Spatio-temporal patterns of microbial communities in a hydrologically dynamic pristine aquifer

Iron coatings on carbonate rocks shape the attached bacterial aquifer community

Most studies of groundwater ecosystems target planktonic microbes, which are easily obtained via water samples. In contrast, little is known about the diversity and function of microbes adhering to rock surfaces, particularly to consolidated rocks. To investigate microbial attachment to rock surfaces, we incubated rock chips from fractured aquifers in limestone-mudstone alternations in bioreactors fed with groundwater from two wells representing oxic and anoxic conditions. Half of the chips were coated with iron oxides, representing common secondary mineralization in fractured rock. Our time-series analysis showed bacteria colonizing the chips within two days, reaching cell numbers up to 4.16 × 105 cells/mm2 after 44 days. Scanning electron microscopy analyses revealed extensive colonization but no multi-layered biofilms, with chips from oxic bioreactors more densely colonized than from anoxic ones. Estimated attached-to-planktonic cell ratios yielded values of up to 106: 1 and 103: 1, for oxic and anoxic aquifers, respectively. We identified distinct attached and planktonic communities with an overlap between 17 % and 42 %. Oxic bioreactors were dominated by proteobacterial genera Aquabacterium and Rhodoferax, while Rheinheimera and Simplicispira were the key players of anoxic bioreactors. Motility, attachment, and biofilm formation traits were predicted in major genera based on groundwater metagenome-assembled genomes and reference genomes. Early rock colonizers appeared to be facultative autotrophs, capable of fixing CO2 to synthesize biomass and a biofilm matrix. Late colonizers were predicted to possess biofilm degrading enzymes such as beta-glucosidase, beta-galactosidase, amylases. Fe-coated chips of both bioreactors featured more potential iron reducers and oxidizers than bare rock chips. As secondary minerals can also serve as energy source, they might favor primary production and thus contribute to subsurface ecosystem services like carbon fixation. Since most subsurface microbes seem to be attached, their contribution to ecosystem services should be considered in future studies.

Responses of microbial communities subjected to hydrodynamically induced disturbances in an organic contaminated site

Organic contaminated sites have gained significant attention as a prominent contributor to shallow groundwater contamination. However, limited knowledge exists regarding the impact of hydrodynamic effects on microbially mediated contaminant degradation at such sites. In this study, we investigated the distribution characteristics and community structure of prokaryotic microorganisms at the selected site during both wet and dry seasons, with a particular focus on their environmental adaptations. The results revealed significant seasonal variations (P < 0.05) in the α-diversity of prokaryotes within groundwater. The dry season showed more exclusive OTUs than the wet season. The response of prokaryotic metabolism to organic pollution pressure in different seasons was explored by PICRUSt2, and enzymes associated with the degradation of organic pollutants were identified based on the predicted functions. The results showed that hormesis was considered as an adaptive response of microbial communities under pollution stress. In addition, structural equation models demonstrated that groundwater level fluctuations can, directly and indirectly, affect the abundance and diversity of prokaryotes through other factors such as oxidation reduction potential (ORP), dissolved oxygen (DO), and naphthalene (Nap). Overall, our findings imply that the taxonomic composition and functional properties of prokaryotes in groundwater in organic contaminated sites is influenced by the interaction between seasonal variations and characteristics of organic pollution. The results provide new insights into microbiological processes in groundwater systems in organic contaminated sites.

Diazotrophic community in the sediments of Poyang Lake in response to water level fluctuations

Water level fluctuations (WLFs) are typical characteristic of floodplain lakes and dominant forces regulating the structure and function of lacustrine ecosystems. The sediment diazotrophs play important roles in contributing bioavailable nitrogen to the aquatic environment. However, the relationship between the diazotrophic community and WLFs in floodplain lakes is unknown. In this paper, we carried out a comprehensive investigation on the alpha diversity, abundance, composition and co-occurrence network of the sediment diazotrophs during different water level phases in Poyang Lake. There were no regular variation patterns in the alpha diversity and abundance of the sediment diazotrophs with the water level phase transitions. The relative abundance of some diazotrophic phyla (including Alphaproteobacteria, Deltaproteobacteri, Euryarchaeota, and Firmicutes) and genera (including Geobacter, Deferrisoma, Desulfuromonas, Rivicola, Paraburkholderia, Methylophilus, Methanothrix, Methanobacterium, and Clostridium) was found to change with the water level phase transitions. The results of ANOSIM, PerMANOVA, and DCA at the OTU level showed that the diazotrophic community structure in the low water level phase was significantly different from that in the two high water level phases, while there was no significant difference between the two high water level phases. These results indicated that the diazotrophic community was affected by the declining water level in terms of the composition, while the rising water level contributed to the recoveries of the diazotrophic community. The diazotrophs co-occurrence network was disrupted by the declining water level, but it was strengthened by the rising water level. Moreover, redundancy analysis showed that the variation of the diazotrophic community composition was mostly related to sediment total nitrogen (TN) and total phosphorous (TP). Interestingly, the levels of sediment TN and TP were also found to vary with the water level phase transitions. Therefore, it might be speculated that the WLFs may influence the sediment TN and TP, and in turn influence the diazotrophic community composition. These data can contribute to broadening our understanding of the ecological impacts of WLFs and the nitrogen fixation process in floodplain lakes.

Rapid Consumption of Dihydrogen Injected into a Shallow Aquifer by Ecophysiologically Different Microbes

The envisaged future dihydrogen (H2) economy requires a H2 gas grid as well as large deep underground stores. However, the consequences of an unintended spread of H2 through leaky pipes, wells, or subterranean gas migrations on groundwater resources and their ecosystems are poorly understood. Therefore, we emulated a short-term leakage incident by injecting gaseous H2 into a shallow aquifer at the TestUM test site and monitored the subsequent biogeochemical processes in the groundwater system. At elevated H2 concentrations, an increase in acetate concentrations and a decrease in microbial α-diversity with a concomitant change in microbial β-diversity were observed. Additionally, microbial H2 oxidation was indicated by temporally higher abundances of taxa known for aerobic or anaerobic H2 oxidation. After H2 concentrations diminished below the detection limit, α- and β-diversity approached baseline values. In summary, the emulated H2 leakage resulted in a temporally limited change of the groundwater microbiome and associated geochemical conditions due to the intermediate growth of H2 consumers. The results confirm the general assumption that H2, being an excellent energy and electron source for many microorganisms, is quickly microbiologically consumed in the environment after a leakage.

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.

