The endolithic bacterial diversity of shallow bedrock ecosystems

Effect of tire wear particle accumulation on nitrogen removal and greenhouse gases abatement in bioretention systems: Soil characteristics, microbial community, and functional genes

Tire wear particles (TWPs), as predominant microplastics (MPs) in road runoff, can be captured and retained by bioretention systems (BRS). This study aimed to investigate the effect of TWPs accumulation on nitrogen processes, focusing on soil characteristics, microbial community, and functional genes. Two groups of lab-scale bioretention columns containing TWPs (0 and 100 mg g-1) were established. The removal efficiencies of NH4+-N and TN in BRS significantly decreased by 7.60%-24.79% and 1.98%-11.09%, respectively, during the 101 days of TWPs exposure. Interestingly, the emission fluxes of N2O and CO2 were significantly decreased, while the emission flux of CH4 was substantially increased. Furthermore, prolonged TWPs exposure significantly influenced the contents of soil organic matter (increased by 27.07%) and NH4+-N (decreased by 42.15%) in the planting layer. TWPs exposure also significantly increased dehydrogenase activity and substrate-induced respiration rate, thereby promoting microbial metabolism. Microbial sequencing results revealed that TWPs decreased the relative abundance of nitrifying bacteria (Nitrospira and Nitrosomonas) and denitrifying bacteria (Dechloromonas and Thauera), reducing the nitrification rate by 42.24%. PICRUSt2 analysis further indicated that TWPs changed the relative abundance of functional genes related to nitrogen and enzyme-coding genes.

In situ incubation of iron(II)-bearing minerals and Fe(0) reveals insights into metabolic flexibility of chemolithotrophic bacteria in a nitrate polluted karst aquifer

Groundwater nitrate pollution is a major reason for deteriorating water quality and threatens human and animal health. Yet, mitigating groundwater contamination naturally is often complicated since most aquifers are limited in bioavailable carbon. Since metabolically flexible microbes might have advantages for survival, this study presents a detailed description and first results on our modification of the BacTrap© method, aiming to determine the prevailing microbial community's potential to utilize chemolithotrophic pathways. Our microbial trapping devices (MTDs) were amended with four different iron sources and incubated in seven groundwater monitoring wells for ∼3 months to promote growth of nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOxB) in a nitrate-contaminated karst aquifer. Phylogenetic analysis based on 16S rRNA gene sequences implies that the identity of the iron source influenced the microbial community's composition. In addition, high throughput amplicon sequencing revealed increased relative 16S rRNA gene abundances of OTUs affiliated to genera such as Thiobacillus, Rhodobacter, Pseudomonas, Albidiferax, and Sideroxydans. MTD-derived enrichments set up with Fe(II)/nitrate/acetate to isolate potential NRFeOxB, were dominated by e.g., Acidovorax spp., Paracoccus spp. and Propionivibrio spp. MTDs are a cost-effective approach for investigating microorganisms in groundwater and our data not only solidifies the MTD's capacity to provide insights into the metabolic flexibility of the aquifer's microbial community, but also substantiates its metabolic potential for anaerobic Fe(II) oxidation.

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.

The enrichment of more functional microbes induced by the increasing hydraulic retention time accounts for the increment of autotrophic denitrification performance

With pyrite (FeS2) and polycaprolactone (PCL) as electron donors, three denitrification systems, namely FeS2-based autotrophic denitrification (PAD) system, PCL-supported heterotrophic denitrification (PHD) system and split-mixotrophic denitrification (PPMD) system, were constructed and operated under varying hydraulic retention times (HRT, 1-48 h). Compared with PAD or PHD, the PPMD system could achieve higher removals of NO3--N and PO43--P, and the effluent SO42- concentration was greatly reduced to 7.28 mg/L. Similarly, the abundance of the dominant genera involved in the PAD (Thiobacillus, Sulfurimonas, and Ferritrophicum, etc.) or PHD (Syntrophomonas, Desulfomicrobium, and Desulfovibrio, etc.) process all increased in the PPMD system. Gene prediction completed by PICRUSt2 showed that the abundance of the functional genes involved in denitrification and sulfur oxidation all increased with the increase of HRT. This also accounted for the increased contribution of autotrophic denitrification to total nitrogen removal in the PPMD system. In addition, the analysis of metabolic pathways disclosed the specific conversion mechanisms of nitrogen and sulfur inside the reactor.

