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

Published online by Cambridge University Press:  23 July 2012

P. Marmonier ,
G. Archambaud ,
N. Belaidi ,
N. Bougon ,
P. Breil ,
E. Chauvet ,
C. Claret ,
J. Cornut ,
T. Datry  and
M.-J. Dole-Olivier
...Show all authors
P. Marmonier*
Affiliation:
Université de Lyon, Université de Lyon 1, UMR-CNRS 5023 LEHNA, 43 Bd du 11 Novembre1918, F-69622 Villeurbanne Cedex, France
G. Archambaud
Affiliation:
Cemagref Aix-en-Provence, Hydrobiologie-EEC, 13182 Aix-en-Provence Cedex 5, France
N. Belaidi
Affiliation:
Département de biologie et environnement, Université de Tlemcen, DZ-13000 Tlemcen, Algeria
N. Bougon
Affiliation:
Cemagref Lyon, UR MALY, 3bis quai Chauveau, 69336 Lyon Cedex 09, France
P. Breil
Affiliation:
Cemagref Lyon – UR Hydrologie Hydraulique, 3bis quai Chauveau, 69336 Lyon Cedex 09, France
E. Chauvet
Affiliation:
Université de Toulouse, UPS, INPT, EcoLab (Laboratoire d'Écologie Fonctionnelle et Environnement), Bât. 4R1, 118 Route de Narbonne, 31062 Toulouse Cedex 9, France CNRS, Ecolab, 31055 Toulouse Cedex 4, France
C. Claret
Affiliation:
Institut Méditerranéen d'Écologie et de Paléoécologie IMEP, UMR-CNRS 6116, Université Paul-Cézanne Aix-Marseille 3, 13397 Marseille Cedex 20, France
J. Cornut
Affiliation:
Université de Toulouse, UPS, INPT, EcoLab (Laboratoire d'Écologie Fonctionnelle et Environnement), Bât. 4R1, 118 Route de Narbonne, 31062 Toulouse Cedex 9, France CNRS, Ecolab, 31055 Toulouse Cedex 4, France
T. Datry
Affiliation:
Cemagref Lyon, UR MALY, 3bis quai Chauveau, 69336 Lyon Cedex 09, France
M.-J. Dole-Olivier
Affiliation:
Université de Lyon, Université de Lyon 1, UMR-CNRS 5023 LEHNA, 43 Bd du 11 Novembre1918, F-69622 Villeurbanne Cedex, France
B. Dumont
Affiliation:
Cemagref Aix-en-Provence, Hydrobiologie-EEC, 13182 Aix-en-Provence Cedex 5, France
N. Flipo
Affiliation:
École des Mines de Paris, Géoscience Départment, Fontainebleau Cedex, France
A. Foulquier
Affiliation:
Université de Lyon, Université de Lyon 1, UMR-CNRS 5023 LEHNA, 43 Bd du 11 Novembre1918, F-69622 Villeurbanne Cedex, France Cemagref Lyon, UR MALY, 3bis quai Chauveau, 69336 Lyon Cedex 09, France
M. Gérino
Affiliation:
Université de Toulouse, UPS, INPT, EcoLab (Laboratoire d'Écologie Fonctionnelle et Environnement), Bât. 4R1, 118 Route de Narbonne, 31062 Toulouse Cedex 9, France CNRS, Ecolab, 31055 Toulouse Cedex 4, France
A. Guilpart
Affiliation:
INR-Agrocampus-Ouest, UMR 985 Écologie et Santé des Ecosystèmes, 65 rue de St Brieuc, 35042 Rennes Cedex, France
F. Julien
Affiliation:
Université de Toulouse, UPS, INPT, EcoLab (Laboratoire d'Écologie Fonctionnelle et Environnement), Bât. 4R1, 118 Route de Narbonne, 31062 Toulouse Cedex 9, France CNRS, Ecolab, 31055 Toulouse Cedex 4, France
C. Maazouzi
Affiliation:
Université de Lyon, Université de Lyon 1, UMR-CNRS 5023 LEHNA, 43 Bd du 11 Novembre1918, F-69622 Villeurbanne Cedex, France
D. Martin
Affiliation:
Université de Lyon, Université de Lyon 1, UMR-CNRS 5023 LEHNA, 43 Bd du 11 Novembre1918, F-69622 Villeurbanne Cedex, France
F. Mermillod-Blondin
Affiliation:
Université de Lyon, Université de Lyon 1, UMR-CNRS 5023 LEHNA, 43 Bd du 11 Novembre1918, F-69622 Villeurbanne Cedex, France
B. Montuelle
Affiliation:
Cemagref Lyon, UR MALY, 3bis quai Chauveau, 69336 Lyon Cedex 09, France INRA, UMR CARTEL, Route de Corzent, BP 511, 74203 Thonon-les-Bains, France
Ph. Namour
Affiliation:
Cemagref Lyon, UR MALY, 3bis quai Chauveau, 69336 Lyon Cedex 09, France Université de Lyon, Université Lyon 1, Institut des Sciences Analytiques, UMR 5280, F-69622 Villeurbanne, France
S. Navel
Affiliation:
Université de Lyon, Université de Lyon 1, UMR-CNRS 5023 LEHNA, 43 Bd du 11 Novembre1918, F-69622 Villeurbanne Cedex, France
D. Ombredane
Affiliation:
INR-Agrocampus-Ouest, UMR 985 Écologie et Santé des Ecosystèmes, 65 rue de St Brieuc, 35042 Rennes Cedex, France
T. Pelte
Affiliation:
Ministère de l'Environnement, Agence de l'Eau Rhône-Méditerrannée and Corse, 2-4 Allée de Lodz, 69363 Lyon Cedex 07, France
C. Piscart
Affiliation:
Université de Lyon, Université de Lyon 1, UMR-CNRS 5023 LEHNA, 43 Bd du 11 Novembre1918, F-69622 Villeurbanne Cedex, France
M. Pusch
Affiliation:
Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
S. Stroffek
Affiliation:
Ministère de l'Environnement, Agence de l'Eau Rhône-Méditerrannée and Corse, 2-4 Allée de Lodz, 69363 Lyon Cedex 07, France
A. Robertson
Affiliation:
Department of Life Sciences – Roehampton University, Holybourne Avenue, London SW15 4JD, UK
J.-M. Sanchez-Pérez
Affiliation:
Université de Toulouse, UPS, INPT, EcoLab (Laboratoire d'Écologie Fonctionnelle et Environnement), Bât. 4R1, 118 Route de Narbonne, 31062 Toulouse Cedex 9, France CNRS, Ecolab, 31055 Toulouse Cedex 4, France
S. Sauvage
Affiliation:
Université de Toulouse, UPS, INPT, EcoLab (Laboratoire d'Écologie Fonctionnelle et Environnement), Bât. 4R1, 118 Route de Narbonne, 31062 Toulouse Cedex 9, France CNRS, Ecolab, 31055 Toulouse Cedex 4, France
A. Taleb
Affiliation:
Département de biologie et environnement, Université de Tlemcen, DZ-13000 Tlemcen, Algeria
M. Wantzen
Affiliation:
Université de Tours, UMR 6173 CITERES, Département IMACOF, 33 allée F. de Lesseps, 37204 Tours Cedex 03, France
Ph. Vervier
Affiliation:
Université de Toulouse, UPS, INPT, EcoLab (Laboratoire d'Écologie Fonctionnelle et Environnement), Bât. 4R1, 118 Route de Narbonne, 31062 Toulouse Cedex 9, France CNRS, Ecolab, 31055 Toulouse Cedex 4, France Acceptables Avenirs Prologue, La Pyrénéenne, BP 27201, 31672 Labège Cedex, France
*
*Corresponding author: [email protected]

Abstract

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Fifty years after the hyporheic zone was first defined (Orghidan, 1959), there are still gaps in the knowledge regarding the role of biodiversity in hyporheic processes. First, some methodological questions remained unanswered regarding the interactions between biodiversity and physical processes, both for the study of habitat characteristics and interactions at different scales. Furthermore, many questions remain to be addressed to help inform our understanding of invertebrate community dynamics, especially regarding the trophic niches of organisms, the functional groups present within sediment, and their temporal changes. Understanding microbial community dynamics would require investigations about their relationship with the physical characteristics of the sediment, their diversity, their relationship with metabolic pathways, their interactions with invertebrates, and their response to environmental stress. Another fundamental research question is that of the importance of the hyporheic zone in the global metabolism of the river, which must be explored in relation to organic matter recycling, the effects of disturbances, and the degradation of contaminants. Finally, the application of this knowledge requires the development of methods for the estimation of hydrological exchanges, especially for the management of sediment clogging, the optimization of self-purification, and the integration of climate change in environmental policies. The development of descriptors of hyporheic zone health and of new metrology is also crucial to include specific targets in water policies for the long-term management of the system and a clear evaluation of restoration strategies.