From the Mountain to the Valley: Drivers of Groundwater Prokaryotic Communities along an Alpine River Corridor

Rivers are the “tip of the iceberg”, with the underlying groundwater being the unseen freshwater majority. Microbial community composition and the dynamics of shallow groundwater ecosystems are thus crucial, due to their potential impact on ecosystem processes and functioning. In early summer and late autumn, samples of river water from 14 stations and groundwater from 45 wells were analyzed along a 300 km transect of the Mur River valley, from the Austrian alps to the flats at the Slovenian border. The active and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The dataset was used to challenge ecological concepts and assembly processes in shallow aquifers. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse and richer in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use.

Groundwater Microbiology of an Urban Open-Loop Ground Source Heat Pump with High Methane

Ground source heat pumps (GSHPs) are low-carbon alternatives to gas boilers for decarbonizing heating. Open-loop GSHP systems abstract groundwater, pass it through a heat exchanger, and return it to ground or surface water. Groundwater samples from the top and base of an abstraction and a recharge borehole of an open-loop GSHP system in Cardiff, UK were assessed, and compared to two local boreholes in the same aquifer. Groundwater samples were taken when the GSHP system was active (once) and inactive (twice) and analyzed for changes in geochemistry, viable cell counts, and microbial community (16S rRNA gene sequencing). The GSHP had a distinct geochemistry and microbial community compared to the control boreholes, and the abstraction borehole showed greater variability than the recharge borehole. The microbial community of the GSHP system showed an increase in relative abundance of genera involved in oxidation of methane and methylated compounds, of which Methylotenera was the most abundant (up to 83.9% of 16S rRNA gene sequences). There were also changes in genera associated with nitrification (Nitrospira, Nitrosomonas) and those with potential for sulfur and iron cycling (Rhodoferax). Methane concentration was analyzed after identification of methylotrophs and found that methane concentrations were up to 2855 μg L^-1 , thus likely having had a significant impact on the bacterial communities present. Understanding the microbiology and biogeochemistry of GSHP systems provides insight into potential issues with local infrastructure and long-term system performance, and supports modeling to maximize efficient and sustainable use of the subsurface.

Matrix-associated microbial communities in a nitrogen-removing on-site wastewater treatment system are largely structured by niche processes

On-site wastewater treatment systems (OWTSs) can be designed to promote microbial communities with naturally occurring metabolic functions desirable to wastewater treatment. Among such OWTSs are nitrogen-removing biofilters (NRBs), comprising a sand layer overlying a sand-lignocellulose (sand-lc) layer and intended to promote sequential nitrification and denitrification. The design of NRBs is based on the hypothesis that niche processes like environmental selection strongly structure the microbial communities, which predicts that immigrating wastewater communities and matrix-associated communities will be distinct and that the matrix communities in the two layers will be distinct. We characterized NRB microbial communities by 16S ribosomal RNA amplicon sequencing. Selection of the matrix-associated communities was indicated by clear differences from the immigrating community. For matrix-associated communities, alpha and beta diversity differed between the matrix layers, as did the relative abundances of many functional groups and genera. Functional groups with strict metabolisms were nearly exclusively detected in either the sand (ammonia and nitrite oxidizers) or sand-lc layer (methanogens), consistent with the niche hypothesis. Contrary to expectations, denitrifiers as a functional group were not present at greater relative abundance in the sand-lc than sand matrix because of a portfolio effect: some denitrifying genera were more abundant in the sand layer, whereas others were more abundant in the sand-lc layer. This study reveals niche processes acting at different levels of community organization for different biogeochemical functions, a crucial consideration in designing effective and reliable OWTSs to mitigate nitrogen pollution.

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.

Substrate-restricted methanogenesis and limited volatile organic compound degradation in highly diverse and heterogeneous municipal landfill microbial communities

Microbial communities in landfills transform waste and generate methane in an environment unique from other built and natural environments. Landfill microbial diversity has predominantly been observed at the phylum level, without examining the extent of shared organismal diversity across space or time. We used 16S rRNA gene amplicon and shotgun metagenomic sequencing to examine the taxonomic and functional diversity of the microbial communities inhabiting a Southern Ontario landfill. The microbial capacity for volatile organic compound degradation in leachate and groundwater samples was correlated with geochemical conditions. Across the landfill, 25 bacterial and archaeal phyla were present at >1% relative abundance within at least one landfill sample, with Patescibacteria, Bacteroidota, Firmicutes, and Proteobacteria dominating. Methanogens were neither numerous nor particularly abundant, and were predominantly constrained to either acetoclastic or methylotrophic methanogenesis. The landfill microbial community was highly heterogeneous, with 90.7% of organisms present at only one or two sites within this interconnected system. Based on diversity measures, the landfill is a microbial system undergoing a constant state of disturbance and change, driving the extreme heterogeneity observed. Significant differences in geochemistry occurred across the leachate and groundwater wells sampled, with calcium, iron, magnesium, boron, meta and para xylenes, ortho xylenes, and ethylbenzene concentrations contributing most strongly to observed site differences. Predicted microbial degradation capacities indicated a heterogeneous community response to contaminants, including identification of novel proteins implicated in anaerobic degradation of key volatile organic compounds.

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.

Bottom-Up Control of the Groundwater Microbial Food-Web in an Alpine Aquifer

Groundwater ecosystems are typically poor in organic carbon and productivity sustaining a low standing stock of microbial biomass. In consequence, microbial food webs in oligotrophic groundwater are hypothesized to be bottom-up controlled. To date, quantitative information on groundwater microbial communities, food web interactions, and carbon flow is relatively lacking in comparison to that of surface waters. Studying a shallow, porous alpine aquifer we collected data on the numbers of prokaryotes, virus-like particles and heterotrophic nanoflagellates (HNFs), the concentration of dissolved (DOC) and assimilable organic carbon (AOC), bacterial carbon production (BCP), and physical-chemical conditions for a 1 year hydrological cycle. The potential effects of protozoan grazing and viral lysis onto the prokaryotic biomass was tested. Flow of organic carbon through the microbial food web was estimated based on data from the literature. The abundance of prokaryotes in groundwater was low with 6.1 ± 6.9 × 104 cells mL–1, seasonally influenced by the hydrological dynamics, with higher densities coinciding with a lower groundwater table. Overall, the variability in cell numbers was moderate, and so it was for HNFs (179 ± 103 HNFs mL–1) and virus-like particles (9.6 ± 5.7 × 105 VLPs mL–1). The virus to prokaryotes and prokaryote to HNF ratios ranged between 2–230 and 33–2,084, respectively. We found no evidence for a viral control of prokaryotic biomass, and the biomass of HNFs being bottom-up controlled. First estimations point at carbon use efficiencies of 0.2–4.2% with prokaryotic production, and carbon consumed and recycled by HNFs and phages to be of minor importance. This first groundwater microbial food web analysis strongly hints at a bottom-up control on productivity and standing stock in oligotrophic groundwater ecosystems. However, direct measurement of protozoan grazing and phage mediated lysis rates of prokaryotic cells are urgently needed to deepen our mechanistic understanding. The effect of microbial diversity on the population dynamics still needs to be addressed.

