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)

Factors Influencing Microbial Contamination of Groundwater: A Systematic Review of Field-Scale Studies

Pathogenic microorganisms released onto the soil from point or diffuse sources represent a public health concern. They can be transported by rainwater that infiltrates into subsoil and reach the groundwater where they can survive for a long time and contaminate drinking water sources. As part of the SCA.Re.S. (Evaluation of Health Risk Related to the Discharge of Wastewater on the Soil) project, we reviewed a selection of field-scale studies that investigated the factors that influenced the fate of microorganisms that were transported from the ground surface to the groundwater. A total of 24 studies published between 2003 and 2022 were included in the review. These studies were selected from the PubMed and Web of Science databases. Microbial contamination of groundwater depends on complex interactions between human activities responsible for the release of contaminants onto the soil, and a range of environmental and biological factors, including the geological, hydraulic, and moisture characteristics of the media traversed by the water, and the characteristics and the viability of the microorganisms, which in turn depend on the environmental conditions and presence of predatory species. Enterococci appeared to be more resistant in the underground environment than thermotolerant coliforms and were suggested as a better indicator for detecting microbial contamination of groundwater.

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.

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.

Effects of a long-term operation wetland for wastewater treatment on the spatial pattern and function of microbial communities in groundwater

Constructed wetlands have been used globally for wastewater treatment owing to low energy inputs and operating costs. However, the impact of their long-term operation on groundwater microbial communities is still unclear. This study aims to investigate the effects and further reveal the linkage between a large-scale surface flow constructed wetland (in operation for 14 years) and groundwater. Changes in the characteristics of groundwater microbial communities and their potential influencing factors were studied based on hydrochemical analysis, Illumina MiSeq sequencing, and multivariate statistical analysis methods. Results show that the long-term operation wetland significantly elevated groundwater nutrient levels and increased the risk of ammonia nitrogen pollution compared to background values. An apparent heterogeneity of microbial communities exhibited in the vertical direction and a similarity in the horizontal direction. Wetland operations substantially altered the structure of microbial communities at 3, 5, and 12 m depths, particularly a reduced abundance of denitrifying and chemoheterotrophic functional genera. The formation and evolution of groundwater microbial community structure mainly subjected to the contributions of dissolved oxygen (33.70%), total nitrogen (21.40%), dissolved organic carbon (11.09%), and pH (10.60%) variations resulted from the wetland operation and largely differed in depths. A combined effect of these factors on the groundwater should be concerned for such a long-term running wetland system. This study provides a new insight into the responses of groundwater microbial community structure driving by wetland operation and a better understanding of corresponding variation of microbial-based geochemical processes.

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 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.