Groundwater Microorganisms Research Articles

Microbial production of methyl-uranium via the Wood-Ljungdahl pathway

The misuse of uranium is a major threat to human health and the environment. In microbial ecosystems, microbes deploy various strategies to cope with uranium-induced stress. However, the exact ecological strategies and mechanisms underlying uranium tolerance in microbes remain unclear. Therefore, this study aimed to investigate the survival strategies and tolerance mechanisms of microbial communities in uranium-contaminated soil and groundwater. Microbial co-occurrence networks and molecular biology techniques were used to analyze the properties of microbes in groundwater and soil samples from various depths of uranium-contaminated areas in Northwest China. Uranium pollution altered microbial ecological strategies. Uranium stress facilitated the formation of microbial community structures, leading to symbiosis. Furthermore, microbes primarily resisted uranium hazards by producing polysaccharides and phosphate groups that chelate uranium, releasing phosphate substances that precipitate uranium, and reducing U(VI) through sulfate- and iron-reducing processes. The relative abundance of metal-methylation genes in soil microorganisms positively correlated with uranium concentration, indicating that soil microorganisms can produce methyl uranium via the Wood-Ljungdahl pathway. Furthermore, soil and groundwater microorganisms demonstrated different responses to uranium stress. This study provides new insights into microbial responses to uranium stress and novel approaches for the bioremediation of uranium-contaminated sites.

Hydrogeochemical differences drive distinct microbial community assembly and arsenic biotransformation in unconfined and confined groundwater of the geothermal system

High‑arsenic (As) groundwater in geothermal aquifers poses a serious threat to public health. Assembly processes governing groundwater microbial community related to As biotransformation are still unexplored in geothermal groundwater across different aquifers. To fill this gap, groundwater microorganisms, community assembly processes, and microbially metabolic coupling of carbon (C), nitrogen (N), phosphorus (P), sulfur (S), and arsenic (As) were investigated in unconfined and confined groundwater in the thermal reservoirs of the Guide Basin. The difference in groundwater hydrogeochemicals led to the heterogeneity of the microbial community and microbially mediated C, N, P, S, and As cycling between unconfined and confined groundwater. Higher temperature and As concentrations, low nutrient supply, and reduced conditions in confined groundwater supported stronger interspecific coexistence and environmental selection, thus promoting the proliferation of As-resistant microorganisms (ARMs) and simplifying the community assemblage. Abundant available nutrient supply and oxidizing conditions supported an increased species diversity and metabolic functionality in unconfined groundwater. S oxidizers, C fixation, and C degradation bacteria potentially contributed to the decreased As concentrations in unconfined groundwater. However, ARMs, ammonification, and anaerobic ammonia-oxidizing bacteria potentially caused As mobilization in confined groundwater. Overall, our results give a comprehensive insight into the interaction between As and microorganisms in geothermal groundwater.

Microbial Metagenomics Revealed the Diversity and Distribution Characteristics of Groundwater Microorganisms in the Middle and Lower Reaches of the Yangtze River Basin.

Groundwater is one of the important freshwater resources on Earth and is closely related to human activities. As a good biological vector, a more diverse repertory of antibiotic resistance genes in the water environment would have a profound impact on human medical health. Therefore, this study conducted a metagenomic sequencing analysis of water samples from groundwater monitoring points in the middle and lower reaches of the Yangtze River to characterize microbial community composition and antibiotic resistance in the groundwater environment. Our results show that different microbial communities and community composition were the driving factors in the groundwater environment, and a diversity of antibiotic resistance genes in the groundwater environment was detected. The main source of antibiotic resistance gene host was determined by correlation tests and analyses. In this study, metagenomics was used for the first time to comprehensively analyze microbial communities in groundwater systems in the middle and lower reaches of the Yangtze River basin. The data obtained from this study serve as an invaluable resource and represent the basic metagenomic characteristics of groundwater microbial communities in the middle and lower reaches of the Yangtze River basin. These findings will be useful tools and provide a basis for future research on water microbial community and quality, greatly expanding the depth and breadth of our understanding of groundwater.

