Selective pressure on microbial communities in a drinking water aquifer - Geochemical parameters vs. micropollutants

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.

Bioaugmentation has temporary effect on anaerobic pesticide biodegradation in simulated groundwater systems

Groundwater is the most important source for drinking water in The Netherlands. Groundwater quality is threatened by the presence of pesticides, and biodegradation is a natural process that can contribute to pesticide removal. Groundwater conditions are oligotrophic and thus biodegradation can be limited by the presence and development of microbial communities capable of biodegrading pesticides. For that reason, bioremediation technologies such as bioaugmentation (BA) can help to enhance pesticide biodegradation. We studied the effect of BA using enriched mixed inocula in two column bioreactors that simulate groundwater systems at naturally occurring redox conditions (iron and sulfate-reducing conditions). Columns were operated for around 800 days, and two BA inoculations (BA1 and BA2) were conducted in each column. Inocula were enriched from different wastewater treatment plants (WWTPs) under different redox-conditions. We observed a temporary effect of BA1, reaching 100% removal efficiency of the pesticide 2,4-D after 100 days in both columns. In the iron-reducing column, 2,4-D removal was in general higher than under sulfate-reducing conditions demonstrating the influence of redox conditions on overall biodegradation. We observed a temporary shift in microbial communities after BA1 that is relatable to the increase in 2,4-D removal efficiency. After BA2 under sulfate-reducing conditions, 2,4-D removal efficiency decreased, but no change in the column microbial communities was observed. The present study demonstrates that BA with a mixed inoculum can be a valuable technique for improving biodegradation in anoxic groundwater systems at different redox-conditions.

Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes

Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.

Actinomycetota, a central constituent microbe during long-term exposure to diazinon, an organophosphorus insecticide

Microbial biodegradation is a primary pesticide remediation pathway. Despite diazinon is one of the most frequently used organophosphate insecticides worldwide, its effect on soil microbial community remains obscure. We hypothesize that diazinon exposure reshapes microbial community, among them increased microbes may play a crucial role in diazinon degradation. To investigate this, we collected soil from an organic farming environment, introduced diazinon, cultivated it in a greenhouse, and then assessed its effects on soil microbiomes at three distinct time points: 20, 40, and 270 days after treatment (DAT). Results from HPLC showed that the level of diazinon was gradually degraded by 98.8% at 270 DAT when compared with day zero, whereas 16S rRNA gene analysis exhibited a significant reduction in the bacterial diversity, especially at the early two time points, indicating that diazinon may exert selection pressure to the bacteria community. Here, the relative abundance of phylum Actinomycetota increased at 20 and 40 DATs. In addition, the bacterial functional gene profile employing PICRUSt2 prediction also revealed that diazinon exposure induced the genomic function related to xenobiotics biodegradation and metabolism in soil, such as CYB5B, hpaC, acrR, and ppkA. To validate if bacterial function is caused by increased relative abundance in diazinon enriched soil, further bacteria isolation resulted in obtaining 25 diazinon degradation strains out of 103 isolates. Notably, more than 70% (18 out of 25) isolates are identified as phylum Actinomycetota, which empirically confirms and correlates microbiome and PICRUSt2 results. In conclusion, this study provides comprehensive information from microbiome analysis to obtaining several bacteria isolates responsible for diazinon degradation, revealing that the phylum Actinomycetota is as a key taxon that facilitates microbial biodegradation in diazinon spoiled soil. This finding may assist in developing a strategy for microbial detoxification of diazinon, such as using an Actinomycetota rich synthetic community (SynCom).

Influence of redox condition and inoculum on micropollutant biodegradation by soil and activated sludge communities

Micropollutant biodegradation is selected by the interplay among environmental conditions and microbial community composition. This study investigated how different electron acceptors, and different inocula with varying microbial diversity, pre-exposed to distinct redox conditions and micropollutants, affect micropollutant biodegradation. Four tested inocula comprised of agricultural soil (Soil), sediment from a ditch in an agricultural field (Ditch), activated sludge from a municipal WWTP (Mun AS), and activated sludge from an industrial WWTP (Ind AS). Removal of 16 micropollutants was investigated for each inoculum under aerobic, nitrate reducing, iron reducing, sulfate reducing, and methanogenic conditions. Micropollutant biodegradation was highest under aerobic conditions with removal of 12 micropollutants. Most micropollutants were biodegraded by Soil (n = 11) and Mun AS inocula (n = 10). A positive correlation was observed between inoculum community richness and the number of different micropollutants a microbial community initially degraded. The redox conditions to which a microbial community had been exposed appeared to positively affect micropollutant biodegradation performance more than pre-exposure to micropollutants. Additionally, depletion of the organic carbon present in the inocula resulted in lower micropollutant biodegradation and overall microbial activities, suggesting that i) an additional carbon source is needed to promote micropollutant biodegradation; and ii) overall microbial activity can be a good indirect indicator for micropollutant biodegradation activity. These results could help to develop novel micropollutant removal strategies.

Effects of a long-term operation wetland for wastewater treatment on the spatial pattern and function of microbial communities in groundwater

Constructed wetlands have been used globally for wastewater treatment owing to low energy inputs and operating costs. However, the impact of their long-term operation on groundwater microbial communities is still unclear. This study aims to investigate the effects and further reveal the linkage between a large-scale surface flow constructed wetland (in operation for 14 years) and groundwater. Changes in the characteristics of groundwater microbial communities and their potential influencing factors were studied based on hydrochemical analysis, Illumina MiSeq sequencing, and multivariate statistical analysis methods. Results show that the long-term operation wetland significantly elevated groundwater nutrient levels and increased the risk of ammonia nitrogen pollution compared to background values. An apparent heterogeneity of microbial communities exhibited in the vertical direction and a similarity in the horizontal direction. Wetland operations substantially altered the structure of microbial communities at 3, 5, and 12 m depths, particularly a reduced abundance of denitrifying and chemoheterotrophic functional genera. The formation and evolution of groundwater microbial community structure mainly subjected to the contributions of dissolved oxygen (33.70%), total nitrogen (21.40%), dissolved organic carbon (11.09%), and pH (10.60%) variations resulted from the wetland operation and largely differed in depths. A combined effect of these factors on the groundwater should be concerned for such a long-term running wetland system. This study provides a new insight into the responses of groundwater microbial community structure driving by wetland operation and a better understanding of corresponding variation of microbial-based geochemical processes.

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.

Investigating a broad range of emerging contaminants in a set of anthropogenically impacted environmental compartments

Environmental compartments are repositories of probably thousands of emerging contaminants (ECs) released along with treated/untreated wastewater. Despite extensive studies on the detection of ECs in surface water, other environmental compartments such as sediments and groundwater are yet to be thoroughly investigated. To assess the heavy anthropogenic impact on the environment, 24 environmental samples comprising of surface water, sediment and groundwater collected from the Yamuna River basin of India were analyzed via target and suspect screening. The surface water and sediment samples were collected from upstream and downstream of densely populated cities and towns situated along the heavily contaminated river Yamuna. The groundwater samples were collected from shallow drinking water wells of the catchment. Liquid chromatography tandem mass-spectroscopy was used to quantify 10 widely consumed pharmaceuticals in the samples. The study also analyzed the potential health hazards posed by the quantified contaminants. In order to evaluate further, the surface water and groundwater samples were subjected to high resolution mass spectrometry (HRMS) screening against a library resulting in a list of 450 ECs in the surface water and 309 ECs in the groundwater. Agricultural chemicals and pharmaceuticals found abundantly in the samples and half of whom were reported first time. The risk quotient was calculated to assess the potential hazard of the target analytes.