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

Atmospheric transport models are often used to simulate the distribution of greenhouse gases (GHGs). This can be in the context of forward modelling of tracer transport using surface-atmosphere fluxes, or flux estimation through inverse modelling, whereby atmospheric tracer measurements are used in combination with simulated transport. In both of these contexts, transport errors can bias the results and should therefore be minimized. Here, we analyze transport uncertainties in the commonly-used Weather Research and Forecasting (WRF) model coupled with the greenhouse gas module (WRF-GHG), enabling passive tracer transport simulation of CO2 and CH4. As a mesoscale numerical weather prediction model, WRF's transport is constrained by global meteorological fields via initialization and at the lateral boundaries of the domain of interest. These global fields were generated by assimilating various meteorological data to increase the accuracy of modeled fields. However, in limited-domain models like WRF, the winds in the centre of the domain can deviate considerably from these driving fields. As the accuracy of the wind speed and direction is critical to the prediction of tracer transport, maintaining a close link to the observations across the simulation domain is desired. On the other hand, a too close link to the global meteorological fields can degrade performance at smaller spatial scales that are better represented by the mesoscale model. In this work, we evaluated the performance of strategies for keeping WRF's meteorology compatible with meteorological observations. To avoid the complexity of assimilating meteorological observations directly, two main strategies of coupling WRF-GHG with ERA5 meteorological reanalysis data were tested over a two-month-long simulation over the European domain: (a) restarting the model daily with fresh initial conditions from ERA5, and (b) nudging the atmospheric winds, temperatures and moisture to those of ERA5 continuously throughout the simulation period, using WRF's built-in four-dimensional data assimilation (FDDA) in grid-nudging mode. Meteorological variables as well as simulated mole fractions of CO2 and CH4 were compared against observations to assess the performance of the different strategies. We also compared planetary boundary layer height (PBLH) with radiosonde-derived estimates. Either nudging or daily restarts similarly improved the meteorology and GHG transport in our simulations, with a small advantage of using both methods in combination. However, notable differences in soil moisture were found that accumulated over the course of the simulation when not using frequent restarts. The soil moisture drift had an impact on the simulated PBLH, presumably via changing the Bowen ratio. This is partially mitigated through nudging without requiring daily restarts, although not entirely alleviated. Soil moisture drift did not have a noticeable impact on GHG performance in our case, likely because it was dominated by other errors. However, since PBLH is critical for accurately simulating GHG transport, we recommend transport model setups that tie soil moisture to observations. Our method of frequently re-initializing simulations with meteorological reanalysis fields proved suitable for this purpose. [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]

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]