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

Key role of NH4+-N in the removal of oxacillin during managed aquifer recharge: Reconsidering the recharge limitation

Frequent occurrence of trace antibiotics in reclaimed water is concerning, which inevitably causes aquifer contamination in the case of managed aquifer recharge (MAR). Global governments have formulated strict reclaimed water standards to ensure the safety of water reuse. Recent studies have found that improved antibiotics removal is intimately associated with high ammonia-oxidizing activity. However, the role of NH4+-N in the removal of residual antibiotics of reclaimed water during MAR remains unknown. NH4+-N removal and the effects of ammonia oxidation on antibiotics biodegradation in the aquifer are the most significant facts for solving the above collision. In this work, the effects of NH4+-N (0, 1 and 5 mg/L) in a model refractory antibiotic (oxacillin (OXA), 100 μg/L) attenuation were deciphered by employing three individual simulated MAR columns, which so called N0, N1 and N5. The results showed that 5 mg/L NH4+-N in influent upregulated the abundance of amo genes by 28.9 %-68.0 % in N5. And the enriched functional genes encoding key degradation enzymes enhanced the OXA removal by 18.7 % and alleviated the oxidative stress caused by antibiotics. Subsequently, antibiotic resistance genes (ARGs), mobile gene elements (MGEs) and human bacterial pathogens (HBPs) abundance were all significantly decreased. Moreover, the intimate association between ammonia-oxidizing microorganisms (AOM) and candidate OXA degraders based on microbial network analysis further supported the significance of AOM on OXA biodegradation. This study provides comprehensive evidence that appropriate amounts of NH4+-N are beneficial in antibiotics and antibiotic resistance risk reduction, providing compelling insights for refine NH4+-N recharge limitation.

Differential microbiome features in lake-river systems of Taihu basin in response to water flow disturbance

Introduction

In riverine ecosystems, dynamic interplay between hydrological conditions, such as flow rate, water level, and rainfall, significantly shape the structure and function of bacterial and microeukaryotic communities, with consequences for biogeochemical cycles and ecological stability. Lake Taihu, one of China's largest freshwater lakes, frequently experiences cyanobacterial blooms primarily driven by nutrient over-enrichment and hydrological changes, posing severe threats to water quality, aquatic life, and surrounding human populations. This study explored how varying water flow disturbances influence microbial diversity and community assembly within the interconnected river-lake systems of the East and South of Lake Taihu (ET&ST). The Taipu River in the ET region accounts for nearly one-third of Lake Taihu's outflow, while the ST region includes the Changdougang and Xiaomeigang rivers, which act as inflow rivers. These two rivers not only channel water into Lake Taihu but can also cause the backflow of lake water into the rivers, creating distinct river-lake systems subjected to different intensities of water flow disturbances.

Methods

Utilizing high-throughput sequencing, we selected 22 sampling sites in the ET and ST interconnected river-lake systems and conducted seasonally assessments of bacterial and microeukaryotic community dynamics. We then compared differences in microbial diversity, community assembly, and co-occurrence networks between the two regions under varying hydrological regimes.

Results and discussion

This study demonstrated that water flow intensity and temperature disturbances significantly influenced diversity, community structure, community assembly, ecological niches, and coexistence networks of bacterial and eukaryotic microbes. In the ET region, where water flow disturbances were stronger, microbial richness significantly increased, and phylogenetic relationships were closer, yet variations in community structure were greater than in the ST region, which experienced milder water flow disturbances. Additionally, migration and dispersal rates of microbes in the ET region, along with the impact of dispersal limitations, were significantly higher than in the ST region. High flow disturbances notably reduced microbial niche width and overlap, decreasing the complexity and stability of microbial coexistence networks. Moreover, path analysis indicated that microeukaryotic communities exhibited a stronger response to water flow disturbances than bacterial communities. Our findings underscore the critical need to consider the effects of hydrological disturbance on microbial diversity, community assembly, and coexistence networks when developing strategies to manage and protect river-lake ecosystems, particularly in efforts to control cyanobacterial blooms in Lake Taihu.

Carbon-fixing bacteria in diverse groundwaters of karst area: Distribution patterns, ecological interactions, and driving factors

The biological carbon pump in karst areas is of great significance for maintaining the effectiveness of karst carbon sinks. However, the spatial distribution and carbon-fixing potential of microorganisms in different aquifers within karst areas remain poorly understood. In this study, the distribution patterns, ecological roles, and environmental drivers of microbiota associated with CO2 fixation were investigated in karst groundwater (KW), porous groundwater (PW), fractured groundwater (FW), and surface water (SW) within a typical karst watershed, located in Guilin, southwest China. KW, PW, and FW displayed the similar community structure and indicative carbon-fixing bacteria composition, which were dominated by chemoautotrophic bacteria compared to SW. Higher abundances of indicative carbon-fixing bacteria and carbon-fixing genes, as well as richer proportions of microbial-derived DOC, indicated the more significant microbial carbon-fixing potential in KW and PW. At the profile of KW, a carbon-fixing hotspot was discovered at the depths of 0-50 m. Correlation analysis between carbon-fixing bacteria and DOC revealed that the chemoautotrophic process driven by nitrogen and sulfur oxidation predominated the microbial carbon fixation in groundwater. Co-occurrence network analysis demonstrated that carbon-fixing bacteria exhibited cooperation with other bacterial taxa in KW, while competition was the dominant interaction in PW. Moreover, carbon-fixing bacteria was found to lead bacterial assembly more deterministic in KW. The analysis of environmental factors and microbial diversity illustrated that inorganic carbon and redox state drove community variations across groundwaters. Structural equation model (SEM) further confirmed that ORP was the primary factor influencing the carbon fixation potential. This study provides a new insight into biological carbon fixation in karst aquatic systems, which holds significance in the accurate assessment of karst carbon sinks.