A Comparative Metagenomic Analysis of Specified Microorganisms in Groundwater for Non-Sterilized Pharmaceutical Products

In pharmaceutical manufacturing, ensuring product safety involves the detection and identification of microorganisms with human pathogenic potential, including Burkholderia cepacia complex (BCC), Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, Staphylococcus aureus, Clostridium sporogenes, Candida albicans, and Mycoplasma spp., some of which may be missed or not identified by traditional culture-dependent methods. In this study, we employed a metagenomic approach to detect these taxa, avoiding the limitations of conventional cultivation methods. We assessed the groundwater microbiome’s taxonomic and functional features from samples collected at two locations in the spring and summer. All datasets comprised 436–557 genera with Proteobacteria, Bacteroidota, Firmicutes, Actinobacteria, and Cyanobacteria accounting for > 95% of microbial DNA sequences. The aforementioned species constituted less than 18.3% of relative abundance. Escherichia and Salmonella were mainly detected in Hot Springs, relative to Jefferson, while Clostridium and Pseudomonas were mainly found in Jefferson relative to Hot Springs. Multidrug resistance efflux pumps and BlaR1 family regulatory sensor-transducer disambiguation dominated in Hot Springs and in Jefferson. These initial results provide insight into the detection of specified microorganisms and could constitute a framework for the establishment of comprehensive metagenomic analysis for the microbiological evaluation of pharmaceutical-grade water and other non-sterile pharmaceutical products, ensuring public safety.

Characterization the microbial diversity and functional genes in the multi-component contaminated groundwater in a petrochemical site.

Microorganisms in groundwater at petroleum hydrocarbon (PHC)-contaminated sites are crucial for PHC natural attenuation. Studies mainly focused on the microbial communities and functions in groundwater contaminated by PHC only. However, due to diverse raw and auxiliary materials and the complex production processes, in some petrochemical sites, groundwater suffered multi-component contamination, but the microbial structure remains unclear. To solve the problem, in the study, a petrochemical enterprise site, where the groundwater suffered multi-component pollution by PHC and sulfates, was selected. Using hydrochemistry, 16S rRNA gene, and metagenomic sequencing analyses, the relationships among electron acceptors, microbial diversity, functional genes, and their interactions were investigated. Results showed that different production processes led to different microbial structures. Overall, pollution reduced species richness but increased the abundance of specific species. The multi-component contamination multiplied a considerable number of hydrocarbon-degrading and sulfate-reducing microorganisms, and the introduced sulfates might have promoted the biodegradation of PHC. PRACTITIONER POINTS: The compound pollution of the site changed the microbial community structure. Sulfate can promote the degradation of petroleum hydrocarbons by hydrocarbon-degrading microorganisms. The combined contamination of petroleum hydrocarbons and sulfates will decrease the species richness but increase the abundance of endemic species.

Rock Surface Colonization by Groundwater Microorganisms in an Aquifer System in Quebec, Canada

Rock Surface Colonization by Groundwater Microorganisms in an Aquifer System in Quebec, Canada

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.

Allochthonous Groundwater Microorganisms Affect Coastal Seawater Microbial Abundance, Activity and Diversity

AbstractSubmarine groundwater discharge (SGD) is a globally important process supplying nutrients and trace elements to the coastal environment, thus playing a pivotal role in sustaining marine primary productivity. Along with nutrients, groundwater also contains allochthonous microbes that are discharged from the terrestrial subsurface into the sea. Currently, little is known about the interactions between groundwater‐borne and coastal seawater microbial populations, and groundwater microbes' role upon introduction to coastal seawater populations. Here, we investigated seawater microbial abundance, activity and diversity in a site strongly influenced by SGD. In addition, through laboratory‐controlled bottle incubations, we mimicked different mixing scenarios between groundwater and seawater. Our results demonstrate that the addition of 0.1 μm filtered groundwater stimulated heterotrophic activity and increased microbial abundance compared to control coastal seawater, whereas 0.22 μm filtration treatments induced primary productivity and Synechococcus growth. 16S rRNA gene sequencing showed a strong shift from a SAR11‐rich community in the control samples to Rhodobacteraceae dominance in the <0.1 μm treatment, in agreement with Rhodobacteraceae enrichment in the SGD field site. These results suggest that microbes delivered by SGD may affect the abundance, activity and diversity of intrinsic microbes in coastal seawater, highlighting the cryptic interplay between groundwater and seawater microbes in coastal environments, which has important implications for carbon cycling.

