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Abstract The functions of soils are intimately linked to its aggregated structure. Microaggregates formed during pedogenesis from a vast variety of mineral, organic, and biotic materials are the smallest conceivable compounds at the basis of soil structural hierarchy. Qualitative hypotheses and concepts on how aggregates form are quite elaborate, but the consistent quantitative application within a mechanistic and physically rigorous framework is still missing. This is partly caused by the fact that such an endeavor requires the combination of synergistic concepts on the transport of particles and their interactions affected by shape, size, and surface properties in aqueous suspension. Here we present a novel quantitative approach for the formation of soil microaggregates in silico that integrates diffusion-limited cluster-cluster aggregation with a probabilistic attachment following the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory of particle interactions. To represent universal mineral shapes found in soils, we implemented spherical, plate-like as well as rod-like particle morphologies inspired by weathered silicates, secondary clay minerals and pedogenic iron oxides. In this way, we developed a model that produces an explicit three-dimensional structure of aggregates emerging from hetero- as well as homo-aggregation in response to the chemical milieu. We then exploited the 3D morphology to assess functional properties of aggregates exemplified with the water retention curve and pore size distribution. Highlights • A model for the formation of explicit 3D structure of microaggregates is developed • Diffusion-limited aggregation and DLVO theory are conceptually combined • Modeled structure is used to assess microaggregate functions (e.g. water retention) • A numerical tool that implements the approach is provided [ABSTRACT FROM AUTHOR]

Abstract: All soils harbor microaggregates, i.e., compound soil structures smaller than 250 µm. These microaggregates are composed of diverse mineral, organic and biotic materials that are bound together during pedogenesis by various physical, chemical and biological processes. Consequently, microaggregates can withstand strong mechanical and physicochemical stresses and survive slaking in water, allowing them to persist in soils for several decades. Together with the physiochemical heterogeneity of their surfaces, the three‐dimensional structure of microaggregates provides a large variety of ecological niches that contribute to the vast biological diversity found in soils. As reported for larger aggregate units, microaggregates are composed of smaller building units that become more complex with increasing size. In this context, organo‐mineral associations can be considered structural units of soil aggregates and as nanoparticulate fractions of the microaggregates themselves. The mineral phases considered to be the most important as microaggregate forming materials are the clay minerals and Fe‐ and Al‐(hydr)oxides. Within microaggregates, minerals are bound together primarily by physicochemical and chemical interactions involving cementing and gluing agents. The former comprise, among others, carbonates and the short‐range ordered phases of Fe, Mn, and Al. The latter comprise organic materials of diverse origin and probably involve macromolecules and macromolecular mixtures. Work on microaggregate structure and development has largely focused on organic matter stability and turnover. However, little is known concerning the role microaggregates play in the fate of elements like Si, Fe, Al, P, and S. More recently, the role of microaggregates in the formation of microhabitats and the biogeography and diversity of microbial communities has been investigated. Little is known regarding how microaggregates and their properties change in time, which strongly limits our understanding of micro‐scale soil structure dynamics. Similarly, only limited information is available on the mechanical stability of microaggregates, while essentially nothing is known about the flow and transport of fluids and solutes within the micro‐ and nanoporous microaggregate systems. Any quantitative approaches being developed for the modeling of formation, structure and properties of microaggregates are, therefore, in their infancy. We respond to the growing awareness of the importance of microaggregates for the structure, properties and functions of soils by reviewing what is currently known about the formation, composition and turnover of microaggregates. We aim to provide a better understanding of their role in soil function, and to present the major unknowns in current microaggregate research. We propose a harmonized concept for aggregates in soils that explicitly considers the structure and build‐up of microaggregates and the role of organo‐mineral associations. We call for experiments, studies and modeling endeavors that will link information on aggregate forming materials with their functional properties across a range of scales in order to better understand microaggregate formation and turnover. Finally, we hope to inspire a novel cohort of soil scientists that they might focus their research on improving our understanding of the role of microaggregates within the system of aggregates and so help to develop a unified and quantitative concept of aggregation processes in soils. [ABSTRACT FROM AUTHOR]

