Filip J. R. Meysman

Quantifying Food Web Flows Using Linear Inverse Models

The quantitative mapping of food web flows based on empirical data is a crucial yet difficult task in ecology. The difficulty arises from the under-sampling of food webs, because most data sets are incomplete and uncertain. In this article, we review methods to quantify food web flows based on empirical data using linear inverse models (LIM). The food web in a LIM is described as a linear function of its flows, which are estimated from empirical data by inversemodeling. The under-sampling of food webs implies that infinitely many different solutions exist that are consistent with a given data set. The existing approaches to food web LIM select a single solution from this infinite set by invoking additional assumptions: either a specific selection criterion that has no solid ecological basis is used or the data set is artificially upgraded by assigning fixed values to, for example, physiological parameters. Here, we advance a likelihood approach (LA) that follows a different solution philosophy. Rather than singling out one particular solution, the LA generates a large set of possible solutions from which the marginal probability density function (mPDF) of each flow and correlations between flows can be derived. The LA is exemplified with an example model of a soil food web and is made available in the open-source R-software. Moreover, we show how stoichiometric data, stable isotope signatures, and fatty acid compositions can be included in the LIM to alleviate the under-sampling problem. Overall, LIM prove to be a powerful tool in food web research, which can bridge the gap between empirical data and the analysis of food web structures.

Natural occurrence of microbial sulphur oxidation by long-range electron transport in the seafloor

Recently, a novel mode of sulphur oxidation was described in marine sediments, in which sulphide oxidation in deeper anoxic layers was electrically coupled to oxygen reduction at the sediment surface. Subsequent experimental evidence identified that long filamentous bacteria belonging to the family Desulfobulbaceae likely mediated the electron transport across the centimetre-scale distances. Such long-range electron transfer challenges some long-held views in microbial ecology and could have profound implications for sulphur cycling in marine sediments. But, so far, this process of electrogenic sulphur oxidation has been documented only in laboratory experiments and so its imprint on the seafloor remains unknown. Here we show that the geochemical signature of electrogenic sulphur oxidation occurs in a variety of coastal sediment environments, including a salt marsh, a seasonally hypoxic basin, and a subtidal coastal mud plain. In all cases, electrogenic sulphur oxidation was detected together with an abundance of Desulfobulbaceae filaments. Complementary laboratory experiments in intertidal sands demonstrated that mechanical disturbance by bioturbating fauna destroys the electrogenic sulphur oxidation signal. A survey of published geochemical data and 16S rRNA gene sequences identified that electrogenic sulphide oxidation is likely present in a variety of marine sediments with high sulphide generation and restricted bioturbation, such as mangrove swamps, aquaculture areas, seasonally hypoxic basins, cold sulphide seeps and possibly hydrothermal vent environments. This study shows for the first time that electrogenic sulphur oxidation occurs in a wide range of marine sediments and that bioturbation may exert a dominant control on its natural distribution.

Reactive transport in aquatic ecosystems: Rapid model prototyping in the open source software R

The concentrations of many natural compounds are altered by chemical and biological transformations, and physical processes such as adsorption and transport. Their fate can be predicted using reactive transport models that describe reaction and advective and dispersive movement of these components in their natural environment. Recently a number of software packages have been implemented in the open source software R that allow one to implement reactive transport models. Central to this is the ReacTran R-package, a comprehensive collection of functions for modeling reactive components that may be distributed over multiple phases, whose dynamics are coupled through biological and geochemical reactions, and that are transported in one-, two- or three-dimensional domains with simple geometries. Dedicated solution methods are in R-packages deSolve and rootSolve. The modeling packages facilitate the simulation of reaction and transport of components for spatial scales ranging from micrometers to kilometers and spanning multiple time-scales. As they are influenced in similar ways, the same functions can solve biogeochemical models of the sediment, groundwater, rivers, estuaries, lakes or water columns, experimental setups, or even describe reaction and transport within flat, cylindrical or spherical bodies, such as organisms, aggregates, or the dispersion of individuals on flat surfaces and so on. We illustrate the use of R for reactive transport modeling by three applications spanning several orders of magnitude with respect to spatial and temporal scales. They comprise (1) a model of an experimental flow-through sediment reactor, where fitting so-called breakthrough curves are used to derive sulfate reduction rates in an estuarine sediment, (2) a conservative and reactive tracer addition experiment in a small stream, which implements the concept of river spiraling, and (3) a 2-D and 3-D model that describes oxygen dynamics in the upper layers of the sediment, interspersed with several hotspots of increased reaction intensities. The packages ReacTran, deSolve and rootSolve are implemented in the software R and thus available for all popular platforms (Linux, Windows, Mac). Models implemented using this software are short and easily readable, yet they are efficiently solved. This makes R extremely well suited for rapid model prototyping.