Spatiotemporal successions of N, S, C, Fe, and As cycling genes in groundwater of a wetland ecosystem: Enhanced heterogeneity in wet season

Microorganisms in wetland groundwater play an essential role in driving global biogeochemical cycles. However, largely due to the dynamics of spatiotemporal surface water-groundwater interaction, the spatiotemporal successions of biogeochemical cycling in wetland groundwater remain poorly delineated. Herein, we investigated the seasonal coevolution of hydrogeochemical variables and microbial functional genes involved in nitrogen, carbon, sulfur, iron, and arsenic cycling in groundwater within a typical wetland, located in Poyang Lake Plain, China. During the dry season, the microbial potentials for dissimilatory nitrate reduction to ammonium and ammonification were dominant, whereas the higher potentials for nitrogen fixation, denitrification, methane metabolism, and carbon fixation were identified in the wet season. A likely biogeochemical hotspot was identified in the area located in the low permeable aquifer near the lake, characterized by reducing conditions and elevated levels of Fe2+ (6.65–17.1 mg/L), NH4+ (0.57–3.98 mg/L), total organic carbon (1.02–1.99 mg/L), and functional genes. In contrast to dry season, higher dissimilarities of functional gene distribution were observed in the wet season. Multivariable statistics further indicated that the connection between the functional gene compositions and hydrogeochemical variables becomes less pronounced as the seasons transition from dry to wet. Despite this transition, Fe2+ remained the dominant driving force on gene distribution during both seasons. Gene-based co-occurrence network displayed reduced interconnectivity among coupled C-N-Fe-S cycles from the dry to the wet season, underpinning a less complex and more destabilizing occurrence pattern. The rising groundwater level may have contributed to a reduction in the stability of functional microbial communities, consequently impacting ecological functions. Our findings shed light on microbial-driven seasonal biogeochemical cycling in wetland groundwater.

Responses of microbial complexes to freezing/thawing in the surface and groundwater interaction zone

This paper presents the research results of the activity of microbial communities (MCs) in relation to humic substances after cyclic freeze-thaw. Groundwater from different aquifer depths from wells at different distances from the riverbank filtration (RBF) zone and river water were used as inoculum. Cyclic freeze-thaw (CFT) was carried out in two stages: the first freezing lasted 30 days at -18°C; then 5 cycles of freezing and thawing were carried out alternately after 7 days. Two types of thawing conditions were created: slow thawing from -18°C to +4°C and fast thawing from -18°C to +23°C. Growth activity on peptone, an easily available substrate, confirmed the survival of the MCs from groundwater and river water after CFT. The maximum activity after CFT with sodium humate (HNa) at a thawing temperature of 4°C was shown by MCs from a depth of 41 m from wells 1,500 m off the bank. It was comparable to the MC activity in river water during the observation period. At a thawing temperature of 23°C, microorganisms in river and groundwater from wells close to the bank were highly active, regardless of the carbon source composition during the CFT period. The growth activity of MCs was affected by the thawing temperature of 23°C in distant wells following CFT, depending on the water sampling depth. Thus, in MCs from depths of 21 m and 41 m, the activity increased with the distribution of easy-to-access co-substrate. The thawing temperature had an impact on the change in the spectral characteristics of HNa after CFT. The distance of the wells from the bank affected the aromatic compound contribution to the composition of the HNa transformation products (λ =275 nm). At a temperature of 23°C, the aromatic compound values were higher in the MCs of river water and wells located in the RBF zone compared to those at 4°C. Slow thawing at 4°C had a positive effect on the transformation of humic substances by microorganisms from distant wells due to their natural adaptation potential.