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 (MnIVO 2) into metastable feitknechtite (β-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. [Display omitted] • Birnessite reductively transforms into feitknechtite and manganite. • Low-molecular-weight organic acids readily oxidize in presence of manganese oxides. • Organic acids oxidize from lactate to pyruvate, acetate, oxalate, and inorganic C. • Multivariate statistics of XRD and FTIR spectra reveals mineral phase transitions. • Abiotic alteration thermodynamically stabilizes pedogenic manganese phases. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract: Column outflow experiments operated at steady state flow conditions do not allow the identification of rate limited release processes. This requires an alternative experimental methodology. In this study, the aim was to apply such a methodology in order to identify and quantify effective release rates of heavy metals from granular wastes. Column experiments were conducted with demolition waste and municipal waste incineration (MSWI) bottom ash using different flow velocities and multiple flow interruptions. The effluent was analyzed for heavy metals, DOC, electrical conductivity and pH. The breakthrough-curves were inversely modeled with a numerical code based on the advection–dispersion equation with first order mass-transfer and nonlinear interaction terms. Chromium, Copper, Nickel and Arsenic are usually released under non-equilibrium conditions. DOC might play a role as carrier for those trace metals. By inverse simulations, generally good model fits are derived. Although some parameters are correlated and some model deficiencies can be revealed, we are able to deduce physically reasonable release-mass-transfer time scales. Applying forward simulations, the parameter space with equifinal parameter sets was delineated. The results demonstrate that the presented experimental design is capable of identifying and quantifying non-equilibrium conditions. They show also that the possibility of rate limited release must not be neglected in release and transport studies involving inorganic contaminants. [Copyright &y& Elsevier]

We present a new analytical procedure for the extraction and determination of natural estrogens in soils based on pressurised liquid extraction and GC–MS determination. After testing twelve solvents, acetone proved to be the most efficient extractant. The optimum extraction temperature is 60°C. Soil extracts have to be purified and concentrated by C-18 solid phase extraction. The dried extracts are derivatised by N-methyl-N-(trimethylsilyl)trifluoro-acetamide before measurement by GC–MS. Recoveries of 79–103% with relative standard deviations ⩽13% document reliability of this method. Further, rapidity of extraction and a low detection limit (1ngkg−1) represent an improvement of estrogen analysis in soils compared to established procedures. [Copyright &y& Elsevier]

Abstract: Soil organic carbon (OC) stocks are highly variable at the forest stand level. In order to analyse spatial variability at the stand scale, a study was conducted on a Luvisol developed from loess in Thuringia, Germany. At a 10,000 m2 beech (Fagus sylvatica L.) forest site, soil samples were taken at 54 points from the litter layer and the complete solum whose thickness varied between 0.24 m and 0.96 m. With a sampling scheme that incorporated a minimum horizontal sampling distance of 0.2 m, OC stocks in the litter layer and the solum were characterised by ordinary statistics and geostatistics. With respect to the vertical distribution of OC stocks, results showed that the OC stocks were 0.4 kg OC m−2 in the litter layer, 3.0 kg OC m−2 in the solum 0–0.12 m depth, and 4.5 kg OC m−2 in the solum >0.12 m depth. This highlighted the importance of subsoils in terrestrial carbon balances. No spatial pattern was observed in the litter layer, whereas semivariograms of OC stocks in the solum 0–0.12 m depth and the solum >0.12 m depth exhibited a range of less than 5.4 m. The nugget variance accounted for around 20% of the sill in the solum 0–0.12 m depth and for over 40% of the sill in the solum >0.12 m depth. These results emphasised the high small scale variability at the stand scale. Ordinary and spatial correlation indicated that the OC stocks are strongly affected by the thickness of the solum, whereas a relation between the distance to the nearest tree and the magnitude of OC stocks was not found. Considering the variability of the study area, the minimum detectable difference (MDD) of OC stocks for n =9 was 0.3 kg OC m−2 in the litter layer, 2.0 kg OC m−2 in the solum 0–0.12 m depth, and 3.6 kg OC m−2 in the solum >0.12 m depth. At this site more than 300 samples would be required to detect a relative OC stock change of 10% in the solum. [Copyright &y& Elsevier]

