Pore-Scale Heterogeneities Improve the Degradation of a Self-Inhibiting Substrate: Insights from Reactive Transport Modeling.

In situ bioremediation is a common remediation strategy for many groundwater contaminants. It was traditionally believed that (in the absence of mixing-limitations) a better in situ bioremediation is obtained in a more homogeneous medium where the even distribution of both substrate and bacteria facilitates the access of a larger portion of the bacterial community to a higher amount of substrate. Such conclusions were driven with the typical assumption of disregarding substrate inhibitory effects on the metabolic activity of enzymes at high concentration levels. To investigate the influence of pore matrix heterogeneities on substrate inhibition, we use a numerical approach to solve reactive transport processes in the presence of pore-scale heterogeneities. To this end, a rigorous reactive pore network model is developed and used to model the reactive transport of a self-inhibiting substrate under both transient and steady-state conditions through media with various, spatially correlated, pore-size distributions. For the first time, we explore on the basis of a pore-scale model approach the link between pore-size heterogeneities and substrate inhibition. Our results show that for a self-inhibiting substrate, (1) pore-scale heterogeneities can consistently promote degradation rates at toxic levels, (2) the effect reverses when the concentrations fall to levels essential for microbial growth, and (3) an engineered combination of homogeneous and heterogeneous media can increase the overall efficiency of bioremediation.

Toward Improved Bioremediation Strategies: Response of BAM-Degradation Activity to Concentration and Flow Changes in an Inoculated Bench-Scale Sediment Tank.

Compound-specific isotope analysis (CSIA) can reveal mass-transfer limitations during biodegradation of organic pollutants by enabling the detection of masked isotope fractionation. Here, we applied CSIA to monitor the adaptive response of bacterial degradation in inoculated sediment to low contaminant concentrations over time. We characterized Aminobacter sp. MSH1 activity in a flow-through sediment tank in response to a transient supply of elevated 2,6-dichlorobenzamide (BAM) concentrations as a priming strategy and took advantage of an inadvertent intermittence to investigate the effect of short-term flow fluctuations. Priming and flow fluctuations yielded improved biodegradation performance and increased biodegradation capacity, as evaluated from bacterial activity and residual concentration time series. However, changes in isotope ratios in space and over time evidenced that mass transfer became increasingly limiting for degradation of BAM at low concentrations under such stimulated conditions, and that activity decreased further due to bacterial adaptation at low BAM (µg/L) levels. Isotope ratios, in conjunction with residual substrate concentrations, therefore helped identifying underlying limitations of biodegradation in such a stimulated system, offering important insight for future optimization of remediation schemes.

Spatial Control of Microbial Pesticide Degradation in Soil: A Model-Based Scenario Analysis.

Microbial pesticide degraders are heterogeneously distributed in soil. Their spatial aggregation at the millimeter scale reduces the frequency of degrader-pesticide encounter and can introduce transport limitations to pesticide degradation. We simulated reactive pesticide transport in soil to investigate the fate of the widely used herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) in response to differently aggregated distributions of degrading microbes. Four scenarios were defined covering millimeter scale heterogeneity from homogeneous (pseudo-1D) to extremely heterogeneous degrader distributions and two precipitation scenarios with either continuous light rain or heavy rain events. Leaching from subsoils did not occur in any scenario. Within the topsoil, increasing spatial heterogeneity of microbial degraders reduced macroscopic degradation rates, increased MCPA leaching, and prolonged the persistence of residual MCPA. In heterogeneous scenarios, pesticide degradation was limited by the spatial separation of degrader and pesticide, which was quantified by the spatial covariance between MCPA and degraders. Heavy rain events temporarily lifted these transport constraints in heterogeneous scenarios and increased degradation rates. Our results indicate that the mild millimeter scale spatial heterogeneity of degraders typical for arable topsoil will have negligible consequences for the fate of MCPA, but strong clustering of degraders can delay pesticide degradation.

Magnitude of Diffusion- and Transverse Dispersion-Induced Isotope Fractionation of Organic Compounds in Aqueous Systems.

