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There is growing concern about environmentally released man-made chemicals suspected to be responsible for a number of adverse effects on endocrine function in wildlife species and possibly also in humans. Sex hormones are of particular interest due to their regulatory role in developmental processes such as sexual differentiation. Endogenous hormones of human or animal origin as well as exogenous sex steroids used for contraception or as anabolics for farm animals are excreted and reach the environment. We investigated the transport of the synthetic growth promoters trenbolone (TbOH) and melengestrol acetate (MGA) in agricultural soil by means of column experiments with aggregated soil materials (Ap and Bt horizons of a Luvisol). Column effluent concentrations and depth profiles of TbOH and MGA were determined with sensitive enzyme immunoassay systems and HPLC (RP-18), respectively. All procedures were confirmed by liquid chromatography-mass spectrometry. Small amounts of TbOH and MGA passed the columns very quickly. However, both hormones exhibited a high affinity to the organic matter of both horizons leading to a high retardation within the upper layers of the soil columns. Although we cannot deduce whether hormones of animal origin reach the ground water under field conditions, our model experiments show that their transition can be presumed. [Copyright &y& Elsevier]

Earthworms are one of the main producers of large biopores (> 2 mm i.d.) in soil, hence affecting the infiltration and flow of water, transport of particles and nutrients as well as soil aeration. During rain events that lead to ponding conditions, earthworm burrows may serve as short circuits between the top- and subsoil, thereby bypassing the soil matrix. Yet, burrow wall characteristics and their continuity with increasing soil depth may have a severe impact on the amount and time scales of water flow and matter transport.In this study, we investigated the wettability and properties of earthworm burrow walls of Lumbricus terrestris in three depths (15, 30 and 50 cm) compared to the bulk soil. The wettability was inferred from water drop penetration time (WDPT) tests. Fourier transform infrared (FTIR) spectroscopy of burrow wall samples were analyzed for the presence of hydrophobic moieties of organic matter (OM). Scanning electron microscopy (SEM) was used to visually explore the burrow wall structure and accumulation with organic matter and microorganisms. Elemental distribution on the burrow walls was investigated with energy dispersive X-ray (EDX) spectroscopy. Earthworm burrow walls were more hydrophobic in all depths compared to the soil matrix. Long-chained aliphatic hydrocarbons, indicated by strong CH2 and CH3 vibrations in FTIR spectra, are suspected to cause water repellency. Such substances are accumulated along burrow walls during decomposition of organic matter and plant residues as well as deposition of cutaneous earthworm mucus. Larger plant residues, microorganisms and fungal hyphae as well as earthworm and microbial extracellular polymeric substances were identified along burrow walls by SEM. Clay minerals along the burrow walls were aligned. Thus, the burrow wall structure was found to be smoother compared to the soil matrix. The recurrent up- and downward burrowing and migration of earthworms and their feeding behavior and application of radial pressure on the walls results in the burrow wall characteristics (displacement of OM and minerals, aggregation and formation of organo-mineral associations and compaction) and consequently in a lower porosity and bulk density in the innermost burrow wall. Hence, lateral water transfer through the burrow wall might be impeded. However, differences in water repellency and chemical composition between the burrow walls and the soil matrix were decreasing with increasing depth. This in turn implies, that upon ponding conditions, the infiltrating water is translocated faster through the topsoil, yet may spread easier in the subsoil. This will also comprise the dissolved, colloidal and particulate organic matter and microorganisms. Thus, biopores may have a severe effect not only on the environmental conditions and biogeochemical cycles in the subsoil, but also on the habitat and established communities. [ABSTRACT FROM AUTHOR]

