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Title: Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies

Abstract

The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of water, nutrients, and organic matter occur in response to variations in discharge and riverbed properties. Within this region, a confluence of surface-derived organic carbon and subsurface nitrogen (in the form of nitrate) has been shown to stimulate microbial activity and transformations of carbon and nitrogen species. For example, production of gases such as CO 2, N 2 and N 2O indicate hyporheic zones might have a significant effect on energy and nutrient flows between the atmosphere and the subsurface. Managed and seasonal river stage changes and geomorphology-controlled sediment texture drive water flow within the HZ of the Columbia River. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the HZ, the grain size distributions for sediment samples taken across 320 m of shoreline were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of carbon and nitrogen oxidizers were found to explain the variability in many biogeochemical attributes. Microbial community analysismore » revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae, together comprising ~20% of the total community across all samples, but scant ammonia-oxidizing Bacteria. Network analysis of operational taxonomic units and the measured geophysical, chemical, and functional parameters showed negative relationships between abundance-based modules of organisms and sand and mud contents, and positive relationships with total organic carbon. The relationships identified in this work indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Some member populations of these sub-communities appear to respond directly to environmental conditions, while others may be dependent on the function of the first group. For example, nitrification is a strong primary response to the observed conditions, and this activity appears to support a larger heterotrophic community. Relationships between facies and hydrobiogeochemical properties enables facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.« less

Authors:
 [1];  [2];  [2];  [1];  [1];  [2];  [2];  [3];  [4];  [2];  [5]
  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Energy and Environment Directorate
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental and Biological Sciences Directorate
  3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Graphic Design
  4. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental and Biological Sciences Directorate; Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
  5. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Physical and Computational Sciences Directorate
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1406700
Report Number(s):
PNNL-SA-121286
Journal ID: ISSN 2045-2322; 48473; KP1702030
Grant/Contract Number:  
AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
58 GEOSCIENCES; 54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; Hyporheic Zone; Biogeochemistry; Facies; Microbial Communities; Environmental Molecular Sciences Laboratory

Citation Formats

Hou, Zhangshuan, Nelson, William C., Stegen, James C., Murray, Christopher J., Arntzen, Evan V., Crump, Alex R., Kennedy, David W., Perkins, M. C., Scheibe, Timothy D., Fredrickson, Jim K., and Zachara, John M. Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies. United States: N. p., 2017. Web. doi:10.1038/s41598-017-12275-w.
Hou, Zhangshuan, Nelson, William C., Stegen, James C., Murray, Christopher J., Arntzen, Evan V., Crump, Alex R., Kennedy, David W., Perkins, M. C., Scheibe, Timothy D., Fredrickson, Jim K., & Zachara, John M. Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies. United States. doi:10.1038/s41598-017-12275-w.
Hou, Zhangshuan, Nelson, William C., Stegen, James C., Murray, Christopher J., Arntzen, Evan V., Crump, Alex R., Kennedy, David W., Perkins, M. C., Scheibe, Timothy D., Fredrickson, Jim K., and Zachara, John M. Wed . "Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies". United States. doi:10.1038/s41598-017-12275-w. https://www.osti.gov/servlets/purl/1406700.
@article{osti_1406700,
title = {Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies},
author = {Hou, Zhangshuan and Nelson, William C. and Stegen, James C. and Murray, Christopher J. and Arntzen, Evan V. and Crump, Alex R. and Kennedy, David W. and Perkins, M. C. and Scheibe, Timothy D. and Fredrickson, Jim K. and Zachara, John M.},
abstractNote = {The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of water, nutrients, and organic matter occur in response to variations in discharge and riverbed properties. Within this region, a confluence of surface-derived organic carbon and subsurface nitrogen (in the form of nitrate) has been shown to stimulate microbial activity and transformations of carbon and nitrogen species. For example, production of gases such as CO2, N2 and N2O indicate hyporheic zones might have a significant effect on energy and nutrient flows between the atmosphere and the subsurface. Managed and seasonal river stage changes and geomorphology-controlled sediment texture drive water flow within the HZ of the Columbia River. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the HZ, the grain size distributions for sediment samples taken across 320 m of shoreline were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of carbon and nitrogen oxidizers were found to explain the variability in many biogeochemical attributes. Microbial community analysis revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae, together comprising ~20% of the total community across all samples, but scant ammonia-oxidizing Bacteria. Network analysis of operational taxonomic units and the measured geophysical, chemical, and functional parameters showed negative relationships between abundance-based modules of organisms and sand and mud contents, and positive relationships with total organic carbon. The relationships identified in this work indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Some member populations of these sub-communities appear to respond directly to environmental conditions, while others may be dependent on the function of the first group. For example, nitrification is a strong primary response to the observed conditions, and this activity appears to support a larger heterotrophic community. Relationships between facies and hydrobiogeochemical properties enables facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.},
doi = {10.1038/s41598-017-12275-w},
journal = {Scientific Reports},
number = 1,
volume = 7,
place = {United States},
year = {2017},
month = {9}
}

