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Nonmotile microorganisms often enter new habitats by co-transport with motile microorganisms. Here, we report that also lytic phages can co-transport with hyphal-riding bacteria and facilitate bacterial colonization of a new habitat. This is comparable to the concept of biological invasions in macroecology. In analogy to invasion frameworks in plant and animal ecology, we tailored spatially organized, water-unsaturated model microcosms using hyphae of Pythium ultimum as invasion paths and flagellated soil-bacterium Pseudomonas putida KT2440 as carrier for co-transport of Escherichia virus T4. P. putida KT2440 efficiently dispersed along P. ultimum to new habitats and dispatched T4 phages across air gaps transporting ≈0.6 phages bacteria−1. No T4 displacement along hyphae was observed in the absence of carrier bacteria. If E. coli occupied the new habitat, T4 co-transport fueled the fitness of invading P. putida KT2440, while the absence of phage co-transport led to poor colonization followed by extinction. Our data emphasize the importance of hyphal transport of bacteria and associated phages in regulating fitness and composition of microbial populations in water-unsaturated systems. As such co-transport seems analogous to macroecological invasion processes, hyphosphere systems with motile bacteria and co-transported phages could be useful models for testing hypotheses in invasion ecology. [ABSTRACT FROM AUTHOR]

Summary: Microbial populations often display different degrees of heterogeneity in their substrate assimilation, that is, anabolic heterogeneity. It has been shown that nutrient limitations are a relevant trigger for this behaviour. Here we explore the dynamics of anabolic heterogeneity under nutrient replete conditions. We applied time‐resolved stable isotope probing and nanoscale secondary ion mass spectrometry to quantify substrate assimilation by individual cells of Pseudomonas putida, P. stutzeri and Thauera aromatica. Acetate and benzoate at different concentrations were used as substrates. Anabolic heterogeneity was quantified by the cumulative differentiation tendency index. We observed two major, opposing trends of anabolic heterogeneity over time. Most often, microbial populations started as highly heterogeneous, with heterogeneity decreasing by various degrees over time. The second, less frequently observed trend, saw microbial populations starting at low or very low heterogeneity, and remaining largely stable over time. We explain these trends as an interplay of metabolic history (e.g. former growth substrate or other nutrient limitations) and metabolic fitness (i.e. the fine‐tuning of metabolic pathways to process a defined growth substrate). Our results offer a new viewpoint on the intra‐population functional diversification often encountered in the environment, and suggests that some microbial populations may be intrinsically heterogeneous. [ABSTRACT FROM AUTHOR]

Functional stability of microbial ecosystems subjected to disturbances is essential for maintaining microbial ecosystem services such as the biodegradation of organic contaminants in terrestrial environments. Functional responses to disturbances are thus an important aspect which is, however, not well understood yet. Here, we present a microbial simulation model to investigate key processes for the recovery of biodegradation. We simulated single disturbances with different spatiotemporal characteristics and monitored subsequent recovery of the biodegradation dynamics. After less intense disturbance events local regrowth governs biodegradation recovery. After highly intense disturbance events the disturbance pattern's spatial configuration is decisive and processes governing local functional recovery vary depending on habitat location with respect to the spatial disturbance pattern. Local regrowth may be unimportant when bacterial dispersal from undisturbed habitats is high. Hence, our results suggest that spatial dynamics are crucial for the robust delivery of the ecosystem service biodegradation under disturbances in terrestrial environments. [ABSTRACT FROM AUTHOR]

Fungi and bacteria form various associations that are central to numerous environmental processes. In the so-called fungal highway, bacteria disperse along fungal mycelium. We developed a novel tool for the in situ isolation of bacteria moving along fungal hyphae as well as for the recovery of fungi potentially involved in dispersal, both of which are attracted towards a target culture medium. We present the validation and the results of the first in situ test. Couples of fungi and bacteria were isolated from soil. Amongst the enriched organisms, we identified several species of fast-growing fungi (Fusarium sp. and Chaetomium sp.), as well as various potentially associated bacterial groups, including Variovorax soli, Olivibacter soli, Acinetobacter calcoaceticus, and several species of the genera Stenotrophomonas, Achromobacter and Ochrobactrum. Migration of bacteria along fungal hyphae across a discontinuous medium was confirmed in most of the cases. Although the majority of the bacteria for which migration was confirmed were also positive for flagellar motility, not all motile bacteria dispersed using their potential fungal partner. In addition, the importance of hydrophobicity of the fungal mycelial surface was confirmed. Future applications of the columns include targeting different types of microorganisms and their interactions, either by enrichment or by state of the art molecular biological methods. [ABSTRACT FROM AUTHOR]

