harbor, Dry Tortugas National Park, Florida

Article

Full-text available

May 2000

Biologically enhanced pore water irrigation affects the course of early diagenesis in shallow marine sediments, as illustrated here for the carbonate sediments from North Key Harbor, Dry Tortugas National Park, Florida. Whereas macrofaunal activity at the study site extends approximately 15 cm below the water-sediment interface, measured O2 microprofiles only show O2 penetration to depths of a few mm. This apparent discrepancy can be explained by considering the 3-D O2 distribution in the burrowed sediments. Calculations based on an idealized tube model for burrow irrigation show that measureable O2 concentrations are limited to the immediate vicinity of burrows. Given the observed burrow density (705 ± 15 m-2), a randomly positioned O2 microprofile has a high probability (>90%) to fall outside the reach of radial O2 diffusion from burrows. Hence, the shallow penetration depths recorded at the site do not exclude a much deeper supply of O2 in the sediment via the burrows. Other characteristic features observed in the upper 15-20 cm of the sediments, in particular, the absence of SO42- depletion and the presence of subsurface maxima in the profiles of NH4+ and TCO2, are also the result of pore water irrigation. These features are reproduced by the multicomponent reactive transport model STEADYSED1. Results of the model simulations indicate that bacterial SO42- reduction is the dominant pathway of organic carbon degradation, but that consumption of SO42- in the sediments is compensated by its enhanced transport by irrigation. Thus, depth profiles of SO42- may be poor indicators of the importance of SO42- reduction in irrigated sediments.

Microbiological and Geochemical Characterization of Microbial Fe(III) Reduction in Salt Marsh Sediments

Article

Full-text available

Apr 2000

Population densities of anaerobic Fe(III)-reducing bacteria (FeRB) and aerobic heterotrophs were inversely correlated in the surficial (0-2 cm) layers of Sapelo Island, Georgia, salt marsh sediments. In surficial sediments where densities of aerobic heterotrophs were low, the density of culturable FeRB correlated positively with the concentration of amorphous Fe(III) oxyhydroxides extractable by ascorbate. High FeRB densities and a decrease with depth of ascorbate-extractable Fe(III) were observed in the upper 6 cm of a tidal creek core. Culturable sulfate-reducing bacteria (SRB) and SRB-targeted rRNA signals were also detected in the upper 6-cm depth. The disappearance of FeRB below 6 cm, however, coincided with a large increase in the abundance of SRB. Thus, when FeRB are not limited by the availability of readily reducible amorphous Fe(III) oxyhydroxides, FeRB may outcompete SRB for growth substrates. Shewanella putrefaciens- and Geobacteraceae-targeted rRNA signals were at or below detection limits in all sediment samples, indicating that these FeRB are not predominant members of the active FeRB populations. The ubiquitous presence of FeRB at the sites studied challenges the traditional view that dissimilatory Fe(III) reduction is not an important pathway of organic carbon oxidation in salt marsh sediments.

Applied Regression Analysis and Other Multivariate Methods. 2nd ed

Article

Jan 1988

On weighted-mean schemes for the finite-difference approximation to the advection-diffusion equation

Article

Dec 1977

The weighted-mean scheme is a method for constructing finite-difference approximations of second-order partial differential equations of the advection-diffusion type using only the center and adjacent points in each space direction. The scheme tends to a centered-difference formulation for strongly diffusive cases and to an upstream formulation for strongly advective cases. The error of approximation is O (h 2 ) or better, when h tends to zero, and the scheme assures stability and convergence to all iterative methods no matter how large the grid size. The scheme thus makes it possible to choose the biggest grid size suitable for each specific problem thereby reducing the computing time considerably. DOI: 10.1111/j.2153-3490.1977.tb00763.x

A comparison of methods for the quantification of bacterial sulfate reduction in coastal marine sediments

Article

Jan 1978

Bo Barker Jørgensen

Actual-palaeontology and neoichnology of salt marshes near Sapelo Island, Georgia

Article

Jan 1977

Distribution of Fiddler Crabs in Georgia Salt Marshes

Article

Apr 1958

John M. Teal

A multicomponent reactive transport model of early diagenesis: Application to redox cycling in coastal marine sediments

