Response and recovery of a pristine groundwater ecosystem impacted by toluene contamination - A meso-scale indoor aquifer experiment

Co-migration behavior of toluene coupled with trichloroethylene and the response of the pristine groundwater ecosystems - A mesoscale indoor experiment

Experimental scale and sampling precision are the main factors limiting the accuracy of migration and transformation assessments of complex petroleum-based contaminants in groundwater. In this study, a mesoscale indoor aquifer device with high environmental fidelity and monitoring accuracy was constructed, in which dissolved toluene and trichloroethylene were used as typical contaminants in a 1.5-year contaminant migration experiment. The process was divided into five stages, namely, pristine, injection, accumulation, decrease, and recovery, and characteristics such as differences in contaminant migration, the responsiveness of environmental factors, and changes in microbial communities were investigated. The results demonstrated that the mutual dissolution properties of the contaminants increased the spread of the plume and confirmed that toluene possessed greater mobility and natural attenuation than trichloroethylene. Attenuation of the contaminant plume proceeded through aerobic degradation, nitrate reduction, and sulfate reduction phases, accompanied by negative feedback from characteristic ion concentrations, dissolved oxygen content, the oxidation-reduction potential and microbial community structure of the groundwater. This research evaluated the migration and transformation characteristics of typical petroleum-based pollutants, revealed the response mechanism of the ecosystem to pollutant, provided a theoretical basis for predicting pollutant migration and formulating control strategies.

Machine Learning Modeling Based on Microbial Community for Prediction of Natural Attenuation in Groundwater

Natural attenuation is widely adopted as a remediation strategy, and the attenuation potential is crucial to evaluate whether remediation goals can be achieved within the specified time. In this work, long-term monitoring of indigenous microbial communities as well as benzene, toluene, ethylbenzene, and xylene (BTEX) and chlorinated aliphatic hydrocarbons (CAHs) in groundwater was conducted at a historic pesticide manufacturing site. A machine learning approach for natural attenuation prediction was developed with random forest classification (RFC) followed by either random forest regression (RFR) or artificial neural networks (ANNs), utilizing microbiological information and contaminant attenuation rates for model training and cross-validation. Results showed that the RFC could accurately predict the feasibility of natural attenuation for both BTEX and CAHs, and it could successfully identify the key genera. The RFR model was sufficient for the BTEX natural attenuation rate prediction but unreliable for CAHs. The ANN model showed better performance in the prediction of the attenuation rates for both BTEX and CAHs. Based on the assessments, a composite modeling method of RFC and ANN was proposed, which could reduce the mean absolute percentage errors. This study reveals that the combined machine learning approach under the synergistic use of field microbial data has promising potential for predicting natural attenuation.

Microbial assembly and co-occurrence network in an aquifer under press perturbation

Purpose

Thousands of aquifers worldwide have been polluted by leachate from landfills and many more remained threatened. Microbial communities from these environments play a crucial role in mediating biodegradation and maintaining the biogeochemical cycles, but their co-occurrence and assembly mechanism have not been investigated.

Method

Here, we coupled network analysis with multivariate statistics to assess the relative importance of deterministic versus stochastic microbial assembly in an aquifer undergoing intrinsic remediation, using 16S metabarcoding data generated through Illumina MiSeq sequencing of the archaeal/bacterial V3–V4 hypervariable region.

Results

Results show that both the aquifer-wide and localised community co-occurrences deviate from expectations under null models, indicating the predominance of deterministic processes in shaping the microbial communities. Further, the amount of variation in the microbial community explained by the measured environmental variables was 55.3%, which illustrates the importance of causal factors in forming the structure of microbial communities in the aquifer. Based on the network topology, several putative keystone taxa were identified which varied remarkably among the wells in terms of their number and composition. They included Nitrospira, Nitrosomonadaceae, Patulibacter, Legionella, uncharacterised Chloroflexi, Vicinamibacteriales, Neisseriaceae, Gemmatimonadaceae, and Steroidobacteraceae. The putative keystone taxa may be providing crucial functions in the aquifer ranging from nitrogen cycling by Nitrospira, Nitrosomonadaceae, and Steroidobacteraceae, to phosphorous bioaccumulation by Gemmatimonadaceae.