Some bacteria have the unique capacity of synthesising ice-nucleation-active (INA) proteins and exposing them at their outer membrane surface. As INA bacteria enter the atmosphere, they may impact the formation of clouds and precipitation. We studied members of airborne bacterial communities for their capacity to catalyse ice formation and we report on the excretion of INA proteins by airborne Pseudomonas sp. We also observed for the first time that INA biological fragments <220 nm were present in precipitation samples (199 and 482 INA fragments per L of precipitation), which confirms the presence of submicron INA biological fragments in the atmosphere. During 14 precipitation events, strains affiliated with the genus Pseudomonas , which are known to carry ina genes, were dominant. A screening for INA properties revealed that ∼12% of the cultivable bacteria caused ice formation at ≤−7 °C. They had likely been emitted to the atmosphere from terrestrial surfaces, e.g. by convective transport. We tested the ability of isolated INA strains to produce outer membrane vesicles and found that two isolates could do so. However, only very few INA vesicles were released per INA cell. Thus, the source of the submicron INA proteinaceous particles that we detected in the atmosphere remains to be elucidated. [ABSTRACT FROM AUTHOR]

Exfoliated graphite (EG) exhibits exceptional sorption capacity for petroleum and dissolved hydrocarbons owing to its highly hydrophobic surface and wide pore size distribution. The high price of preparing EG, however, restricts its application. Methods which increase the rate or extent of sorption to EG even further are thus longed for. Here, we assess the effects of weak direct current (DC) fields on the sorption of the polycyclic aromatic hydrocarbon phenanthrene (PHE) to EG. DC applied to an ionic solution in a solid matrix invokes electroosmotic flow (EOF), i.e., the surface charge-induced movement of the solution. EG was exposed to weak DC fields in the presence of dissolved PHE to test if EOF increases transport of PHE to poorly accessible sorption sites. DC fields increased PHE sorption rates in EG sevenfold and reduced the desorption rate of sorbed PHE by >99%. EOF thus appeared to be highly effective in translocating PHE into pores, which contribute most of the sorption sites, but are difficult to access in the absence of EOF by molecular diffusion only. The observed ‘power of power’ may be used to kinetically regulate the interaction of sorbates with EG or other porous sorbents in environmental (bio-) technology. [ABSTRACT FROM AUTHOR]

A systematic investigation of environmentally relevant transformation processes of alpha-hexachlorocyclohexane ( α -HCH) was performed in order to explore the potential of compound specific stable isotope analysis (CSIA) to characterize reaction mechanisms. The carbon isotope enrichment factors ( ɛ C ) for the chemical transformations of α -HCH via direct photolysis, indirect photolysis (UV/H 2 O 2 ), hydrolysis, electro-reduction or reduction by Fe 0 were quantified and compared to those previously published for biodegradation. Hydrogen abstraction by hydroxyl radicals generated by UV/H 2 O 2 led to ɛ C of −1.9 ± 0.2‰ with an apparent kinetic carbon isotope effect (AKIE C ) of 1.012 ± 0.001. Dehydrochlorination by alkaline hydrolysis yielded ɛ C of −7.6 ± 0.4‰ with AKIE C of 1.048 ± 0.003. Dechlorination either by homolytic bond cleavage in direct photolysis ( ɛ C = −2.8 ± 0.2‰) or single-electron transfer in electro-reduction ( ɛ C = −3.8 ± 0.4‰) corresponded to AKIE C of 1.017 ± 0.001 and 1.023 ± 0.003, respectively. Dichloroelimination catalyzed by Fe 0 via two-electron transfers resulted in ɛ C of −4.9 ± 0.1‰. AKIE C values assuming either a concerted or a stepwise mechanism were 1.030 ± 0.0006 and 1.015 ± 0.0003, respectively. Contrary to biodegradation, no enantioselectivity of α -HCH was observed in chemical reactions, which might be used to discriminate chemical and biological in situ transformations. [ABSTRACT FROM AUTHOR]

The performance of biodegradation of organic pollutants in soil often depends on abiotic conditions and the bioavailability of these pollutants to degrading bacteria. In this context, bacterial dispersal is an essential aspect. Recent studies on the potential promotion of bacterial dispersal by fungal hyphae raised the idea of specifically applying fungal networks to accelerate bacterial degradation processes in situ. Our objective is to investigate these processes and their performance via simulation modelling and address the following questions: (1) Under what abiotic conditions can dispersal networks significantly improve bacterial degradation? and (2) To what extent does the spatial configuration of the networks influence the degradation performance? To answer these questions, we developed a spatially explicit bacterial colony model, which is applied to controlled laboratory experiments with Pseudomonas putida G7 organisms as a case study. Using this model, we analyzed degradation performance in response to different environmental scenarios and showed that conditions of limited bacterial dispersal also limit degradation performance. Under such conditions, dispersal networks have the highest potential for improving the bioavailability of pollutants to bacteria. We also found that degradation performance significantly varies with the spatial configuration of the dispersal networks applied and the time horizon over which performance is assessed. Regarding future practical applications, our results suggest that (1) fungal networks may dramatically improve initially adverse conditions for biodegradation of pollutants in soil, and (2) the network's spatial structure and accessibility are decisive for the success of such tasks. [Copyright &y& Elsevier]