Impact of harmful algal bloom severity on bacterial communities in a full-scale biological filtration system for drinking water treatment

The occurrence of harmful algal blooms (HABs) in freshwater environments has been expanded worldwide with growing frequency and severity. HABs can pose a threat to public water supplies, raising concerns about safety of treated water. Many studies have provided valuable information about the impacts of HABs and management strategies on the early-stage treatment processes (e.g., pre-oxidation and coagulation/flocculation) in conventional drinking water treatment plants (DWTPs). However, the potential effect of HAB-impacted water in the granular media filtration has not been well studied. Biologically-active filters (BAFs), which are used in drinking water treatment and rely largely on bacterial community interactions, have not been examined during HABs in full-scale DWTPs. In this study, we assessed the bacterial community structure of BAFs, functional profiles, assembly processes, and bio-interactions in the community during both severe and mild HABs. Our findings indicate that bacterial diversity in BAFs significantly decreases during severe HABs due to the predominance of bloom-associated bacteria (e.g., Spingopyxis, Porphyrobacter, and Sphingomonas). The excitation-emission matrix combined with parallel factor analysis (EEM-PARAFAC) confirmed that filter influent affected by the severe HAB contained a higher portion of protein-like substances than filter influent samples during a mild bloom. In addition, BAF community functions showed increases in metabolisms associated with intracellular algal organic matter (AOM), such as lipids and amino acids, during severe HABs. Further ecological process and network analyses revealed that severe HAB, accompanied by the abundance of bloom-associated taxa and increased nutrient availability, led to not only strong stochastic processes in the assembly process, but also a bacterial community with lower complexity in BAFs. Overall, this study provides deeper insights into BAF bacterial community structure, function, and assembly in response to HABs.

Nanoscale zero-valent iron alleviate antibiotic resistance risk during managed aquifer recharge (MAR) by regulating denitrifying bacterial network

The frequent occurrence of antibiotics in reclaimed water is concerning, in the case of managed aquifer recharge (MAR), it inevitably hinders further water purification and accelerates the evolutionary resistance in indigenous bacteria. In this study, we constructed two column reactors and nanoscale zero-valent iron (nZVI) amendment was applied for its effects on water quality variation, microbial community succession, and antibiotic resistance genes (ARGs) dissemination, deciphered the underlying mechanism of resistance risk reduction. Results showed that nZVI was oxidized to iron oxides in the sediment column, and total effluent iron concentration was within permissible limits. nZVI enhanced NO3--N removal by 15.5% through enriching denitrifying bacteria and genes, whereas made no effects on oxacillin (OXA) removal. In addition, nZVI exhibited a pivotal impact on ARGs and plasmids decreasing. Network analysis elucidated that the diversity and richness of ARG host declined with nZVI amendment. Denitrifying bacteria play a key role in suppressing horizontal gene transfer (HGT). The underlying mechanisms of inhibited HGT included the downregulated SOS response, the inhibited Type-Ⅳ secretion system and the weakened driving force. This study afforded vital insights into ARG spread control, providing a reference for future applications of nZVI in MAR.

The effects of heavy rain on the fate of urban and agricultural pollutants in the riverside area around weirs using multi-isotope, microbial data and numerical simulation

The increase in extreme heavy rain due to climate change is a critical factor in the fate of urban and agricultural pollutants in aquatic system. Nutrients, including NO3- and PO43-, are transported with surface and seepage waters into rivers, lakes and aquifers and can eventually lead to algal blooms. δ15N-NO3-, δ18O-NO3-, and δ11B combined with hydrogeochemical and microbial data for groundwater and surface water samples were interpreted to evaluate the fate of nutrients in a riverside area around weirs in Daegu, South Korea. Most of the ions showed similar concentrations in the groundwater samples before and after heavy rain while concentrations of major ions in surface water samples were diluted after heavy rain. However, Si, PO43-, Zn, Ce, La, Pb, Cu and a number of waterborne pathogens increased in surface water after heavy rain. The interpretation of δ11B, δ15N-NO3-, and δ18O-NO3- values using a Bayesian mixing model revealed that sewage and synthetic fertilizers were the main sources of contaminants in the groundwater and surface water samples. δ18O and SiO2 interpreted using the Bayesian mixing model indicated that the groundwater component in the surface water increased from 4.4 % to 17.9 % during the wet season. This is consistent with numerical simulation results indicating that the direct surface runoff and the groundwater baseflow contributions to the river system had also increased 6.4 times during the wet season. The increase in proteobacteria and decrease of actinobacteria in the surface water samples after heavy rain were also consistent with an increase of surface runoff and an increased groundwater component in the surface water. This study suggests that source apportionment based on chemical and multi-isotope data combined with numerical modeling approaches can be useful for identifying main hydrological and geochemical processes in riverside areas around weirs and can inform suggestions of effective methods for water quality management.

New progress in the deep understanding of the biocake layer property: Combined effect of neglected protein secondary structure, morphology, and mechanism

The application of magnetic fields (MFs) and magnetic particles (MPs) in water treatment has attracted widespread attention due to their stability, strong biological compatibility, and less chemical consumption. This study introduced MPs and MFs to GDM and probed their effects on filtration performance. Predeposited large MPs (P-large) and batch-added little MPs (B-little) intervened biocake layer development, forming more open and porous structures, they also reduced biomass secretion, resulting in flux increases of 13 % in P-large and 40 % in B-little than P-little, respectively. Besides, MFs controlled MPs distribution on the biocake layer, resulting in forming of more rough and open structures. A relatively lower magnetic field of 20 mT facilitated biomass secretion, while a higher magnetic field of 50 mT decreased biomass. Furthermore, applying magnetic fields decreased the ratios of α-helix and β-sheet, and increased random coil percentage. Thus, applying magnetic field mediation would contribute to the flux improvements in I-20 and I-50 by 29 % and 32 % relative to I-0. Economic analysis suggested introducing MPs and MFs to GDM was economically feasible, synergy of MPs and MFs had more economic advantages on the community scale and MPs-assisted GDM had significant economic advantages on both community and household scales. Future works should focus on developing new technologies for the recycling of MPs and membranes. This study provided new insight into the protein secondary structures associated with GDM performance and would encourage new sustainable MFs and MPs-assisted GDM technological developments.

