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Title: On Modeling Ensemble Transport of Metal Reducing Motile Bacteria

Abstract

Many metal reducing bacteria are motile with their run-and-tumble behavior exhibiting series of flights and waiting-time spanning multiple orders of magnitude. While several models of bacterial processes do not consider their ensemble motion, some models treat motility using an advection diffusion equation (ADE). In this study, Geobacter and Pelosinus, two metal reducing species, are used in micromodel experiments for study of their motility characteristics. Trajectories of individual cells on the order of several seconds to few minutes in duration are analyzed to provide information on (1) the length of runs, and (2) time needed to complete a run (waiting or residence time). A Continuous Time Random Walk (CTRW) model to predict ensemble breakthrough plots is developed based on the motility statistics. The results of the CTRW model and an ADE model are compared with the real breakthrough plots obtained directly from the trajectories. The ADE model is shown to be insufficient, whereas a coupled CTRW model is found to be good at predicting breakthroughs at short distances and at early times, but not at late time and long distances. The inadequacies of the simple CTRW model can possibly be improved by accounting for correlation in run length and waiting time.

Authors:
 [1];  [1];  [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [3]; ORCiD logo [4]
  1. Desert Research Inst., Reno, NV (United States). Div. of Hydrologic Sciences
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Energy and Environment Directorate
  3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab.
  4. Brigham Young Univ., Provo, UT (United States). Dept. of Chemistry and Biochemistry
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1577077
Report Number(s):
PNNL-SA-134947
Journal ID: ISSN 2045-2322
Grant/Contract Number:  
AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Yang, Xueke, Parashar, Rishi, Sund, Nicole L., Plymale, Andrew E., Scheibe, Timothy D., Hu, Dehong, and Kelly, Ryan T. On Modeling Ensemble Transport of Metal Reducing Motile Bacteria. United States: N. p., 2019. Web. doi:10.1038/s41598-019-51271-0.
Yang, Xueke, Parashar, Rishi, Sund, Nicole L., Plymale, Andrew E., Scheibe, Timothy D., Hu, Dehong, & Kelly, Ryan T. On Modeling Ensemble Transport of Metal Reducing Motile Bacteria. United States. doi:10.1038/s41598-019-51271-0.
Yang, Xueke, Parashar, Rishi, Sund, Nicole L., Plymale, Andrew E., Scheibe, Timothy D., Hu, Dehong, and Kelly, Ryan T. Thu . "On Modeling Ensemble Transport of Metal Reducing Motile Bacteria". United States. doi:10.1038/s41598-019-51271-0. https://www.osti.gov/servlets/purl/1577077.
@article{osti_1577077,
title = {On Modeling Ensemble Transport of Metal Reducing Motile Bacteria},
author = {Yang, Xueke and Parashar, Rishi and Sund, Nicole L. and Plymale, Andrew E. and Scheibe, Timothy D. and Hu, Dehong and Kelly, Ryan T.},
abstractNote = {Many metal reducing bacteria are motile with their run-and-tumble behavior exhibiting series of flights and waiting-time spanning multiple orders of magnitude. While several models of bacterial processes do not consider their ensemble motion, some models treat motility using an advection diffusion equation (ADE). In this study, Geobacter and Pelosinus, two metal reducing species, are used in micromodel experiments for study of their motility characteristics. Trajectories of individual cells on the order of several seconds to few minutes in duration are analyzed to provide information on (1) the length of runs, and (2) time needed to complete a run (waiting or residence time). A Continuous Time Random Walk (CTRW) model to predict ensemble breakthrough plots is developed based on the motility statistics. The results of the CTRW model and an ADE model are compared with the real breakthrough plots obtained directly from the trajectories. The ADE model is shown to be insufficient, whereas a coupled CTRW model is found to be good at predicting breakthroughs at short distances and at early times, but not at late time and long distances. The inadequacies of the simple CTRW model can possibly be improved by accounting for correlation in run length and waiting time.},
doi = {10.1038/s41598-019-51271-0},
journal = {Scientific Reports},
number = 1,
volume = 9,
place = {United States},
year = {2019},
month = {10}
}

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Works referenced in this record:

Role of chemotaxis in the transport of bacteria through saturated porous media
journal, June 2007


Multicomponent reactive transport modeling of uranium bioremediation field experiments
journal, October 2009