The high cost of commercial lipases limits their industrial application in the production of biodiesel or fatty acid methyl esters (FAME). This disadvantage has encouraged the search for lipase-producing microorganisms (LPMs) as potential whole cell catalysts for FAME production. The aim of this study, therefore, was to evaluate innovative procedures for easy selection and testing of LPMs as a low-cost whole cell catalyst, based on catalytic performance, methanol tolerance and physico-chemical cell surface properties. The latter (in particular the cell surface hydrophobicity and charge) were analyzed because of their crucial role in microbial adhesion to surfaces and the concomitant increase in cell immobilization and bioavailability of hydrophobic substrates. Biocatalysis experiments performed in the presence of nutrient, rapeseed oil and methanol were an effective tool for studying and identifying, in just two experiments, the capacity of different LPMs as biocatalysts in organic media, as well as the methanol tolerance of the cell and the lipase. This indicates the potential for using live microorganisms for FAME production. Another finding was that the inhibitory effect of methanol is more significant for lipase activity than LPM growth, indicating that the way in which alcohol is supplied to the reaction is a crucial step in FAME production by biocatalysts. According to these results, the application of these innovative assessments should simplify the search for new strains which are able to effectively catalyze the FAME production process. [Copyright &y& Elsevier]

The solvent-tolerant strain Pseudomonas putida DOT-T1E was grown in batch fermentations in a 5-liter bioreactor in the presence and absence of 10% (vol/vol) of the organic solvent 1-decanol. The growth behavior and cellular energetics, such as the cellular ATP content and the energy charge, as well as the cell surface hydrophobicity and charge, were measured in cells growing in the presence and absence of 1-decanol. Although the cells growing in the presence of 1-decanol showed an about 10% reduced growth rate and a 48% reduced growth yield, no significant differences were measured either in the ATP and potassium contents or in the energy charge, indicating that the cells adapted completely at the levels of membrane permeability and energetics. Although the bacteria needed additional energy for adaptation to the presence of the solvent, they were able to maintain or activate electron transport phosphorylation, allowing homeostasis of the ATP level and energy charge in the presence of the solvent, at the price of a reduced growth yield. On the other hand, significantly enhanced cell hydrophobicities and more negative cell surface charges were observed in cells grown in the presence of 1-decanol. Both reactions occurred within about 10 min after the addition of the solvent and were significantly different after killing of the cells with toxic concentrations of HgCl2. This adaptation of the surface properties of the bacterium to the presence of solvents seems to be very similar to previously observed reactions on the level of lipopolysaccharides, with which bacteria adapt to environmental stresses, such as heat shock, antibiotics, or low oxygen content. The results give clear physiological indications that the process with P. putida DOT-T1E as the biocatalyst and 1-decanol as the solvent is a stable system for two-phase biotransformations that will allow the production of fine chemicals in economically sound amounts. [ABSTRACT FROM AUTHOR]

Interactions with solid matrices control the persistence and (bio-)degradability of hydrophobic organic chemicals (HOC). Approaches influencing the rate or extent of HOC interactions with matrices are thus longed for. When a direct current (DC) electric field is applied to a matrix immersed in an ionic solution, it invokes transport processes including electromigration, electrophoresis, and electroosmotic flow (EOF). EOF is the surface charge-induced movement of pore fluids. It has the potential to mobilize uncharged organic contaminants and, hence, to influence their interactions with sorbing geo-matrices (i.e. geo-sorbents). Here, we assessed the effects of weak DC electric fields on sorption and desorption of phenanthrene (PHE) in various mineral and carbonaceous geo-sorbents. We found that DC fields significantly changed the rates and extent of PHE sorption and desorption as compared to DC-free controls. A distinct correlation between the Gibbs free energy change (Δ G °) and electrokinetic effects such as the EOF velocity was observed; in case of mineral sorbents EOF limited (or even inhibited) PHE sorption and increased its desorption. In strongly sorbing carbonaceous geo-sorbents, however, EOF significantly increased the rates of PHE sorption and reduced PHE desorption by > 99% for both activated charcoal and exfoliated graphite. Based on our findings, an approach linking Δ G ° and EOF velocity was developed to estimate DC-induced PHE sorption and desorption benefits on mineral and carbonaceous sorbents. We conclude that such kinetic regulation gives rise to future technical applications that may allow modulating sorption processes e.g. in response to fluctuating sorbate concentrations in contaminated water streams. DC electric fields significantly influence the rates and extents of sorption and desorption of phenanthrene to mineral and carbonaceous model geo-sorbents by electroosmotic flow. Image 1 • DC electric fields strongly change PAH interactions with (non-electrode) sorbents. • DC effects correlate to the electroosmotic flow velocity and ΔG° of PAH sorption. • DC fields increase PAH sorption to and reduce PAH desorption from strong sorbents. • DC fields limit PAH sorption to and promote PAH desorption from weak sorbents. [ABSTRACT FROM AUTHOR]