In the aeration zone, transients of water-saturation, fluid flow, (re-)distribution and cycling of matter and energy may strongly control the compartmentalization of subsurface ecosystems. Especially, seasonal or episodic dynamics of flow and flow paths within the aeration zone, cause transient groundwater flow partitioning that guides the quality evolution and ecology of groundwater resources. However, flow dynamics and matter cycling within the aeration zone are typically less explored and considered in resource modeling and management. This is particularly the case for topographic recharge areas with large aeration zones, themselves lacking productive groundwater bodies, but most important for the quality of the seepage. In the Hainich Critical Zone Exploratory (central Germany), we investigate the interplay of aeration zone dynamics for groundwater quality evolution along a hillslope monitoring transect. In the widely-distributed setting of alternating mixed carbonate-/siliciclastic bedrock, lysimeters, aeration zone collectors and multi-level monitoring wells were installed to access the subsurface compartments down to ~90 m. From up to eight years of monitoring weather, ground temperatures, multi-depth hydraulic heads and non-conservative environmental tracers, we were able to reconstruct hidden phenomena like localized recharge and fluctuating perched groundwater that also cause flow transients in the phreatic zone. Likely shaping the subsurface ecosystems, we found aeration zone-loading of waters, that bypass the argillaceous, oxygen-deficient overburden and cause, for instance, oxygenation of the main aquifer by seasonally ascending flow. Furthermore, our data highlight the role of (multiple) snowmelts that strongly contribute to the groundwater budget in our hillslope terrain with temperate climate. [ABSTRACT FROM AUTHOR]

The terrestrial deep biosphere hosts up to 20% of the earth’s biomass. Whereas life in deepsaline waters is suggested to be sustained mainly by H2 and CO2, microbes in shallowgroundwaters still receive input from recently fixed organic carbon. Within the researchcentre AquaDiva, we aim to understand the links between the surface and subsurfacebiogeosphere, especially how organisms inhabiting the subsurface reflect and influence theirenvironment, and affect water and matter transiting the subsurface. To achieve this, we haveconstructed a novel infrastructure, the Hainich Critical Zone Exploratory (CZE), whichprovides an excellent platform to access groundwater and aquifer rock material fromoligotrophic limestone aquifer assemblages along with soil and seepage from the respectivegroundwater recharge areas. We tracked the formation of the groundwater microbiome and the differentiation of thepredominant Cand. Patescibacteria under distinct hydrochemical regimes. Network,correlation analysis and time series allowed us to postulate different biological andhydrochemical drivers for community assembly of planktonic microbiota, with implicationsfor subsurface carbon cycling. Furthermore, our data showed the existence of a unique rockmatrix microbiome. Shallow weathered limestones contained bacterial groups most likelyoriginating from soil habitats. Low-permeable mudstones, containing mainly oligotrophicheterotrophs and thiosulfate-oxidizing autotrophs, showed similarities betweensurface-near samples and deep samples, without relation to rock type and bulk rockpermeability. The bacterial communities found on fracture surfaces of limestonesubsamples were distinct from their matrix counterparts and ranged from organic matterdecomposers in outcrop areas to autotrophs in downdip positions that receive limitedsurface input. By comparing the stable and radiogenic carbon isotope compositions ofmicrobial phospholipid-derived fatty acids (PLFAs) with those of the potentialmicrobial C sources, we determined that subsurface groundwater microbiomesappeared to assimilate up to 70% ancient organic matter derived from rocks, despite thepresence of younger organic matter. These signatures challenge the current paradigmand point to an intensive internal cycling of carbon independent of surface input. [ABSTRACT FROM AUTHOR]

[Display omitted] • An experimental-pedogenesis study on initial soil formation in carbonate rock. • The intricate role of organic matter (OM) for structure formation is unraveled. • A multitude of pedogenic processes already operates during early stages of weathering. • OM strongly slows down the dissolution kinetics of carbonate host rock. • OM provokes a rapid and pronounced evolution of microstructure and topography. Soil aggregation and the translocation of clay and organic matter are significant pedogenic processes that manifest in diagnostic horizons in mature soil. Yet, their onset might date to much earlier stages of soil development where host rock weathering is dominant and litter from pioneer vegetation is the only input of organic matter. We present a time-lapse experimental-pedogenesis study on early host rock weathering that shows the formation of aggregates and clay translocation in response to irrigation with and without organic matter released from a litter layer. The presence of organic matter increases total carbonate dissolution capacity and results in a characteristic surface morphology, while simultaneously slowing down the dissolution rate. With the dissolution of carbonates, clay minerals of the host rock and iron from pyrite are released. Controlled by the presence of organic matter, both are either transported with the seepage water or form crusts and aggregates from clay minerals and freshly precipitated secondary iron oxides. Our study shows that the interplay of dissolution, neoformation of secondary minerals, translocation, and aggregation of organic matter and clay-sized minerals shape soil structure evolution during early pedogenesis in carbonate host rocks. [ABSTRACT FROM AUTHOR]

