Influence of Hydrological Perturbations and Riverbed Sediment Characteristics on Hyporheic Zone Respiration of CO2 and N2

Newcomer, Michelle E.; Hubbard, Susan S.; Fleckenstein, Jan H.; Maier, Ulrich; Schmidt, Christian; Thullner, Martin; Ulrich, Craig; Flipo, Nicolas; Rubin, Yoram

doi:10.1002/2017JG004090

Title: Influence of Hydrological Perturbations and Riverbed Sediment Characteristics on Hyporheic Zone Respiration of CO₂ and N₂

Journal Article · Thu Feb 22 00:00:00 EST 2018 · Journal of Geophysical Research. Biogeosciences

DOI:https://doi.org/10.1002/2017JG004090· OSTI ID:1561881

^[1];

^[2]; Maier, Ulrich ^[3];

^[2];

^[4]; Ulrich, Craig ^[1];

^[5];

^[6]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Climate and Ecosystem Sciences Division
Helmholtz-Centre for Environmental Research (UFZ), Leipzig (Germany). Dept. of Hydrogeology
Univ. of Göttingen, Göttingen (Germany). Geoscience Centre, Dept. of Applied Geology
Helmholtz-Centre for Environmental Research (UFZ), Leipzig (Germany). Dept. of Environmental Microbiology
MINES ParisTech, PSL Research Univ., Paris (France). Geosciences Dept.
Univ. of California, Berkeley, CA (United States). Dept. of Civil and Environmental Engineering

Rivers in climatic zones characterized by dry and wet seasons often experience periodic transitions between losing and gaining conditions across the river-aquifer continuum. Infiltration shifts can stimulate hyporheic microbial biomass growth and cycling of riverine carbon and nitrogen leading to major exports of biogenic CO₂ and N₂ to rivers. In this study, we develop and test a numerical model that simulates biological-physical feedback in the hyporheic zone. We used the model to explore different initial conditions in terms of dissolved organic carbon availability, sediment characteristics, and stochastic variability in aerobic and anaerobic conditions from water table fluctuations. Our results show that while highly losing rivers have greater hyporheic CO₂ and N₂ production, gaining rivers allowed the greatest fraction of CO₂ and N₂ production to return to the river. Hyporheic aerobic respiration and denitrification contributed 0.1–2 g/m²/d of CO₂ and 0.01–0.2 g/m²/d of N₂; however, the suite of potential microbial behaviors varied greatly among sediment characteristics. We found that losing rivers that consistently lacked an exit pathway can store up to 100% of the entering C/N as subsurface biomass and dissolved gas. Finally, our results demonstrate the importance of subsurface feedbacks whereby microbes and hydrology jointly control fate of C and N and are strongly linked to wet-season control of initial sediment conditions and hydrologic control of seepage direction. These results provide a new understanding of hydrobiological and sediment-based controls on hyporheic zone respiration, including a new explanation for the occurrence of anoxic microzones and large denitrification rates in gravelly riverbeds.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1561881

Journal Information:: Journal of Geophysical Research. Biogeosciences, Vol. 123, Issue 3; ISSN 2169-8953

Publisher:: American Geophysical UnionCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 36 works

Citation information provided by
Web of Science

References (123)

