scholarly journals Trait-specific dispersal of bacteria in heterogeneous porous environments: from pore to porous medium scale

2020 ◽  
Vol 17 (164) ◽  
pp. 20200046 ◽  
Author(s):  
David Scheidweiler ◽  
Filippo Miele ◽  
Hannes Peter ◽  
Tom J. Battin ◽  
Pietro de Anna
Keyword(s):  
Preferential Flow ◽  
Cell Attachment ◽  
Flow Direction ◽  
Time Lapse ◽  
Breakthrough Curves ◽  
Porous System ◽  
Dispersal Patterns ◽  
Multi Scale ◽  
Motile Cells ◽  
Hydrodynamic Shear

The dispersal of organisms controls the structure and dynamics of populations and communities, and can regulate ecosystem functioning. Predicting dispersal patterns across scales is important to understand microbial life in heterogeneous porous environments such as soils and sediments. We developed a multi-scale approach, combining experiments with microfluidic devices and time-lapse microscopy to track individual bacterial trajectories and measure the overall breakthrough curves and bacterial deposition profiles: we, then, linked the two scales with a novel stochastic model. We show that motile cells of Pseudomonas putida disperse more efficiently than non-motile mutants through a designed heterogeneous porous system. Motile cells can evade flow-imposed trajectories, enabling them to explore larger pore areas than non-motile cells. While transported cells exhibited a rotation in response to hydrodynamic shear, motile cells were less susceptible to the torque, maintaining their body oriented towards the flow direction and thus changing the population velocity distribution with a significant impact on the overall transport properties. We also found, in a separate set of experiments, that if the suspension flows through a porous system already colonized by a biofilm, P. putida cells are channelled into preferential flow paths and the cell attachment rate is increased. These two effects were more pronounced for non-motile than for motile cells. Our findings suggest that motility coupled with heterogeneous flows can be beneficial to motile bacteria in confined environments as it enables them to actively explore the space for resources or evade regions with unfavourable conditions. Our study also underlines the benefit of a multi-scale approach to the study of bacterial dispersal in porous systems.

Microbial dispersal throgh dead-end cavities

2021 ◽  
Author(s):  
David Scheidweiler ◽  
Ankur Deep Bordoloi ◽  
Pietro de Anna
Keyword(s):  
Porous Media ◽  
Time Lapse ◽  
Breakthrough Curves ◽  
Bacterial Cells ◽  
Dispersal Patterns ◽  
Microbial Life ◽  
Sedimentary Environments ◽  
Escherichia Coli Cells ◽  
Dead End

<p>Predicting dispersal patterns is important to understand microbial life in porous media as soils and sedimentary environments. We studied active and passive dispersal of bacterial cells in porous media characterized by two main pore features: fast channels and dead-end cavities. We combined experiments with microfluidic devices and time-lapse microscopy to track individual bacterial trajectories and measure the breakthrough curves and pore scale bacterial abundance. Escherichia coli cells dispersed more efficiently than the non-motile mutants showing a different retention in the dead-end pores. Our findings highlight the role of diffusion dominated dead-end pores on the dispersal of microorganisms in porous media.</p>

Motility of the Limulus blood cell

1979 ◽  
Vol 37 (1) ◽  
pp. 169-180
Author(s):  
P.B. Armstrong
Keyword(s):  
Tissue Culture ◽  
Time Lapse ◽  
Coelomic Fluid ◽  
Cellular Motility ◽  
Paraffin Oil ◽  
Motile Cells ◽  
Direct Microscopic Examination ◽  
High Concentrations ◽  
Glass Surfaces

The sole cell type (the amoebocyte) found in the coelomic fluid of the horseshoe crab, Limulus polyphemus can be stimulated to become motile by extravasation or trauma. Motility was studied using time-lapse microcinematography and direct microscopic examination of cells in tissue culture and in gill leaflets isolated from young animals. Phase-contrast and Nomarski differential-interference contrast optics were employed. Both in culture and in the gills, motile cells showed 2 interconvertible morphological types: the contracted cell, which was compact and rounded and had a relatively small area of contact with the substratum, and a flattened from with a larger area of contact. In both morphological types, motility involved the protrusion of hyaline pseudopods followed by flow of granular endoplasm forward in the pseudoplod. Cellular motility in vivo (in the gill leaflet) was morphologically identical to that displayed in tissue culture. In culture, motility was unaffected by the nature of the substratum: cells were indistinguishable on fluid (paraffin oil) or solid (glass) substrata or on hydrophobic (paraffin oil, siliconized glass) or hydrophilic (clean glass) surfaces. Cells migrated and spread on agar surfaces. Cell motility was unaffected by high concentrations (100 micrograms/ml) of the microtubule-depolymerizing agent colcemid and was abolished by cytochalasin B at 1 microgram/ml.

scholarly journals Form and function in hillslope hydrology: characterization of subsurface flow based on response observations

