Importance of inner-sphere P-O-Fe bonds in natural and synthetic mineral-organic associations.

Sorption of organic molecules on mineral surfaces can occur through several binding mechanisms of varying strength. Here, we investigated the importance of inner-sphere P-O-Fe bonds in synthetic and natural mineral-organic associations. Natural organic matter such as water extracted soil organic matter (WESOM) and extracellular polymeric substances (EPS) from liquid bacterial cultures were adsorbed to goethite and examined by FTIR spectroscopy and P K-edge NEXAFS spectroscopy. Natural particles from a Bg soil horizon (Gleysol) were subjected to X-ray fluorescence (XRF) mapping, NanoSIMS imaging, and NEXAFS spectro-microscopy at the P K-edge. Inner-sphere P-O-Fe bonds were identified for both, adsorbed EPS extracts and adsorbed WESOMs. Characteristic infrared peaks for P-O-Fe stretching vibrations are present but cannot unambiguously be interpreted due to possible interferences with mono- and polysaccharides. For the Bg horizon, P was only found on Fe oxides, covering the entire surface at different concentrations, but not on clay minerals. Linear combination fitting of NEXAFS spectra indicates that this adsorbed P is mainly a mixture of orthophosphate and organic P compounds. By combining atomic force microscopy (AFM) images with STXM-generated C and Fe distribution maps, we show that the Fe oxide surfaces were fully coated with organic matter. In contrast, clay minerals revealed a much lower C signal. The C NEXAFS spectra taken on the Fe oxides had a substantial contribution of carboxylic C, aliphatic C, and O-alkyl C, which is a composition clearly different from pure adsorbed EPS or aromatic-rich lignin-derived compounds. Our data show that inner-sphere P-O-Fe bonds are important for the association of Fe oxides with soil organic matter. In the Bg horizon, carboxyl groups and orthophosphate compete with the organic P compounds for adsorption sites.

Reductive transformation of birnessite by low-molecular-weight organic acids.

Soil biogeochemistry is intrinsically coupled to the redox cycling of iron and manganese. Oxidized manganese forms various (hydr)oxides that may reductively transform and dissolve, thereby serving as electron acceptors for microbial metabolisms. Furthermore, manganese oxides might reduce purely abiotically by oxidation of dissolved Mn2+ in a specific route of transformation from birnessite (MnIVO2) into metastable feitknechtite (ß-MnIIIOOH) and stable manganite (γ-MnIIIOOH). In natural soil solutions, however, dissolved Mn2+ is not abundant and organic substances such as low-molecular-weight organic acids (LMWOA) may be oxidized and serve as an electron donor for manganese oxide reduction instead. We investigated whether LMWOA would impact the transformation of birnessite at a temperature of 290 ± 2 K under ambient pressure for up to 1200 d. We found that birnessite was reductively transformed into feitknechtite, which subsequently alters into the more stable manganite without releasing Mn2+ into the solution. Instead, LMWOA served as electron donors and were oxidized from lactate into pyruvate, acetate, oxalate, and finally, inorganic carbon. We conclude that the reductive transformation of short-range ordered minerals like birnessite by the abiotic oxidation of LMWOA is a critical process controlling the abundance of LMWOA in natural systems besides their microbial consumption. Our results further suggest that the reduction of MnIV oxides not necessarily results in their dissolution at neutral and alkaline pH but also forms more stable MnIII oxyhydroxides with less oxidative degradation potential for organic contaminants.

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.

Exposure of humic acid-coated goethite colloids to groundwater does not affect their adsorption of metal(loid)s and their impact on Daphnid mobility.

