Biostimulation with oxygen and electron donors supports micropollutant biodegradation in an experimentally simulated nitrate-reducing aquifer

The availability of suitable electron donors and acceptors limits micropollutant natural attenuation in oligotrophic groundwater. This study investigated how electron donors with different biodegradability (humics, dextran, acetate, and ammonium), and different oxygen concentrations affect the biodegradation of 15 micropollutants (initial concentration of each micropollutant = 50 μg/L) in simulated nitrate reducing aquifers. Tests mimicking nitrate reducing field conditions showed no micropollutant biodegradation, even with electron donor amendment. However, 2,4-dichlorophenoxyacetic acid and mecoprop were biodegraded under (micro)aerobic conditions with and without electron donor addition. The highest 2,4-dichlorophenoxyacetic acid and mecoprop biodegradation rates and removal efficiencies were obtained under fully aerobic conditions with amendment of an easily biodegradable electron donor. Under microaerobic conditions, however, amendment with easily biodegradable dissolved organic carbon (DOC) inhibited micropollutant biodegradation due to competition between micropollutants and DOC for the limited oxygen available. Microbial community composition was dictated by electron acceptor availability and electron donor amendment, not by micropollutant biodegradation. Low microbial community richness and diversity led to the absence of biodegradation of the other 13 micropollutants (such as bentazon, chloridazon, and carbamazepine). Finally, adaptation and potential growth of biofilms interactively determined the location of the micropollutant removal zone relative to the point of amendment. This study provides new insight on how to stimulate in situ micropollutant biodegradation to remediate oligotrophic groundwaters as well as possible limitations of this process.

Effect of dissolved organic carbon on micropollutant biodegradation by aquifer and soil microbial communities

Groundwater, a major source of drinking water worldwide, is often contaminated with micropollutants. Although microbial communities in aquifers and soils have the capability to biodegrade some micropollutants, this process is limited in situ. Biostimulation with dissolved organic carbon (DOC) is known to promote micropollutant biodegradation, but the role of DOC biodegradability is still poorly understood. This study investigated how three DOC types with different biodegradability (humics, dextran and acetate) affect the biodegradation of 15 micropollutants by aquifer and soil microbial communities under aerobic and nitrate reducing conditions. Although originating from different environments, both communities were able to biodegrade the same 4 micropollutants under aerobic conditions - 2,4-D, MCPP, chloridazon (CLZ) and chloridazon-desphenyl. However, DOC addition only affected MCPP biodegradation, promoting MCPP biodegradation regardless of DOC biodegradability. Biodegradation of 2,4-D, MCPP and CLZ under aerobic conditions was observed after a lag phase, whose duration differed per compound. 2,4-D was biodegraded first and fully. Aquifer community was able to degrade about half of the initial MCPP concentration (removal efficiency of 49.3 ± 11.7%). CLZ was fully biodegraded by the aquifer community, but not by the soil community, possibly due to substrate competition with organics originating from the inoculum. Therefore, the natural organic carbon present in the inocula and in environmental systems can influence micropollutant biodegradation. Under nitrate reducing conditions micropollutant biodegradation was not observed nor biostimulated by DOC addition. The results also highlight the importance of sufficient exposure time to trigger in situ micropollutant biodegradation.

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.

Effect of 4-chloro-2-methylphenoxy acetic acid on tomato gene expression and rhizosphere bacterial communities under inoculation with phosphate-solubilizing bacteria

The herbicide 4-chloro-2-methylphenoxy acetic acid (MCPA) is widely used to control the spread of broad-leaved weeds in agricultural soils, though it remains unclear how tomato plants cope with the phytotoxic effects of MCPA at the molecular level. In this study, RNA-seq and Illumina MiSeq were used to sequence bacterial communities in tomato rhizosphere soils treated with MCPA and the phosphate-solubilizing bacterial strain N3. The results showed that MCPA induced abnormal growth of lateral roots in tomato seedlings and reduced uptake of the nutrients N, P, and K as well as the hormone (ABA and GA3) levels. Inoculation with strain N3 increased nutrient uptake by roots and increased levels of the hormones ABA, ZEA, and JA in tomato seedlings and also increased the abundance of the phyla Proteobacteria and Gemmatimonadetes in soil under MCPA treatment. GO functional groups in which differentially expressed genes (DEGs) are involved included DNA binding transcription factor activity, transcriptional regulator activity, enzyme inhibitor activity, and cell wall biogenesis. The highest numbers of DEGs are annotated to ribosome, photosynthesis, and carbon metabolism categories. Our findings provide valuable information for the application of strain N3, which is beneficial for reducing the toxic effect of MCPA on vegetable plants.