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Works referenced in this record:

Evaluation of a laser-diffraction-size analyzer for use with natural sediments
journal, July 1986


Multivariate regression models for panel data
journal, January 1982


Abundance and Diversity of Ammonia-Oxidizing Microorganisms in the Sediments of Jinshan Lake
journal, July 2014


UCHIME improves sensitivity and speed of chimera detection
journal, June 2011


Abundance and composition of ammonia-oxidizing bacteria and archaea in different types of soil in the Yangtze River estuary
journal, October 2012

  • Li, Xiao-ran; Xiao, Yi-ping; Ren, Wen-wei
  • Journal of Zhejiang University SCIENCE B, Vol. 13, Issue 10
  • DOI: 10.1631/jzus.B1200013

The effects of long term nitrogen deposition on extracellular enzyme activity in an Acer saccharum forest soil
journal, September 2002


Distribution of sediment ammonia-oxidizing microorganisms in plateau freshwater lakes
journal, January 2015

  • Liu, Yong; Zhang, Jingxu; Zhao, Lei
  • Applied Microbiology and Biotechnology, Vol. 99, Issue 10
  • DOI: 10.1007/s00253-014-6341-z

Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set
journal, January 2002


Denitrifïcations in Sediments from the Hyporheic Zone Adjacent to a Small Forested Stream
journal, June 1990

  • Duff, John H.; Triska, Frank J.
  • Canadian Journal of Fisheries and Aquatic Sciences, Vol. 47, Issue 6
  • DOI: 10.1139/f90-133

Influence of hyporheic zone characteristics on the structure and activity of microbial assemblages
journal, September 2013

  • Nogaro, Geraldine; Datry, Thibault; Mermillod-Blondin, Florian
  • Freshwater Biology, Vol. 58, Issue 12
  • DOI: 10.1111/fwb.12233

Influence of streambed sediment clogging on microbial processes in the hyporheic zone: Influence of clogging on microbial processes
journal, January 2010


The relation of stream sediment surface area, grain size and composition to trace element chemistry
journal, July 1987


Influence of base flow stream bank seepage on riparian zone nitrogen biogeochemistry
journal, June 2007


The influence of stream sediment particle size on bacterial abundance and community composition
journal, August 2006


The Distinction between Grain Size and Mineral Composition in Sedimentary-Rock Nomenclature
journal, July 1954

  • Folk, Robert L.
  • The Journal of Geology, Vol. 62, Issue 4
  • DOI: 10.1086/626171

The role of organisms in hyporheic processes: gaps in current knowledge, needs for future research and applications
journal, January 2012

  • Marmonier, P.; Archambaud, G.; Belaidi, N.
  • Annales de Limnologie - International Journal of Limnology, Vol. 48, Issue 3
  • DOI: 10.1051/limn/2012009

Bacterial community dynamics in the hyporheic zone of an intermittent stream
journal, December 2011

  • Febria, Catherine M.; Beddoes, Paul; Fulthorpe, Roberta R.
  • The ISME Journal, Vol. 6, Issue 5
  • DOI: 10.1038/ismej.2011.173

