Groundwater Bacterial Communities Research Articles

Underpinning the ecological response of mixed chlorinated volatile organic compounds (CVOCs) associated with contaminated and bioremediated groundwaters: A potential nexus of microbial community structure and function for strategizing efficient bioremediation

Understanding the structure, dynamics, and functionality of microbial communities is essential for developing sustainable and effective bioremediation strategies, particularly for sites contaminated with mixed chlorinated volatile organic compounds (CVOCs), which can make the biodegradation process more complex and challenging. In this study, 16S rRNA amplicon sequencing revealed a significant change in microbial distribution in response to CVOCs contamination. The loss of sensitive taxa such as Proteobacteria and Acidobacteriota was observed, while CVOCs-resistant taxa such as Campilobacterota were found significantly enriched in contaminated sites. Additionally, varying abundances of crucial enzymes involved in the sequential biodegradation of CVOCs were expressed depending on the contamination level. Association analysis revealed that specific genera such as Sulfurospirillum, Azospira, Trichlorobacter, Acidiphilium, and Magnetospririllum could relatively survive under higher levels of CVOC contamination, whereas pH, ORP and temperature had a negative influence in their abundance and distribution. However, Dechloromonas, Thiobacillus, Pseudarcicella, Hydrogenophaga, and Sulfuritalea showed a negative relationship with CVOC contamination, highlighting their sensitivity towards CVOC contamination. These findings provide valuable insights into the relationship among ecological responses, the groundwater bacterial community, and their functionality in response to mixed CVOC contamination, offering a fundamental basis for developing effective and sustainable bioremediation strategies for CVOC-contaminated groundwater systems.

Correlation Between the Diversity Characteristics of Groundwater Bacterial Community and Environmental Factors in Typical Industrial Areas

In order to investigate the composition and diversity of groundwater bacterial communities in typical industrial areas in Shanghai, the Illumina MiSeq high-throughput technology was adopted to explore the correlation and response mechanism of groundwater bacterial communities and environmental factors in typical industries, combined with the analysis of groundwater tri-nitrogen, heavy metals, organic matter, and other indicators. The results showed that the ammonia nitrogen in the groundwater of the petrochemical industry was 64.49%, 32.46%, and 113.91% higher than that of the textile industry, metal products industry, and other industries (P<0.05), respectively. The main detectable indicators of organic matter were total petroleum hydrocarbons (TPH) and volatile phenol. The mass concentration of volatile phenol in groundwater of the petrochemical industry was significantly higher than that of the textile industry, metal products industry, and other industries (P<0.05). The mass concentration of arsenic in the metal products industry was 49.26% and 50.59% higher than that in the petrochemical industry and other industries (P<0.05), respectively. Chloride, manganese, sulfate, etc., were significantly different in different industries (P<0.05). The Shannon index of groundwater in the textile industry was the highest at 3.14, whereas the Shannon index and Ace index of the groundwater in the metal products industry were as low as at 2.42 and 960.46, respectively. The dominant bacterial phylum in groundwater in the industrial area was Proteobacteria, accounting for 80.05%-86.18%. Arsenic, mercury, TPH, etc. were the main influencing factors in groundwater in industrial areas, whereas the nitrifying bacteria, denitrifying bacteria, and organic matter-degrading bacteria were mostly related to groundwater environmental factors. The results of this study can provide theoretical support for groundwater pollution risk management and microbial remediation in petrochemical and metal product industrial areas.

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.

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.

Patterns of groundwater bacterial communities along the petroleum hydrocarbon gradient