Draft genomes of two phenanthrene-degrading bacterial isolates from oil sands process-affected water (OSPW) in Alberta, Canada were sequenced. Both isolates grew in close association on agar plates and were difficult to obtain axenically. They represent novel Pseudomonas chengduensis and Sphingobium sp. strains with genomes of 5.5 and 4.1 Mbases length, respectively., Competing Interests: The authors declare no conflict of interest.

Biofiltration is a simple and low-cost method for the cleanup of contaminated water. However, the reduced availability of dissolved chemicals to surface-attached degrader bacteria may limit its efficient use at certain hydraulic loadings. When a direct current (DC) electric field is applied to an immersed packed bed, it invokes electrokinetic processes, such as electroosmotic water flow (EOF). EOF is a surface-charge-induced plug-flow-shaped movement of pore fluids. It acts at a nanometer distance above surfaces and allows the change of microscale pressure-driven flow profiles and, hence, the availability of dissolved contaminants to microbial degraders. In laboratory percolation columns, we assessed the effects of a weak DC electric field ( E = 0.5 V·cm -1 ) on the biodegradation of waterborne naphthalene (NAH) by surface-attached Pseudomonas fluorescens LP6a. To vary NAH bioavailability, we used different NAH concentrations ( C 0 = 2.7, 5.1, or 7.8 × 10 -5 mol·L -1 ) and Darcy velocities typical for biofiltration ( U ¯ = 0.2-1.2 × 10 -4 m·s -1 ). In DC-free controls, we observed higher specific degradation rates ( q c ) at higher NAH concentrations. The q c depended on U ¯ , suggesting bioavailability restrictions depending on the hydraulic residence times. DC fields consistently increased q c and resulted in linearly increasing benefits up to 55% with rising hydraulic loadings relative to controls. We explain these biodegradation benefits by EOF-altered microscale flow profiles allowing for better NAH provision to bacteria attached to the collectors even though the EOF was calculated to be 100-800 times smaller than bulk water flow. Our data suggest that electrokinetic approaches may give rise to future technical applications that allow regulating biodegradation, for example, in response to fluctuating hydraulic loadings.

Sorption to activated carbon is a common approach to reducing environmental risks of waterborne perfluorooctanoic acid (PFOA), while effective and flexible approaches to PFOA sorption are needed. Variations in temperature or the use of electrokinetic phenomena (electroosmosis and electromigration) in the presence of external DC electric fields have been shown to alter the contaminant sorption of contaminants. Their role in PFOA sorption, however, remains unclear. Here, we investigated the joint effects of DC electric fields and the temperature on the sorption of PFOA on activated carbon. Temperature-dependent batch and column sorption experiments were performed in the presence and absence of DC fields, and the results were evaluated by using different kinetic sorption models. We found an emerging interplay of DC and temperature on PFOA sorption, which was linked via the liquid viscosity (η) of the electrolyte. For instance, the combined presence of a DC field and low temperature increased the PFOA loading up to 38% in 48 h relative to DC-free controls. We further developed a model that allowed us to predict temperature- and DC field strength-dependent electrokinetic benefits on the drivers of PFOA sorption kinetics (i.e., intraparticle diffusivity and the film mass transfer coefficient). Our insights may give rise to future DC- and temperature-driven applications for PFOA sorption, for instance, in response to fluctuating PFOA concentrations in contaminated water streams.