WGCNA: an R package for weighted correlation network analysis
journal, December 2008


Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria
journal, September 2009

  • Martens-Habbena, Willm; Berube, Paul M.; Urakawa, Hidetoshi
  • Nature, Vol. 461, Issue 7266
  • DOI: 10.1038/nature08465

Permeability as a Function of the Size Parameters of Unconsolidated Sand
journal, December 1943

  • Krumbein, W. C.; Monk, G. D.
  • Transactions of the AIME, Vol. 151, Issue 01
  • DOI: 10.2118/943153-G

Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
journal, June 2007

  • Wang, Q.; Garrity, G. M.; Tiedje, J. M.
  • Applied and Environmental Microbiology, Vol. 73, Issue 16
  • DOI: 10.1128/AEM.00062-07

Mechanical composition of clastic sediments
journal, January 1914

  • Udden, J. A.
  • Geological Society of America Bulletin, Vol. 25, Issue 1
  • DOI: 10.1130/GSAB-25-655

Bayesian Regularization for Normal Mixture Estimation and Model-Based Clustering
journal, September 2007


Influence of Bed-Sediment Features on the Interstitial Habitat Available for Macroinvertebrates in 15 French Streams
journal, January 2003

  • Gayraud, Sebastien; Philippe, Michel
  • International Review of Hydrobiology, Vol. 88, Issue 1
  • DOI: 10.1002/iroh.200390007

Resistance, resilience, and redundancy in microbial communities
journal, August 2008

  • Allison, S. D.; Martiny, J. B. H.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue Supplement 1
  • DOI: 10.1073/pnas.0801925105

Microbial community changes along the active seepage site of one cold seep in the Red Sea
journal, July 2015


Plotting partial correlation and regression in ecological studies
journal, January 2008


Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions: Ammonia-oxidizing bacteria and archaea
journal, March 2010


Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray
journal, October 2007


How Many Clusters? Which Clustering Method? Answers Via Model-Based Cluster Analysis
journal, August 1998


Lateral hyporheic exchange throughout the Mississippi River network
journal, May 2014

  • Kiel, Brian A.; Bayani Cardenas, M.
  • Nature Geoscience, Vol. 7, Issue 6
  • DOI: 10.1038/ngeo2157

Genome Sequence of Chthoniobacter flavus Ellin428, an Aerobic Heterotrophic Soil Bacterium
journal, April 2011

  • Kant, R.; van Passel, M. W. J.; Palva, A.
  • Journal of Bacteriology, Vol. 193, Issue 11
  • DOI: 10.1128/Jb.00295-11

Perspectives on Defining and Delineating Hyporheic Zones
journal, March 1993

  • White, David S.
  • Journal of the North American Benthological Society, Vol. 12, Issue 1
  • DOI: 10.2307/1467686

Biogeochemical Processes and Microbial Characteristics across Groundwater−Surface Water Boundaries of the Hanford Reach of the Columbia River
journal, November 2003

  • Moser, Duane P.; Fredrickson, James K.; Geist, David R.
  • Environmental Science & Technology, Vol. 37, Issue 22
  • DOI: 10.1021/es034457v

Characterizing seasonal changes in physicochemistry and bacterial community composition in hyporheic sediments
journal, July 2009


Biogeochemical Hot Spots and Hot Moments at the Interface of Terrestrial and Aquatic Ecosystems
journal, June 2003


Parafluvial Nitrogen Dynamics in a Desert Stream Ecosystem
journal, December 1994

  • Holmes, Robert M.; Fisher, Stuart G.; Grimm, Nancy B.
  • Journal of the North American Benthological Society, Vol. 13, Issue 4
  • DOI: 10.2307/1467844

Importance of surface-subsurface exchange in stream ecosystems: The hyporheic zone
journal, January 1995


Spatial distribution of ammonia-oxidizing archaea and bacteria across eight freshwater lakes in sediments from Jiangsu of China
journal, March 2014