Dynamics of microbiotic patterns reveal surface water groundwater interactions in intermittent and perennial streams

Exchange between groundwater (GW), hyporheic zone waters (HZ) and surface waters (SW) is critical for water quality, quantity, and the ecological health and functioning of all three ecosystems. Hydrological exchange is particularly important in intermittent creeks, such as in the Murray Darling Basin, Australia, where stream reaches shift from losing to gaining depending on the volume of surface flows. In this study we used hydrochemistry to identify SW-GW exchange and combined this with eDNA data to analyse the response of eukaryote and prokaryote communities to differing flow conditions within intermittent and perennial stream reaches. Our study suggested that SW and GW microbial communities were only around 30% similar. Differences in microbiota between SW, HZ and GW habitats were driven by changes in relative abundances of surface water dominant organisms (such as those capable of photosynthesis) as well as anaerobic taxa typical of GW environments (e.g., methanogens), with GW and HZ microbial communities becoming increasingly different to those in SW as flow ceased in intermittent creeks. Fine-scale hydrologic changes were identified through microbial communities in the perennial Maules Creek, indicating the importance of GW-SW exchange to biotic communities. This study highlights the importance of flow in shaping microbial communities and biogeochemical cycling within intermittent creeks and their connected alluvial aquifers. Our results suggest that microbiota may prove a useful indicator of SW-GW exchange, and in some circumstances, may be more sensitive in demonstrating fine-scale changes in SW-GW interactions than water chemistry. This knowledge furthers our understanding of GW-SW exchange and its impacts on ecological health.

Identification of groundwater microbial communities and their connection to the hydrochemical environment in southern Laizhou Bay, China

The microbial community plays an important role in the biogeochemical cycle in coastal groundwater ecosystems. However, the composition and controlling factors of the microbial community in coastal closed groundwater systems (CCGSs) with high salinity have rarely been studied. Here, we investigated and analyzed the hydrochemical characteristics and microbial community composition of seven brine samples with high total dissolved solid (TDS) values ranging from 74.5 to 132.3 g/L within and across three coastal saltworks (Yangkou, Hanting, and Changyi) in southern Laizhou Bay (SLB). The bacterial diversity was independent of salinity. Compared with those of low-salinity groundwater, the diversity of the microbial community in brine was lower, but the richness was slightly higher. There was a significant correlation between the microbial community diversity and groundwater sources, which indicated that the microbial communities were affected by groundwater sources. A comparison of the microbial community compositions of the three saltworks showed that the Hanting and Changyi saltworks had similar microbial communities due to their similar sampling depths. In addition, the main force shaping the differences in the microbial communities in both coastal open groundwater systems (COGSs) and CCGSs was identified as the hydraulic connection with the seawater controlled by hydrogeological conditions formed throughout geological history. This study can help to elucidate the biogeochemical processes in coastal aquifers.

Substrate type and plant phenolics influence epiphytic bacterial assembly during short-term succession

In natural ecosystems, large amounts of epiphytic bacteria live on the surfaces of submerged plants or non-biological substrates. Although it contributes greatly to host plant health or ecological functions in waters, little is known about the temporal dynamics and assembly mechanisms of epiphytic bacteria. To test whether host plant chemistry leads to divergent community dynamics, we investigated the fine scale temporal community successions of both epiphytic bacteria and the bacterioplankton of the surrounding water in two submerged plants and one non-biological artificial substance. We first observed differentiated epiphytic or surrounding water bacterial communities for different substrates in small spaces (approximately 1 m × 1 m). Selection played dominant roles in affecting the assembly of epiphytic bacteria in the high-phenolic plant Hydrilla verticillata, while for the artificial substance and the low-phenolic plant Vallisneria natans, drift and dispersal drove the assembly of both epiphytic bacteria and bacterioplankton. The higher selection may also contribute to higher turnover rates in both bacterioplankton and epiphytic communities of H. verticillata, with the latter changing drastically in approximately one week. Epiphytic bacteria in H. verticillata developed more complex networks with a higher proportion of positive links, suggesting that more intense interactions such as mutualism or facilitation may exist within epiphytic bacterial communities of the high-phenolic plant. Our results also implied that for the submerged macrophytes used in biological purification, the dynamics of epiphytic biofilm in the purification-related functional capacities might also be considered.

Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL

Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput Fluidigm^TM functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Further analyses of representative functional genes affiliated with N₂ fixation (nifH), methane oxidation (pmoA), and sulfate reduction (dsrB, and aprA), suggested functional redundancy within the shallow aquifer microbiomes. While more diversified functional gene taxa were observed for the suspended microbial communities than the attached ones except for pmoA, different levels of changes over time and space were observed between these functional genes. Notably, deterministic and stochastic ecological processes shaped the assembly of microbial communities and functional gene reservoirs differently. While homogenous selection was the prevailing process controlling assembly of microbial communities, the neutral processes (e.g., dispersal limitation, drift and others) were more important for the functional genes. The results suggest complex and changing shallow aquifer microbiomes, whose functionality and assembly vary even between the spatially proximate habitats and fractions. This research underscored the importance to include all the interface components for a more holistic understanding of the biogeochemical processes in aquifer ecosystems, which is also instructive for practical applications.

