Natural attenuation and enhanced bioremediation of organic contaminants in groundwater

Exploring bacterial community assembly in vadose and saturated zone soil for tailored bioremediation of a long-term hydrocarbon-contaminated site

Indigenous soil microbial communities play a pivotal role in the in situ bioremediation of contaminated sites. However, research on the distribution characteristics of microbial communities at various soil depths remains limited. In particular, there is little information on the assembly of microbial communities, especially those with degradation potential, in the vadose and saturated zones of hydrocarbon-contaminated sites. In this study, 18 soil samples were collected from the vadose zone and saturated zone at a long-term hydrocarbon-contaminated site. The diversity, composition, and driving factors of assembly of the soil bacterial community were determined by high-throughput sequencing analysis. Species richness and diversity were significantly higher in the vadose zone soils than in the saturated zone soils. Significant differences in abundance at both the phylum and genus levels were observed between the two zones. Soil bacterial community assembly was driven by the combination of pollution stress and nutrients in the vadose zone but by nutrient limitations in the saturated zone. The abundance of dechlorinating bacteria was greater in the saturated zone soils than in the vadose zone soils. Compared with contaminant concentrations, nutrient levels had a more pronounced impact on the abundance of dechlorinating bacteria. In addition, the interactions among dechlorinating bacterial populations were stronger in the saturated zone soils than in the vadose zone soils. These findings underscore the importance of comprehensively understanding indigenous microbial communities, especially those with degradation potential, across different soil layers to devise specific, effective in situ bioremediation strategies for contaminated sites.

Costus speciosus (Koen ex. Retz.) Sm.: a suitable plant species for remediation of crude oil and mercury-contaminated soil

The aim of this study was to evaluate the efficiency of Costus speciosus (Koen ex. Retz.) Sm. in the degradation of crude oil and reduction of mercury (Hg) from the contaminated soil in pot experiments in the net house for 180 days. C. speciosus was transplanted in soil containing 19150 mg kg-1 crude oil and 3.2 mg kg-1 Hg. The study includes the evaluation of plant biomass, height, root length, total petroleum hydrocarbon (TPH) degradation, and Hg reduction in soil, TPH, and Hg accumulation in plants grown in fertilized and unfertilized pots, chlorophyll production, and rhizospheric most probable number (MPN) at 60-day interval. The average biomass production and heights of C. speciosus in contaminated treatments were significantly (p < 0.05) lower compared to the unvegetated control. Plants grown in contaminated soil showed relatively reduced root surface area compared to the uncontaminated treatments. TPH degradation in planted fertilized, unplanted, and planted unfertilized pot was 63%, 0.8%, and 38%, respectively. However, compared to unvegetated treatments, TPH degradation was significantly higher (p < 0.05) in vegetated treatments. A comparison of fertilized and unfertilized soils showed that TPH accumulation in plant roots and shoots was relatively higher in fertilized soils. Hg degradation in soil was significantly (p < 0.05) more in planted treatment compared to unplanted treatments. The fertilized soil showed relatively more Hg degradation in soil and its accumulation in roots and shoots of plants in comparison to unfertilized soil. MPN in treatments with plants was significantly greater (p < 0.05) than without plants. The plant's ability to produce biomass, chlorophyll, break down crude oil, reduce Hg levels in soil, and accumulate TPH and Hg in roots and shoots of the plant all point to the possibility of using this plant to remove TPH and Hg from soil.

Potential and limitations for monitoring of pesticide biodegradation at trace concentrations in water and soil

Pesticides application on agricultural fields results in pesticides being released into the environment, reaching soil, surface water and groundwater. Pesticides fate and transformation in the environment depend on environmental conditions as well as physical, chemical and biological degradation processes. Monitoring pesticides biodegradation in the environment is challenging, considering that traditional indicators, such as changes in pesticides concentration or identification of pesticide metabolites, are not suitable for many pesticides in anaerobic environments. Furthermore, those indicators cannot distinguish between biotic and abiotic pesticide degradation processes. For that reason, the use of molecular tools is important to monitor pesticide biodegradation-related genes or microorganisms in the environment. The development of targeted molecular (e.g., qPCR) tools, although laborious, allowed biodegradation monitoring by targeting the presence and expression of known catabolic genes of popular pesticides. Explorative molecular tools (i.e., metagenomics & metatranscriptomics), while requiring extensive data analysis, proved to have potential for screening the biodegradation potential and activity of more than one compound at the time. The application of molecular tools developed in laboratory and validated under controlled environments, face challenges when applied in the field due to the heterogeneity in pesticides distribution as well as natural environmental differences. However, for monitoring pesticides biodegradation in the field, the use of molecular tools combined with metadata is an important tool for understanding fate and transformation of the different pesticides present in the environment.

iChip increases the success of cultivation of TBT-resistant and TBT-degrading bacteria from estuarine sediment

Standard methods of microbial cultivation only enable the isolation of a fraction of the total environmental bacteria. Numerous techniques have been developed to increase the success of isolation and cultivation in the laboratory, some of which derive from diffusion chambers. In a diffusion chamber, environmental bacteria in agar medium are put back in the environment to grow as close to their natural conditions as possible, only separated from the environment by semi-permeable membranes. In this study, the iChip, a device that possesses hundreds of mini diffusion chambers, was used to isolate tributyltin (TBT) resistant and degrading bacteria. IChip was shown to be efficient at increasing the number of cultivable bacteria compared to standard methods. TBT-resistant strains belonging to Oceanisphaera sp., Pseudomonas sp., Bacillus sp. and Shewanella sp. were identified from Liverpool Dock sediment. Among the isolates in the present study, only members of Pseudomonas sp. were able to use TBT as a sole carbon source. It is the first time that members of the genus Oceanisphaera have been shown to be TBT-resistant. Although iChip has been used in the search for molecules of biomedical interest here we demonstrate its promising application in bioremediation.

Agricultural practices linked to shifts in groundwater microbial structure and denitrifying bacteria

Irrigation enhances the connectivity between the surface and groundwater by facilitating the transport of energy sources and oxygen. When combined with fertilisers, the impact on groundwater microbial communities and their interactions with nitrogen cycling in aquifers is poorly understood. This study examines the impact of different landuses (irrigated and non-irrigated) on groundwater microbial communities. A total of 38 wells accessing shallow aquifers in three sub-catchments of the Murray Darling Basin, Australia, were sampled for water chemistry and microbial community structure using environmental DNA (eDNA) techniques. All sub-catchments showed evidence of intense irrigation and groundwater contamination with total nitrogen, nitrates and phosphorus concentrations often well above background, with total nitrogen concentrations up to 70 mg/L and nitrate concentration up to 18 mg/L. Across sub-catchments there was high microbial diversity, with differences in community structure and function between catchments and landuses. Of the 1100 operational taxonomic units (OTUs) recorded, 47 OTUs were common across catchments with species from Woesearchaeota, Nitrospirales, Nitrosopumilales and Acidobacter taxonomic groups contributing greatly to groundwater microbial communities. Within non-irrigated sites, groundwaters contained similar proportions of nitrifying and denitrifying capable taxa, whereas irrigated sites had significantly higher abundances of microbes with nitrifying rather than denitrifying capabilities. Microbial diversity was lower in irrigated sites in the Macquarie catchment. These results indicate that irrigated landuses impact microbial community structure and diversity within groundwaters and suggest that the ratios of denitrifying to nitrifying capable microbes as well as specific orders (e.g., Nitrososphaerales) may be useful to indicate long-term nitrogen contamination of groundwaters. Such research is important for understanding the biogeochemical processes that are key predictors of redox state and contamination of groundwater by N species and other compounds. This will help to predict human impacts on groundwater microbial structure, diversity, and ecosystem functions, aiding the long-term management groundwater resources.