Spatial and temporal aspects of the transition from connection to disconnection between rivers, lakes and groundwater Brunner, Philip; Simmons, Craig T.; Cook, Peter G. Journal of Hydrology, Vol. 376, Issue 1-2 https://doi.org/10.1016/j.jhydrol.2009.07.023	journal	September 2009
Biogeochemical modelling at the river scale: plankton and periphyton dynamics Flipo, Nicolas; Even, Stephanie; Poulin, Michel Ecological Modelling, Vol. 176, Issue 3-4 https://doi.org/10.1016/j.ecolmodel.2004.01.012	journal	September 2004
Comparison of nitrification rates in three branches of the lower river Rhine Admiraal, Wim; Botermans, YvesJ. H. Biogeochemistry, Vol. 8, Issue 2 https://doi.org/10.1007/BF00001317	journal	September 1989
Does streambed heterogeneity matter for hyporheic residence time distribution in sand-bedded streams? Tonina, Daniele; de Barros, Felipe P. J.; Marzadri, Alessandra Advances in Water Resources, Vol. 96 https://doi.org/10.1016/j.advwatres.2016.07.009	journal	October 2016
Impacts of rainfall spatial variability on hydrogeological response Sapriza-Azuri, Gonzalo; Jódar, Jorge; Navarro, Vicente Water Resources Research, Vol. 51, Issue 2 https://doi.org/10.1002/2014WR016168	journal	February 2015
Labile dissolved organic carbon supply limits hyporheic denitrification Zarnetske, Jay P.; Haggerty, Roy; Wondzell, Steven M. Journal of Geophysical Research, Vol. 116, Issue G4 https://doi.org/10.1029/2011JG001730	journal	January 2011
Electrical and hydraulic vertical variability in channel sediments and its effects on streamflow depletion due to groundwater extraction Chen, Xunhong; Burbach, Mark; Cheng, Cheng Journal of Hydrology, Vol. 352, Issue 3-4 https://doi.org/10.1016/j.jhydrol.2008.01.004	journal	May 2008
Mediterranean-climate streams and rivers: geographically separated but ecologically comparable freshwater systems Bonada, Núria; Resh, Vincent H. Hydrobiologia, Vol. 719, Issue 1 https://doi.org/10.1007/s10750-013-1634-2	journal	August 2013
River-Aquifer Interactions, Geologic Heterogeneity, and Low-Flow Management Fleckenstein, Jan H.; Niswonger, Richard G.; Fogg, Graham E. Ground Water, Vol. 44, Issue 6 Understanding https://doi.org/10.1111/j.1745-6584.2006.00190.x	journal	November 2006
In situ quantification of spatial and temporal variability of hyporheic exchange in static and mobile gravel-bed rivers Rosenberry, Donald O.; Klos, P. Zion; Neal, Andrew Hydrological Processes, Vol. 26, Issue 4 https://doi.org/10.1002/hyp.8154	journal	May 2011
Experimental and numerical assessment of transient stream–aquifer exchange during disconnection Rivière, A.; Gonçalvès, J.; Jost, A. Journal of Hydrology, Vol. 517 https://doi.org/10.1016/j.jhydrol.2014.05.040	journal	September 2014
The clogging of coarse gravel river beds by fine sediment Sch�lchli, Ueli Hydrobiologia, Vol. 235-236, Issue 1 https://doi.org/10.1007/BF00026211	journal	July 1992
Contributions of algae to GPP and DOC production in an Alaskan fen: effects of historical water table manipulations on ecosystem responses to a natural flood Wyatt, Kevin H.; Turetsky, Merritt R.; Rober, Allison R. Oecologia, Vol. 169, Issue 3 https://doi.org/10.1007/s00442-011-2233-4	journal	December 2011
Estimation of stream-aquifer exchanges at regional scale using a distributed model: Sensitivity to in-stream water level fluctuations, riverbed elevation and roughness Baratelli, Fulvia; Flipo, Nicolas; Moatar, Florentina Journal of Hydrology, Vol. 542 https://doi.org/10.1016/j.jhydrol.2016.09.041	journal	November 2016
Biophysical controls on organic carbon fluxes in fluvial networks Battin, Tom J.; Kaplan, Louis A.; Findlay, Stuart Nature Geoscience, Vol. 1, Issue 2 https://doi.org/10.1038/ngeo101	journal	January 2008
Porosity and Permeability in Sediment Mixtures Kamann, Patrick J.; Ritzi, Robert W.; Dominic, David F. Ground Water, Vol. 45, Issue 4 https://doi.org/10.1111/j.1745-6584.2007.00313.x	journal	July 2007
Characterisation of river–aquifer exchange fluxes: The role of spatial patterns of riverbed hydraulic conductivities Tang, Q.; Kurtz, W.; Brunner, P. Journal of Hydrology, Vol. 531 https://doi.org/10.1016/j.jhydrol.2015.08.019	journal	December 2015
The response of river nitrification to changes in wastewater treatment (The case of the lower Seine River downstream from Paris) Aissa-Grouz, Najla; Garnier, Josette; Billen, Gilles Annales de Limnologie - International Journal of Limnology, Vol. 51, Issue 4 https://doi.org/10.1051/limn/2015031	journal	January 2015