Terrestrial dissolved organic matter inputs drive the temporal dynamics of riverine bacterial ecological networks and assembly processes

Rivers receive, transport, and are reactors of terrestrial dissolved organic matter (DOM) and are highly influenced by changes in hydrological conditions and anthropogenic disturbances, but the effect of DOM composition on the dynamics of the bacterial community in rivers is poorly understood. We conducted a seasonal field sampling campaign at two eutrophic river mouth sites to examine how DOM composition influences the temporal dynamics of bacterial community networks, assembly processes, and DOM-bacteria associations. DOM composition and seasonal factors explained 34.7% of the variation in bacterial community composition, and 14.4% was explained purely by DOM composition where specific UV absorbance (SUVA254) as an indicator of aromaticity was the most important predictor. Significant correlations were observed between SUVA254 and the topological features of subnetworks of interspecies and DOM-bacteria associations, indicating that high DOM aromaticity results in more complex and connected networks of bacteria. The bipartite networks between bacterial taxa and DOM molecular formulae (identified by ultrahigh-resolution mass spectrometry) further revealed less specialized bacterial processing of DOM molecular formulae under the conditions of high water level and DOM aromaticity in summer than in winter. A shift in community assembly processes from stronger homogeneous selection in summer to higher stochasticity in winter correlated with changes in DOM composition, and more aromatic DOM was associated with greater similarity in bacterial community composition. Our results highlight the importance of DOM aromaticity as a predictor of the temporal dynamics of riverine bacterial community networks and assembly.

Unveiling the biogeochemical mechanism of nitrate in the vadose zone-groundwater system: Insights from integrated microbiology, isotope techniques, and hydrogeochemistry

Clarifying the biogeochemical mechanism of nitrate (NO3-) in the vadose zone-groundwater system, particularly in agricultural contexts, is crucial for mitigating groundwater NO3- pollution. However, comprehensive studies on the impacts of changes in chemical indicators and microbial communities on NO3- are still lacking. This paper aims to address this gap by employing hydrogeochemistry, stable isotopes, and microbial techniques to assess the NO3- biogeochemical processes in the vadose zone-groundwater system. The findings suggested that NO3- in upper soil layers was primarily influenced by plant root absorption, assimilation, and nitrification processes. The oxygen contents gradually decreased with the nitrification process, resulting in the occurrence of the denitrification. However, denitrification predominantly occurred in the 60-80 cm soil layer in the study area. The limited thickness of the denitrification layer results in less NO3- consumption, leading to increased NO3- leaching into groundwater. Hydrochemical and isotopic characteristics further indicated that groundwater NO3- concentrations were mainly controlled by nitrification, followed by denitrification and mixing processes. The 16S rRNA sequencing analysis revealed great influences of soil sampling depths and groundwater NO3- concentrations on the microbial community structure. Additionally, the PICRUSt2-based prediction results demonstrated a stronger potential for dissimilatory reduction of NO3- to ammonium (DNRA) in both soil and groundwater compared to the other processes, potentially due to the widespread presence of the nrfH functional genes. However, the chemical indicators and isotopes used in this study did not support the occurrence of DNRA process in the vadose zone-groundwater system. This finding highlights the importance of an integrated approach combining microbiological, isotopic, and hydrogeochemical data to comprehensive understanding biogeochemical processes. The study developed a conceptual model elucidating the NO3- biogeochemical processes in the vadose zone-groundwater system within an agricultural area, contributing to enhanced comprehension and advancement of sustainable management practices for groundwater nitrogen.

Linking Groundwater to Surface Discharge Ecosystems: Archaeal, Bacterial, and Eukaryotic Community Diversity and Structure in Quebec (Canada)

Aquifer systems are composed of water flowing from surface recharge areas, to the subsurface and back to the surface in discharge regions. Groundwater habitats harbor a large microbial biomass and diversity, potentially contributing to surface aquatic ecosystems. Although this contribution has been widely studied in marine environments, very little is known about the connection between underground and surface microbial communities in freshwater settings. Therefore, in this study, we used amplicon sequencing to analyze the archaeal, bacterial, and eukaryotic community diversity and structure in groundwater and surface water samples, spanning the vast regions of the Laurentides and Lanaudières in the Quebec province (Canada). Our results show significant differences between subsurface and surface taxa; with more fungi, Amoebozoa, and chemolithoautotrophic prokaryotes involved in nitrogen-, sulfur-, and iron-cycling dominating the underground samples; while algae, ciliates, methanogens, and Actinobacteria dominate the surface discharge waters. Microbial source tracking suggested that only a small portion of the microbial communities in the groundwater contributed to the surface discharge communities. However, many taxa were shared between both habitats, with a large range of functional diversity, likely explaining their survival in both subsurface and surface water ecosystems.

Effect of Snowmelt on Groundwater Bacterial Community Composition and Potential Role of Surface Environments as Microbial Seed Bank in Two Distinct Aquifers from the Region of Quebec, Canada

Events of groundwater recharge are associated with changes in the composition of aquifer microbial communities but also abiotic conditions. Modification in the structure of the community can be the result of different environmental condition favoring or hindering certain taxa, or due to the introduction of surface-derived taxa. Yet, in both cases, the local hydrogeochemical settings of the aquifer is likely to affect the amount of variation observed. Therefore, in our study, we used 16S rRNA gene sequencing to assess how microbial communities change in response to snowmelt and the potential connectivity between subsurface and surface microbiomes in two distinct aquifers located in the region of Vaudreuil-Soulanges (Québec, Canada). At both sites, we observed an increase in groundwater level and decrease in temperature following the onset of snow melt in March 2019. Bacterial community composition of each aquifer was significantly different (p < 0.05) between samples collected prior and after groundwater recharge. Furthermore, microbial source tracking results suggested a low contribution of surface environments to the groundwater microbiome except for in the months associated with recharge (March 2019 and April 2019). Overall, despite differences in soil permeability between both sites, the period of snow melt was followed by important changes in the composition of microbial communities from aquifers.