Field Test of In Situ Groundwater Treatment Applying Oxygen Diffusion and Bioaugmentation Methods in an Area with Sustained Total Petroleum Hydrocarbon (TPH) Contaminant Flow

Contamination of groundwater by petroleum hydrocarbons is a widespread environmental problem in many regions. Contamination of unsaturated and saturated zones could also pose a significant risk to human health. The main purpose of the study was to assess the efficiency of biodegradation of total petroleum hydrocarbon (TPH) in situ, in an area with loam and sandy loam soils, and to identify features and characteristics related to groundwater treatment in an area with a persistent flow of pollutants. We used methods of biostimulation (oxygen as stimulatory supplement) and bioaugmentation to improve water quality. Oxygen was added to the groundwater by diffusion through silicone tubing. The efficiency of groundwater treatment was determined by detailed monitoring. Implementation of the applied measure resulted in an average reduction in TPH concentration of 73.1% compared with the initial average concentration (4.33 mg/L), and in the local area, TPH content was reduced by 95.5%. The authors hope that this paper will contribute to a better understanding of the topic of groundwater treatment by in situ biodegradation of TPH. Further studies on this topic are particularly needed to provide more data and details on the efficiency of groundwater treatment under adverse geological conditions.

Modelling bioelectrochemical denitrification in absence of electron donors for groundwater treatment

Microbial electrochemical technologies (METs) have become a widely studied technology in recent years due to the need for sustainable biotechnologies. The scope of this work is the development of a mechanistic biokinetic model, based on first principles and a robust thermodynamic basis, to provide a theoretical accurate description of a MET system that would treat water contaminated with nitrate, the most common aquifer water pollutant, in absence of external electron donors. The model aims at describing the complex processes occurring including the competition between bioelectroactive and non-bioelectroactive reactions as well as the dynamics and kinetics of multiple bioelectrochemical reactions (both in series and in parallel) taking place in the same electrode. The bioelectrochemical denitrification of groundwater was then evaluated using the model as a case study. The evaluation focused on theoretical removal rates and energy expenditure, as well as the effect of key design parameters on the system's performance. The model successfully described how changes in the applied voltage and/or hydraulic retention time may impact the performance in terms of removal rate and effluent quality. The theoretical results also predict that the impact of electrode area is potentially more significant on the energy efficiency rather than on the effluent quality.

Biostimulation is a valuable tool to assess pesticide biodegradation capacity of groundwater microorganisms

Groundwater is the main source for drinking water production globally. Groundwater unfortunately can contain micropollutants (MPs) such as pesticides and/or pesticide metabolites. Biological remediation of MPs in groundwater requires an understanding of natural biodegradation capacity and the conditions required to stimulate biodegradation activity. Thus, biostimulation experiments are a valuable tool to assess pesticide biodegradation capacity of field microorganisms. To this end, groundwater samples were collected at a drinking water abstraction aquifer at two locations, five different depths. Biodegradation of the MPs BAM, MCPP and 2,4-D was assessed in microcosms with groundwater samples, either without amendment, or amended with electron acceptor (nitrate or oxygen) and/or carbon substrate (dissolved organic carbon (DOC)). Oxygen + DOC was the most successful amendment resulting in complete biodegradation of 2,4-D in all microcosms after 42 days. DOC was most likely used as a growth substrate that enhanced co-metabolic 2,4-D degradation with oxygen as electron acceptor. Different biodegradation rates were observed per groundwater sample. Overall, microorganisms from the shallow aquifer had faster biodegradation rates than those from the deep aquifer. Higher microbial activity was also observed in terms of CO₂ production in the microcosms with shallow groundwater. Our results seem to indicate that shallow groundwater contains more active microorganisms, possibly due to their exposure to higher concentrations of both DOC and MPs. Understanding field biodegradation capacity is a key step towards developing further bioremediation-based technologies. Our results show that biostimulation has real potential as a technology for remediating MPs in aquifers in order to ensure safe drinking production.

Spatiotemporal and seasonal dynamics in the microbial communities of a landfill-leachate contaminated aquifer

The microbiome of an aquifer contaminated by landfill leachate and undergoing intrinsic remediation was characterised using 16S rRNA metabarcoding. The archaeal/bacterial V3-V4 hypervariable region of the 16S rRNA gene was sequenced using Illumina MiSeq, and multivariate statistics were applied to make inferences. Results indicate that the aquifer recharge and aquifer sediment samples harbour different microbial communities compared to the groundwater samples. While Proteobacteria dominated both the recharge and groundwater samples, Acidobacteria dominated the aquifer sediment. The most abundant genera detected from the contaminated aquifer were Polynucleobacter, Rhodoferax, Pedobacter, Brevundimonas, Pseudomonas, Undibacterium, Sulfurifustis, Janthinobacterium, Rhodanobacter, Methylobacter and Aquabacterium. The result also shows that the microbial communities of the groundwater varied spatially, seasonally and interannually, although the interannual variation was significant for only one of the wells. Variation partitioning analysis indicates that water chemistry and well distance are intercorrelated and they jointly accounted for most of the variation in microbial composition. This implies that the species composition and water chemistry characteristics have a similar spatial structuring, presumably caused by the landfill leachate plume. The study improves our understanding of the dynamics in subsurface microbial communities in space and time.

Insights into enhanced biodegradation of sulfadimethoxine by catalyst: Transcriptomic responses and free radical interactions

The occurrence of sulfonamides in the environment is a severe global threat to public health due to the increasing prevalence of antibiotic selection pressure that may lead to the development of antibiotic resistance. We report an enhanced biodegradation of sulfadimethoxine (SDM) by Phanerochaete chrysosporium (Pc) with lignocellulosic biomass (Lb) using Fe₃O₄-ZSM-5 as a catalyst (Pc/Fe₃O₄-ZSM-5/Lb). SDM was completely degraded within 4 days at pH 7.0 in the Pc/Fe₃O₄-ZSM-5/Lb system. Transcriptomic, metabolites and free radical analyses were performed to explore the detailed molecular mechanisms of SDM degradation. A total of 246 genes of Pc in the Pc/Fe₃O₄-ZSM-5/Lb system exhibited significant upregulation compared to that in Pc alone. Upregulated genes encoding cellulases, cytochrome P450, cellobiose quinone oxidoreductase, and cellobiose dehydrogenase were involved in SDM degradation in the Pc/Fe₃O₄-ZSM-5/Lb system. In addition, genes encoding glutathione S-transferase and cytochrome P450 genes related to oxidative stress and detoxification were all significantly upregulated (P < 0.01). Electron paramagnetic resonance revealed the generation of OH suggesting a free radical pathway could be catalyzed by Fe₃O₄-ZSM-5 and the enzymes. These findings of catalyst-assisted SDM biodegradation will be valuable for remediation of antibiotics from contaminated wastewater.