Hydrological mediated denitrification in groundwater below a seasonal flooded restored riparian zone: Denitrification in groundwater below flooded riparian zone Kolbjørn Jensen, Jannick; Engesgaard, Peter; Johnsen, Anders R. Water Resources Research, Vol. 53, Issue 3 https://doi.org/10.1002/2016WR019581	journal	March 2017
Estimating ecosystem metabolism from continuous multi-sensor measurements in the Seine River Escoffier, N.; Bensoussan, N.; Vilmin, L. Environmental Science and Pollution Research, Vol. 25, Issue 24 https://doi.org/10.1007/s11356-016-7096-0	journal	June 2016
Simulating bioclogging effects on dynamic riverbed permeability and infiltration: BIOCLOGGING, DYNAMIC RIVERBED PERMEABILITY, AND INFILTRATION Newcomer, Michelle E.; Hubbard, Susan S.; Fleckenstein, Jan H. Water Resources Research, Vol. 52, Issue 4 https://doi.org/10.1002/2015WR018351	journal	April 2016
Multi-method assessment of connectivity between surface water and shallow groundwater: the case of Limarí River basin, north-central Chile Oyarzún, Ricardo; Barrera, Felisa; Salazar, Pamela Hydrogeology Journal, Vol. 22, Issue 8 https://doi.org/10.1007/s10040-014-1170-9	journal	July 2014
Riverbed Clogging Associated with a California Riverbank Filtration System: An Assessment of Mechanisms and Monitoring Approaches Ulrich, Craig; Hubbard, Susan S.; Florsheim, Joan Journal of Hydrology, Vol. 529 https://doi.org/10.1016/j.jhydrol.2015.08.012	journal	October 2015
Pore-scale modeling of biological clogging due to aggregate expansion: A material mechanics approach Dupin, Hubert J.; Kitanidis, Peter K.; McCarty, Perry L. Water Resources Research, Vol. 37, Issue 12 https://doi.org/10.1029/2001WR000306	journal	December 2001
Assessment of nitrate pollution in the Grand Morin aquifers (France): Combined use of geostatistics and physically based modeling Flipo, Nicolas; Jeannée, Nicolas; Poulin, Michel Environmental Pollution, Vol. 146, Issue 1 https://doi.org/10.1016/j.envpol.2006.03.056	journal	March 2007
Modeling biofilm dynamics and hydraulic properties in variably saturated soils using a channel network model Rosenzweig, Ravid; Furman, Alex; Dosoretz, Carlos Water Resources Research, Vol. 50, Issue 7 https://doi.org/10.1002/2013WR015211	journal	July 2014
Characterization of the key pathways of dissimilatory nitrate reduction and their response to complex organic substrates in hyporheic sediments Lansdown, K.; Trimmer, M.; Heppell, C. M. Limnology and Oceanography, Vol. 57, Issue 2 https://doi.org/10.4319/lo.2012.57.2.0387	journal	February 2012
Hydraulic Conductivity of Soils from Grain-Size Distribution: New Models Boadu, Fred Kofi Journal of Geotechnical and Geoenvironmental Engineering, Vol. 126, Issue 8 https://doi.org/10.1061/(ASCE)1090-0241(2000)126:8(739)	journal	August 2000
Seasonal Reassembly of a River food web: Floods, Droughts, and Impacts of fish Power, Mary E.; Parker, Michael S.; Dietrich, William E. Ecological Monographs, Vol. 78, Issue 2 https://doi.org/10.1890/06-0902.1	journal	May 2008
Using temperature modeling to investigate the temporal variability of riverbed hydraulic conductivity during storm events Mutiti, Samuel; Levy, Jonathan Journal of Hydrology, Vol. 388, Issue 3-4 https://doi.org/10.1016/j.jhydrol.2010.05.011	journal	July 2010
Modeling Microbially Induced Carbon Degradation in Redox-Stratified Subsurface Environments: Concepts and Open Questions Thullner, Martin; Regnier, Pierre; Van Cappellen, Philippe Geomicrobiology Journal, Vol. 24, Issue 3-4 https://doi.org/10.1080/01490450701459275	journal	July 2007
Modeling of a microbial growth experiment with bioclogging in a two-dimensional saturated porous media flow field Thullner, Martin; Schroth, Martin H.; Zeyer, Josef Journal of Contaminant Hydrology, Vol. 70, Issue 1-2 https://doi.org/10.1016/j.jconhyd.2003.08.008	journal	May 2004
Interaction between water flow and spatial distribution of microbial growth in a two-dimensional flow field in saturated porous media Thullner, Martin; Mauclaire, Laurie; Schroth, Martin H. Journal of Contaminant Hydrology, Vol. 58, Issue 3-4 https://doi.org/10.1016/S0169-7722(02)00033-5	journal	October 2002
A physical explanation for the development of redox microzones in hyporheic flow Briggs, Martin A.; Day‐Lewis, Frederick D.; Zarnetske, Jay P. Geophysical Research Letters, Vol. 42, Issue 11 https://doi.org/10.1002/2015GL064200	journal	June 2015
Primary production in headwater streams of the Seine basin: The Grand Morin river case study Flipo, Nicolas; Rabouille, Christophe; Poulin, Michel Science of The Total Environment, Vol. 375, Issue 1-3 https://doi.org/10.1016/j.scitotenv.2006.12.015	journal	April 2007
Modeling the impact of microbial activity on redox dynamics in porous media Thullner, Martin; Van Cappellen, Philippe; Regnier, Pierre Geochimica et Cosmochimica Acta, Vol. 69, Issue 21 https://doi.org/10.1016/j.gca.2005.04.026	journal	November 2005