Keywords

River sedimentinvertebratesmicrobial communitiesriver management
Type
Research Article
Information
Annales de Limnologie - International Journal of Limnology , Volume 48 , Issue 3 , 2012 , pp. 253 - 266
Copyright
© EDP Sciences, 2012

References

Aller, R.C., 1982. The effects of macrobenthos on chemical properties of marine sediment and overlying water. In: McCall, P.L. and Tevesz, M.J.S. (eds.), Animal Sediment Relations. The Biogenic Alteration of Sediments, Plenum Publishing Corporation, New York, 53–102.CrossRefGoogle Scholar
Aller, R.C., 1994. Bioturbation and remineralization of sedimentary organic matter: effects of redox oscillation. Chem. Geol., 114, 331–345.CrossRefGoogle Scholar
Atalah, J., Otto, S.A., Anderson, M.J., Costello, M.J., Lenz, M. and Wahl, M., 2007. Temporal variance of disturbance did not affect diversity and structure of a marine fouling community in north-eastern. New Zealand. Mar. Biol., 153, 199–211.CrossRefGoogle Scholar
Baker, M.A., Dahm, C.N. and Valett, H.M., 1999. Acetate retention and metabolism in the hyporheic zone of a mountain stream. Limnol. Oceanogr., 44, 1530–1539.CrossRefGoogle Scholar
Bärlocher, F., Seena, S., Wilson, K.P. and Williams, D.D., 2008. Raised water temperature lowers diversity of hyporheic aquatic hyphomycetes. Freshwater Biol., 53, 368–379.Google Scholar
Battin, T.J., 2000. Hydrodynamics is a major determinant of streambed biofilm activity: From the sediment to the reach scale. Limnol. Oceanogr., 45, 1308–1319.CrossRefGoogle Scholar
Battin, T.J., Wille, A., Sattler, B. and Psenner, R., 2001. Phylogenetic and functional heterogeneity of sediment biofilms along environmental gradients in a glacial stream. Appl. Environ. Microbiol., 67, 799–807.CrossRefGoogle Scholar
Bencala, K.E., 1993. A perspective on stream-catchment connections. J. N. Am. Benthol. Soc., 12, 44–47.CrossRefGoogle Scholar
Bencala, K.E., 2000. Hyporheic zone hydrological processes. Hydrol. Process., 14, 2797–2798.3.0.CO;2-6>CrossRefGoogle Scholar
Birgand, F., Skaggs, R.W., Chescheir, G.M. and Gilliam, J.W., 2007. Nitrogen removal in streams of agricultural catchments – a literature review. Crit. Rev. Environ. Sci. Technol., 37, 381–487.CrossRefGoogle Scholar
Bouletreau, S., Garabetian, F., Sauvage, S. and Sánchez-Pérez, J.M., 2006. Assessing the importance of self-generated detachment process in river biofilm models. Freshwater Biol., 51, 901–912.CrossRefGoogle Scholar
Boulton, A.J., 2000. The functional role of the hyporheos. Verh. Int. Ver. Theor. Angew. Limnol., 27, 51–63.Google Scholar
Boulton, A.J., 2005. Chances and challenges in the conservation of groundwater-dependent ecosystems. Aquat. Conserv.: Mar. Freshwater Ecosyst., 15, 319–323.CrossRefGoogle Scholar
Boulton, A.J., Scarsbrook, M.R., Quinn, J.M. and Burrell, G.P., 1997. Land-use effects on the hyporheic ecology of five small streams near Hamilton, New Zealand. N. Z. J. Mar. Freshwater Res., 31, 609–622.CrossRefGoogle Scholar
Boulton, A.J., Findlay, S., Marmonier, P., Stanley, E.H. and Valett, H.M., 1998. The functional significance of the hyporheic zone in streams and rivers. Annu. Rev. Ecol. Syst., 29, 59–81.CrossRefGoogle Scholar
Boulton, A.J., Fenwick, G.D., Hancock, P.J. and Harvey, M.S., 2008. Biodiversity, functional roles and ecosystem services of groundwater invertebrates. Invertebr. Syst., 22, 103–116.CrossRefGoogle Scholar
Boulton, A.J., Datry, T., Kasahara, T., Mutz, M. and Stanford, J.A., 2010. Ecology and management of the hyporheic zone: stream–groundwater interactions of running waters and their floodplains. J. N. Am. Benthol. Soc., 29, 26–40.CrossRefGoogle Scholar
Bretschko, G. and Leichtfried, M., 1987. The determination of organic matter in river sediments. Arch. Hydrobiol. Suppl., 68, 403–417.Google Scholar
Bretschko, G. and Leichtfried, M., 1988. Distribution of organic matter and fauna in a second order alpine gravel stream (RITRODAT-Lunz).  Verh. Int. Verein. Limnol., 23, 1333–1339.Google Scholar
Bridge, J., 2005. High resolution in-situ monitoring of hyporheic zone biogeochemistry, Science Report SC030155/SR3, Environment Agency, Bristol, 51 p.