Energy Taxis toward Redox-Active Surfaces Decreases the Transport of Electroactive Bacteria in Saturated Porous Media

The fate and transport of bacteria in porous media are essential for bioremediation and water quality control. However, the influence of biological activities like extracellular electron transfer (EET) and swimming motility toward granular media on cell transport remains unknown. Here, electroactive bacteria with higher Fe(III) reduction abilities were found to demonstrate greater retention in ferrihydrite-coated sand. Increasing the concentrations of the electron donor (1-10 mM lactate), shuttle (0-50 μM anthraquinone-2,6-disulfonate), and acceptor (ferrihydrite, MnO₂, or biochar) under flow conditions significantly reduced Shewanella oneidensis MR-1's mobility through redox-active porous media. The deficiency of EET ability or flagellar motion and inhibition of intracellular proton motive force, all of which are essential for energy taxis, enhanced MR-1's transport. It was proposed that EET could facilitate MR-1 to sense, tactically move toward, and attach on redox-active media surface, eventually improving its retention. Positive linear correlations were established among parameters describing MR-1's energy taxis ability (relative taxis index), cell transport behavior (dispersion coefficient and relative change of effluent percentage), and redox activity of media surface (reduction potential or electron-accepting rate), providing novel insights into the critical impacts of bacterial microscale motility on macroscale cell transport through porous media.

Impact of Transgenic Arabidopsis thaliana Plants on Herbicide Isoproturon Phytoremediation through Expressing Human Cytochrome P450-1A2

The excessive use of herbicides is a major cause of many environmental problems. The use of isoproturon herbicide as a weed controller has been a common practice globally. Phytoremediation technology can help in cleaning up polluted areas. In this paper the ability of CYP1A2 transgenic A. thaliana plants in the phytoremediation of isoproturon herbicides has been investigated. We tested the capability of P450-1A2 overexpression on the detoxification and degradation of isoproturon. We explored the toxic effect of isoproturon on the plant phenotypic characteristics, including the primary root length, rosette diameter, and fresh, dry weight for transgenic and wild type A. thaliana. The results revealed that no morphological changes appeared on CYP1A2 transgenic plants with a high tolerance to isoproturon herbicide applications either via foliar spraying or supplementation of the growth medium. Deleterious effects were observed on the morphological characteristics of plants of the wild type grown in soil under different treatments with isoproturon. The transgenic A. thaliana plants exhibited a vigorous growth even at high doses of isoproturon treatments. In contrast, the growth of the wild type was significantly impaired with doses above 50 µM isoproturon. The transgenic A. thaliana plants expressing P450-1A2 were able to metabolize the phenylurea herbicide isoproturon. Therefore, this method can be determined as a potential bioremediation agent.

Diversity of bacteria and archaea in the groundwater contaminated by chlorinated solvents undergoing natural attenuation

Chlorinated solvents (CS)-contaminated groundwater poses serious risks to the environment and public health. Microorganisms play a vital role in efficient remediation of CS. In this study, the microbial community (bacterial and archaeal) composition of three CS-contaminated groundwater wells located at an abandoned chemical factory which covers three orders of magnitude in concentration (0.02-16.15 mg/L) were investigated via 16S rRNA gene high-throughput sequencing. The results indicated that Proteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal groups at the phylum level in groundwater, respectively. The major bacterial genera (Flavobacterium sp., Mycobacterium sp. and unclassified Parcubacteria taxa, etc.) and archaeal genera (Thaumarchaeota Group C3, Miscellaneous Crenarchaeotic Group and Miscellaneous Euryarchaeotic Group, etc.) might be involved in the dechlorination processes. In addition, Pearson's correlation analyses showed that alpha diversity of the bacterial community was not significantly correlated with CS concentration, while alpha diversity of archaeal community greatly decreased with the increased contamination of CS. Moreover, partial Mantel test indicated that oxidation-reduction potential, dissolved oxygen, temperature and methane concentration were major drivers of bacterial and archaeal community composition, whereas CS concentration had no significant impact, indicating that both indigenous bacterial and archaeal community compositions are capable of withstanding elevated CS contamination. This study improves our understanding of how the natural microbial community responds to high CS-contaminated groundwater.

Occurrence and transformation of phenoxy acids in aquatic environment and photochemical methods of their removal: a review

The article presents the behavior of phenoxy acids in water, the levels in aquatic ecosystems, and their transformations in the water environment. Phenoxy acids are highly soluble in water and weakly absorbed in soil. These highly mobile compounds are readily transported to surface and groundwater. Monitoring studies conducted in Europe and in other parts of the world indicate that the predominant phenoxy acids in the aquatic environment are mecoprop, 4-chloro-2-methylphenoxyacetic acid (MCPA), dichlorprop, 2,4-dichlorophenoxyacetic acid (2,4-D), and their metabolites which are chlorophenol derivatives. In water, the concentrations of phenoxy acids are effectively lowered by hydrolysis, biodegradation, and photodegradation, and a key role is played by microbial decomposition. This process is determined by the qualitative and quantitative composition of microorganisms, oxygen levels in water, and the properties and concentrations of phenoxy acids. In shallow and highly insolated waters, phenoxy acids can be decomposed mainly by photodegradation whose efficiency is determined by the form of the degraded compound. Numerous studies are underway on the use of advanced oxidation processes (AOPs) to remove phenoxy acids. The efficiency of phenoxy acid degradation using AOPs varies depending on the choice of oxidizing system and the conditions optimizing the oxidation process. Most often, methods combining UV radiation with other reagents are used to oxidize phenoxy acids. It has been found that this solution is more effective compared with the oxidation process carried out using only UV.

Assessing toluene biodegradation under temporally varying redox conditions in a fractured bedrock aquifer using stable isotope methods

In complex hydrogeological settings little is known about the extent of temporally varying redox conditions and their effect on aromatic hydrocarbon biodegradation. This study aims to assess the impact of changing redox conditions over time on aromatic hydrocarbon biodegradation in a fractured bedrock aquifer using stable isotope methods. To that end, four snapshots of highly spatio-temporally resolved contaminant and redox sensitive species concentrations, as well as stable isotope ratio profiles, were determined over a two-years time period in summer 2016, spring 2017, fall 2017 and summer 2018 in a toluene contaminated fractured bedrock aquifer. The concentration profiles of redox sensitive species and stable isotope ratio profiles for dissolved inorganic carbon (DIC) and sulfate (δ¹³C_DIC, δ³⁴S_SO4, δ¹⁸O_SO4) revealed that the aquifer alternates between oxidising (spring 2017/summer 2018) and reducing conditions (summer 2016/fall 2017). This alternation was attributed to a stronger aquifer recharge with oxygen-rich meltwater in spring 2017/summer 2018 compared to summer 2016/fall 2017. The temporally varying redox conditions coincided with various extents of toluene biodegradation revealed by the different magnitude of heavy carbon (¹³C) and hydrogen (²H) isotope enrichment in toluene. This indicated that the extent of toluene biodegradation and its contribution to plume attenuation was controlled by the temporally changing redox conditions. The highest toluene biodegradation was observed in summer 2016, followed by spring 2017 and fall 2017, whereby these temporal changes in biodegradation occurred throughout the whole plume. Thus, under temporally varying recharge conditions both the core and the fringe of a contaminant plume can be replenished with terminal electron acceptors causing biodegradation in the whole plume and not only at its distal end as previously suggested by the plume fringe concept. Overall, this study highlights the importance of highly temporally resolved groundwater monitoring to capture temporally varying biodegradation rates and to accurately predict biodegradation-induced contaminant attenuation in fractured bedrock aquifers.