Simultaneous partial nitrification, denitrification, and phosphorus removal in sequencing batch reactors via controlled reduced aeration and short-term sludge retention time decrease

Simultaneous bio-treatment processes of organic carbon (C)-, nitrogen (N)-, and phosphorus (P)-containing wastewater are challenged by insufficient carbon sources in the effluent. In the present study, two parallel anaerobic/aerobic sequencing batch reactors (R-1 and R-2) treating low C/N (≤4) wastewater were employed using different partial nitrification start-up strategies, controlled reduced aeration, and decreased sludge retention time. Advanced removal efficiencies for NH4+-N (≥96%), total nitrogen (TN, ≥86%), PO43--P (≥95%), and CODintra (≥91%) were realized, with TN and PO43--P effluent concentrations of 10.0 ± 3.5 and 0.11 ± 0.3 mg/L in R-1 and 9.28 ± 4.0 and 0.11 ± 0.1 mg/L in R-2, respectively. Higher nitrite accumulation rate (nearly 100%) and TN (121.1 ± 0.7 mg TN/g VSS·d) and P (12.5 ± 0.6 mg PO43--P/g VSS·d) removal loadings were obtained in R-2 by a thorough elimination of nitrite-oxidizing bacteria. Moreover, different microbial structures and nutrient removal pathways were identified. Denitrifying glycogen-accumulating organisms (Candidatus Competibacter) and phosphorus-accumulating organisms (PAOs) (Tetrasphaera) removed N and P with partial nitrification-endogenous denitrification pathways and aerobic P removal in R-1. In R-2, aerobic denitrifying bacteria (Psychrobacter) and PAOs ensured N and P removal through the partial nitrification-aerobic denitrification and aerobic P removal pathways. Compared to R-1, R-2 offers greater efficiency, convenience, and scope to further reduce carbon-source demand.

A glimpse of the paleome in endolithic microbial communities

BACKGROUND

The terrestrial subsurface is home to a significant proportion of the Earth's microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments mainly by using 16S rRNA gene surveys. To obtain more insights about biomass of consolidated rocks and the metabolic status of endolithic microbiomes, we investigated interbedded limestone and mudstone from the vadose zone, fractured aquifers, and deep aquitards.

RESULTS

By adapting methods from microbial archaeology and paleogenomics, we could recover sufficient DNA for downstream metagenomic analysis from seven rock specimens independent of porosity, lithology, and depth. Based on the extracted DNA, we estimated between 2.81 and 4.25 × 105 cells × g-1 rock. Analyzing DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens, all obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay indicating that water saturation and not flow is controlling subsurface microbial survival. Decoding the taxonomy and functional potential of paleome communities revealed increased abundances for sequences affiliated with chemolithoautotrophs and taxa such as Cand. Rokubacteria. We also found a broader metabolic potential in terms of aromatic hydrocarbon breakdown, suggesting a preferred utilization of sedimentary organic matter in the past.

CONCLUSIONS

Our study suggests that limestones function as archives for genetic records of past microbial communities including those sensitive to environmental stress at modern times, due to their specific conditions facilitating long-term DNA preservation. Video Abstract.

Adaptation of the Endolithic Biome in Antarctic Volcanic Rocks

Endolithic microorganisms, ranging from microeukaryotes to bacteria and archaea, live within the cracks and crevices of rocks. Deception Island in Antarctica constitutes an extreme environment in which endoliths face environmental threats such as intense cold, lack of light in winter, high solar radiation in summer, and heat emitted as the result of volcanic eruptions. In addition, the endolithic biome is considered the harshest one on Earth, since it suffers added threats such as dryness or lack of nutrients. Even so, samples from this hostile environment, collected at various points throughout the island, hosted diverse and numerous microorganisms such as bacteria, fungi, diatoms, ciliates, flagellates and unicellular algae. These endoliths were first identified by Scanning Electron Microscopy (SEM). To understand the molecular mechanisms of adaptation of these endoliths to their environment, genomics techniques were used, and prokaryotic and eukaryotic microorganisms were identified by metabarcoding, sequencing the V3-V4 and V4-V5 regions of the 16S and 18S rRNA genes, respectively. Subsequently, the sequences were analyzed by bioinformatic methods that allow their metabolism to be deduced from the taxonomy. The results obtained concluded that some of these microorganisms have activated the biosynthesis routes of pigments such as prodigiosin or flavonoids. These adaptation studies also revealed that microorganisms defend themselves against environmental toxins by activating metabolic pathways for the degradation of compounds such as ethylbenzene, xylene and dioxins and for the biosynthesis of antioxidant molecules such as glutathione. Finally, these Antarctic endolithic microorganisms are of great interest in astrobiology since endolithic settings are environmentally analogous to the primitive Earth or the surfaces of extraterrestrial bodies.