Engineered humic acid-coated goethite (HA-Goe) colloids find increasing application in in situ remediation of metal(loid)-polluted groundwater. Once introduced into the subsurface, the colloids interact with groundwater altering their physicochemical properties. In comparison to freshly synthesized, unreacted HA-Goe colloids, such alterations could reduce the adsorption affinity towards metal(loid)s and also result in altered ecotoxicological effects. In our study, HA-Goe colloids were exposed to two groundwaters (low vs. high concentrations of metal(loid)s) from two metal(loid)-contaminated sites for 87 days. We investigated (i) the course of HA-Goe ecotoxicity (Daphnia magna immobilization tests), (ii) HA-Goe adsorption properties (multi-element solutions containing As, Cu, Zn, Ni and Co), and (iii) changes in the chemical composition as well as in the mineral and aggregate properties of HA-Goe. The adsorption affinity of HA-Goe decreased in the order As ≈ Cu ≫ Zn > Ni ≈ Co. The metal(loid) adsorption occurred rapidly after mixing prior to the first sampling, while the duration of ongoing exposition to groundwater had no effect on the adsorption of these metal(loid)s. We neither observed a desorption of humic acids from the goethite surface nor alterations in the mineralogy, crystallinity, and surface properties of HA-Goe. Standardized Daphnia magna immobilization tests showed an increased number of mobile organisms with increasing exposure time of HA-Goe to both groundwaters. The decrease in HA-Goe-mediated immobilization of D. magna was strongest within the first 30 d. We attribute this to a shift to smaller sizes due to the breakdown of large HA-Goe aggregates, particularly within the first 30 d. The breakdown of these µm-sized aggregates may result mainly from the repeated shaking of the HA-Goe suspensions. Our study confirms within this particular setting that the tested HA-Goe colloids are suitable for the long-term immobilization of metal(loid)s, while lethal effects on D. magna were negligible.

Groundwater bacterial communities evolve over time in response to recharge.

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

The mechanisms of gravity-constrained aggregation in natural colloidal suspensions.

Colloidal settlement in natural aqueous suspensions is effectively compensated by diffusive movement if particles resist aggregation - a state known as colloidal stability. However, if the settling velocity increases upon aggregation, complex structural features emerge from the directional movement induced by gravity. We present a comprehensive modeling study on the evolution of an aggregated three-dimensional structure due to diffusion, surface interactions, and gravity. The systematic investigation of particle geometry and size revealed three mechanisms: (I) aggregation due to spatial confinement of settled particles, (II) aggregation due to differential settling, whereby fast and slow particles collide, (III) inhibition of aggregation due to fractionation of particles with different settling velocity. A 3D visualization tool allowed us to follow the subtle interplay of these mechanisms and the highly dynamic hierarchical self-assembly of aggregates. It revealed how the balance of the different interactions determines the actual rate of aggregation.

Event-driven dynamics of the total mobile inventory in undisturbed soil account for significant fluxes of particulate organic carbon.

Considerable portions of the total mobile inventory of soil seepage are the diverse colloidal and larger suspended materials that essentially contribute to pedogenesis, soil functioning, and nutritional supply of subsurface ecosystems. However, the size- and material-spectra of the total mobile inventory, and field-scale factors controlling its long-term seasonal and episodic dynamics in undisturbed soil, are scarcely investigated so far. In a 4.5-year field-scale study, we utilized automated tension-controlled lysimeters optimized for in situ-sampling of total mobile inventory. Covering different land uses in a low-mountain groundwater recharge area in central Germany, seepage of top- and subsoil was collected at least biweekly and analyzed by hydrochemical and spectromicroscopic techniques (SEM/EDX, nanoparticle tracking analysis). In undisturbed soil, diverse mineral-, mineral-organic, organic, and bioparticles (microbial cells, biotic detritus) up to 75 µm was mobile. Atmospheric forcing was the major factor that governed transport of the total mobile inventory, causing considerable seasonality in seepage pH and certain solutes (e.g. sulphate), as well as episodic fluctuation of particulates. Especially episodic high-flow events, like those following snow melts and lasting rainstorms, primarily contributed to the export of inorganic/organic matter beyond the subsoil-regolith boundary. Individual infiltration events during winter accounted for up to 80% of annual fluxes of particulate organic carbon. On average, a significant proportion of 21% of the mobile organic carbon belonged to the >0.45 µm fraction. The pedological setting and land use mostly impacted the solute signature but were of minor importance for the particle load. Our ongoing monitoring provides evidence of significant episodic nutrient fluxes and unveiled pronounced temporal patterns of field-scale pH fluctuations. We conclude that dynamics of the total mobile inventory, including particulates >0.45 µm must be considered in approaches that budget carbon and elemental fluxes, but also in concepts and models on nutrient cycles and subsurface ecosystem functioning.

