Data-driven approach to identify field-scale biogeochemical transitions using geochemical and geophysical data and hidden Markov models: Development and application at a uranium-contaminated aquifer

Water Resources Research

Volumn 49, Issue 10, 2013, Pages 6412-6424

  Chen, Jinsong ^a   Hubbard, Susan S ^a   Williams, Kenneth H ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

bioremediation; complex resistivity; groundwater; hidden Markov model; spectral IP; uranium

Indexed keywords

COMPLEX RESISTIVITY; DATA-DRIVEN APPROACH; DEVELOPMENT AND APPLICATIONS; GEOPHYSICAL OBSERVATIONS; HIDDEN MARKOV RANDOM FIELDS; INDUCED POLARIZATION; SPECTRAL IP; URANIUM CONCENTRATION;

AQUIFERS; BIOREMEDIATION; BIOTECHNOLOGY; COMPLEX NETWORKS; GROUNDWATER; GROUNDWATER POLLUTION; GROUNDWATER RESOURCES; HIDDEN MARKOV MODELS; NONINVASIVE MEDICAL PROCEDURES; POLLUTION; URANIUM;

BIOGEOCHEMISTRY;

AQUIFER POLLUTION; BIOREMEDIATION; DATA ACQUISITION; GEOCHEMICAL METHOD; GEOPHYSICAL METHOD; MARKOV CHAIN; POLLUTION CONTROL; PROBABILITY; SUBSURFACE FLOW; TIME SERIES; URANIUM;

EID: 84885000200     PISSN: 00431397     EISSN: 19447973     Source Type: Journal    
DOI: 10.1002/wrcr.20524     Document Type: Article

References (36)