Article

Jan 1996
GEOCHIM COSMOCHIM AC

Numerical Recipes (Fortran Version)

Book

Jan 1990

Emanation of radon-222 from marine sediments

Article

Mar 1979
MAR CHEM

The behavior of radon in the sea-floor region provides a useful test of theories which describe mass transport in sediments. We have made measurements of Rn-222 and Ra-226 in near-bottom waters and near-surface sediments at the same location. The distribution of radon in sediments can be described by a simplified diagenetic equation when advection, adsorption, and bioturbation are ignored. Sediment measurements show a radon deficit relative to radium emanation. A reasonable balance is found between integrated radon deficit in sediment and radon surplus in the overlying water.In most cores radium increased with depth in the top 10 cm of sediment. This implies that bioturbation and other mixing processes do not homogenize the radium concentration in the zone of diffusive radon loss, and that radium is diffusing out of the sediments.Radon leakage is less than that predicted by previous authors. Radon leakage depends upon the physical distribution of radium in marine sediments. We present a model that predicts leakage of 30–40% for normal deep-sea sediments, in agreement with measured values.Radon surplus in near-bottom waters depends upon the radium distribution, radon leakage, and effective diffusion coefficients. These in turn depend on the properties of the sediment, such as composition, accumulation rate, and porosity. As we learn how these factors interact we may be able to infer sedimentary features from measurements of radon in overlying waters.

Sulfate reduction in the salt marshes at Sapelo Island, Georgia

Article

Jan 1983

Sulfate reduction rates were measured in stands of Spartina alterniflora at Sapelo Island, Georgia, in November 1980 by injecting tracer amounts of Â³âµSOâ/sup 2 -/ into cores, incubating overnight, and analyzing for the incorporation of Â³âµS into reduced sulfur compounds. Qualitatively, sulfate reduction in the Georgia marsh is very similar to that in the Massachusetts marshes the authors have studied: FeSÂ² (pyrite or marcasite) is the major end product. Lesser amounts of soluble sulfides, iron monosulfides, and elemental sulfur are also formed. The rate of sulfate reduction (determined by the same method)is significantly lower during November in Georgia than in the Great Sippewissett Marsh in Massachusetts, 0.090 vs. 0.27 moles SOâ/sup 2 -/xmâ»Â²xdâ»Â¹ in stands of short Spartina. The lower rates in Georgia may reflect a lower rate of organic carbon input by below ground production. Sulfate reduction appears to be the major form of respiration in the sediments of salt marshes in Georgia as well as in Massachusetts.

Radon222 tracing of sediment-water chemical transport in an estuarine sediment

Article

May 1984

In situ benthic chamber flux measurements and ²²² Rn deficiency core measurements were made in fine‐grained sediments of the White Oak River estuary during August through October 1980. Benthic chamber flux values ranged from 27 to 60 atoms·m s ‒2 ·s ‒1 ; on a given date triplicate emplacements yielded a range of <30%. Apparent whole sediment diffusivities calculated from the fluxes measured yielded coefficients ranging from 0.35 to 1.6 × 10 ‒5 cm s ² ·s ‒1 , within the range expected for control of sediment‐water transport by molecular diffusion. Sampling and analytical problems with accurate radon‐radium disequilibrium measurements in small‐diameter cores appear to compromise their usefulness for studying sediment‐water transport at our site. ²²² Rn values determined in 17‐cm‐long sectioned cores never reached secular equilibrium activities of ²²⁶ Ra.

Radon 222 distribution and transport across the sediment-water interface in the Hudson River estuary

Article

Sep 1977

Radon 222 concentrations in waters of the Hudson River estuary show little consistent vertical, axial, or seasonal variation. The median of 106 summer measurements is 1.43 +- 0.25 dpm/1, and the median of 17 winter measurements is 1.30 +- 0.35 dpm/1. A budget is constructed for the water column which balances the rate of radon input against the rate of radon loss for two regions, one of which is broad and shallow and the other narrow and deep. The primary supply of radon for these two regions is from the sediments (75--90%), with minor inputs from radium 226 decay in the water column, stream runoff, and tidal pumping of groundwater. Loss of radon occurs by evasion to the atmosphere and decay in the water column in roughly equal amounts. The activity of mobile radon in sediments (per wet sediment volume) is 0.33 +- 0.10 dpm/cmÂ³ in the broad, shallow area of the estuary and 0.42 +- 0.11 dpm/cmÂ³ in the narrow, deep reach immediately upstream. When these value are used, the flux supplied by molecular diffusion is approximately 40% of the total input. Constant physical stirring of the upper few centimeters of sediments by bottom currents over large areas and stochastic reworking to somewhat greater depth in localized sediment deposits appear to be primarily responsible for augmenting the flux from sediments provided by molecular diffusion.