ANCIENT PRACTICE TO MODERN TECHNOLOGY: RIVERBANK FILTRATION (RBF) FOR DRINKING WATER

ABSTRACT This study focuses on applying riverbank filtration (RBF) in Malaysia, aiming to address water quality challenges caused by river water pollution, particularly the presence of harmful pathogens that can lead to waterborne diseases. Malaysia heavily relies on surface water as its primary source of potable water, making it crucial to explore practical and sustainable technologies for water treatment. Riverbank filtration is a promising low-cost, environmentally friendly technology that has shown significant potential in reducing the concentration of harmful bacteria and contaminants in water supplies. However, research into RBF's effectiveness in Malaysia has been limited, warranting further investigation and understanding of its application. The study emphasizes the importance of protecting surface water from contamination and conducting risk assessments of microorganisms in groundwater, particularly in the context of RBF implementation. A thorough understanding of the movement and retention of pathogenic bacteria in the aquifer is vital for optimizing RBF's efficiency and ensuring drinking water safety. Moreover, the study highlights the significance of considering soil properties and characteristics to determine suitable sites for RBF application. By providing valuable insights into RBF's potential benefits and capacity to address water quality issues, this research contributes to the advancement of sustainable water resource management in Malaysia, offering a promising solution for safeguarding public health and water security in the country. KEYWORDS: Riverbank filtration (RBF), drinking water, pathogenic pollutants

Degradation of nuclear fuel debris analog by siderophore-releasing microorganisms

ABSTRACT In damaged Fukushima Daiichi NPP reactors, groundwater microorganisms have continuously seeped into contaminated water. We investigated the effect of a siderophore-releasing microorganism (SB) on fuel debris analogs. Fuel debris analog pellet samples (FDAPS) and powder samples containing CeO2 (an alternative to UO2)-ZrO2 solid solution and metallic iron were formed. FDAPSs were contacted with SB on a membrane filter placed on agar medium for 50 days. With the addition of SB, Fe-containing degradation products were detected by SEM-EDX analyses on FDAPSs, on the filter, and on the agar medium, revealing that some fractions of Fe ions were dissolved and precipitated on FDAPSs, and the rest became detached from FDAPSs and migrated through the filter. The SB-derived degradation differed from those by P. fluorescens and Na-citrate solution. The RBS and ERDA spectrometry analyses identified the degradation products as Fe oxyhydroxides. Although Zr was detected in small amounts in the Fe area by SEM-EDX and by SIMS analyses, the dissolution of Zr may be limited. These results clarify that the presence of SB accelerates the degradation of fuel debris in which Fe metal regions are preferentially degraded, and some fraction of Fe were detached and migrated from the fuel debris analog.

Microorganisms in Soil and Groundwater of Epe and Laje Solid Waste Dumpsites in Ondo Town, Nigeria

The menace of open dumps is a serious concern in Nigeria because of its associated health hazards. In this work, microorganisms in soil and groundwater of Epe and Laje dumpsites which are two major dumpsites in Ondo metropolis, Nigeria were investigated using standard techniques. Bacteria isolates were later identified based on their colonial morphology, cellular morphology and their biochemical characteristics while cotton in blue lactophenol technique was used for fungal identification. Epe had higher bacteria counts (cfu/ml) in both top soil (122.0 ×106) and subsoil (72.0 ×106) when compared with bacteria counts in Laje top soil (97.0 ×106) and subsoil (52.0 ×106). Similarly, Epe also had higher fungi counts (sfu/ml) in both top (25.5× 106) and subsoil (11.5× 106), comparably with fungi counts in Laje top soil (17.0×106) and subsoil (9.5×106)). Meanwhile, total heterotrophic bacteria counts (cfu/ml) of the ground water samples was higher in Epe (42.0 x106 ) and Laje (27.0x106) in comparison with total heterotrophic fungi count (sfu/ml) in Epe (14.0x106) and Laje groundwater samples (10.5x106). Identified isolates included Staphylococcus aureus, Streptococcus spp, Escherichia coli, Micrococcus luteus, Proteus spp (bacteria) and Mucor spp, Aspergillus niger and Fusarium spp (fungi). Remarkably, these isolates are organisms of medical importance, suggesting serious health threats to the residents around the dumpsites.

Microbial community structural response to variations in physicochemical features of different aquifers.