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.

The endolithic bacterial diversity of shallow bedrock ecosystems.

Terrestrial subsurface microbial communities are not restricted to the fluid-filled void system commonly targeted during groundwater sampling but are able to inhabit and dwell in rocks. However, compared to the exploration of the deep biosphere, endolithic niches in shallow sedimentary bedrock have received little interest so far. Despite the potential contribution of rock matrix dwellers to matter cycling and groundwater resource quality, their identity and diversity patterns are largely unknown. Here, we investigated the bacterial diversity in twenty-two rock cores in common limestone-mudstone alternations that differed in rock permeabilities and other geostructural and petrological factors. 16S rRNA gene analysis showed the existence of a unique rock matrix microbiome compared to surrounding groundwater. Typically, shallow weathered limestones contained bacterial groups most likely originating from soil habitats. In low-permeable mudstones, we found similar communities of oligotrophic heterotrophs, and thiosulfate-oxidizing autotrophs, without relation to depth, rock type and bulk rock permeability. In fractured limestone, the bacterial communities of fracture surfaces were distinct from their matrix counterparts and ranged from organic matter decomposers in outcrop areas to autotrophs in downdip positions that receive limited surface input. Contrastingly, rock matrices from lithologically corresponding, but highly isolated environments, were dominated by spore-forming bacteria, oligotrophic heterotrophs and hydrogen-oxidizing autotrophs. Neither depth, matrix permeability nor major mineralogy dominantly controlled the endolithic bacterial diversity. Instead, a combination of subsurface factors drives the supply of niches by fluids, matter and energy as well as the (re)dispersal conditions that likely shape bacterial diversity.

First insights into the living groundwater mycobiome of the terrestrial biogeosphere.

Although fungi play important roles in biogeochemical cycling in aquatic ecosystems and have received a great deal of attention, much remains unknown about the living fractions of fungal communities in aquifers of the terrestrial subsurface in terms of diversity, community dynamics, functional roles, the impact of environmental factors and presence of fungal pathogens. Here we address this gap in knowledge by using RNA-based high throughput pair-end illumina sequencing analysis of fungal internal transcribed spacer (ITS) gene markers, to target the living fractions of groundwater fungal communities from fractured alternating carbonate-/siliciclastic-rock aquifers of the Hainich Critical Zone Exploratory. The probed levels of the hillslope multi-storey aquifer system differ primarily in their oxygen and nitrogen content due to their different connections to the surface. We discovered highly diverse living fungal communities (384 Operational Taxonomic Units, OTUs) with different taxonomic affiliations and ecological functions. The observed fungal communities primarily belonged to three phyla: Ascomycota, Basidiomycota and Chytridiomycota. Perceived dynamics in the composition of living fungal communities were significantly shaped by the concentration of ammonium in the moderately agriculturally impacted aquifer system. Apart from fungal saprotrophs, we also detected living plant and animal pathogens for the first time in this aquifer system. This work also demonstrates that the RNA-based high throughput pair-end illumina sequencing method can be used in future for water quality monitoring in terms of living fungal load and subsequent risk assessments. In general, this study contributes towards the growing knowledge of aquatic fungi in terrestrial subsurface biogeosphere.

Nitrogen Loss from Pristine Carbonate-Rock Aquifers of the Hainich Critical Zone Exploratory (Germany) Is Primarily Driven by Chemolithoautotrophic Anammox Processes.