Predicted tortuosity of muds

Tortuosity figures prominently in geochemical, hydrological, and geophysical calculations concerned with sediments, but it is a difficult parameter to measure. Past theoretical models for predicting the tortuosity from porosity data do not work with marine muds, and scientists and engineers have had to resort to entirely empirical models, without a mechanistic explanation and with unknown predictive power. We offer the first geometric model for the dependence of tortuosity on porosity in marine muds; the model is based on the tortuosity of separated layers of nonoverlapping disks. The fitted geometric constant in this model indicates that natural marine sediments act as if their fabric were made of disks with thickness:diameter ratios very close to 1:2, which indicates a blocklike fabric with respect to diffusion. The model was also applied to predict the tortuosity of a variety of sediments and soils not in the original database, and it provides a satisfactory prediction of the mean trend in these data.

Oxidation and Origin of Organic Matter in Surficial Eastern Mediterranean Hemipelagic Sediments

Aerobic mineralisation of Corg in surface sedimentsof the deep (>2000 m water depth) eastern Mediterranean Sea has been quantified by analysis of detailedbox core Corg concentration versus depth profiles and the modelling environment for early diageneticproblems MEDIA. The reactive fraction comprises 60–80% of the total Corg reachingthe sediments and is largely oxidised within the surficial 10 cm. A non-reactive C orgfraction (GNR) dominates at depths >10 cm, and makes up20–40% of the total C org flux to the sediments. First-order rateconstants for decomposition of the reactive fraction calculated from theC org profiles range from 5.4 × 10-3 to8.0 × 10-3 y-1 to 8.0 × 10-3 y-1. Total mineralization rates in thesurface sediment are between 1.7 and 2.6 μmol C cm-2 y-1 and thus are typical for oligotrophic, deep-seaenvironments. The low fluxes and rapid remineralisation of C org are accompanied by210Pbexcess surface mixed layers which are only 2 cm deep, among the thinnest reported for oxygenated marine sediments.Model results indicate a mismatch between the C org profiles and O2 microprofileswhich were measured onboard ship. This can be attributed to a combination of decompression artefactsaffecting onboard measurement of the O2 profiles or the leakage ofoxygen into the core during handling on deck. Furthermore, the used Db values, based on 210Pb, may not befully appropriate; calculations with higher Db values improve the O2 fits. The surficial sedimentδ13C org values of ∼ -22‰ become less negative with increasing depth and decreasing C orgconcentrations. The major δ13C change occurs in the top 3 to 4 cm and coincides with the interval weremost of the organic carbon oxidation takes place. This indicates that the reactive fractionof organic matter, commonly assumed to be marine, has a more negative δ13C orgthan the refractory fraction, usually held to be terrestrial. Palaeoproductivity estimates calculated from thesediment data by means of literature algorithms yield low surface productivities(12–88 gC m-2 y-1), which are in good agreement with field measurements of primary productivity in otherstudies. Such values are, however, significantly lower than those indicated by recent productivitymaps of the area derived from satellite imagery (>100 gC m-2 y-1).

Microbial carbon metabolism associated with electrogenic sulphur oxidation in coastal sediments

Recently, a novel electrogenic type of sulphur oxidation was documented in marine sediments, whereby filamentous cable bacteria (Desulfobulbaceae) are mediating electron transport over cm-scale distances. These cable bacteria are capable of developing an extensive network within days, implying a highly efficient carbon acquisition strategy. Presently, the carbon metabolism of cable bacteria is unknown, and hence we adopted a multidisciplinary approach to study the carbon substrate utilization of both cable bacteria and associated microbial community in sediment incubations. Fluorescence in situ hybridization showed rapid downward growth of cable bacteria, concomitant with high rates of electrogenic sulphur oxidation, as quantified by microelectrode profiling. We studied heterotrophy and autotrophy by following 13C-propionate and -bicarbonate incorporation into bacterial fatty acids. This biomarker analysis showed that propionate uptake was limited to fatty acid signatures typical for the genus Desulfobulbus. The nanoscale secondary ion mass spectrometry analysis confirmed heterotrophic rather than autotrophic growth of cable bacteria. Still, high bicarbonate uptake was observed in concert with the development of cable bacteria. Clone libraries of 16S complementary DNA showed numerous sequences associated to chemoautotrophic sulphur-oxidizing Epsilon- and Gammaproteobacteria, whereas 13C-bicarbonate biomarker labelling suggested that these sulphur-oxidizing bacteria were active far below the oxygen penetration. A targeted manipulation experiment demonstrated that chemoautotrophic carbon fixation was tightly linked to the heterotrophic activity of the cable bacteria down to cm depth. Overall, the results suggest that electrogenic sulphur oxidation is performed by a microbial consortium, consisting of chemoorganotrophic cable bacteria and chemolithoautotrophic Epsilon- and Gammaproteobacteria. The metabolic linkage between these two groups is presently unknown and needs further study.