Monitoring of the effects of a temporally limited heat stress on microbial communities in a shallow aquifer

Aquifer thermal energy storage (ATES) is a key concept for the use of renewable energy resources. Interest in ATES performed at high temperature (HT-ATES; > 60 °C) is increasing due to higher energetic efficiencies. HT-ATES induces temperature fluctuations that exceed the natural variability in shallow aquifers, which could lead to adverse effects in subsurface ecosystems by altering the groundwater chemistry, biodiversity, and microbial metabolic activity, resulting in changes of the groundwater quality, biogeochemical processes, and ecosystem functions. The aim of this study was to emulate the initial operating phase of a HT-ATES system with a short-term infiltration of warm water into Pleistocene sandur sediment and, consequently, to monitor the thermal effects on the groundwater microbiome inhabiting an imitated affected space of an HT-ATES system. Therefore, local groundwater was withdrawn, heated up to 75 °C, and re-infiltrated into a shallow aquifer located near Wittstock/Dosse (Brandenburg, Germany) for around five days. Groundwater samples taken regularly before and after the infiltration were analyzed by 16S rRNA gene amplicon sequencing for microbial diversity analyses as well as total cell counting. During the infiltration, a thermal plume with groundwater temperatures increasing from 9 ± 2 to up to ~65 °C was recorded. The highest temperature at which groundwater samples were taken was 34.9 °C, a temperature typically arising in the affected space of an HT-ATES system. The microbial communities in the groundwater were mainly composed of Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, and Actinobacteria, and the total cell numbers ranged from 3.2 * 10⁴ to 3.1 * 10⁶ cells ml^-1. Neither the compositions of the microbial communities nor the total number of cells in groundwater were significantly changed upon moderate temperature increase, indicating that the diverse groundwater microbiome was resilient to the temporally limited heat stress.

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.

Spatiotemporal and seasonal dynamics in the microbial communities of a landfill-leachate contaminated aquifer

The microbiome of an aquifer contaminated by landfill leachate and undergoing intrinsic remediation was characterised using 16S rRNA metabarcoding. The archaeal/bacterial V3-V4 hypervariable region of the 16S rRNA gene was sequenced using Illumina MiSeq, and multivariate statistics were applied to make inferences. Results indicate that the aquifer recharge and aquifer sediment samples harbour different microbial communities compared to the groundwater samples. While Proteobacteria dominated both the recharge and groundwater samples, Acidobacteria dominated the aquifer sediment. The most abundant genera detected from the contaminated aquifer were Polynucleobacter, Rhodoferax, Pedobacter, Brevundimonas, Pseudomonas, Undibacterium, Sulfurifustis, Janthinobacterium, Rhodanobacter, Methylobacter and Aquabacterium. The result also shows that the microbial communities of the groundwater varied spatially, seasonally and interannually, although the interannual variation was significant for only one of the wells. Variation partitioning analysis indicates that water chemistry and well distance are intercorrelated and they jointly accounted for most of the variation in microbial composition. This implies that the species composition and water chemistry characteristics have a similar spatial structuring, presumably caused by the landfill leachate plume. The study improves our understanding of the dynamics in subsurface microbial communities in space and time.

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.

Influence of stormwater infiltration systems on the structure and the activities of groundwater biofilms: Are the effects restricted to rainy periods?

Stormwater infiltration systems (SIS) have been set up to collect and infiltrate urban stormwater runoff in order to reduce flooding and to artificially recharge aquifers. Such practices produce environmental changes in shallow groundwater ecosystems like an increase in organic matter concentrations that could drive changes in structure and functions of groundwater microbial communities. Previous works suggested that SIS influence groundwater physico-chemistry during either rainy and dry period but no study has examined the impact of SIS on groundwater microorganisms during both periods. This study aimed to fill this gap by assessing SIS impacts on groundwater quality parameters in three SIS with vadose zone thickness < 3 m during two contrasting meteorological conditions (rainy/dry periods). Physicochemical (dissolved organic carbon and nutrient concentrations) and microbial variables (biomass, dehydrogenase and hydrolytic activities, and bacterial community structure) were assessed on SIS-impacted and non-SIS-impacted zones of the aquifers for the three SIS. Using clay beads incubated in the aquifer to collect microbial biofilm, we show that SIS increased microbial activities, bacterial richness and diversity in groundwater biofilms during the rainy period but not during the dry period. In contrast, the significant differences in dissolved organic carbon and nutrient concentrations, biofilm biomass and bacterial community structures (Bray-Curtis distances, relative abundances of main bacterial orders) measured between SIS-impacted and non-SIS-impacted zones of the aquifer were comparable during the two periods. These results suggest that structural indicators of biofilm like biomass were probably controlled by long-term effects of SIS on concentrations of dissolved organic matter and nutrients whereas biofilm activities and bacterial richness were temporally stimulated by stormwater runoff infiltrations during the rainy period. This decoupling between the structural and functional responses of groundwater biofilms to stormwater infiltration practices suggests that biofilms functions were highly reactive to fluxes associated with aquifer recharge events.

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.

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

Riverbank filtration has gained increasing importance for balancing rising groundwater demands and securing drinking water supplies. While microbial communities are the pillar of vital ecosystem functions in groundwater, the impact of riverbank filtration on these communities has been understudied so far. Here, we followed changes in microbial community composition based on 16S rRNA gene amplicon sequence variants (ASVs) in an initially pristine shallow porous aquifer in response to surface water intrusion during the early stages of induced riverbank filtration over a course of seven weeks. We further analyzed sediment cores for imprints of river-derived ASVs after seven weeks of riverbank filtration. The onset of the surface water intrusion caused loss of taxa and significant changes in community composition, revealing low disturbance resistance of the initial aquifer microbial communities. SourceTracker analysis revealed that proportions of river-derived ASVs in the groundwater were generally <25%, but locally could reach up to 62% during a period of intense precipitation. However, variation partitioning showed that the impact of dispersal of river-derived ASVs on changes in aquifer microbial community composition was overall outweighed by species sorting due to changes in environmental conditions caused by the infiltrating river water. Proportions of river-derived ASVs on aquifer sediments were <0.5%, showing that taxa transported from the river into the aquifer over the course of the study mainly resided as planktonic microorganisms in the groundwater. Our study demonstrates that groundwater microbial communities react sensitively to changes in environmental conditions caused by surface water intrusion, whereas mass effects resulting from the influx of river-derived taxa play a comparatively minor role.

Linkage Between Dissolved Organic Matter Transformation, Bacterial Carbon Production, and Diversity in a Shallow Oligotrophic Aquifer: Results From Flow-Through Sediment Microcosm Experiments

Aquifers are important reservoirs for organic carbon. A fundamental understanding of the role of groundwater ecosystems in carbon cycling, however, is still missing. Using sediment flow-through microcosms, long-term (171d) experiments were conducted to test two scenarios. First, aquifer sediment microbial communities received dissolved organic matter (DOM) at low concentration and typical to groundwater in terms of composition (DOM-1x). Second, sediments received an elevated concentration of DOM originating from soil (DOM-5x). Changes in DOM composition were analyzed via NMR and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Carbon production, physiological adaptations and biodiversity of groundwater, and sediment prokaryotic communities were monitored by total cell counts, substrate use arrays, and deep amplicon sequencing. The experiments showed that groundwater microbial communities do not react very fast to the sudden availability of labile organic carbon from soil in terms of carbon degradation and biomass production. It took days to weeks for incoming DOM being efficiently degraded and pronounced cell production occurred. Once conditioned, the DOM-1x supplied sediments mineralized 294(±230) μgC L⁻¹_sed d⁻¹, 10-times less than the DOM-5x fed sediment communities [2.9(±1.1) mgC L⁻¹_sed d⁻¹]. However, the overall biomass carbon production was hardly different in the two treatments with 13.7(±4.8) μgC L⁻¹_sed d⁻¹ and 14.3(±3.5) μgC L⁻¹_sed d⁻¹, respectively, hinting at a significantly lower carbon use efficiency with higher DOM availability. However, the molecularly more diverse DOM from soil fostered a higher bacterial diversity. Taking the irregular inputs of labile DOM into account, shallow aquifers are assumed to have a low resilience. Lacking a highly active and responsive microbial community, oligotrophic aquifers are at high risk of contamination with organic chemicals.