Determining whether aqueous diffusion and dispersion lead to significant isotope fractionation is important for interpreting the isotope ratios of organic contaminants in groundwater. We performed diffusion experiments with modified Stokes diaphragm cells and transverse-dispersion experiments in quasi-two-dimensional flow-through sediment tank systems to explore isotope fractionation for benzene, toluene, ethylbenzene, 2,6-dichlorobenzamide, and metolachlor at natural isotopic abundance. We observed very small to negligible diffusion- and transverse-dispersion-induced isotope enrichment factors (ε < -0.4 ‰), with changes in carbon and nitrogen isotope values within ±0.5‰ and ±1‰, respectively. Isotope effects of diffusion did not show a clear correlation with isotopologue mass with calculated power-law exponents ß close to zero (0.007 < ß < 0.1). In comparison to ions, noble gases, and labeled compounds, three aspects stand out. (i) If a mass dependence is derived from collision theory, then isotopologue masses of polyatomic molecules would be affected by isotopes of multiple elements resulting in very small expected effects. (ii) However, collisions do not necessarily lead to translational movement but can excite molecular vibrations or rotations minimizing the mass dependence. (iii) Solute-solvent interactions like H-bonds can further minimize the effect of collisions. Modeling scenarios showed that an inadequate model choice, or erroneous choice of ß, can greatly overestimate the isotope fractionation by diffusion and, consequently, transverse dispersion. In contrast, available data for chlorinated solvent and gasoline contaminants at natural isotopic abundance suggest that in field scenarios, a potential additional uncertainty from aqueous diffusion or dispersion would add to current instrumental uncertainties on carbon or nitrogen isotope values (±1‰) with an additional ±1‰ at most.

Mass-Transfer-Limited Biodegradation at Low Concentrations-Evidence from Reactive Transport Modeling of Isotope Profiles in a Bench-Scale Aquifer.

Organic contaminant degradation by suspended bacteria in chemostats has shown that isotope fractionation decreases dramatically when pollutant concentrations fall below the (half-saturation) Monod constant. This masked isotope fractionation implies that membrane transfer is slow relative to the enzyme turnover at µg L-1 substrate levels. Analogous evidence of mass transfer as a bottleneck for biodegradation in aquifer settings, where microbes are attached to the sediment, is lacking. A quasi-two-dimensional flow-through sediment microcosm/tank system enabled us to study the aerobic degradation of 2,6-dichlorobenzamide (BAM), while collecting sufficient samples at the outlet for compound-specific isotope analysis. By feeding an anoxic BAM solution through the center inlet port and dissolved oxygen (DO) above and below, strong transverse concentration cross-gradients of BAM and DO yielded zones of low (µg L-1) steady-state concentrations. We were able to simulate the profiles of concentrations and isotope ratios of the contaminant plume using a reactive transport model that accounted for a mass-transfer limitation into bacterial cells, where apparent isotope enrichment factors *ε decreased strongly below concentrations around 600 µg/L BAM. For the biodegradation of organic micropollutants, mass transfer into the cell emerges as a bottleneck, specifically at low (µg L-1) concentrations. Neglecting this effect when interpreting isotope ratios at field sites may lead to a significant underestimation of biodegradation.

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.

Introduction of a new platform for parameter estimation of kinetically complex environmental systems.

A modeling framework (ReKinSim - Reaction Kinetics Simulator) is introduced, within which biogeochemical reactions in environmental systems can be described and inversely fitted to experimental data. Three key features of this simulation environment are: (1) a generic mathematical tool for solving sets of unlimited, arbitrary, non-linear ordinary differential equations; (2) no limitation to the number or type of reactions or other influential dynamics (e.g., isotope fractionation or small-scale mass-transfer limitations); (3) an easy to use and flexible module for nonlinear data-fitting. It allows users to easily define any kinetic model by a set of biogeochemical reactions relevant to the experimental application and to obtain the values of the kinetic parameters by fitting of the model to data. By allowing users to include the environmentally related processes and solving them along with the chemical kinetics, ReKinSim helps the user to elucidate the extent that these processes are controlled by factors other than kinetics. The novelty of the presented program primary lays in its unique combination of flexibility, computational efficiency and user-friendliness. ReKinSim's usability is showcased by four case studies of varying complexity, and compared against a set of currently available modeling tools.

Mycelium-Like Networks Increase Bacterial Dispersal, Growth, and Biodegradation in a Model Ecosystem at Various Water Potentials.