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.

The pesticide mineralization capacity in sand filter units of drinking water treatment plants (DWTP): Consistency in time and relationship with intake water and sand filter characteristics

Sand filters (SFs) are commonly applied in drinking water treatment plants (DWTPs) for removal of iron and manganese but also show potential for microbial degradation of pesticide residues. The latter is advantageous in case the intake water contains pesticide residues. However, whether this involves mineralization suggesting no generation of harmful transformation products, its consistency over time, and how this ability relates to physicochemical and biological characteristics of the DWTP intake water and the SFs is unknown. The capacity to mineralize the herbicides bentazon and 2-methyl-4-chlorophenoxyacetic acid (MCPA) was examined in SF samples from 11 DWTPs differing in operation, intake water composition and pesticide contamination level. MCPA was mineralized in all biologically active SFs while mineralization of bentazon occurred rarely. Mineralization of both compounds was consistent in time and across samples taken from different SF units of the same DWTP. Kinetic modelling of mineralization curves suggested the occurrence of growth linked bentazon and MCPA mineralization in several SF samples. Multivariate analysis correlating intake water/SF characteristics with pesticide mineralization indicated that pesticide mineralization capacity depended on a range of intake water characteristics, but was not necessarily explained by the presence of the pesticide in the intake water and hence the in situ exposure of the SF community to the pesticide. This was supported by testing a sample from DWTP Kluizen for its capacity to mineralize 5 other pesticides including pesticides not present or occasionally present in the intake water. All of those pesticides were mineralized as well.

Methanotrophic contribution to biodegradation of phenoxy acids in cultures enriched from a groundwater-fed rapid sand filter

Drinking water supply is in many parts of the world based on groundwater. Groundwater often contains methane, which can be oxidized by methanotrophs upon aeration. Sand from rapid sand filters fed with methane-rich groundwater can remove some pesticides (Hedegaard and Albrechtsen in Water Res 48:71-81, 2014). We enriched methanotrophs from filter sand and investigated whether they could drive the degradation of various pesticides. To enrich for methanotrophs, we designed and operated four laboratory-scale, continuously methane-fed column reactors, inoculated with filter sand and one control column fed with tap water. When enrichments were obtained, methane was continuously supplied to three reactors, while the fourth was starved for methane for 1 week, and the reactors were spiked with ten pesticides at groundwater-relevant concentrations (2.1-6.6 μg/L). Removal for most pesticides was not detected at the investigated contact time (1.37 min). However, the degradation of phenoxy acids was observed in the methanotrophic column reactor starved for methane, while it was not detected in the control column indicating the importance of methanotrophs. Phenoxy acid removal, using dichlorprop as a model compound, was further investigated in batch experiments with methanotrophic biomass collected from the enrichment reactors. Phenoxy acid removal (expressed per gram of matrix sand) was substantially improved in the methanotrophic enrichment compared to parent filter sand. The presence of methane did not clearly impact dichlorprop removal but did impact mineralization. We suggest that other heterotrophs are responsible for the first step in dichlorprop degradation, while the subsequent steps including ring-hydroxylation are driven by methanotrophs.

Metagenomics: Probing pollutant fate in natural and engineered ecosystems

Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.

Impact of dry-wet and freeze-thaw events on pesticide mineralizing populations and their activity in wetland ecosystems: A microcosm study

Riparian wetlands are proposed to mitigate diffuse pollution of surface water by pesticides in agricultural landscapes. Wetland ecosystems though are highly dynamic environments and seasonal disturbances such as freezing and drying can affect microbial population sizes in the sediment and their functionality including pesticide biodegradation, which has hardly been studied. This study examined the effect of artificially induced dry-wet or freeze-thaw events on the mineralization of the pesticides isoproturon (IPU) and 2-methoxy-4-chlorophenoxy acetic acid (MCPA) in wetland microcosms, either without or with prior enrichment of IPU/MCPA degrading populations. Without prior enrichment, mineralization of IPU and MCPA was significantly reduced after exposure to especially freeze-thaw events, as evidenced by lower mineralization rates and longer lag times compared to non-exposed microcosms. However, herbicide mineralization kinetics correlated poorly with cell numbers of herbicide mineralizers as estimated by a most probable number (MPN) approach and the number of IPU and MCPA mineralizers was unexpectedly higher in freeze-thaw and dry-wet cycle exposed setups compared to the control setups. This suggested that the observed effects of season-bound disturbances were due to other mechanisms than decay of pesticide mineralizers. In addition, in systems in which the growth of pesticide mineralizing bacteria was stimulated by amendment of IPU and MCPA, exposure to a freeze-thaw or dry-wet event only marginally affected the herbicide mineralization kinetics. Our results show that season bound environmental disturbances can affect pesticide mineralization kinetics in wetlands but that this effect can depend on the history of pesticide applications.