Use of bacteria community analysis to distinguish groundwater recharge sources to shallow wells

In this study, bacteria community analysis was performed to supplement a preexisting evaluation of nitrate contamination in drinking water wells at a coastal site in Old Lyme, CT. Given well usage and coastal hydrogeologic conditions, the source(s) of nitrate contamination in domestic wells could not be discerned between local septic systems or a nearby farm where organic fertilizers were used. Groundwater bacteria communities are known to be sensitive to a variety of environmental conditions. As such, they are potentially useful in distinguishing groundwater recharge sources. Groundwater samples collected from wells were analyzed using polymerase chain reactions (PCR) and 16S rRNA sequencing to determine the bacteria distributions in each well. The biostatistical analysis of the data using Bray-Curtis nonmetric multidimensional scaling and permutational multivariate analysis of variance revealed three distinct bacteria community distributions that coincided with three different areas on the site. Additionally, principal component analysis (PCA) of the water quality data revealed that wells with similar bacteria shared similar water quality, all of which was indicative of local recharge. These findings suggested that the domestic well nitrate contamination was derived from local septic systems rather than the farm. Septic indicator analysis using ultra-performance liquid chromatography-tandem mass spectrometry determined the presence of caffeine in domestic wells, which was consistent with the conclusions from the bacteria analysis, PCA, and the known hydrogeologic conditions. The low cost, ease of sample collection, and growing availability of bioinformatics laboratory services and software are conducive to the application of microbial community analysis as a supplemental tool for groundwater investigations.

Seasonal Patterns of Dominant Microbes Involved in Central Nutrient Cycles in the Subsurface

Microbial communities play a key role for central biogeochemical cycles in the subsurface. Little is known about whether short-term seasonal drought and rewetting events influence the dominant microbes involved in C- and N-cycles. Here, we applied metaproteomics at different subsurface sites in winter, summer and autumn from surface litter layer, seepage water at increasing subsoil depths and remote located groundwater from two wells within the Hainich Critical Zone Exploratory, Germany. We observed changes in the dominance of microbial families at subsurface sampling sites with increasing distances, i.e., Microcoleaceae dominated in topsoil seepage, while Candidatus Brocadiaceae dominated at deeper and more distant groundwater wells. Nitrifying bacteria showed a shift in dominance from drought to rewetting events from summer by Nitrosomandaceae to autumn by Candidatus Brocadiaceae. We further observed that the reductive pentose phosphate pathway was a prominent CO₂-fixation strategy, dominated by Woeseiaceae in wet early winter, which decreased under drought conditions and changed to a dominance of Sphingobacteriaceae under rewetting conditions. This study shows that increasing subsurface sites and rewetting event after drought alter the dominances of key subsurface microbes. This helps to predict the consequences of annual seasonal dynamics on the nutrient cycling microbes that contribute to ecosystem functioning.

Comparison of the groundwater microbial community in a salt-freshwater mixing zone during the dry and wet seasons

To gain a better understanding of the microbial community in salt-freshwater mixing zones, in this study, the influence of seasonal variation on the groundwater microbial community was evaluated by high throughput 16S rDNA gene sequencing. The results showed that notable changes in microbial community occurred in a salt-freshwater mixing zone and the groundwater samples in the dry season were more saline than those in the wet season. The increase in precipitation during the wet season relieved local seawater intrusion. Microbial diversity varied greatly with seasons, while no obvious change pattern was found. Proteobacteria was identified as the dominant phylum in all samples. The genus Hydrogenophaga dominated in the dry season, while the genus Acidovorax dominated in the wet season. Dissolved oxygen affected the diversity of the microbial communities during the dry and wet season, while groundwater level had a strong influence on the structure of microbial communities. Phylogenetic molecular network analysis of the microbial communities indicated that increased seawater intrusion led to a more compact microbial network and strengthening the groundwater microbial interactions.

Responses of Rotifer Community to Microhabitat Changes Caused by Summer-Concentrated Rainfall in a Shallow Reservoir, South Korea

Empirical studies suggest that the structural heterogeneity of aquatic ecosystem microhabitat is determined by the diversity and abundance of macrophytes. However, excessive accumulation of free-floating macrophytes on the water surface can reduce the biomass of submerged macrophytes, resulting in a relatively simplified habitat structure. We hypothesized that heavy summer rainfall disrupts the growth of free-floating macrophytes covering much of the Jangcheok Reservoir’s water surface, thereby resulting in a more complex habitat structure by allowing development of a more diverse of macrophytic community. We divided long-term (2008–2017) monitoring data (rainfall, macrophytes, and rotifers) into two groups: Rainy and Dry years, corresponding to years with annual rainfall higher and lower than the total annual average, respectively. We found that summer densities of rotifers fell sharply in Rainy years, but increased continuously in Dry years. This trend resulted in greater autumn densities in Rainy relative to Dry years, which we attributed to changes in habitat related to differential macrophyte development. Moderate disturbance of the water surface caused by high summer rainfall can promote growth of submerged macrophytes by creating large areas of open water and therefore a more complex autumnal microhabitat structure, resulting in seasonal variations in rotifer community structures and populations. Moreover, a highly complex microhabitat structure restricts foraging activity of fish (i.e., Lepomis macrochirus) that prey on rotifers. Based on these findings, we suggest that summer-concentrated rainfall plays an important role in supporting the density and species diversity of rotifers.