Sulfate reduction and methane oxidation in continental margin sediments influenced by irrigation (South-East Atlantic off Namibia)

Article

Mar 2000
GEOCHIM COSMOCHIM AC

Sulfate reduction rates (SRR) and concentrations of SO42−, H2S, pyrite sulfur, total sulfur, CH4, and organic carbon were measured with high depth resolution through the entire length of the SO42−-zone and well into the CH4-zone at two continental slope stations in the eastern South Atlantic (Benguela upwelling area). The sediments were characterized by a high organic carbon content of approx. 7.5% at GeoB 3703 and 3.7% at GeoB 3714. At GeoB 3703 SO42− concentrations decreased linearly with depth to about 40 μM at the sulfate-methane transition zone (SMT) at 3.5 m, while at GeoB 3714, SO42− remained at sea water concentration in the top 2 m of the sediment and then decreased linearly to about 70 μM at the SMT at 6 m. Direct rate measurements of SRR (35SO42−) showed that the highest SRR occurred within the surface 3–5 cm with peak rates of up to 20 and 7 nmol SO42− cm−3 day−1 at GeoB 3703 and GeoB 3714, respectively. SRR decreased quasi-exponentially with depth at GeoB 3703 and the cumulative SRR over the length of the SO42− zone resulted in an areal SRR (SRRarea) of 1114–3493 μmol m−2 day−1 (median value: 2221 μmol m−2 day−1) at GeoB 3703 with more than 80% of the total sulfate reduction proceeding in the top 30 cm sediment. At GeoB 3714 SRR exhibited more scatter with a cumulative SRRarea of 398–1983 μmol m−2 day−1 (median value: 1251 μmol m−2 day−1) and with >60% of the total sulfate reduction occurring below a depth of 30 cm due partially to a deeply buried zone of sulfate reduction located between 3 and 5 m depths. SRR peaks were also observed in SMT of both cores, ostensibly associated with methane oxidation, but with rates about 10 times lower than at the surface. Modeled SRR balanced both methane oxidation rates and measured SRR within the SMT, but severely underestimated by up to 89% the total SRRarea that were obtained from direct measurements. Modeled and measured SRR were reconciled by including solute transport by irrigation described by a non-local pore water exchange function (α) which had values of up to 0.3 year−1 in the top sediment, and decreased exponentially to zero (i.e., no irrigation) at 2–3 meters (i.e., above SMT). These results suggested that co-existing sulfate reduction processes and linear SO42−-gradients can be maintained by a non-local transport mechanism such as irrigation, by which pore water in tubes or burrows is exchanged with bottom waters by activities of tube-dwelling animals, or some similar physical transport phenomenon (i.e., bubble ebullition). Further support for an irrigation mechanism was found in the observations of open tubes of up to 8 mm (ID) at depths down to 6 m, which also contained fecal pellets, indicating that these tubes were or had been inhabited.

Applied Regression Analysis and Other Multivariate Models

Article

Sep 1979

Sulphate Reduction, Organic Matter Decomposition and Pyrite Formation [and Discussion]