Groundwater contamination by petroleum hydrocarbons has become a worldwide environmental problem. Despite that microorganisms played an important role in biogeochemical processes such as hydrocarbon degradation, comprehensive understanding of the structure, function, and interactions of groundwater bacterial communities in petroleum hydrocarbon-contaminated sites is still lacking. Here we investigated the groundwater bacterial communities along a total petroleum hydrocarbon gradient (TPH: 0.01–2.09 mg/L) at an abandoned chemical factory site by sequencing microbial 16 S rRNA gene amplicons. Results showed that hydrocarbon contamination in groundwater reduced the bacterial diversity, and favored the growth of some species, such as members of the β-, γ-Proteobacteria and Planctomycetes. TPH exerted profound selection pressure on the bacterial community, as the variation of community structure along the TPH gradient were significantly correlated with the petroleum hydrocarbon tolerance of the community (r = 0.362; p < 0.001). Other geochemical variables of the groundwater, including pH, sampling depth, oxidation-reduction potential, temperature, and dissolved oxygen, also influenced the community structure. Variations in bacterial community structure thus altered the functional potential, with significantly higher alkane (alkB and alkH) and PAH (nahF and phdK) degradation gene abundances in the relatively high contaminated sampling wells. By conducting the ecological network analysis, we identified a potentially important ecological module relating to petroleum hydrocarbon degradation, which is mainly composed of members of Proteobacteria. This suggested the potential metabolic cross-feeding relationship of Proteobacteria in utilizing petroleum hydrocarbon. These findings illustrate an overall picture of bacterial communities involved in a petroleum hydrocarbon contamination site and provided useful information for groundwater restoration and environmental management.

Determining the primary sources of groundwater bacterial communities in a large-scale plain area: Microbial source tracking and interpretation for different land use patterns

Groundwater quality has been profoundly affected by human activities, especially in large-scale plain areas with high population density. However, it remains unclear how groundwater has been influenced, especially at the microbial community level. Here, a metagenome-based microbial source tracking (MST) technique was used to track the sources of groundwater microbial communities associated with land use patterns in three-dimensional space in a large-scale plain area in the middle of the Yangtze River Basin. Although groundwater and surface water bacterial communities were different, there was considerable evidence of bacterial seeding from surface water to groundwater. Furthermore, the aquaculture pond was found to be the main contributor to the groundwater microbial community (~41.0 % interpretation rate in both rainy and dry seasons). The contribution of farmland to the groundwater microbial community (39.2 %) was similar to that of the aquaculture pond during the rainy season, while it was higher than that during the dry season (29.9 %); however, the contribution of microbes from the lake to groundwater was low (6.9–8.7 %). Further, antibiotic resistance genes (ARGs) and bacteria co-occurrence networks of aquaculture ponds and groundwater were more alike than those of other investigated aquatic systems. In addition, aquaculture ponds could bring non-negligible negative impacts to groundwater, such as pathogen infiltration and ARG enrichment. This work highlights the importance of the use of MST combined with land use patterns to reliably track the sources of groundwater microbial communities in large-scale plain areas and provides a deeper insight into the sources of groundwater pollution and protection of groundwater from a microbial perspective.

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.

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.

The impact of heavy rain event on groundwater microbial communities in Xikuangshan, Hunan Province, P.R. China

With the increase of the frequency and intensity of extreme precipitation in the context of global warming, the subsequent impact on groundwater ecosystem is urgently needed to be investigated. To understand the impact of heavy rain event (HRE) on groundwater microbial communities, sampling campaigns were conducted at Xikuangshan (XKS), the world largest antimony deposit, in dry period (DP) without precipitation and wet period with an HRE, respectively. Samples were subsequently subjected to high throughput sequencing, function prediction by FAPROTAX and physicochemical properties analysis. Results demonstrated that HRE significantly shifted the bacterial compositions, potential functions and microbial interactions. Betaproteobacteria dominated in DP, whereas Gammaproteobacteria was abundant in HRE. Microbial functions such as aromatic compound degradation, nitrate reduction, sulfate respiration and methanol oxidation were enriched in HRE. Moreover, HRE also disturbed microbial interactions and resulted in a loosely connected and less stable co-occurrence network of bacterial communities. Multiple variables such as pH, Sb, PO43−, Eh ect. controlled groundwater bacterial communities and predicted functions during HRE and DP, whereas Sb concentration was the most important one. Our results firstly demonstrated that HRE results in significant variations in the composition, potential functions and interactions of bacterial communities in high-Sb groundwater and enhanced our understanding on the response of microbial community to extreme precipitation in the context of global warming.