Soil organisms are recognized as ecosystem engineers and key for aggregation in soil due to bioturbation, organic matter (OM) decomposition, and excretion of biogenic OM. The activity of soil organisms is beneficial for soil quality, functions, and nutrient cycling. These attributions are based on field-scale observations that link the presence and activity of organisms to spatiotemporal changes in soil properties and can be traced back to the formation of biogenic aggregates. This biogenic formation pathway encompasses a cascade of processes so far not discussed comprehensively. A more general approach needs to consider the activity and feedback loops between soil biota, the active release of biogenic OM by excretion, the interaction of biogenic OM with soil constituents, the formation of organo-mineral associations, and how these become incorporated in aggregated structures. Especially the function of biogenically excreted OM, which is quite complex in composition, is controversial as it permits or inhibits aggregation. This review analyzes the various roles of biogenically excreted OM may take as an aggregation agent. We will show that its function depends on the interplay of numerous factors, including environmental conditions, variety of OM producers, composition and availability of biogenically excreted OM, and type of interacting mineral phase. We consider biogenically excreted OM to affect aggregate formation in three different ways: (I) as a bridging agent which promotes the aggregation due to surface modifications and attraction, (II) as a separation agent which favors the formation, mobility, and transport of organo-mineral associations and inhibits their further inclusion into aggregates, and (III) as a gluing agent which mediates aggregate stability, after an external force provokes a close approach of soil particles. We conclude that biogenically excreted OM takes these functional roles simultaneously and to a varying extent across spatiotemporal scales. Hence, biogenically excreted OM is involved in the surface modification of soil particles, in the enmeshment and gluing of particles into soil aggregates, in the (im-)mobilization, and in facilitating the transport of particles. All that depends on the interplay of a hierarchy of factors comprising the local soil community's composition, the properties of biogenically excreted OM, and the conditions of the immediate environment. • Cross-scale consideration of the influence of biogenic organic matter on aggregation. • Mineral interactions with mucus, extracellular polymeric substances, and root exudates. • Critical discussion of biogenic organic matter as aggregation promoting and inhibiting agent. • Function of biogenic organic matter as bridging, separation, and gluing agent. • Biogenically induced aggregation is governed by the interplay of different species. [ABSTRACT FROM AUTHOR]

Abstract: It is not clear from the literature whether heavy grazing leads to a deterioration of physical and chemical parameters of topsoils in steppe ecosystems. We sampled five sites in northern China with different grazing intensities, ranging from ungrazed since 1979 to heavily grazed, at 540 sampling points to a depth of 0–4 cm. Each sample was analysed for bulk density, organic carbon (OC), total nitrogen (N), total sulphur (S) and pH. The dataset was analysed using general statistics and explorative analysis (ANOVA, Kruskal–Wallis). As a result of the large number of samples, we were able to detect a change in the mean value of all parameters of less than 10%, with a statistical power of 90% and a level of significance of 0.01. Bulk density increased significantly with increasing grazing intensity. Organic carbon, total N and total S concentrations decreased significantly with increasing grazing intensity. No effect on the pH or C/N ratio was detected. Significant differences in C/S and N/S ratios between differently grazed plots were found. These differences point towards a relative accumulation of sulphur in grazed compared to ungrazed areas following an increased organic matter decline or lower inputs of diluting litter. Elemental stocks of the upper 4 cm were calculated for OC, total N and total S using the measured bulk densities. The data revealed significantly lower amounts for all three elements on the heavily grazed site, but no significant differences for the other areas. In addition, elemental stocks were calculated using an equivalent mass instead of bulk density to take into account changes in bulk density following grazing. This revealed a highly significant decrease for OC, total N and total S with increasing grazing intensity. OC, total N and total S concentrations respond similarly to different grazing intensities, showing highly significant positive correlations. OC concentrations and bulk densities were significantly negatively correlated. We found effects of grazing cessation only in the long-term, as no ameliorating effects of reduced or excluded grazing could be detected five years after grazing cessation. After 25 years of exclusion, significantly different values were found for all parameters. Thus, physical and chemical parameters of steppe topsoils deteriorated significantly following heavy grazing, remained stable if grazing was reduced or excluded for five years, and recovered significantly after 25 years of grazing exclusion. [Copyright &y& Elsevier]