Despite the high relevance of anaerobic ammonium oxidation (anammox) for nitrogen loss from marine systems, its relative importance compared to denitrification has less been studied in freshwater ecosystems, and our knowledge is especially scarce for groundwater. Surprisingly, phospholipid fatty acids (PLFA)-based studies identified zones with potentially active anammox bacteria within two superimposed pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory (CZE; Germany). We found anammox to contribute an estimated 83% to total nitrogen loss in suboxic groundwaters of these aquifer assemblages at rates of 3.5-4.7 nmol L-1 d-1, presumably favored over denitrification by low organic carbon availability. Transcript abundances of hzsA genes encoding hydrazine synthase exceeded nirS and nirK transcript abundances encoding denitrifier nitrite reductase by up to two orders of magnitude, providing further support of a predominance of anammox. Anammox bacteria, dominated by groups closely related to Cand. Brocadia fulgida, constituted up to 10.6% of the groundwater microbial community and were ubiquitously present across the two aquifer assemblages with indication of active anammox bacteria even in the presence of 103 µmol L-1 oxygen. Co-occurrence of hzsA and amoA gene transcripts encoding ammonia mono-oxygenase suggested coupling between aerobic and anaerobic ammonium oxidation under suboxic conditions. These results clearly demonstrate the relevance of anammox as a key process driving nitrogen loss from oligotrophic groundwater environments, which might further be enhanced through coupling with incomplete nitrification.

Archaeal Diversity and CO2 Fixers in Carbonate-/Siliciclastic-Rock Groundwater Ecosystems.

Groundwater environments provide habitats for diverse microbial communities, and although Archaea usually represent a minor fraction of communities, they are involved in key biogeochemical cycles. We analysed the archaeal diversity within a mixed carbonate-rock/siliciclastic-rock aquifer system, vertically from surface soils to subsurface groundwater including aquifer and aquitard rocks. Archaeal diversity was also characterized along a monitoring well transect that spanned surface land uses from forest/woodland to grassland and cropland. Sequencing of 16S rRNA genes showed that only a few surface soil-inhabiting Archaea were present in the groundwater suggesting a restricted input from the surface. Dominant groups in the groundwater belonged to the marine group I (MG-I) Thaumarchaeota and the Woesearchaeota. Most of the groups detected in the aquitard and aquifer rock samples belonged to either cultured or predicted lithoautotrophs (e.g., Thaumarchaeota or Hadesarchaea). Furthermore, to target autotrophs, a series of 13CO2 stable isotope-probing experiments were conducted using filter pieces obtained after filtration of 10,000 L of groundwater to concentrate cells. These incubations identified the SAGMCG Thaumarchaeota and Bathyarchaeota as groundwater autotrophs. Overall, the results suggest that the majority of Archaea on rocks are fixing CO2, while archaeal autotrophy seems to be limited in the groundwater.

Disentangling the root- and detritus-based food chain in the micro-food web of an arable soil by plant removal.

Soil food web structure and function is primarily determined by the major basal resources, which are living plant tissue, root exudates and dead organic matter. A field experiment was performed to disentangle the interlinkage of the root-and detritus-based soil food chains. An arable site was cropped either with maize, amended with maize shoot litter or remained bare soil, representing food webs depending on roots, aboveground litter and soil organic matter as predominant resource, respectively. The soil micro-food web, i.e. microorganisms and nematodes, was investigated in two successive years along a depth transect. The community composition of nematodes was used as model to determine the changes in the rhizosphere, detritusphere and bulk soil food web. In the first growing season the impact of treatments on the soil micro-food web was minor. In the second year plant-feeding nematodes increased under maize, whereas after harvest the Channel Index assigned promotion of the detritivore food chain, reflecting decomposition of root residues. The amendment with litter did not foster microorganisms, instead biomass of Gram-positive and Gram-negative bacteria as well as that of fungi declined in the rooted zone. Likely higher grazing pressure by nematodes reduced microbial standing crop as bacterial and fungal feeders increased. However, populations at higher trophic levels were not promoted, indicating limited flux of litter resources along the food chain. After two years of bare soil microbial biomass and nematode density remained stable, pointing to soil organic matter-based resources that allow bridging periods with deprivation. Nematode communities were dominated by opportunistic taxa that are competitive at moderate resource supply. In sum, removal of plants from the system had less severe effects than expected, suggesting considerable food web resilience to the disruption of both the root and detrital carbon channel, pointing to a legacy of organic matter resources in arable soils.