Abstract: Continued input of airplane de-icing/anti-icing fluids (ADAF) to runway adjacent soils may result in the depletion of soil-borne terminal electron acceptors. We studied the transport and transformation of propylene glycol (PG), the major constituent of many ADAF, in topsoil and subsoil samples using saturated column experiments at 4 °C and 20 °C. The export of soil-borne DOC was generally high, non-exhaustive and rate limited. Retardation of added PG was negligible. Rapid PG degradation was observed only in topsoil materials high in organic matter at 20 °C. At 4 °C, no significant degradation was observed. Thus, under unfavorable, i.e., wet and cold conditions typical for winter de-icing operations, PG and its metabolites will be relocated to deeper soil horizons or even to the groundwater. In subsoil materials, PG degradation was very slow and incomplete. We found that subsoil degradation depended on the import of active microorganisms originating from the organic-rich topsoil material. The degradation efficiency is strongly influenced by the flow velocity, i.e., the residence time of PG in the soil column. Poorly crystalline iron(III) and manganese(IV) (hydr)oxides are used during microbial respiration acting as terminal electron acceptors. This results in the formation and effective relocation of reduced and mobile Fe and Mn species. Long-term application of ADAF to runway adjacent soil as well as the lasting consumption of Fe and Mn will tend to decrease the soil redox potential. Without proper counteractive measures, this will eventually favor the development of methanogenic conditions. [Copyright &y& Elsevier]

Abstract: Charred organic matter is assumed to contain heavily condensed polycyclic aromatic domains with a considerable proportion of core carbons. To examine their possible underestimation using variable amplitude (VA) cross polarization (CP) magic angle spinning (MAS) 13C nuclear magnetic resonance (NMR), the condensation degree of a peat subjected to thermal oxidation at 350°C for up to 180s was examined by means of elemental analysis and various NMR techniques. For comparison, commercially available barbeque charcoal and charred organic residues collected from a fire-affected soil from Southern Spain were analyzed. The atomic H/C ratios of the aromatic moiety of the chars revealed that on average every second to third C is connected to a proton. Dipolar dephasing NMR data confirm the high extent of and are in agreement with relatively small clusters of six aromatic rings connected by approximately two bridging CS. Alternatively, benzanthracene-like structures with two to five bridging CS are possible. The CP time (T CH) and the 1H and 13C spin lattice relaxation times in the rotating frame (T 1ρH; T 1ρC) of the chars suggest the presence of crystalline and amorphous domains. Both fractions fulfill the condition T CH < t c < T 1ρH which is required for C-detection with the CP-technique. Reliability of the CP-technique was supported by experiments with standards consisting of charred material and untreated peat mixed in defined ratios. The analysis of 13C spin lattice relaxation indicated saturation of some O-alkyl and alkyl C in the Bloch decay (BD) NMR spectrum of the untreated peat. This may explain its higher aromatic C intensity compared to the respective CP MAS NMR spectrum. [Copyright &y& Elsevier]

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]

Simplified equations are used in common approaches to describe cross polarization (CP) dynamics of solids. The CP behavior may be modulated by several nuclei interactions and physicochemical sample properties. At high magnetic fields and spinning speeds, these modulations can obscure the results. To elucidate their impact on the CP behavior of natural organic materials variable contact time (VCT) experiments were acquired with a high temporal resolution for two coal samples. The measurements were distinctly influenced by interfering fluctuations. Conventional approaches showed insufficient flexibility in terms of degrees of freedom to calculate the CP dynamics. The use of an original fundamental equation as model resulted in sufficient flexibility for such heterogeneous systems. The best results were obtained assuming a two component system. On these conditions a differentiation between amorphous and crystalline domains within the coal samples was enabled. [Copyright &y& Elsevier]

• Multi-directional flow phenomena are intrinsic features of topographic highs. • Multi-directional flow shapes groundwater quality and intrinsic vulnerability. • We present a scheme for exploratory analysis of dis-/continuous groundwater data. • Large sets of environmental tracers are required in mixed-lithology flow systems. • Interacting aeration zone/phreatic flow dynamics shape ecosystem compartmentalization. Multi-directional fluid flow and transport dynamics as intrinsic characteristics of hillslope flow regimes can strongly contribute to the quality evolution of groundwater resources and compartmentalization of subsurface ecosystems. However, their extent and importance in topographic highs (groundwater recharge areas) is typically less investigated, because productive groundwater bodies and thus monitoring activities are frequently lacking. In the Hainich Critical Zone Exploratory, we explored the hydrogeological functioning of the widely distributed setting of thin-bedded, alternating mixed carbonate-/siliciclastic bedrock, by using basic environmental timeseries. Up to 8-year records of weather parameters, ground temperatures, multi-depth hydraulic heads, and non-conservative tracers, were exploited applying a scheme for the exploratory analysis of dis-/continuous groundwater quality data. We identified transient, multi-directional flow dynamics, comprising fluctuating perched groundwater, localized recharge and groundwater mounding in the aeration zone that modify and partly reverse flow patterns in the phreatic zone. This interplay of flow dynamics within the hillslope aeration and phreatic zone causes significant re-distribution (e.g. oxygen, nitrate) that even overcome the "protective cover" of thick argillaceous strata by supplying surface-sourced substances to deep groundwater resources. As a factor for ecosystem compartmentalization, our results further suggest to carefully consider the hillslope multi-directional flow and matter exchange in biogeochemical models, as well as in resource protection and groundwater management practices. [ABSTRACT FROM AUTHOR]

