This laboratory study advances our understanding of sediment transport in vegetated regions, by describing the impact of stem density on the critical velocity, Ucrit, at which sediment motion is initiated. Sparse emergent vegetation was modeled with rigid cylinders arranged in staggered arrays of different stem densities. The sediment transport rate, Qs, was measured over a range of current speeds using digital imaging, and the critical velocity was selected as the condition at which the magnitude of Qs crossed the noise threshold. For both grain sizes considered here (0.6–0.85 mm and 1.7–2 mm), Ucrit decreased with increasing stem density. This dependence can be explained by a threshold condition based on turbulent kinetic energy, kt, suggesting that near‐bed turbulence intensity may be a more important control than bed shear stress on the initiation of sediment motion. The turbulent kinetic energy model unified the bare bed and vegetated channel measurements.

Previous studies have shown that sediment transport models based on bed shear stress ( ) are not accurate for regions with vegetation. The present study demonstrated that the inaccuracy arises from the influence of vegetation-generated turbulence. Bed-load transport rate, Q s , and near-bed velocity were measured in a sediment-recirculating flume with model vegetation of different vegetation volume fractions ( ) and with bare sand beds. At the same , the measured Q s increased with increasing , suggesting that vegetation-generated turbulence, which also increased with increasing , was augmenting the bed-load transport. At the same near-bed turbulent kinetic energy, k t , the Q s measured in both bare and vegetated channels agreed within uncertainty, suggesting that k t may be a more universal predictor of bed-load transport than bed shear stress. A -based bed-load transport model was reinterpreted as a k t -based model. The new k t -based model predicted the Q s measurements for both bare and vegetated channels.Plain Language Summary Aquatic vegetated habitats, including wetlands and mangroves, are disappearing at an annual rate of 1% to 7%. These ecosystems provide habitat important to fisheries, enhance water quality by filtering nutrients from runoff, and also protect coastal regions from storm surge and waves. To mitigate the loss of these habitats, restoration projects import sediment to eroded areas. The success of the restoration depends on its ability to retain sediment, so that restoration design requires a good understanding of sediment transport within vegetated landscapes. However, this understanding is currently lacking, and many restoration projects fail due to unanticipated sediment loss from the restored regions. The goal of our study was to develop a predictive model for sediment transport in regions with vegetation. Using laboratory experiments with a model vegetation, we first showed that existing sediment transport models, based on studies without vegetation, underestimate by orders of magnitude the sediment transport in vegetated regions. Second, we demonstrated that the enhanced sediment transport was caused by vegetation-generated turbulence. Finally, we proposed and verified a new model for sediment transport that incorporates the role of vegetation-generated turbulence, which we believe will be an important guide for future coastal and riverine restoration projects.

The shear stress at the bed of a channel influences important benthic processes such as sediment transport. Several methods exist to estimate the bed shear stress in bare channels without vegetation, but most of these are not appropriate for vegetated channels due to the impact of vegetation on the velocity profile and turbulence production. This study proposes a new model to estimate the bed shear stress in both vegetated and bare channels with smooth beds. The model, which is supported by measurements, indicates that for both bare and vegetated channels with smooth beds, within a viscous sublayer at the bed, the viscous stress decreases linearly with increasing distance from the bed, resulting in a parabolic velocity profile at the bed. For bare channels, the model describes the velocity profile in the overlap region of the Law of the Wall. For emergent canopies of sufficient density (frontal area per unit canopy volume a ! 4:3 m 21 ), the thickness of the linear-stress layer is set by the stem diameter, leading to a simple estimate for bed shear stress.

