Microbial atrazine breakdown in a karst groundwater system and its effect on ecosystem energetics

Microbial hydrolysis of atrazine in contaminated groundwater

Degradation of the widespread herbicide atrazine has been intensively studied in soils, while its degradation in groundwater has received less attention. This work studied atrazine degradation in contaminated groundwater adjacent to its production plant. The degradation potential was first explored in groundwater enrichment cultures. A broad potential for microbial atrazine degradation was observed when atrazine served as the sole nitrogen source, even when incubated with nitrate. Hydroxyatrazine was formed by the cultures, while desethylatrazine and desisopropylatrazine were not detected. Both the atzA and the trzN genes were identified by quantitative PCR analysis, with a clear dominance of atzA. Carbon isotope enrichments throughout the degradation process varied between the different cultures, with ε values ranging from -0.6 to -5.5‰. This implies corresponding uncertainties when using compound-specific isotope analysis to estimate degradation extents. In the field samples, in-situ degradation was reflected by a high percentage of metabolites, with hydroxyatrazine accounting for >95% of the metabolites in most wells. Both atzA and trzN were detected in the groundwater at quantities of ≈10² to 10⁶ copies mL^-1, with a dominance of atzA over trzN. These results provide evidence of the high potential for atrazine hydrolysis in the contaminated groundwater.

Reactive transport of micropollutants in laboratory aquifers undergoing transient exposure periods

Groundwater quality is of increasing concern due to the ubiquitous occurrence of micropollutant mixtures. Stream-groundwater interactions near agricultural and urban areas represent an important entry pathway of micropollutants into shallow aquifers. Here, we evaluated the biotransformation of a micropollutant mixture (i.e., caffeine, metformin, atrazine, terbutryn, S-metolachlor and metalaxyl) during lateral stream water flow to adjacent groundwater. We used an integrative approach combining concentrations and transformation products (TPs) of the micropollutants, compound-specific isotope analysis (δ¹³C and δ¹⁵N), sequencing of 16S rRNA gene amplicons and reactive transport modeling. Duplicate laboratory aquifers (160 cm × 80 cm × 7 cm) were fed with stream water and subjected over 140 d to three successive periods of micropollutant exposures as pulse-like (6000 μg L^-1) and constant (600 μg L^-1) injections under steady-state conditions. Atrazine, terbutryn, S-metolachlor and metalaxyl persisted in both aquifers during all periods (<10 % attenuation). Metformin attenuation (up to 14 %) was only observed from 90 d onwards, suggesting enhanced degradation over time. In contrast, caffeine dissipated during all injection periods (>90 %), agreeing with fast degradation rates (t_1/2 < 3 d) in parallel microcosm experiments and detection of TPs (theobromine and xanthine). Significant stable carbon isotope fractionation (Δδ¹³C ≥ 6.6 ‰) was observed for caffeine in both aquifers, whereas no enrichment in ¹⁵N occurred. A concentration dependence of caffeine biotransformation in the aquifers was further suggested by model simulations following Michaelis-Menten kinetics. Changes in bacterial community composition reflected long-term bacterial adaptation to micropollutant exposures. Altogether, the use of an integrative approach can help to understand the interplay of subsurface hydrochemistry, bacterial adaptations and micropollutants biotransformation during stream-groundwater interactions.

Seasonal variations of microbial community structure, assembly processes, and influencing factors in karst river

The physicochemical properties and microbial communities have significant annual and seasonal changes in karst aquifers. To explore the changes of microbial community and their relationships with environmental factors, water samples were collected from a typical karst river. Microbial communities in winter (Jan-2017 and Jan-2019) were stable with high similarity in spite of the 2 years sampling interval, but the microbial communities in Aug-2017 was different from that in Aug-2018. In four sampling times, there were 275 shared genera, whose average relative abundance ranging from 89.04 to 96.27%. The winter and summer specific genera were mainly from the recharge of tributary site K6 and discharge of waste water treatment plant (K2 and K3), respectively. The deterministic processes had a more significant effect on the microbial community assembly in winter than that in summer, which was affected by environmental pressure from pollution. Furthermore, antibiotics and inorganic nitrogen pollution affected element cycles of nitrogen and sulfur indirectly through microbial ecological modules in karst river, and the denitrification and desulfurization processes were potentially inhibited. These findings contributed to understand the changes and its assembly mechanism of microbial community, as well as the feedback to environment in polluted karst river.