Changes in groundwater bacterial community during cyclic groundwater‐table variations

AbstractColumn experiments containing an aquifer sand were subjected to static and oscillating water tables to investigate the impact of natural fluctuations and rainfall infiltration on the groundwater bacterial community just below the phreatic surface, and its association with the geochemistry. Once the columns were established, the continuously saturated zone was anoxic in all three columns. The rate of soil organic matter (SOM) mineralization was higher when the water table varied cyclically than when it was static due to the greater availability of NO3− and SO42−. Natural fluctuations in the water table resulted in a similar NO3− concentration to that observed with a static water table but the cyclic wetting of the intermittently saturated zone resulted in a higher SO42− concentration. Rainfall infiltration induced cyclic water‐table variations resulted in a higher NO3− concentration than those in the other two columns, and a SO42− concentration intermediate between those columns. As rainwater infiltration resulted in slow downward displacement of the groundwater, it is inferred that NO3− and SO42− were being mobilized from the vadose zone. NO3− was mainly released by SOM mineralization (which was enhanced by the infiltration of oxygenated rainwater), but the larger amount of SO42− release required a second mechanism (possibly desorption). Different groundwater bacterial communities evolved from initially similar populations due to the different groundwater histories.

Evaluation of groundwater bacterial community composition to inform waterborne pathogen vulnerability assessments

Microbial water quality evaluations are essential for determining the vulnerability of subsurface drinking water sources to fecal pathogen intrusion. Rather than directly monitor waterborne pathogens using culture- or enumeration-based techniques, the potential of assessing bacterial community using 16S rRNA gene amplicon sequencing to support these evaluations was investigated. A framework for analyzing 16S rRNA gene amplicon sequencing results featuring negative-binomial generalized linear models is demonstrated, and applied to bacterial taxa sequences in purge water samples collected from a shallow, highly aerobic, unconfined aquifer. Bacterial taxa relevant as indicators of fecal source and surface connectivity were examined using this approach. Observed sequences of Escherichia, a genus suggestive of fecal source, were consistently detected but not confirmed by culture-based methods. On the other hand, episodic appearance of anaerobic taxa sequences in this highly aerobic environment, namely Clostridia and Bacteroides, warrants further investigation as potential indicators of fecal contamination. Betaproteobacteria sequences varied significantly on a seasonal basis, and therefore may be linked to understanding surface-water groundwater interactions at this site. However, sequences that are often encountered in surface water bodies (Cyanobacteria and Flavobacteriia) were notably absent or present at very low levels, suggesting that microbial transport from surface-derived sources may be rather limited. This work demonstrates the utility of 16S rRNA gene amplicon sequencing for contextualizing and complementing conventional microbial techniques, allowing for hypotheses about source and transport processes to be tested and refined.

Shift in Natural Groundwater Bacterial Community Structure Due to Zero-Valent Iron Nanoparticles (nZVI).

Toxic and persistent contaminants in groundwater are technologically difficult to remediate. Remediation techniques using nanoparticles (NPs) such as nZVI (Zero-Valent Iron) are applicable as in situ reduction or oxidation agents and give promising results for groundwater treatment. However, these NP may also represent an additional contamination in groundwater. The aims of this study are to assess the impact of nZVI on the nitrate-reducing potential, the abundance and the structure of a planktonic nitrate-reducing bacterial community sampled in groundwater from a multicontaminated site. An active nitrate-reducing bacterial community was obtained from groundwater samples, and inoculated into batch reactors containing a carbon substrate, nitrate and a range of nZVI concentrations (from 0 to 70.1 mg Fe.L-1). Physical (pH, redox potential), chemical ( concentrations) and biological (DNA, RNA) parameters were monitored during 1 week, as well as nZVI size distribution and mortality of bacteria. Nitrate-reducing activity was temporally stopped in the presence of nZVI at concentrations higher than 30 mg L-1, and bacterial molecular parameters all decreased before resuming to initial values 48 h after nZVI addition. Bacterial community composition was also modified in all cultures exposed to nZVI as shown by CE-SSCP fingerprints. Surprisingly, it appeared overall that bacteria viability was lower for lower nZVI concentrations. This is possibly due to the presence of larger, less reactive NP aggregates for higher nZVI concentrations, which inhibit bacterial activity but could limit cell mortality. After 1 week, the bacterial cultures were transplanted into fresh media without nZVI, to assess their resilience in terms of activity. A lag-phase, corresponding to an adaptation phase of the community, was observed during this step before nitrate reduction reiterated, demonstrating the community’s resilience. The induction by nZVI of modifications in the bacterial community composition and thus in its metabolic potentials, if also occurring on site, could affect groundwater functioning on the long term following nZVI application. Further work dedicated to the study of nZVI impact on bacterial community directly on site is needed to assess a potential impact on groundwater functioning following nZVI application.