High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer

Understanding microbial community structure and function within the subsurface is critical to assessing overall quality and maintenance of groundwater; however, the factors that determine microbial community assembly, structure, and function in groundwater systems and their impact on water quality remains poorly understood. In this study, three shallow wells (FW301, FW303, FW305) in a non-contaminated shallow aquifer in the ENIGMA-Oak Ridge Field Research Center (Oak Ridge, TN) were sampled approximately 3 times a week over a period of three months to measure changes in groundwater geochemistry and microbial diversity. It was expected that the sampled microbial diversity from two historic field wells (FW301, FW303) would be relatively stable, while diversity from a newer well (FW305) would be less stable over time. The wells displayed some degree of hydrochemical variability over time unique to each well, with FW303 being overall the most stable well and FW301 being the most dynamic based upon dissolved oxygen, conductivity, and nitrate. Community analysis via ss-rRNA paired-end sequencing and distribution-based clustering revealed higher OTU richness, diversity, and variability in groundwater communities of FW301 than the other two wells for diversity binned over all time points. Microbial community composition of a given well was on average > 50% dissimilar to any other well at a given time (days), yet, functional gene diversity as measured with GeoChip remained relatively constant. Similarities in community structure across wells were observed with respect to the presence of 20 shared bacterial groups in all samples in all wells, although at varying levels over the tested time period. Similarity percentage (SIMPER) analysis revealed that variability in FW301 was largely attributed to low abundance, highly-transient populations, while variability in the most hydrochemically stable well (FW303) was due to fluctuations in more highly abundant and frequently present taxa. Additionally, the youngest well FW305 showed a dramatic shift in community composition towards the end of the sampling period that was not observed in the other wells, suggesting possible succession events over time. Time-series analysis using vector auto-regressive models and Granger causality showed unique relationships between richness and geochemistry over time in each well. These results indicate temporally dynamic microbial communities over short time scales, with day-to-day population shifts in local community structure influenced by available source community diversity and local groundwater hydrochemistry.

Characterizing microbial diversity and community composition of groundwater in a salt-freshwater transition zone

A salt-freshwater transition zone due to seawater intrusion to groundwater promotes changes in microbial diversity and community composition in a coastal aquifer. The main purpose of this study is to explore the effect of seawater intrusion on the groundwater quality in a salt-freshwater transition zone and identify the microbial fingerprints of seawater intrusion. The changes in microbial community diversity response to the seawater intrusion were characterized by comparing the community structures of the microbes in fresh groundwater, seawater, and salty groundwater from various monitoring wells at different depths using the high throughput 16S rDNA gene sequencing. Results show that seawater had the lowest taxon richness and evenness, and the irrigation water had the highest richness and evenness. Statistical analysis showed that DO%, ORP, and Cl^- affected microbial distribution in the groundwater; while DO% was a main environmental factor influencing microbial community diversity. The analysis of microbial community structures indicates that the order Oceanospirillales and the family Alteromonadaceae could be used as indicators of seawater intrusion.

Are dominant microbial sub-surface communities affected by water quality and soil characteristics?

Subsurface microorganisms must deal with quite extreme environmental conditions. The lack of light, oxygen, and potentially nutrients are the main environmental stresses faced by subsurface microbial communities. Likewise, environmental disruptions providing an unbalanced positive input of nutrients force microorganisms to adapt to varying conditions, visible in the changes in microbial community diversity. In order to test microbial community adaptation to environmental changes, we performed a study in a surface Managed Aquifer Recharge facility, consisting of a settlement basin (two-day residence time) and an infiltration pond. Data on groundwater hydrochemistry, soil texture, and microbial characterization was compiled from surface water, groundwater, and soil samples at two distinct recharge operation conditions. Multivariate statistics by means of Principal Component Analysis (PCA) was the technique used to map the relevant dimensionality reduced combinations of input variables that properly describe the system behavior. The methodology selected allows including variables of different nature and displaying very different range values. Strong differences in the microbial assemblage under recharge conditions were found, coupled to hydrochemistry and grain-size distribution variables. Also, some microbial groups displayed correlations with either carbon or nitrogen cycles, especially showing abundant populations of denitrifying bacteria in groundwater. A significant correlation was found between Methylotenera mobilis and the concentrations of NO₃ and SO₄, and also between Vogesella indigofera and the presence of DOC in the infiltrating water. Also, microbial communities present at the bottom of the pond correlated with representative descriptors of soil grain size distribution.

Seasonal microbial variation accounts for arsenic dynamics in shallow alluvial aquifer systems

Determining the temporal variation of microbial communities in groundwater systems is essential to improve our understanding of hydrochemical dynamics in aquifers, particularly as it relates to the fate of redox-sensitive contaminants like arsenic (As). Therefore, a high-resolution hydrobiogeochemical investigation was conducted in the As-affected alluvial aquifer systems of the Jianghan Plain. In two 25 m-deep monitoring wells, the seasonal variation in the composition of groundwater microbial communities was positively correlated with the change in groundwater level (R = 0.47 and 0.39 in NH03B and NH05B, respectively, P <  0.01), implying that the latter could be a primary driver of the seasonal microbial dynamics. In response to the fluctuating groundwater level, iron (Fe) reducers within the Desulfuromonadales were dominant (9.9 ± 4.7% among different sampling sites) in groundwater microbial communities during the monsoon season and associated with high concentrations of Fe(II) and As, while the predominance (16.7 ± 15.2% among different sampling sites) of iron-oxidizers the Gallionellaceae was accompanied by low Fe(II) and As in the non-monsoon season. These results suggest that microbially-mediated iron reduction/oxidation may have governed the seasonal mobilization/scavenging of As in groundwater. Our results provide new insights into mechanisms responsible for seasonal variations in groundwater As concentrations in similar aquifer systems.

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 10 days 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.

Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments

Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.

Diversity and predictive metabolic pathways of the prokaryotic microbial community along a groundwater salinity gradient of the Pearl River Delta, China

Almost half of the groundwater in the Pearl River Delta (PRD) contains salt water originally derived from paleo-seawater due to the Holocene transgression, which then generates intense physicochemical gradients in the mixing zone between freshwater and saltwater. Although some studies have been conducted on the hydrological and geochemical characteristics of groundwater in the PRD to monitor the intrusion of seawater, little attention has been paid to the microbial community of this particular region. In this study, we implemented a high-throughput sequencing analysis to characterize the microbial communities along a salinity gradient in the PRD aquifer, China. Our results indicated that the microbial community composition varied significantly depending on the salinity of the aquifer. The presence of abundant anaerobic microorganisms of the genera Desulfovibrio and Methanococcus in certain saltwater samples may be responsible for the gas generation of H₂S and CH₄ in the stratum. In saline water samples (TDS > 10 g/L), the linear discriminant analysis effect size (LEfSe) analysis found two biomarkers that usually live in marine environments, and the aquifers of the PRD still contained large quantity of saltwater, indicating that the impact of the paleo-seawater has lasted to this day. The predictive metagenomic analysis revealed that the metabolic pathways present in the groundwater samples studied, included the degradation of pesticides and refractory organics (dichlorodiphenyltrichloroethane (DDT), atrazine and polycyclic aromatic hydrocarbons), matter cycling (methane, nitrogen and sulfur), and inorganic ion and mineral metabolites. This study can help enhance our understanding of the composition of the microbial assemblages and its implications as an environmental indicator in an aquifer affected by saltwater intrusion.