Nitrate with enriched heavy oxygen isotope linked to changes in nitrogen source and transformation as groundwater table rises

Nitrate is a significant constituent of the total nitrogen pool in shallow aquifers and poses an escalating threat to groundwater resources, making it crucial to comprehend the source, conversion, and elimination of nitrogen using appropriate techniques. Although dual-isotope dynamics in nitrate have been widely used, uncertainties remain regarding the asynchronously temporal changes in δ¹⁸O-NO₃^- and δ¹⁵N-NO₃^- observed in hypoxic aquifers. This study aimed to investigate changes in nitrogen sources and transformations using temporal changes in field-based NO₃^- isotopic composition, hydro-chemical variables, and environmental DNA profiling, as the groundwater table varied. The results showed that the larger enrichment in δ¹⁸O-NO₃^- (+13‰) compared with δ¹⁵N-NO₃^- (-2‰) on average during groundwater table rise was due to a combination of factors, including high ¹⁸O-based atmospheric N deposition, canopies nitrification, and soil nitrification transported vertically by rainfalls, and ¹⁸O-enriched O₂ produced through microbial and root respiration within denitrification. The strong association between functional gene abundance and nitrogen-related indicators suggests that anammox was actively processed with nitrification but in small bacterial population during groundwater table rise. Furthermore, bacterial species associated with nitrogen-associated gradients provided insight into subsurface nitrogen transformation, with Burkholderiaceae species and Pseudorhodobacter potentially serving as bioindicators of denitrification, while Candidatus Nitrotogn represents soil nitrification. Fluctuating groundwater tables can cause shifts in hydro-chemical and isotopic composition, which in turn can indicate changes in nitrogen sources and transformations. These changes can be used to improve input sources for mixture models and aid in microbial remediation of nitrate.

The ecology of bacterial communities in groundwater of industrial areas: Diversity, composition, network, and assembly

Groundwater provides freshwater resources necessary for mankind, but its quality is significantly impacted by anthropologic activities. The unique characteristics of groundwater provide a special niche for bacterial colonization. To maintain the sustainability of groundwater ecosystem, a good understanding of the influencing factors and assembly mechanisms for bacterial communities is necessary. Here, we investigated the bacterial communities of groundwater from two industrial zones in Shanghai, a highly industrialized city, during the wet and dry seasons using the high-throughput sequencing technology. Our study uncovered the significant effects of season, geographical location, and industrial type on the diversity and composition of groundwater bacterial communities, particularly, we found that season was the most dominant factor with much stronger influences (give the explanation 17.7%) in comparison with geographical location (8.8%) and industrial type (7.5%). Co-occurrence networks revealed that geographical location explained more variations of bacterial ecological network than season did. Both distance-decay of similarities and variation partitioning analyses indicated that the assembly of groundwater bacterial communities was more governed by environmental filtering compared to spatial-related dispersal. Finally, null model analysis suggested the role of stochastic processes, including dispersal and drift, in shaping the groundwater bacterial communities cannot be ignored. These findings would benefit to improve our understanding of the bacterial communities in groundwater ecosystem and provide a theoretical foundation for groundwater health management.

Estimation of nutrient sources and fate in groundwater near a large weir-regulated river using multiple isotopes and microbial signatures

The excessive input of nutrients into groundwater can accelerate eutrophication in associated surface water systems. This study combined hydrogeochemistry, multi isotope tracers, and microbiological data to estimate nutrient sources and the effects of groundwater-surface water interactions on the spatiotemporal variation of nutrients in groundwater connected to a large weir-regulated river in South Korea. δ11B and δ15N-NO3- values, in combination with a Bayesian mixing model, revealed that manure and sewage contributed 40 % and 25 % respectively to groundwater nitrate, and 42 % and 27 % to nitrate in surface water during the wet season. In the dry season, the source apportionment was similar for groundwater while the sewage contribution increased to 52 % of nitrate in river water. River water displayed a high correlation between NO3- concentration and cyanobacteria (Microcystis and Prochlorococcus) in the wet season. The mixing model using multiple isotopes indicated that manure-derived nutrients delivered with increased contributions of groundwater to the river during the wet season governed the occurrence of cyanobacterial blooms in the river. We postulate that the integrated approach using multi-isotopic and microbiological data is highly effective for evaluating nutrient sources and for delineating hydrological interactions between groundwater and surface water, as well as for investigating surface water quality including eutrophication in riverine and other surface water systems.

Application of phosphorus amendments reduces metal uptake and increases yield of Oryza saliva L. (rice) in Cd/Cu-contaminated paddy field

To alleviate worldwide food safety issues caused by metal contamination, an easily available material is urgently needed for extensive application. In this study, calcium magnesium phosphate fertiliser (Pcm) was applied to a Cd/Cu co-contaminated paddy field in comparison with limestone and organic fertiliser. The results showed that only Pcm is effective in simultaneously reducing Cd uptake by 56.7% and Cu uptake by 36.2% in Oryza saliva L. (rice). The rice yield, reduced mainly by Cu, also increased by 30.1% with respect to the enhancement of soil pH, cation exchange capacity and availability of phosphorus, as well as the reduction in availabilities of Cd and Cu. Additionally, Pcm dramatically shaped the bacterial community structure, with Proteobacteria and Firmicutes predominant in the soils. The beneficial genera Exiguobacterium, Citrobacter, and Acinetobacter, which are vital for phosphate dissolution and Cd/Cu immobilisation, were also enriched. The results demonstrated that the application of Pcm at 0.4% (w:w) was able to enhance both crop quantity and quality in Cd/Cu co-contaminated paddy fields by reducing Cu/Cd availability, promoting rice yield, and reshaping bacterial community structures.