Hydro-biogeochemical impacts of fugitive methane on a shallow unconfined aquifer

Oil and gas development can result in natural gas migration into shallow groundwater. Methane (CH₄), the primary component of natural gas, can subsequently react with solutes and minerals in the aquifer to create byproducts that affect groundwater chemistry. Hydro-biogeochemical processes induced by fugitive gas from leaky oil and gas wells are currently not well understood. We monitored the hydro-biogeochemical responses of a controlled natural gas release into a well-studied Pleistocene beach sand aquifer (Canadian Forces Base Borden, Ontario, Canada). Groundwater samples were collected before, during, and up to 700 days after gas injection and analyzed for pH, major and minor ions, alkalinity, dissolved gases, stable carbon isotope ratios of CO₂ and CH₄, and microbial community composition. Gas injection resulted in a dispersed plume of free and dissolved phase natural gas, affecting groundwater chemistry in two distinct temporal phases. Initially (i.e. during and immediately after gas injection), pH declined and major ions and trace elements fluctuated; at times increasing above baseline concentrations. Changes in the short-term were due to invasion of deep groundwater with elevated total dissolved solids entrained with the upward migration of free phase gas and, reactions that were instigated through the introduction of constituents other than CH₄ present in the injected gas (e.g. CO₂). At later times, more pronounced aerobic and anaerobic CH₄ oxidation led to subtle increases in major ions (e.g. Ca²⁺, H₄SiO₄) and trace elements (e.g. As, Cr). Microbial community profiling indicated a persistent perturbation to community composition with a conspicuous ingrowth of taxa implicated in aerobic CH₄ oxidation as well anaerobic S, N and Fe species metabolism.

Potential impact of hydrodynamic shear force in aquifer thermal energy storage on dissolved organic matter releasement: A vigorous shaking batch study

The combination of bioremediation and aquifer thermal energy storage (ATES) has become attractive because of the possibility of solving environmental and energy problems simultaneously. While the impact of ATES on groundwater quality due to temperature change has received ample attention in literature, the effect of the greatly enhanced groundwater flow velocity on groundwater quality has not yet received sufficient scientific attention. To fill this gap in understanding, we conducted a simple yet straightforward experiment to illustrate the impact of hydrodynamic shear force due to the water flow by ATES on the release of dissolved organic matter, which can potentially be advantageous to bioremediation. Vigorous shaking conditions were applied to simulate the enhanced dynamics at the ATES well center and nearby. As the indicators of dissolved organic matter, COD and TOC concentrations were significantly impacted by shaking. COD increased from 5.4 mgO₂/L to 36.3 mgO₂/L during horizontal shaking. The maximum COD level was determined as 33.8 mgO₂/L during orbital shaking, while the TOC level was growing from 6.7 to 28.7 mg C/L. Meanwhile, redox potential (with initial level -100 mV) was decreasing to -450 mV synchronously with the elevating COD and TOC level. Temperature was also revealed as a significant factor in the organic matter releasement. Microbial iron reduction was deemed to occur, yet sulfate reduction was not initiated during the whole experiment. Eventually, the structure of the soil-water matrix has been changed due to the extensive hydraulic and particle collisions, resulting in blackish appearance and thicker layer of fine particles. Overall, the findings advance our understanding of the role of the ATES-induced water flow in the subsurface biogeochemistry and give insight into the perspective of the combination of bioremediation and ATES. In general, an increase in dissolved organic matter can be expected due to the increased shear force at high flow conditions in the ATES system.

Synergistic plant-microbes interactions in the rhizosphere: a potential headway for the remediation of hydrocarbon polluted soils

Soil pollution is an unavoidable evil; many crude-oil exploring communities have been identified to be the most ecologically impacted regions around the world due to hydrocarbon pollution and their concurrent health risks. Several clean-up technologies have been reported on the removal of hydrocarbons in polluted soils but most of them are either very expensive, require the integration of advanced mechanization and/or cannot be implemented in small scale. However, "Bioremediation" has been reported as an efficient, cost-effective and environment-friendly technology for clean-up of hydrocarbon"s contaminated soils. Here, we suggest the implementation of synergistic mechanism of bioremediation such as the use of rhizosphere mechanism which involves the actions of plant and microorganisms, which involves the exploitation of plant and microorganisms for effective and speedy remediation of hydrocarbon"s contaminated soils. In this mechanism, plant"s action is synergized with the soil microorganisms through the root rhizosphere to promote soil remediation. The microorganisms benefit from the root metabolites (exudates) and the plant in turn benefits from the microbial recycling/solubilizing of mineral nutrients. Harnessing the abilities of plants and microorganisms is a potential headway for cost-effective clean-up of hydrocarbon"s polluted sites; such technology could be very important in countries with great oil producing activities/records over many years but still developing.

Do composition and diversity of bacterial communities and abiotic conditions of spring water reflect characteristics of groundwater ecosystems exposed to different agricultural activities?

Modern agricultural practices have undeniably increased global food production. On the other hand, agricultural practices not only lead to a degradation of natural ecosystems but also affect the functioning of ecosystems and the related services they provide. Even though impacts of anthropogenic activities vary across ecosystems, freshwater ecosystems are among those affected to a higher degree. In comparison to surface water ecosystems, groundwater ecosystems are less affected by anthropogenic pollutants, as the overlaying soil retains organic and inorganic substances. However, it has become evident that the excessive use of fertilizers has led to the eutrophication of many aquifers. Bacterial communities, which significantly contribute to the cycling of matter due to their metabolic capacities, are prone to environmental perturbations, and structural variation of bacterial communities may consequently affect the functioning of groundwater ecosystems. Our present paper intends to evaluate the impact of anthropogenic activities on environmental conditions as well as on the structural properties of bacterial communities in groundwater. We repeatedly sampled emerging groundwater at five spring sites belonging to different catchments and determined the concentration of abiotic variables as well as the diversity and composition of bacterial communities on a local scale. We hypothesized that anthropogenic activities influence the concentration of abiotic variables, especially of nitrate, as well as the composition and diversity of bacterial communities in groundwater. Our results show that underground spring catchment areas only slightly differ regarding the concentration of abiotic variables as well as the structure of bacterial communities. Furthermore, abiotic variables, presumably influenced by anthropogenic activities, do not correlate with the diversity and composition of bacterial communities. Although supported only by circumstantial evidence, we suggest that upwelling groundwater from the deeper aquifer affects the diversity and composition of bacterial communities, and we argue that bacterial communities act as useful indicators for environmental changes.