Article

Jul 1985
PHILOS T R SOC A

Laboratory, field, and theoretical studies have shown that the rate of bacterial sulphate reduction during early diagenesis depends primarily on the reactivity of sedimentary organic matter whose decomposition follows first-order kinetics, with rate constants varying over six orders of magnitude. Decay rates decrease with decreasing sediment burial rate and, for a given sediment, with depth, because of the successive utilization by bacteria of less and less reactive organic compounds. High burial (and bioturbation) rates enable reactive compounds to become available for sulphate reduction, at depth, which otherwise would be destroyed by molecular oxygen at or above the sediment--water interface. An important consequence of bacterial sulphate reduction is the formation of sedimentary pyrite, FeS2. In normal marine sediments (those deposited in oxygenated bottom waters) pyrite formation is limited by the concentration and reactivity of organic matter, whereas in euxinic (sulphidic) basins pyrite is limited by the abundance and reactivity of detrital iron minerals, and in non-saline swamp and lake sediments by the low levels of dissolved sulphate found in fresh water. Because of these differences in limiting factors, the three environments can be distinguished in both modern sediments and ancient rocks by plots of organic carbon, C against pyrite sulphur, S. Values of the C:S ratio based on theoretical calculations indicate that worldwide the bulk of organic matter burial has shifted considerably between these environments over Phanerozoic time.

Gas exchange in a Georgia salt mars

Article

Apr 1961

The oxygen consumption of the undisturbed marsh surface, of well-stirred mud samples, and of above- and below-ground portions of Spartina was measured as were oxygen and rcdox profiles and sediment particle size. All but the uppermost fraction of the sediment was oxygen free and the intensity of reduction was high in all but the best drained areas an d was not correlated with amount of reduced material present. The latter was, however, roughly correlated with primary productivity. The rate of energy degradation of the bac- teria living in the marsh mud was increased about 25 times when they were supplied with oxygen. Spartina, the major marsh producer, consumes more oxygen than any other group. Next in importance are the bacteria of the mud.

Benthic oxygen fluxes on the Washington shelf and slope: A comparison of in situ microelectrode and chamber flux measurements

Article

May 1992

Benthic oxygen fluxes calculated from in situ microelectrode profiles arc compared with benthic flux chamber O2 uptake measurements on a transect of eight stations across the continental shelf and three stations on the slope of Washington State. Station depths ranged from 40 to 630 m and bottom-water oxygen concentrations were 127-38 FM. The fluxes measured by the two methods were similar on the slope, but on the shelf, the chamber flux exceeded the microelectrode flux by as much as a factor of 3-4. We attribute this difference to pore-water irrigation, a process which apparently accounts for the oxidation of a significant amount of organic C in the continental shelf sediments. Combining our diffusive flux data with other data demonstrates clearly that the bottom- water oxygen concentration must play some significant role in determining the sedimentary oxygen consumption rate. Numerical simulation of the microelectrode 0, profiles suggests that roughly half the diffusive 0, flux must be consumed within - 1 mm of the sediment surface. If this conclusion is correct, then the magnitude of the diffusive flux depends both on the bottom-water oxygen concentration and on the supply rate of labile C to the sediment surf'ace.

Diffusion-Coefficients In Nearshore Marine-Sediments

Article

May 1982

The formation resistivity factor, F, necessary to calculate bulk sediment diffusion coefficients of interstitial solutes from free solution diffusion coefficients, can be estimated from f the sediment porosity. Empirical relationships between F and f indicate that F » f -2 for unlithified marine sands or muds when 0.7 ≥ f and F » f -2.5 to f -3 for high porosity muds when f > 0.7.

Sediment-water exchange in shallow water estuarine sediments

Article

Aug 1984

Pore water profiles in shallow estuarine sediments of Puget Sound show the characteristics of enhanced interstitial-water transport by animal activity. Using an in situ 3H experiment and dissolved silicate profiles we evaluate the transport parameter due to animal activity in the surface 20 cm of sediments to be 1-5 × 10-7 s-1 which is in the range of similar parameters determined in other nearshore environments in the U.S. The fluxes of alkalinity, ammonia and silicate across the sediment-water interface due to biological processes are greater than that by one-dimensional molecular diffusion. For the metals Fe, Mn, Cu, Ni and Cd the dominant transport mechanism depends upon the depth at which the metal is released to the pore waters. Probably the most important effect of biological activity on metal remobilization is the removal of sulfide from the pore waters, via ventilation of sediments with oxic overlying water, allowing the enrichment of dissolved metals which might otherwise be very low in concentration due to insoluble sulfide formation. The result is a greatly enhanced flux of metals to the bottom waters.

