Using geochemical indicators to distinguish high biogeochemical activity in floodplain soils and sediments
Abstract
A better understanding of how microbial communities interact with their surroundings in physically and chemically heterogeneous subsurface environments will lead to improved quantification of biogeochemical reactions and associated nutrient cycling. This paper develops a methodology to predict potential elevated rates of biogeochemical activity (microbial “hotspots”) in subsurface environments by correlating microbial DNA and aspects of the community structure with the spatial distribution of geochemical indicators in subsurface sediments. Multiple linear regression models of simulated precipitation leachate, HCl and hydroxylamine extractable iron and manganese, total organic carbon (TOC), and microbial community structure were used to identify sample characteristics indicative of biogeochemical hotspots within fluvially-derived aquifer sediments and overlying soils. The method has been applied to (a) alluvial materials collected at a former uranium mill site near Rifle, Colorado and (b) relatively undisturbed floodplain deposits (soils and sediments) collected along the East River near Crested Butte, Colorado. At Rifle, 16 alluvial samples were taken from 8 sediment cores, and at the East River, 46 soil/sediment samples were collected across and perpendicular to 3 active meanders and an oxbow meander. Regression models using TOC and TOC combined with extractable iron and manganese results were determined to be the best fitting statistical models ofmore »
- Authors:
-
- Colorado School of Mines, Golden, CO (United States). Hydrologic Sciences and Engineering Program
- Colorado School of Mines, Golden, CO (United States). Dept. of Civil and Environmental Engineering
- Colorado School of Mines, Golden, CO (United States). Dept. of Applied Mathematics and Statistics
- Desert Research Inst. (DRI), Reno, NV (United States). Division of Hydrologic Sciences
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1471023
- Alternate Identifier(s):
- OSTI ID: 1324027
- Grant/Contract Number:
- AC02-05CH11231; 737 AC02-05CH11231
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Science of the Total Environment
- Additional Journal Information:
- Journal Volume: 563-564; Journal ID: ISSN 0048-9697
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 58 GEOSCIENCES; 59 BASIC BIOLOGICAL SCIENCES; microbial DNA; extractable metals; floodplain geochemistry
Citation Formats
Kenwell, Amy, Navarre-Sitchler, Alexis, Prugue, Rodrigo, Spear, John R., Hering, Amanda S., Maxwell, Reed M., Carroll, Rosemary W. H., and Williams, Kenneth H. Using geochemical indicators to distinguish high biogeochemical activity in floodplain soils and sediments. United States: N. p., 2016.
Web. doi:10.1016/j.scitotenv.2016.04.014.
Kenwell, Amy, Navarre-Sitchler, Alexis, Prugue, Rodrigo, Spear, John R., Hering, Amanda S., Maxwell, Reed M., Carroll, Rosemary W. H., & Williams, Kenneth H. Using geochemical indicators to distinguish high biogeochemical activity in floodplain soils and sediments. United States. https://doi.org/10.1016/j.scitotenv.2016.04.014
Kenwell, Amy, Navarre-Sitchler, Alexis, Prugue, Rodrigo, Spear, John R., Hering, Amanda S., Maxwell, Reed M., Carroll, Rosemary W. H., and Williams, Kenneth H. 2016.
"Using geochemical indicators to distinguish high biogeochemical activity in floodplain soils and sediments". United States. https://doi.org/10.1016/j.scitotenv.2016.04.014. https://www.osti.gov/servlets/purl/1471023.
