Chemotaxis under flow disorder shapes microbial dispersion in porous media

Anna, Pietro de; Pahlavan, Amir A.; Yawata, Yutaka; Stocker, Roman; Juanes, Rubén

doi:10.1038/s41567-020-1002-x

Cited by 54 publications

(43 citation statements)

References 42 publications

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“…These intertwined effects complicate the mechanistic understanding of the observed impacts of chemotaxis and motility in such complex environments as the rhizosphere or the GI tract, where grains, surfaces or the mucus affect swimming patterns (de Anna et al . 2020 ; Figueroa-Morales et al . 2019 ; Frangipane et al .…”

Section: Discussionmentioning

confidence: 99%

Multiple functions of flagellar motility and chemotaxis in bacterial physiology

Colin

Laganenka

et al. 2021

FEMS Microbiology Reviews

163

118

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Most swimming bacteria are capable of following gradients of nutrients, signaling molecules and other environmental factors that affect bacterial physiology. This tactic behavior became one of the most-studied model systems for signal transduction and quantitative biology, and underlying molecular mechanisms are well characterized in Escherichia coli and several other model systems. In this review, we focus primarily on less understood aspect of bacterial chemotaxis, namely its physiological relevance for individual bacterial cells and for bacterial populations. As evident from multiple recent studies, even for the same bacterial species flagellar motility and chemotaxis might serve multiple roles, depending on the physiological and environmental conditions. Among these, finding sources of nutrients and more generally locating niches that are optimal for growth appear to be one of the major functions of bacterial chemotaxis, which could explain many chemoeffector preferences as well as flagellar gene regulation. Chemotaxis might also generally enhance efficiency of environmental colonization by motile bacteria, which involves intricate interplay between individual and collective behaviors and trade-offs between growth and motility. Finally, motility and chemotaxis play multiple roles in collective behaviors of bacteria including swarming, biofilm formation and autoaggregation, as well as in their interactions with animal and plant hosts.

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Section: Discussionmentioning

confidence: 99%

Multiple functions of flagellar motility and chemotaxis in bacterial physiology

Colin

Laganenka

et al. 2021

FEMS Microbiology Reviews

163

118

View full text Add to dashboard Cite

show abstract

“…8,9 However, one of the problems researchers face when trying to optimize these processes is the limited understanding of the role that bacterial motility plays at the pore scale [10][11][12][13][14] and its coupling to local chemical gradients. 15 Indeed, we now know that flagellated microorganisms such as E. coli, or sperm cells display a great variety of swimming behaviors like upstream motions, [16][17][18] drift trajectories on surfaces 19,20 or helicoidal trajectories in a flow. 21,22 These motions contribute significantly to the trapping of bacteria in pores as well as in determining their localization in a channeled flow 23 and their hydrodynamic dispersion.…”

Section: Introductionmentioning

confidence: 99%

The influence of motility on bacterial accumulation in a microporous channel

et al. 2021

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“…Flow channelization is an ubiquitous phenomenon in subsurface media with implications in many engineering endeavors including groundwater management (Charbeneau 2006;Freeze and Cherry 1979;Šimnek et al 2003;LeBlanc et al 1991), oil and gas recovery (Middleton et al 2015;Orr and Taber 1984;Wong 1988), and geotechnical engineering (Dullien 1992;Bear 1988). Observations of nonuniform flow distribution have been reported at the pore-and continuum-scales in laboratory studies (Kurotori et al 2019;Datta et al 2013;Carrel et al 2018;Morales et al 2017;Holzner et al 2015;de Anna et al 2021), field experiments (Goeppert et al 2020;Bianchi et al 2011;Zheng et al 2011;Abelin et al 1991;Guihéneuf et al 2014;Le Borgne et al 2006;Rasmuson and Neretnieks 1986;Winograd and Pearson 1976;Flury et al 1994;Hendrickx and Flury 2001) and numerical simulations (Alim et al 2017;Meyer and Bijeljic 2016;Tyukhova and Willmann 2016;Siena et al 2014Siena et al , 2019Nissan and Berkowitz 2019;Puyguiraud et al 2019;Kang et al 2014;Bijeljic et al 2013;Fiori et al 2011Fiori et al , 2013Zinn and Harvey 2003;Hyman 2020). The multi-scale structural heterogeneity of porous and...…”

Section: Introductionmentioning

confidence: 99%

Flow Path Resistance in Heterogeneous Porous Media Recast into a Graph-Theory Problem

et al. 2021

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This work aims to describe the spatial distribution of flow from characteristics of the underlying pore structure in heterogeneous porous media. Thousands of two-dimensional samples of polydispersed granular media are used to (1) obtain the velocity field via direct numerical simulations, and (2) conceptualize the pore network as a graph in each sample. Analysis of the flow field allows us to distinguish preferential from stagnant flow regions and to quantify how channelized the flow is. Then, the graph’s edges are weighted by geometric attributes of their corresponding pores to find the path of minimum resistance of each sample. Overlap between the preferential flow paths and the predicted minimum resistance path determines the accuracy in individual samples. An evolutionary algorithm is employed to determine the “fittest” weighting scheme (here, the channel’s arc length to pore throat ratio) that maximizes accuracy across the entire dataset while minimizing over-parameterization. Finally, the structural similarity of neighboring edges is analyzed to explain the spatial arrangement of preferential flow within the pore network. We find that connected edges within the preferential flow subnetwork are highly similar, while those within the stagnant flow subnetwork are dissimilar. The contrast in similarity between these regions increases with flow channelization, explaining the structural constraints to local flow. The proposed framework may be used for fast characterization of porous media heterogeneity relative to computationally expensive direct numerical simulations. Article Highlights A quantitative assessment of flow channeling is proposed that distinguishes pore-scale flow fields into preferential and stagnant flow regions. Geometry and topology of the pore network are used to predict the spatial distribution of fast flow paths from structural data alone. Local disorder of pore networks provides structural constraints for flow separation into preferential v stagnant regions and informs on their velocity contrast.

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Chemotaxis under flow disorder shapes microbial dispersion in porous media

Cited by 54 publications

References 42 publications

Multiple functions of flagellar motility and chemotaxis in bacterial physiology

Multiple functions of flagellar motility and chemotaxis in bacterial physiology

The influence of motility on bacterial accumulation in a microporous channel

Flow Path Resistance in Heterogeneous Porous Media Recast into a Graph-Theory Problem

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