Conclusion

Collectively, the findings provide answers to fundamental ecological questions which improve our understanding of the microbial ecology of landfill leachate plumes, an ecosystem that remains understudied.

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

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

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.

Influence of stormwater infiltration systems on the structure and the activities of groundwater biofilms: Are the effects restricted to rainy periods?

Stormwater infiltration systems (SIS) have been set up to collect and infiltrate urban stormwater runoff in order to reduce flooding and to artificially recharge aquifers. Such practices produce environmental changes in shallow groundwater ecosystems like an increase in organic matter concentrations that could drive changes in structure and functions of groundwater microbial communities. Previous works suggested that SIS influence groundwater physico-chemistry during either rainy and dry period but no study has examined the impact of SIS on groundwater microorganisms during both periods. This study aimed to fill this gap by assessing SIS impacts on groundwater quality parameters in three SIS with vadose zone thickness < 3 m during two contrasting meteorological conditions (rainy/dry periods). Physicochemical (dissolved organic carbon and nutrient concentrations) and microbial variables (biomass, dehydrogenase and hydrolytic activities, and bacterial community structure) were assessed on SIS-impacted and non-SIS-impacted zones of the aquifers for the three SIS. Using clay beads incubated in the aquifer to collect microbial biofilm, we show that SIS increased microbial activities, bacterial richness and diversity in groundwater biofilms during the rainy period but not during the dry period. In contrast, the significant differences in dissolved organic carbon and nutrient concentrations, biofilm biomass and bacterial community structures (Bray-Curtis distances, relative abundances of main bacterial orders) measured between SIS-impacted and non-SIS-impacted zones of the aquifer were comparable during the two periods. These results suggest that structural indicators of biofilm like biomass were probably controlled by long-term effects of SIS on concentrations of dissolved organic matter and nutrients whereas biofilm activities and bacterial richness were temporally stimulated by stormwater runoff infiltrations during the rainy period. This decoupling between the structural and functional responses of groundwater biofilms to stormwater infiltration practices suggests that biofilms functions were highly reactive to fluxes associated with aquifer recharge events.

Long-term redox conditions in a landfill-leachate-contaminated groundwater

Indicators of redox conditions; oxygen, sulphate, nitrate, ammonium, iron and manganese, and in addition, bicarbonate and total organic carbon were studied in groundwater samples contaminated by leachate emanating from Revdalen Landfill (Norway). Based on these variables, the study aimed to deduce the redox conditions in the aquifer. Literature on landfill leachate contamination of confined aquifers is scarce and to the best of our knowledge, this study, which describes long-term analysis of redox chemistry, is the first of its kind in such an environment. Groundwater samples were monitored for a period of 24 years, enabling us to describe redox conditions on both short-term and long-term bases. Levels of measured parameters in the contaminated aquifer varied spatially and with time, but were generally elevated except oxygen; pH (4.9-8.8), oxygen (0-11.3 mg/L), sulphate (0-28 mg/L), nitrate (0-16 mg N/L), ammonium (0.02-40 mg/L), iron (0-99 mg/L), manganese (0.06-16 mg/L), bicarbonate (22-616 mg/L) and total organic carbon (1.3-47 mg/L). From the result, levels of iron, manganese, nitrate and ammonium violated the Norwegian drinking water norms. However, iron, ammonium, total organic carbon and bicarbonate showed strong attenuation along the groundwater flow path. By contrast, oxygen, nitrate and sulphate increased farther out in the plume. The redox conditions that developed in the aquifer were similar to those previously reported for phreatic aquifers, structuring by proximity to the landfill as sulphate-reducing, iron-reducing, manganese-reducing, nitrate-reducing, and finally aerobic condition. Eventually, there was an apparent breakdown of this system due to ecosystem shift in the landfill when leachable reduced ions were depleted and the landfill became aerobic. Overall, the redox framework provided remarkable attenuation to contaminants, and thus prevented potential degradation of ecological health due to the landfill leachate.