Structural and Functional Changes of Groundwater Bacterial Community During Temperature and pH Disturbances.

In this study, we report the characteristics of a microbial community in sampled groundwater and elucidate the effects of temperature and pH disturbances on bacterial structure and nitrogen-cycling functions. The predominant phyla of candidate OD1, candidate OP3, and Proteobacteria represented more than half of the total bacteria, which clearly manifested as a "low nucleic acid content (LNA) bacteria majority" type via flow cytometric fingerprint. The results showed that LNA bacteria were more tolerant to rapid changes in temperature and pH, compared to high nucleic acid content (HNA) bacteria. A continuous temperature increase test demonstrated that the LNA bacterial group was less competitive than the HNA bacterial group in terms of maintaining their cell intactness and growth potential. In contrast, the percentage of intact LNA bacteria was maintained at nearly 70% with pH decrease, despite a 50% decrease in total intact cells. Next-generation sequencing results revealed strong resistance and growth potential of phylum Proteobacteria when the temperature increased or the pH decreased in groundwater, especially for subclasses α-, β-, and γ-Proteobacteria. In addition, relative abundance of nitrogen-related functional genes by qPCR showed no difference in nitrifiers or denitrifiers within 0.45μm-captured and 0.45μm-filterable bacteria due to phylogenetic diversity. One exception was the monophyletic anammox bacteria that belong to the phylum Planctomycetes, which were mostly captured on a 0.45-μm filter. Furthermore, we showed that both temperature increase and pH decrease could enhance the denitrification potential, whereas the nitrification and anammox potentials were weakened.

Clay beads as artificial trapping matrices for monitoring bacterial distribution among urban stormwater infiltration systems and their connected aquifers.

Stormwater infiltration systems (SIS) have been developed to limit surface runoff and flooding in urban areas. The impacts of such practices on the ecological and biological quality of groundwater ecosystems remain poorly studied due to the lack of efficient methodologies to assess microbiological quality of aquifers. In the present study, a monitoring method based on the incubation of artificial matrices (clay beads) is presented to evaluate microbial biomass, microbial activities, and bacterial community structure. Four microbial variables (biomass, dehydrogenase and hydrolytic activities, bacterial community structures) were measured on clay beads incubated in three urban water types (stormwater surface runoffs, SIS-impacted and non-impacted groundwaters) for six SIS. Analyses based on next-generation sequencing (NGS) of partial rrs (16S rRNA) PCR products (V5-V6) were used to compare bacterial community structures of biofilms on clay beads after 10days of incubation with those of waters collected from the same sampling points at three occasions. Biofilm biomass and activities on clay beads were indicative of nutrient transfers from surface to SIS-impacted groundwaters. Biofilms allowed impacts of SIS on groundwater bacterial community structures to be determined. Although bacterial communities on clay beads did not perfectly match those of waters, clay beads captured the most abundant bacterial taxa. They also captured bacterial taxa that were not detected in waters collected at three occasions during the incubation, demonstrating the integrative character of this approach. Monitoring biofilms on clay beads also allowed the tracking of bacterial genera containing species representing health concerns.

Toward Integrative Bacterial Monitoring of Metolachlor Toxicity in Groundwater.