• Groundwater microbiomes are less stable through time than previously thought. • Over six years, the communities showed temporal patterns and gradual succession. • Temporal patterns in groundwater microbiomes are driven by recharge events. • Over half of the groundwater taxa originated from recharge-related sources. 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. [Display omitted] [ABSTRACT FROM AUTHOR]

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. Unlabelled Image • Mobile inventory comprises solutes, colloids, and larger particles of diverse origin • Field-scale release dynamics and importance of controlling factors are unknown • We optimized tension-controlled lysimeters for total inventory sampling • Episodic events rather than seasonality govern particle release • >20% of total mobile organic carbon exported from soil is larger than >0.45 μm [ABSTRACT FROM AUTHOR]

Forecasting atmospheric CO2 concentrations on synoptic timescales (∼ days) can benefit the planning of field campaigns by better predicting the location of important gradients. One aspect of this, accurately predicting the day-to-day variation in biospheric fluxes, poses a major challenge. This study aims to investigate the feasibility of using a diagnostic light-use-efficiency model, the Vegetation Photosynthesis Respiration Model (VPRM), to forecast biospheric CO2 fluxes on the timescale of a few days. As input, the VPRM model requires downward shortwave radiation, 2 m temperature, and enhanced vegetation index (EVI) and land surface water index (LSWI), both of which are calculated from MODIS reflectance measurements. Flux forecasts were performed by extrapolating the model input into the future, i.e., using downward shortwave radiation and temperature from a numerical weather prediction (NWP) model, as well as extrapolating the MODIS indices to calculate future biospheric CO2 fluxes with VPRM. A hindcast for biospheric CO2 fluxes in Europe in 2014 has been done and compared to eddy covariance flux measurements to assess the uncertainty from different aspects of the forecasting system. In total the range-normalized mean absolute error (normalized) of the 5 d flux forecast at daily timescales is 7.1 %, while the error for the model itself is 15.9 %. The largest forecast error source comes from the meteorological data, in which error from shortwave radiation contributes slightly more than the error from air temperature. The error contribution from all error sources is similar at each flux observation site and is not significantly dependent on vegetation type. [ABSTRACT FROM AUTHOR]

Abstract A combined study of facies and diagenesis variations was carried out with the aim to understand small-scale heterogeneities in porosity and permeability of sandstones within a 219 m completely cored Middle Buntsandstein succession from central Germany. The well Erfurt 1/12 (EF-FB 1/12) allows studying aquifer quality variations by taking 49 plug samples of fresh rock material for thin section analyses and petrophysical measurements. This potential Buntsandstein aquifer is composed of varying portions of sandstones, mudstones and sandstone-mudstone interlayers, which were deposited on a large terminal fan system and in a large playa-lake in the basin centre. A fluvial channel and a sandflat depositional environment can be distinguished. Both are composed of varying amounts of channel-, sandsheet- and floodplain sediments of mainly massive, cross-bedded, horizontally laminated and ripple cross-bedded sandstones. Best aquifer potential occurs in the horizontally laminated and cross-bedded sandstones within channels of the fluvial environment, and in the massive sandstones of channels in sandflat deposits. Aquifer quality does not decrease with increasing depth or stratigraphic position. Instead, it is controlled by grain size and diagenetic evolution. Four diagenesis types were distinguished: (1) cementation type (CT), (2) leaching type (LT), (3) illite type (IT) and (4) mixed type (MT). Best aquifer quality was found in the leaching type (LT) consisting of larger grain sizes (medium sand), which led to the formation of a large primary pore network. Our data suggest a strong relation of hydraulic parameters not only with different facies types, architectural elements and depositional environments, but particularly with compaction and cementation during burial, and dissolution by meteoric water during subsequent uplift history. Thereby, present horizons with good hydraulic properties relate to this complex interaction of sedimentary facies and diagenetic evolution, but are restricted to only very local areas with no relevance for basin-wide fluid flow in the subsurface. Highlights • Highest permeability values are in fluvial horizontal laminated channel sandstones. • Poor aquifer potential occurs in horizontal laminated sandflat sandstones. • Improved hydraulic properties relate to cement leaching during uplift. • Good aquifer quality is restricted to small isolated areas/volumes. • Horizons with high aquifer potential have no relevance for basin-wide fluid flow. [ABSTRACT FROM AUTHOR]