@article{osti_1471023,
title = {Using geochemical indicators to distinguish high biogeochemical activity in floodplain soils and sediments},
author = {Kenwell, Amy and Navarre-Sitchler, Alexis and Prugue, Rodrigo and Spear, John R. and Hering, Amanda S. and Maxwell, Reed M. and Carroll, Rosemary W. H. and Williams, Kenneth H.},
abstractNote = {A better understanding of how microbial communities interact with their surroundings in physically and chemically heterogeneous subsurface environments will lead to improved quantification of biogeochemical reactions and associated nutrient cycling. This paper develops a methodology to predict potential elevated rates of biogeochemical activity (microbial “hotspots”) in subsurface environments by correlating microbial DNA and aspects of the community structure with the spatial distribution of geochemical indicators in subsurface sediments. Multiple linear regression models of simulated precipitation leachate, HCl and hydroxylamine extractable iron and manganese, total organic carbon (TOC), and microbial community structure were used to identify sample characteristics indicative of biogeochemical hotspots within fluvially-derived aquifer sediments and overlying soils. The method has been applied to (a) alluvial materials collected at a former uranium mill site near Rifle, Colorado and (b) relatively undisturbed floodplain deposits (soils and sediments) collected along the East River near Crested Butte, Colorado. At Rifle, 16 alluvial samples were taken from 8 sediment cores, and at the East River, 46 soil/sediment samples were collected across and perpendicular to 3 active meanders and an oxbow meander. Regression models using TOC and TOC combined with extractable iron and manganese results were determined to be the best fitting statistical models of microbial DNA (via 16S rRNA gene analysis). Finally, fitting these models to observations in both contaminated and natural floodplain deposits, and their associated alluvial aquifers, demonstrates the broad applicability of the geochemical indicator based approach.},
doi = {10.1016/j.scitotenv.2016.04.014},
url = {https://www.osti.gov/biblio/1471023},
journal = {Science of the Total Environment},
issn = {0048-9697},
number = ,
volume = 563-564,
place = {United States},
year = {Sun May 01 00:00:00 EDT 2016},
month = {Sun May 01 00:00:00 EDT 2016}
}
Web of Science
Works referenced in this record:
Using streamlines to simulate stochastic reactive transport in heterogeneous aquifers: Kinetic metal release and transport in CO2 impacted drinking water aquifers
journal, February 2013
- Atchley, Adam L.; Maxwell, Reed M.; Navarre-Sitchler, Alexis K.
- Advances in Water Resources, Vol. 52
ParCrunchFlow: an efficient, parallel reactive transport simulation tool for physically and chemically heterogeneous saturated subsurface environments
journal, April 2015
- Beisman, James J.; Maxwell, Reed M.; Navarre-Sitchler, Alexis K.
- Computational Geosciences, Vol. 19, Issue 2
Geochemical, mineralogical and microbiological characteristics of sediment from a naturally reduced zone in a uranium-contaminated aquifer
journal, August 2012
- Campbell, K. M.; Kukkadapu, R. K.; Qafoku, N. P.
- Applied Geochemistry, Vol. 27, Issue 8
Competitive Exclusion of Sulfate Reduction by Fe(lll)-Reducing Bacteria: A Mechanism for Producing Discrete Zones of High-Iron Ground Water
journal, January 1992
- Chapelle, Francis H.; Lovley, Derek R.
- Ground Water, Vol. 30, Issue 1
Numerical simulation of organic carbon, nitrate, and nitrogen isotope behavior during denitrification in a riparian zone
journal, June 2004
- Chen, David J. Z.; MacQuarrie, Kerry T. B.
- Journal of Hydrology, Vol. 293, Issue 1-4
Trace metal behaviour in estuarine and riverine floodplain soils and sediments: A review
journal, June 2009
- Du Laing, G.; Rinklebe, J.; Vandecasteele, B.
- Science of The Total Environment, Vol. 407, Issue 13
Feedbacks Between Hydrological Heterogeneity and Bioremediation Induced Biogeochemical Transformations
journal, July 2009
- Englert, A.; Hubbard, S. S.; Williams, K. H.
- Environmental Science & Technology, Vol. 43, Issue 14
Assessment of Soil Microbial Community Structure by Use of Taxon-Specific Quantitative PCR Assays
journal, July 2005
- Fierer, N.; Jackson, J. A.; Vilgalys, R.
- Applied and Environmental Microbiology, Vol. 71, Issue 7
Groundwater-surface water interactions: New methods and models to improve understanding of processes and dynamics
journal, November 2010
- Fleckenstein, Jan H.; Krause, Stefan; Hannah, David M.
- Advances in Water Resources, Vol. 33, Issue 11
Iron Speciation in Dissimilatory Fe(III)-reducing Cultures
journal, May 2011
- García-Balboa, C.; Vicente, M. S.; Blázquez, M. L.
- Geomicrobiology Journal, Vol. 28, Issue 4
Assessment of the geochemical reactivity of Fe-DOM complexes in wetland sediment pore waters using a nitroaromatic probe compound
journal, March 2009
- Hakala, J. Alexandra; Fimmen, Ryan L.; Chin, Yu-Ping
- Geochimica et Cosmochimica Acta, Vol. 73, Issue 5
Reaction- and sample-specific inhibition affect standardization of qPCR assays of soil bacterial communities
journal, April 2013
- Hargreaves, Sarah K.; Roberto, Alescia A.; Hofmockel, Kirsten S.
- Soil Biology and Biochemistry, Vol. 59
Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR
journal, December 2004
- Henry, Sonia; Baudoin, Ezékiel; López-Gutiérrez, Juan C.