Fungal mycelia serve as effective dispersal networks for bacteria in water-unsaturated environments, thereby allowing bacteria to maintain important functions, such as biodegradation. However, poor knowledge exists on the effects of dispersal networks at various osmotic (Ψo) and matric (Ψm) potentials, which contribute to the water potential mainly in terrestrial soil environments. Here we studied the effects of artificial mycelium-like dispersal networks on bacterial dispersal dynamics and subsequent effects on growth and benzoate biodegradation at ΔΨo and ΔΨm values between 0 and -1.5 MPa. In a multiple-microcosm approach, we used a green fluorescent protein (GFP)-tagged derivative of the soil bacterium Pseudomonas putida KT2440 as a model organism and sodium benzoate as a representative of polar aromatic contaminants. We found that decreasing ΔΨo and ΔΨm values slowed bacterial dispersal in the system, leading to decelerated growth and benzoate degradation. In contrast, dispersal networks facilitated bacterial movement at ΔΨo and ΔΨm values between 0 and -0.5 MPa and thus improved the absolute biodegradation performance by up to 52 and 119% for ΔΨo and ΔΨm, respectively. This strong functional interrelationship was further emphasized by a high positive correlation between population dispersal, population growth, and degradation. We propose that dispersal networks may sustain the functionality of microbial ecosystems at low osmotic and matric potentials.

Effects of Facilitated Bacterial Dispersal on the Degradation and Emission of a Desorbing Contaminant.

The quantitative relationship between a compound's availability for biological removal and ecotoxicity is a key issue for retrospective risk assessment and remediation approaches. Here, we investigated the impact of facilitated bacterial dispersal at a model soil-atmosphere interface on the release, degradation, and outgassing of a semivolatile contaminant. We designed a laboratory microcosm with passive dosing of phenanthrene (PHE) to a model soil-atmosphere interface (agar surface) in the presence and absence of glass fibers known to facilitate the dispersal of PHE-degrading Pseudomonas fluorescens LP6a. We observed that glass fibers (used as a model to mimic a fungal hyphal network) resulted in (i) increased bacterial surface coverage, (ii) effective degradation of matrix-bound PHE, and (iii) substantially reduced PHE emission to locations beyond the contamination zone even at low bacterial surface coverage. Our data suggest that bacterial dispersal networks such as mycelia promote the optimized spatial arrangement of microbial populations to allow for effective contaminant degradation and reduction of potential hazard to organisms beyond a contaminated zone.

Kinetics of Substrate Biodegradation under the Cumulative Effects of Bioavailability and Self-Inhibition.

Microbial degradation is an important process in many environments controlling for instance the cycling of nutrients or the biodegradation of contaminants. At high substrate concentrations toxic effects may inhibit the degradation process. Bioavailability limitations of a degradable substrate can therefore either improve the overall dynamics of degradation by softening the contaminant toxicity effects to microorganisms, or slow down the biodegradation by reducing the microbial access to the substrate. Many studies on biodegradation kinetics of a self-inhibitive substrate have mainly focused on physiological responses of the bacteria to substrate concentration levels without considering the substrate bioavailability limitations rising from different geophysical and geochemical dynamics at pore-scale. In this regard, the role of bioavailability effects on the kinetics of self-inhibiting substrates is poorly understood. In this study, we theoretically analyze this role and assess the interactions between self-inhibition and mass transfer-limitations using analytical/numerical solutions, and show the findings practical relevance for a simple model scenario. Although individually self-inhibition and mass-transfer limitations negatively impact biodegradation, their combined effect may enhance biodegradation rates above a concentration threshold. To our knowledge, this is the first theoretical study describing the cumulative effects of the two mechanisms together.

Influence of mass transfer on stable isotope fractionation.