Self-rescue of nitrogen-cycling bacteria under β-lactam antibiotics stress during managed aquifer recharge (MAR): Microbial collaboration and anti-resistance

Storing reclaimed water via managed aquifer recharge (MAR) is an effective strategy for alleviating groundwater overdraft and achieving water resource recycling simultaneously. However, β-lactam antibiotics in the reclaimed water can induce stress on aquifer system, reshape microbial community, and affect the emergence and prevalence of antibiotic resistance genes (ARGs). In this study, three sandy soil columns (H 1.5 m, ID 14 cm) were employed to simulate MAR, and synthetic reclaimed water containing either amoxicillin (AMO), ampicillin (AMP) or oxacillin (OXA) was continuously recharged for 120 d The temporal and spatial attenuation of β-lactams and nitrogen was studied, and microbial collaboration and the resistance mechanism were elaborated. Biodegradation is the main pathway for β-lactams elimination, AMO and AMP were eliminated when migrating 30 cm, while the attenuation of OXA experienced in the whole column with final removal efficiency of 82%. Moreover, refractory OXA induced more ARGs production, and approximately 10% and 13% higher than that of AMO and AMP columns. Efflux pump and antibiotics inactivation were the two major resistance mechanisms. NO₃^--N gradually decreased (by 26%, 38%, and 49% for AMO, AMP, and OXA, respectively) along the recharge direction. Microbial co-occurrence network revealed that nitrogen-cycling bacteria were the keystone species in aquifer community, and ammonation provided NH₄⁺-N for the nitrification process of ammonia-oxidizing archaea (AOA), promoting the further denitrification for nitrogen removal in MAR process. Nitrogen-cycling bacteria were the key and active ARG hosts, which could keep nitrogen transformation activity under antibiotics stress. In sum, nitrogen-cycling bacteria exhibited intimate collaboration and elastic resistance in response to the malnutrition environment and β-lactams exposure during MAR.

Meta-analysis addressing the characterization and risk identification of antibiotics and antibiotic resistance genes in global groundwater

Antimicrobial resistance (AMR) is one of the significant global issues to public health. Compared to other aquatic environments, research on AMR in groundwater is scarce. In the study, a meta-analysis was conducted to explore the characteristics and risks of antibiotics and antibiotic resistance genes (ARGs) in global groundwater, using a data set of antibiotic concentrations collected from publications during 2000-2021 and a large-scale metagenomes of groundwater samples (n = 330). The ecotoxicological risks of antibiotics in the global groundwater were evaluated using mixture risk quotient with concentration addition model to consider the synergistic effects of multiple antibiotics. Bioinformatic annotations identified 1413 ARGs belonging to 37 ARG types in the global groundwater, dominated by rifamycin, polyketide, and quinolone resistance genes and including some emerging ARGs such as mcr-family and carbapenem genes. Relatively, the level of ARGs in the groundwater from spring was significantly higher (ANOVA, p < 0.01) than those from the riparian zone, sand and deep aquifer. Similarly, metal resistance genes (MRGs) were prevalent in the global groundwater, and network analysis suggested the MRGs presented non-random co-occurrence with the ARGs in such environments. Taxonomic annotations showed Proteobacteria, Actinobacteria, Eukaryota, Acidobacteria and Thaumarchaeota were the dominant phylum in the groundwater, and the microbial community largely shaped profile of ARGs in the environment. Notably, the ARGs presented co-occurrence with mobile genetic elements, virulence factors and human bacterial pathogens, indicating potential dissemination risk of ARGs in the groundwater. Furthermore, an omics-based approach was used for health risk assessment of antibiotic resistome and screened out 152 risk ARGs in the global groundwater. Comparatively, spring and cold creek presented higher risk index, which deserves more attention to ensure the safety of water supply.

From Recharge, to Groundwater, to Discharge Areas in Aquifer Systems in Quebec (Canada): Shaping of Microbial Diversity and Community Structure by Environmental Factors

Groundwater recharge and discharge rates and zones are important hydrogeological characteristics of aquifer systems, yet their impact on the formation of both subterranean and surface microbiomes remains largely unknown. In this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community of seven different aquifers, including the recharge and discharge areas of each system. The connectivity between subsurface and surface microbiomes was evaluated at each site, and the temporal succession of groundwater microbial communities was further assessed at one of the sites. Bacterial and archaeal community composition varied between the different sites, reflecting different geological characteristics, with communities from unconsolidated aquifers being distinct from those of consolidated aquifers. Our results also revealed very little to no contribution of surface recharge microbial communities to groundwater communities as well as little to no contribution of groundwater microbial communities to surface discharge communities. Temporal succession suggests seasonal shifts in composition for both bacterial and archaeal communities. This study demonstrates the highly diverse communities of prokaryotes living in aquifer systems, including zones of groundwater recharge and discharge, and highlights the need for further temporal studies with higher resolution to better understand the connectivity between surface and subsurface microbiomes.

On the hidden diversity and niche specialization of the microbial realm of subterranean estuaries

Subterranean estuaries (STEs) modulate the chemical composition of continental groundwater before it reaches the coast, but their microbial community is poorly known. Here, we explored the microbial ecology of two neighbouring, yet contrasting STEs (Panxón and Ladeira STEs; Ría de Vigo, NW Iberian Peninsula). We investigated microbial composition (16S rRNA gene sequencing), abundance, heterotrophic production and their geochemical drivers. A total of 10,150 OTUs and 59 phyla were retrieved from porewater sampled during four surveys covering each STE seepage face. In both STEs, we find a very diverse microbial community composed by abundant cosmopolitans and locally restricted rare taxa. Porewater oxygen and dissolved organic matter are the main environmental predictors of microbial community composition. More importantly, the high variety of benthic microbiota links to biogeochemical processes of different elements in STEs. The oxygen-rich Panxón beach showed strong associations of the ammonium oxidizing archaea Nitrosopumilales with the heterotrophic community, thus acting as a net source of nitrogen to the coast. On the other hand, the prevailing anoxic conditions of Ladeira beach promoted the dominance of anaerobic heterotrophs related to the degradation of complex and aromatic compounds, such as Dehalococcoidia and Desulfatiglans, and the co-occurrence of methane oxidizers and methanogens.