Quantification of pH-dependent speciation of organic compounds with spectroscopy and chemometrics.

Fluorescence and UV/Vis spectra of aqueous solutions with numerous organic compounds are a superposition of single spectra of the chemical species present. Thus, an isolation of individual spectra with chemometrics is required for their quantification. We investigated UV/Vis spectra and fluorescence excitation-emission matrices of vanillic acid, salicylic acid, phenoxyacetic acid and phthalic acid with positive matrix factorization (PMF) and non-negativity constrained parallel factor analysis (PARAFAC) in combination with the law of mass action. In consideration of the pH-dependent speciation of organic acids, we first reconstructed the pH-specific spectra of each compound. Using these spectra as known components in a constrained algorithm, we could successfully quantify species of multiple compounds and reconstruct the solution pH. In addition, we estimated the uncertainty of reconstructed spectra and concentrations in order to assess the most probable number of components for PMF/PARAFAC. Therefore, we could derive a framework to reconstruct the number of relevant species and their individual concentration present in spectroscopic data of aqueous solutions containing multiple organic compounds.

Candidate Brocadiales dominates C, N and S cycling in anoxic groundwater of a pristine limestone-fracture aquifer.

Groundwater-associated microorganisms are known to play an important role in the biogeochemical C, N and S cycling. Metaproteomics was applied to characterize the diversity and the activity of microbes to identify key species in major biogeochemical processes in the anoxic groundwater of a pristine karstic aquifer located in Hainich, central Germany. Sampling was achieved by pumping 1000L water from two sites of the upper aquifer assemblage and filtration on 0.3µm glass filters. In total, 3808 protein groups were identified. Interestingly, the two wells (H4/2 and H5/2) differed not only in microbial density but also in the prevalence of different C, N and S cycling pathways. The well H5/2 was dominated by the anaerobic ammonia-oxidizing (anammox) candidate Brocadiales (31%) while other orders such as Burkholderiales (2%) or Nitrospirales (3%) were less abundant. Otherwise, the well H4/2 featured only low biomass and remarkably fewer proteins (391 to 3631 at H5/2). Candidate Brocadiales was affiliated to all major carbon fixation strategies, and to the cycling of N and S implying a major role in biogeochemical processes of groundwater aquifers. The findings of our study support functions which can be linked to the ecosystem services provided by the microbial communities present in aquifers. SIGNIFICANCE: Subsurface environments especially the groundwater ecosystems represent a large habitat for microbial activity. Microbes are responsible for energy and nutrient cycling and are massively involved in the planet's sustainability. Microbial diversity is tremendous and the central question in current microbial ecology is "Who eats what, where and when?". In this study, we characterize a natural aquifer inhabiting microbial community to obtain evidence for the phylogenetic diversity and the metabolic activity by protein abundance and we highlight important biogeochemical cycling processes. The aquifer was dominated by Candidatus Brocadiales while other phylotypes such as Burkholderiales, Caulobacterales and Nitrospirales were less abundant. The candidate comprised all major carbon fixation strategies, ammonification, anammox and denitrification as well as assimilatory sulfate reduction. Our findings have broad implications for the understanding of microbial activities in this aquifer and consequently specific functions can be linked to the ecosystem services provided by the microbial communities present in aquifers.

Schwertmannite formation at cell junctions by a new filament-forming Fe(II)-oxidizing isolate affiliated with the novel genus Acidithrix.

