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Sandy sediments of lowland streams are typically transported at low flow in the form of migrating ripples. In these bedforms, microbial communities spanning all trophic guilds (heterotrophic bacteria, fungi, photoautotrophic and phagotrophic protists) are exposed to highly frequent moving–resting cycles of sediment grains. Up to date, it is unknown to what extent ripple migration impacts community metabolism and composition as well as the vertical zonation of sediment-associated multitrophic microbial communities compared to stationary sediments. We hypothesize that, as a result of mechanical abrasion and limited light supply, migrating ripple sediments have lower microbial abundance, diversity, metabolism and resource acquisition and no vertical zonation compared to stationary sediments. We collected samples from five lowland streams in north-eastern Germany between May and June 2020. The coarser and better sorted sediments of migrating ripples had a higher oxygen concentration and less organic matter than stationary sediments. Photosynthetic pigments, potential extracellular enzyme activities, bacterial cell counts, and fungal gene copies were lower in migrating ripples than in stationary sediments. In contrast, cell-specific bacterial production was higher in migrating ripples. Metabarcoding revealed that bedform migration was important in shaping the community structure of bacteria, fungi, and phagotrophic protists. Dry mass-related net community production, respiration, and bacterial production were higher in superficial compared to underlying layers irrespective of sediment transport. By modulating the abundance, diversity, and structure of different trophic guilds of microbial communities and their resource acquisition, migrating bedforms create streambed heterogeneity, shaping regional biodiversity and the flow of matter through the benthic food web.

Climate change and erosion from agricultural areas cause increased drying periods and bedform migration of riverbeds, respectively, worldwide. Both sediment drying and bedform migration can independently stress the microbial community residing in the riverbed. Here, we investigated the microbial response after exposure to these stressors with a focus on long-term recovery. We conducted an in situ experiment to investigate the long-term (8 months) functional and structural recovery of benthic microbial communities from either sediment drying (episodic severe stressor) or bedform migration (frequent moderate stressor). Stressed sediment associated communities were rewetted (dried sediments) and immobilized (migrated sediments) and exposed in the River Spree (north-eastern Germany) to initiate the recovery process. We then evaluated the microbial function (community respiration, net community production and extracellular enzymatic activities) as well as the bacterial, fungal and diatom community structure (16S rRNA gene and ITS region metabarcoding, and microscopic diatom morphotype classification). We observed different recovery times for community respiration (less than 7 days) and gross primary production (more than 5 months), implying a shift toward net heterotrophy in the first few months after stress exposure. Similarly, we observed a strong autotrophic community response (particularly associated with the diatoms Navicula and Fragilaria), especially in migrated sediments. The bacterial and fungal community response to sediment drying was stronger than to bedform migration (particularly associated with the bacterium Flavobacterium and the fungi Alternaria sp. and Aureobasidium pullulans). Our results show that sediment drying and bedform migration had a significant impact on the microbial community function and structure, which persisted for several months after the stress. Due to the surprising long period of recovery, successive stress events combined with seaso

Climate change and erosion from agricultural areas cause increased drying periods and bedform migration of riverbeds, respectively, worldwide. Both sediment drying and bedform migration can independently stress the microbial community residing in the riverbed. Here, we investigated the microbial response after exposure to these stressors with a focus on long-term recovery. We conducted an in situ experiment to investigate the long-term (8 months) functional and structural recovery of benthic microbial communities from either sediment drying (episodic severe stressor) or bedform migration (frequent moderate stressor). Stressed sediment associated communities were rewetted (dried sediments) and immobilized (migrated sediments) and exposed in the River Spree (north-eastern Germany) to initiate the recovery process. We then evaluated the microbial function (community respiration, net community production and extracellular enzymatic activities) as well as the bacterial, fungal and diatom community structure (16S rRNA gene and ITS region metabarcoding, and microscopic diatom morphotype classification). We observed different recovery times for community respiration (less than 7 days) and gross primary production (more than 5 months), implying a shift toward net heterotrophy in the first few months after stress exposure. Similarly, we observed a strong autotrophic community response (particularly associated with the diatoms Navicula and Fragilaria), especially in migrated sediments. The bacterial and fungal community response to sediment drying was stronger than to bedform migration (particularly associated with the bacterium Flavobacterium and the fungi Alternaria sp. and Aureobasidium pullulans). Our results show that sediment drying and bedform migration had a significant impact on the microbial community function and structure, which persisted for several months after the stress. Due to the surprising long period of recovery, successive stress events combined with seaso

