Influence of Microbial Growth on Hydraulic Properties of Pore Networks

From laboratory experiments it is known that bacterial biomass is able to influence the hydraulic properties of saturated porous media, an effect called bioclogging. To interpret the observations of these experiments and to predict possible bioclogging effects on the field scale it is necessary to use transport models, which are able to include bioclogging. For these models it is necessary to know the relation between the amount of biomass and the hydraulic conductivity of the porous medium. Usually these relations were determined using bundles of parallel pore channels and do not account for interconnections between the pores in more than one dimension. The present study uses two-dimensional pore network models to study the effects of bioclogging on the pore scale. Numerical simulations were done for two different scenarios of the growth of biomass in the pores. Scenario 1 assumes microbial growth in discrete colonies clogging particular pores completely. Scenario 2 assumes microbial growth as a biofilm growing on the wall of each pore. In both scenarios the hydraulic conductivity was reduced by at least two orders of magnitude, but for the colony scenario much less biomass was needed to get a maximal clogging effect and a better agreement with previously published experimental data could be found. For both scenarios it was shown that heterogeneous pore networks could be clogged with less biomass than more homogeneous one

Elucidating the impact of micro-scale heterogeneous bacterial distribution on biodegradation

Groundwater microorganisms hardly ever cover the solid matrix uniformly–instead they form micro-scale colonies. To which extent such colony formation limits the bioavailability and biodegradation of a substrate is poorly understood. We used a high-resolution numerical model of a single pore channel inhabited by bacterial colonies to simulate the transport and biodegradation of organic substrates. These high-resolution 2D simulation results were compared to 1D simulations that were based on effective rate laws for bioavailability-limited biodegradation. We (i) quantified the observed bioavailability limitations and (ii) evaluated the applicability of previously established effective rate concepts if microorganisms are heterogeneously distributed. Effective bioavailability reductions of up to more than one order of magnitude were observed, showing that the micro-scale aggregation of bacterial cells into colonies can severely restrict the bioavailability of a substrate and reduce in situ degradation rates. Effective rate laws proved applicable for upscaling when using the introduced effective colony sizes

Global-scale quantification of mineralization pathways in marine sediments: A reaction-transport modeling approach

[1] The global-scale quantification of organic carbon (Corg) degradation pathways in marine sediments is difficult to achieve experimentally due to the limited availability of field data. In the present study, a numerical modeling approach is used as an alternative to quantify the major metabolic pathways of Corg oxidation (Cox) and associated fluxes of redox-sensitive species fluxes along a global ocean hypsometry, using the seafloor depth (SFD) as the master variable. The SFD dependency of the model parameters and forcing functions is extracted from existing empirical relationships or from the NOAA World Ocean Atlas. Results are in general agreement with estimates from the literature showing that the relative contribution of aerobic respiration to Cox increases from 80% in deep-sea sediments. Sulfate reduction essentially follows an inversed SFD dependency, the other metabolic pathways (denitrification, Mn and Fe reduction) only adding minor contributions to the global-scale mineralization of Corg. The hypsometric analysis allows the establishment of relationships between the individual terminal electron acceptor (TEA) fluxes across the sediment-water interface and their respective contributions to the Corg decomposition process. On a global average, simulation results indicate that sulfate reduction is the dominant metabolic pathway and accounts for approximately 76% of the total Cox, which is higher than reported so far by other authors. The results also demonstrate the importance of bioirrigation for the assessment of global species fluxes. Especially at shallow SFD most of the TEAs enter the sediments via bioirrigation, which complicates the use of concentration profiles for the determination of total TEA fluxes by molecular diffusion. Furthermore, bioirrigation accounts for major losses of reduced species from the sediment to the water column prohibiting their reoxidation inside the sediment. As a result, the total carbon mineralization rate exceeds the total flux of oxygen into the sediment by a factor of 2 globally