Common herbicides such as metolachlor (MET), and their transformation products, are frequently detected in groundwater worldwide. Little is known about the response of groundwater bacterial communities to herbicide exposure, and its potential use for ecotoxicological assessment. The response of bacterial communities exposed to different levels of MET from the Ariège alluvial aquifer (Southwest of France) was investigated in situ and in laboratory experiments. Variations in both chemistry and bacterial communities were observed in groundwater, but T-RFLP analysis did not allow to uncover a pesticide-specific effect on endogenous bacterial communities. To circumvent issues of hydrogeochemical and seasonal variations in situ, groundwater samples from two monitoring wells of the Ariège aquifer with contrasting records of pesticide contamination were exposed to different levels of MET in laboratory experiments. The standard Microtox® acute toxicity assay did not indicate toxic effects of MET, even at 5 mg L-1 (i.e., 1000-fold higher than in contaminated groundwater). Analysis of MET transformation products and compound-specific isotope analysis (CSIA) in laboratory experiments demonstrated MET biodegradation but did not correlate with MET exposure. High-throughput sequencing analysis (Illumina MiSeq) of bacterial communities based on amplicons of the 16S rRNA gene revealed that bacterial community differed mainly by groundwater origin rather than by its response to MET exposure. OTUs correlating with MET addition ranged between 0.4 to 3.6% of the total. Predictive analysis of bacterial functions impacted by pesticides using PICRUSt suggested only minor changes in bacterial functions with increasing MET exposure. Taken together, results highlight MET biodegradation in groundwater, and the potential use of bacterial communities as sensitive indicators of herbicide contamination in aquifers. Although detected effects of MET on groundwater bacterial communities were modest, this study illustrates the potential of integrating DNA- and isotopic analysis-based approaches to improve ecotoxicological assessment of pesticide-contaminated aquifers. GRAPHICAL ABSTRACTAn integrative approach was develop to investigate in situ and in laboratory experiments the response of bacterial communities exposed to different levels of MET from the Ariége alluvial aquifer (Southwest of France).

Carbon cycling and food web interaction in groundwater ecosystems - key drivers and major limitations

Groundwater ecosystems are naturally low in productivity (oligotrophic) reflected by a comparably low standing stock of biomass and slow growth and reproduction of organisms. On the other hand, aquifers are, due to their dimensions, enormous (interim) reservoirs of carbon. However, since we typically lack detailed information on carbon and energy flow through groundwater food webs, it is difficult to predict effects of climate and global change on groundwater ecosystems performance with regard to ‘sink’ or ‘source’ of carbon. Applying stable isotope analysis, high end mass spectrometry, and flow cytometry in addition to a suite of established methods in microbiology and geochemistry, we started to dissect, at selected sites, the various pools and fluxes of organic carbon in aquifers, including dissolved organic matter, particulate organic matter, and organisms. Moreover we investigated the link between carbon (organic and inorganic) and microbial growth and productivity. Last but not least, we tried to uncover food sources for groundwater fauna and the connection to microbes. The work was done in collaboration with Roland Hofmann, Katrin Hug, Marion Gallus, Lucas Fillinger, Marina Spona-Friedl, Alexander Braun, Ramona Brejcha (Institute of Groundwater Ecology at the Helmholtz Zentrum München, Germany) and Jenny Uhl, Norbert Hertkorn, and Philip Schmitt-Kopplin (Research Unit Analytical Biogeochemistry at the Helmholtz Zentrum München). Groundwater rarely contained less than 1 mg/L DOC, however, with only a small fraction being readily biodegradable (BDOC, AOC). Unrecognized, 10-100 times the amount of organic carbon dissolved in groundwater was found to be adsorbed to the sediment matrix. Cell numbers and activities of microbes in aquifers typically ranged 1-3 orders below values from surface waters. In fact, carbon use efficiency (CUE) of groundwater bacterial communities was considerably lower than values from other oligotrophic aquatic environments, with a mean value of 5% (200 samples from 100 sites). There is ample evidence that biogeochemical processes are primarily linked to the sediment associated microbial communities that outnumber their suspended counterparts in terms of biomass and activity by 1-4 orders of magnitude. While groundwater fauna at many sites seem to live on plant derived organic matter and cannibalism, we also collected evidence for chemolithoautotrophic primary production fueling groundwater food webs.

Southern South Australian groundwater microbe diversity.

Groundwater is increasingly used globally for domestic, industrial and agricultural production. While many studies have focused on groundwater as a resource, the diverse ecosystems within are often ignored. Here, we assess 54 Southern South Australian groundwater microbial communities from the populated part of the state to assess their status and dynamics in isolated groundwater systems. We observed a strong site-to-site individuality in groundwater bacterial communities, likely due to the isolated nature of groundwater bodies leading to unique ecosystems. Rank abundance analysis indicates bacterial diversity is maintained even at low abundances and that the distribution fits classical ecological models for strong competition in resource-limited environments. Combined, our data indicates that despite overrepresentation of pollutant-associated bacterial orders in and around the Adelaide metropolitan area, microbial communities remain diverse and show little evidence of converging on a common pollutant-effected community.