The organization of microbial communities in marine sediment relies on complex biotic and abiotic interactions. Among them, the interaction between fungi and bacteria plays a crucial role building specific microbial assemblages, resulting in metabolic networks adapted to environmental conditions. The fungal-bacterial interaction (FBI) includes bacterial translocation via fungal mycelia, allowing bacterial dispersion, and ecological niche colonization. In order to demonstrate that the translocation of bacteria through fungal mycelia involves bacterial selection, the mycelia of two fungi isolated from marine coastal sediment, Alternaria destruens F10.81 and Fusarium pseudonygamai F5.76, showing different strategies for uptake of polycyclic aromatic hydrocarbon (PAH), homogenous internalization and vacuole forming respectively, were used to translocate bacteria through hydrophobic hydrocarbon contaminated sediments. A. destruens F10.81 selected four specific bacteria, while bacterial selection by F. pseudonygamai F5.76 was not evident. Among the bacteria selected by A. destruens F10.81, Spirochaeta litoralis, known as strictly anaerobic bacterium, was identified, indicating that A. destruens F10.81 selects and transports both aerobic and anaerobic bacteria. Such a result is consistent with the observed formation of anoxic micro-niches in areas surrounding and affected by fungal hyphae. Our findings provide new insights on the selection and dispersion of bacterial communities by fungi, which are crucial for the organization of microbial communities and their functioning in coastal PAH-contaminated sediments. IMPORTANCE The study provides advances for understanding fungal-bacterial relationships, particularly on the selection and dispersion of bacterial communities by fungi, which are crucial for the organization of microbial communities and their functioning in coastal PAH-contaminated sediments. The transportation of bacteria via fungal hyphae (fungal highway) results in bacterial selection; in particular, fungal hyphae offer adequate conditions for the transport of both aerobic and anaerobic bacteria through hydrophobic patches for the colonization of novel niches.

Bile acids are crucial for the uptake of dietary lipids and can shape the gut-microbiome composition. This latter function is associated with the toxicity of bile acids and can be modulated by bile acid modifying bacteria such as Eggerthella lenta , but the molecular details of the interaction of bacteria depending on bile acid modifications are not well understood. In order to unravel the molecular response to bile acids and their metabolites, we cultivated eight strains from a human intestinal microbiome model alone and in co-culture with Eggerthella lenta in the presence of cholic acid (CA) and deoxycholic acid (DCA). We observed growth inhibition of particularly gram-positive strains such as Clostridium ramosum and the gram-variable Anaerostipes cacae by CA and DCA stress. C. ramosum was alleviated through co-culturing with Eggerthella lenta . We approached effects on the membrane by zeta potential and genotoxic and metabolic effects by (meta)proteomic and metabolomic analyses. Co-culturing with Eggerthella lenta decreased both CA and DCA by the formation of oxidized and epimerized bile acids. Eggerthella lenta also produces microbial bile salt conjugates in a co-cultured species-specific manner. This study highlights how the interaction with other bacteria can influence the functionality of bacteria.

Background: To disperse in water-unsaturated environments, such as the soil, bacteria rely on the availability and structure of water films forming on biotic and abiotic surfaces, and, especially, along fungal mycelia. Dispersal along such "fungal highways" may be driven both by mycelial physical properties and by interactions between bacteria and fungi. However, we still do not have a way to disentangle the biotic and abiotic elements., Results: We designed and 3D printed two devices establishing stable liquid films that support bacteria dispersal in the absence of biotic interactions. The thickness of the liquid film determined the presence of hydraulic flow capable of transporting non-motile cells. In the absence of flow, only motile cells can disperse in the presence of an energy source. Non-motile cells could not disperse autonomously without flow but dispersed as "hitchhikers" when co-inoculated with motile cells., Conclusions: The 3D printed devices can be used as an abiotic control to study bacterial dispersal on hydrated surfaces, such as plant roots and fungal hyphae networks in the soil. By teasing apart the abiotic and biotic dimensions, these 3D printed devices will stimulate further research on microbial dispersal in soil and other water-unsaturated environments., (© 2022. The Author(s).)

Anoxic microsites arising in fungal biofilms may foster the presence of obligate anaerobes. Here, we analyzed whether and to which degree hyphae of Coprinopsis cinerea thriving in oxic habitats enable the germination, growth, and dispersal of the obligate anaerobic soil bacterium Clostridium acetobutylicum. Time-resolved optical oxygen mapping, microscopy, and metabolite analysis revealed the formation and persistence of anoxic circum hyphal niches, allowing for spore germination, growth, and fermentative activity of the obligate anaerobe in an otherwise inhabitable environment. Hypoxic liquid films containing 80% ± 10% of atmospheric oxygen saturation around single air-exposed hyphae thereby allowed for efficient clostridial dispersal amid spatially separated (>0.5 cm) anoxic sites. Hyphae hence may serve as good networks for the activity and spatial organization of obligate anaerobic bacteria in oxygenated heterogeneous environments such as soil. IMPORTANCE Although a few studies have reported on the presence of anoxic microniches in fungal biofilms, knowledge of the effects of fungal oxygen consumption on bacterial-fungal interactions is limited. Here, we demonstrate the existence and persistence of oxygen-free zones in air-exposed mycelia enabling spore germination, growth, fermentative activity, and dispersal of the obligate anaerobe. Our study points out a previously overlooked role of aerobic fungi in creating and bridging anoxic microniches in ambient oxic habitats. Air-exposed hyphae hence may act as a scaffold for activity and dispersal of strictly anaerobic microbes. Given the short-term tolerance of strict anaerobes to oxygen and reduced oxygen content in the mycosphere, hyphae can promote spatial organization of both obligate anaerobic and aerobic bacteria. Such finding may be important for a better understanding of previously observed co-occurrences of aerobes and anaerobes in well-aerated habitats such as upland soils.