Organic particles including microorganisms are a significant fraction of the mobile organic matter (MOM) pool that contributes to initial pedogenesis. Still, the dynamics and the interplay of the multitude of processes that control the mobilization, transport, and retention of MOM are vastly unclear. We studied this interplay using an ‘artificial soil’ as model for a young, unstructured soil with defined initial composition employing a novel two-layer column experiment. The upstream layer was composed of a mixture of well-defined mineral phases, a sterile organic matter source and a diverse, natural microbial inoculant mimicking an organic-rich topsoil. The downstream layer, mimicking the subsoil, was composed of the mineral phases, only. Columns were run under water-unsaturated flow conditions with multiple flow interruptions to reflect natural flow regimes and to detect possible non-equilibrium processes. Pore system changes caused by flow were inspected by scanning electron microscopy and computed micro-tomography. MOM-related physicochemical effluent parameters and bacterial community diversity and abundance were assessed by molecular analysis of the effluent and the solid phase obtained after the long-term irrigation experiment (75 d). Tomographic data showed homogeneous packing of the fine-grained media (sandy loam). During flow, the initially single-grain structured artificial soil showed no connected macropores. In total, 6% of the initial top layer organic matter was mobile. The release and transport of particulate (1.2%) and dissolved organic matter (4.8%) including bacteria were controlled by non-equilibrium conditions. Bacterial cells were released and selectively transported to downstream layer resulting in a depth-dependent and selective establishment of bacterial communities in the previously sterile artificial soil. This study underlines the importance of bacterial transport from the surface or topsoil for colonization and maturation of downstream compartments. This initial colonization of pristine surfaces is the major step in forming biogeochemical interfaces - the prominent locations of intensive biological activity and element turnover that seem to play a major role for the functioning of soil. [ABSTRACT FROM AUTHOR]

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 1000 L water from two sites of the upper aquifer assemblage and filtration on 0.3 μm 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. [ABSTRACT FROM AUTHOR]

• Groundwater dissolved organic matter (DOM) connects microbial and geochemical spheres. • We demonstrate 5-years DOM (metabolomics) monitoring by mass spectrometry. • DOM-feature fingerprints are highly variable but converge periodically across sites. • An association of this convergence with discharge/recharge flows is evident. • DOM dynamics add insight to responses of groundwater to climatic events / extremes. 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. [Display omitted] [ABSTRACT FROM AUTHOR]

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 × 103 to 6 × 106 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 Sulfuricellaand 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. [ABSTRACT FROM AUTHOR]

We followed the abundance and compared the diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the groundwater of two superimposed pristine limestone aquifers located in the Hainich region (Thuringia, Germany) over 22 months. Groundwater obtained from the upper aquifer (12 m depth) was characterized by low oxygen saturation (0-20%) and low nitrate concentrations (0-20 μM), contrasting with 50-80% oxygen saturation and 40-200 μM nitrate in the lower aquifer (48 m and 88 m depth). Quantitative PCR targeting bacterial and archaeal amoA and 16S rRNA genes suggested a much higher ammonia oxidizer fraction in the lower aquifer (0.4-7.8%) compared with the upper aquifer (0.01-0.29%). In both aquifers, AOB communities were dominated by one phylotype related to Nitrosomonas ureae, while AOA communities were more diverse. Multivariate analysis of amoA DGGE profiles revealed a stronger temporal variation of AOA and AOB community composition in the upper aquifer, pointing to a stronger influence of surface environments. Parallel fluctuations of AOA, AOB, and total microbial abundance suggested that hydrological factors (heavy rain falls, snow melt) rather than specific physicochemical parameters were responsible for the observed community dynamics. [ABSTRACT FROM AUTHOR]