Brunke, M. and Gonser, T., 1999. Hyporheic invertebrates – the clinal nature of interstitial communities structured by hydrological exchange and environmental gradients. J. N. Am. Benthol. Soc., 18, 344–362.CrossRefGoogle Scholar
Buffington, J.M. and Tonina, D., 2009. Hyporheic exchange in mountain rivers II: effects of channel morphology on mechanics, scales, and rates of exchange. Geogr. Compass, 3, 1038–1062.CrossRefGoogle Scholar
Burns, A. and Ryder, D.S., 2001. Potential for biofilms as biological indicators in Australian riverine systems. Ecol. Manage. Rest., 2, 53–63.CrossRefGoogle Scholar
Burt, T., Pinay, G. and Sabater, S., 2010. What do we still need to know about the ecohydrology of riparian zones? Ecohydrology, 3, 373–377.CrossRefGoogle Scholar
Cardenas, M.B., Wilson, J.L. and Zlotnik, V.A., 2004. Impact of heterogeneity, bed forms, and stream curvature on subchannel hyporheic exchange. Water Resour. Res., 40, W08307.CrossRefGoogle Scholar
Carpenter, S.R., Fisher, S.G., Grimm, N.B. and Kitchell, J.F., 1992. Global change and freshwater ecosystems. Annu. Rev. Ecol. Syst., 23, 119–139.CrossRefGoogle Scholar
Chamberlain, P.M., Bull, I.D., Black, H.I.J., Ineson, P. and Evershed, R.P., 2006. Collembolan trophic preferences determined using fatty acid distributions and compound-specific stable carbon isotope values. Soil Biol. Biochem., 38, 1275–1281.CrossRefGoogle Scholar
Claret, C., Marmonier, P., Boissier, J.M., Fontvieille, D. and Blanc, P., 1997. Nutrient transfer between parafluvial interstitial water and river water: influence of gravel bar heterogeneity. Freshwater Biol., 37, 657–670.CrossRefGoogle Scholar
Claret, C., Marmonier, P. and Bravard, J.P., 1998. Seasonal dynamics of nutrient and biofilm in interstitial habitats of two contrasting riffles in a regulated large river. Aquat. Sci., 60, 33–55.CrossRefGoogle Scholar
Claret, C., Boulton, A.J., Dole-Olivier, M.J. and Marmonier, P., 2001. Functional processes versus state variables: interstitial organic matter pathways in floodplain habitats. Can. J. Fish. Aquat. Sci., 58, 1594–1602.CrossRefGoogle Scholar
Clement, J.C., Pinay, G. and Marmonier, P., 2002. Seasonal dynamics of denitrification along topohydrosequences in three different riparian wetlands. J. Environ. Qual., 31, 1025–1037.CrossRefGoogle ScholarPubMed
Clement, J.C., Shrestha, J., Ehrenfeld, J.G. and Jaffe, P.R., 2005. Ammonium oxidation coupled to dissimilatory reduction of iron under anaerobic conditions in wetland soils. Soil Biol. Biochem., 37, 2323–2328.CrossRefGoogle Scholar
Cooling, M.P. and Boulton, A.J., 1993. Aspects of the hyporheic zone below the terminus of a South Australian arid-zone stream. Aust. J. Mar. Freshwater Res., 44, 411–426.CrossRefGoogle Scholar
Cornut, J., Elger, A., Lambrigot, D., Marmonier, P. and Chauvet, E., 2010. Early stages of leaf decomposition are mediated by aquatic fungi in the hyporheic zone of woodland streams. Freshwater Biol., 55, 2541–2556.CrossRefGoogle Scholar
Corti, R., Datry, T., Drummond, L. and Learned, S., 2011. Natural variation in immersion and emersion affects breakdown and invertebrate colonization of leaf litter in temporary river. Aquat. Sci., 73, 537–550.CrossRefGoogle Scholar
Crenshaw, C.L., Valett, H.M. and Tank, J.L., 2002. Effects of coarse particulate organic matter on fungal biomass and invertebrate density in the subsurface of a head- water stream. J. N. Am. Benthol. Soc., 21, 28–42.CrossRefGoogle Scholar
Creuzé des Châtelliers, M. and Reygrobellet, J.L., 1990. Interactions between geomorphological processes, benthic and hyporheic communities: first results on a by-passed canal of the French upper Rhône river. Regul. Riv., 5, 139–158.CrossRefGoogle Scholar
Dahm, C.N. and Valett, H.M., 1996. Hyporheic zones. In: Methods in Stream Ecology, A. H. F. R. a. L. G., Academic Press, San Diego, California, 53–74.Google Scholar
Dahm, C.N., Trotter, E.H. and Sedell, J.R., 1987. Role of anaerobic zones and processes in stream ecosystem productivity. In: Averett, R.C. and McKnight, D.M. (eds.), Chemical Quality of Water and the Hydrologic Cycle, Lewis Publishers, Chelsea, 157–178.Google Scholar
Dahm, C.N., Grimm, N.B., Marmonier, P., Valett, H.M. and Vervier, P., 1998. Nutrient Dynamics at the interface between surface waters and ground waters. Freshwater Biol., 40, 427–451.CrossRefGoogle Scholar
Danielopol, D.L., 1989. Groundwater fauna associated to riverine aquifers. J. N. Am. Benthol. Soc., 8, 18–35.CrossRefGoogle Scholar
Danielopol, D.L., 2000. Biodiversity in groundwater: a large-scale view. Trends Ecol. Evol., 15, 223–224.CrossRefGoogle ScholarPubMed
Datry, T. and Larned, S.T., 2008. River flow controls ecological processes and invertebrate assemblages in subsurface flowpaths of an ephemeral river reach. Can. J. Fish. Aquat. Sci., 65, 1532–1544.CrossRefGoogle Scholar
Datry, T., Corti, R., Claret, C. and Philippe, M., 2011. Flow intermittence controls leaf litter breakdown in a French temporary alluvial river: the “drying memory”. Aquat. Sci., 73, 471–483.CrossRefGoogle Scholar
Datry, T., Malard, F., Niedereitter, R. and Gibert, J., 2003. Video logging for examining biogenic structures in deep heterogeneous subsurface sediments. C. R. Acad. Sci. Biol., 326, 589–597.Google ScholarPubMed
Datry, T., Larned, S.T. and Scarsbrook, M.R., 2007. Responses of hyporheic invertebrate assemblages to large-scale variation in flow permanence and surface-subsurface exchange. Freshwater Biol., 52, 1452–1462.CrossRefGoogle Scholar
Descloux, S., Datry, T., Philippe, M. and Marmonier, P., 2010. Comparison of different techniques to assess surface and subsurface streambed colmation with fine sediments. Int. Rev. Hydrobiol, 95, 520–540.CrossRefGoogle Scholar
Doering, M., Uehlinger, U., Rotach, A., Schläpfer, D. and Tockner, K., 2006. Large-scale expansion and contraction dynamics along an unconstrained alpine alluvial corridor (Tagliamento River, Northeast Italy). Earth Surf. Process. Landforms, 32, 1693–1704.CrossRefGoogle Scholar
Dole-Olivier, M.J., Marmonier, P. and Beffy, J.L., 1997. Response of invertebrates to lotic disturbance: is the hyporheic zone a patchy refugium? Freshwat. Biol., 37, 257–276.CrossRefGoogle Scholar
Dukes, J.S. and Mooney, H.A., 1999. Does global change increase the success of biological invaders? Trends Ecol. Evol., 14, 135–139.CrossRefGoogle ScholarPubMed
Engstrom, P., Penton, C.R. and Devol, A.H., 2009. Anaerobic ammonium oxidation in deep-sea sediments off the Washington margin. Limnol. Oceanogr., 54, 1643–1652.CrossRefGoogle Scholar
European Community, 2000. Directive 2000/60/EC of the European Parliament and of the Council establishing a framework for the Community action in the field of water policy.