Contaminant concentration versus flow velocity: drivers of biodegradation and microbial growth in groundwater model systems

Aromatic hydrocarbons belong to the most abundant contaminants in groundwater systems. They can serve as carbon and energy source for a multitude of indigenous microorganisms. Predictions of contaminant biodegradation and microbial growth in contaminated aquifers are often vague because the parameters of microbial activity in the mathematical models used for predictions are typically derived from batch experiments, which don’t represent conditions in the field. In order to improve our understanding of key drivers of natural attenuation and the accuracy of predictive models, we conducted comparative experiments in batch and sediment flow-through systems with varying concentrations of contaminant in the inflow and flow velocities applying the aerobic Pseudomonas putida strain F1 and the denitrifying Aromatoleum aromaticum strain EbN1. We followed toluene degradation and bacterial growth by measuring toluene and oxygen concentrations and by direct cell counts. In the sediment columns, the total amount of toluene degraded by P. putida F1 increased with increasing source concentration and flow velocity, while toluene removal efficiency gradually decreased. Results point at mass transfer limitation being an important process controlling toluene biodegradation that cannot be assessed with batch experiments. We also observed a decrease in the maximum specific growth rate with increasing source concentration and flow velocity. At low toluene concentrations, the efficiencies in carbon assimilation within the flow-through systems exceeded those in the batch systems. In all column experiments the number of attached cells plateaued after an initial growth phase indicating a specific “carrying capacity” depending on contaminant concentration and flow velocity. Moreover, in all cases, cells attached to the sediment dominated over those in suspension, and toluene degradation was performed practically by attached cells only. The observed effects of varying contaminant inflow concentration and flow velocity on biodegradation could be captured by a reactive-transport model. By monitoring both attached and suspended cells we could quantify the release of new-grown cells from the sediments to the mobile aqueous phase. Studying flow velocity and contaminant concentrations as key drivers of contaminant transformation in sediment flow-through microcosms improves our system understanding and eventually the prediction of microbial biodegradation at contaminated sites.

Mineral Ecology: Surface Specific Colonization and Geochemical Drivers of Biofilm Accumulation, Composition, and Phylogeny

This study tests the hypothesis that surface composition influences microbial community structure and growth of biofilms. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the phylogenetic and taxonomic variability in microbial communities as a function of surface type (carbonate, silicate, aluminosilicate), media pH, and carbon and phosphate availability. Using high-throughput pyrosequencing, we found that surface type significantly controlled ~70–90% of the variance in phylogenetic diversity regardless of environmental pressures. Consistent patterns also emerged in the taxonomy of specific guilds (sulfur-oxidizers/reducers, Gram-positives, acidophiles) due to variations in media chemistry. Media phosphate availability was a key property associated with variation in phylogeny and taxonomy of whole reactors and was negatively correlated with biofilm accumulation and α-diversity (species richness and evenness). However, mineral-bound phosphate limitations were correlated with less biofilm. Carbon added to the media was correlated with a significant increase in biofilm accumulation and overall α-diversity. Additionally, planktonic communities were phylogenetically distant from those in biofilms. All treatments harbored structurally (taxonomically and phylogenetically) distinct microbial communities. Selective advantages within each treatment encouraged growth and revealed the presence of hundreds of additional operational taxonomix units (OTU), representing distinct consortiums of microorganisms. Ultimately, these results provide evidence that mineral/rock composition significantly influences microbial community structure, diversity, membership, phylogenetic variability, and biofilm growth in subsurface communities.

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation

Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads), and biogeochemical parameters are monitored by quantifying 53 metals, 12 organic acids, 14 anions, and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community and responded to DO. This also directly influenced the pH, and so the biotic impacts of DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part not only by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.

Online flow cytometry reveals microbial dynamics influenced by concurrent natural and operational events in groundwater used for drinking water treatment

Detailed measurements of physical, chemical and biological dynamics in groundwater are key to understanding the important processes in place and their influence on water quality – particularly when used for drinking water. Measuring temporal bacterial dynamics at high frequency is challenging due to the limitations in automation of sampling and detection of the conventional, cultivation-based microbial methods. In this study, fully automated online flow cytometry was applied in a groundwater system for the first time in order to monitor microbial dynamics in a groundwater extraction well. Measurements of bacterial concentrations every 15 minutes during 14 days revealed both aperiodic and periodic dynamics that could not be detected previously, resulting in total cell concentration (TCC) fluctuations between 120 and 280 cells μL⁻¹. The aperiodic dynamic was linked to river water contamination following precipitation events, while the (diurnal) periodic dynamic was attributed to changes in hydrological conditions as a consequence of intermittent groundwater extraction. Based on the high number of measurements, the two patterns could be disentangled and quantified separately. This study i) increases the understanding of system performance, ii) helps to optimize monitoring strategies, and iii) opens the possibility for more sophisticated (quantitative) microbial risk assessment of drinking water treatment systems.

Spatial and temporal variability of bacterial communities in high alpine water spring sediments

Water springs are complex, fragile and taxa-rich environments, especially in highly dynamic ecosystems such as glacier forefields experiencing glacier retreat. Bacterial communities are important actors in alpine water body metabolism, and have shown both high seasonal and spatial variations. Seven springs from a high alpine valley (Matsch Valley, South Tyrol, Italy) were examined via a multidisciplinary approach using both hydrochemical and microbiological techniques. Amplified ribosomal intergenic spacer analysis (ARISA) and electric conductivity (EC) measurements, as well as elemental composition and water stable isotopic analyses, were performed. Our target was to elucidate whether and how bacterial community structure is influenced by water chemistry, and to determine the origin and extent of variation in space and time. There existed variations in both space and time for all variables measured. Diversity values more markedly differed at the beginning of summer and then at the end; the extent of variation in space was prevalent over the time scale. Bacterial community structural variation responded to hydrochemical parameter changes; moreover, the stability of the hydrochemical parameters played an important role in shaping distinctive bacterial communities.