The community structure of groundwater microorganisms has a significant impact on groundwater quality. However, the relationships between the microbial communities and environmental variables in groundwater of different recharge and disturbance types are not fully understood. In this study, measurements of groundwater physicochemical parameters and 16S rDNA high-throughput sequencing technology were used to assess the interactions between hydrogeochemical conditions and microbial diversity in Longkou coastal aquifer (LK), Cele arid zone aquifer (CL), and Wuhan riverside hyporheic zone aquifer (WH). Redundancy analysis indicated that the primary chemical parameters affecting the microbial community composition were NO3 -, Cl-, and HCO3 -. The species and quantity of microorganisms in the river-groundwater interaction area were considerably higher than those in areas with high salinity [Shannon: WH (6.28) > LK (4.11) > CL (3.96); Chao1: WH (4,868) > CL (1510) > LK (1,222)]. Molecular ecological network analysis demonstrated that the change in microbial interactions caused by evaporation was less than that caused by seawater invasion under high-salinity conditions [(nodes, links): LK (71,192) > CL (51,198)], whereas the scale and nodes of the microbial network were greatly expanded under low-salinity conditions [(nodes, links): WH (279,694)]. Microbial community analysis revealed that distinct differences existed in the classification levels of the different dominant microorganism species in the three aquifers. Environmental physical and chemical conditions selected the dominant species according to microbial functions. Gallionellaceae, which is associated with iron oxidation, dominated in the arid zones, while Rhodocyclaceae, which is related to denitrification, led in the coastal zones, and Desulfurivibrio, which is related to sulfur conversion, prevailed in the hyporheic zones. Therefore, dominant local bacterial communities can be used as indicators of local environmental conditions.

Microbial community composition and environmental response characteristics of typical brackish groundwater in the North China Plain

(Objective)To reveal the microbial community composition of regional shallow porous brackish groundwater and its response characteristics to groundwater environment, (Method)the first and second aquifers in Taocheng District, Hengshui City were selected, and 10 groundwater source samples were collected for hydrochemical analysis and microbial 16S RNA gene V4-V5 regional sequencing. (Results)The results showed that the shallow brackish groundwater in the study area is weakly alkaline and has high ion content. The spatial zonation of the abundance and diversity of groundwater microorganisms is obvious. The number of endemic bacteria in groundwater from upstream, midstream to downstream is 11, 135 and 22 respectively, with a total of 22 bacteria. Proteobacteria is the most dominant in groundwater level, and there are obvious differences in different sections. At the genus level, the main dominant species in each group and sample are Pseudomonas and Hydrogenophaga. In terms of composition difference, Pseudohongiella, Pseudorhodobacter and Limnohabitans are the representatives of UR, MR and LR. (Conclusion)On the whole, the composition of flora in groundwater is sensitive and closely related to hydrochemical processes. Species abundance is affected by alkaline and high salinity environmental indicators, while species diversity is related to depth and DO in weak reduction environment.

A starch-based controlled-release targeted nutrient agent to stimulate the activity of volatile chlorinated hydrocarbon-degrading indigenous microflora present in groundwater

Volatile chlorinated hydrocarbons (VCHs) contaminated groundwater has a low indigenous microorganism population, and lack of nutrient substrates involved in degradation reactions, resulting in a weak natural remediation ability of groundwater ecosystems. In this study, based on the principle of degradation of VCHs by indigenous microorganisms in groundwater, and combined with biostimulation and controlled-release technology, we developed a starch-based encapsulated targeted bionutrient (YH-1) with easy uptake, good stability, controllable slow-release migration, and long timeliness for the remediation of groundwater contaminated by VCHs by indigenous microorganisms. The results showed that YH-1 is easily absorbed by microorganisms and can rapidly initiate itself to stimulate the microbial degradation of VCHs, and the degradation rate of various VCH components within 7 days was 82.38–92.38 %. The release rate of nutrient components in YH-1 increases with increasing VCH concentrations in groundwater; this could effectively prolong the action time of nutrient components, while also improving the degradation efficiency of pollutants with a sustained effect of more than 15 days. Simultaneously, owing to the fluidity, water solubility, and biodegradability of YH-1 in lithologic media, YH-1 injection did not cause blockage of the lithologic media in the aquifer. Through YH-1 stimulation, indigenous microorganisms grew rapidly in the underground environment, the diversity of microbial communities and the total number of species increased, and the correlation between genera strengthened. Simultaneously, YH-1 improved the ability of microbial community to convert inorganic electron donors/acceptors, thereby strengthening the co-metabolic mechanism between microorganisms. Additionally, there was a significant increase in the percentage of many microorganisms (e.g., Sphingomonas, Janthinobacterium, Duganella, etc.) that mediated the reductive dechlorination process and were redox inorganic electron donors/acceptors. This was conducive to the reductive dechlorination process of VCHs and achieved the efficient degradation of VCHs.