Fauvet, G., Claret, C. and Marmonier, P., 2001. Influence of benthic and interstitial processes on nutrient changes along a regulated reach of a large river (Rhône River, France). Hydrobiologia, 445, 121–131.CrossRefGoogle Scholar
Fellows, C.S., Valett, H.M. and Dahm, C.N., 2001. Whole-stream metabolism in two montane streams: Contribution of the hyporheic zone. Limnol. Oceanogr., 46, 523–531.CrossRefGoogle Scholar
Feris, K.P., Ramsey, P.W., Frazar, C., Rillig, M.C., Gannon, J.E. and Holben, W.E., 2003. Structure and seasonal dynamics of hyporheic zone microbial communities in free-stone Rivers of the western United States. Microb. Ecol., 46, 200–215.Google ScholarPubMed
Feris, K.P., Ramsey, P.W., Frazar, C., Rillig, M.C., Moore, J.N., Gannon, J.E. and Holben, W.E., 2004. Seasonal dynamics of shallow-hyporheic-zone microbial community structure along a heavy-metal contamination gradient. Appl. Environ. Microbiol., 70, 2323–2331.CrossRefGoogle ScholarPubMed
Findlay, S. and Sobczak, W.V., 1996. Variability in removal of dissolved organic carbon in hyporheic sediments. J. N. Am. Benthol. Soc., 15, 35–41.CrossRefGoogle Scholar
Findlay, S., Strayer, D., Goumbala, C. and Gould, K., 1993. Metabolism of streamwater dissolved organic carbon in the shallow hyporheic zone. Limnol. Oceanogr., 38, 1493–1499.CrossRefGoogle Scholar
Fisher, S.G., Grimm, N.B., Marti, E., Holmes, R.M. and Jones, J.B., 1998. Material spiraling in stream corridors: a telescoping ecosystem model. Ecosystems, 1, 19–34.CrossRefGoogle Scholar
Fischer, H., Sukhodolov, A., Wilczek, S. and Engelhardt, C., 2003. Effects of flow dynamics and sediment movement on microbial activity in a lowland river. River Res. Appl., 19, 473–482.CrossRefGoogle Scholar
Fischer, H., Kloep, F., Wilzcek, S. and Pusch, M.T., 2005. A river's liver – microbial processes within the hyporheic zone of a large lowland river. Biogeochemistry, 76, 349–371.CrossRefGoogle Scholar
Fowler, R.T. and Scarsbrook, M.R., 2002. Influence of hydrologic exchange patterns on water chemistry and hyporheic invertebrate communities in three gravel-bed rivers. N. Z. J. Mar. Freshwater Res., 36, 471–482.CrossRefGoogle Scholar
Gaudes, A., Artigas, J. and Munoz, I., 2010. Species traits and resilience of floods and drought in a Mediterranean stream. Mar. Freshwater Res., 61, 1336–1347.CrossRefGoogle Scholar
Gerino, M., Frignani, M., Mugnai, C., Bellucci, L.G., Prevedelli, D., Valentini, A., Castelli, A., Delmotte, S. and Sauvage, S., 2007. Bioturbation in the Venice lagoon: rates and relationship to organisms. Acta Oecol., 32, 14–25.CrossRefGoogle Scholar
Gessner, M.O., Chauvet, E. and Dobson, M., 1999. A perspective on leaf litter breakdown in streams. Oikos, 85, 377–384.CrossRefGoogle Scholar
Gibert, J., Ginet, R., Mathieu, J. and Reygrobellet, J.L., 1981. Structure et fonctionnement des écosystèmes du Haut-Rhône français. IX – Analyse des peuplements de deux stations phréatiques alimentant des bras morts. Int. J. Speleol., 11, 141–158.CrossRefGoogle Scholar
Gibert, J., Dole-Olivier, M.J., Marmonier, P. and Vervier, P. 1990. Surface water-Groundwater ecotones. In: Naiman, R.J. and Décamps, H. (eds.), Ecology and Management of Aquatic-Terrestrial Ecotones, Partenon Publications, London, 199–225.Google Scholar
Gilbert, F., Bonin, P. and Stora, G., 1995. Effect of bioturbation on denitrification in a marine sediment from the West Mediterranean littoral. Hydrobiologia, 304, 49–58.CrossRefGoogle Scholar
Gilbert, F., Stora, G. and Bonin, P., 1998. Influence of bioturbation on denitrification activity in Mediterranean coastal sediments: an in situ experimental approach. Mar. Ecol. Prog. Ser., 163, 99–107.CrossRefGoogle Scholar
Gilbert, F., Hulth, S. and Aller, R.C., 2003. The influence of macrofaunal burrow spacing and diffusive scaling on sedimentary nitrification and denitrification: an experimental and model approach. J. Mar. Res., 61, 101–125.CrossRefGoogle Scholar
Gooseff, M.N., Anderson, J.K., Wondzell, S.M., LaNier, J. and Haggerty, R., 2006. A modelling study of hyporheic exchange pattern and the sequence size, and spacing of stream bedforms in mountain stream networks, Oregon, USA. Hydrol. Proc., 20, 2443–2457.CrossRefGoogle Scholar
Graça, M.A., 2001. The Role of Invertebrates on Leaf Litter Decomposition in Streams – a Review. Int. Rev. Hydrobiol., 86, 383–393.3.0.CO;2-D>CrossRefGoogle Scholar
Greenwood, R., Mills, G.A. and Roig, B., 2007. Introduction to emerging tools and their use in water monitoring. Trends Anal. Chem., 26, 263–267.CrossRefGoogle Scholar
Griebler, C. and Lueders, T., 2009. Towards a conceptual understanding of microbial biodiversity in groundwater ecosystems. Freshwater Biol., 54, 649–677.CrossRefGoogle Scholar
Grimm, N.B. and Fisher, S.G., 1984. Exchange between interstitial and surface water: implications for stream metabolism and nutrient cycling. Hydrobiologia, 111, 219–228.CrossRefGoogle Scholar
Gurevitch, J. and Padilla, D.K., 2004. Are invasions a major cause of extinctions?  Trends Ecol. Evol., 19, 470–474.CrossRefGoogle Scholar
Hakenkamp, C. and Morin, A., 2000. The importance of meiofauna to lotic ecosystem functioning.  Freshwater Biol., 44, 165–175.CrossRefGoogle Scholar
Hancock, P.J., Boulton, A.J. and Humphreys, W.F., 2005. Aquifers and hyporheic zones: Towards an ecological understanding of groundwater. Hydrogeol. J., 13, 98–111.CrossRefGoogle Scholar
Harvey, B.N., Johnson, M.L., Kiernan, J.D. and Green, P.G., 2011. Net dissolved inorganic nitrogen production in hyporheic mesocosms with contrasting sediment size distributions. Hydrobiologia, 658, 343–352.CrossRefGoogle Scholar