A new acidophilic iron-oxidizing strain (C25) belonging to the novel genus Acidithrix was isolated from pelagic iron-rich aggregates ('iron snow') collected below the redoxcline of an acidic lignite mine lake. Strain C25 catalysed the oxidation of ferrous iron [Fe(II)] under oxic conditions at 25 °C at a rate of 3.8 mM Fe(II) day(-1) in synthetic medium and 3.0 mM Fe(II) day(-1) in sterilized lake water in the presence of yeast extract, producing the rust-coloured, poorly crystalline mineral schwertmannite [Fe(III) oxyhydroxylsulfate]. During growth, rod-shaped cells of strain C25 formed long filaments, and then aggregated and degraded into shorter fragments, building large cell-mineral aggregates in the late stationary phase. Scanning electron microscopy analysis of cells during the early growth phase revealed that Fe(III)-minerals were formed as single needles on the cell surface, whereas the typical pincushion-like schwertmannite was observed during later growth phases at junctions between the cells, leaving major parts of the cell not encrusted. This directed mechanism of biomineralization at specific locations on the cell surface has not been reported from other acidophilic iron-oxidizing bacteria. Strain C25 was also capable of reducing Fe(III) under micro-oxic conditions which led to a dissolution of the Fe(III)-minerals. Thus, strain C25 appeared to have ecological relevance for both the formation and transformation of the pelagic iron-rich aggregates at oxic/anoxic transition zones in the acidic lignite mine lake.

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.

Constraints of propylene glycol degradation at low temperatures and saturated flow conditions.

During snowmelt, the infiltration of large amounts of propylene glycol (PG), the major compound of many aircraft deicing fluids, affects redox processes and poses a contamination risk for the groundwater. To gain a better understanding about the degradation of PG and the associated biogeochemical processes under these conditions, we conducted saturated soil column experiments at 4 °C. During two successive PG pulses, we monitored the effect of the runway deicer formate (FO) and changing redox conditions on PG degradation. Furthermore, we applied first-order and simplified Monod kinetics to describe PG and FO transport. The transport of 50 mg l(-1) PG showed three stages of microbial degradation, which were defined as lag phase, aerobic phase, and anaerobic phase. During the second pulse, lag effects diminished due to the already accomplished microbial adaption, and the initial degradation rate of PG increased. Degradation of PG was most efficient during aerobic conditions (aerobic phase), while the subsequent drop of the redox potential down to -300 mV decreased the degradation rate (anaerobic phase). Formate addition decreased the overall degradation of PG by 50 and 15 % during the first and second pulse, illustrating the inhibitory effect of FO on PG degradation. The concurrent increase of Fe(III), organic carbon, and the turbidity in the column effluent after PG and FO application suggest the combined export of Fe adsorbed to fragments of detached biofilm. Neither the first-order nor the simplified Monod model was able to reconstruct the dynamic breakthrough of 50 mg l(-1) PG. The breakthrough of 1,000 mg l(-1), however, was described reasonably well with first-order kinetics. At low temperature and high water saturation, the application of first-order degradation kinetics seems therefore appropriate to describe the transport of high concentrations of PG.

Size- and composition-dependent toxicity of synthetic and soil-derived Fe oxide colloids for the nematode Caenorhabditis elegans.

Colloidal iron oxides (FeOx) are increasingly released to the environment due to their use in environmental remediation and biomedical applications, potentially harming living organisms. Size and composition could affect the bioavailability and toxicity of such colloids. Therefore, we investigated the toxicity of selected FeOx with variable aggregate size and variably composed FeOx-associated organic matter (OM) toward the nematode Caenorhabditis elegans. Ferrihydrite colloids containing citrate were taken up by C. elegans with the food and accumulated inside their body. The toxicity of ferrihydrite, goethite, and akaganeite was dependent on aggregate size and specific surface area, with EC50 values for reproduction ranging from 4 to 29 mg Fe L(-1). Experiments with mutant strains lacking mitochondrial superoxide dismutase (sod-2) showed oxidative stress for two FeOx and Fe(3+)-ions, however, revealed that it was not the predominant mechanism of toxicity. The OM composition determined the toxicity of mixed OM-FeOx phases on C. elegans. FeOx associated with humic acids or citrate were less toxic than OM-free FeOx. In contrast, soil-derived ferrihydrite, containing proteins and polysaccharides from mobile OM, was even more toxic than OM-free Fh of similar aggregate size. Consequently, the careful choice of the type of FeOx and the type of associated OM may help in reducing the ecological risks if actively applied to the subsurface.