Redox conditions and a moderate anthropogenic impairment of groundwater quality reflected on the microbial functional traits in a volcanic aquifer

Groundwater is an important freshwater resource and hosts specialized microbial assemblages providing fundamental ecosystem services. The current knowledge on the role of aquatic microorganisms in subsurface ecosystems is still limited. This work aimed to explore the links between groundwater hydrogeochemical properties and microbial community traits in a volcanic unconfined aquifer, moderately impacted by anthropic activities. The main physical and chemical parameters of groundwater samples were analyzed, along with microbial biomass (total cell counts, ATP-active biomass concentration), potential metabolic activity, and physiological profiles at the microbial community level (Biolog ™ EcoPlates). The results showed the coexistence of oxidizing and reducing groundwater conditions across the study area. We discriminated two groups of oxidizing/reducing groundwater samples (Ox and Red), each including two subgroups with different chemical conditions attributed to contrasting levels of anthropogenic impact for non-intensive agricultural practices and waste disposal activities (Ox − and Ox + ; Red − and Red +). Although the microbial biomass was likely not affected by changing redox, the microbial metabolic potential and functional diversity changed significantly. In the Ox samples, the community-level physiological profiles were different, mainly owing to the utilization of carboxylic acids (Ox − > Ox +) and carbohydrates (Ox + > Ox −). In the Red samples, a wider set of organic substrates were consumed by the microbial communities, including those less bioavailable (e.g., phenols). Significant differences were also found between Red − and Red + , mainly owing to the relative increase in the utilization of amino acids in Red − , polymers and amines in Red + , along with the active biomass. By reflecting the local redox conditions and moderate levels of anthropogenic impact, the applied approach highlighted changes of microbial metabolic potential and physiological profiles that imply direct repercussions on biogeochemical cycling and the ecosystem services provided by groundwater microorganisms.

Bacterial Necromass Is Rapidly Metabolized by Heterotrophic Bacteria and Supports Multiple Trophic Levels of the Groundwater Microbiome.

ABSTRACTPristine groundwater is a highly stable environment with microbes adapted to dark, oligotrophic conditions. Input events like heavy rainfalls can introduce the excess particulate organic matter, including surface-derived microorganisms, thereby disturbing the groundwater microbiome. Some surface-derived bacteria will not survive this translocation, leading to an input of necromass to the groundwater. Here, we investigated the effects of necromass addition to the microbial community in fractured bedrock groundwater, using groundwater mesocosms as model systems. We followed the uptake of 13C-labeled necromass by the bacterial and eukaryotic groundwater community quantitatively and over time using a complementary protein-stable and DNA-stable isotope probing approach. Necromass was rapidly depleted in the mesocosms within 4 days, accompanied by a strong decrease in Shannon diversity and a 10-fold increase in bacterial 16S rRNA gene copy numbers. Species of Flavobacterium, Massilia, Rheinheimera, Rhodoferax, and Undibacterium dominated the microbial community within 2 days and were identified as key players in necromass degradation, based on a 13C incorporation of >90% in their peptides. Their proteomes comprised various proteins for uptake and transport functions and amino acid metabolization. After 4 and 8 days, the autotrophic and mixotrophic taxa Nitrosomonas, Limnohabitans, Paucibacter, and Acidovorax increased in abundance with a 13C incorporation between 0.5% and 23%. Likewise, eukaryotes assimilated necromass-derived carbon either directly or indirectly. Our data point toward a fast and exclusive uptake of labeled necromass by a few specialists followed by a concerted action of groundwater microorganisms, including autotrophs presumably fueled by released, reduced nitrogen and sulfur compounds generated during necromass degradation.IMPORTANCE Subsurface microbiomes provide essential ecosystem services, like the generation of drinking water. These ecosystems are devoid of light-driven primary production, and microbial life is adapted to the resulting oligotrophic conditions. Modern groundwater is most vulnerable to anthropogenic and climatic impacts. Heavy rainfalls, which will increase with climate change, can result in high surface inputs into shallow aquifers by percolation or lateral flow. These inputs include terrestrial organic matter and surface-derived microbes that are not all capable to flourish in aquatic subsurface habitats. Here, we investigated the response of groundwater mesocosms to the addition of bacterial necromass, simulating event-driven surface input. We found that the groundwater microbiome responds with a rapid bloom of only a few primary degraders, followed by the activation of typical groundwater autotrophs and mixotrophs, as well as eukaryotes. Our results suggest that this multiphase strategy is essential to maintain the balance of the groundwater microbiome to provide ecosystem services.