[Display omitted] 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. [ABSTRACT FROM AUTHOR]

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]

Background: Our understanding of C storage in soils lacks insights investigating organic matter (OM) depletion, often studied in bare fallow systems. The content of coarse rock fragments is often excluded, whereas it may affect C storage. Aims: We aim to contribute to a better understanding of the impact of bare fallow on C storage mechanisms in the soil as influenced by its coarse rock fragment contents. We investigated whether bare fallow induced a depletion of C in OM fractions and analyzed to which extent this affected soil aggregate size distribution and the C loading of the clay‐sized fraction. Methods: A comparison of 14 years bare fallow management with adjacent cropped soils located in Selhausen (Germany) provided a gradient of coarse rock fragments of 34%–71%, from which sites with three different fine earth (FE) contents were compared. Across the FE gradient, we isolated particulate OM and mineral‐associated OM fractions, obtained microaggregate and macroaggregate size fractions, and quantified the C loading. Results: Bare fallow management induced an OM depletion at lower contents of FE. There, the management influence was more concentrated onto less FE volume. The contribution of both particulate and mineral‐associated OM fractions to the C in the low‐FE soils decreased. The C loading increased under bare fallow, compared to cropped soil. In the low‐FE soil, we also found less macroaggregates, whereas the C content decreased in some microaggregate size fractions. Conclusions: A high content of coarse rock fragments can enhance OM depletion decreasing mineral‐associated and particulate C under bare fallow. [ABSTRACT FROM AUTHOR]

Background: Soil organisms influence pedogenesis on a molecular level through the production of biopolymers which interact with soil minerals depending on their molecular properties. Specifically, biopolymers impact structure formation by inhibiting aggregation as a separation agent or promoting aggregation as a bridging agent. Mucus is a biopolymer excreted by earthworms that consists mainly of proteins, polysaccharides, and, to a lesser extent, lipids. However, despite earthworms' fundamental contribution to soil quality and structuring via bioturbation, the role of mucus in aggregation still has to be unraveled. Aims: Our study explores the role of cutaneous earthworm mucus (CEM) of Lumbricus terrestris L. for the formation of organo–mineral associations and aggregates, a sub‐process of pedogenesis. Methods: We conducted batch experiments with goethite and CEM at different pH values and varying CEM concentrations to form mucus–goethite associations. Employing the newly formed mucus–goethite associations, we explored the (homo‐/hetero‐)aggregation with quartz particles as a function of the loading of surfaces with mucus‐C and CEM concentrations in solution. Results: Our results suggest that the molecular structure of CEM constituents (especially proteins) is sensitive to pH. We found that the adsorption of CEM to goethite depends on pH and concentration. Polysaccharides of CEM adsorbed preferentially under acidic conditions (pH 3) and at low CEM concentration (6 mg mucus‐C L–1). In contrast, stronger adsorption of proteins was observed at higher CEM concentrations (30 mg mucus‐C L–1). In subsequent aggregation experiments, the hetero‐aggregation rate of organo–mineral associations and quartz decreased at low C‐loadings. Conversely, the rate increased at high loadings compared to the CEM‐free reference. Furthermore, electrostatic/steric repulsion (separation agent) inhibited the aggregation between goethite particles at high CEM concentrations in the solution (mineral/mucus ratio of 17). However, at a low CEM supply (mineral/mucus ratio of >83), CEM took the role of a bridging agent. Conclusions: The composition, function, and (im‐)mobilization of CEM and corresponding organo–mineral associations in earthworm‐influenced soil structures are shaped by the structure/reactivity of CEM affected by environmental parameters. Formation and aggregation of mucus–mineral associations contribute to nutrient/carbon storage and are involved in the structure formation in soil. [ABSTRACT FROM AUTHOR]