Cable bacteria generate a firewall against euxinia in seasonally hypoxic basins

Significance Seasonal hypoxia is increasing in coastal areas worldwide, as more nutrients are delivered to the coastal ocean and water temperatures are rising due to climate change. Hypoxia reaches a particularly harmful stage when sulfide, which is highly toxic for marine life, is released to the bottom water. Here, we document a natural microbial mechanism that counteracts the release of free sulfide, thus preventing the most adverse stage of seasonal hypoxia. Electricity-generating cable bacteria produce a large pool of oxidized sedimentary iron minerals, which efficiently bind free sulfide. As cable bacteria are likely abundant in many seasonally hypoxic basins worldwide, their “firewall” mechanism may be widespread. Seasonal oxygen depletion (hypoxia) in coastal bottom waters can lead to the release and persistence of free sulfide (euxinia), which is highly detrimental to marine life. Although coastal hypoxia is relatively common, reports of euxinia are less frequent, which suggests that certain environmental controls can delay the onset of euxinia. However, these controls and their prevalence are poorly understood. Here we present field observations from a seasonally hypoxic marine basin (Grevelingen, The Netherlands), which suggest that the activity of cable bacteria, a recently discovered group of sulfur-oxidizing microorganisms inducing long-distance electron transport, can delay the onset of euxinia in coastal waters. Our results reveal a remarkable seasonal succession of sulfur cycling pathways, which was observed over multiple years. Cable bacteria dominate the sediment geochemistry in winter, whereas, after the summer hypoxia, Beggiatoaceae mats colonize the sediment. The specific electrogenic metabolism of cable bacteria generates a large buffer of sedimentary iron oxides before the onset of summer hypoxia, which captures free sulfide in the surface sediment, thus likely preventing the development of bottom water euxinia. As cable bacteria are present in many seasonally hypoxic systems, this euxinia-preventing firewall mechanism could be widely active, and may explain why euxinia is relatively infrequently observed in the coastal ocean.

Cable Bacteria Control Iron–Phosphorus Dynamics in Sediments of a Coastal Hypoxic Basin

Phosphorus is an essential nutrient for life. The release of phosphorus from sediments is critical in sustaining phytoplankton growth in many aquatic systems and is pivotal to eutrophication and the development of bottom water hypoxia. Conventionally, sediment phosphorus release is thought to be controlled by changes in iron oxide reduction driven by variations in external environmental factors, such as organic matter input and bottom water oxygen. Here, we show that internal shifts in microbial communities, and specifically the population dynamics of cable bacteria, can also induce strong seasonality in sedimentary iron-phosphorus dynamics. Field observations in a seasonally hypoxic coastal basin demonstrate that the long-range electrogenic metabolism of cable bacteria leads to a dissolution of iron sulfides in winter and spring. Subsequent oxidation of the mobilized ferrous iron with manganese oxides results in a large stock of iron-oxide-bound phosphorus below the oxic zone. In summer, when bottom water hypoxia develops and cable bacteria are undetectable, the phosphorus associated with these iron oxides is released, strongly increasing phosphorus availability in the water column. Future research should elucidate whether formation of iron-oxide-bound phosphorus driven by cable bacteria, as observed in this study, contributes to the seasonality in iron-phosphorus cycling in aquatic sediments worldwide.

Cold-water coral reefs and adjacent sponge grounds: hotspots of benthic respiration and organic carbon cycling in the deep sea

Cold-water coral reefs and adjacent sponge grounds are distributed widely in the deep ocean, where only a small fraction of the surface productivity reaches the seafloor as detritus. It remains elusive how these hotspots of biodiversity can thrive in such a food-limited environment, as data on energy flow and organic carbon utilization are critically lacking. Here we report in situ community respiration rates for cold-water coral and sponge ecosystems obtained by the non-invasive aquatic Eddy Correlation technique. Oxygen uptake rates over coral reefs and adjacent sponge grounds in the Traena Coral Field (Norway) were 9-20 times higher than those of the surrounding soft sediments. These high respiration rates indicate strong organic matter consumption, and hence suggest a local focusing onto these ecosystems of the downward flux of organic matter that is exported from the surface ocean. Overall, our results show that coral reefs and adjacent sponge grounds are hotspots of carbon processing in the food-limited deep ocean, and that these deep-sea ecosystems play a more prominent role in marine biogeochemical cycles than previously recognized.

Reactive transport in surface sediments I. Mexity and software quality

Analysis of three recent diagenetic model codes (OMEXDIA, CANDI and STEADYSED) revealed that codes have a rigid, static and problem-specific character, leaving little autonomy for the application user. The resulting lack of flexibility and extensibility, and the associated need for ground-level reprogramming, constitutes a major barrier for potential model users. Present codes have apparently passed a critical threshold of code complexity, above which code development becomes time-consuming and expensive using the present procedure-oriented techniques. We have explored the advantages of object-oriented technology and the concept of a problem-solving environment to improve the quality of software for reactive transport modelling. A general blueprint for an object-oriented code for modelling early diagenesis is presented. The MEDIA environment consists of a toolbox of building blocks (element, species and process objects), which can be combined freely by the user to construct new models (without the need for recompilation). An object-oriented database stores current objects and accommodates new user-defined building blocks. Altogether, it is advocated that by improving the software quality, one can substantially lower the threshold for using model codes as an integrated data-aualysis tool.