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.

A newly developed consortium with a highly efficient thiocyanate degradation capacity: A comprehensive investigation of the degradation and detoxification potential

Thiocyanate-containing wastewater harms ecosystems and can cause serious damage to animals and plants, so it is urgent to treat it effectively. In this study, a new efficient thiocyanate-degrading consortium was developed and its degradation characteristics were studied. It was found that up to 154.64 mM thiocyanate could be completely degraded by this consortium over 6 days of incubation, with a maximum degradation rate of 1.53 mM h^-1. High-throughput sequencing analysis showed that Thiobacillus (77.78%) was the predominant thiocyanate-degrading bacterial genus. Plant toxicology tests showed that the germination index of mung bean and rice seeds cultured with media obtained after thiocyanate degradation by the consortium increased by 94% and 84.83%, respectively, compared with the control group without thiocyanate degradation. Cytotoxicity tests showed that thiocyanate without degradation significantly decreased the Neuro-2a cell activity and mitochondrial membrane potential; induced reactive oxygen species generation and apoptosis; increased the cellular Ca²⁺ concentration; and damaged the cell nucleus and DNA. Furthermore, the thiocyanate degradation products produced the consortium were almost totally non-toxic, revealing the same characteristics as those of the control using distilled water. This study shows that the consortium has a high degradation efficiency and detoxification characteristics, as well as great application potential in bioremediation of industrial thiocyanate-containing wastewater.

Rapid start-up and advanced nutrient removal of simultaneous nitrification, endogenous denitrification and phosphorus removal aerobic granular sequence batch reactor for treating low C/N domestic wastewater

The rapid start-up and advanced nutrient removal of simultaneous nitrification, endogenous denitrification, and phosphorus (P) removal aerobic granular sequence batch reactor (SNEDPR-AGSBR) is a challenge in the treatment of low carbon/nitrogen (C/N) domestic sewage. In this study, the feasibility of the SNEDPR-AGSBR process was examined in an exceedingly single-stage anaerobic/aerobic/anoxic sequencing batch reactor for treating low C/N ratio (3.3-5.0) domestic sewage. The initial results showed that accompanied by the rapid formation of the mature aerobic granular sludge based on the selection for slow-growing organisms, the rapid start-up (38 d) of the SNEDPR-AGSBR process was successfully realized. The formed mature aerobic granules had a dense structure with an average diameter of 667.7 μm and SVI₃₀ of 30.0 mL/g. Two conditions for achieving the competitive balance between phosphorus-accumulating organisms/denitrifying phosphorus-accumulating organisms (PAOs/DPAOs) and glycogen accumulating organisms/denitrifying glycogen accumulating organisms (GAOs/DGAOs) were revealed by the long-term operation results. First, the dissolved oxygen (DO) concentration needed to be decreased to 3.0 mg/L in the aerobic phase, and then, the aerobic and anoxic phase hydraulic retention time (HRT) should be increased to 3.0 h. Notably, high removal efficiencies for NH₄⁺-N (100%), total nitrogen (84.3%), and P (91.8%) of the SNEDPR-AGSBR process were stably obtained with a low C/N ratio of 3.9 domestic sewage. Simultaneous nitrification and endogenous denitrification (SNED) efficiency of 61.6% was achieved during a long-term operation of 142 days. Finally, microbial community analysis confirmed that GAOs (Defluviicoccus)/DGAOs (Candidatus_Competibacter) were responsible for the removal N, and PAOs (Acinetobacter, Candidatus_Accumulibacter, Hypomicrobinm)/DPAOs (Pseudomonas and Dechloromonas) ensured P removal.