Soil characteristics and redox properties of infiltrating water are determinants of microbial communities at managed aquifer recharge sites

In this study, we conducted a meta-analysis of soil microbial communities at three, pilot-scale field sites simulating shallow infiltration for managed aquifer recharge (MAR). We evaluated shifts in microbial communities after infiltration across site location, through different soils, with and without carbon-rich amendments added to test plots. Our meta-analysis aims to enable more effective MAR basin design by identifying potentially important interactions between soil physical-geochemical parameters and microbial communities across several geographically separate MAR basins. We hypothesized infiltration and carbon amendments would lead to common changes in subsurface microbial communities at multiple field sites but instead found distinct differences. Sites with coarser (mainly sandy) soil had large changes in diversity and taxa abundance, while sites with finer soils had fewer significant changes in genera, despite having the greatest increase in nitrogen cycling. Below test plots amended with a carbon-rich permeable reactive barrier, we observed more nitrate removal and a decrease in genera capable of nitrification. Multivariate statistics determined that the soil texture (a proxy for numerous soil characteristics) was the main determinant of whether the microbial community composition changed because of infiltration. These results suggest that microbial communities in sandy soil with carbon-rich amendments are most impacted by infiltration. Soil composition is a critical parameter that links between microbial communities and nutrient cycling during infiltration and could influence the citing and operation of MAR to benefit water quality and supply.

Microbial diversity and geochemistry of groundwater impacted by steel slag leachates

To understand long-term impacts of steel slag material on aquifer geochemistry and microbial communities, we conducted four sampling campaigns in the Gier alluvial groundwater (Loire, France). In its northern part, the aquifer flows under a 200,000 m³ steel slag exhibiting high levels of chromium and molybdenum. Geochemical analyses of the water table revealed the existence of water masses with different chemical signatures. They allowed us to identify an area particularly contaminated by leachates from the slag heap, whatever the sampling period. Water samples from this area were compared to non-contaminated samples, with geochemical characteristics similar to the river samples. To follow changes in microbial communities, the V3-V4 region of 16 s rRNA gene was sequenced. Overall, we observed lower diversity indices in contaminated areas, with higher relative abundances of Verrucomicrobiota and Myxococcota phyla, while several Proteobacteria orders exhibited lower relative abundances. In particular, one single genus among the Verrucomicrobiota, Candidatus Omnitrophus, represented up to 36 % of total taxon abundance in areas affected by steel slag leachates. A large proportion of taxa identified in groundwater were also detected in the upstream river, indicating strong river-groundwater interactions. Our findings pave the way for future research work on C. Omnitrophus remediation capacities.

Microbial response to biogeochemical profile in a perpendicular riverbank filtration site

Due to extensive water exchanges and abundant active biochemical compositions, active and complex hydrogeochemical processes often exist in riverbank filtration (RBF). The distribution of microbes is considered to be profoundly affected by these processes and is considered to impact the hydrogeochemical processes and the migration and transformation of water pollutants in turn and then impact the water quality. The distribution of microbes and their response to the physiochemical properties along a vertical RBF profile perpendicular to the Songhua River in Northeast China was explored by using 16 S rRNA and redundancy analysis (RDA). The results showed that various microbes were found in the vertical riparian filter (RBF) curve, including Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, and Firmicutes. With increasing depth (vertical) and distance from the river (lateral), the microbial community and diversity in the RBF sediment profile decreased. Nitrospirota, Pseudomonas, Gammaproteobacteria, Ochrobactrum, Acinetobacter and Desulfobacterota of the RBF core taxa were also significantly correlated with the biotransformation behavior of typical groundwater pollutants (ammonia, Fe, Mn and S). The amount of As in the RBF is too low to sustain microbial survival. Some microbes in RBF can also degrade natural organic pollutants. This study not only revealed the spatial distribution of geological microbes under the impact of hydrological processes but also lays a foundation for the further study of the hydrobiogeochemical processes of active biochemical compositions in groundwater and water quality evolution, which is of positive significance to ensure the quality safety of the drinking water supplied by RBFs.

High biodiversity and distinct assembly patterns of microbial communities in groundwater compared with surface water

The differences in bacterial community assembly mechanism between surface water and groundwater, as well as the driving factors of environmental factors, are still unknown. Here we aimed to answer these questions by analyzing microbial community samples from surface water and groundwater. We observed a strong connection between microbial communities in surface water and groundwater and several human pathogens are shared between surface water and groundwater; however, the richness and diversity of groundwater microbial communities were greater than those of surface water, regardless of the season. Additionally, bacterial community compositions of surface water and groundwater differed significantly between seasons. Most importantly, the groundwater community exhibited a highly deterministic assembly process (56% contributed by deterministic process, with neutral community model R² = 0.277) compared with surface water (51% contributed by deterministic process, with R² = 0.526). This study provides a deep understanding of the effects of environmental factors on surface water and groundwater microbial communities, to better protect water resources.

The biogeochemical responses of hyporheic groundwater to the long-run managed aquifer recharge: Linking microbial communities to hydrochemistry and micropollutants

Interactions of surface water and groundwater (SW-GW) in hyporheic zones produce biogeochemical hotspots. However, response patterns of hyporheic groundwater to external influences remain unclear. In this study, three datasets (hydrochemistry, antibiotics, and microbiome) were collected over a hydrological year to explore the influence of a 12-year managed aquifer recharge (MAR) project. We observed that the long-term MAR practice elevated nutrient and antibiotic levels while reduced redox potential in hyporheic groundwater, and these impacts depended on decreasing SW-GW interaction intensity with aquifer depth. In contrast, the long-term MAR practice increased community dissimilarity of 30-m groundwater but had little impact on 50-m or 80-m groundwater. Moreover, hyporheic community assembly was dominated by dispersal limitation, and thereby co-varied hydrochemistry and antibiotics only attributed to small community variability. The long-term MAR practice decreased species-interaction intensity and changed the abundance of metabolic functions in hyporheic groundwater. Furthermore, predicted community functions involving carbon, nitrogen, sulfur, and manganese cycles for 30-m groundwater showed higher abundances than those for 50- and 80-m groundwater. Collectively, we showed that hyporheic groundwater was sensitive to the SW-GW interaction and human activities, with the interactions of hydrochemistry, contaminants, and microbiome linking to hyporheic groundwater quality and ecosystem functioning.