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

Contaminant back-diffusion from low-permeability layers as affected by groundwater velocity: A laboratory investigation by box model and image analysis

Low-permeability lenses represent potential sources of long-term release when filled from contaminant solute through direct contact with dissolved plumes. The redistribution of contaminant from low to high permeability aquifer zones (Back-Diffusion) was studied. Redistribution causes a long plume tail, commonly regarded as one of the main obstacles to effective groundwater remediation. Laboratory tests were performed to reproduce the redistribution process and to investigate the effect of pumping water on the remediation time of these contaminated low-permeability lenses. The test section used is representative of clay/silt lenses (k≈1∗10^-10m/s/k≈1∗10^-7m/s) in a sand aquifer (k≈1∗10^-3m/s). Hence, an image analysis procedure was used to estimate the diffusive flux of contaminant released by these low-permeability zones. The proposed technique was validated performing a mass balance of a lens saturated by a known quantity of tracer. For each test, performed using a different groundwater velocity, the diffusive fluxes of contaminant released by lenses were compared and the remediation times of the low-permeability zones calculated. For each lens, the obtained remediation timeframes were used to define an analytical relation vs groundwater velocity and the coefficients of these relations were matched to grain size of the low-permeability lenses. Results show that an increase of the velocity field is not useful to diminish the total depletion times as the process mainly diffusive. This is significant when the remediation approach relies on pumping technology.

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition

Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion of the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems.

Combination of aquifer thermal energy storage and enhanced bioremediation: Biological and chemical clogging

Interest in the combination concept of aquifer thermal energy storage (ATES) and enhanced bioremediation has recently risen due to the demand for both renewable energy technology and sustainable groundwater management in urban areas. However, the impact of enhanced bioremediation on ATES is not yet clear. Of main concern is the potential for biological clogging which might be enhanced and hamper the proper functioning of ATES. On the other hand, more reduced conditions in the subsurface by enhanced bioremediation might lower the chance of chemical clogging, which is normally caused by Fe(III) precipitate. To investigate the possible effects of enhanced bioremediation on clogging with ATES, we conducted two recirculating column experiments with differing flow rates (10 and 50mL/min), where enhanced biological activity and chemically promoted Fe(III) precipitation were studied by addition of lactate and nitrate respectively. The pressure drop between the influent and effluent side of the column was used as a measure of the (change in) hydraulic conductivity, as indication of clogging in these model ATES systems. The results showed no increase in upstream pressure during the period of enhanced biological activity (after lactate addition) under both flow rates, while the addition of nitrate lead to significant buildup of the pressure drop. However, at the flow rate of 10mL/min, high pressure buildup caused by nitrate addition could be alleviated by lactate addition. This indicates that the risk of biological clogging is relatively small in the investigated areas of the mimicked ATES system that combines enhanced bioremediation with lactate as substrate, and furthermore that lactate may counter chemical clogging.

Towards an integrated understanding of how micro scale processes shape groundwater ecosystem functions

Micro scale processes are expected to have a fundamental role in shaping groundwater ecosystems and yet they remain poorly understood and under-researched. In part, this is due to the fact that sampling is rarely carried out at the scale at which microorganisms, and their grazers and predators, function and thus we lack essential information. While set within a larger scale framework in terms of geochemical features, supply with energy and nutrients, and exchange intensity and dynamics, the micro scale adds variability, by providing heterogeneous zones at the micro scale which enable a wider range of redox reactions. Here we outline how understanding micro scale processes better may lead to improved appreciation of the range of ecosystems functions taking place at all scales. Such processes are relied upon in bioremediation and we demonstrate that ecosystem modelling as well as engineering measures have to take into account, and use, understanding at the micro scale. We discuss the importance of integrating faunal processes and computational appraisals in research, in order to continue to secure sustainable water resources from groundwater.

Effects of synthetic iron and aluminium oxide surface charge and hydrophobicity on the formation of bacterial biofilm

In this research, bacterial cell attachments to hematite, goethite and aluminium hydroxide were investigated. The aim was to study the effects of these minerals' hydrophobicity and pH-dependent surface charge on the extent of biofilm formation using six genetically diverse bacterial strains: Rhodococcus spp. (RC92 & RC291), Pseudomonas spp. (Pse1 & Pse2) and Sphingomonas spp. (Sph1 & Sph2), which had been previously isolated from contaminated environments. The surfaces were prepared in a way that was compatible with the naturally occurring coating process in aquifers: deposition of colloidal particles from the aqueous phase. The biofilms were evaluated using a novel, in situ and non-invasive technique developed for this purpose. A manufactured polystyrene 12-well plate was used as the reference surface to be coated with synthesized minerals by deposition of their suspended particles through evaporation. Planktonic phase growth indicates that it is independent of the surface charge and hydrophobicity of the studied surfaces. The hydrophobic similarities failed to predict biofilm proliferation. Two of the three hydrophilic strains formed extensive biofilms on the minerals. The third one, Sph2, showed anomalies in contrast to the expected electrostatic attraction between the minerals and the cell surface. Further research showed how the solution's ionic strength affects Sph2 surface potential and shapes the extent of its biofilm formation; reducing the ionic strength from ≈200 mM to ≈20 mM led to a tenfold increase in the number of cells attached to hematite. This study provides a technique to evaluate biofilm formation on metal-oxide surfaces, under well-controlled conditions, using a simple yet reliable method. The findings also highlight that cell numbers in the planktonic phase do not necessarily show the extent of cell attachment, and thorough physicochemical characterization of bacterial strains, substrata and the aquifer medium is fundamental to successfully implementing any bioremediation projects.

Biodegradation of isoproturon by Pseudoxanthomonas sp. isolated from herbicide-treated wheat fields of Tarai agro-ecosystem, Pantnagar

A gram-negative, rod-shaped, isoproturon (IPU) utilizing bacterium was isolated from herbicide-applied wheat fields of Tarai agro-ecosystem, Pantnagar. The phylogenetic sequence analysis based on 16S rRNA sequence revealed that the isolate could be a distinct species within the genus Pseudomonas. The isolate was a close relative of Pseudoxanthomonas japonensis (95 % similarity) and designated as K2. The bacterial isolate showed positive reaction for oxidase, catalase, and 20 carbohydrates using KB009 Part A and B HiCarbohydrate™ Kit. Degradation experiments were conducted using 200 mg l^-1 initial IPU as a source of carbon at different pH and temperatures. Maximum IPU degradation by K2 was observed at pH 7.0 and 30 °C, while least degradation at 6.5 pH and 25 °C. Addition of dextrose along with IPU as an auxiliary carbon source increased IPU degradation by 4.72 %, as compared to the IPU degradation without dextrose under optimum conditions. 4-isopropylaniline was detected as a degradation by-product in the medium. The present study demonstrated the IPU metabolizing capacity of a novel bacterial isolate K2 that can be a better choice for the remediation of IPU-contaminated sites.

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.