- Journal of Microbiological Methods, Vol. 59, Issue 3
Detection and Enumeration of Sulphate-Reducing Bacteria in Estuarine Sediments by Competitive PCR
journal, April 2004
- Kondo, Ryuji; Nedwell, David B.; Purdy, Kevin J.
- Geomicrobiology Journal, Vol. 21, Issue 3
Physicochemical Heterogeneity Controls on Uranium Bioreduction Rates at the Field Scale
journal, December 2011
- Li, Li; Gawande, Nitin; Kowalsky, Michael B.
- Environmental Science & Technology, Vol. 45, Issue 23
Dissimilatory Fe(III) and Mn(IV) reduction
journal, June 1991
- Lovley, D. R.
- Microbiological Reviews, Vol. 55, Issue 2
Riparian nitrogen dynamics in two geomorphologically distinct tropical rain forest watersheds: subsurface solute patterns
journal, June 1992
- McDowell, Williiam H.; Bowden, William B.; Asbury, Clyde E.
- Biogeochemistry, Vol. 18, Issue 2
Terminal electron accepting processes in the alluvial sediments of a headwater stream
journal, December 2000
- Morrice, John A.; Dahm, Clifford N.; Valett, H. Maurice
- Journal of the North American Benthological Society, Vol. 19, Issue 4
The influence of physical heterogeneity on microbial degradation and distribution in porous media
journal, May 1997
- Murphy, Ellyn M.; Ginn, Timothy R.; Chilakapati, Ashokkumar
- Water Resources Research, Vol. 33, Issue 5
Cyanobacterial construction of hot spring siliceous stromatolites in Yellowstone National Park: Cyanobacterial diversity of YNP stromatolites
journal, February 2012
- Pepe-Ranney, Charles; Berelson, William M.; Corsetti, Frank A.
- Environmental Microbiology, Vol. 14, Issue 5
Patterns of denitrification rates in European alluvial soils under various hydrological regimes
journal, February 2007
- Pinay, G.; Gumiero, B.; Tabacchi, E.
- Freshwater Biology, Vol. 52, Issue 2
Fringe-Controlled Natural Attenuation of Phenoxy Acids in a Landfill Plume: Integration of Field-Scale Processes by Reactive Transport Modeling
journal, August 2006
- Prommer, Henning; Tuxen, Nina; Bjerg, Poul L.
- Environmental Science & Technology, Vol. 40, Issue 15
Intra-meander hyporheic flow in alluvial rivers: HYPORHEIC EXCHANGE IN MEANDERING RIVERS
journal, December 2008
- Revelli, Roberto; Boano, Fulvio; Camporeale, Carlo
- Water Resources Research, Vol. 44, Issue 12
Spatial Relations of Topography, Lithology and Water Quality in a Large River Floodplain: Spatial Relations in a Floodplain
journal, May 2011
- Schilling, K. E.; Jacobson, P.
- River Research and Applications, Vol. 28, Issue 9
Improving qPCR efficiency in environmental samples by selective removal of humic acids with DAX-8
journal, April 2011
- Schriewer, A.; Wehlmann, A.; Wuertz, S.
- Journal of Microbiological Methods, Vol. 85, Issue 1
Modelling Microbial Degradation Coupled to Reactive Transport in Groundwater: A Benchmark Analysis
journal, December 2011
- Sena, Clara; Molinero, Jorge; Ajima, Shuji
- Mathematical Geosciences, Vol. 44, Issue 2
Oxygen-consuming processes at the profundal and littoral sediment-water interface of a small meso-eutrophic lake (Lake Vechten, The Netherlands)
journal, September 1991
- Sweerts, Jean-Pierre R. A.; Bär-Gilissen, Marie-Jose; Cornelese, Adi A.
- Limnology and Oceanography, Vol. 36, Issue 6
Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE
journal, September 2004
- Throbäck, Ingela Noredal; Enwall, Karin; Jarvis, à Sa
- FEMS Microbiology Ecology, Vol. 49, Issue 3
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
Works referencing / citing this record:
Factors controlling seasonal groundwater and solute flux from snow-dominated basins
journal, June 2018
- Carroll, Rosemary W. H.; Bearup, Lindsay A.; Brown, Wendy
- Hydrological Processes, Vol. 32, Issue 14
Inhibitory Effects of Sulfate and Nitrate Reduction on Reductive Dechlorination of PCP in a Flooded Paddy Soil
journal, March 2018
- Xu, Yan; Xue, Lili; Ye, Qi
- Frontiers in Microbiology, Vol. 9