More Like this

1. Fluidic bacterial diodes rectify magnetotactic cell motility in porous environments

   https://doi.org/10.1038/s41467-021-26235-6  

   Waisbord, Nicolas ; Dehkharghani, Amin ; Guasto, Jeffrey S. ( October 2021 , Nature Communications)

   Directed motility enables swimming microbes to navigate their environment for resources via chemo-, photo-, and magneto-taxis. However, directed motility competes with fluid flow in porous microbial habitats, affecting biofilm formation and disease transmission. Despite this broad importance, a microscopic understanding of how directed motility impacts the transport of microswimmers in flows through constricted pores remains unknown. Through microfluidic experiments, we show that individual magnetotactic bacteria directed upstream through pores display three distinct regimes, whereby cells swim upstream, become trapped within a pore, or are advected downstream. These transport regimes are reminiscent of the electrical conductivity of a diode andmore »are accurately predicted by a comprehensive Langevin model. The diode-like behavior persists at the pore scale in geometries of higher dimension, where disorder impacts conductivity at the sample scale by extending the trapping regime over a broader range of flow speeds. This work has implications for our understanding of the survival strategies of magnetotactic bacteria in sediments and for developing their use in drug delivery applications in vascular networks.

   « less
2. Imaging the emergence of bacterial turbulence: Phase diagram and transition kinetics

   https://doi.org/10.1126/sciadv.abd1240  

   Peng, Yi ; Liu, Zhengyang ; Cheng, Xiang ( April 2021 , Science Advances)

   We experimentally study the emergence of collective bacterial swimming, a phenomenon often referred to as bacterial turbulence. A phase diagram of the flow of 3D Escherichia coli suspensions spanned by bacterial concentration, the swimming speed of bacteria, and the number fraction of active swimmers is systematically mapped, which shows quantitative agreement with kinetic theories and demonstrates the dominant role of hydrodynamic interactions in bacterial collective swimming. We trigger bacterial turbulence by suddenly increasing the swimming speed of light-powered bacteria and image the transition to the turbulence in real time. Our experiments identify two unusual kinetic pathways, i.e., the one-step transitionmore »with long incubation periods near the phase boundary and the two-step transition driven by long-wavelength instabilities deep inside the turbulent phase. Our study provides not only a quantitative verification of existing theories but also insights into interparticle interactions and transition kinetics of bacterial turbulence.« less
3. Mangrove roots model suggest an optimal porosity to prevent erosion

   https://doi.org/10.1038/s41598-021-88119-5  

   Kazemi, Amirkhosro ; Castillo, Luciano ; Curet, Oscar M. ( December 2021 , Scientific Reports)

   Abstract Mangrove swamps are extremely productive ecosystems providing many ecological services in coastal regions. The hydrodynamic interactions of mangrove roots and water flow have been proposed as a key element to mitigate erosion. Several studies reveal that precise prediction of the morphological evolution of coastal areas, in the face of global warming and the consequent sea-level rise, requires an understanding of interactions between root porosity (the fraction of the volume of void space over the total volume), water flows, and sediment transport. Water flows around the mangrove prop roots create a complex energetic process that mixes up sediments and generatesmore »a depositional region posterior to the roots. In this work, we investigated the boundary layer behind permeable arrays of cylinders (patch) that represent the mangrove roots to explore the impact of patch porosity on the onset of sediment transport. The flow measurements were performed in a vertical plane along the water depth downstream of the mangrove root models. A high-resolution Particle Image Velocimetry (PIV) was used in a flume to observe the impact of porosity on the mean flow, velocity derivatives, skin friction coefficient, and production of turbulent kinetic energy for Reynolds number of 2500 (based on patch diameter length-scale). Here, we proposed a predictive model for critical velocity for incipient motion that takes into account the mangrove roots porosity and the near-bed turbulence effect. It is found that the patch with the $$\phi =47\%$$ ϕ = 47 % porosity, has the maximum critical velocity over which the sediment transport initiates. We found the optimum porosity has the minimum sediment erosion and creates negative vorticity sources near the bed that increases the critical velocity. This signifies an optimum porosity for the onset of sediment transport consistent with the porosity of mangroves in nature. The phenomenological model is elucidated based on an analysis of the vorticity evolution equation for viscous incompressible flows. For the optimum porous patch, a sink of vorticity was formed which yielded to lower the near-bed turbulence and vorticity. The minimum velocity fluctuations were sufficient to initiate the boundary layer transition, however, the viscous dissipation dominated the turbulence production to obstruct the sediment transport. This work identified the pivotal role of mangrove root porosity in sediment transport in terms of velocity and its derivatives in wall-bounded flows. Our work also provides insight into the sediment transport and erosion processes that govern the evolution of the shapes of shorelines.« less
4. Fluid deformation in random steady three-dimensional flow

   https://doi.org/10.1017/jfm.2018.654  

   Lester, Daniel R. ; Dentz, Marco ; Le Borgne, Tanguy ; de Barros, Felipe P. ( November 2018 , Journal of Fluid Mechanics)