1. Akaike, H., (1973), Information theory and an extension of the maximum likelihood principle, in Second International Symposium on Information Theory, edited by, B. N. Petrov, and, F. Csaki, pp. 267-281, Akademiai Kiado, Budapest.
2. Anderson, R. T., et al. (2003), Stimulating the in-situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer, (Pubitemid 37280308)
3. Armstrong, R., and, J. Ajo-Franklin, (2011), Investigating biomineralization using synchrotron based X-ray computed microtomography, Geophys. Res. Lett., 38, L08406, doi: 10.1029/2011GL046916.
4. Binley, A., and, A. Kemna, (2005), DC resistivity and induced polarization methods, in Hydrogeophysics, edited by, Y. Rubin, and, S. Hubbard, pp. 129-156, Springer, Dordrecht, Netherlands.
5. Chen, J., S. Hubbard, K. Williams, S. Pride, L. Li, C. Steefel, and, L. Slater, (2009), A state-space Bayesian framework for estimating biogeochemical transformations using time-lapse geophysical data, Water Resour. Res., 45, W08420, doi: 10.1029/2008WR007698.
6. Chen, J., S. S. Hubbard, K. H. Williams, A. Flores-Orozco, and, A. Kemna, (2012), Estimating the spatiotemporal distribution of geochemical parameters associated with biostimulation using spectral induced polarization data and hierarchical Bayesian models, Water Resour. Res., 48, W05555, doi: 10.1029/2011WR010992.
7. Davis, C. A., E. Atekwana, E. Atekwana, L. D. Slater, S. Rossbach, and, M. R. Mormile, (2006), Microbial growth and biofilm formulation in geologic media is detected with complex conductivity measurements, Geophys. Res. Lett., 33, L18403, doi: 10.1029/2006GL027312. (Pubitemid 351147900)
8. Dempster, A. P., N. M. Laird, and, D. B. Rubin, (1977), Maximum likelihood from incomplete data via the EM algorithm (with discussion), J. R. Stat. Soc., Ser. B, 39, 1-38.
9. Druhan, J. L., C. I. Steefel, S. Molins, K. H. Williams, M. E. Conrad, and, D. J. DePaolo, (2012), Timing the onset of sulfate reduction over multiple subsurface acetate amendments by measurement and modeling of sulfur isotope fractionation, Environ. Sci. Technol., 46 (16), 8895-8902.
10. Fang, Y., S. B. Yabusaki, S. J. Morrison, J. P. Amonette, and, P. E. Long, (2009), Multicomponent reactive transport modeling of uranium bioremediation field experiments, Geochim. Cosmochim. Acta, 73 (20), 6029-6051.
11. Flores Orozco, A., K. H. Williams, P. E. Long, S. S. Hubbard, and, A. Kemna, (2011), Using complex resistivity imaging to infer biogeochemical processes associated with bioremediation of an uranium contaminated aquifer, J. Geophys. Res., 116, G03001, doi: 10.1029/2010JG001591.
12. Hughes, J. P., and, P. Guttorp, (1994), A class of stochastic models for relating synoptic atmospheric patterns to regional hydrologic phenomena, Water Resour. Res., 30, 1535-1546. (Pubitemid 24404201)
13. Kemna, A, (2000), Tomographic inversion of complex resistivity: Theory and application, PhD Thesis, Ruhr-University Bochum, Bochum, Germany.
14. Li, L., C. I. Steefel, M. B. Kowalsky, A. Englert, and, S. Hubbard, (2010), Effects of physical and geochemical heterogeneities on mineral transformation and biomass accumulation during biostimulation experiments at Rifle, Colorado, J. Contam. Hydrol., 112, 45-63.
15. Lu, Z., and, L. M. Berliner, (1998), Markov switching time series models with application to daily runoff series, Water Resour. Res., 35 (2), 523-534.
16. Nico, P. S., B. D. Stewart, and, S. Fendorf, (2009), Incorporation of oxidized uranium into Fe (Hydr)oxides during Fe(II) catalyzed remineralization, Environ. Sci. Technol., 43, 7391-7396.
17. Ntarlagiannis, D., K. H. Williams, L. Slater, and, S. S. Hubbard, (2005), Low-frequency electrical response to microbial induced sulfide precipitation, J. Geophys. Res., 110, G02009, doi: 10.1029/2005JG000024.
18. Pelton, W. H., S. H. Ward, P. G. Hallof, W. R. Sill, and, P. H. Nelson, (1978), Mineral discrimination and removal of inductive coupling with multi-frequency IP, Geophysics, 43 (3), 588-609. (Pubitemid 8594745)
19. Personna, Y. R., D. Ntarlagiannis, L. Slater, N. Yee, M. O'Brien, and, S. S. Hubbard, (2008), Spectral induced polarization and electrodic potential monitoring of microbially mediated iron sulfide transformations, J. Geophys. Res., 113, G02020, doi: 10.1029/2007JG000614.
20. Revil, A., (2012), Spectral induced polarization of shaly sands: Influence of electrical double layer, Water Resour. Res., 48, W02517, doi: 10.1029/2011WR011260.
21. Schwarz, G. E., (1978), Estimating the dimension of a model, Ann. Stat., 6 (2), 461-464.
22. Slater, L., D. Ntarlagiannis, Y. R. Personna, and, S. S. Hubbard, (2007), Pore-scale spectral induced polarization signatures associated with FeS biomineral transformations, Geophys. Res. Lett., 34, L21404, doi: 10.1029/2007GL031840. (Pubitemid 351149078)
23. Venables, W. N., and, B. D. Ripley, (1999), Modern Applied Statistics With S-Plus, 3rd ed., Springer, New York.
24. Visser, I., (2011), Seven things to remember about hidden Markov models: A tutorial on Markovian models for time series, J. Math. Psychol., 55, 403-415.
25. Visser, I., and, M. Speekenbrink, (2010), depmixS4: An R package for hidden Markov models, J. Stat. Software, 36 (7), 1-21.
26. Vrionis, H. A., R. T. Anderson, I. Ortiz-Bernad, K. R. O'Neill, C. T. Resch, A. D. Peacock, R. Dayvault, D. C. White, P. E. Long, and, D. R. Lovley, (2005), Microbiological and geochemical heterogeneity in an in-situ uranium bioremediation field site, Appl. Environ. Microbiol., 71 (10), 6308-6318. (Pubitemid 41460528)
27. Wan, J., W. Dong, and, T. K. Tokunaga, (2011), Method to attenuate U(VI) mobility in acidic waste plumes using humic acids, Environ. Sci. Technol., 45, 2331-2337.
28. Williams, K. H., D. Ntarlagiannis, L. Slater, A. Dohnalkova, S. S. Hubbard, and, J. Banfield, (2005), Geophysical imaging of stimulated microbial bioremediation, Environ. Sci. Technol., 39 (19), 7592-7600. (Pubitemid 41407491)
29. Williams, K. H., A. Kemna, M. Wilkins, J. Druhan, E. Arntzen, L. N'Guessan, P. E. Long, S. S. Hubbard, and, J. F. Banfield, (2009), Geophysical monitoring of coupled microbial and geochemical processes during stimulated subsurface bioremediation, Environ. Sci. Technol., 43 (17), 6717-6723.
30. Williams, K. H., et al. (2011), Acetate availability and its influence on sustainable bioremediation of uranium-contaminated groundwater, Geomicrobiol. J., 28, 519-539.
31. Wong, J., (1979), An electrochemical model of the induced-polarization phenomenon in disseminated sulfide ores, Geophysics, 44 (7), 1245-1265. (Pubitemid 9471830)
32. Wu, Y., R. Versteeg, L. Slater, and, D. LaBrecque, (2009), Calcite precipitation dominates the electrical signatures of zero valent iron columns under simulated field conditions, J. Contam. Hydrol., 106, 131-143.
33. Wu, Y., J. B. Ajo-Franklin, N. Spycher, S. S. Hubbard, G. Zhang, K. H. Williams, J. Taylor, Y. Fujita, and, R. Smith, (2011), Geophysical monitoring and reactive transport modeling of ureolytically-driven calcium carbonate precipitation, Geochem. Trans., 12, doi: 10.1186/1467-4866-12-7.
34. Yabusaki, S. B., et al. (2007), Uranium removal from groundwater via in situ biostimulation: Field-scale modeling of transport and biological processes, J. Contam. Hydrol., 93, 216-235. (Pubitemid 47088023)
35. Zucchini, W., and, P. Guttorp, (1991), A hidden Markov model for space-time precipitation, Water Resour. Res., 27, 1917-1923.
36. Zucchini, W., and, I. L. MacDonald, (2009), Hidden Markov Models for Time Series: An Introduction using R, CRC Press, New York.