Biodegradation of contaminants is a common remediation strategy for subsurface environments. To monitor the success of such remediation means a quantitative assessment of biodegradation at the field scale is required. Nevertheless, the reliable quantification of the in situ biodegradation process it is still a major challenge. Compound-specific stable isotope analysis has become an established method for the qualitative analysis of biodegradation in the field and this method is also proposed for a quantitative analysis. However, to use stable isotope data to obtain quantitative information on in situ biodegradation requires among others knowledge on the influence of mass transfer processes on the observed stable isotope fractionation. This paper reviews recent findings on the influence of mass transfer processes on stable isotope fractionation and on the quantitative interpretation of isotope data. Focus will be given on small-scale mass transfer processes controlling the bioavailability of contaminants. Such bioavailability limitations are known to affect the biodegradation rate and have recently been shown to affect stable isotope fractionation, too. Theoretical as well as experimental studies addressing the link between bioavailability and stable isotope fractionation are reviewed and the implications for assessing biodegradation in the field are discussed.

Phase-specific stable isotope fractionation effects during combined gas-liquid phase exchange and biodegradation.

Stable isotope fractionation of toluene under dynamic phase exchange was studied aiming at ascertaining the effects of gas-liquid partitioning and biodegradation of toluene stable isotope composition in liquid-air phase exchange reactors (Laper). The liquid phase consisted of a mixture of aqueous minimal media, a known amount of a mixture of deuterated (toluene-d) and non-deuterated toluene (toluene-h), and bacteria of toluene degrading strain Pseudomonas putida KT2442. During biodegradation experiments, the liquid and air-phase concentrations of both toluene isotopologues were monitored to determine the observable stable isotope fractionation in each phase. The results show a strong fractionation in both phases with apparent enrichment factors beyond -800‰. An offset was observed between enrichment factors in the liquid and the gas phase with gas-phase values showing a stronger fractionation in the gas than in the liquid phase. Numerical simulation and parameter fitting routine was used to challenge hypotheses to explain the unexpected experimental data. The numerical results showed that either a very strong, yet unlikely, fractionation of the phase exchange process or a - so far unreported - direct consumption of gas phase compounds by aqueous phase microorganisms could explain the observed fractionation effects. The observed effect can be of relevance for the analysis of volatile contaminant biodegradation using stable isotope analysis in unsaturated subsurface compartments or other environmental compartment containing a gas and a liquid phase.

Modeling population patterns of chemotactic bacteria in homogeneous porous media.

The spatio-temporal distribution of subsurface microorganisms determines their efficiency in providing essential ecosystem services such as the degradation of organic matter, the remineralization of carbon and nitrogen, or the remediation of anthropogenic contaminants. Populations of motile, chemotactic bacteria have been shown to be capable of pattern formation even in the absence of environmental heterogeneities. Focusing on the water saturated domain of the subsurface (e.g., aquatic sediments, porous aquifers), we analyze this innate capability of bacterial populations in an idealized model of a homogeneous, saturated porous medium. Considering a linear array of connected, identical microhabitats populated by motile, chemotactic bacterial cells, we identify prerequisites for pattern formation, analyze types of patterns, and assess their impact on substrate utilization. In our model, substrate supplied to the microhabitats facilitates bacterial growth, and microbial cells can migrate between neighboring microhabitats due to (i) random motility, (ii) chemotaxis towards substrate, and (iii) self-attraction. A precondition for inhomogeneous population patterns is analytically derived, stating that patterns are possible if the self-attraction exceeds a threshold defined by the random motility and the steady state population density in the microhabitats. An individual-based implementation of the model shows that static and dynamic population patterns can unfold. Degradation efficiency is highest for homogeneous bacterial distributions and decreases as pattern formation commences. If during biostimulation efforts the carrying capacity of the microhabitats is successively increased, simulation results show that degradation efficiency can unexpectedly decrease when the pattern formation threshold is crossed.

Dissolved organic carbon enhances the mass transfer of hydrophobic organic compounds from nonaqueous phase liquids (NAPLs) into the aqueous phase.

The hypothesis that dissolved organic carbon (DOC) enhances the mass transfer of hydrophobic organic compounds from nonaqueous phase liquids (NAPLs) into the aqueous phase above that attributable to dissolved molecular diffusion alone was tested. In controlled experiments, mass transfer rates of five NAPL-phase PAHs (log K(OW) 4.15-5.39) into the aqueous phase containing different concentrations of DOC were measured. Mass transfer rates were increased by up to a factor of 4 in the presence of DOC, with the greatest enhancement being observed for more hydrophobic compounds and highest DOC concentrations. These increases could not be explained by dissolved molecular diffusion alone, and point to a parallel DOC-mediated diffusive pathway. The nature of the DOC-mediated diffusion pathway as a function of the DOC concentration and PAH sorption behavior to the DOC was investigated using diffusion-based models. The DOC-enhanced mass transfer of NAPL-phase hydrophobic compounds into the aqueous phase has important implications for their bioremediation as well as bioconcentration and toxicity.