Aquifer recharge with stormwater runoff in urban areas: Influence of vadose zone thickness on nutrient and bacterial transfers from the surface of infiltration basins to groundwater

Stormwater infiltration systems (SIS) have been built in urban areas to reduce the environmental impacts of stormwater runoff. Infiltration basins allow the transfer of stormwater runoff to aquifers but their abilities to retain contaminants depend on vadose zone properties. This study assessed the influence of vadose zone thickness (VZT) on the transfer of inorganic nutrients (PO43−, NO3−, NH4+), dissolved organic carbon (total -DOC- and biodegradable -BDOC-) and bacteria. A field experiment was conducted on three SIS with a thin vadose zone (<3 m) and three SIS with a thick vadose zone (>10 m). Water samples were collected at three times during a rainy period of 10 days in each infiltration basin (stormwater runoff), in the aquifer impacted by infiltration (impacted groundwater) and in the same aquifer but upstream of the infiltration area (non-impacted groundwater). Inorganic nutrients, organic matter, and dissolved oxygen (DO) were measured on all water samples. Bacterial community structures were investigated on water samples through a next-generation sequencing (NGS) scheme of 16S rRNA gene amplicons (V5-V6). The concentrations of DO and phosphate measured in SIS-impacted groundwaters were significantly influenced by VZT due to distinct biogeochemical processes occurring in the vadose zone. DOC and BDOC were efficiently retained in the vadose zone, regardless of its thickness. Bacterial transfers to the aquifer were overall low, but data obtained on day 10 indicated a significant bacterial transfer in SIS with a thin vadose zone. Water transit time and water saturation of the vadose zone were found important parameters for bacterial transfers. Most bacterial taxa (>60%) from impacted groundwaters were not detected in stormwater runoff and in non-impacted groundwaters, indicating that groundwater bacterial communities were significantly modified by processes associated with infiltration (remobilization of bacteria from vadose zone and/or species sorting).

Investigating antibiotics, antibiotic resistance genes, and microbial contaminants in groundwater in relation to the proximity of urban areas.

Groundwater is an essential public and drinking water supply and its protection is a goal for global policies. Here, we investigated the presence and prevalence of antibiotic residues, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and microbial contamination in groundwater environments at various distances from urban areas. Antibiotic concentrations ranged from below detection limit to 917 ng/L, being trimethoprim, macrolide, and sulfonamide the most abundant antibiotic classes. A total of eleven ARGs (aminoglycoside, β-lactam, chloramphenicol, Macrolide-Lincosamide-Streptogramin B - MLSB, sulfonamide, and tetracycline), one antiseptic resistance gene, and two MGEs were detected by qPCR with relative abundances ranging from 6.61 × 10-7 to 2.30 × 10-1 copies/16S rRNA gene copies. ARGs and MGEs were widespread in the investigated groundwater environments, with increased abundances not only in urban, but also in remote areas. Distinct bacterial community profiles were observed, with a higher prevalence of Betaproteobacteria and Bacteroidetes in the less-impacted areas, and that of Firmicutes in the contaminated groundwater. The combined characteristics of increased species diversity, distinct phylogenetic composition, and the possible presence of fecal and/or pathogenic bacteria could indicate different types of contamination. Significant correlations between ARGs, MGEs and specific taxa within the groundwater bacterial community were identified, revealing the potential hosts of resistance types. Although no universal marker gene could be determined, a co-selection of int1, qacEΔ1 and sulI genes, a proxy group for anthropogenic pollution, with the tetC, tetO, tetW resistance genes was identified. As the tet group was observed to follow the pattern of environmental contamination for the groundwater samples investigated in this study, our results strongly support the proposal of this group of genes as an environmental tracer of human impact. Overall, the present study investigated several emerging contaminants in groundwater habitats that may be included in monitoring programs to enable further regulatory and protection measures.

Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation.

The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L. Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. Across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges, indicating niche-specific responses of these autochthonous populations. Altogether, our findings suggest that monitored natural attenuation is an appropriate remediation strategy for DCM contamination, and that high-throughput sequencing technologies are a robust method for assessing the potential role of biodegrading bacterial assemblages in the apparent reduction of DCM concentrations in environmental scenarios.