The draft genome sequences of two Sphingobium strains that are hexachlorocyclohexane (HCH) degraders are presented. The strains were isolated from HCH-contaminated soil in Kitengela, Kenya. Both genomes possess the lin genes responsible for HCH degradation and gene clusters for degradation of other xenobiotic compounds.

The pH of an environment is both a driver and the result of diversity and functioning of microbial habitats such as the area affected by fungal hyphae (mycosphere). Here we used a novel pH-sensitive bioreporter, Synechocystis sp. PCC6803&#95;peripHlu, and ratiometric fluorescence microscopy, to spatially and temporally resolve the mycosphere pH at the micrometre scale. Hyphae of the basidiomycete Coprionopsis cinerea were allowed to overgrow immobilised and homogeneously embedded pH bioreporters in an agarose microcosm. Signals of >700 individual cells in an area of 0.4 × 0.8 mm were observed over time and used to create highly resolved (3 × 3 µm) pH maps using geostatistical approaches. C. cinerea changed the pH of the agarose from 6.9 to ca. 5.0 after 48 h with hyphal tips modifying pH in their vicinity up to 1.8 mm. pH mapping revealed distinct microscale spatial variability and temporally stable gradients between pH 4.4 and 5.8 over distances of ≈20 µm. This is the first in vivo mapping of a mycosphere pH landscape at the microscale. It underpins the previously hypothesised establishment of pH gradients serving to create spatially distinct mycosphere reaction zones., (© 2021. The Author(s).)

We present the draft genome sequence of Fusarium equiseti strain K3, a fungus isolated from a hexachlorocyclohexane (HCH)-contaminated soil (Kitengela, Kenya). The 37.88-Mb draft genome sequence consists of 206 contigs, 12,311 predicted protein-coding sequences, and 261 tRNA sequences. This genome sequence contributes to our understanding of fungal-bacterial interactions during hexachlorocyclohexane degradation.

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.

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.

Surfactant-enhanced remediation (SER) is considered as a promising and efficient remediation approach. This review summarizes and discusses main drivers on the application of SER in removing polycyclic aromatic hydrocarbons (PAHs) from contaminated soil and water. The effect of PAH-PAH interactions on SER efficiency is, for the first time, illustrated in an SER review. Interactions between mixed PAHs could enhance, decrease, or have no impact on surfactants' solubilization power towards PAHs, thus affecting the optimal usage of surfactants for SER. Although SER can transfer PAHs from soil/non-aqueous phase liquids to the aqueous phase, the harmful impact of PAHs still exists. To decrease the level of PAHs in SER solutions, a series of SER-based integrated cleanup technologies have been developed including surfactant-enhanced bioremediation (SEBR), surfactant-enhanced phytoremediation (SEPR) and SER-advanced oxidation processes (SER-AOPs). In this review, the general considerations and corresponding applications of the integrated cleanup technologies are summarized and discussed. Compared with SER-AOPs, SEBR and SEPR need less operation cost, yet require more treatment time. To successfully achieve the field application of surfactant-based technologies, massive production of the cost-effective green surfactants (i.e. biosurfactants) and comprehensive evaluation of the drivers and the global cost of SER-based cleanup technologies need to be performed in the future., (Copyright © 2017. Published by Elsevier Ltd.)