Identification of novel toluene monooxygenase genes in a hydrocarbon-polluted sediment using sequence- and function-based screening of metagenomic libraries

The microbial potential for toluene degradation within sediments from a tar oil-contaminated site in Flingern, Germany, was assessed using a metagenomic approach. High molecular weight environmental DNA from contaminated sediments was extracted, purified, and cloned into fosmid and BAC vectors and transformed into Escherichia coli. The fosmid library was screened by hybridization with a PCR amplicon of the α-subunit of the toluene 4-monooxygenase gene to identify genes and pathways encoding toluene degradation. Fourteen clones were recovered from the fosmid library, among which 13 were highly divergent from known tmoA genes and several had the closest relatives among Acinetobacter species. The BAC library was transferred to the heterologous hosts Cupriavidus metallidurans (phylum Proteobacteria) and Edaphobacter aggregans (phylum Acidobacteria). The resulting libraries were screened for expression of toluene degradation in the non-degradative hosts. From expression in C. metallidurans, three novel toluene monooxygenase-encoding operons were identified that were located on IncP1 plasmids. The E. aggregans-hosted BAC library led to the isolation of a cloned genetic locus putatively derived from an Acidobacteria taxon that contained genes involved in aerobic and anaerobic toluene degradation. These data suggest the important role of plasmids in the spread of toluene degradative capacity and indicate putative novel tmoA genes present in this hydrocarbon-polluted environment.

Biogeochemical gradients above a coal tar DNAPL

Naturally occurring distribution and attenuation processes can keep hydrocarbon emissions from dense non aqueous phase liquids (DNAPL) into the adjacent groundwater at a minimum. In a historically coal tar DNAPL-impacted site, the de facto absence of a plume sparked investigations regarding the character of natural attenuation and DNAPL resolubilization processes at the site. Steep vertical gradients of polycyclic aromatic hydrocarbons, microbial community composition, secondary water quality and redox-parameters were found to occur between the DNAPL-proximal and shallow waters. While methanogenic and mixed-electron acceptor conditions prevailed close to the DNAPL, aerobic conditions and very low dissolved contaminant concentrations were identified in three meters vertical distance from the phase. Comprehensive two-dimensional gas chromatography-mass spectrometry (GC×GC-MS) proved to be an efficient tool to characterize the behavior of the present complex contaminant mixture. Medium to low bioavailability of ferric iron and manganese oxides of aquifer samples was detected via incubation with Shewanella alga and evidence for iron and manganese reduction was collected. In contrast, 16S rDNA phylogenetic analysis revealed the absence of common iron reducing bacteria. Aerobic hydrocarbon degraders were abundant in shallow horizons, while nitrate reducers were dominating in deeper aquifer regions, in addition to a low relative abundance of methanogenic archaea. Partial Least Squares - Canonical Correspondence Analysis (PLS-CCA) suggested that nitrate and oxygen concentrations had the greatest impact on aquifer community structure in on- and offsite wells, which had a similarly high biodiversity (H' and Chao1). Overall, slow hydrocarbon dissolution from the DNAPL appears to dominate natural attenuation processes. This site may serve as a model for developing legal and technical strategies for the treatment of DNAPL-impacted sites where contaminant plumes are absent or shrinking.

New Bio-Indicators for Long Term Natural Attenuation of Monoaromatic Compounds in Deep Terrestrial Aquifers

Deep subsurface aquifers despite difficult access, represent important water resources and, at the same time, are key locations for subsurface engineering activities for the oil and gas industries, geothermal energy, and CO2 or energy storage. Formation water originating from a 760 m-deep geological gas storage aquifer was sampled and microcosms were set up to test the biodegradation potential of BTEX by indigenous microorganisms. The microbial community diversity was studied using molecular approaches based on 16S rRNA genes. After a long incubation period, with several subcultures, a sulfate-reducing consortium composed of only two Desulfotomaculum populations was observed able to degrade benzene, toluene, and ethylbenzene, extending the number of hydrocarbonoclastic-related species among the Desulfotomaculum genus. Furthermore, we were able to couple specific carbon and hydrogen isotopic fractionation during benzene removal and the results obtained by dual compound specific isotope analysis (𝜀C = -2.4‰ ± 0.3‰; 𝜀H = -57‰ ± 0.98‰; AKIEC: 1.0146 ± 0.0009, and AKIEH: 1.5184 ± 0.0283) were close to those obtained previously in sulfate-reducing conditions: this finding could confirm the existence of a common enzymatic reaction involving sulfate-reducers to activate benzene anaerobically. Although we cannot assign the role of each population of Desulfotomaculum in the mono-aromatic hydrocarbon degradation, this study suggests an important role of the genus Desulfotomaculum as potential biodegrader among indigenous populations in subsurface habitats. This community represents the simplest model of benzene-degrading anaerobes originating from the deepest subterranean settings ever described. As Desulfotomaculum species are often encountered in subsurface environments, this study provides some interesting results for assessing the natural response of these specific hydrologic systems in response to BTEX contamination during remediation projects.

Enhanced Retention of Chemotactic Bacteria in a Pore Network with Residual NAPL Contamination

Nonaqueous-phase liquid (NAPL) contaminants are difficult to eliminate from natural aquifers due, in part, to the heterogeneous structure of the soil. Chemotaxis enhances the mixing of bacteria with contaminant sources in low-permeability regions, which may not be readily accessible by advection and dispersion alone. A microfluidic device was designed to mimic heterogeneous features of a contaminated groundwater aquifer. NAPL droplets (toluene) were trapped within a fine pore network, and bacteria were injected through a highly conductive adjacent macrochannel. Chemotactic bacteria (Pseudomonas putida F1) exhibited greater accumulation near the pore network at 0.5 m/day than both the nonchemotactic control and the chemotactic bacteria at a higher groundwater velocity of 5 m/day. Chemotactic bacteria accumulated in the vicinity of NAPL droplets, and the accumulation was 15% greater than a nonchemotactic mutant. Indirect evidence showed that chemotactic bacteria were retained within the contaminated low-permeability region longer than nonchemotactic bacteria at 0.25 m/day. This retention was diminished at 5 m/day. Numerical solutions of the bacterial-transport equations were consistent with the experimental results. Because toluene is degraded by P. putida F1, the accumulation of chemotactic bacteria around NAPL sources is expected to increase contaminant consumption and improve the efficiency of bioremediation.

Biodegradation of cis-1,2-Dichloroethene in Simulated Underground Thermal Energy Storage Systems

Underground thermal energy storage (UTES) use has showed a sharp rise in numbers in the last decades, with aquifer thermal energy storage (ATES) and borehole thermal energy storage (BTES) most widely used. In many urban areas with contaminated aquifers, there exists a desire for sustainable heating and cooling with UTES and a need for remediation. We investigated the potential synergy between UTES and bioremediation with batch experiments to simulate the effects of changing temperature and liquid exchange that occur in ATES systems, and of only temperature change occurring in BTES systems on cis-DCE reductive dechlorination. Compared to the natural situation (NS) at a constant temperature of 10 °C, both UTES systems with 25/5 °C for warm and cold well performed significantly better in cis-DCE (cis-1,2-dichloroethene) removal. The overall removal efficiency under mimicked ATES and BTES conditions were respectively 13 and 8.6 times higher than in NS. Inoculation with Dehalococcoides revealed that their initial presence is a determining factor for the dechlorination process. Temperature was the dominating factor when Dehalococcoides abundance was sufficient. Stimulated biodegradation was shown to be most effective in the mimicked ATES warm well because of the combined effect of suitable temperature, sustaining biomass growth, and regular cis-DCE supply.