A Method-of-Lines Code for Carbon and Nutrient Diagenesis in Aquatic Sediments

Article

Jun 1996
COMPUT GEOSCI-UK

Bernard P. Boudreau

The computer code CANDI successfully models organic matter, oxidant, nutrient, by-product, and pH diagenesis in aquatic sediments. It is stable for a wide range of burial velocities, and can deal with depth-dependent transport processes and properties (e.g. bio-diffusivities that disappear with sediment depth). It correctly reproduces the accepted sequence of oxidants, and it is remarkably good at preserving mass. Whereas it is flexible in its present form, the subroutines can also be altered to adopt any kinetics, diffusivities, porosity functions, and initial conditions.

Seasonal cycles of particle and solute transport processes in nearshore sediments: 222Rn226Ra and 234Th238U disequilibrium at a site in Buzzards Bay, MA

Article

Apr 1987
GEOCHIM COSMOCHIM AC

Radiochemical measurements leading to the estimation of particle mixing rates and irrigation rates in the sediments of a site in Buzzards Bay, Massachusetts, have been made over two nearly full seasonal cycles. Both particle mixing and sediment irrigation show significant seasonal variability at this site; the variability is consistent with biologically driven transport mechanisms. disequilibrium measurements were used to estimate particle mixing rates: based on three cores taken from December through March and four taken from June through October, a cold-season average mixing rate of 5.6 cm2/yr and a warm-season average rate of 17 cm2/yr were found. Excess 234Th inventories in the upper 5 cm of the sediments also varied seasonally, with a cold-season average value of 1.8 dpm/cm2, significantly less than both the warm-season value of 3.4 dpm/cm2 and the predicted average value for Buzzards Bay (≈3 dpm/cm2). disequilibrium in sediment pore waters was used to estimate sediment irrigation. Based on a total of seven cores, three seasonal groupings of results were made: (1) December through March, when 222Rn deficits could be explained by vertical molecular diffusion alone, (2) early summer (June), when irrigation was important to at least 20 cm, the maximum depth of the sampled region, and (3) early fall, when irrigation was important to about 10 cm. A nonlocal exchange/vertical molecular diffusion model (Emersonet al., 1984) was used to obtain quantitative estimates of irrigation rates; when the exchange parameter was allowed to vary exponentially with depth below the sediment-water interface, model Rn deficit profiles fit measured profiles quite well.

On weighted‐mean schemes for the finite‐difference approximation to the advection‐diffusion equation

Article

Dec 1977

The weighted-mean scheme is a method for constructing finite-difference approximations of second-order partial differential equations of the advection-diffusion type using only the center and adjacent points in each space direction. The scheme tends to a centered-difference formulation for strongly diffusive cases and to an upstream formulation for strongly advective cases. The error of approximation is O(h2) or better, when h tends to zero, and the scheme assures stability and convergence to all iterative methods no matter how large the grid size. The scheme thus makes it possible to choose the biggest grid size suitable for each specific problem thereby reducing the computing time considerably.