Variation of bacterial community and alkane monooxygenase gene abundance in diesel n-alkane contaminated subsurface environment under seasonal water table fluctuation

n-Alkanes, the main component of diesel fuel, are common light non-aqueous phase liquids (LNAPLs) that threaten ecological security. The subsurface from vadose zone, through fluctuating zone, to saturated zone, is a critical multi-interface earth layer which significantly affects the biodegradation processes of n-alkanes. A pilot-scale diesel contaminated aquifer column experiment has been undertaken to investigate the variations of bacterial community and alkane monooxygenase (alkB) gene abundance in these zones due to water-table fluctuations. The n-alkanes formed a layer immediately above the water table, and when this was raised, they were carried upwards through the fluctuating zone into the vadose zone. Water content and n-alkanes component C10-C12 are main factors influencing bacterial community variation in the vadose zone, while C10-C12 is a key driving factor shaping bacterial community in the fluctuating zone. The most abundant bacterial phyla at all three zones were Proteobacteria, Firmicutes and Actinobacteria, but moisture-niche selection determined their relative abundance. The intermittent wetting cycle resulted in higher abundance of Proteobacteria, and lower abundance of Actinobacteria in the vadose and fluctuating zones in comparison to the control column with a static water-table. The abundances of the alkB gene variants were relatively uniform in different zones, probably because the bacterial populations harboring alkB gene are habituated to biogenic n-alkanes rather than responding to diesel fuel contamination. The variation in the bacterial populations with height due to moisture-niche selection had very little effect on the alkB gene abundance, possibly because numerous species in both phyla (Proteobacteria and Actinobacteria) carry an alkB gene variant. Nevertheless, the drop in the water table caused a short-term spike in alkB gene abundance in the saturated zone, which is most likely associated with transport of solutes or colloids from the fluctuating zone to bacteria species in the saturated zone, so a fluctuating water table could potentially increase n-alkane biodegradation function.

Decreased levels and ecological risks of disinfection by-product chloroform in a field-scale artificial groundwater recharge project by colloid supplement

To bolster freshwater supply, artificial groundwater recharge with recycled water has increasingly attracted research attentions and interests. However, artificial groundwater recharge has potential risks to groundwater quality, as recharge water disinfection is frequently used for pathogen inactivation and causes the concerns of disinfection by-products (DBPs). Colloid supplement is a good approach solving this problem, but its roles in mitigating DBPs remains unclear. In this study, we collected 20 groundwater and soil samples from a field-scale groundwater recharge project, and explored the impacts of silica colloids on chloroform migration and groundwater bacterial communities during the recharge process. Water physicochemical variables changed along the recharge time, and colloid supplement significantly reduced chloroform formation and slowed its migration in groundwater. Bacterial communities in groundwater, river water and recharge water were significantly different. Gammaproteobacteria in recharge water (71.7%) was more abundant than in river water (30.5%) and groundwater (33.5%), while Actinobacteria dominated groundwater (40.6%). After recharge, Gammaproteobacteria increased more with colloid supplement (75.7%) than without (52.6%), attributing to its dominance in soils (74.6%). Our results suggested more bacterial lineages released from soils into aquifer by silica colloid supplement, owing to the competitive adsorption encouraging microbial transfer, especially Gram-negative bacteria. Our findings unraveled the effects of colloid supplement on chloroform formation and migration during artificial groundwater recharge, which consequently altered groundwater bacterial communities, and offered valuable suggestions for the safety management of DBPs in aquifer recharge.

Surface Water Intrusion, Land Use Impacts, and Bacterial Community Composition in Shallow Groundwater Wells Supplying Potable Water in Sparsely Populated Areas of a Boreal Region

Rural communities often rely on groundwater for potable water supply. In this study, untreated groundwater samples from 28 shallow groundwater wells in Finland (<10 m deep and mostly supplying untreated groundwater to <200 users in rural areas) were assessed for physicochemical water quality, stable water isotopes, microbial water quality indicators, host-specific microbial source tracking (MST) markers, and bacterial community composition, activity, and diversity (using amplicon sequencing of the 16S rRNA gene and 16S rRNA). Indications of surface water intrusion were identified in five wells, and these indications were found to be negatively correlated, overall, with bacterial alpha diversity (based on amplicon sequencing of the 16S rRNA gene). High levels of turbidity, heterotrophs, and iron compromised water quality in two wells, with values up to 2.98 nephelometric turbidity units (NTU), 16,000 CFU/ml, and 2,300 μg/liter, respectively. Coliform bacteria and general fecal indicator Bacteroidales bacteria (GenBac3) were detected in 14 and 10 wells, respectively (albeit mostly at low levels), and correlations were identified between microbial, physicochemical, and environmental parameters, which may indicate impacts from nearby land use (e.g., agriculture, surface water, road salt used for deicing). Our results show that although water quality was generally adequate in most of the studied wells, the continued safe use of these wells should not be taken for granted.

IMPORTANCE Standard physicochemical water quality analyses and microbial indicator analyses leave much of the (largely uncultured) complexity of groundwater microbial communities unexplored. This study combined these standard methods with additional analyses of stable water isotopes, bacterial community data, and environmental data about the surrounding areas to investigate the associations between physicochemical and microbial properties of 28 shallow groundwater wells in Finland. We detected impaired groundwater quality in some wells, identified potential land use impacts, and revealed indications of surface water intrusion which were negatively correlated with bacterial alpha diversity. The potential influence of surface water intrusion on groundwater wells and their bacterial communities is of particular interest and warrants further investigation because surface water intrusion has previously been linked to groundwater contamination, which is the primary cause of waterborne outbreaks in the Nordic region and one of the major causes in the United States and Canada.

The effect of periodic disturbances and carrying capacity on the significance of selection and drift in complex bacterial communities

Understanding how periodical disturbances affect the community assembly processes is vital for predicting temporal dynamics in microbial communities. However, the effect of dilutions as disturbances are poorly understood. We used a marine bacterial community to investigate the effect of disturbance (+/-) and carrying capacity (high/low) over 50 days in a dispersal-limited 2 × 2 factorial study in triplicates, with a crossover in the disturbance regime between microcosms halfway in the experiment. We modelled the rate of change in community composition between replicates and used this rate to quantify selection and ecological drift. The disturbed communities increased in Bray-Curtis similarity with 0.011 ± 0.0045 (Period 1) and 0.0092 ± 0.0080 day-1 (Period 2), indicating that selection dominated community assembly. The undisturbed communities decreased in similarity at a rate of -0.015 ± 0.0038 day-1 in Period 1 and were stable in Period 2 at 0.00050 ± 0.0040 day-1, suggesting drift structured community assembly. Interestingly, carrying capacity had minor effects on community dynamics. This study is the first to show that stochastic effects are suppressed by periodical disturbances resulting in exponential growth periods due to density-independent biomass loss and resource input. The increased contribution of selection as a response to disturbances implies that ecosystem prediction is achievable.