2017 ◽  
Vol 21 (7) ◽  
pp. 3727-3748 ◽  
Author(s):  
Lisa Angermann ◽  
Conrad Jackisch ◽  
Niklas Allroggen ◽  
Matthias Sprenger ◽  
Erwin Zehe ◽  
...  
Keyword(s):  
Preferential Flow ◽  
Explanatory Power ◽  
Subsurface Flow ◽  
Time Lapse ◽  
Storm Event ◽  
Monitoring Methods ◽  
Catchment Scale ◽  
Flow Paths ◽  
Form And Function ◽  
And Function

Abstract. The phrase form and function was established in architecture and biology and refers to the idea that form and functionality are closely correlated, influence each other, and co-evolve. We suggest transferring this idea to hydrological systems to separate and analyze their two main characteristics: their form, which is equivalent to the spatial structure and static properties, and their function, equivalent to internal responses and hydrological behavior. While this approach is not particularly new to hydrological field research, we want to employ this concept to explicitly pursue the question of what information is most advantageous to understand a hydrological system. We applied this concept to subsurface flow within a hillslope, with a methodological focus on function: we conducted observations during a natural storm event and followed this with a hillslope-scale irrigation experiment. The results are used to infer hydrological processes of the monitored system. Based on these findings, the explanatory power and conclusiveness of the data are discussed. The measurements included basic hydrological monitoring methods, like piezometers, soil moisture, and discharge measurements. These were accompanied by isotope sampling and a novel application of 2-D time-lapse GPR (ground-penetrating radar). The main finding regarding the processes in the hillslope was that preferential flow paths were established quickly, despite unsaturated conditions. These flow paths also caused a detectable signal in the catchment response following a natural rainfall event, showing that these processes are relevant also at the catchment scale. Thus, we conclude that response observations (dynamics and patterns, i.e., indicators of function) were well suited to describing processes at the observational scale. Especially the use of 2-D time-lapse GPR measurements, providing detailed subsurface response patterns, as well as the combination of stream-centered and hillslope-centered approaches, allowed us to link processes and put them in a larger context. Transfer to other scales beyond observational scale and generalizations, however, rely on the knowledge of structures (form) and remain speculative. The complementary approach with a methodological focus on form (i.e., structure exploration) is presented and discussed in the companion paper by Jackisch et al.(2017).

Integrated reservoir characterization: Beyond tomography

Geophysics ◽  
1995 ◽  
Vol 60 (2) ◽  
pp. 354-364 ◽  
Author(s):  
Larry Lines ◽  
Henry Tan ◽  
Sven Treitel ◽  
John Beck ◽  
Richard Chambers ◽  
...  
Keyword(s):  
History Matching ◽  
Preferential Flow ◽  
Reservoir Characterization ◽  
Seismic Anisotropy ◽  
Flow Direction ◽  
Geophysical Methods ◽  
Reservoir Properties ◽  
Traveltime Tomography ◽  
Sonic Log ◽  
Primary Water

In 1992, there was a collaborative effort in reservoir geophysics involving Amoco, Conoco, Schlumberger, and Stanford University in an attempt to delineate variations in reservoir properties of the Grayburg unit in a West Texas [Formula: see text] pilot at North Cowden Field. Our objective was to go beyond traveltime tomography in characterizing reservoir heterogeneity and flow anisotropy. This effort involved a comprehensive set of measurements to do traveltime tomography, to image reflectors, to analyze channel waves for reservoir continuity, to study shear‐wave splitting for borehole stress‐pattern estimation, and to do seismic anisotropy analysis. All these studies were combined with 3-D surface seismic data and with sonic log interpretation. The results are to be validated in the future with cores and engineering data by history matching of primary, water, and [Formula: see text] injection performance. The implementation of these procedures should provide critical information on reservoir heterogeneities and preferential flow direction. Geophysical methods generally indicated a continuous reservoir zone between wells.

scholarly journals Detecting infiltrated water and preferential flow pathways through time-lapse ground-penetrating radar surveys

2020 ◽  
Vol 726 ◽  
pp. 138511 ◽  
Author(s):  
Simone Di Prima ◽  
Thierry Winiarski ◽  
Rafael Angulo-Jaramillo ◽  
Ryan D. Stewart ◽  
Mirko Castellini ◽  
...  
Keyword(s):  
Ground Penetrating Radar ◽  
Preferential Flow ◽  
Time Lapse ◽  
Flow Pathways ◽  
Preferential Flow Pathways ◽  
Ground Penetrating

Multi-scale preferential flow processes in an urban streambed under variable hydraulic conditions

2019 ◽  
Vol 573 ◽  
pp. 168-179 ◽  
Author(s):  
Farzaneh MahmoodPoor Dehkordy ◽  
Martin A. Briggs ◽  
Frederick D. Day-Lewis ◽  
Kamini Singha ◽  
Ashton Krajnovich ◽  
...  
Keyword(s):  
Preferential Flow ◽  
Multi Scale ◽  
Hydraulic Conditions ◽  
Flow Processes

scholarly journals Tracing Septic Pollution Sources Using Synthetic DNA Tracers: Proof of Concept