The impacts of aquatic vegetation on bed load transport rate and bedform characteristics were quantified using flume measurements with model emergent vegetation. First, a model for predicting the turbulent kinetic energy, kt, in vegetated channels from channel average velocity U and vegetation volume fraction ϕ was validated for mobile sediment beds. Second, using data from several studies, the predicted kt was shown to be a good predictor of bed load transport rate, Qs, allowing Qs to be predicted from U and ϕ for vegetated channels. The control of Qs by kt was explained by statistics of individual grain motion recorded by a camera, which showed that the number of sediment grains in motion per bed area was correlated with kt. Third, ripples were observed and characterized in channels with and without model vegetation. For low vegetation solid volume fraction (ϕ ≤ 0.012), the ripple wavelength was constrained by stem spacing. However, at higher vegetation solid volume fraction (ϕ=0.025), distinct ripples were not observed, suggesting a transition to sheet flow, which is sediment transport over a plane bed without the formation of bedforms. The fraction of the bed load flux carried by migrating ripples decreased with increasing ϕ, again suggesting that vegetation facilitated the formation of sheet flow.

Soil absorbs about 20% of anthropogenic carbon emissions annually, and clay is one of the key carbon-capture materials. Although sorption to clay is widely assumed to strongly retard the microbial decomposition of soil organic matter, enhanced degradation of clay-associated organic carbon has been observed under certain conditions. The conditions in which clay influences microbial decomposition remain uncertain because the mechanisms of clay-organic carbon interactions are not fully understood. Here we reveal the spatiotemporal dynamics of carbon sorption and release within model clay aggregates and the role of enzymatic decomposition by directly imaging a transparent smectite clay on a microfluidic chip. We demonstrate that clay-carbon protection is due to the quasi-irreversible sorption of high molecular-weight sugars within clay aggregates and the exclusion of bacteria from these aggregates. We show that this physically-protected carbon can be enzymatically broken down into fragments that are released into solution. Further, we suggest improvements relevant to soil carbon models.

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Diversity–invasion resistance relationships are often variable and sensitive to environmental conditions such as resource availability. Resource stoichiometry, the relative concentration of different elements in the environment, has been shown to have strong effects on the physiology and interactions between different species. Yet, its role for diversity–invasion resistance relationships is still poorly understood. Here, we explored how the ratio of nitrogen (N) and phosphorus affects the productivity and invasion resistance of constructed microbial communities by a plant pathogenic bacterium, Ralstonia solanacearum . We found that resource stoichiometry and species identity effects affected the invasion resistance of communities. Both high N concentration and resident community diversity constrained invasions, and two resident species, in particular, had strong negative effects on the relative density of the invader and the resident community productivity. While resource stoichiometry did not affect the mean productivity of the resident community, it favoured the growth of two species that strongly constrained invasions turning the slope of productivity–invasion resistance relationship more negative. Together our findings suggest that alterations in resource stoichiometry can change the community resistance to invasions by having disproportionate effects on species growth, potentially explaining changes in microbial community composition under eutrophication.

The spread of pathogenic bacteria in unsaturated porous media, where air and liquid coexist in pore spaces, is the major cause of soil contamination by pathogens, soft rot in plants, food spoilage, and many pulmonary diseases. However, visualization and fundamental understanding of bacterial transport in unsaturated porous media are currently lacking, limiting the ability to address the above contamination- and disease-related issues. Here, we demonstrate a previously unreported mechanism by which bacterial cells are transported in unsaturated porous media. We discover that surfactant-producing bacteria can generate flows along corners through surfactant production that changes the wettability of the solid surface. The corner flow velocity is on the order of several millimeters per hour, which is the same order of magnitude as bacterial swarming, one of the fastest known modes of bacterial surface translocation. We successfully predict the critical corner angle for bacterial corner flow to occur based on the biosurfactant-induced change in the contact angle of the bacterial solution on the solid surface. Furthermore, we demonstrate that bacteria can indeed spread by producing biosurfactants in a model soil, which consists of packed angular grains. In addition, we demonstrate that bacterial corner flow is controlled by quorum sensing, the cell–cell communication process that regulates biosurfactant production. Understanding this previously unappreciated bacterial transport mechanism will enable more accurate predictions of bacterial spreading in soil and other unsaturated porous media.