Groundwater metabolome responds to recharge in fractured sedimentary strata

Understanding the sources, structure and fate of dissolved organic matter (DOM) in groundwater is paramount for the protection and sustainable use of this vital resource. On its passage through the Critical Zone, DOM is subject to biogeochemical conversions. Therefore, it carries valuable cross-habitat information for monitoring and predicting the stability of groundwater ecosystem services and assessing these ecosystems' response to fluctuations caused by external impacts such as climatic extremes. Challenges arise from insufficient knowledge on groundwater metabolite composition and dynamics due to a lack of consistent analytical approaches for long-term monitoring. Our study establishes groundwater metabolomics to decipher the complex biogeochemical transport and conversion of DOM. We explore fractured sedimentary bedrock along a hillslope recharge area by a 5-year untargeted metabolomics monitoring of oxic perched and anoxic phreatic groundwater. A summer with extremely high temperatures and low precipitation was included in the monitoring. Water was accessed by a monitoring well-transect and regularly collected for liquid chromatography-mass spectrometry (LC-MS) investigation. Dimension reduction of the resulting complex data set by principal component analysis revealed that metabolome dissimilarities between distant wells coincide with transient cross-stratal flow indicated by groundwater levels. Time series of the groundwater metabolome data provides detailed insights into subsurface responses to recharge dynamics. We demonstrate that dissimilarity variability between groundwater bodies with contrasting aquifer properties coincides with recharge dynamics. This includes groundwater high- and lowstands as well as recharge and recession phases. Our monitoring approach allows to survey groundwater ecosystems even under extreme conditions. Notably, the metabolome was highly variable lacking seasonal patterns and did not segregate by geographical location of sampling wells, thus ruling out vegetation or (agricultural) land use as a primary driving factor. Patterns that emerge from metabolomics monitoring give insight into subsurface ecosystem functioning and water quality evolution, essential for sustainable groundwater use and climate change-adapted management.

From Surface to Subsurface: Diversity, Composition, and Abundance of Sessile and Endolithic Bacterial, Archaeal, and Eukaryotic Communities in Sand, Clay and Rock Substrates in the Laurentians (Quebec, Canada)

Microbial communities play an important role in shallow terrestrial subsurface ecosystems. Most studies of this habitat have focused on planktonic communities that are found in the groundwater of aquifer systems and only target specific microbial groups. Therefore, a systematic understanding of the processes that govern the assembly of endolithic and sessile communities is still missing. This study aims to understand the effect of depth and biotic factors on these communities, to better unravel their origins and to compare their composition with the communities detected in groundwater. To do so, we collected samples from two profiles (~0–50 m) in aquifer sites in the Laurentians (Quebec, Canada), performed DNA extractions and Illumina sequencing. The results suggest that changes in geological material characteristics with depth represent a strong ecological and phylogenetical filter for most archaeal and bacterial communities. Additionally, the vertical movement of water from the surface plays a major role in shallow subsurface microbial assembly processes. Furthermore, biotic interactions between bacteria and eukaryotes were mostly positive which may indicate cooperative or mutualistic potential associations, such as cross-feeding and/or syntrophic relationships in the terrestrial subsurface. Our results also point toward the importance of sampling both the geological formation and groundwater when it comes to studying its overall microbiology.

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

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

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

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.

Groundwater bacterial communities evolve over time in response to recharge

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

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

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

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

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

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.

Complex food webs coincide with high genetic potential for chemolithoautotrophy in fractured bedrock groundwater