Groundwater contaminated with short-chain chlorinated paraffins and microbial responses

The vertical migrations of toxic and persistent short-chain chlorinated paraffins (SCCPs) in soils as well as the microbial responses have been reported, however, there is a paucity of data on the resulting groundwater contamination. Here, we determined the concentration and congener profile of SCCPs in the groundwater beneath a production plant of chlorinated paraffins (CPs) and characterized the microbial community to explore their responses to SCCPs. Results showed that SCCPs ranged from not detected to 70.3 μg/L, with C₁₃-CPs (11.2-65.8%) and Cl₇-CPs (27.2-50.6%), in mass ratio, as the dominant groups. Similar to the distribution pattern in soils, SCCPs in groundwater were distributed in hotspot pattern. CP synthesis was the source of SCCPs in groundwater and the entire contamination plume significantly migrated downgradient, while there was an apparent hysteresis of C₁₃-CP migration. Groundwater microbial community was likely shaped by both hydrogeological condition (pH and depth) and SCCPs. Specifically, the microbial community responded to the contamination by forming a co-occurrence network with "small world" feature, where Desulfobacca, Desulfomonile, Ferritrophicum, Methylomonas, Syntrophobacter, Syntrophorhabdus, Syntrophus, and Thermoanaerobaculum were the keystone taxa. Furthermore, the interrelations between bacterial taxa and SCCPs indicated that the microbial community might cooperate to achieve the dechlorination and mineralization of SCCPs through either anaerobic organohalide respiration mainly functioned by the keystone taxa, or cometabolic degradation processes functioned by Aquabacterium and Hydrogenophaga. Results of this study would provide a better understanding of the environmental behavior and ecological effects of SCCPs in groundwater systems.

Groundwater bacterial communities evolve over time in response to recharge

Time series analyses are a crucial tool for uncovering the patterns and processes shaping microbial communities and their functions, especially in aquatic ecosystems. Subsurface aquatic environments are perceived to be more stable than surface oceans and lakes, due to the lack of sunlight, the absence of photosysnthetically-driven primary production, low temperature variations, and oligotrophic conditions. However, periodic groundwater recharge should affect the structure and succession of groundwater microbiomes. To disentangle the long-term temporal changes in bacterial communities of shallow fractured bedrock groundwater, and identify the drivers of the observed patterns, we analysed bacterial 16S rRNA gene sequencing data for samples collected monthly from three groundwater wells over a six-year period (n = 230) along a hillslope recharge area. We showed that the bacterial communities in the groundwater of limestone-mudstone alternations were not stable over time and exhibited non-linear dissimilarity patterns which corresponded to periods of groundwater recharge. Further, we observed an increase in dissimilarity over time (generalized additive model P < 0.001) indicating that the successive recharge events result in communities that are increasingly more dissimilar to the initial reference time point. The sampling period was able to explain up to 29.5% of the variability in bacterial community composition and the impact of recharge events on the groundwater microbiome was linked to the strength of the recharge and local environmental selection. Many groundwater bacteria originated from the recharge-related sources (mean = 66.5%, SD = 15.1%) and specific bacterial taxa were identified as being either enriched or repressed during recharge events. Overall, similar to surface aquatic environments, the microbiomes in shallow fractured-rock groundwater vary through time, though we revealed groundwater recharges as unique driving factors for these patterns. The high temporal resolution employed here highlights the dynamics of bacterial communities in groundwater, which is an essential resource for the provision of clean drinking water; understanding the biological complexities of these systems is therefore crucial.

Microbial intrusion and seasonal dynamics in the groundwater microbiome of a porous basaltic rock aquifer used as municipal water reservoir

Groundwater is a key resource for safe drinking water supply. Yet unconfined aquifers can be vulnerable to microbial contamination during extreme weather events that lead to surface runoff. The current study characterises the groundwater microbiome of a porous basaltic rock aquifer in South-West Iceland used for drinking water extraction and analyses the microbial community dynamics during surface runoff. The groundwater microbial community sampled from 12 wells across the extraction area contained over 745 prokaryotic genera and was phylogenetically similar between wells and most seasons, representing a diverse but homogenous ecosystem. The largest seasonal variation in the microbial community composition was detected during a period of concurrent snow melt and high precipitation leading to surface runoff. This period was characterised by an increased abundance of soil-associated taxa in the groundwater microbiome and specifically of taxa assigned to Aeromonas and Bacillus. A field experiment simulating high surface runoff around a groundwater well confirmed the increased abundance of surface soil microorganisms in the well water, indicating vulnerability of groundwater towards surface microbial intrusion during extreme weather events. As such events are likely to increase due to climate change, novel water management tools such as microbial community analysis could help ensure drinking water safety.

The microbial dimension of submarine groundwater discharge: current challenges and future directions

Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, the microbial dimension of SGD remains poorly understood. SGD can influence marine microbial communities through supplying chemical compounds and microorganisms, and in turn, microbes at the land–ocean transition zone determine the chemistry of the groundwater reaching the ocean. However, compared with inland groundwater, little is known about microbial communities in coastal aquifers. Here, we review the state of the art of the microbial dimension of SGD, with emphasis on prokaryotes, and identify current challenges and future directions. Main challenges include improving the diversity description of groundwater microbiota, characterized by ultrasmall, inactive and novel taxa, and by high ratios of sediment-attached versus free-living cells. Studies should explore microbial dynamics and their role in chemical cycles in coastal aquifers, the bidirectional dispersal of groundwater and seawater microorganisms, and marine bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization and linking taxonomy to activity but also considering the entire groundwater–marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, microbial ecology) are needed to frame the study of terrestrial and aquatic microorganisms beyond the limits of their presumed habitats, and to foster our understanding of SGD processes and their influence in coastal biogeochemical cycles.