Cryoturbation, the burial of topsoil material into deeper soil horizons by repeated freeze-thaw events, is an important storage mechanism for soil organic matter (SOM) in permafrost-affected soils. Besides abiotic conditions, microbial community structure and the accessibility of SOM to the decomposer community are hypothesized to control SOM decomposition and thus have a crucial role in SOM accumulation in buried soils. We surveyed the microbial community structure in cryoturbated soils from nine soil profiles in the northeastern Siberian tundra using high-throughput sequencing and quantification of bacterial, archaeal and fungal marker genes. We found that bacterial abundances in buried topsoils were as high as in unburied topsoils. In contrast, fungal abundances decreased with depth and were significantly lower in buried than in unburied topsoils resulting in remarkably low fungal to bacterial ratios in buried topsoils. Fungal community profiling revealed an associated decrease in presumably ectomycorrhizal (ECM) fungi. The abiotic conditions (low to subzero temperatures, anoxia) and the reduced abundance of fungi likely provide a niche for bacterial, facultative anaerobic decomposers of SOM such as members of the Actinobacteria, which were found in significantly higher relative abundances in buried than in unburied topsoils. Our study expands the knowledge on the microbial community structure in soils of Northern latitude permafrost regions, and attributes the delayed decomposition of SOM in buried soils to specific microbial taxa, and particularly to a decrease in abundance and activity of ECM fungi, and to the extent to which bacterial decomposers are able to act as their functional substitutes.

Abstract. Ecosystem models often rely on heuristic descriptions of autotrophic growth that fail to reproduce various stationary and dynamic states of phytoplankton cellular composition observed in laboratory experiments. Here, we present the integration of an advanced phytoplankton growth model within a coupled three-dimensional physicalbiogeochemical model and the application of the model system to the southern North Sea (SNS) defined on a relatively high resolution ( ∼ 1.5-4.5 km) curvilinear grid. The autotrophic growth model, recently introduced by Wirtz and Kerimoglu (2016), is based on a set of novel concepts for the allocation of internal resources and operation of cellular metabolism. The coupled model system consists of the General Estuarine Transport Model (GETM) as the hydrodynamical driver, a lower-trophic-level model and a simple sediment diagenesis model. We force the model system with realistic atmospheric and riverine fluxes, background turbidity caused by suspended particulate matter (SPM) and open ocean boundary conditions. For a simulation for the period 2000-2010, we show that the model system satisfactorily reproduces the physical and biogeochemical states of the system within the German Bight characterized by steep salinity; nutrient and chlorophyll (Chl) gradients, as inferred from comparisons against observation data from long-term monitoring stations; sparse in situ measurements; continuous transects; and satellites. The model also displays skill in capturing the formation of thin chlorophyll layers at the pycnocline, which is frequently observed within the stratified regions during summer. A sensitivity analysis reveals that the vertical distributions of phytoplankton concentrations estimated by the model can be qualitatively sensitive to the description of the light climate and dependence of sinking rates on the internal nutrient reserves. A non-acclimative (fixed-physiology) version of the model predicted entirely different vertical profiles, suggesting that accounting for physiological flexibility might be relevant for a consistent representation of the vertical distribution of phytoplankton biomass. Our results point to significant variability in the cellular chlorophyll-to-carbon ratio (Chl : C) across seasons and the coastal to offshore transition. Up to 3-fold-higher Chl : C at the coastal areas in comparison to those at the offshore areas contribute to the steepness of the chlorophyll gradient. The model also predicts much higher phytoplankton concentrations at the coastal areas in comparison to its non-acclimative equivalent. Hence, findings of this study provide evidence for the relevance of physiological flexibility, here reflected by spatial and seasonal variations in Chl : C, for a realistic description of biogeochemical fluxes, particularly in the environments displaying strong resource gradients.