The impact of floods on infiltration rates in a disconnected stream: THE IMPACT OF FLOODS ON INFILTRATION RATES Chen, Wenfu; Huang, Chihchao; Chang, Minhsiang Water Resources Research, Vol. 49, Issue 12 https://doi.org/10.1002/2013WR013762	journal	December 2013
Impact of microbial growth on water flow and solute transport in unsaturated porous media: IMPACT OF MICROBIAL GROWTH ON UNSATURATED FLOW Yarwood, R. R.; Rockhold, M. L.; Niemet, M. R. Water Resources Research, Vol. 42, Issue 10 https://doi.org/10.1029/2005WR004550	journal	October 2006
Redox chemistry of iron and manganese minerals in river-recharged aquifers: A model interpretation of a column experiment Matsunaga, T.; Karametaxas, G.; von Gunten, H. R. Geochimica et Cosmochimica Acta, Vol. 57, Issue 8 https://doi.org/10.1016/0016-7037(93)90107-8	journal	April 1993
Hyporheic exchange and streambed filtration of suspended particles: STREAMBED FILTRATION OF SUSPENDED PARTICLES Karwan, Diana L.; Saiers, James E. Water Resources Research, Vol. 48, Issue 1 https://doi.org/10.1029/2011WR011173	journal	January 2012
The importance of the riparian zone and in-stream processes in nitrate attenuation in undisturbed and agricultural watersheds – A review of the scientific literature Ranalli, Anthony J.; Macalady, Donald L. Journal of Hydrology, Vol. 389, Issue 3-4 https://doi.org/10.1016/j.jhydrol.2010.05.045	journal	August 2010
Spatial and temporal variations in streambed hydraulic conductivity quantified with time-series thermal methods Hatch, Christine E.; Fisher, Andrew T.; Ruehl, Chris R. Journal of Hydrology, Vol. 389, Issue 3-4 https://doi.org/10.1016/j.jhydrol.2010.05.046	journal	August 2010
Denitrification in the Mississippi River network controlled by flow through river bedforms Gomez-Velez, Jesus D.; Harvey, Judson W.; Cardenas, M. Bayani Nature Geoscience, Vol. 8, Issue 12 https://doi.org/10.1038/ngeo2567	journal	October 2015
Numerical analysis of biological clogging in two-dimensional sand box experiments Kildsgaard, Jesper; Engesgaard, Peter Journal of Contaminant Hydrology, Vol. 50, Issue 3-4 https://doi.org/10.1016/S0169-7722(01)00109-7	journal	August 2001
Hyporheic zone denitrification: Controls on effective reaction depth and contribution to whole-stream mass balance: Scaling hyporheic flow controls on stream denitrification Harvey, Judson W.; Böhlke, J. K.; Voytek, Mary A. Water Resources Research, Vol. 49, Issue 10 https://doi.org/10.1002/wrcr.20492	journal	October 2013
The effect of losing and gaining flow conditions on hyporheic exchange in heterogeneous streambeds: HYPORHEIC EXCHANGE IN HETEROGENEOUS STREAMBEDS Fox, A.; Laube, G.; Schmidt, C. Water Resources Research, Vol. 52, Issue 9 https://doi.org/10.1002/2016WR018677	journal	September 2016
The natural greenhouse effect of atmospheric oxygen (O ₂ ) and nitrogen (N ₂ ) : NATURAL GREENHOUSE EFFECT OF O Höpfner, M.; Milz, M.; Buehler, S. Geophysical Research Letters, Vol. 39, Issue 10 https://doi.org/10.1029/2012GL051409	journal	May 2012
Single discharge events increase reactive efficiency of the hyporheic zone: DISCHARGE EVENTS INCREASE REACTIVITY Trauth, Nico; Fleckenstein, Jan H. Water Resources Research, Vol. 53, Issue 1 https://doi.org/10.1002/2016WR019488	journal	January 2017
Heterogeneous or homogeneous? Implications of simplifying heterogeneous streambeds in models of losing streams Irvine, Dylan J.; Brunner, Philip; Franssen, Harrie-Jan Hendricks Journal of Hydrology, Vol. 424-425 https://doi.org/10.1016/j.jhydrol.2011.11.051	journal	March 2012
Oscillatory modes of extended Nile River records (A.D. 622–1922) Kondrashov, D. Geophysical Research Letters, Vol. 32, Issue 10 https://doi.org/10.1029/2004GL022156	journal	January 2005
River-aquifer interactions in a semi-arid environment stressed by groundwater abstraction: River-aquifer interactions in a semi-arid environment McCallum, Andrew M.; Andersen, Martin S.; Giambastiani, Beatrice M. S. Hydrological Processes, Vol. 27, Issue 7 https://doi.org/10.1002/hyp.9229	journal	April 2012
Reporting of Stream-Aquifer Flow Distribution at the Regional Scale with a Distributed Process-Based Model Pryet, A.; Labarthe, B.; Saleh, F. Water Resources Management, Vol. 29, Issue 1 https://doi.org/10.1007/s11269-014-0832-7	journal	October 2014
Diel fluctuations of DOC generated by algae in a piedmont stream1: Stream DOC diel fluctuations Kaplan, Louis A.; Bott, Thomas L. Limnology and Oceanography, Vol. 27, Issue 6 https://doi.org/10.4319/lo.1982.27.6.1091	journal	November 1982