Ecology and management of the hyporheic zone: stream–groundwater interactions of running waters and their floodplains
journal, March 2010

  • Boulton, Andrew J.; Datry, Thibault; Kasahara, Tamao
  • Journal of the North American Benthological Society, Vol. 29, Issue 1
  • DOI: 10.1899/08-017.1

Sediment Ammonia-Oxidizing Microorganisms in Two Plateau Freshwater Lakes at Different Trophic States
journal, June 2015


A Scale of Grade and Class Terms for Clastic Sediments
journal, July 1922

  • Wentworth, Chester K.
  • The Journal of Geology, Vol. 30, Issue 5
  • DOI: 10.1086/622910

Relationships of chloroform fumigation–incubation to soil organic matter pools
journal, March 1999


Global Ecological Pattern of Ammonia-Oxidizing Archaea
journal, February 2013


Wastewater Effluent Impacts Ammonia-Oxidizing Prokaryotes of the Grand River, Canada
journal, September 2013

  • Sonthiphand, Puntipar; Cejudo, Eduardo; Schiff, Sherry L.
  • Applied and Environmental Microbiology, Vol. 79, Issue 23
  • DOI: 10.1128/Aem.02202-13

Surface-subsurface interactions in stream ecosystems
journal, June 1996


Heterotrophic cultures of microalgae: Metabolism and potential products
journal, January 2011


A new look at the statistical model identification
journal, December 1974


Inter-disciplinary perspectives on processes in the hyporheic zone
journal, November 2010

  • Krause, S.; Hannah, D. M.; Fleckenstein, J. H.
  • Ecohydrology, Vol. 4, Issue 4
  • DOI: 10.1002/eco.176

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
journal, October 2009

  • Schloss, P. D.; Westcott, S. L.; Ryabin, T.
  • Applied and Environmental Microbiology, Vol. 75, Issue 23, p. 7537-7541
  • DOI: 10.1128/AEM.01541-09

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
journal, November 2003


QIIME allows analysis of high-throughput community sequencing data
journal, April 2010

  • Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
  • Nature Methods, Vol. 7, Issue 5
  • DOI: 10.1038/nmeth.f.303

Determination of Hydraulic Conductivity from Grain-Size Distribution for Different Depositional Environments: J. Rosas et al
journal, June 2013

  • Rosas, Jorge; Lopez, Oliver; Missimer, Thomas M.
  • Groundwater, Vol. 52, Issue 3
  • DOI: 10.1111/gwat.12078

Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment
journal, March 2015


The Functional Significance of the Hyporheic zone in Streams and Rivers
journal, November 1998


Experimental Study of the Porosity and Permeability of Clastic Sediments
journal, November 1935

  • Fraser, H. J.
  • The Journal of Geology, Vol. 43, Issue 8, Part 1
  • DOI: 10.1086/624388

Abundance and community composition of ammonia-oxidizing archaea and bacteria in two different zones of Lake Taihu
journal, August 2012

  • Zeng, Jin; Zhao, Da-Yong; Huang, Rui
  • Canadian Journal of Microbiology, Vol. 58, Issue 8
  • DOI: 10.1139/W2012-078

Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China
journal, October 2015


Comparative Analysis of Denitrifying Activities of Hyphomicrobium nitrativorans, Hyphomicrobium denitrificans, and Hyphomicrobium zavarzinii
journal, May 2015

  • Martineau, Christine; Mauffrey, Florian; Villemur, Richard
  • Applied and Environmental Microbiology, Vol. 81, Issue 15
  • DOI: 10.1128/Aem.00848-15

Wastewater Treatment Effluent Reduces the Abundance and Diversity of Benthic Bacterial Communities in Urban and Suburban Rivers
journal, January 2013

  • Drury, Bradley; Rosi-Marshall, Emma; Kelly, John J.
  • Applied and Environmental Microbiology, Vol. 79, Issue 6
  • DOI: 10.1128/Aem.03527-12

Size Frequency Distributions of Sediments and the Normal Phi Curve
journal, January 1938