Modeling suspended particulate matter (SPM) dynamics is essential to calculate sediment transport budgets and to provide relevant knowledge for the understanding of biogeochemical cycles in coastal waters. Natural flocs are characterized by their size, shape, structure and density that determine their settling velocity and therefore their vertical as well as horizontal transport. During transport, several processes, in particular aggregation and fragmentation, alter these particle properties. In the present study, we compare two different 0D modeling approaches for flocculation processes, a size classbased (SCB) model and a distribution-based (DB) model that follows the first moment of the particle distribution function. The study leads to an improved understanding of both models, which aim to better resolve SPM dynamics in spatial and ecosystem models in the near future. Both models are validated using data from laboratory experiments. The time evolution of the particle dynamics subjected to tidal forcing is represented equally well by both models, in particular in terms of (i) the mean diameter, (ii) the computed mean settling velocity and (iii) the particle size distribution. A sensitivity study revealed low sensitivity to changes in the collision efficiency and initial conditions, but a high sensitivity with respect to the particles' fractal dimension. The latter is an incitation to enhance the knowledge on processes related to changes of fractal dimension in order to further improve SPM transport models. The limitations of both models are discussed. The model intercomparison revealed that the SCB model is useful for studies focussing on the time evolution of floc distributions, especially under highly variable conditions. By contrast, the DB model is more suitable for studies dealing with larger spatial scales and, moreover, with coupled marine physical-biogeochemical systems, as it is computationally very effective.

Abstract. Marine aggregates are the vector for biogenically bound carbon and nutrients from the euphotic zone to the interior of the oceans. To improve the representation of this biological carbon pump in the global biogeochemical HAMburg Ocean Carbon Cycle (HAMOCC) model, we implemented a novel Microstructure, Multiscale, Mechanistic, Marine Aggregates in the Global Ocean (M4AGO) sinking scheme. M4AGO explicitly represents the size, microstructure, heterogeneous composition, density and porosity of aggregates and ties ballasting mineral and particulate organic carbon (POC) fluxes together. Additionally, we incorporated temperature-dependent remineralization of POC. We compare M4AGO with the standard HAMOCC version, where POC fluxes follow a Martin curve approach with (i) linearly increasing sinking velocity with depth and (ii) temperature-independent remineralization. Minerals descend separately with a constant speed. In contrast to the standard HAMOCC, M4AGO reproduces the latitudinal pattern of POC transfer efficiency, as recently constrained by Weber et al. (2016). High latitudes show transfer efficiencies of ≈0.25±0.04, and the subtropical gyres show lower values of about 0.10±0.03. In addition to temperature as a driving factor for remineralization, diatom frustule size co-determines POC fluxes in silicifier-dominated ocean regions, while calcium carbonate enhances the aggregate excess density and thus sinking velocity in subtropical gyres. Prescribing rising carbon dioxide (CO2) concentrations in stand-alone runs (without climate feedback), M4AGO alters the regional ocean atmosphere CO2 fluxes compared to the standard model. M4AGO exhibits higher CO2 uptake in the Southern Ocean compared to the standard run, while in subtropical gyres, less CO2 is taken up. Overall, the global oceanic CO2 uptake remains the same. With the explicit representation of measurable aggregate properties, M4AGO can serve as a test bed for evaluating the impact of aggregate-associated processes on global biogeochemical cycles and, in particular, on the biological carbon pump.

Anaerobic oxidation of ammonium (anammox) in oxygen minimum zones (OMZs) is a major pathway of oceanic nitrogen loss. Ammonium released from sinking particles has been suggested to fuel this process. During cruises to the Peruvian OMZ in April–June 2017 we found that anammox rates are strongly correlated with the volume of small particles (128–512 µm), even though anammox bacteria were not directly associated with particles. This suggests that the relationship between anammox rates and particles is related to the ammonium released from particles by remineralization. To investigate this, ammonium release from particles was modelled and theoretical encounters of free-living anammox bacteria with ammonium in the particle boundary layer were calculated. These results indicated that small sinking particles could be responsible for ~75% of ammonium release in anoxic waters and that free-living anammox bacteria frequently encounter ammonium in the vicinity of smaller particles. This indicates a so far underestimated role of abundant, slow-sinking small particles in controlling oceanic nutrient budgets, and furthermore implies that observations of the volume of small particles could be used to estimate N-loss across large areas.