Side Effects of Pesticides and Metabolites in Groundwater: Impact on Denitrification

The impact of two pesticides (S-metolachlor and propiconazole) and their respective main metabolites (ESA-metolachlor and 1,2,4-triazole) on bacterial denitrification in groundwater was studied. For this, the denitrification activity and the bacterial diversity of a microbial community sampled from a nitrate-contaminated groundwater were monitored during 20 days in lab experiments in the presence or absence of pesticides or metabolites at 2 or 10 μg/L. The kinetics of nitrate reduction along with nitrite and N₂O production all suggested that S-metolachlor had no or only little impact, whereas its metabolite ESA-metolachlor inhibited denitrification by 65% at 10 μg/L. Propiconazole and 1,2,4-triazole also inhibited denitrification at both concentrations, but to a lesser extent (29–38%) than ESA-metolachlor. When inhibition occurred, pesticides affected the reduction of nitrate into nitrite step. However, no significant differences were detected on the abundance of nitrate reductase narG and napA genes, suggesting an impact of pesticides/metabolites at the protein level rather than on denitrifying bacteria abundance. 16S rRNA gene Illumina sequencing indicated no major modification of bacterial diversity in the presence or absence of pesticides/metabolites, except for ESA-metolachlor and propiconazole at 10 μg/L that tended to increase or decrease Shannon and InvSimpson indices, respectively. General growth parameters suggested no impact of pesticides, except for propiconazole at 10 μg/L that partially inhibited acetate uptake and induced a decrease in microbial biomass. In conclusion, pesticides and metabolites can have side effects at environmental concentrations on microbial denitrification in groundwater and may thus affect ecosystem services based on microbial activities.

Cave Drip Water-Related Samples as a Natural Environment for Aromatic Hydrocarbon-Degrading Bacteria

Restricted contact with the external environment has allowed the development of microbial communities adapted to the oligotrophy of caves. However, nutrients can be transported to caves by drip water and affect the microbial communities inside the cave. To evaluate the influence of aromatic compounds carried by drip water on the microbial community, two limestone caves were selected in Brazil. Drip-water-saturated and unsaturated sediment, and dripping water itself, were collected from each cave and bacterial 16S rDNA amplicon sequencing and denaturing gradient gel electrophoresis (DGGE) of naphthalene dioxygenase (ndo) genes were performed. Energy-dispersive X-ray spectroscopy (EDX) and atomic absorption spectroscopy (AAS) were performed to evaluate inorganic nutrients, and GC was performed to estimate aromatic compounds in the samples. The high frequency of Sphingomonadaceae in drip water samples indicates the presence of aromatic hydrocarbon-degrading bacteria. This finding was consistent with the detection of naphthalene and acenaphthene and the presence of ndo genes in drip-water-related samples. The aromatic compounds, aromatic hydrocarbon-degrading bacteria and 16S rDNA sequencing indicate that aromatic compounds may be one of the sources of energy and carbon to the system and the drip-water-associated bacterial community contains several potentially aromatic hydrocarbon-degrading bacteria. To the best of our knowledge, this is the first work to present compelling evidence for the presence of aromatic hydrocarbon-degrading bacteria in cave drip water.

High Microbial Diversity Despite Extremely Low Biomass in a Deep Karst Aquifer

Despite the importance of karst aquifers as a source of drinking water, little is known about the role of microorganisms in maintaining the quality of this water. One of the limitations in exploring the microbiology of these environments is access, which is usually limited to wells and surface springs. In this study, we compared the microbiology of the Madison karst aquifer sampled via the potentiometric lakes of Wind Cave with surface sampling wells and a spring. Our data indicated that only the Streeter Well (STR), which is drilled into the same hydrogeologic domain as the Wind Cave Lakes (WCL), allowed access to water with the same low biomass (1.56-9.25 × 10³ cells mL^-1). Filtration of ∼300 L of water from both of these sites through a 0.2 μm filter allowed the collection of sufficient cells for DNA extraction, PCR amplification of 16S rRNA gene sequences, and identification through pyrosequencing. The results indicated that bacteria (with limited archaea and no detectable eukaryotic organisms) dominated both water samples; however, there were significant taxonomic differences in the bacterial populations of the samples. The STR sample was dominated by a single phylotype within the Gammaproteobacteria (Order Acidithiobacillales), which dramatically reduced the overall diversity and species richness of the population. In WCL, despite less organic carbon, the bacterial population was significantly more diverse, including significant contributions from the Gammaproteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Planctomycetes, Fusobacter, and Omnitrophica phyla. Comparisons with similar oligotrophic environments suggest that karst aquifers have a greater species richness than comparable surface environs. These data also demonstrate that Wind Cave provides a unique opportunity to sample a deep, subterranean aquifer directly, and that the microbiology of such aquifers may be more complex than previously anticipated.