Anthropogenic perturbation of the carbon fluxes from land to ocean

A substantial amount of the atmospheric carbon taken up on land through photosynthesis and chemical weathering is transported laterally along the aquatic continuum from upland terrestrial ecosystems to the ocean. So far, global carbon budget estimates have implicitly assumed that the transformation and lateral transport of carbon along this aquatic continuum has remained unchanged since pre-industrial times. A synthesis of published work reveals the magnitude of present-day lateral carbon fluxes from land to ocean, and the extent to which human activities have altered these fluxes. We show that anthropogenic perturbation may have increased the flux of carbon to inland waters by as much as 1.0 Pg C yr-1 since pre-industrial times, mainly owing to enhanced carbon export from soils. Most of this additional carbon input to upstream rivers is either emitted back to the atmosphere as carbon dioxide (~0.4 Pg C yr-1) or sequestered in sediments (~0.5 Pg C yr-1) along the continuum of freshwater bodies, estuaries and coastal waters, leaving only a perturbation carbon input of ~0.1 Pg C yr-1 to the open ocean. According to our analysis, terrestrial ecosystems store ~0.9 Pg C yr-1 at present, which is in agreement with results from forest inventories but significantly differs from the figure of 1.5 Pg C yr-1 previously estimated when ignoring changes in lateral carbon fluxes. We suggest that carbon fluxes along the land–ocean aquatic continuum need to be included in global carbon dioxide budgets.Peer reviewe

Microbial controls on the biogeochemical dynamics in the subsurface

SCOPUS: ar.kinfo:eu-repo/semantics/publishe

Influence of Microbial Growth on Hydraulic Properties of Pore Networks

ISSN:0169-3913ISSN:1573-163

How the chemotactic characteristics of bacteria can determine their population patterns

Highlights • An individual-based model was developed and coupled to a pore-network model. • The bacterial distribution patterns were geostatistically analyzed. • The effects from bacterial chemotactic properties on bacterial distribution patterns were examined. • The additional influences from structural heterogeneities were examined. Abstract Spatial distribution of soil microorganisms is relevant for the functioning and performance of many ecosystem processes such as nutrient cycling or biodegradation of organic matters and contaminants. Beside the multitude of abiotic environmental factors controlling the distribution of microorganisms in soil systems, many microbial species exhibit chemotactic behavior by directing their movement along concentration gradients of nutrients or of chemoattractants produced by cells of their own kind. This chemotactic ability has been shown to promote the formation of complex distribution patterns even in the absence of environmental heterogeneities. Microbial population patterns in heterogeneous soil systems might be, hence, the result of the interplay between the heterogeneous environmental conditions and the microorganisms' intrinsic pattern formation capabilities. In this modeling study, we combined an individual-based modeling approach with a reactive pore-network model to investigate the formation of bacterial patterns in homogeneous and heterogeneous porous media. We investigated the influence of different bacterial chemotactic sensitivities (toward both substrate and bacteria) on bacterial distribution patterns. The emerging population patterns were classified with the support of a geostatistical approach, and the required conditions for the formation of any specific pattern were analyzed. Results showed that the chemotactic behavior of the bacteria leads to non-trivial population patterns even in the absence of environmental heterogeneities. The presence of structural pore scale heterogeneities had also an impact on bacterial distributions. For a range of chemotactic sensitivities, microorganisms tend to migrate preferably from larger pores toward smaller pores and the resulting distribution patterns thus resembled the heterogeneity of the pore space. The results clearly indicated that in a porous medium like soil the distribution of bacteria may not only be related to the external constraints but also to the chemotactic behavior of the bacterial cells

Applying the Rayleigh Approach for Stable Isotope-Based Analysis of VOC Biodegradation in Diffusion-Dominated Systems

Compound-specific stable isotope analysis (CSIA) has become an established tool for assessing biodegradation in the subsurface. Diffusion-dominated vapor phase transport thereby is often excluded from quantitative assessments due to the problem of diffusive mixing of concentrations with different isotopic signatures for CSIA interpretation. In soils and other unsaturated porous media volatile organic compounds (VOCs) however, are mainly transported via gas-phase diffusion and may thus prohibit a CSIA-based quantitative assessment of the fate of VOCs. The present study presents and verifies a concept for the assessment of biodegradation-induced stable isotope fractionation along a diffusive transport path of VOCs in unsaturated porous media. For this purpose data from batch and column toluene biodegradation experiments in unsaturated porous media were combined with numerical reactive transport simulations; both addressing changes of concentration and stable isotope fractionation of toluene. The numerical simulations are in good agreement with the experiment data, and our results show that the presented analytically derived assessment concept allows using the slope of the Rayleigh plot to obtain reasonable estimates of effective in situ fractionation factors in spite of diffusion-dominated transport. This enlarges the application range of CSIA and provides a mean for a better understanding of VOC fate in the unsaturated subsurface