Rates of As and Trace-Element Mobilization Caused by Fe Reduction in Mixed BTEX-Ethanol Experimental Plumes

Biodegradation of organic matter, including petroleum-based fuels and biofuels, can create undesired secondary water-quality effects. Trace elements, especially arsenic (As), have strong adsorption affinities for Fe(III) (oxyhydr)-oxides and can be released to groundwater during Fe-reducing biodegradation. We investigated the mobilization of naturally occurring As, cobalt (Co), chromium (Cr), and nickel (Ni) from wetland sediments caused by the introduction of benzene, toluene, ethylbenzene, and xylenes (BTEX) and ethanol mixtures under iron- and nitrate-reducing conditions, using in situ push-pull tests. When BTEX alone was added, results showed simultaneous onset and similar rates of Fe reduction and As mobilization. In the presence of ethanol, the maximum rates of As release and Fe reduction were higher, the time to onset of reaction was decreased, and the rates occurred in multiple stages that reflected additional processes. The concentration of As increased from <1 μg/L to a maximum of 99 μg/L, exceeding the 10 μg/L limit for drinking water. Mobilization of Co, Cr, and Ni was observed in association with ethanol biodegradation but not with BTEX. These results demonstrate the potential for trace-element contamination of drinking water during biodegradation and highlight the importance of monitoring trace elements at natural and enhanced attenuation sites.

Electro-assisted groundwater bioremediation: fundamentals, challenges and future perspectives

Bioremediation is envisaged as an important way to abate groundwater contamination, but the need for chemical addition and limited bioavailability of electron donors/acceptors or contaminants hamper its application. As a promising means to enhance such processes, electrochemical system has drawn considerable attention, as it offers distinct advantages in terms of environmental benignity, controllability and treatment efficiency. Meanwhile, there are also potential risks and considerable engineering challenges for its practical application. This review provides a first comprehensive introduction of this emerging technology, discusses its potential applications and current challenges, identifies the knowledge gaps, and outlooks the future opportunities to bring it to field application. The need for a better understanding on the microbiology under electrochemical stimulation and the future requirements on process monitoring, modeling and evaluation protocols and field investigations are highlighted.

Quantitative analysis of chemotaxis towards toluene by Pseudomonas putida in a convection-free microfluidic device

Chemotaxis has been shown to be beneficial for the migration of soil-inhabiting bacteria towards industrial chemical pollutants, which they degrade. Many studies have demonstrated the importance of this microbial property under various circumstances; however, few quantitative analyses have been undertaken to measure the two essential parameters that characterize the chemotaxis of bioremediation bacteria: the chemotactic sensitivity coefficient χ(0) and the chemotactic receptor constant K(c). The main challenge to determine these parameters is that χ(0) and K(c) are coupled together in non-linear mathematical models used to evaluate them. In this study we developed a method to accurately measure these parameters for Pseudomonas putida in the presence of toluene, an important pollutant in groundwater contamination. Our approach uses a multilayer microfluidic device to expose bacteria to a convection-free linear chemical gradient of toluene that is stable over time. The bacterial distribution within the gradient is measured in terms of fluorescence intensity, and is then used to fit the parameters Kc and χ(0) with mathematical models. Critically, bacterial distributions under chemical gradients at two different concentrations were used to solve for both parameters independently. To validate the approach, the chemotaxis parameters of Escherichia coli strains towards α-methylaspartate were experimentally derived and were found to be consistent with published results from related work.

Detection of Dehalococcoides spp. by peptide nucleic acid fluorescent in situ hybridization

Chlorinated solvents including tetrachloroethene (perchloroethene and trichloroethene), are widely used industrial solvents. Improper use and disposal of these chemicals has led to a widespread contamination. Anaerobic treatment technologies that utilize Dehalococcoides spp. can be an effective tool to remediate these contaminated sites. Therefore, the aim of this study was to develop, optimize and validate peptide nucleic acid (PNA) probes for the detection of Dehalococcoides spp. in both pure and mixed cultures. PNA probes were designed by adapting previously published DNA probes targeting the region of the point mutations described for discriminating between the Dehalococcoides spp. strain CBDB1 and strain 195 lineages. Different fixation, hybridization and washing procedures were tested. The results indicated that the PNA probes hybridized specifically and with a high sensitivity to their corresponding lineages, and that the PNA probes developed during this work can be used in a duplex assay to distinguish between strain CBDB1 and strain 195 lineages, even in complex mixed cultures. This work demonstrates the effectiveness of using PNA fluorescence in situ hybridization to distinguish between two metabolically and genetically distinct Dehalococcoides strains, and they can have strong implications in the monitoring and differentiation of Dehalococcoides populations in laboratory cultures and at contaminated sites.

Temperature dependent redox zonation and attenuation of wastewater-derived organic micropollutants in the hyporheic zone

The hyporheic zone - a spatially fluctuating ecotone connecting surface water and groundwater - is considered to be highly reactive with regard to the attenuation of organic micropollutants. In the course of the presented study an undisturbed sediment core was taken from the infiltration zone of a bank filtration site in Berlin and operated under controlled laboratory conditions with wastewater-influenced surface water at two different temperatures, simulating winter and summer conditions. The aim was to evaluate the fate of site-relevant micropollutants, namely metoprolol, iopromide, diclofenac, carbamazepine, acesulfame, tolyltriazole, benzotriazole, phenazone and two phenazone type metabolites, within the first meter of infiltration dependent on the prevailing temperature. A change in temperature resulted in a development of significantly distinct redox conditions. Both temperature dependencies and related redox dependencies were identified for all micropollutants except for benzotriazole and carbamazepine, which behaved persistent under all conditions. For the remaining compounds degradation rate constants generally decreased from warm and oxic/penoxic/suboxic over cold and oxic/penoxic to warm and manganese reducing (transition zone). Individual degradation rate constants ranged from 0 (e.g. diclofenac, acesulfame and tolyltriazole in the transition zone) to 1.4×10(-4)s(-1) for metoprolol under warm conditions within the oxic to suboxic zone.

Intrinsic potential for immediate biodegradation of toluene in a pristine, energy-limited aquifer

Pristine and energy-limited aquifers are considered to have a low resistance and resilience towards organic pollution. An experiment in an indoor aquifer system revealed an unexpected high intrinsic potential for the attenuation of a short-term toluene contamination. A 30 h pulse of 486 mg of toluene, used as a model contaminant, and deuterated water (D2O) through an initially pristine, oxic, and organic carbon poor sandy aquifer revealed an immediate aerobic toluene degradation potential. Based on contaminant and tracer break-through curves, as well as mass balance analyses and reactive transport modelling, a contaminant removal of 40 % over a transport distance of only 4.2 m in less than one week of travel time was obtained. The mean first-order degradation rate constant was λ = 0.178 day(-1), corresponding to a half-life time constant T1/2 of 3.87 days. Toluene-specific stable carbon isotope analysis independently proved that the contaminant mass removal can be attributed to microbial biodegradation. Since average doubling times of indigenous bacterial communities were in the range of months to years, the aerobic biodegradation potential observed is assumed to be present and active in the pristine, energy-limited groundwater ecosystems at any time. Follow-up experiments and field studies will help to quantify the immediate natural attenuation potential of aquifers for selected priority contaminants and will try to identify the key-degraders within the autochthonous microbial communities.