Atrazine Transport through a Soil-Epikarst System

Row crop and livestock production contaminate soils and groundwater of the karst aquifers within south-central Kentucky's Pennyroyal Plateau. Transport of atrazine from field application to the epikarstic drainage system beneath a field with active row-crop farming was investigated. The Crumps Cave study site is a shallow autogenic drainage system with a recharge area of ∼1 ha that contains two epikarst drains (WF-1 and WF-2) which were monitored for atrazine, deethylatrazine (DEA), and deisopropylatrazine (DIA) concentrations from January 2011 to May 2012. Atrazine concentrations in both drains did not increase above winter background levels for nearly 2 mo after application when levels suddenly spiked and reached peak concentrations for the study during an event in May 2011. Atrazine, DEA, and DIA were detected in 100% of samples, and metabolites accounted for 54 to 94% of the monthly total loads, except in May 2011. Median dealkylated metabolite/atrazine ratios (DMAR) were ∼5:1 at both sites, and seasonal DMAR patterns corresponded with changes in soil temperature. These data support the hypothesis that a combination of sorption and degradation in the soil column above the epikarst controlled the transport of atrazine and its metabolites. This resulted in delayed atrazine transport after application and prolonged transport of atrazine and its weakly sorbed metabolites to the epikarst aquifer. Management practices that reduce herbicide inputs, such as diverse crop rotations, cover crops, and use of low-rate and strong-sorbing herbicides, would improve groundwater quality in areas of the Corn Belt with intensive row cropping on karst topography.

Hydrogeological characteristics influencing the occurrence of pesticides and pesticide metabolites in groundwater across the Republic of Ireland

Pesticide contamination of water is a potential environmental issue which may impact the quality of drinking water. The full extent of pesticide contamination is not fully understood due to complex fate pathways in the subsurface. Groundwater pesticide occurrence was investigated at seven agricultural sites in different hydrogeological settings to identify where pesticide occurrence dominated in temperate maritime climatic conditions. In Ireland, six cereal dominated sites in the South East and one grassland site in the West were investigated. Soil and subsoils varied from acid brown earths with high permeability to clay and silt rich tills with lower permeability. Over a 2year monitoring period, 730 samples were collected from a network of dedicated wells and springs across the seven sites. Multi-nested piezometers were installed in intergranular, fissured and karstic type aquifers to target shallow, transition and deeper groundwaters. Several springs were also sampled and the network included a confined aquifer. Groundwater was analysed for nine pesticide active ingredients and eight metabolites. Mecoprop and 2,4-D were the most frequently detected active ingredients above the instrument detection limit, accounting for 36% and 26% of the 730 samples collected and analysed. Phenoxyacetic acid was the most frequently detected and widespread metabolite found in 39% of samples collected at all seven sites. Where the European Union drinking water standard of 0.1μg/L was exceeded, metabolites accounted for the majority of exceedances with 3,5-dichlorobenzoic acid (DBA) and phenoxyacetic acid (PAC) dominating. Highest detections were encountered in sites with well drained soils underlain by gravel and limestone aquifers and within gravel lenses in lower permeability subsoil. Across the seven sites pesticide detections were mostly associated with metabolites and the environmental impact of many of these is unknown as they have received little attention in groundwater previously.

Effect of pesticides and metabolites on groundwater bacterial community

We assessed the effect of pesticides, especially commonly detected herbicides, on bacterial communities in groundwater. To this end, we used a combined approach with i) triazine-spiked experiments at environmentally relevant concentrations (1 and 10μg/L) in waters with contrasting contamination histories, and ii) in situ monitoring in a rural aquifer, where many additional biotic and abiotic parameters also affect the community. Microbial community was characterized by fingerprinting techniques (CE-SSCP), gene presence (atzA/B/C/D/E/F and amoA genes) and abundance (16S RNA, napA and narG genes). During triazine-spiked experiments, the bacterial community structure in reference water was modified following an exposure to atrazine (ATZ) and/or its metabolite desethylatrazine (DEA) at 1μg/L; in historically-contaminated water, the bacterial community structure was modified following an exposure to 10μg/L ATZ/DEA. Similarly, biodiversity indices and biomass in the reference water appeared affected at lower triazine concentrations than in the historically-contaminated water, though these end-points are less sensitive than the community structure. Our results thus suggest that the history of contamination induced a community tolerance to the tested triazines. ATZ and DEA were not degraded during the experiment and this was consistent with the absence of atz genes involved in their degradation in none of the tested conditions. In field monitoring, triazines that represent a historical and diffuse contamination of groundwater, participate in the microbial community structure, confirming the triazine effect observed under laboratory conditions. Other herbicides, such as chloroacetanilides that are applied today, did not appear to affect the whole community structure; they however induced a slight, but significant, increase in the abundance of nitrate-reducing bacteria. To our best knowledge, this is the first study on the microbial ecotoxicology of pesticides and their metabolites at environmentally relevant concentrations in groundwater.