The seepage-mediated translocation of soil microorganisms across the soil-regolith boundary plays a central role in connecting surface and subsurface habitats. However, field studies targeting the factors controlling the dynamics of this translocation are still rare. We aimed to disentangle the effects of taxonomic identity, soil type, land use, and hydrological season on the translocation of bacteria over 1.5 years. Seepage-mediated bacterial transport was assessed using tension-controlled lysimeters in various soil types of a low-mountain groundwater recharge area under a temperate climate. Susceptibility to transport with seepage was primarily taxon-specific while influence by land use played only a minor role. The estimated total export of cells from soil ranged from 5.2 × 1011 to 1.3 × 1012 cells per m2 during a six-months-period and was 1.5 times higher during hydrological winter than in summer. In winter, low ionic strength seepage likely favored the export of bacterial groups with cell sizes of less than 1 μm such as Cand. Patescibacteria or Bdellovibrionaceae , or extracellular stages of potential pathogens of eukaryotes (Chlamydiales , Rickettsiales). Cand. Patescibacteria alone accounted for 40% of the cells exported in winter. Mobile cells contributed 1.3–2.1% to the total organic carbon exported from topsoil and subsoil. Our results demonstrate that substantial bacterial biomass is continuously exported from soils to subsurface environments. Export is strongly driven by the susceptibility of specific bacterial taxa to undergo translocation, and by seasonal infiltration regime. Enhanced introduction of bacterivorous or potential pathogenic taxa from soil to groundwater upon recharge may represent an important controlling factor for bacterial interaction networks or trophic interactions in groundwater food webs. [Display omitted] • Soil seepage-mediated microbial transport connects surface and subsurface habitats. • Susceptibility to seepage-mediated transport was highly taxon-specific. • Estimated total cell export in winter was 1.5 times than that in the summer. • High infiltration favored export of small-sized taxa such as Cand. Patescibacteria. [ABSTRACT FROM AUTHOR]

Structures of colloidal compounds in soil, including organo–mineral and mineral–mineral associations, are considered as composite building units (CBUs) that may combine into soil microaggregates. Despite the ubiquitous occurrence of CBUs, the major formation mechanisms are rather obscure and little is known about whether they form primarily during weathering of the parent rocks or by aggregation processes from the soil suspension. We studied the formation of CBUs from suspensions composed of minerals and organic matter typical for temperate soils (i.e. quartz, goethite, illite and extracellular polymeric substances [EPS]). Without EPS, we found CBUs formed as mineral–mineral associations by hetero coagulation of illite and quartz that is bridged by goethite. The presence of EPS, in contrast, led to the formation of a stable suspension of clay‐sized CBUs with no involvement of quartz. We explained this by the rapid formation of organo–mineral CBUs made of EPS‐associated goethite and EPS‐associated illite. The sorption of EPS to goethite screened its surface charge, thereby reducing the electrostatic attraction between goethite and illite. This interaction effectively impeded the formation of mineral–mineral CBUs. Moreover, interactions of EPS with goethite resulted in a marked decrease of the phosphorus/carbon ratio in the suspension. This suggested a preferred adsorption of phosphorus‐containing EPS constituents to goethite and in turn to a compositional fractionation of EPS constituents between the solid and liquid phase as shown by Fourier‐transform infrared spectroscopy with attenuated total reflection (FTIR–ATR). Laser light diffraction measurements revealed a shift from the fine silt fraction to that of the fine sand that also supports the role of EPS as a 'binding' agent. Highlights: Composite building units (CBUs) form in suspensions with different mineral and organic components.Both, hetero mineral–mineral and organo–mineral CBUs were formed.The initial composition of the suspension controls type and properties of resulting CBUs.Depending on the mineral surfaces, EPS may serve as a separation or binding agent. [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]

[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]