Groundwater ecosystems face the challenge of energy limitation due to the absence of light-driven primary production. Lack of space and low oxygen availability might further contribute to generally assumed low food web complexity. Chemolithoautotrophy provides additional input of carbon within the subsurface, however, we still do not understand how abundances of chemolithoautotrophs, differences in surface carbon input, and oxygen availability control subsurface food web complexity. Using a molecular approach, we aimed to disentangle the different levels of potential trophic interactions in oligotrophic groundwater along a hillslope setting of alternating mixed carbonate-/siliciclastic bedrock with contrasting hydrochemical conditions and hotspots of chemolithoautotrophy. Across all sites, groundwater harbored diverse protist communities including Ciliophora, Cercozoa, Centroheliozoa, and Amoebozoa but correlations with hydrochemical parameters were less pronounced for eukaryotes compared to bacteria. Ciliophora-affiliated reads dominated the eukaryotic data sets across all sites. DNA-based evidence for the presence of metazoan top predators such as Cyclopoida (Arthropoda) and Stenostomidae (Platyhelminthes) was only found at wells where abundances of functional genes associated with chemolithoautotrophy were 10-100 times higher compared to wells without indications of these top predators. At wells closer to recharge areas with presumably increased inputs of soil-derived substances and biota, fungi accounted for up to 85% of the metazoan-curated eukaryotic sequence data, together with a low potential for chemolithoautotrophy. Although we did not directly observe higher organisms, our results point to the existence of complex food webs with several trophic levels in oligotrophic groundwater. Chemolithoautotrophy appears to provide strong support to more complex trophic interactions, feeding in additional biomass produced by light-independent CO₂-fixation.

Environmental selection shapes the formation of near-surface groundwater microbiomes

Hydrodynamics drives both stochastic and deterministic community assembly in aquatic habitats, by translocating microbes across geographic barriers and generating changes in selective pressures. Thus, heterogeneity of hydrogeological settings and episodic surface inputs from recharge areas might play important roles in shaping and maintaining groundwater microbial communities. Here we took advantage of the Hainich Critical Zone Exploratory to disentangle mechanisms of groundwater microbiome differentiation via a three-year observation in a setting of mixed carbonate-siliciclastic alternations along a hillslope transect. Variation partitioning of all data elucidated significant roles of hydrochemistry (35.0%) and spatial distance (18.6%) but not of time in shaping groundwater microbiomes. Groundwater was dominated by rare species (99.6% of OTUs), accounting for 25.9% of total reads, whereas only 26 OTUs were identified as core species. The proximity to the recharge area gave prominence to high microbial diversity coinciding with high surface inputs. In downstream direction, the abundance of rare OTUs decreased whereas core OTUs abundance increased up to 47% suggesting increasing selection stress with a higher competition cost for colonization. In general, environmental selection was the key mechanism driving the spatial differentiation of groundwater microbiomes, with N-compounds and dissolved oxygen as the major determinants, but it was more prominent in the upper aquifer with low flow velocity. Across the lower aquifer with higher flow velocity, stochastic processes appeared to be additionally important for community assembly. Overall, this study highlights the impact of surface and subsurface conditions, as well as flow regime and related habitat accessibility, on groundwater microbiomes assembly.

Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions

Despite the widely observed predominance of Cand. Patescibacteria in subsurface communities, their input source and ecophysiology are poorly understood. Here we study mechanisms of the formation of a groundwater microbiome and the subsequent differentiation of Cand. Patescibacteria. In the Hainich Critical Zone Exploratory, Germany, we trace the input of microorganisms from forested soils of preferential recharge areas through fractured aquifers along a 5.4 km hillslope well transect. Cand. Patescibacteria were preferentially mobilized from soils and constituted 66% of species-level OTUs shared between seepage and shallow groundwater. These OTUs, mostly related to Cand. Kaiserbacteraceae, Cand. Nomurabacteraceae, and unclassified UBA9983 at the family level, represented a relative abundance of 71.4% of the Cand. Patescibacteria community at the shallowest groundwater well, and still 44.4% at the end of the transect. Several Cand. Patescibacteria subclass-level groups exhibited preferences for different conditions in the two aquifer assemblages investigated: Cand. Kaiserbacteraceae surprisingly showed positive correlations with oxygen concentrations, while Cand. Nomurabacteraceae were negatively correlated. Co-occurrence network analysis revealed a central role of Cand. Patescibacteria in the groundwater microbial communities and pointed to potential associations with specific organisms, including abundant autotrophic taxa involved in nitrogen, sulfur and iron cycling. Strong associations among Cand. Patescibacteria themselves further suggested that for many groups within this phylum, distribution was mainly driven by conditions commonly supporting a fermentative life style without direct dependence on specific hosts. We propose that import from soil, and community differentiation driven by hydrochemical conditions, including the availability of organic resources and potential hosts, determine the success of Cand. Patescibacteria in groundwater environments.