Nitrate and ammonia as nitrogen sources for deep subsurface microorganisms

We investigated the N-utilizing bacterial community in anoxic brackish groundwater of the low and intermediate level nuclear waste repository cave in Olkiluoto, Finland, at 100 m depth using ¹⁵N-based stable isotope probing (SIP) and enrichment with ^14∕15N-ammonium or ^14∕15N-nitrate complemented with methane. Twenty-eight days of incubation at 12°C increased the concentration of bacterial 16S rRNA and nitrate reductase (narG) gene copies in the substrate amended microcosms simultaneously with a radical drop in the overall bacterial diversity and OTU richness. Hydrogenophaga/Malikia were enriched in all substrate amended microcosms and Methylobacter in the ammonium and ammonium+methane supplemented microcosms. Sulfuricurvum was especially abundant in the nitrate+methane treatment and the unamended incubation control. Membrane-bound nitrate reductase genes (narG) from Polarimonas sp. were detected in the original groundwater, while Burkholderia, Methylibium, and Pseudomonas narG genes were enriched due to substrate supplements. Identified amoA genes belonged to Nitrosomonas sp. ¹⁵N-SIP revealed that Burkholderiales and Rhizobiales clades belonging to the minority groups in the original groundwater used ¹⁵N from ammonium and nitrate as N source indicating an important ecological function of these bacteria, despite their low number, in the groundwater N cycle in Olkiluoto bedrock system.

Determining potential for microbial atrazine degradation in agricultural drainage ditches

Passage of agricultural runoff through vegetated drainage ditches has been shown to reduce the amount of pesticides, such as atrazine, exiting out of agricultural watersheds. Previous studies have found that microbial communities in soil from fields treated with atrazine display enhanced rates of atrazine degradation. However, no studies have examined the potential for atrazine degradation in ditches used to drain these lands. The purpose of the current study was to determine the potential of the drainage ditch soil microbial community for atrazine degradation. Soil samples were collected from fields and adjacent drainage ditches and from nonagricultural land with no previous exposure to atrazine. Polymerase chain reaction analysis indicated widespread presence of atrazine degradation genes in fields and ditches. Potential for degradation was determined by following the decrease of atrazine in spiked soil samples over a 28-d incubation period. Greater than 95% of atrazine was degraded in field and ditch soils, whereas only 68.5 ± 1.3% was degraded in the nonagricultural control. Comparison with autoclaved soil samples indicated the primary mechanism of atrazine degradation in agricultural soils was microbially mediated, whereas its breakdown in nonagricultural soil appeared to be the byproduct of abiotic processes. Therefore, microbial communities in drainage ditch sediments have the potential to play a role in atrazine removal from agricultural runoff by breaking down atrazine deposited in sediments and limiting the amount of this herbicide carried into downstream ecosystems.

Mass effects meet species sorting: transformations of microbial assemblages in epiphreatic subsurface karst water pools

We investigated the transformations of the microbial communities in epiphreatic karst cave pools with different flooding frequencies. Fingerprinting of 16S rRNA genes was combined with microscopic and sequence analysis to examine if source water would transport comparable microbial inocula into the pools at consecutive flood events, and to assess possible effects of residence time on the microbial assemblages during stagnant periods. Variability in the concentrations of dissolved organic carbon and conductivity indicated differences between floods and changes of pool water over time. High numbers of Betaproteobacteria affiliated with Methylophilaceae and Comamonadaceae were introduced into the pools during floodings. While the former persisted in the pools, the latter exhibited considerable microdiversification. These Betaproteobacteria might thus represent core microbial groups in karst water. A decrease in the estimated total diversity of the remaining bacterial taxa was apparent after a few weeks of residence: Some were favoured by stagnant conditions, whereas the majority was rapidly outcompeted. Thus, the microbial communities consisted of different components governed by complementary assembly mechanisms (dispersal versus environmental filtering) upon introduction into the pools. High overlap of temporary and persistent community members between samplings from two winters, moreover, reflected the seasonal recurrence of the studied microbial assemblages.

Occurrence and dynamics of micropollutants in a karst aquifer

Karst systems represent important yet vulnerable drinking water resources. A wide spectrum of pollutants may be released into karst groundwater from agriculture, livestock farming, private households, and industry. This work provides an overview on the occurrence and dynamics of micropollutants in a karst system of the Swiss Jura. Ten months of intensive monitoring for micropollutants confirmed that the swallow hole draining an agricultural plain was the main entry path for pesticides into the karst system and the two connected springs. Elevated fungicide concentrations in winter and occasional quantification of pharmaceuticals suggested wood- or façade treatment and domestic sewer as additional sources of contamination. A continuous atrazine signal in the low ng/L range might affect the autochthonous endokarst microbial community and represents a potential risk for the human population through karst groundwater.