MOM encompass dissolved and colloidal, but also particulate matter and biota. It is suggested to impact the architecture and functioning of subsurface compartments in various ways, for instance as key components in biogeochemical cycling, as substrate and microbial actor. Yet, the understanding of conditions and relevance under which MOM is released in topsoil and translocated to downstream compartments is still in its infancy, as long-term and high-resolution field studies are essentially lacking. To overcome this knowledge gap, we operate, in addition to a groundwater monitoring well transect, 22 tension-supported lysimeters in topsoil and subsoil, covering different land use in the topographic recharge area of the Hainich Critical Zone Exploratory (NW-Thuringia, central Germany). Besides the collection and physico-/chemical and spectroscopic analysis of soil seepage, we furthermore analyze precipitation and groundwater on a regular and event-scale cycle. Generally, our results suggest that the composition of soil-born MOM is largely controlled by the "formation environment" (soil group, parent rock, land use). However, both, episodic infiltration events (rainstorms, snow melts) and seasonal moisture fluctuations are major factors of MOM release. Especially, episodic events cause mobilization of significant amounts of the particulate OM fraction. Mobile particulate substances, present in all seepage and groundwater samples, were mainly comprised of dispersed mineral particles (e.g. carbonate particles, clay minerals), mineral-organic particulates, but also diverse bioparticles and biotic detritus make up as considerable fraction. Our long-term field study, allowing to track mobile substances within the Critical Zone, demonstrates the importance of the particulate fraction of soil-born MOM, released under natural transient conditions, that may significantly contribute to subsurface ecosystem development, supply, and functioning. [ABSTRACT FROM AUTHOR]

Plant-derived mucilage and microbially produced extracellular polymeric substances (EPS) by fungi or bacteria are known to be crucial for the formation and stabilization of organo-mineral associations and soil aggregates (Six et al., 2004; Totsche et al., 2018). Especially the interactions between organism-produced complex mixtures of macromolecules (e.g. microbial EPS) and typical constituents of the soil mineral phase like iron oxides and clay minerals were intensively investigated. Although the role of earthworms in improving soil quality has been stated already by Charles Darwin (Brown et al., 2000), surprisingly little is known on the interactions of earthworm mucus with the soil mineral phase and experimental studies are vastly lacking. With our study, we contribute to closing this knowledge gap by studying the interactions between soil minerals (goethite and illite) and earthworm mucus with completely mixed batch reactor experiments. Mucus is a nutrient rich extracellular polymeric substance excreted by earthworms to facilitate their movement through soils. We focused on mucus from anecic (Lumbricus terrestris) and endogeic (Aporrectodea caliginosa) earthworm species, mainly composed of proteins and carbohydrates. For both mucus types, we observed strong adsorption to the mineral phases of goethite and illite. A fractionation of mucus between the solid (minerals) and liquid (supernatants) phase was determined that resulted from preferred adsorption of phosphorus-containing mucus constituents to goethite. This adsorption results in the formation of organo-mineral associations which serve as composite building unit for soil microaggregates. Mucus adsorption further alters the isoelectric point (IEP) of the associate compared to the pure mineral phases. The IEP of organo-mineral associations with goethite decreased, while that with illite increased in comparison to the bare minerals. The adsorption of organic carbon and the specific accumulation of phosphorous to goethite points to the importance of earthworm influenced organo-mineral associations for the nutrient cycles. Additionally, the specific surface properties of these organo-mineral associations could influence their paths and translocation in the soil massively, with regard to preferential flows inside the earthworm formed burrow systems.References:Brown, G.G., Barois, I. & Lavelle, P. 2000. Regulation of soil organic matter dynamics and microbial activity in the drilosphere and the role of interactions with other edaphic functional domains. European Journal of Soil Biology, 36, 177-198.Six, J., Bossuyt, H., Degryze, S. & Denef, K. 2004. A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics. Soil & Tillage Research, 79, 7-31.Totsche, K.U., Amelung, W., Gerzabek, M.H., Guggenberger, G., Klumpp, E., Knief, C. et al. 2018. Microaggregates in soils. Journal of Plant Nutrition and Soil Science, 181, 104-136. [ABSTRACT FROM AUTHOR]

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. Unlabelled Image • Bacterial patterns differ between niches of high- and low-bulk rock permeability • Depth and matrix permeability are minor controls of endolithic diversity. • Surface input or isolation control endolithic bacterial communities • Oligotrophic heterotrophs dominate bacterial communities in isolated niches • Bacterial communities on fracture surfaces differ from those inside the matrices. [ABSTRACT FROM AUTHOR]

Forecasting atmospheric CO2 concentrations on synoptic time scales (~ 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 research 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 time scale 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 day 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, which fail to accurately predict cloud cover, leading to overestimated shortwave radiation in the model. 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]