Aquatic carbon cycling in the conterminous United States and implications for terrestrial carbon accounting Butman, David; Stackpoole, Sarah; Stets, Edward Proceedings of the National Academy of Sciences, Vol. 113, Issue 1 https://doi.org/10.1073/pnas.1512651112	journal	December 2015
Bioclogging in porous media: Model development and sensitivity to initial conditions Brovelli, A.; Malaguerra, F.; Barry, D. A. Environmental Modelling & Software, Vol. 24, Issue 5 https://doi.org/10.1016/j.envsoft.2008.10.001	journal	May 2009
Pathways of organic carbon oxidation in three continental margin sediments Canfield, D. E.; Jørgensen, B. B.; Fossing, H. Marine Geology, Vol. 113, Issue 1-2 https://doi.org/10.1016/0025-3227(93)90147-N	journal	July 1993
Nitrate attenuation in groundwater: A review of biogeochemical controlling processes Rivett, Michael O.; Buss, Stephen R.; Morgan, Philip Water Research, Vol. 42, Issue 16 https://doi.org/10.1016/j.watres.2008.07.020	journal	October 2008
Upscaling Nitrogen Removal Capacity from Local Hotspots to Low Stream Orders’ Drainage Basins Pinay, Gilles; Peiffer, Stefan; De Dreuzy, Jean-Raynald Ecosystems, Vol. 18, Issue 6 https://doi.org/10.1007/s10021-015-9878-5	journal	May 2015
Drought-induced discontinuities in the source and degradation of dissolved organic matter in a Mediterranean river Casas-Ruiz, Joan P.; Tittel, Jörg; von Schiller, Daniel Biogeochemistry, Vol. 127, Issue 1 https://doi.org/10.1007/s10533-015-0173-5	journal	December 2015
Groundwater–surface-water interactions: current research directions Larned, Scott T.; Gooseff, Michael N.; Packman, Aaron I. Freshwater Science, Vol. 34, Issue 1 https://doi.org/10.1086/679491	journal	March 2015
Correlations of Permeability and Grain Size Shepherd, Russell G. Ground Water, Vol. 27, Issue 5 https://doi.org/10.1111/j.1745-6584.1989.tb00476.x	journal	September 1989
Characterizing Precipitation Variability and Trends in the World’s Mediterranean-Climate Areas Deitch, Matthew; Sapundjieff, Michele; Feirer, Shane Water, Vol. 9, Issue 4 https://doi.org/10.3390/w9040259	journal	April 2017
Influence of aquifer and streambed heterogeneity on the distribution of groundwater discharge Kalbus, E.; Schmidt, C.; Molson, J. W. Hydrology and Earth System Sciences, Vol. 13, Issue 1 https://doi.org/10.5194/hess-13-69-2009	journal	January 2009
Modelling the fate of nitrite in an urbanized river using experimentally obtained nitrifier growth parameters Raimonet, Mélanie; Vilmin, Lauriane; Flipo, Nicolas Water Research, Vol. 73 https://doi.org/10.1016/j.watres.2015.01.026	journal	April 2015
Dissolved organic carbon and its utilization in a riverine wetland ecosystem Mann, CarrollJ.; Wetzel, RobertG. Biogeochemistry, Vol. 31, Issue 2 https://doi.org/10.1007/BF00000941	journal	November 1995
Pluri-annual sediment budget in a navigated river system: The Seine River (France) Vilmin, Lauriane; Flipo, Nicolas; de Fouquet, Chantal Science of The Total Environment, Vol. 502 https://doi.org/10.1016/j.scitotenv.2014.08.110	journal	January 2015
Net dissolved inorganic nitrogen production in hyporheic mesocosms with contrasting sediment size distributions Harvey, Brett N.; Johnson, Michael L.; Kiernan, Joseph D. Hydrobiologia, Vol. 658, Issue 1 https://doi.org/10.1007/s10750-010-0504-4	journal	October 2010
Algal mats and insect emergence in rivers under Mediterranean climates: towards photogrammetric surveillance Power, M.; Lowe, R.; Furey, P. Freshwater Biology, Vol. 54, Issue 10 https://doi.org/10.1111/j.1365-2427.2008.02163.x	journal	October 2009
Flow extremes and benthic organic matter shape the metabolism of a headwater Mediterranean stream Acuna, Vicenc; Giorgi, Adonis; Munoz, Isabel Freshwater Biology, Vol. 49, Issue 7 https://doi.org/10.1111/j.1365-2427.2004.01239.x	journal	July 2004
Hyporheic flow and residence time distributions in heterogeneous cross-bedded sediment: HYPORHEIC FLOW IN HETEROGENEOUS SEDIMENT Sawyer, Audrey Hucks; Cardenas, M. Bayani Water Resources Research, Vol. 45, Issue 8 https://doi.org/10.1029/2008WR007632	journal	August 2009
Biofilm-induced bioclogging produces sharp interfaces in hyporheic flow, redox conditions, and microbial community structure: BIOCLOGGING-INDUCED BIOCHEMICAL ZONATION Caruso, Alice; Boano, Fulvio; Ridolfi, Luca Geophysical Research Letters, Vol. 44, Issue 10 https://doi.org/10.1002/2017GL073651	journal	May 2017
Factors Governing Sustainable Groundwater Pumping near a River Zhang, Yingqi; Hubbard, Susan; Finsterle, Stefan Ground Water, Vol. 49, Issue 3 https://doi.org/10.1111/j.1745-6584.2010.00743.x	journal	August 2010