Aquifer recharge viewed through the lens of microbial community ecology: Initial disturbance response, and impacts of species sorting versus mass effects on microbial community assembly in groundwater during riverbank filtration

Riverbank filtration has gained increasing importance for balancing rising groundwater demands and securing drinking water supplies. While microbial communities are the pillar of vital ecosystem functions in groundwater, the impact of riverbank filtration on these communities has been understudied so far. Here, we followed changes in microbial community composition based on 16S rRNA gene amplicon sequence variants (ASVs) in an initially pristine shallow porous aquifer in response to surface water intrusion during the early stages of induced riverbank filtration over a course of seven weeks. We further analyzed sediment cores for imprints of river-derived ASVs after seven weeks of riverbank filtration. The onset of the surface water intrusion caused loss of taxa and significant changes in community composition, revealing low disturbance resistance of the initial aquifer microbial communities. SourceTracker analysis revealed that proportions of river-derived ASVs in the groundwater were generally <25%, but locally could reach up to 62% during a period of intense precipitation. However, variation partitioning showed that the impact of dispersal of river-derived ASVs on changes in aquifer microbial community composition was overall outweighed by species sorting due to changes in environmental conditions caused by the infiltrating river water. Proportions of river-derived ASVs on aquifer sediments were <0.5%, showing that taxa transported from the river into the aquifer over the course of the study mainly resided as planktonic microorganisms in the groundwater. Our study demonstrates that groundwater microbial communities react sensitively to changes in environmental conditions caused by surface water intrusion, whereas mass effects resulting from the influx of river-derived taxa play a comparatively minor role.

Linkage Between Dissolved Organic Matter Transformation, Bacterial Carbon Production, and Diversity in a Shallow Oligotrophic Aquifer: Results From Flow-Through Sediment Microcosm Experiments

Aquifers are important reservoirs for organic carbon. A fundamental understanding of the role of groundwater ecosystems in carbon cycling, however, is still missing. Using sediment flow-through microcosms, long-term (171d) experiments were conducted to test two scenarios. First, aquifer sediment microbial communities received dissolved organic matter (DOM) at low concentration and typical to groundwater in terms of composition (DOM-1x). Second, sediments received an elevated concentration of DOM originating from soil (DOM-5x). Changes in DOM composition were analyzed via NMR and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Carbon production, physiological adaptations and biodiversity of groundwater, and sediment prokaryotic communities were monitored by total cell counts, substrate use arrays, and deep amplicon sequencing. The experiments showed that groundwater microbial communities do not react very fast to the sudden availability of labile organic carbon from soil in terms of carbon degradation and biomass production. It took days to weeks for incoming DOM being efficiently degraded and pronounced cell production occurred. Once conditioned, the DOM-1x supplied sediments mineralized 294(±230) μgC L⁻¹_sed d⁻¹, 10-times less than the DOM-5x fed sediment communities [2.9(±1.1) mgC L⁻¹_sed d⁻¹]. However, the overall biomass carbon production was hardly different in the two treatments with 13.7(±4.8) μgC L⁻¹_sed d⁻¹ and 14.3(±3.5) μgC L⁻¹_sed d⁻¹, respectively, hinting at a significantly lower carbon use efficiency with higher DOM availability. However, the molecularly more diverse DOM from soil fostered a higher bacterial diversity. Taking the irregular inputs of labile DOM into account, shallow aquifers are assumed to have a low resilience. Lacking a highly active and responsive microbial community, oligotrophic aquifers are at high risk of contamination with organic chemicals.

The D-A-(C) index: A practical approach towards the microbiological-ecological monitoring of groundwater ecosystems