The bed of fluvial ecosystems plays a major role in global biogeochemical cycles. All fluvial sediments migrate and although responses of aquatic organisms to such movements have been recorded there is no theoretical framework on how the frequency of sediment movement affects streambed ecology and biogeochemistry. We here developed a theoretical framework describing how the moving-resting frequencies of fine-grained sediments constrain streambed communities across spatial scales. Specifically, we suggest that the most drastic impact on benthic and hyporheic communities will exist when ecological and biogeochemical processes are at the same temporal scale as the sediment moving-resting frequency. Moreover, we propose that the simultaneous occurrence of streambed patches differing in morphodynamics should be considered as an important driver of metacommunity dynamics. We surmise that the frequency of patch transition will add new dimensions to the understanding of biogeochemical cycling and metacommunities from micro-habitat to segment scales. This theoretical framework is important for fluvial ecosystems with frequent sediment movement, yet it could be applied to any other dynamic habitat.

Stream sediments move at low flow forming migrating ripples. These ripples can cover substantial areas where benthic communities experience erosion-resting cycles of sand grains. Sediment surface and interstitial space is colonized by meiobenthos, an assemblage of microscopic invertebrates. Here we describe how sediment migration influences the structure of the meiobenthic community. We sampled migrating and stationary sediment patches in five streams. Sediments in migrating ripple patches were characterized by coarser grain size and higher oxygen concentration, but less organic matter and chlorophyll than stationary patches. Meiobenthos was more abundant in the superficial layer of stationary sediment compared to the underlying layer, whereas comparable abundances were observed in both layers of migrating patches. This suggests that ripple migration enhances the vertical mixing of interstitial communities. Among the environmental drivers measured, meiobenthos community structure was most related to sediment transport regime: Rotatoria were more abundant in migrating patches, whereas Chironomidae, Ceratopogonidae, Copepoda and Hydrachnidia were more abundant in stationary patches. Body-size structure was affected by sediment migration, with fewer larger organisms in migrating ripples. By modifying the distribution of benthic resources and of meiobenthic consumers, ripple migration likely affects energy flow paths through benthic food webs.

Sandy streambeds are mobile even at low flow velocities at which sediments can be transported as bedload, more specifically as migrating ripples. Small variations in discharge can result in transitions between sediment transport and no‐transport. Despite being inherent processes of streams and rivers, the effect of sediment transport and transport regime transition on the phototrophic and heterotrophic activity of streambed microbial communities remains unclear. We performed a microcosm experiment mimicking sediment transport as migrating ripples (i.e., migrating) and no sediment transport (i.e., stationary), and their transition to observe the response of the phototrophic and heterotrophic microbial community. Both net community production and community respiration were respectively 77% and 40% suppressed in migration sediments compared to stationary sediments. In migrating sediments, a combination of mechanical stress, light limitation and limited habitable area likely hampered microbial metabolism. Stationary conditions facilitated an active community of phototrophs, mainly diatoms, as indicated by high net community production, high rates of dissolved organic carbon release and silicon retention. After transitioning migrating to stationary and vice versa, differences were maintained regardless of the change in mechanical stress and associated stressors, most likely as a result of the interaction between their antecedent transport conditions and developmental stage that shaped the microbial community. Our results indicate that sediment transported as migrating ripples at low flow velocity can strongly modulate streambed metabolism, and discharge oscillations resulting in sediment transport transitions will result in a mosaic of microbial activity and biomass that will emerge at larger scales determining reach scale metabolism.

The interaction of the water residence time (RT) in hyporheic sediments with the sediment metabolic rates is believed to be a key factor controlling whole stream metabolism. However, due to the methodological difficulties, there is little data that investigates this fundamental theory of aquatic ecology. Here, we report on progress made to combine numerical modelling with a series of modification to laboratory flumes overcoming methodological difficulties e.g. by creating steady flow paths for assessment of metabolic rates. To model the biogeochemical performance and to validate the model results, sediment structures were introduced in both, the model and the flumes, leading to differing RT distributions. Furthermore, the DOC supply in the flumes was manipulated to test the whole stream metabolic response with regard to RT distributions. In the flumes, hydraulic conditions were assessed using conservative tracer and heat as tracer. Metabolic activity was assessed using oxygen dynamics as a proxy of community respiration (CR). Residence time and metabolic processes were modelled using a multicomponent reactive transport code called MIN3P and calibrated with regard to the hydraulic conditions using the results obtained from the flume experiments. Monod type expressions were used to implement metabolic activity terms in the model. Using the results of the hydrological process model, a sensitivity analysis of the impact of RT distributions on the metabolic activity could yield supporting proof of an existing link between the two.