Vertical Distribution of Ammonia-Oxidizing Archaea and Bacteria in Sediments of a Eutrophic Lake
journal, May 2013


Insights into the phylogeny and coding potential of microbial dark matter
journal, July 2013

  • Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander
  • Nature, Vol. 499, Issue 7459
  • DOI: 10.1038/nature12352

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012

  • Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
  • The ISME Journal, Vol. 6, Issue 8
  • DOI: 10.1038/ismej.2012.8

Environmental factors shaping the ecological niches of ammonia-oxidizing archaea
journal, September 2009


Brazos River bar [Texas]; a study in the significance of grain size parameters
journal, March 1957


Assessing biological soil quality with chloroform fumigation-incubation: Why subtract a control?
journal, November 1999

  • Franzluebbers, A. J.; Haney, R. L.; Hons, F. M.
  • Canadian Journal of Soil Science, Vol. 79, Issue 4
  • DOI: 10.4141/S99-010

Niche separation of ammonia-oxidizing bacteria across a tidal freshwater marsh
journal, November 2008


The effects of stream substratum texture on interstitial conditions and bacterial biofilms: Methodological strategies
journal, March 2013


Depth-related changes of sediment ammonia-oxidizing microorganisms in a high-altitude freshwater wetland
journal, March 2014

  • Liu, Yong; Zhang, Jingxu; Zhang, Xiaoling
  • Applied Microbiology and Biotechnology, Vol. 98, Issue 12
  • DOI: 10.1007/s00253-014-5651-5

Correlations of Permeability and Grain Size
journal, September 1989


Horizontal hydraulic conductivity of shallow streambed sediments and comparison with the grain-size analysis results
journal, May 2011

  • Lu, Chengpeng; Chen, Xunhong; Cheng, Cheng
  • Hydrological Processes, Vol. 26, Issue 3
  • DOI: 10.1002/hyp.8143

Relationships between bacteria and grain surfaces in intertidal sediments1: Bacteria in intertidal sediments
journal, September 1983


Nitrogen processing in the hyporheic zone of a pastoral stream
journal, July 2004


Habitat Heterogeneity and Associated Microbial Community Structure in a Small-Scale Floodplain Hyporheic Flow Path
journal, May 2009


Clogging Processes in Hyporheic Interstices of an Impounded River, the Danube at Vienna, Austria
journal, July 2003

  • Blaschke, Alfred Paul; Steiner, Karl-Heinz; Schmalfuss, Roland
  • International Review of Hydrobiology, Vol. 88, Issue 34
  • DOI: 10.1002/iroh.200390034

Abundance and community structure of ammonia-oxidizing microorganisms in reservoir sediment and adjacent soils
journal, August 2013

  • Wang, Xiaoyan; Wang, Cui; Bao, Linlin
  • Applied Microbiology and Biotechnology, Vol. 98, Issue 4
  • DOI: 10.1007/s00253-013-5174-5

Coupled transport and reaction kinetics control the nitrate source-sink function of hyporheic zones: HYPORHEIC N SOURCE-SINK CONTROLS
journal, November 2012

  • Zarnetske, Jay P.; Haggerty, Roy; Wondzell, Steven M.
  • Water Resources Research, Vol. 48, Issue 11
  • DOI: 10.1029/2012WR011894

Human and Environmental Impacts on River Sediment Microbial Communities
journal, May 2014


Multivariate Regression Analyses for Categorical Data
journal, September 1992

  • Liang, Kung-Yee; Zeger, Scott L.; Qaqish, Bahjat
  • Journal of the Royal Statistical Society: Series B (Methodological), Vol. 54, Issue 1
  • DOI: 10.1111/j.2517-6161.1992.tb01862.x

Generalized Linear Models
journal, January 1972

  • Nelder, J. A.; Wedderburn, R. W. M.
  • Journal of the Royal Statistical Society. Series A (General), Vol. 135, Issue 3
  • DOI: 10.2307/2344614

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    Microbial Community Structure and Metabolic Potential of the Hyporheic Zone of a Large Mid-Stream Channel Bar
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