Benthic fluxes in San Francisco Bay

Article

Jan 1985

Measurements of benthic fluxes have been made on four occasions between February 1980 and February 1981 at a channel station and a shoal station in South San Francisco Bay, using in situ flux chambers. On each occasion replicate measurements of easily measured substances such as radon, oxygen, ammonia, and silica showed a variability (±1σ) of 30% or more over distances of a few meters to tens of meters, presumably due to spatial heterogeneity in the benthic community. Fluxes of radon were greater at the shoal station than at the channel station because of greater macrofaunal irrigation at the former, but showed little seasonal variability at either station. At both stations fluxes of oxygen, carbon dioxide, ammonia, and silica were largest following the spring bloom. Fluxes measured during different seasons ranged over factors of 2–3, 3, 4–5, and 3–10 (respectively), due to variations in phytoplankton productivity and temperature. Fluxes of oxygen and carbon dioxide were greater at the shoal station than at the channel station because the net phytoplankton productivity is greater there and the organic matter produced must be rapidly incorporated in the sediment column. Fluxes of silica were greater at the shoal station, probably because of the greater irrigation rates there. N + N (nitrate + nitrite) fluxes were variable in magnitude and in sign. Phosphate fluxes were too small to measure accurately. Alkalinity fluxes were similar at the two stations and are attributed primarily to carbonate dissolution at the shoal station and to sulfate reduction at the channel station. The estimated average fluxes into South Bay, based on results from these two stations over the course of a year, are (in mmol m−2d−1):O2= −27 ± 6; TCO2= 23 ± 6; Alkalinity = 9 ± 2; N + N = −0.3 ± 0.5; NH3 = 1.4 ± 0.2; PO4 = 0.1 ± 0.4; Si = 5.6 ± 1.1. These fluxes are comparable in magnitude to those in other temperate estuaries with similar productivity, although the seasonal variability is smaller, probably because the annual temperature range in San Francisco Bay is smaller. Budgets constructed for South San Francisco Bay show that large fractions of the net annual productivity of carbon (about 90%) and silica (about 65%) are recycled by the benthos. Substantial rates of simultaneous nitrification and denitrification must occur in shoal areas, apparently resulting in conversion to N2 of 55% of the particulate nitrogen reaching the sediments. In shoal areas, benthic fluxes can replace the water column standing stocks of ammonia in 2–6 days and silica in 17–34 days, indicating the importance of benthic fluxes in the maintenance of productivity. Pore water profiles of nutrients and Rn-222 show that macrofaunal irrigation is extremely important in transport of silica, ammonia, and alkalinity. Calculations of benthic fluxes from these profiles are less accurate, but yield results consistent with chamber measurements and indicate that most of the NH3, SiO2, and alkalinity fluxes are sustained by reactions occurring throughout the upper 20–40 cm of the sediment column. In contrast, O2, CO2, and N + N fluxes must be dominated by reactions occurring within the upper one cm of the sediment-water interface. While most data support the statements made above, a few flux measurements are contradictory and demonstrate the complexity of benthic exchange.

Biological enhancement of solute exchange between sediments and bottom water on the Washington continental shelf

Article

Dec 1984
CONT SHELF RES

Solute exchange between the interstitial waters and overlying waters on the Washington continental shelf was investigated based on measurements of the pore-water sulfate distribution and sulfate reduction rates as well as through models describing the distribution of sulfate in anaerobic pore waters. The depth-integrated sulfate reduction rate greatly exceeded the influx of sulfate attributable to molecular diffusion and sediment accumulation acting on the measured vertical sulfate gradients, and indicated that additional transport mechanisms must have been operating. Sediment mixing was probably not the primary mechanism since high eddy diffusivities would be required to depths of 30 cm to maintain the observed sulfate distribution, whereas previously measured210Pb distributions indicated sediment mixing is primarily restricted to depths <7 cm. Irrigation of bottom water through animal burrows was the most likely mechanism. To describe this process, a general diffusive irrigation coefficient, B, was formulated. Vertical profiles of B showed the main irrigation zone occurred between 2 and 10 cm with reduced irrigation rates occurring below this. These coefficients calculated from the sulfate distribution were similar to ones calculated from previously published radon measurements at the same stations, indicating that this formulation of irrigation exchange may be useful in modelling the exchange of dissolved solutes between the pore water and the bottom water.

Quantifying solute distributions in the bioturbated zone of marine sediments by defining an average microenvironment

Article

Dec 1980
GEOCHIM COSMOCHIM AC

Robert Curwood Aller

The bioturbated zone of marine sediments is a region having a complex, time-dependent geometry of diffusion and chemical reactions. It is possible to simplify this geometry by postulating an average sediment microenvironment and modelling it as representative of the sediment body as a whole. The microenvironment is assumed to correspond to a single, tube-dwelling animal together with its surrounding sediment and can be represented by a finite hollow cylinder. A transport-reaction model derived from this postulate produces good agreement between observed and predicted pore water profiles using realistic physical constants. The average vertical distributions of pore water solutes and their sediment-water fluxes are influenced by the presence of irrigated burrows to varying degrees depending on the kind of reactions governing their behavior. Pore water profiles of solutes, such as NH+4, subject to zero order reaction rates are highly sensitive to the abundance and sizes of burrows while the net flux of the constituent across the sediment-water interface is not. In contrast, profiles of solutes such as Si that are subject to first order reaction rates are less sensitive to the presence of irrigated burrows but net fluxes are greatly affected. Average pore water concentrations, fluxes of solutes like Si and the apparent one-dimensional diffusion coefficients required to match vertical gradients with measured solute fluxes, are influenced by both the size and spacing of burrows. Because of the range of solute concentrations within the microenvironment at any given depth it is not strictly valid to make detailed solubility calculations on the basis of average pore water concentrations within the bioturbated zone.