  • Fang, Yilin; Yabusaki, Steven B.; Morrison, Stan J.
  • Geochimica et Cosmochimica Acta, Vol. 73, Issue 20
  • DOI: 10.1016/j.gca.2009.07.019

Twitching motility of bacteria with type-IV pili: Fractal walks, first passage time, and their consequences on microcolonies
journal, November 2017


Transverse Mixing Enhancement due to Bacterial Random Motility in Porous Microfluidic Devices
journal, October 2011

  • Singh, Rajveer; Olson, Mira Stone
  • Environmental Science & Technology, Vol. 45, Issue 20
  • DOI: 10.1021/es201706w

Stimulating the In Situ Activity of Geobacter Species To Remove Uranium from the Groundwater of a Uranium-Contaminated Aquifer
journal, October 2003


Model-based analysis of the role of biological, hydrological and geochemical factors affecting uranium bioremediation
journal, March 2011

  • Zhao, Jiao; Scheibe, Timothy D.; Mahadevan, R.
  • Biotechnology and Bioengineering, Vol. 108, Issue 7
  • DOI: 10.1002/bit.23096

E. coli Superdiffusion and Chemotaxis—Search Strategy, Precision, and Motility
journal, August 2009


Pelosinus defluvii sp. nov., isolated from chlorinated solvent-contaminated groundwater, emended description of the genus Pelosinus and transfer of Sporotalea propionica to Pelosinus propionicus comb. nov.
journal, August 2011

  • Moe, W. M.; Stebbing, R. E.; Rao, J. U.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 62, Issue Pt 6
  • DOI: 10.1099/ijs.0.033753-0

Bacterial motility: How do pili pull?
journal, November 2000


Modeling microbial transport in porous media: Traditional approaches and recent developments
journal, June 2007


Anomalous Fluctuations in the Orientation and Velocity of Swarming Bacteria
journal, July 2016


Microbiological and Geochemical Heterogeneity in an In Situ Uranium Bioremediation Field Site
journal, October 2005


Idling Time of Motile Bacteria Contributes to Retardation and Dispersion in Sand Porous Medium
journal, May 2011

  • Liu, Jun; Ford, Roseanne M.; Smith, James A.
  • Environmental Science & Technology, Vol. 45, Issue 9
  • DOI: 10.1021/es104041t

Finite-size effects on bacterial population expansion under controlled flow conditions
journal, March 2017

  • Tesser, Francesca; Zeegers, Jos C. H.; Clercx, Herman J. H.
  • Scientific Reports, Vol. 7, Issue 1
  • DOI: 10.1038/srep43903

Molecular Analysis of the In Situ Growth Rates of Subsurface Geobacter Species
journal, December 2012

  • Holmes, Dawn E.; Giloteaux, Ludovic; Barlett, Melissa
  • Applied and Environmental Microbiology, Vol. 79, Issue 5
  • DOI: 10.1128/AEM.03263-12

Motile Behavior of Bacteria
journal, January 2000


How the Motility Pattern of Bacteria Affects Their Dispersal and Chemotaxis
journal, December 2013


Large variability in the motility of spiroplasmas in media of different viscosities
journal, November 2018


Anomalous transport in laboratory-scale, heterogeneous porous media
journal, January 2000

  • Berkowitz, Brian; Scher, Harvey; Silliman, Stephen E.
  • Water Resources Research, Vol. 36, Issue 1
  • DOI: 10.1029/1999WR900295

Geobacter pickeringii sp. nov., Geobacter argillaceus sp. nov. and Pelosinus fermentans gen. nov., sp. nov., isolated from subsurface kaolin lenses
journal, January 2007

  • Shelobolina, E. S.; Nevin, K. P.; Blakeney-Hayward, J. D.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 1
  • DOI: 10.1099/ijs.0.64221-0

Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments
journal, December 2003

  • Methe, B. A.; Nelson, K. E.; Eisen, J. A.
  • Science, Vol. 302, Issue 5652, p. 1967-1969
  • DOI: 10.1126/science.1088727

Enhanced diffusion due to motile bacteria
journal, August 2004

  • Kim, Min Jun; Breuer, Kenneth S.
  • Physics of Fluids, Vol. 16, Issue 9
  • DOI: 10.1063/1.1787527