Highlights • Core and intact polar GDGTs in groundwater are reported. • These can be used to trace soil input to groundwater. • Both bacteria- and archaea-derived GDGTs were mainly produced within groundwater. • Cycling rate of GDGTs in groundwater is lower than in surface soils. Abstract Groundwater ecosystems host diverse and complex microbial communities that play important roles in the biogeochemical processing of organic matter and in the maintenance of drinking water quality. Here we investigated the microbial community in suspended particulate matter (SPM) of biogeochemically distinct groundwaters (Hainich Critical Zone Exploratory) by analyzing branched and isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs) from bacteria and archaea, respectively. The contributions of those lipids derived from dead and living organisms were determined by analyses of the core lipid distributions of core and intact polar GDGTs. We compared the groundwater GDGT distributions to the ones from soils of potential recharge areas and with archaeal 16S rRNA-gene based community reconstructions to estimate their origin in these terrestrial subsurface environments and thus their potential use for evaluating soil inputs into groundwater. In soils, the relative abundance of intact polar branched GDGTs (brGDGTs) was lower than that of isoprenoid GDGTs (isoGDGTs; 2% vs 5% of total GDGTs), while the opposite trend (71% vs 22% of total GDGTs) was observed in the core lipid pools. This supports previous observations that soil brGDGT-producing bacteria might be more active and thus have higher regeneration rates than the isoGDGT-producing archaea. We found similar trends in the groundwater that might indicate higher activity (i.e., cell division) of brGDGT-producing bacteria than of isoGDGT-producing archaea. The higher relative abundance of the hexamethylated brGDGT in the groundwater SPM (mean 65 ± 9%, n = 5) than in soils (mean 16 ± 7%, n = 22) indicated an in situ origin of brGDGT-producing bacteria. Higher contributions of penta- and tetra-methylated brGDGTs, which suggested some inputs from soil bacteria, was only detected in two out of seven groundwater samples. The strong correlation between core and intact polar isoGDGTs (R2 = 0.99, n = 7) in groundwater SPM indicated low disturbance (e.g., surface inputs) and suggested indigenous archaeal communities in the groundwater. This was supported by the results from a previous 16S rRNA-gene study that detected distinct archaeal groups in soils and groundwater. This first GDGT study in groundwater demonstrated that even dynamic karstic subsurface environments host an indigenous bacterial and archaeal community that is adapted to the living conditions. Furthermore, fast recharge events are likely detectable using tetraether lipids from the soil microbial community. [ABSTRACT FROM AUTHOR]

Abstract 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. Highlights • First RNA-based study using Illumina platform studying fungi in the aquifer system. • A diverse pool of living aquatic fungal species detected in subsurface aquifers. • NH 4 + and TIC supply correlate with the living fungal community composition in the aquifers. • Saprotrophs along with animal and plant pathogens were most frequently detected living functional groups. [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]

Substantial amounts of organic matter are mobilized from upper soil layers during extreme precipitation events. This results in considerable fluxes of carbon from plant-associated topsoil to deeper mineral soil and to groundwater. Microbes constitute an important part of this mobile organic matter (MOM) pool. Previous work has shown that specific bacteria associated with the rhizosphere of decaying maize roots were selectively transported with seepage water upon snowmelt in winter. However, effective mechanisms of mobilization and also possible distinctions to microbial transport for living root systems remain poorly understood. In the present study, bacteria in seepage water were sampled from lysimeters at an experimental maize field after extreme rain events in summer. We show that a distinctive subset of rhizoplane-associated bacterial populations was mobilized after summer rain, especially including abundant members of the Bacteroidetes , representing a microbial conduit for fresh plant-derived carbon inputs into deeper soil layers. Marked distinctions of seepage communities were not observed between lysimeters with a different relative contribution of preferential vs. matrix flow. Time-resolved analyses of seepage water during an artificial rain event revealed temporal patterns in the mobilization of certain lineages, with members of the Chitinophagaceae , Sphingomonadaceae , and Bradyrhizobiaceae preferentially mobilized in early and late seepage fractions, and members of the candidate phyla Parcubacteria and Microgenomates mobilized mostly in intermediate fractions. While average bacterial cell counts were at ∼10 7  ml −1 in seepage water, the recovery of amended fluorescently labeled cells of Arthrobacter globiformis was low (0.2–0.6%) over seepage events. Still, mobilized bacteria clearly have the potential to influence bacterial activities and communities in subsoils. These findings demonstrate that dynamic hydraulic events must be considered for a better understanding of the connectivities between microbial populations and communities in soil, as well as of the links between distinct carbon pools over depth. [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]