Seasonal variations of bioirrigation in coastal sediments: Modelling of field data

Article

Mar 2000
GEOCHIM COSMOCHIM AC

In near-shore and coastal margin sediments remineralization of organic carbon is significantly affected by biologically mediated solute exchange caused by burrow-dwelling infauna. Although irrigation rates have been determined for various environments, little is known about their seasonal variations and their coupling to the food-supply or the oxygen level in bottom waters. These aspects have been investigated at two sites in the Kiel Bight by modelling pore water concentrations of Cl, which is a suitable tracer for transport processes. A very similar temporal pattern of irrigation was determined at both sites. In spring and fall the effect of bioirrigation on the pore water concentration of Cl is important at both sites, and a more than two to five fold enhancement of solute exchange, relative to diffusional transport, was calculated. The temporal pattern of bioirrigation correlates with that of the Chl.-a (eq) inventory of the surface sediments. Enhanced irrigation rates follow the settling of plankton blooms in this region. During the summer, when low oxygen levels were observed in bottom waters, overall irrigation rates are low. Furthermore, the relative importance of irrigation processes operating close to the sediment surface increases suggesting an upward movement and migration of burrow-dwelling organisms in response to low O2-concentrations. Because bioirrigation is an important transport process coupling organic carbon flux, remineralization at the seafloor, and redox zonation in the sediment quantifying the seasonal cycle of the irrigation intensity represents a step forward in the dynamic understanding of benthic processes.

The use of Radon-222 as a Tracer of Sediment Irrigation and Mixing on the Washington Continental Shelf

Article

Jul 1981
MAR GEOL

Observations of the natural radioisotope Rn-222 were used in conjunction with radiochemical, biological, and sedimentological techniques to investigate the irrigation and mixing of sediment at three sites (about 90 m water depth) along the Washington continental shelf. The Rn-222 deficit (difference between observed and predicted concentrations) within the seabed was greatest near the Columbia River during the summer. Molecular diffusion at most locations and times could account for only a portion of the deficit; irrigation and mixing of the seabed explain the remainder. Biological mixing (bioturbation) and physical irrigation (wave and tidal pumping) have relatively little effect on the Rn-222 deficit. Physical mixing (erosion and deposition) has a significant effect soon after a major erosion event (storm); however, no such event occurred prior to the observations. The conclusion is that biological irrigation and molecular diffusion are the primary causes of the Rn-222 deficit, and that biological irrigation is responsible for the observed spatial and temporal variations in the deficit. Therefore, biological irrigation is greatest near the Columbia River during the summer. The spatial increase of irrigation near the Columbia is probably due to a relatively large population of tube-dwelling, filter-feeding polychaetes. The temporal increases of irrigation during the summer is probably due to annual growth cycles of the benthic community, and is not due to water temperature changes.

A global model for the early diagenesis of organic carbon and organic phosphorus in marine sediments

Article

Apr 1995
GEOCHIM COSMOCHIM AC

Sediments are the main repository in the oceanic cycles of carbon (C) and phosphorus (P). In order to relate the deposition of organic C and organic P from the water column, and ultimate burial in sediments, we present a model for the early diagenesis of organic matter in marine sediments. This general diagenetic model was developed for inclusion in global circulation models and is based on a single master variable, the sedimentation rate. The processes included are sediment advection, particle mixing by bioturbation, porewater diffusion, organic matter degradation by aerobic respiration, sulfate reduction, and methanogenesis. Deposition fluxes of organic C and organic P, and the bottomwater concentrations of O2 and SO4= are used as input for the sediment model. First-order kinetics are assumed for the degradation of organic C and organic P (one-G model).Despite the model's simplicity, the model quantitatively reproduces the rates of organic matter oxidation and the burial fluxes of organic C and P. The predicted trends of oxygen penetration depth and the relative importance of oxygen and sulfate reduction are in good agreement with field observations. The model appears to account for the critical biogeochemical and transport processes that control the fate of organic matter in sediments.