Impact of cell density on microbially induced stable isotope fractionation.

Quantification of microbial contaminant biodegradation based on stable isotope fractionation analysis (SIFA) relies on known, invariable isotope fractionation factors. The microbially induced isotope fractionation is caused by the preferential cleavage of bonds containing light rather than heavy isotopes. However, a number of non-isotopically sensitive steps preceding the isotopically sensitive bond cleavage may affect the reaction kinetics of a degradation process and reduce the observed (i.e., the macroscopically detectable) isotope fractionation. This introduces uncertainty to the use of isotope fractionation for the quantification of microbial degradation processes. Here, we report on the influence of bacterial cell density on observed stable isotope fractionation. Batch biodegradation experiments were performed under non-growth conditions to quantify the toluene hydrogen isotope fractionation by exposing Pseudomonas putida mt-2(pWWO) at varying cell densities to different concentrations of toluene. Observed isotope fractionation depended significantly on the cell density. When the cell density rose from 5 x 10(5) to 5 x 10(8)cells/mL, the observed isotope fractionation declined by 70% and went along with a 55% decrease of the degradation rates of individual cells. Theoretical estimates showed that uptake-driven diffusion to individual cells depended on cell density via the overlap of the cells' diffusion-controlled boundary layers. Our data suggest that biomass effects on SIFA have to be considered even in well-mixed systems such as the cell suspensions used in this study.

Quantitation and Comparison of Phenotypic Heterogeneity Among Single Cells of Monoclonal Microbial Populations.

Phenotypic heterogeneity within microbial populations arises even when the cells are exposed to putatively constant and homogeneous conditions. The outcome of this phenomenon can affect the whole function of the population, resulting in, for example, new "adapted" metabolic strategies and impacting its fitness at given environmental conditions. Accounting for phenotypic heterogeneity becomes thus necessary, due to its relevance in medical and applied microbiology as well as in environmental processes. Still, a comprehensive evaluation of this phenomenon requires a common and unique method of quantitation, which allows for the comparison between different studies carried out with different approaches. Consequently, in this study, two widely applicable indices for quantitation of heterogeneity were developed. The heterogeneity coefficient (HC) is valid when the population follows unimodal activity, while the differentiation tendency index (DTI) accounts for heterogeneity implying outbreak of subpopulations and multimodal activity. We demonstrated the applicability of HC and DTI for heterogeneity quantitation on stable isotope probing with nanoscale secondary ion mass spectrometry (SIP-nanoSIMS), flow cytometry, and optical microscopy datasets. The HC was found to provide a more accurate and precise measure of heterogeneity, being at the same time consistent with the coefficient of variation (CV) applied so far. The DTI is able to describe the differentiation in single-cell activity within monoclonal populations resolving subpopulations with low cell abundance, individual cells with similar phenotypic features (e.g., isotopic content close to natural abundance, as detected with nanoSIMS). The developed quantitation approach allows for a better understanding on the impact and the implications of phenotypic heterogeneity in environmental, medical and applied microbiology, microbial ecology, cell biology, and biotechnology.

Computational pore network modeling of the influence of biofilm permeability on bioclogging in porous media.

For many years, controversy has surrounded the use of biofilm models to describe the distribution of microbial biomass in natural or artificial porous media. This use is often advocated on the basis of the relative mathematical simplicity of the biofilm concept, and of the widespread availability of analytical solutions or numerical implementations. However, microscopic observations consistently point to a patchy, rather than homogeneous, distribution of microorganisms at the pore scale in many porous media of interest, even under conditions of severe bioclogging. Also, bioclogging models involving biofilms tend to underpredict the extent of permeability reductions in all be the coarse-textured materials. In this context, computer simulations described in the present article show that some of the limitations of biofilm models to describe the bioclogging of porous media are linked to the common constitutive assumption that biofilms are impermeable, that is, that nutrient transport occurs through the biofilms only by molecular diffusion. When this restriction is alleviated and liquid flow is allowed in the biofilms, the level of bioclogging achievable by a given biomass is very significantly increased and is comparable to that observed in experiments. In addition, the distribution of microorganisms becomes patchy and exhibits a self-organized periodic pattern with pores either entirely filled with biomass or without any biomass at all, again similar to published microscopic observations. These results suggest that biofilm models should not be ruled out a priori for the quantitative description of bioclogging in porous media, as long as biofilms are allowed to be permeable.