The effect of sampling rate on observed statistics in a correlated random walk
journal, August 2013

  • Rosser, G.; Fletcher, A. G.; Maini, P. K.
  • Journal of The Royal Society Interface, Vol. 10, Issue 85
  • DOI: 10.1098/rsif.2013.0273

Swarming bacteria migrate by Lévy Walk
journal, September 2015

  • Ariel, Gil; Rabani, Amit; Benisty, Sivan
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms9396

Modeling Microorganism Transport and Survival in the Subsurface
journal, January 2014

  • Bradford, Scott A.; Wang, Yusong; Kim, Hyunjung
  • Journal of Environment Quality, Vol. 43, Issue 2
  • DOI: 10.2134/jeq2013.05.0212

Effect of motility on the transport of bacteria populations through a porous medium
journal, January 2019


Diffusion of Bacterial Cells in Porous Media
journal, January 2016


Analysis of Bacterial Random Motility in a Porous Medium Using Magnetic Resonance Imaging and Immunomagnetic Labeling
journal, February 2003

  • Sherwood, Juli L.; Sung, James C.; Ford, Roseanne M.
  • Environmental Science & Technology, Vol. 37, Issue 4
  • DOI: 10.1021/es011210u

2D motility tracking of Pseudomonas putida KT2440 in growth phases using video microscopy
journal, May 2011

  • Davis, Michael L.; Mounteer, Leslie C.; Stevens, Lindsey K.
  • Journal of Bioscience and Bioengineering, Vol. 111, Issue 5
  • DOI: 10.1016/j.jbiosc.2011.01.007

An analysis of hydrodispersive transfer in aquifers
journal, February 1980


Changes in Protein Expression Across Laboratory and Field Experiments in Geobacter bemidjiensis
journal, February 2015

  • Merkley, Eric D.; Wrighton, Kelly C.; Castelle, Cindy J.
  • Journal of Proteome Research, Vol. 14, Issue 3
  • DOI: 10.1021/pr500983v

Processes in microbial transport in the natural subsurface
journal, August 2002


Divergent Aquifer Biogeochemical Systems Converge on Similar and Unexpected Cr(VI) Reduction Products
journal, August 2014

  • Beller, Harry R.; Yang, Li; Varadharajan, Charuleka
  • Environmental Science & Technology, Vol. 48, Issue 18
  • DOI: 10.1021/es5016982

Evaluation of bacterial run and tumble motility parameters through trajectory analysis
journal, April 2018


Variably saturated flow and multicomponent biogeochemical reactive transport modeling of a uranium bioremediation field experiment
journal, November 2011

  • Yabusaki, Steven B.; Fang, Yilin; Williams, Kenneth H.
  • Journal of Contaminant Hydrology, Vol. 126, Issue 3-4
  • DOI: 10.1016/j.jconhyd.2011.09.002

Modeling microbial processes in porous media
journal, March 2000


Enrichment of Members of the Family Geobacteraceae Associated with Stimulation of Dissimilatory Metal Reduction in Uranium-Contaminated Aquifer Sediments
journal, May 2002


Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1
journal, October 2012

  • Beller, Harry R.; Han, Ruyang; Karaoz, Ulas
  • Applied and Environmental Microbiology, Vol. 79, Issue 1
  • DOI: 10.1128/AEM.02496-12

Genetic Identification of a PilT Motor in Geobacter sulfurreducens Reveals a Role for Pilus Retraction in Extracellular Electron Transfer
journal, October 2016

  • Speers, Allison M.; Schindler, Bryan D.; Hwang, Jihwan
  • Frontiers in Microbiology, Vol. 7
  • DOI: 10.3389/fmicb.2016.01578

Monitored natural attenuation forum: Highlights from a panel discussion
journal, January 2007


Flagella and Pili-Mediated Near-Surface Single-Cell Motility Mechanisms in P. aeruginosa
journal, April 2011


Random walk patterns of a soil bacterium in open and confined environments
journal, January 2015


Transverse Bacterial Migration Induced by Chemotaxis in a Packed Column with Structured Physical Heterogeneity
journal, August 2009

  • Wang, Meng; Ford, Roseanne M.
  • Environmental Science & Technology, Vol. 43, Issue 15
  • DOI: 10.1021/es901001t