Groundwater is not only a vital resource, but also one of the largest terrestrial aquatic ecosystems on Earth. However, to date, ecological criteria are often not considered in routine groundwater monitoring, mainly because of the lack of suitable ecological assessment tools. Prokaryotic microorganisms are ubiquitous in groundwater ecosystems even under the harshest conditions, making them ideal bioindicators for ecological monitoring. We have developed a simple, inexpensive approach that enables ecological groundwater monitoring based on three microbiological parameters that can be easily integrated into existing routine monitoring practices: prokaryotic cell density (D) measured by flow cytometry; activity (A) measured as prokaryotic intracellular ATP concentrations using a simple cell-lysis-luminescence assay; and, as an optional parameter, the bioavailable carbon (C) measured as the concentration of assimilable organic carbon in a simple batch growth assay. We analyzed data for three case studies of different disturbances representing some of the main threats to groundwater ecosystems, i.e. organic contamination with hydrocarbons, surface water intrusion, and agricultural land use. For all three disturbances, disturbed samples could be reliably distinguished from undisturbed samples based on a single index value obtained from multivariate outlier analyses of the microbial variables. We could show that this multivariate approach allowed for a significantly more sensitive and reliable detection of disturbed samples compared to separate univariate outlier analyses of the measured variables. Furthermore, a comparison of non-contaminated aquifers from nine different regions across Germany revealed distinct multivariate signatures along the three microbial variables, which should be considered when applying our approach in practice. In essence, our approach offers a practical tool for the detection of disturbances of groundwater ecosystems based on microbial parameters which can be seamlessly extended in the future by additional parameters for higher sensitivity as well as flexibility.

Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale

The southern Gulf of Mexico (sGoM) is highly susceptible to receiving environmental impacts due to the recent increase in oil-related activities. In this study, we assessed the changes in the bacterioplankton community structure caused by a simulated oil spill at mesocosms scale. The 16S rRNA gene sequencing analysis indicated that the initial bacterial community was mainly represented by Gamma-proteobacteria, Alpha-proteobacteria, Flavobacteriia, and Cyanobacteria. The hydrocarbon degradation activity, measured as the number of culturable hydrocarbonoclastic bacteria (CHB) and by the copy number of the alkB gene, was relatively low at the beginning of the experiment. However, after four days, the hydrocarbonoclastic activity reached its maximum values and was accompanied by increases in the relative abundance of the well-known hydrocarbonoclastic Alteromonas. At the end of the experiment, the diversity was restored to similar values as those observed in the initial time, although the community structure and composition were clearly different, where Marivita, Pseudohongiella, and Oleibacter were detected to have differential abundances on days eight–14. These changes were related with total nitrogen (p value = 0.030 and r² = 0.22) and polycyclic aromatic hydrocarbons (p value = 0.048 and r² = 0.25), according to PERMANOVA. The results of this study contribute to the understanding of the potential response of the bacterioplankton from sGoM to crude oil spills.

Contaminant concentration versus flow velocity: drivers of biodegradation and microbial growth in groundwater model systems

Aromatic hydrocarbons belong to the most abundant contaminants in groundwater systems. They can serve as carbon and energy source for a multitude of indigenous microorganisms. Predictions of contaminant biodegradation and microbial growth in contaminated aquifers are often vague because the parameters of microbial activity in the mathematical models used for predictions are typically derived from batch experiments, which don’t represent conditions in the field. In order to improve our understanding of key drivers of natural attenuation and the accuracy of predictive models, we conducted comparative experiments in batch and sediment flow-through systems with varying concentrations of contaminant in the inflow and flow velocities applying the aerobic Pseudomonas putida strain F1 and the denitrifying Aromatoleum aromaticum strain EbN1. We followed toluene degradation and bacterial growth by measuring toluene and oxygen concentrations and by direct cell counts. In the sediment columns, the total amount of toluene degraded by P. putida F1 increased with increasing source concentration and flow velocity, while toluene removal efficiency gradually decreased. Results point at mass transfer limitation being an important process controlling toluene biodegradation that cannot be assessed with batch experiments. We also observed a decrease in the maximum specific growth rate with increasing source concentration and flow velocity. At low toluene concentrations, the efficiencies in carbon assimilation within the flow-through systems exceeded those in the batch systems. In all column experiments the number of attached cells plateaued after an initial growth phase indicating a specific “carrying capacity” depending on contaminant concentration and flow velocity. Moreover, in all cases, cells attached to the sediment dominated over those in suspension, and toluene degradation was performed practically by attached cells only. The observed effects of varying contaminant inflow concentration and flow velocity on biodegradation could be captured by a reactive-transport model. By monitoring both attached and suspended cells we could quantify the release of new-grown cells from the sediments to the mobile aqueous phase. Studying flow velocity and contaminant concentrations as key drivers of contaminant transformation in sediment flow-through microcosms improves our system understanding and eventually the prediction of microbial biodegradation at contaminated sites.