The transformation of leaf litter, a key process in aquatic systems, is known to be reduced with decreasing oxygen concentrations, mainly due to lower abundance of and/or less active shredding macroinvertebrates. Aquatic fungi and phagotrophic protists involved in leaf litter processing can tolerate low oxygen, but little is known about their role in leaf litter processing under these conditions.We aimed to unravel the importance of phagotrophic protists within microbially mediated leaf litter processing under contrasting oxic conditions. We hypothesised that respiration, abundance of aquatic bacteria and biomass of aquatic fungi, and thus leaf litter processing, are enhanced in the presence of phagotrophic protists, both under normoxic and low oxic conditions. Lower leaf processing was expected under low oxic than under normoxic conditions.In microcosms, oxygen concentration was adjusted to either normoxic or low. For a total of 105 days, leaf litter was cocultivated with three microbial communities: (i) a multispecies bacterial community enriched from stream leaf litter, (ii) the aquatic fungus Heliscus lugdunensis added to the bacterial community and (iii) the phagotrophic protist Glaucoma scintillans added to the bacteria–fungi community.Oxic condition had no significant effect on microbially mediated leaf mass loss. The leaf mass loss was faster in the presence of the aquatic fungus and further accelerated by adding the phagotrophic protist. After 105 days, leaf mass remaining approximated 64–79%, 57–68% and 55–61% of initial leaf mass in the bacteria, bacteria–fungi, and bacteria–fungi–phagotrophic protist communities, respectively.Under both oxic conditions, the lower leaf toughness indicated that the aquatic fungus had the potential to process leaf structural components more efficiently than bacteria alone. The combination of lower ergosterol concentrations and enhanced leaf mass loss indicated that phagotrophic protists stimulated the effi

Sandy stream-bed sediments colonized by a diverse ciliate community are subject to various disturbance regimes. In microcosms, we investigated the effect of sediment shifting on the colonization dynamics of 3 ciliate morphotypes differing in morphology, behavior and feeding strategy. The dynamics of the ciliate morphotypes inhabiting sediment pore water and overlying water were observed at 3 sediment shifting frequencies: (1) stable sediments, (2) periodically shifting sediments such as migrating ripples, and (3) continuously shifting sediments as occurring during scour events of the uppermost sediment. Sediment shifting significantly affected the abundance and growth rate of the ciliate morphotypes. The free-swimming filter feeder Dexiostoma campylum was vulnerable to washout by sediment shifting since significantly higher numbers occurred in the overlying water than in pore water. Abundance of D. campylum only increased in pore water of stable sediments. On the contrary, the vagile grasper feeder Chilodonella uncinata and the sessile filter feeder Vorticella convallaria had positive growth rates and successfully colonized sediments that shifted periodically and continuously. Thus, the spatio-temporal pattern of sediment dynamics acts as an essential factor of impact on the structure, distribution and function of ciliate communities in sand-bed streams.

Aquatic heterotrophic protists structure biofilm morphology and stimulate organic matter processing, but knowledge about their effects on the activity of surface-associated communities is still missing. Microcosm experiments revealed that the community respiration of young biofilms (7 d old) at mineral surfaces was not affected by co-cultivation with the raptorial feeder Chilodonella uncinata or the suspension feeder Tetrahymena pyriformis. However, grazing by both ciliates reduced the bacterial abundance and probably enhanced nutrient availability by recycling. Our data indicated an increased individual bacterial activity under grazing pressure, resulting in no net effect on the community respiration. In a second experiment, the respiration of leaf-associated microbial communities composed of the fungus Heliscus lugdunensis and a multispecies bacterial assemblage was significantly enhanced in the presence of T. pyriformis after 7 d of incubation. The stimulation was observed under both normoxic (turbulent) and hypoxic (turbulent and stagnant) conditions. After longer incubation, presumably matching an advanced phase of leaf degradation, T. pyriformis did not affect community respiration exposed to hypoxic stagnant conditions. In contrast to former studies, no impact of protists on leaf mass loss was observed. By stimulating leaf-associated community respiration, protists seem to affect processes involved in the initial phase of leaf processing.