Groundwater Isolation Governs Chemistry and Microbial Community Structure along Hydrologic Flowpaths

This study deals with the effects of hydrodynamic functioning of hard-rock aquifers on microbial communities. In hard-rock aquifers, the heterogeneous hydrologic circulation strongly constrains groundwater residence time, hydrochemistry, and nutrient supply. Here, residence time and a wide range of environmental factors were used to test the influence of groundwater circulation on active microbial community composition, assessed by high throughput sequencing of 16S rRNA. Groundwater of different ages was sampled along hydrogeologic paths or loops, in three contrasting hard-rock aquifers in Brittany (France). Microbial community composition was driven by groundwater residence time and hydrogeologic loop position. In recent groundwater, in the upper section of the aquifers or in their recharge zone, surface water inputs caused high nitrate concentration and the predominance of putative denitrifiers. Although denitrification does not seem to fully decrease nitrate concentrations due to low dissolved organic carbon concentrations, nitrate input has a major effect on microbial communities. The occurrence of taxa possibly associated with the application of organic fertilizers was also noticed. In ancient isolated groundwater, an ecosystem based on Fe(II)/Fe(III) and S/SO₄ redox cycling was observed down to several 100 of meters below the surface. In this depth section, microbial communities were dominated by iron oxidizing bacteria belonging to Gallionellaceae. The latter were associated to old groundwater with high Fe concentrations mixed to a small but not null percentage of recent groundwater inducing oxygen concentrations below 2.5 mg/L. These two types of microbial community were observed in the three sites, independently of site geology and aquifer geometry, indicating hydrogeologic circulation exercises a major control on microbial communities.

Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability

Unchanging physicochemical conditions and nutrient sources over long periods of time in cave and karst subsurface habitats, particularly aquifers, can support stable ecosystems, termed autochthonous microbial endokarst communities (AMEC). AMEC existence is unknown for other karst settings, such as epigenic cave streams. Conceptually, AMEC should not form in streams due to faster turnover rates and seasonal disturbances that have the capacity to transport large quantities of water and sediment and to change allochthonous nutrient and organic matter sources. Our goal was to investigate whether AMEC could form and persist in hydrologically active, epigenic cave streams. We analyzed bacterial diversity from cave water, sediments, and artificial substrates (Bio-Traps®) placed in the cave at upstream and downstream locations. Distinct communities existed for the water, sediments, and Bio-Trap® samplers. Throughout the study period, a subset of community members persisted in the water, regardless of hydrological disturbances. Stable habitat conditions based on flow regimes resulted in more than one contemporaneous, stable community throughout the epigenic cave stream. However, evidence for AMEC was insufficient for the cave water or sediments. Community succession, specifically as predictable exogenous heterotrophic microbial community succession, was evident from decreases in community richness from the Bio-Traps®, a peak in Bio-Trap® community biomass, and from changes in the composition of Bio-Trap® communities. The planktonic community was compositionally similar to Bio-Trap® initial colonizers, but the downstream Bio-Trap® community became more similar to the sediment community at the same location. These results can help in understanding the diversity of planktonic and attached microbial communities from karst, as well as microbial community dynamics, stability, and succession during disturbance or contamination responses over time.

Biodegradation: Updating the concepts of control for microbial cleanup in contaminated aquifers

Biodegradation is one of the most favored and sustainable means of removing organic pollutants from contaminated aquifers but the major steering factors are still surprisingly poorly understood. Growing evidence questions some of the established concepts for control of biodegradation. Here, we critically discuss classical concepts such as the thermodynamic redox zonation, or the use of steady state transport scenarios for assessing biodegradation rates. Furthermore, we discuss if the absence of specific degrader populations can explain poor biodegradation. We propose updated perspectives on the controls of biodegradation in contaminant plumes. These include the plume fringe concept, transport limitations, and transient conditions as currently underestimated processes affecting biodegradation.

Large fractions of CO2-fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds

The traditional view of the dependency of subsurface environments on surface-derived allochthonous carbon inputs is challenged by increasing evidence for the role of lithoautotrophy in aquifer carbon flow. We linked information on autotrophy (Calvin-Benson-Bassham cycle) with that from total microbial community analysis in groundwater at two superimposed-upper and lower-limestone groundwater reservoirs (aquifers). Quantitative PCR revealed that up to 17% of the microbial population had the genetic potential to fix CO2 via the Calvin cycle, with abundances of cbbM and cbbL genes, encoding RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) forms I and II, ranging from 1.14 × 10(3) to 6 × 10(6) genes liter(-1) over a 2-year period. The structure of the active microbial communities based on 16S rRNA transcripts differed between the two aquifers, with a larger fraction of heterotrophic, facultative anaerobic, soil-related groups in the oxygen-deficient upper aquifer. Most identified CO2-assimilating phylogenetic groups appeared to be involved in the oxidation of sulfur or nitrogen compounds and harbored both RubisCO forms I and II, allowing efficient CO2 fixation in environments with strong oxygen and CO2 fluctuations. The genera Sulfuricella and Nitrosomonas were represented by read fractions of up to 78 and 33%, respectively, within the cbbM and cbbL transcript pool and accounted for 5.6 and 3.8% of 16S rRNA sequence reads, respectively, in the lower aquifer. Our results indicate that a large fraction of bacteria in pristine limestone aquifers has the genetic potential for autotrophic CO2 fixation, with energy most likely provided by the oxidation of reduced sulfur and nitrogen compounds.

Evaluating the performance of water purification in a vegetated groundwater recharge basin maintained by short-term pulsed infiltration events

Infiltration of surface water constitutes an important pillar in artificial groundwater recharge. However, insufficient transformation of organic carbon and nutrients, as well as clogging of sediments often cause major problems. The attenuation efficiency of dissolved organic carbon (DOC), nutrients and pathogens versus the risk of bioclogging for intermittent recharge were studied in an infiltration basin covered with different kinds of macrovegetation. The quality and concentration of organic carbon, major nutrients, as well as bacterial biomass, activity and diversity in the surface water, the porewater, and the sediment matrix were monitored over one recharge period. Additionally, the numbers of viral particles and Escherichia coli were assessed. Our study showed a fast establishment of high microbial activity. DOC and nutrients have sustainably been reduced within 1.2 m of sediment passage. Numbers of E. coli, which were high in the topmost centimetres of sediment porewater, dropped below the detection limit. Reed cover was found to be advantageous over bushes and trees, since it supported higher microbial activities along with a good infiltration and purification performance. Short-term infiltration periods of several days followed by a break of similar time were found suitable for providing high recharge rates, and good water purification without the risk of bioclogging.