2019 ◽  
Vol 12 ◽  
pp. 117862211986379 ◽  
Author(s):  
Christine B Georgakakos ◽  
Paul L Richards ◽  
M Todd Walter
Keyword(s):  
Preferential Flow ◽  
Quantitative Polymerase Chain Reaction ◽  
Breakthrough Curves ◽  
Septic Systems ◽  
Proof Of Concept ◽  
Septic System ◽  
Flow Paths ◽  
Synthetic Dna ◽  
Preferential Flow Paths ◽  
Polymerase Chain

Contamination from septic systems is one of the most difficult sources of nonpoint source (NPS) pollution to quantify. Quantification is difficult in part because locating malfunctioning septic systems within a watershed is challenging. This study used synthetic-DNA-based tracers to track flows from 2 septic systems. Sample DNA was quantified using quantitative polymerase chain reaction (qPCR). This technology could be especially useful for simultaneously assessing multiple septic systems because there are essentially infinite unique combinations of DNA bases such that unique tracers could be engineered for each septic system. Two studies were conducted: the first, to determine whether the tracers move through septic systems (experiment 1), and the second, to determine whether the tracers were detectable at watershed scales (experiment 2). In both cases, clear, although complex, breakthrough curves were detected. Experiment 1 revealed possible preferential flow paths that might not have been otherwise obvious, indicative of short circuiting systems. This proof of concept suggests that these tracers could be applied to watersheds suspected of experiencing NPS septic system pollution.

scholarly journals Technical Note: The use of an interrupted-flow centrifugation method to characterise preferential flow in low permeability media

2015 ◽  
Vol 12 (1) ◽  
pp. 67-92
Author(s):  
R. A. Crane ◽  
M. O. Cuthbert ◽  
W. Timms
Keyword(s):  
Preferential Flow ◽  
Molecular Diffusion ◽  
Breakthrough Curves ◽  
Technical Note ◽  
Dual Porosity ◽  
Low Permeability ◽  
Efficiency Coefficient ◽  
Transport Modelling ◽  
Induced Flow ◽  
Interrupted Flow

Abstract. We present an interrupted-flow centrifugation technique to characterise preferential flow in low permeability media. The method entails a minimum of three phases: centrifuge induced flow, no flow and centrifuge induced flow, which may be repeated several times in order to most effectively characterise multi-rate mass transfer behaviour. In addition, the method enables accurate simulation of relevant in situ total stress conditions during flow by selecting an appropriate centrifugal force level. We demonstrate the utility of the technique for characterising the hydraulic properties of smectite clay dominated core samples. All samples exhibited a non-Fickian tracer breakthrough (early tracer arrival), combined with a decrease in tracer concentration immediately after each period of interrupted-flow. This is indicative of dual (or multi) porosity behaviour, with solute migration predominately via advection during induced flow, and via molecular diffusion (between the preferential flow network(s) and the low hydraulic conductivity domain) during interrupted-flow. Tracer breakthrough curves were simulated using a bespoke dual porosity model with excellent agreement between the data and model output (Nash–Sutcliffe model efficiency coefficient was >0.97 for all samples). In combination interrupted-flow centrifuge experiments and dual porosity transport modelling are shown to be a powerful method to characterise preferential flow in low permeability media.

scholarly journals Covariance-constrained difference inversion of time-lapse electrical resistivity tomography data

Geophysics ◽  
2016 ◽  
Vol 81 (5) ◽  
pp. E311-E322 ◽  
Author(s):  
Thomas Hermans ◽  
Andreas Kemna ◽  
Frédéric Nguyen
Keyword(s):  
Electrical Resistivity ◽  
Electrical Resistivity Tomography ◽  
Time Lapse ◽  
Breakthrough Curves ◽  
Time Dimension ◽  
Resistivity Tomography ◽  
Shallow Subsurface ◽  
Direct Measurements ◽  
Active Processes ◽  
Low Sensitivity

Hydrogeophysics has become a major field of research in the past two decades, and time-lapse electrical resistivity tomography (ERT) is one of the most popular techniques to monitor passive and active processes in shallow subsurface reservoirs. Time-lapse inversion schemes have been developed to refine inversion results, but they mostly still rely on a spatial regularization procedure based on the standard smoothness constraint. We have applied a covariance-based regularization operator to the time-lapse ERT inverse problem. We first evaluated the method for surface and crosshole ERT with two synthetic cases and compared the results with the smoothness-constrained inversion (SCI). These tests showed that the covariance-constrained inversion (CCI) better images the target in terms of shape and amplitude. Although more important in low-sensitivity zones, we have observed improvements everywhere in the tomograms. Those synthetic examples also show that an error made in the range or in the type of the variogram model had a limited impact on the resulting image, which still remained better than SCI. We then applied the method to cross-borehole ERT field data from a heat-tracing experiment, in which the comparison with direct measurements showed a strong improvement of the breakthrough curves retrieved from ERT. This method could be extended to the time dimension, which would allow the use of CCI in 4D inversion schemes.

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