Heffernan, J.B., Sponseller, R.A. and Fisher, S.G., 2008. Consequences of a biogeomorphic regime shift for the hyporheic zone of a Sonoran Desert stream. Freshwater Biol., 53, 1954–1968.CrossRefGoogle Scholar
Hendricks, S.P., 1993. Microbial ecology of the hyporheic zone: a perspective integrating hydrology and biology. J. N. Am. Benthol. Soc., 12, 70–78.CrossRefGoogle Scholar
Hendricks, S.P. and White, D.S., 1991. Physicochemical patterns within a hyporheic zone of a Northen Michigan River, with comments on surface water patterns. Can. J. Fish. Aquat. Sci., 48, 1645–1654.CrossRefGoogle Scholar
Hester, E.T. and Doyle, M.W., 2008. In-stream geomorphic structures as drivers of hyporheic exchange. Water Resour. Res., 44, W03417.CrossRefGoogle Scholar
Hinkle, S.R., Duff, J.H., Triska, F.J., Laenen, A., Gates, E.B., Bencala, K.E., Wentz, D.A. and Silva, S.R., 2001. Linking hyporheic flow and nitrogen cycling near the Willametter River – a large river in Oregon, USA. J. Hydrol., 244, 157–180.CrossRefGoogle Scholar
Iribar, A., Sánchez-Pérez, J.M., Lyautey, E. and Garabétian, F., 2008. Differentiated free-living and sediment-attached bacterial community structure inside and outside denitrification hotspots in the river-groundwater interface. Hydrobiologia, 598, 109–121.CrossRefGoogle Scholar
Jetten, M.S.M., Strous, M., Van der Pas-Schoonen, K.T., Schalk, J., Van Dongen, U.G.J.M., Van der Graaf, A.A., Logemann, S., Muyzer, G., Van Loosdrecht, M.C.M. and Kuenen, J.G., 1998. The anaerobic oxidation of ammonium. FEMS Microbiol. Rev., 22, S.421–437.CrossRefGoogle ScholarPubMed
Jones, J.B. and Holmes, R.M., 1996. Surface-subsurface interactions in stream ecosystems. Trends Ecol. Evol., 11, 239–242.CrossRefGoogle ScholarPubMed
Kasahara, T., Datry, T., Mutz, M. and Boulton, A., 2009. Restoration of stream-groundwater linkages in streams and rivers. Mar. Freshwater Res., 60, 976–981.CrossRefGoogle Scholar
Kirchner, J.W., Feng, X.H., Neal, C. and Robson, A.J., 2004. The fine structure of water-quality dynamics: the (high-frequency) wave of the future. Hydrol. Process., 18, 1353–1359.CrossRefGoogle Scholar
Kjellin, J., Hallin, S. and Worman, A., 2007. Spatial variations in denitrification activity in wetland sediments explained by hydrology and denitrifying community structure. Water Res., 41, 4710–4720.CrossRefGoogle ScholarPubMed
Krause, S., Hannah, D.M., Fleckenstein, J.H., Heppell, C.M., Picku, R., Pinay, G., Robertson, A.L. and Wood, P.J., 2011. Inter-disciplinary perspectives on processes in the hyporheic zone. Ecohydrology, 4, 481–499.CrossRefGoogle Scholar
Kristensen, E., Jensen, M.H. and Andersen, T.K., 1985. The impact of polychaete (Nereis virens Sars) burrows on nitrification and nitrate reduction in estuarine sediments. J. Exp. Mar. Biol. Ecol., 85, 75–91.CrossRefGoogle Scholar
Labat, F., Piscart, C., Fontan, B., 2011. First records, pathways and distributions of four new Ponto-Caspian amphipods in France. Limnologica, 41, 290–295.CrossRefGoogle Scholar
Lafont, M., Vivier, A., Nogueira, S., Namour, P. and Breil, P., 2006. Surface and hyporheic oligochaete assemblages in a French suburban stream. Hydrobiologia, 564, 183–193.CrossRefGoogle Scholar
Landmeyer, J.E., Bradley, P.M., Trego, D.A., Hale, K.G. and Haas, J.E., 2010. MTBE, TBA, and TAME Attenuation in Diverse Hyporheic Zones. Ground Water, 48, 30–41.CrossRefGoogle ScholarPubMed
Larned, S.T., Hicks, M.D., Schmidt, J., Davey, A.J.H., Dey, K., Scarsbrook, M., Arscott, D.B. and Woods, R.A., 2008. The Selwyn River of New Zealand: a benchmark system for alluvial plain rivers. River Res. Appl., 24, 1–21.CrossRefGoogle Scholar
Lecerf, A. and Richardson, J.S., 2010. Biodiversity-ecosystem function research: Insights gained from streams. River Res. Appl., 26, 45–54.CrossRefGoogle Scholar
Leduc, D., 2009. Description of Oncholaimus moanae sp. nov. (Nematoda: Oncholaimidae), with notes on feeding ecology based on isotopic and fatty acid composition. J. Mar. Biol. Assoc. UK, 89, 337–344.CrossRefGoogle Scholar
Lefebvre, S., Marmonier, P. and Pinay, G., 2004. Stream regulation and Nitrogen dynamics in sediment interstices: comparison of natural and straightened sectors of a third-order stream. River Res. Appl., 20, 499–512.CrossRefGoogle Scholar
Lefebvre, S., Marmonier, P. and Peiry, J.L., 2006. Nitrogen dynamics in rural streams: differences between geomorphologic units. Int. J. Limnol., 42, 43–52.CrossRefGoogle Scholar
Lefebvre, S., Clement, J.C., Pinay, G., Thenail, C., Durand, P. and Marmonier, P., 2007. 15N-Nitrate signature in streams: effects of land-cover and agriculture practices. Ecol. Appl., 17, 2333–2346.CrossRefGoogle Scholar
Lefebvre, S., Marmonier, P., Pinay, G., Bour, O., Aquilina, L. and Baudry, J., 2005. Nutrient dynamics in interstitial habitats of low-order rural streams with different bedrock geology. Arch. Hydrobiol., 164, 169–191.CrossRefGoogle Scholar
Lewis, D.B., Grimm, N.B., Harms, T.K. and Schade, J.D., 2007. Subsystems, flowpaths, and the spatial variability of nitrogen in fluvial ecosystem. Landscape Ecol., 22, 911–924.CrossRefGoogle Scholar
Lopez-Garcia, P., Gaill, F. and Moreira, D., 2002. Wide bacterial diversity associated with tubes of the vent worm Riftia pachyptila. Environ. Microbiol., 4, 204–215.CrossRefGoogle ScholarPubMed
Lowell, J.L., Gordon, N., Engstrom, D., Stanford, J.A., Holben, W.E. and Gannon, J.E., 2009. Habitat heterogeneity and associated microbial community structure in a small-scale floodplain hyporheic flow path. Microb. Ecol., 58, 611–620.CrossRefGoogle Scholar