Estimation of the water quality of a large urbanized river as defined by the European WFD: what is the optimal sampling frequency? Vilmin, Lauriane; Flipo, Nicolas; Escoffier, Nicolas Environmental Science and Pollution Research, Vol. 25, Issue 24 https://doi.org/10.1007/s11356-016-7109-z	journal	July 2016
Effects of antecedent hydrologic conditions, time dependence, and climate cycles on the suspended sediment load of the Salinas River, California Gray, Andrew B.; Pasternack, Gregory B.; Watson, Elizabeth B. Journal of Hydrology, Vol. 525 https://doi.org/10.1016/j.jhydrol.2015.04.025	journal	June 2015
Continental hydrosystem modelling: the concept of nested stream–aquifer interfaces Flipo, N.; Mouhri, A.; Labarthe, B. Hydrology and Earth System Sciences, Vol. 18, Issue 8 https://doi.org/10.5194/hess-18-3121-2014	journal	January 2014
Sources of and processes controlling CO2 emissions change with the size of streams and rivers Hotchkiss, E. R.; Hall Jr, R. O.; Sponseller, R. A. Nature Geoscience, Vol. 8, Issue 9 https://doi.org/10.1038/ngeo2507	journal	August 2015
The role of organisms in hyporheic processes: gaps in current knowledge, needs for future research and applications Marmonier, P.; Archambaud, G.; Belaidi, N. Annales de Limnologie - International Journal of Limnology, Vol. 48, Issue 3 https://doi.org/10.1051/limn/2012009	journal	January 2012
Diel fluctuations in bacterial activity on streambed substrata during vernal algal blooms: Effects of temperature, water chemistry, and habitat: Diel patterns in streams Kaplan, Louis A.; Bott, Thomas L. Limnology and Oceanography, Vol. 34, Issue 4 https://doi.org/10.4319/lo.1989.34.4.0718	journal	June 1989
Experimental Observations and Numerical Modeling of Coupled Microbial and Transport Processes in Variably Saturated Sand Rockhold, M. L.; Yarwood, R. R.; Niemet, M. R. Vadose Zone Journal, Vol. 4, Issue 2 https://doi.org/10.2136/vzj2004.0087	journal	January 2005
Denitrification in river sediments: relationship between process rate and properties of water and sediment Freshwater Biology, Vol. 39, Issue 3 https://doi.org/10.1046/j.1365-2427.1998.00295.x	journal	May 1998
Connecting large-scale atmospheric circulation, river flow and groundwater levels in a chalk catchment in southern England Lavers, David A.; Hannah, David M.; Bradley, Chris Journal of Hydrology, Vol. 523 https://doi.org/10.1016/j.jhydrol.2015.01.060	journal	April 2015
Nitrification in the Upper Mississippi River: patterns, controls, and contribution to the NO ₃ ⁻ budget Strauss, Eric A.; Richardson, William B.; Bartsch, Lynn A. Journal of the North American Benthological Society, Vol. 23, Issue 1 https://doi.org/10.1899/0887-3593(2004)023<0001:NITUMR>2.0.CO;2	journal	January 2004
Episodic sediment accumulation on Amazonian flood plains influenced by El Niño/Southern Oscillation Aalto, Rolf; Maurice-Bourgoin, Laurence; Dunne, Thomas Nature, Vol. 425, Issue 6957 https://doi.org/10.1038/nature02002	journal	October 2003
Modelling bioclogging in variably saturated porous media and the interactions between surface/subsurface flows: Application to Constructed Wetlands Samsó, Roger; García, Joan; Molle, Pascal Journal of Environmental Management, Vol. 165 https://doi.org/10.1016/j.jenvman.2015.09.045	journal	January 2016
Measurements of riverbed hydraulic conductivity in a semi-arid lowland river system (Murray–Darling Basin, Australia) Taylor, Andrew R.; Lamontagne, Sébastien; Crosbie, Russell S. Soil Research, Vol. 51, Issue 5 https://doi.org/10.1071/SR13090	journal	January 2013
Multicomponent reactive transport modeling in variably saturated porous media using a generalized formulation for kinetically controlled reactions: REACTIVE TRANSPORT MODELING IN VARIABLY SATURATED MEDIA Mayer, K. Ulrich; Frind, Emil O.; Blowes, David W. Water Resources Research, Vol. 38, Issue 9 https://doi.org/10.1029/2001WR000862	journal	September 2002
Climatic, ecophysiological, and phenological controls on plant ecohydrological strategies in seasonally dry ecosystems: ECOHYDROLOGY OF SEASONALLY DRY ECOSYSTEMS Vico, Giulia; Thompson, Sally E.; Manzoni, Stefano Ecohydrology, Vol. 8, Issue 4 https://doi.org/10.1002/eco.1533	journal	August 2014
Atmospheric Rivers, Floods and the Water Resources of California Dettinger, Michael D.; Ralph, Fred Martin; Das, Tapash Water, Vol. 3, Issue 2 https://doi.org/10.3390/w3020445	journal	March 2011
Field assessment of surface water-groundwater connectivity in a semi-arid river basin (Murray-Darling, Australia): SURFACE WATER-GROUNDWATER CONNECTIVITY IN A SEMI-ARID RIVER BASIN Lamontagne, S.; Taylor, A. R.; Cook, P. G. Hydrological Processes, Vol. 28, Issue 4 https://doi.org/10.1002/hyp.9691	journal	January 2013