Research into the biodegradation of soil contaminants has rarely addressed the consequences of predator-prey interactions. Here, we investigated the joint effect of predation and dispersal networks on contaminant degradation by linking spatial abundances of degrader (Pseudomonas fluorescens LP6a) and predator (Bdellovibrio bacteriovorus) bacteria to the degradation of the major soil contaminant phenanthrene (PHE). We used a laboratory microcosm with a PHE passive dosing system and a glass fiber network to facilitate bacterial dispersal. Different predator-to-prey ratios and spatial arrangements of prey and predator inoculation were used to study predation pressure effects on PHE degradation. We observed that predation resulted in (i) enhanced PHE-degradation at low predator counts (PC) compared to controls lacking predation, (ii) reduced PHE-degradation at elevated PC relative to low PC, and (iii) significant effects of the spatial arrangement of prey and predator inoculation on PHE degradation. Our data suggest that predation facilitated by dispersal networks (such as fungal mycelia) may support the build-up of an effective bacterial biomass and, hence, contaminant biodegradation in heterogeneous systems such as soil., (© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Mycolata form a group of Gram-positive bacteria with unique cell envelope structures that are known for their high tolerance against antibiotics and both aromatic and aliphatic hydrocarbons. An important part of the unique surface structure of the mycolata is the presence of long chain α-alkyl-β-hydroxy fatty acids, the mycolic acids. In order to investigate the adaptive changes in the mycolic acid composition, we investigated the composition of mycolic acids during the response both to osmotic stress caused by NaCl and to 4-chlorophenol in Rhodococcus opacus PWD4. This bacterium was chosen as it is known to adapt to different kinds of stresses. In addition, it is a potential biocatalyst in bioremediation as well as for biotechnological applications. In the present study, cells of R. opacus PWD4, grown in liquid cultures, responded to toxic concentrations of NaCl by increasing the ratio between mycolic acids and membrane phospholipid fatty acids (MA/PLFA-ratio). Cells reacted to both NaCl and 4-chlorophenol by decreasing both the average chain length and the unsaturation index of their mycolic acids. These changes in mycolic acid composition correlated with increases in cell surface hydrophobicity and saturation of membrane fatty acids, demonstrating the relation between mycolic acid and phospholipid synthesis and their contribution to cell surface properties of R. opacus PWD4.

Biodegradation of organic chemicals in the vapor phase of soils and vertical flow filters has gained attention as promising approach to clean up volatile organic compounds (VOC). The drivers of VOC biodegradation in unsaturated systems however still remain poorly understood. Here, we analyzed the processes controlling aerobic VOC biodegradation in a laboratory setup mimicking the unsaturated zone above a shallow aquifer. The setup allowed for diffusive vapor-phase transport and biodegradation of three VOC: non-deuterated and deuterated toluene as two compounds of highly differing biodegradability but (nearly) identical physical and chemical properties, and MTBE as (at the applied experimental conditions) non-biodegradable tracer and internal control. Our results showed for toluene an effective microbial degradation within centimeter VOC transport distances despite high gas-phase diffusivity. Degradation rates were controlled by the reactivity of the compounds while oxic conditions were found everywhere in the system. This confirms hypotheses that vadose zone biodegradation rates can be extremely high and are able to prevent the outgassing of VOC to the atmosphere within a centimeter range if compound properties and site conditions allow for sufficiently high degradation rates., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

The extraction of bitumen from oil sands in Alberta (Canada) produces volumes of tailings that are pumped into large anaerobic settling-basins. Beside bitumen, tailings comprise fractions of benzene, toluene, ethylbenzene and xylenes (BTEX) that derive from the application of industrial solvents. Due to their toxicity and volatility, BTEX pose a strong concern for gas- and water-phase environments in the vicinity of the ponds. The examination of two pond profiles showed that concentrations of indigenous BTEX decreased with depth, pointing at BTEX transformation in situ. With depth, the relative contribution of ethylbenzene and xylenes to total BTEX significantly decreased, while benzene increased relatively from 44% to 69%, indicating preferential hydrocarbon degradation. To predict BTEX turnover and residence time, we determined BTEX degradation rates in tailings of different depths in a 180-days microcosm study. In addition, we evaluated the impact of labile organic substrates (e.g. acetate) generally considered to stimulate hydrocarbon degradation and the contribution of sulfate-reducing bacteria (SRB) to BTEX turnover. In all depths, BTEX concentrations significantly decreased due to microbial activity, with degradation rates ranging between 4 and 9 μg kg(-1) d(-1). BTEX biodegradation decreased linearly in correlation with initial concentrations, suggesting a concentration-dependent BTEX transformation. SRB were not significantly involved in BTEX consumption, indicating the importance of methanogenic degradation. BTEX removal decreased to 70-90% in presence of organic substrates presumptively due to an accumulation of acetate that lowered BTEX turnover due to product inhibition. In those assays SRB slightly stimulated BTEX transformation by reducing inhibitory acetate levels., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

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.