Maazouzi, C., Piscart, C., Pihan, J.C. and Masson, G., 2009. Effect of habitat-related resources on fatty acid composition and body weight of the invasive Dikerogammarus villosus in an artificial reservoir. Fundam. Appl. Limnol., 175, 327–338.CrossRefGoogle Scholar
Malard, F., Gallassi, D., Lafont, M., Dolédec, S. and Ward, J.V., 2003. Longitudinal patterns of invertebrates in the hyporheic zone of a glacial river. Freshwater Biol., 48, 1709–1725.CrossRefGoogle Scholar
Malard, F., Uehlinger, U., Zah, R. and Tockner, K., 2006. Flood-pulse and riverscape dynamics in a braided glacial river. Ecology, 87, 704–716.CrossRefGoogle Scholar
Malcolm, I.A., Soulsby, C. and Youngson, A.F., 2006. High frequency logging technologies reveal state dependant hyporheic process dynamics: implications for hydroecological studies. Hydrol. Process., 20, 615–622.CrossRefGoogle Scholar
Marmonier, P., Delettre, Y., Lefebvre, S., Guyon, J. and Boulton, A.J., 2004. A simple technique using wooden stakes to estimate vertical patterns of interstitial oxygenation in the beds of rivers. Arch. Hydrobiol., 160, 133–143.CrossRefGoogle Scholar
Marmonier, P., Piscart, C., Sarriquet, P.E., Azam, D. and Chauvet, E., 2010. Relevance of large litter bag burial for the study of leaf breakdown in the hyporheic zone. Hydrobiologia, 641, 203–214.CrossRefGoogle Scholar
Massa, F., Baglinière, J.L., Prunet, P. and Grimaldi, C., 2000. Survie embryo-larvaire de la truite (Salmo trutta) et conditions chimiques dans la frayère. Cybium, 24 (Suppl.), 129–140.Google Scholar
Matthaei, C.D., Weller, F., Kelly, D.W. and Townsend, C.R., 2006. Impacts of fine sediment addition to tussock, pasture, dairy and deer farming streams in New Zealand. Freshwater Biol., 51, 2154–2172.CrossRefGoogle Scholar
McDermott, M.J., Robertson, A.L., Shaw, P.J. and Milner, A.M., 2010. The hyporheic assemblage of a recently formed stream following deglaciation in Glacier Bay, Alaska. Can. J. Fish. Aquat. Sci., 67, 304–313.CrossRefGoogle Scholar
Mermillod-Blondin, F., Creuzé des Châtelliers, M., Gerino, M. and Gaudet, J.P., 2000. Testing the effect of Limnodrilus sp. (Oligochaeta, Tubificidae) on organic matter and nutrient processing in the hyporheic zone: a microcosm method. Arch. Hydrobiol., 149, 467–487.CrossRefGoogle Scholar
Mermillod-Blondin, F., Gaudet, J.P., Gerino, M. and Creuzé des Châtelliers, M., 2003. Influence of macroinvertebrates on physico-chemical and microbial processes in the hyporheic sediments. Hydrol. Process., 17, 779–794.CrossRefGoogle Scholar
Mermillod-Blondin, F., Nogaro, G., Datry, T., Malard, F. and Gibert, J., 2005. Do tubificid worms influence the fate of organic matter and pollutants in stormwater sediments? Environ. Pollut., 134, 57–69.CrossRefGoogle ScholarPubMed
Mermillod-Blondin, F., Nogaro, G., Vallier, F. and Gibert, J., 2008. Laboratory study highlights the key influences of stormwater sediment thickness and bioturbation by tubificid worms on dynamics of nutrients and pollutants in stormwater retention systems. Chemosphere, 72, 213–223.CrossRefGoogle ScholarPubMed
Meyer, J.L., Sale, M.J., Mulholland, P.J. and LeRoy Poff, N., 1999. Impacts of climate change on aquatic ecosystem functioning and health. J. Am. Water Res. Assoc., 35, 1373–1386.CrossRefGoogle Scholar
Monard, C., Vandenkoornhuyse, P., Le Bot, B., Binet, F., 2011. Relationship between bacterial diversity and function under biotic control: the soil pesticide degraders as a case study. ISME J., 5, 1048–1056.CrossRefGoogle ScholarPubMed
Morrice, J.A., Valett, H.M., Dahm, C.N. and Campana, M.E., 1997. Alluvial characteristics, groundwater–surface water exchange and hydrologic retention in headwater streams. Hydrol. Process., 11, 253–267.3.0.CO;2-J>CrossRefGoogle Scholar
Mulholland, P.J., Marzolf, E.R., Webster, J.R., Hart, D.R. and Hendricks, S.P., 1997. Evidence of hyporheic retention of phosphorus in Walker Branch. Limnol. Oceanogr., 42, 443–451.CrossRefGoogle Scholar
Nalepa, T.F., Fanslow, D.L. and Lang, G.A., 2009. Transformation of the offshore benthic community in Lake Michigan: recent shift from the native amphipod Diporeia spp. to the invasive mussel Dreissena rostriformis bugenis. Freshwater Biol., 54, 466–479.CrossRefGoogle Scholar
Navel, S., Mermillod-Blondin, F., Montuelle, B., Chauvet, E., Simon, L., Piscart, C. and Marmonier, P., 2010. Interactions between fauna and sediment characteristics control plant matter breakdown in river sediments. Freshwater Biol., 55, 753–766.CrossRefGoogle Scholar
Navel, S., Simon, L., Lecuyer, C., Fourel, F. and Mermillod-Blondin, F., 2011. The shredding activity of gammarids facilitates the processing of organic matter by the subterranean amphipod Niphargus rhenorhodanensis. Freshwater Biol., 56, 481–49.CrossRefGoogle Scholar
Navel, S., Mermillod-Blondin, F., Montuelle, B., Chauvet, E., Simon, L. and Marmonier, P., 2011. Water-sediment exchanges control microbial processes associated with leaf litter degradation in the hyporheic zone: a microcosm study., 61, 968–79.Google ScholarPubMed
Nicholls, J.C. and Trimmer, M., 2009. Widespread occurrence of the anammox reaction in estuarine sediments. Aquat. Microbiol. Ecol., 55, 105–113.CrossRefGoogle Scholar
Nikolcheva, L.G., Cockshutt, A.M. and Barlocher, F., 2003. Determining diversity of freshwater fungi on decaying leaves: Comparison of traditional and molecular approaches. Appl. Environ. Microbiol., 69, 2548–2554.CrossRefGoogle ScholarPubMed