Modeling microbial processes in porous media Murphy, Ellyn M.; Ginn, Timothy R. Hydrogeology Journal, Vol. 8, Issue 1 https://doi.org/10.1007/s100409900043	journal	March 2000
Evaluating fine sediment mobilization and storage in a gravel-bed river using controlled reservoir releases Petticrew, E. L.; Krein, A.; Walling, D. E. Hydrological Processes, Vol. 21, Issue 2 https://doi.org/10.1002/hyp.6183	journal	January 2007
Simulation of Microbial Growth Dynamics Coupled to Nutrient and Oxygen Transport in Porous Media Molz, F. J.; Widdowson, M. A.; Benefield, L. D. Water Resources Research, Vol. 22, Issue 8 https://doi.org/10.1029/WR022i008p01207	journal	August 1986
The Influence of Streambed Heterogeneity on Hyporheic Flow in Gravelly Rivers: Y. Zhou etal. Ground Water XX, no. X: XXXX Zhou, YaoQuan; Ritzi, Robert W.; Soltanian, Mohamad Reza Groundwater, Vol. 52, Issue 2 https://doi.org/10.1111/gwat.12048	journal	April 2013
Importance of surface-subsurface exchange in stream ecosystems: The hyporheic zone Findlay, Stuart Limnology and Oceanography, Vol. 40, Issue 1 https://doi.org/10.4319/lo.1995.40.1.0159	journal	January 1995
Carbon fate in a large temperate human-impacted river system: Focus on benthic dynamics: C FATE IN A LARGE HUMAN-IMPACTED RIVER Vilmin, Lauriane; Flipo, Nicolas; Escoffier, Nicolas Global Biogeochemical Cycles, Vol. 30, Issue 7 https://doi.org/10.1002/2015GB005271	journal	July 2016
Metabolism, Gas Exchange, and Carbon Spiraling in Rivers Hall, Robert O.; Tank, Jennifer L.; Baker, Michelle A. Ecosystems, Vol. 19, Issue 1 https://doi.org/10.1007/s10021-015-9918-1	journal	September 2015
Sand aggradation alters biofilm standing crop and metabolism in a low-gradient Lake Superior tributary Marcarelli, Amy M.; Huckins, Casey J.; Eggert, Susan L. Journal of Great Lakes Research, Vol. 41, Issue 4 https://doi.org/10.1016/j.jglr.2015.09.004	journal	December 2015
Comparison of bioclogging effects in saturated porous media within one- and two-dimensional flow systems Thullner, Martin Ecological Engineering, Vol. 36, Issue 2 https://doi.org/10.1016/j.ecoleng.2008.12.037	journal	February 2010
Ambient groundwater flow diminishes nitrate processing in the hyporheic zone of streams: AMBIENT GROUNDWATER AND STREAM N-CYCLING Azizian, Morvarid; Boano, Fulvio; Cook, Perran L. M. Water Resources Research, Vol. 53, Issue 5 https://doi.org/10.1002/2016WR020048	journal	May 2017
Longitudinal transformation of nitrogen and carbon in the hyporheic zone of an N-rich stream: A combined modelling and field study Peyrard, D.; Delmotte, S.; Sauvage, S. Physics and Chemistry of the Earth, Parts A/B/C, Vol. 36, Issue 12 https://doi.org/10.1016/j.pce.2011.05.003	journal	January 2011
Open-channel measurement of denitrification in a large lowland river Ritz, Stephanie; Dähnke, Kirstin; Fischer, Helmut Aquatic Sciences, Vol. 80, Issue 1 https://doi.org/10.1007/s00027-017-0560-1	journal	December 2017
Analysis of pumping-induced unsaturated regions beneath a perennial river: PUMPING-INDUCED UNSATURATED REGIONS Su, Grace W.; Jasperse, James; Seymour, Donald Water Resources Research, Vol. 43, Issue 8 https://doi.org/10.1029/2006WR005389	journal	August 2007
Hydraulic controls of in‐stream gravel bar hyporheic exchange and reactions Trauth, Nico; Schmidt, Christian; Vieweg, Michael Water Resources Research, Vol. 51, Issue 4 https://doi.org/10.1002/2014WR015857	journal	April 2015
River corridor science: Hydrologic exchange and ecological consequences from bedforms to basins: RIVER CORRIDORS FROM BEDFORMS TO BASINS Harvey, Jud; Gooseff, Michael Water Resources Research, Vol. 51, Issue 9 https://doi.org/10.1002/2015WR017617	journal	September 2015
ENSO and Hydrologic Extremes in the Western United States* Cayan, Daniel R.; Redmond, Kelly T.; Riddle, Laurence G. Journal of Climate, Vol. 12, Issue 9 https://doi.org/10.1175/1520-0442(1999)012<2881:EAHEIT>2.0.CO;2	journal	September 1999
Residence times of stream-groundwater exchanges due to transient stream stage fluctuations: BANK STORAGE RESIDENCE TIMES McCallum, James L.; Shanafield, Margaret Water Resources Research, Vol. 52, Issue 3 https://doi.org/10.1002/2015WR017441	journal	March 2016
Pore-network modeling of biofilm evolution in porous media Ezeuko, C. C.; Sen, A.; Grigoryan, A. Biotechnology and Bioengineering, Vol. 108, Issue 10 https://doi.org/10.1002/bit.23183	journal	May 2011
The ecology and biogeochemistry of stream biofilms Battin, Tom J.; Besemer, Katharina; Bengtsson, Mia M. Nature Reviews Microbiology, Vol. 14, Issue 4 https://doi.org/10.1038/nrmicro.2016.15	journal	March 2016