Abstract: The specific surface area of natural particles is an important parameter to quantify processes such as mineral dissolution and sorptive interactions in soils and sediments. In this study, the external specific surface area (SSA), specific edge surface area (ESA) and specific basal surface area (BSA) of an illite (Inter-ILI) and a montmorillonite (Ceratosil) were determined by atomic force microscopy (AFM) and compared with the SSA obtained by N2 gas adsorption (BET) and by liquid adsorption using ethylene glycol monomethyl ether (EGME). For the illite we found an SSA of 41±3m2 g−1 by BET and of 83±5m2 g−1 by analysing 54 particles by AFM. For the montmorillonite BET we estimated a SSA of 61±2m2 g−1, whereas the analysis of 62 particles by AFM images gave a much larger mean SSA of 346±37m2 g−1. We assume that the sample treatment prior to AFM imaging (involving dispersion by NaOH in a dilute dispersion and sonication for 2min) resulted in delamination of the clay mineral particles. The ESA was 5.6±0.4m2 g−1 for the illite, and 15±2m2 g−1 for the montmorillonite. This leads to an ESA/BSA ratio of 0.07 for the illite and 0.05 for the montmorillonite for the delaminated particles. For the untreated, non-delaminated particles we calculated an ESA/BSA ratio of 0.16 for the illite and of 0.27 for the montmorillonite. The specific surface area as estimated by EGME was 112m2 g−1 for the illite and 475m2 g−1 for the montmorillonite, i.e. about 30–40% larger than the respective AFM values. However, this difference in specific surface area was not in agreement with the expected interlayer surface area of both minerals. [Copyright &y& Elsevier]

• We model soil microbial dynamics by a cellular automaton and differential equations. • Simulations are based on CT-scans of microaggregates and realistic parameter values. • Scenarios in silico allowed investigations at scales still inaccessibe ex-situ. • Connectivity, not supply controls microbial degradation at the microaggregate scale. • We contribute to the understanding of metabolic factors driving the Birch effect. Microaggregates are hot spots of microbial activity at a scale that frequently poses a severe experimental challenge or defies a direct observation. Mathematical models that combine the mechanisms of spatially resolved organic matter transport with the processes of organic matter turnover can facilitate the understanding of soil microbial dynamics and the function of soils at these scales. In this study, we investigate microbial population dynamics and the turnover of particulate organic matter (POM) in soil microaggregates. CT images of microaggregates obtained from samples of natural soils serve as basis for selecting the simulation domain. For different levels of water saturation, the fluid (liquid and gas) distribution within the pore space is calculated according to a morphological model. We consider bacteria and POM, which are heterogeneously distributed within the liquid phase. Dissolved organic carbon (DOC) is released by hydrolyzing POM, assuming a reaction following first-order kinetics. DOC spreads by diffusion and can subsequently be consumed by bacteria and turned into CO 2. The growth of bacteria is realized by a cellular automaton framework (CAM) and based on Michaelis–Menten kinetics due to the uptake of DOC. Our simulations show that the heterogeneous distribution of substrate and bacteria results in an overall biodegradation kinetics and CO 2 output that strongly depends on the microaggregate scale (<250μm). Only very specific cases can be distinguished globally, e.g., when the substrates are isolated from bacteria due to a disconnected liquid phase. Locally, however, heterogeneities in substrate distribution impact the development of bacteria populations, e.g., a smaller geodesic distance of bacteria to the substrate promotes bacterial growth locally. [ABSTRACT FROM AUTHOR]

Earthworms are considered as "ecosystem engineers" impacting soil properties as well as nutrient and element cycles. As they move through soil, earthworms secrete cutaneous mucus which is metabolized by soil microorganisms and a source of plant-available nutrients. Earthworm-processed soil contains carbon enriched, earthworm-specific soil aggregates (e.g. casts and middens) in comparison to earthworm unaffected soil. The reason could be that organic polymeric substances in earthworm mucus bind to soil minerals. The objective of this study was to investigate the small-scale interactions between earthworm mucus and secondary soil minerals, e.g. goethite and illite, leading to the formation of organo-mineral associations. We characterized the chemical composition of earthworm mucus by FTIR and 13C-NMR spectroscopy and compared spectra of mucus to microbial extracellular polymeric substances (EPS), an abundant and well-known type of organic matter that binds with soil minerals. Mucus from anecic (Lumbricus terrestris L.) and endogeic (Aporrectodea caliginosa Sav.) earthworm species was dominated by proteins and carbohydrates. Between 21 and 36% of the total organic carbon in the mucus containing treatments adsorbed to illite and goethite, and most of the binding with goethite was associated with phosphorus containing mucus compounds. The surface charge of newly-formed organo-mineral associations was determined by measuring the isoelectric point (IEP). The IEP of mucus-goethite associations was 6.8, which was lower than the bare goethite IEP of 8.4. The zeta potential of mucus-illite associations was greater than bare illite. We conclude that the specific adsorption of earthworm mucus constituents to soil minerals leads to the formation of mucus-mineral associations. These associations contribute to retention of organic substances from earthworm mucus in soil (micro-)aggregates and explain the altered physicochemical properties of earthworm-formed aggregates in comparison to the earthworm unaffected "bulk" soil material. • Mucus composition investigated for two ecological groups of earthworms. • Phosphorus-containing mucus constituents adsorb preferentially to goethite. • Mineral specific adsorption of mucus causes fractionation of mucus compounds. • Formation of mucus-mineral associations screened the surface charge. [ABSTRACT FROM AUTHOR]