Bioremediation via in situ microbial degradation of organic pollutants

Contamination of soil and natural waters by organic pollutants is a global problem. The major organic pollutants of point sources are mineral oil, fuel components, and chlorinated hydrocarbons. Research from the last two decades discovered that most of these compounds are biodegradable under anoxic conditions. This has led to the rise of bioremediation strategies based on the in situ biodegradation of pollutants. Monitored natural attenuation is a concept by which a contaminated site is remediated by natural biodegradation; to evaluate such processes, a combination of chemical and microbiological methods are usually used. Compound specific stable isotope analysis emerged as a key method for detecting and quantifying in situ biodegradation. Natural attenuation processes can be initiated or accelerated by manipulating the environmental conditions to become favorable for indigenous pollutant degrading microbial communities or by adding externally breeded specific pollutant degrading microorganisms; these techniques are referred to as enhanced natural attenuation. Xenobiotic micropollutants, such as pesticides or pharmaceuticals, contaminate diffusively large areas in low concentrations; the biodegradation pattern of such contaminations are not yet understood.

Chemical effectors cause different motile behavior and deposition of bacteria in porous media

We tested the hypothesis whether chemically induced motility patterns of bacteria may affect their transport in porous media. Naphthalene-degrading Pseudomonas putida G7 cells were exposed to glucose, salicylate, and silver nanoparticles (AgNPs) and their motility was assessed by computer-assisted, quantitative swimming and capillary-based taxis determinations. Exposure to salicylate induced smooth movement with few acceleration events and positive taxis, whereas cells exposed to AgNPs exhibited tortuous movement and a repellent response. Although metabolized by strain G7, glucose did not cause attraction and induced a hyper-motile mode of swimming, characterized by a high frequency of acceleration events, high swimming speed (>60 μm s(-1)), and a high tortuosity in the trajectories. Chemically induced motility behavior correlated with distinct modes of attachment to sand in batch assays and breakthrough curves in percolation column experiments. Salicylate significantly reduced deposition of G7 cells in column experiments whereas glucose and AgNPs enhanced attachment and caused filter blocking that resulted in a progressive decrease in deposition. These findings are relevant for bioremediation scenarios that require an optimized outreach of introduced inoculants and in other environmental technologies, such as water disinfection and microbially enhanced oil recovery.

Transverse chemotactic migration of bacteria from high to low permeability regions in a dual permeability microfluidic device

Low permeability regions such as clay lenses are difficult to remediate using conventional treatment methods. Bacterial chemotaxis (directed migration toward a contaminant source) may be helpful in enhancing bioremediation of such contaminated sites. This study experimentally simulates a two-dimensional dual-permeability groundwater contamination scenario using a microfluidic device (MFD) and evaluates transverse chemotactic migration of bacteria from high to low permeability regions under various flow velocities. Chemotaxis of Escherichia coli (E. coli) HCB33 to the chemoattractant dl-aspartic acid was quantified in terms of change in total bacterial counts in pore throats in low permeability regions containing attractant. An increase in total bacterial counts, ranging from 1.09 to 1.74 times, was observed in low permeability regions in experiments under chemotactic conditions. Experiments with no attractant showed no increase in total bacterial counts in low permeability regions. A large increase in bacterial counts in the pore throats just outside the low permeability region was also observed in chemotaxis experiments. The bacterial chemotactic response was observed to decrease linearly with increase in flow velocity, with no observed response at the highest flow velocity (Darcy velocity = 0.22 mm/s), where chemotaxis was offset by advective flow.

Evaluation of a laboratory-scale bioreactive in situ sediment cap for the treatment of organic contaminants

The development of bioreactive sediment caps, in which microorganisms capable of contaminant transformation are placed within an in situ cap, provides a potential remedial design that can sustainably treat sediment and groundwater contaminants. The goal of this study was to evaluate the ability and limitations of a mixed, anaerobic dechlorinating consortium to treat chlorinated ethenes within a sand-based cap. Results of batch experiments demonstrate that a tetrachloroethene (PCE)-to-ethene mixed consortium was able to completely dechlorinate dissolved-phase PCE to ethene when supplied only with sediment porewater obtained from a sediment column. To simulate a bioreactive cap, laboratory-scale sand columns inoculated with the mixed culture were placed in series with an upflow sediment column and directly supplied sediment effluent and dissolved-phase chlorinated ethenes. The mixed consortium was not able to sustain dechlorination activity at a retention time of 0.5 days without delivery of amendments to the sediment effluent, evidenced by the loss of cis-1,2-dichloroethene (cis-DCE) dechlorination to vinyl chloride. When soluble electron donor was supplied to the sediment effluent, complete dechlorination of cis-DCE to ethene was observed at retention times of 0.5 days, suggesting that sediment effluent lacked sufficient electron donor to maintain active dechlorination within the sediment cap. Introduction of elevated contaminant concentrations also limited biotransformation performance of the dechlorinating consortium within the cap. These findings indicate that in situ bioreactive capping can be a feasible remedial approach, provided that residence times are adequate and that appropriate levels of electron donor and contaminant exist within the cap.

Idling time of motile bacteria contributes to retardation and dispersion in sand porous medium

The motility of microorganisms affects their transport in natural systems by altering their interactions with the solid phase of the soil matrix. To assess the effect of these interactions on transport parameters, a series of breakthrough curves (BTCs) for motile and nonmotile bacteria, including E. coli and P. putida species, were measured from a homogeneously packed sand column under three different interstitial velocities of 1 m/d, 5 m/d, and 10 m/d. BTCs for the nonmotile bacteria were nearly identical for all three flow rates, except that the recovery percentage at 1 m/d was reduced by 5% compared to the higher flow rates. In contrast, for the motile bacteria, the recovery percentages were not affected by flow rate, but their BTCs exhibited a higher degree of retardation and dispersion as the flow velocity decreased, which was consistent with increased idling times of the motile strains. The smooth-swimming mutant E. coli HCB437, which is unable to change its swimming direction after encountering the solid surfaces and thus has the largest idling time, also exhibited the greatest degree of retardation and dispersion. All of the experimental observations were compared to results from an advection-dispersion transport model with three fitting parameters: retardation factor (R), longitudinal dispersivity (α(L)), and attachment rate coefficient (k(att)). In addition, the single-collector efficiency (η₀) and collision efficiency (α) were calculated according to the colloid filtration theory (CFT), and confirmed that motile bacteria had lower collision efficiencies than nonmotile bacteria. This is consistent with previously reported observations that motile bacteria can avoid attachment to a solid surface by their active swimming capabilities. By quantifying the effect of bacterial motility on various transport parameters, more robust fate and transport models can be developed for decision-making related to environmental remediation strategies and risk assessment.