Primary Production in Flowing Waters1 Odum, Howard T. Limnology and Oceanography, Vol. 1, Issue 2 https://doi.org/10.4319/lo.1956.1.2.0102	journal	April 1956
Denitrification Across Landscapes and Waterscapes: a Synthesis Seitzinger, S.; Harrison, J. A.; Böhlke, J. K. Ecological Applications, Vol. 16, Issue 6 https://doi.org/10.1890/1051-0761(2006)016[2064:DALAWA]2.0.CO;2	journal	December 2006
Hydrogeologic controls on disconnection between surface water and groundwater: HYDROGEOLOGIC CONTROLS ON THE DISCONNECT Brunner, Philip; Cook, Peter G.; Simmons, Craig T. Water Resources Research, Vol. 45, Issue 1 https://doi.org/10.1029/2008WR006953	journal	January 2009
Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies Hou, Z.; Nelson, W. C.; Stegen, J. C. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-12275-w	journal	September 2017
Microcosms for Aquifer Research: Application to Colonization of Various Sized Particles by Ground-Water Microorganisms Dodds, Walter K.; Randel, Clay A.; Edler, Christopher C. Ground Water, Vol. 34, Issue 4 https://doi.org/10.1111/j.1745-6584.1996.tb02065.x	journal	July 1996
The effect of El Niño Southern Oscillation cycles on the decadal scale suspended sediment behavior of a coastal dry-summer subtropical catchment: DECADAL SCALE PATTERNS IN FLUVIAL SUSPENDED SEDIMENT BEHAVIOR Gray, Andrew B.; Pasternack, Gregory B.; Watson, Elizabeth B. Earth Surface Processes and Landforms, Vol. 40, Issue 2 https://doi.org/10.1002/esp.3627	journal	August 2014
Clogging of an Effluent Dominated Semiarid River: A Conceptual Model of Stream-Aquifer Interactions Treese, Samantha; Meixner, Thomas; Hogan, James F. JAWRA Journal of the American Water Resources Association, Vol. 45, Issue 4 https://doi.org/10.1111/j.1752-1688.2009.00346.x	journal	August 2009
Sediment Fluxes from California Coastal Rivers: The Influences of Climate, Geology, and Topography Andrews, E. D.; Antweiler, Ronald C. The Journal of Geology, Vol. 120, Issue 4 https://doi.org/10.1086/665733	journal	July 2012
Impacts of river bed gas on the hydraulic and thermal dynamics of the hyporheic zone Cuthbert, M. O.; Mackay, R.; Durand, V. Advances in Water Resources, Vol. 33, Issue 11 https://doi.org/10.1016/j.advwatres.2010.09.014	journal	November 2010
Occurrence of Nitrate in Groundwater—A Review Spalding, R. F.; Exner, M. E. Journal of Environment Quality, Vol. 22, Issue 3 https://doi.org/10.2134/jeq1993.00472425002200030002x	journal	January 1993
Characterization of dissolved organic matter from a restored urban marsh and its role in the mobilization of trace metals ElBishlawi, Hagar; Jaffe, Peter R. Chemosphere, Vol. 127 https://doi.org/10.1016/j.chemosphere.2014.12.080	journal	May 2015
Numerical modeling of coupled nitrification–denitrification in sediment perfusion cores from the hyporheic zone of the Shingobee River, MN Sheibley, Richard W.; Jackman, Alan P.; Duff, John H. Advances in Water Resources, Vol. 26, Issue 9 https://doi.org/10.1016/S0309-1708(03)00088-5	journal	September 2003
Extreme winds and precipitation during landfall of atmospheric rivers Waliser, Duane; Guan, Bin Nature Geoscience, Vol. 10, Issue 3 https://doi.org/10.1038/ngeo2894	journal	February 2017
Climate Change and the Episodicity of Sediment Flux of Small California Rivers Inman, Douglas L.; Jenkins, Scott A. The Journal of Geology, Vol. 107, Issue 3 https://doi.org/10.1086/314346	journal	May 1999
Evaluation of infiltration from losing-disconnected rivers using a geophysical characterisation of the riverbed and a simplified infiltration model Crosbie, Russell S.; Taylor, Andrew R.; Davis, Aaron C. Journal of Hydrology, Vol. 508 https://doi.org/10.1016/j.jhydrol.2013.07.045	journal	January 2014

Cited By (4)

Exploring the role of hydraulic conductivity on the contribution of the hyporheic zone to in‐stream nitrogen uptake Mendoza‐Lera, Clara; Ribot, Miquel; Foulquier, Arnaud Ecohydrology, Vol. 12, Issue 7 https://doi.org/10.1002/eco.2139	journal	July 2019
Hydrogeologic Controls of Surface Water‐Groundwater Nitrogen Dynamics Within a Tidal Freshwater Zone Barnes, Rebecca T.; Sawyer, Audrey H.; Tight, Delaney M. Journal of Geophysical Research: Biogeosciences, Vol. 124, Issue 11 https://doi.org/10.1029/2019jg005164	journal	November 2019
Technical note: Water table mapping accounting for river–aquifer connectivity and human pressure Maillot, Mathias; Flipo, Nicolas; Rivière, Agnès Hydrology and Earth System Sciences, Vol. 23, Issue 11 https://doi.org/10.5194/hess-23-4835-2019	journal	January 2019
Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer Mailloux, Brian J.; Kim, Carol; Kichuk, Tess Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-46663-1	journal	July 2019