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. Image 1 • Hydrochemistry explains more microbial variations than spatial distance and time. • Differences in flow velocity between aquifers shape the dominant assembly processes. • N-compounds and dissolved oxygen are the major determinants. • Proximity to the recharge area gave prominence to high microbial diversity. • The abundance of the groundwater core OTUs increases in the downstream direction. [ABSTRACT FROM AUTHOR]

• Glucose addition stimulated microbial activity in soils. • In sands, friction angle decreased while cohesion increased; in loams, compressive strength decreased. • Illite layers in mixed layer clay minerals were turned into smectite. • Microbial cells and EPS enmeshed solid particles. • With decreasing microbial activity, stress-strain properties partly recovered. High inputs of easily available organic matter to the subsurface may quickly activate the native microbial communities, thereby changing soil engineering properties. We studied the effect of glucose addition, an easily available carbon source, on stress-strain properties, mineralogy, and microstructure of several loamy and sandy soils over 30 days in laboratory experiments. During the period of high microbial activity, direct shear tests revealed a reduction of the friction angle of 15–30 % and a raise of cohesion in sands. Unconfined compression tests showed a 20–30 % decrease in the compressive strength of loamy soils. With the decline of microbial activity, the stress-strain properties recovered partially. The alterations of the stress-strain properties with increasing microbial activity were linked to changes in mineralogy and composition. X-ray diffraction showed that the proportion of smectite layers in illite-smectite mixed layer minerals increased, as well as the overall imperfection of clay minerals. Glucose addition resulted in a temporary increase in the content of microaggregates (0.1-0.05 mm). Newly formed linkages of organic matter between solid particles, biofilm formation and direct interaction of cells with mineral surfaces were observed by scanning electron microscopy. Our data show that microbial-mediated processes may adversely influence stress-strain properties of soils and endanger the safety of buildings. [ABSTRACT FROM AUTHOR]

Hypothesis: Host rock weathering and incipient pedogenesis result in the exposition of minerals, e.g., clay minerals in sedimentary limestones. Once exposed, these minerals provide the surfaces for fluid-solid interactions that control the fate of dissolved or suspended compounds such as organic matter and colloids. However, the functional and compositional diversity of organic matter and colloids limits the assessment of reactivity and availability of clay mineral interfaces. Such assessment demands a mobile compound with strong affinity to clay surfaces that is alien to the subsurface., Experiment: We approached this challenge by using poly(ethylene glycol) (PEG) as interfacial tracer in limestone weathering experiments., Findings: PEG adsorption and transport was dependent on the availability of clay mineral surfaces and carbonate dissolution dynamics. In addition, PEG adsorption featured adsorption-desorption hysteresis which retained PEG mass on clay mineral surfaces. This resulted in different PEG transport for experiments conducted consecutively in the same porous medium. As such, PEG transport was reconstructed with a continuum-scale model parametrized by a Langmuir-type isotherm including hysteresis. Thus, we quantified the influence of exposed clay mineral surfaces on the transport of organic colloids in carbonate media. This renders PEG a suitable model colloid tracer for the assessment of clay surface exposition in porous media., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

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 Mn 2+ in a specific route of transformation from birnessite (Mn IV O 2 ) into metastable feitknechtite (β-Mn III OOH) and stable manganite (γ-Mn III OOH). In natural soil solutions, however, dissolved Mn 2+ 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 Mn 2+ 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 Mn IV oxides not necessarily results in their dissolution at neutral and alkaline pH but also forms more stable Mn III oxyhydroxides with less oxidative degradation potential for organic contaminants., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)