The effect of low-pH concrete on microbial community development in bentonite suspensions as a model for microbial activity prediction in future nuclear waste repository

Concrete as an important component of an engineered barrier system in deep geological repositories (DGR) for radioactive waste may come into contact with bentonite, or other clays, rich in indigenous microorganisms, with potentially harmful impacts on barrier integrity. Our study aimed to assess the effect of a concrete environment on indigenous bentonite and groundwater microbial communities as these particular conditions will select for the potentially harmful microorganisms to the concrete in the future DGR. The two-month experiment under anoxic conditions consisted of crushed, aged, low-pH concrete, Czech Ca-Mg bentonite, and anoxic groundwater, with control samples without concrete or with sterile groundwater. The microbial diversity and proliferation were estimated by qPCR and 16S rRNA gene amplicon sequencing. The presence of concrete had a strong effect on microbial diversity and reduced the increase in total microbial biomass, though low-pH concrete harbored indigenous bacteria. The growth of sulfate reducers was also limited in concrete samples. Several genera, such as Massilia, Citrifermentans, and Lacunisphaera, dominant in bentonite controls, were suppressed in concrete-containing samples. In contrast, genera such as Bacillus, Dethiobacter and Anaerosolibacter specifically proliferated in the presence of concrete. Genera such as Thermincola or Pseudomonas exhibited high versatility and proliferated well under both conditions. Because several of the detected bacterial genera are known to affect concrete integrity, further long-term studies are needed to estimate the effect of bentonite and groundwater microorganisms on concrete stability in future DGR.

Biostimulation is a valuable tool to assess pesticide biodegradation capacity of groundwater microorganisms

Groundwater is the main source for drinking water production globally. Groundwater unfortunately can contain micropollutants (MPs) such as pesticides and/or pesticide metabolites. Biological remediation of MPs in groundwater requires an understanding of natural biodegradation capacity and the conditions required to stimulate biodegradation activity. Thus, biostimulation experiments are a valuable tool to assess pesticide biodegradation capacity of field microorganisms. To this end, groundwater samples were collected at a drinking water abstraction aquifer at two locations, five different depths. Biodegradation of the MPs BAM, MCPP and 2,4-D was assessed in microcosms with groundwater samples, either without amendment, or amended with electron acceptor (nitrate or oxygen) and/or carbon substrate (dissolved organic carbon (DOC)). Oxygen + DOC was the most successful amendment resulting in complete biodegradation of 2,4-D in all microcosms after 42 days. DOC was most likely used as a growth substrate that enhanced co-metabolic 2,4-D degradation with oxygen as electron acceptor. Different biodegradation rates were observed per groundwater sample. Overall, microorganisms from the shallow aquifer had faster biodegradation rates than those from the deep aquifer. Higher microbial activity was also observed in terms of CO2 production in the microcosms with shallow groundwater. Our results seem to indicate that shallow groundwater contains more active microorganisms, possibly due to their exposure to higher concentrations of both DOC and MPs. Understanding field biodegradation capacity is a key step towards developing further bioremediation-based technologies. Our results show that biostimulation has real potential as a technology for remediating MPs in aquifers in order to ensure safe drinking production.