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. [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]

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 Fe3+-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. [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]

Biological Mn oxidation is responsible for producing highly reactive and abundant Mn oxide phases in the environment that can mitigate metal contamination. However, little is known about Mn oxidation in low-pH environments, where metal contamination often is a problem as the result of mining activities. We isolated two Mn(II)-oxidizing bacteria (MOB) at pH 5.5 (Duganella isolate AB-14 and Albidiferax isolate TB-2) and nine strains at pH 7 from a former uranium mining site. Isolate TB-2 may contribute to Mn oxidation in the acidic Mn-rich subsoil, as a closely related clone represented 16% of the total community. All isolates oxidized Mn over a small pH range, and isolates from low-pH samples only oxidized Mn below pH 6. Two strains with different pH optima differed in their Fe requirements for Mn oxidation, suggesting that Mn oxidation by the strain found at neutral pH was linked to Fe oxidation. Isolates tolerated Ni, Cu, and Cd and produced Mn oxides with similarities to todorokite and birnessite, with the latter being present in subsurface layers where metal enrichment was associated with Mn oxides. This demonstrates that MOB can be involved in the formation of biogenic Mn oxides in both moderately acidic and neutral pH environments. [ABSTRACT FROM AUTHOR]

To clarify the structure of microbial food webs in groundwater, knowledge about the protist diversity and feeding strategies is essential. We applied cultivation-dependent approaches and molecular methods for further understanding of protist diversity in groundwater. Groundwater was sampled from a karstified aquifer located in the Thuringian Basin (Thuringia, Germany). Cultivable protist abundance estimated up to 8,000 cells/L. Eleven flagellates, 10 naked amoebae, and one ciliate morpho-species were detected in groundwater enrichment cultures. Most of the flagellates morpho-species, typically < 10 μm, were sessile or free swimming suspension feeders, e.g., Spumella spp., Monosiga spp., and mobile, surface-associated forms that grasp biofilms, e.g., Bodo spp. Naked amoebae, typically < 35 μm, that grasp biofilms were represented by, e.g., Vahlkampfia spp., Vannella spp., and Hartmanella spp. The largest fraction of the 18S rRNA gene sequences was affiliated with Spumella-like Stramenopiles. Besides, also sequences affiliated with fungi and metazoan grazers were detected in clone libraries of the groundwater. We hypothesize that small sized protist species take refuge in the structured surface of the fractures and fissures of the karstified aquifer and mainly feed on biofilm-associated or suspended bacteria. [ABSTRACT FROM AUTHOR]

Abstract: The origin and quantity of plant inputs to soil are primary factors controlling the size and structure of the soil microbial community. The present study aimed to elucidate and quantify the carbon (C) flow from both root and shoot litter residues into soil organic, extractable, microbial and fungal C pools. Using the shift in C stable isotope values associated with replacing C3 by C4 plants we followed root- vs. shoot litter-derived C resources into different soil C pools. We established the following treatments: Corn Maize (CM), Fodder Maize (FM), Wheat+maize Litter (WL) and Wheat (W) as reference. The Corn Maize treatment provided root- as well as shoot litter-derived C (without corn cobs) whereas Fodder Maize (FM) provided only root-derived C (aboveground shoot material was removed). Maize shoot litter was applied on the Wheat+maize Litter (WL) plots to trace the incorporation of C4 litter C into soil microorganisms. Soil samples were taken three times per year (summer, autumn, winter) over two growing seasons. Maize-derived C signal was detectable after three to six months in the following pools: soil organic C (Corg), extractable organic C (EOC), microbial biomass (Cmic) and fungal biomass (ergosterol). In spite of the lower amounts of root- than of shoot litter-derived C inputs, similar amounts were incorporated into each of the C pools in the FM and WL treatments, indicating greater importance of the root- than shoot litter-derived resources for the soil microorganisms as a basis for the belowground food web. In the CM plots twice as much maize-derived C was incorporated into the pools. After two years, maize-derived C in the CM treatment contributed 14.1, 24.7, 46.6 and 76.2% to Corg, EOC, Cmic and ergosterol pools, respectively. Fungi incorporated maize-derived C to a greater extent than did total soil microbial biomass. [Copyright &y& Elsevier]

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]