Functional Resistance to Recurrent Spatially Heterogeneous Disturbances Is Facilitated by Increased Activity of Surviving Bacteria in a Virtual Ecosystem.

Bacterial degradation of organic compounds is an important ecosystem function with relevance to, e.g., the cycling of elements or the degradation of organic contaminants. It remains an open question, however, to which extent ecosystems are able to maintain such biodegradation function under recurrent disturbances (functional resistance) and how this is related to the bacterial biomass abundance. In this paper, we use a numerical simulation approach to systematically analyze the dynamic response of a microbial population to recurrent disturbances of different spatial distribution. The spatially explicit model considers microbial degradation, growth, dispersal, and spatial networks that facilitate bacterial dispersal mimicking effects of mycelial networks in nature. We find: (i) There is a certain capacity for high resistance of biodegradation performance to recurrent disturbances. (ii) If this resistance capacity is exceeded, spatial zones of different biodegradation performance develop, ranging from no or reduced to even increased performance. (iii) Bacterial biomass and biodegradation dynamics respond inversely to the spatial fragmentation of disturbances: overall biodegradation performance improves with increasing fragmentation, but bacterial biomass declines. (iv) Bacterial dispersal networks can enhance functional resistance against recurrent disturbances, mainly by reactivating zones in the core of disturbed areas, even though this leads to an overall reduction of bacterial biomass.

Spatiotemporal disturbance characteristics determine functional stability and collapse risk of simulated microbial ecosystems.

Terrestrial microbial ecosystems are exposed to many types of disturbances varying in their spatial and temporal characteristics. The ability to cope with these disturbances is crucial for maintaining microbial ecosystem functions, especially if disturbances recur regularly. Thus, understanding microbial ecosystem dynamics under recurrent disturbances and identifying drivers of functional stability and thresholds for functional collapse is important. Using a spatially explicit ecological model of bacterial growth, dispersal, and substrate consumption, we simulated spatially heterogeneous recurrent disturbances and investigated the dynamic response of pollutant biodegradation - exemplarily for an important ecosystem function. We found that thresholds for functional collapse are controlled by the combination of disturbance frequency and spatial configuration (spatiotemporal disturbance regime). For rare disturbances, the occurrence of functional collapse is promoted by low spatial disturbance fragmentation. For frequent disturbances, functional collapse is almost inevitable. Moreover, the relevance of bacterial growth and dispersal for functional stability also depends on the spatiotemporal disturbance regime. Under disturbance regimes with moderate severity, microbial properties can strongly affect functional stability and shift the threshold for functional collapse. Similarly, networks facilitating bacterial dispersal can delay functional collapse. Consequently, measures to enhance or sustain bacterial growth/dispersal are promising strategies to prevent functional collapses under moderate disturbance regimes.

Mycelium-mediated transfer of water and nutrients stimulates bacterial activity in dry and oligotrophic environments.

Fungal-bacterial interactions are highly diverse and contribute to many ecosystem processes. Their emergence under common environmental stress scenarios however, remains elusive. Here we use a synthetic microbial ecosystem based on the germination of Bacillus subtilis spores to examine whether fungal and fungal-like (oomycete) mycelia reduce bacterial water and nutrient stress in an otherwise dry and nutrient-poor microhabitat. We find that the presence of mycelia enables the germination and subsequent growth of bacterial spores near the hyphae. Using a combination of time of flight- and nanoscale secondary ion mass spectrometry (ToF- and nanoSIMS) coupled with stable isotope labelling, we link spore germination to hyphal transfer of water, carbon and nitrogen. Our study provides direct experimental evidence for the stimulation of bacterial activity by mycelial supply of scarce resources in dry and nutrient-free environments. We propose that mycelia may stimulate bacterial activity and thus contribute to sustaining ecosystem functioning in stressed habitats.