Fine scale spatial variability of microbial pesticide degradation in soil: scales, controlling factors, and implications

Pesticide biodegradation is a soil microbial function of critical importance for modern agriculture and its environmental impact. While it was once assumed that this activity was homogeneously distributed at the field scale, mounting evidence indicates that this is rarely the case. Here, we critically examine the literature on spatial variability of pesticide biodegradation in agricultural soil. We discuss the motivations, methods, and main findings of the primary literature. We found significant diversity in the approaches used to describe and quantify spatial heterogeneity, which complicates inter-studies comparisons. However, it is clear that the presence and activity of pesticide degraders is often highly spatially variable with coefficients of variation often exceeding 50% and frequently displays non-random spatial patterns. A few controlling factors have tentatively been identified across pesticide classes: they include some soil characteristics (pH) and some agricultural management practices (pesticide application, tillage), while other potential controlling factors have more conflicting effects depending on the site or the pesticide. Evidence demonstrating the importance of spatial heterogeneity on the fate of pesticides in soil has been difficult to obtain but modeling and experimental systems that do not include soil's full complexity reveal that this heterogeneity must be considered to improve prediction of pesticide biodegradation rates or of leaching risks. Overall, studying the spatial heterogeneity of pesticide biodegradation is a relatively new field at the interface of agronomy, microbial ecology, and geosciences and a wealth of novel data is being collected from these different disciplinary perspectives. We make suggestions on possible avenues to take full advantage of these investigations for a better understanding and prediction of the fate of pesticides in soil.

The gompertz function can coherently describe microbial mineralization of growth-sustaining pesticides

Mineralization of (14)C-labeled tracers is a common way of studying the environmental fate of xenobiotics, but it can be difficult to extract relevant kinetic parameters from such experiments since complex kinetic functions or several kinetic functions may be needed to adequately describe large data sets. In this study, we suggest using a two-parameter, sigmoid Gompertz function for parametrizing mineralization curves. The function was applied to a data set of 252 normalized mineralization curves that represented the potential for degradation of the herbicide MCPA in three horizons of an agricultural soil. The Gompertz function fitted most of the normalized curves, and trends in the data set could be visualized by a scatter plot of the two Gompertz parameters (rate constant and time delay). For agricultural topsoil, we also tested the effect of the MCPA concentration on the mineralization kinetics. Reduced initial concentrations lead to shortened lag-phases, probably due to reduced need for bacterial growth. The effect of substrate concentration could be predicted by simply changing the time delay of the Gompertz curves. This delay could to some extent also simulate concentration effects for 2,4-D mineralization in agricultural soil and aquifer sediment and 2,6-dichlorobenzamide mineralization in single-species, mineral medium.

Discharge of landfill leachate to streambed sediments impacts the mineralization potential of phenoxy acid herbicides depending on the initial abundance of tfdA gene classes

To understand the role of abundance of tfdA gene classes belonging to β- and γ-proteobacteria on phenoxy acid herbicide degradation, streambed sediments were sampled around three seepage meters (SMs) installed in a landfill-impacted groundwater-surface water interface. Highest herbicide mass discharge to SM3, and lower herbicide mass discharges to SM1 and SM2 were determined due to groundwater discharge rates and herbicide concentrations. SM1-sediment with the lowest abundance of tfdA gene classes had the slowest mineralization, whereas SM2- and SM3-sediments with more abundant tfdA genes had faster mineralization. The observed difference in mineralization rates between discharge zones was simulated by a Monod-based kinetic model, which confirmed the role of abundance of tfdA gene classes. This study suggests presence of specific degraders adapted to slow growth rate and high yield strategy due to long-term herbicide exposure; and thus groundwater-surface water interface could act as a natural biological filter and protect stream water quality.