   The deformation of elementary fluid volumes by velocity gradients is a key process for scalar mixing, chemical reactions and biological processes in flows. Whilst fluid deformation in unsteady, turbulent flow has gained much attention over the past half-century, deformation in steady random flows with complex structure – such as flow through heterogeneous porous media – has received significantly less attention. In contrast to turbulent flow, the steady nature of these flows constrains fluid deformation to be anisotropic with respect to the fluid velocity, with significant implications for e.g. longitudinal and transverse mixing and dispersion. In this study we derive an abmore »initio coupled continuous-time random walk (CTRW) model of fluid deformation in random steady three-dimensional flow that is based upon a streamline coordinate transform which renders the velocity gradient and fluid deformation tensors upper triangular. We apply this coupled CTRW model to several model flows and find that these exhibit a remarkably simple deformation structure in the streamline coordinate frame, facilitating solution of the stochastic deformation tensor components. These results show that the evolution of longitudinal and transverse fluid deformation for chaotic flows is governed by both the Lyapunov exponent and power-law exponent of the velocity probability distribution function at small velocities, whereas algebraic deformation in non-chaotic flows arises from the intermittency of shear events following similar dynamics as that for steady two-dimensional flow.« less
5. The Functional Significance of Bacterial Predators

   https://doi.org/10.1128/mBio.00466-21  

   Hungate, Bruce A. ; Marks, Jane C. ; Power, Mary E. ; Schwartz, Egbert ; van Groenigen, Kees Jan ; Blazewicz, Steven J. ; Chuckran, Peter ; Dijkstra, Paul ; Finley, Brianna K. ; Firestone, Mary K. ; et al ( April 2021 , mBio)

   Lemon, Katherine P. (Ed.)

   ABSTRACT Predation structures food webs, influences energy flow, and alters rates and pathways of nutrient cycling through ecosystems, effects that are well documented for macroscopic predators. In the microbial world, predatory bacteria are common, yet little is known about their rates of growth and roles in energy flows through microbial food webs, in part because these are difficult to quantify. Here, we show that growth and carbon uptake were higher in predatory bacteria compared to nonpredatory bacteria, a finding across 15 sites, synthesizing 82 experiments and over 100,000 taxon-specific measurements of element flow into newly synthesized bacterial DNA. Obligate predatorymore »bacteria grew 36% faster and assimilated carbon at rates 211% higher than nonpredatory bacteria. These differences were less pronounced for facultative predators (6% higher growth rates, 17% higher carbon assimilation rates), though high growth and carbon assimilation rates were observed for some facultative predators, such as members of the genera Lysobacter and Cytophaga , both capable of gliding motility and wolf-pack hunting behavior. Added carbon substrates disproportionately stimulated growth of obligate predators, with responses 63% higher than those of nonpredators for the Bdellovibrionales and 81% higher for the Vampirovibrionales , whereas responses of facultative predators to substrate addition were no different from those of nonpredators. This finding supports the ecological theory that higher productivity increases predator control of lower trophic levels. These findings also indicate that the functional significance of bacterial predators increases with energy flow and that predatory bacteria influence element flow through microbial food webs. IMPORTANCE The word “predator” may conjure images of leopards killing and eating impala on the African savannah or of great white sharks attacking elephant seals off the coast of California. But microorganisms are also predators, including bacteria that kill and eat other bacteria. While predatory bacteria have been found in many environments, it has been challenging to document their importance in nature. This study quantified the growth of predatory and nonpredatory bacteria in soils (and one stream) by tracking isotopically labeled substrates into newly synthesized DNA. Predatory bacteria were more active than nonpredators, and obligate predators, such as Bdellovibrionales and Vampirovibrionales , increased in growth rate in response to added substrates at the base of the food chain, strong evidence of trophic control. This work provides quantitative measures of predator activity and suggests that predatory bacteria—along with protists, nematodes, and phages—are active and important in microbial food webs.« less