A multicomponent reactive transport model of early diagenesis: Application to redox cycling in coastal marine sediments

Article

Aug 1996
GEOCHIM COSMOCHIM AC

STEADYSED1 is a multicomponent reactive transport code for steady-state early diagenesis which fully incorporates the reaction couplings among the elements, C, O, N, S, Fe, and Mn. The model is tested against extensive datasets collected by Canfield et al. (1993a,b) at three coastal marine sites that exhibit high rates of combined iron and manganese (hydr)oxide reduction. It is shown that the model provides a consistent explanation of the entire body of multicomponent multisite observations. The measured concentration profiles of twenty-eight individual porewater and solid sediment species are satisfactorily reproduced. Furthermore, the model predicts the observed distributions of sulfate reduction rates, as well as diagnostic features of the porewater pH profiles.

Numerical Recipes in Fortran 77

Book

Jan 1992

An inverse model for reactive transport in biogeochemical systems : application to biologically-enhanced pore water transport (irrigation) in aquatic sediments

Article

Christof D. Meile

M.S. Herbert L. Windom

Reactive and nonreactive particle dynamics in dense assemblages of the head down deposit feeder Clymenella torquata

Mar 1996
30

N I Craig
G R Lopez

CRAIG, N. I., AND G. R. LOPEZ. 1996. Reactive and nonreactive particle dynamics in dense assemblages of the head down deposit feeder Clymenella torquata, p.30. In S. A. Woodin and others [eds.], 24th Annual Benthic Ecology Meeting, Columbia, South Carolina, March 7-10, 1996.

Quantifying solute distributions in the bioturbated zone of marine sediments by defining an average microenvironment The effect of biogenic irrigation intensity and solute exchange on diagenetic reaction rates in marine sediments

Jan 1980
1955-1965

And J Y J Y Aller
And W J Yingst
Ullman

ALLER, R. C. 1980. Quantifying solute distributions in the bioturbated zone of marine sediments by defining an average microenvironment. Geochim. Cosmochim. Acta 44: 1955-1965. , AND J. Y. ALLER. 1998. The effect of biogenic irrigation intensity and solute exchange on diagenetic reaction rates in marine sediments. J. Mar. Res. 56: 905-936. , J. Y. YINGST, AND W. J. ULLMAN. 1983. Comparative biogeochemistry of water in intertidal Onuphis (polychaeta) and Upogebia (crustacea) burrows: Temporal patterns and causes.

The measurement of sediment irrigation rates: A comparison of the Br tracer and 222Rn/226Ra disequilibrium techniques Seasonal cycles of particle and solute transport processes in nearshore sediments: 222Rn/ 226Ra and 234Th

Jan 1987
927-943

And G T Banta

MARTIN, W. R., AND G. T. BANTA. 1992. The measurement of sediment irrigation rates: A comparison of the Br tracer and 222Rn/226Ra disequilibrium techniques. J. Mar. Res. 50: 125154. , AND F. L. SAYLES. 1987. Seasonal cycles of particle and solute transport processes in nearshore sediments: 222Rn/ 226Ra and 234Th/238U disequilibrium at a site in Buzzards Bay, MA. Geochim. Cosmochim. Acta 51: 927-943.

On the equivalence of nonlocal and radialdiffusion models for porewater irrigation Mathematics of tracer mixing in sediments: III. The theory of nonlocal mixing within sediments A method-of-lines code for carbon and nutrient diagenesis in aquatic sediments Diagenetic models and their implementation

Jan 1984
731735-693

B P Boudreau

BOUDREAU, B. P. 1984. On the equivalence of nonlocal and radialdiffusion models for porewater irrigation. J. Mar. Res. 42: 731735. . 1987. Mathematics of tracer mixing in sediments: III. The theory of nonlocal mixing within sediments. Am. J. Sci. 287: 693-719. . 1996. A method-of-lines code for carbon and nutrient diagenesis in aquatic sediments. Computers Geosci. 22: 479-496. . 1997. Diagenetic models and their implementation. Springer.

Quantifying bioirrigation in aquatic sediments: An inverse modeling approach

Abstract

No full-text available

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