Nogaro, G. and Mermillod-Blondin, F., 2009. Stormwater sediment and bioturbation influences on hydraulic functioning, biogeochemical processes, and pollutant dynamics in laboratory infiltration systems. Environ. Sci. Technol., 43, 3632–3638.CrossRefGoogle ScholarPubMed
Nogaro, G., Mermillod-Blondin, F., François-Carcaillet, F., Gaudet, J.P., Lafont, M. and Gibert, J., 2006. Invertebrate bioturbation can reduce the clogging of sediment: an experimental study using filtration sediment columns. Freshwater Biol., 51, 1458–1473.CrossRefGoogle Scholar
Nogaro, G., Mermillod-Blondin, F., Montuelle, B., Boisson, J.C., Lafont, M., Volat, B. and Gibert, J., 2007. Do tubificid worms influence organic matter processing and fate of pollutants in stormwater sediments deposited at the surface of infiltration systems? Chemosphere, 70, 315–328.CrossRefGoogle ScholarPubMed
Nogaro, G., Mermillod-Blondin, F., Valett, H.M., François-Carcaillet, F., Gaudet, J.P., Lafont, M. and Gibert, J., 2009. Ecosystem engineering at the sediment-water interface: bioturbation and consumer-substrate interaction. Oecologia, 161, 125–138.CrossRefGoogle ScholarPubMed
Nogaro, G., Datry, T., Mermillod-Blondin, F. and Montuelle, B., 2010. Influence of streambed sediment clogging on microbial processes in the hyporheic zone. Freshwater Biol., 55, 1288–1302.CrossRefGoogle Scholar
Ojanguren, A.F. and Braña, F., 2003. Thermal dependence of embryonic growth and development in brown trout. J. Fish Biol., 62, 580–590.CrossRefGoogle Scholar
Orghidan, T., 1959. Ein neuer Lebensraum des unterirdischen Wassers: Der hyporheische Biotop. Arch. Hydrobiol., 55, 392–414.Google Scholar
Orghidan, T., 2010. A new habitat of subsurface waters: the hyporheic biotope. Fundam. Appl. Limnol., 176, 291–302.CrossRefGoogle Scholar
Peyrard, D., Sauvage, S., Vervier, P., Sánchez-Pérez, J.M. and Quintard, M., 2008. A coupled vertically integrated model to describe lateral exchanges between surface and subsurface in large alluvial floodplains with a fully penetrating river. Hydrol. Process., 22, 4257–4273.CrossRefGoogle Scholar
Pinay, G. and Décamps, H., 1988. The role of riparian woods in regulating nitrogen fluxes between the alluvial aquifer and surface water: a conceptual model. Regul. Riv., 2, 507–516.CrossRefGoogle Scholar
Piscart, C., Moreteau, J.C. and Beisel, J.N., 2005. Biodiversity and structure of macroinvertebrate communities along a small permanent salinity gradient (Meurthe River, France). Hydrobiologia, 551, 227–236.CrossRefGoogle Scholar
Piscart, C., Genoel, R., Dolédec, S., Chauvet, E. and Marmonier, P., 2009. Effects of intense agricultural practices on heterotrophic processes in streams. Environ. Pollut., 157, 1011–1018.CrossRefGoogle ScholarPubMed
Piscart, C., Bergerot, B., Lafaille, P. and Marmonier, P., 2010. Are amphipod invaders a threat to regional biodiversity? Biol. Invasions, 12, 853–863.CrossRefGoogle Scholar
Piscart, C., Roussel, J.M., Dick, J.T.A., Grosbois, G. and Marmonier, P., 2011. Effects of coexistence on the habitat use and trophic ecology of interacting native and invasive amphipods. Freshwater Biol., 56, 325–334.CrossRefGoogle Scholar
Poole, G.C., Stanford, J.A., Running, S.W., Frissell, C.A., Woessner, W.W. and Ellis, B.K., 2004. A patch hierarchy approach to modeling surface and subsurface hydrology in complex flood-plain environments. Earth Surf. Process. Landforces, 29, 1259–1274.CrossRefGoogle Scholar
Poole, G.C., O'Daniel, S.J., Jones, K.L., Woessner, W.W., Bernhardt, E.S., Helton, A.M., Stanford, J.A., Boer, B.R. and Beechie, T.J., 2008. Hydrologic spiralling: the role of multiple interactive flow paths in stream ecosystems. River Res. Appl., 24, 1018–1031.CrossRefGoogle Scholar
Puig, M.A., Sabater, F. and Malo, J., 1990. Benthic and hyporheic faunas of mayflies and stoneflies in the Ter River Basin (NE-Spain). In: Campbell, I.C. (ed.), Mayflies and Stoneflies: Life Histories and Biology, Kluwer Academic Publishers, Dordrecht, 255–258.CrossRefGoogle Scholar
Riss, H.W., Meyer, E.I. and Niepagenkemper, O., 2008. A novel and robust device for repeated small-scale oxygen measurement in riverine sediments implications for advanced environmental surveys. Limnol. Oceanogr. Met., 6, 200–207.CrossRefGoogle Scholar
Robertson, A.L. and Wood, P.J., 2010. Ecology of the hyporheic zone: origins, current knowledge and future directions. Fundam. Appl. Limnol., 176, 279–289.CrossRefGoogle Scholar
Romani, A.M. and Sabater, S., 2001. Structure and activity of rock and sand biofilms in a Mediterranean stream. Ecology, 82, 3232–3245.CrossRefGoogle Scholar
Romani, A.M., Fischer, H., Mille-Lindblom, C. and Tranvik, L.J., 2006. Interactions of bacteria and fungi on decomposing litter: Differential extracellular enzyme activities. Ecology, 87, 2559–2569.CrossRefGoogle ScholarPubMed
Ryder, D.S., 2009. Responses of epixylic biofilm metabolism to water level variability in a regulated floodplain river. J. N. Am. J. Benthol. Soc., 23, 214–223.2.0.CO;2>CrossRefGoogle Scholar
Sabater, S., Butturini, A., Clement, J.C., Burt, T., Dowrick, D., Hesfting, M., Maitre, V., Pinay, G., Postolache, C., Rzepecki, M. and Sabater, F.N., 2003. Nitrogen removal by riparian buffers under various N loads along a European climatic gradient: patterns and factors of variation. Ecosystems, 6, 20–30.CrossRefGoogle Scholar
Sánchez-Pérez, J.M., Bouey, C., Sauvage, S., Teissier, S., Antigüedad, I. and Vervier, P., 2003a. A standardized method for measuring in situ denitrification in shallow aquifers: numerical validation and measurements in riparian wetlands. Hydrol. Earth Sci. Syst., 7, 87–96.CrossRefGoogle Scholar