Bacterial degradation is an ecosystem service that offers a promising method for the remediation of contaminated soils. To assess the dynamics and efficiency of bacterial degradation, reliable microbial simulation models, along with the relevant processes, are required. We present an approach aimed at improving reliability by studying the relevance and implications of an important concept from theoretical ecology in the context of a bacterial system: conditional dispersal denoting that the dispersal strategy depends on environmental conditions. Different dispersal strategies, which either incorporate or neglect this concept, are implemented in a bacterial model and results are compared to data obtained from laboratory experiments with Pseudomonas putida colonies growing on glucose agar. Our results show that, with respect to the condition of resource uptake, the model's correspondence to experimental data is significantly higher for conditional than for unconditional bacterial dispersal. In particular, these results support the hypothesis that bacteria disperse less when resources are abundant. We also show that the dispersal strategy has a considerable impact on model predictions for bacterial degradation of resources: disregarding conditional bacterial dispersal can lead to overestimations when assessing the performance of this ecosystem service.

In order to cope with the toxicity imposed by the exposure to environmental hydrocarbons, many bacteria have developed specific adaptive responses such as modifications in the cell envelope. Here we compared the influence of n-alkanols and chlorophenols on the surface properties of the solvent-tolerant bacterium Pseudomonas putida DOT-T1E. In the presence of toxic concentrations of n-alkanols, this strain significantly increased its cell surface charge and hydrophobicity with changes depending on the chain length of the added n-alkanols. The adaptive response occurred within 10 min after the addition of the solvent and was demonstrated to be of physiological nature. Contrary to that, chlorophenols of similar hydrophobicity and potential toxicity as the corresponding alkanols caused only minor effects in the surface properties. To our knowledge, this is the first observation of differences in the cellular adaptive response of bacteria to compound classes of quasi equal hydrophobicity and toxicity. The observed adaptation of the physico-chemical surface properties of strain DOT-T1E to the presence of alkanols was reversible and correlated with changes in the composition of the lipopolysaccharide content of the cells. The reaction is explained by previously described reactions allowing the release of membrane vesicles that was demonstrated for cells affected by 1-octanol and heat shock, whereas no membrane vesicles were released after the addition of chlorophenols.

Rhodococcus erythropolis was found to utilize C5 to C16 n-alkane hydrocarbons as sole source of carbon and energy when growing as planktonic or biofilm cells attached to polystyrene surfaces. Growth rates on even numbered were two- to threefold increased relatively to odd-numbered n-alkanes and depended on the chain length of the n-alkanes. C10-, C12-, C14-, and C16-n-alkanes gave rise to two- to fourfold increased maximal growth rates relative to C5- to C9-hydrocarbons. In reaction to the extremely poor water solubility of the n-alkanes, both planktonic and biofilm cells exhibited distinct adaptive changes. These included the production of surface active compounds and substrate-specific modifications of the physicochemical cell surface properties as expressed by the microbial adhesion to hydrocarbon- and contact angle-based hydrophobicity, as well as the zeta potential of the cells. By contrast, n-alkane-specific alterations of the cellular membrane composition were less distinct. The specificity of the observed autecological changes suggest that R. erythropolis cells may be used in the development and application of sound biocatalytic processes using n-alkanes as substrates or substrate reservoirs or for target-specific bioremediation of oils and combustibles, respectively.

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.

There has been increasing interest in employing electro-bioremediation, a hybrid technology of bioremediation and electrokinetics, to overcome the low bioavailability of hydrophobic organic contaminants (HOC) by homogenizing sorption-retarded HOC and immobilised microorganisms. Present electro-remediation approaches mainly aim at macroscale pollutant extraction and tend to neglect possible impacts of direct current (DC) on the physiology of microorganisms. The effect of weak electric fields (X = 1 V cm(-1)) on the fitness of electrokinetically dispersed fluorene-degrading Sphingomonas sp. LB126 in bench-scale model aquifers was investigated by flow cytometry using propidium iodide (PI) as an indicator that distinguishes between PI-permeable (cells with porous membranes, i.e. dead or vulnerable) and PI-impermeable bacteria. After 15.5 h of DC treatment 56% of all cells recovered were dispersed at the centimetre scale relative to 29% in the absence of DC. There was no overall negative effect of the 15.5-h DC treatment on cell vulnerability, as 7.0% of the DC-treated bacteria exhibited PI-staining compared to 6.5% of the control population. Minor differences were observed in the subpopulation that had been mobilised by electroosmosis with an approximately twofold increase in the percentage of PI-stained cells relative to the control. Enhanced PI staining did not correlate with reduced culturability of the cells on rich-medium agar plates. Relative to the control, DC-treated cells mobilised by electroosmosis were threefold more culturable, confirming earlier data that that PI-cell membrane permeability does not always indicate reduced viability of oligotrophic environmental bacteria. Our findings suggest that electrokinetics is a valuable mechanism to transport viable and culturable polycyclic aromatic hydrocarbon (PAH)-degrading bacteria in soil or sediments.