Sánchez-Pérez, J.M., Vervier, P., Garabétian, F., Sauvage, S., Loubet, M., Rols, J.L., Bariac, T. and Weng, P., 2003b. Nitrogen dynamics in the shallow groundwater of a riparian wetland zone of the Garonne, Southwester France: nitrate inputs, bacterial densities, organic matter supply and denitrification measurements. Hydrol. Earth Sci. Syst., 7, 97–107.CrossRefGoogle Scholar
Sánchez-Pérez, J.M., Gerino, M., Sauvage, S., Dumas, P., Maneux, E., Julien, F., Winterton, P. and Vervier, P., 2009. Effects of nutrient pollution on in-stream nutrient retention in an agricultural watershed. Ann. Limnol. ‐ Int. J. Limnol., 45, 79–92.CrossRefGoogle Scholar
Schmid, P.E. and Schmid-Araya, J.M., 2010. Scale-dependent relations between bacteria, organic matter and invertebrates in a headwater stream. Fundam. Appl. Limnol., 176, 365–375.CrossRefGoogle Scholar
Sebilo, M., Billen, G., Grably, M. and Mariotti, A., 2003. Isotopic composition of nitrate–nitrogen as a marker of riparian and benthic denitrification at the scale of the whole Seine river system. Biogeochemistry, 63, 35–51.CrossRefGoogle Scholar
Sinsabaugh, R.L., Antibus, R.K., Linkins, A.E., McClaugherty, C.A., Rayburn, L., Repert, D. and Weiland, T., 1993. Wood decomposition – nitrogen  and  phosphorous dynamics in relation to extracellular enzyme activity. Ecology, 74, 1596–1593.CrossRefGoogle Scholar
Stanford, J.A. and Ward, J.V., 1988. The hyporheic habitat of river ecosystems. Nature, 335, 64–66.CrossRefGoogle Scholar
Strayer, D.L., 2010. Alien species in fresh waters: ecological effects, interactions with other stressors, and prospects for the future. Freshwat. Biol., 55 (Suppl. 1), 152–174.CrossRefGoogle Scholar
Taleb, A., Belaidi, N., Sanchez-Perez, J.M., Vervier, P., Sauvage, S. and Gagneur, J., 2008. The role of the hyporheic zone in the nitrogen dynamics within a semi-arid gravel bed stream located downstream of a heavily polluted reservoir (Tafna wadi, Algeria).  River Res. Appl., 24, 183–196.CrossRefGoogle Scholar
Thompson, R.C., Moschella, P.S., Jenkins, S.R., Norton, T.A. and Hawkins, S.J., 2005. Differences in photosynthetic marine biofilm between sheltered and moderately exposed rocky shores. Mar. Ecol. Prog. Ser., 296, 53–63.CrossRefGoogle Scholar
Tockner, K., Ward, J.V., Edwards, P.J. and Kollmann, J., 2002. Riverine landscapes: an introduction. Freshwater Biol., 47, 497–500.CrossRefGoogle Scholar
Tonina, D. and Buffington, J.M., 2009. Hyporheic Exchange in Mountain Rivers I: Mechanics and Environmental Effects. Geogr. Compass, 3, 1063–1086.CrossRefGoogle Scholar
Tringe, S.G., von Mering, C., Kobayashi, A., Salamov, A.A., Chen, K., Chang, H.W., Podar, M., Short, J.M., Mathur, E.J., Detter, J.C., Bork, P., Hugenholtz, P. and Rubin, E.M., 2005. Comparative metagenomics of microbial communities. Science, 308, 554–557.CrossRefGoogle ScholarPubMed
Valett, H.M., Morrice, J.A., Dahm, C.N. and Campana, M.E., 1996. Parent lithology, groundwater-surface water exchange and nitrate retention in headwater streams. Limnol. Oceanogr., 41, 333–345.CrossRefGoogle Scholar
Vandenkoornhuyse, P., Dufresne, A., Quaiser, A., Gouesbet, G., Binet, F., Francez, A.J., Mahé, S., Bormans, M., Lagadeuc, Y. and Couée, I., 2010. Integration of molecular functions at the ecosystemic level: breakthroughs and future goals of environmental genomics and post-genomics. Ecol. Lett., 13, 776–791.CrossRefGoogle ScholarPubMed
Vervier, P., Bonvallet-Garey, S., Sauvage, S., Maurice, V. and Sánchez-Pérez, J.M., 2009. Influence of the hyporheic zone on the phosphorus dynamics of a large gravel bed river, Garonne river, France. Hydrol. Process., 23, 1801–1812.CrossRefGoogle Scholar
Ward, J.V. and Voelz, N.J., 1994. Groundwater fauna of the South Platte River system, Colorado. In: Gilbert, J., Danielopol, D.L. and Stanford, J.A. (eds.), Groundwater Ecology, Academic Press, San Diego, 391–423.CrossRefGoogle Scholar
Weng, P., Sánchez-Pérez, J.M., Sauvage, S., Vervier, P. and Giraud, F., 2003. Assessment of the quantitative and qualitative buffer function of an alluvial wetland: Hydrological modelling of a large floodplain (Garonne River, France). Hydrol. Process., 17, 2375–2393.CrossRefGoogle Scholar
Werner, S. and Rothhaupt, K.O., 2007. Effects of the invasive bivalve Corbicula fluminea on settling juveniles and other benthic taxa. J. N. Am. Benthol. Soc., 26, 673–680.CrossRefGoogle Scholar
Williams, D.D. and Hynes, H.B.N., 1974. The occurrence of benthos deep in the substratum of a stream. Freshwater Biol., 4, 233–256.CrossRefGoogle Scholar
Williams, D.D. and Hynes, H.B.N., 1976. The recolonization mechanisms of stream benthos. Oikos, 27, 265–272.CrossRefGoogle Scholar
Williams, J.B., Mills, G., Bamhurst, D., Southern, S. and Garvin, N., 2009. Transport and degradation of a trichloroethylene plume within a stream hyporheic zone. Proc. 2007 Nat. Conf. Environ. Sci. Tech., 4, 189–194.CrossRefGoogle Scholar
Woessner, W.W., 2000. Stream and fluvial plain ground water interactions: rescaling hydrogeologic thought. Ground Water, 38, 423–429.CrossRefGoogle Scholar
Wood, P.J., Gunn, J., Smith, H. and Abas-Kutty, A., 2005. Flow permanence and macroinvertebrate community diversity within groundwater dominated headwater streams and springs. Hydrobiologia, 545, 55–64.CrossRefGoogle Scholar
Wood, P.J., Boulton, A.J., Little, S. and Stubbington, R., 2010. Is the hyporheic zone a refugium for macroinvertebrates during severe low flow conditions? Fundam. Appl. Limnol., 176, 377–390.CrossRefGoogle Scholar