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A River's Liver – Microbial Processes within the Hyporheic Zone of a Large Lowland River

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Abstract

Little is known on microbial activities in the sediments of large lowland rivers despite of their potentially high influence on biogeochemical budgets. Based on field measurements in a variety of sedimentary habitats typical for a large lowland river (Elbe, Germany), we present results on the abundance and production of sedimentary bacteria, the potential activity of a set of extracellular enzymes, and potential nitrification and denitrification rates. A diving bell was used to access the sediments in the central river channel, enabling us to sample down to 1 m sediment depth. Depth gradients of all measures of microbial activity were controlled by sediment structure, hydraulic conditions, as well as by the supply with organic carbon and nitrogen. Microbial heterotrophic activity was tightly coupled with the availability of carbon and nitrogen, whereas chemolithotrophic activity (nitrification rate) was related to the available surface area of particles. In the central bed of the river, bacterial production and extracellular enzyme activity remained high down to the deepest sediment layers investigated. Due to the large inner surface area and their connectivity with the surface water, the shifting sediments in the central channel of the river were microbially highly active There, vertically integrated bacterial production amounted to 0.95 g C m−3 h−1, which was 2.9 to 5.5 times higher than in the nearshore habitats. We conclude that carbon and nitrogen cycling in the river is controlled by the live sediments of the central river channel, which thus represent a “liver function” in the river's metabolism.

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References

  • R.B. Alexander R.A. Smith G.E. Schwarz (2000) ArticleTitleEffect of stream channel size on the delivery of nitrogen to the Gulf of Mexico Nature 403 758–761 Occurrence Handle10.1038/35001562

    Article  Google Scholar 

  • J.D. Allan (1995) Stream Ecology. Structure and Function of Running Waters Chapman & Hall London

    Google Scholar 

  • M.A. Baker C. Dahm H.M. Valett (1999) ArticleTitleAcetate retention and metabolism in the hyporheic zone of a mountain stream Limnol. Oceanogr. 44 1530–1539

    Google Scholar 

  • D. Bastviken J. Ejlertsson L. Tranvik (2001) ArticleTitleSimilar bacterial growth on dissolved organic matter in anoxic and oxic lake water Aquat. Microb. Ecol. 24 41–49

    Google Scholar 

  • D. Bastviken M. Olsson L. Tranvik (2003) ArticleTitleSimultaneous measurements of bacterial production and organic carbon mineralization in oxic and anoxic lake sediments Microb. Ecol. 46 73–82 Occurrence Handle10.1007/s00248-002-1061-9

    Article  Google Scholar 

  • T.J. Battin (2000) ArticleTitleHydrodynamics is a major determinant of streambed biofilm activity: from the sediment to the reach scale Limnol. Oceanogr. 45 1308–1319

    Google Scholar 

  • H. Behrendt D. Opitz (1999) ArticleTitleRetention of nutrients in river systems: dependence on specific runoff and hydraulic load Hydrobiologia 410 111–122 Occurrence Handle10.1023/A:1003735225869

    Article  Google Scholar 

  • L.W. Belser E.L. Mays (1980) ArticleTitleSpecific inhibition of nitrite oxidation by chlorate and its use in assessing nitrification in soil and sediments Appl. Environ. Microbiol. 39 505–510

    Google Scholar 

  • R. Benner J. Lay E. K'nees R.E. Hodson (1988) ArticleTitleCarbon conversion efficiency for bacterial growth on lignocellulose: implications for detritus-based food webs Limnol. Oceanogr. 33 1514–1526

    Google Scholar 

  • C. Bou R. Rouch (1967) ArticleTitleUn nouveau champ de recherches sur la faune aquatique souterraine Comptes Rendus Académie des Sciences Paris 265 369–370

    Google Scholar 

  • M. Brunke H. Fischer (1999) ArticleTitleHyporheic bacteria – relationships to environmental gradients and invertebrates in a prealpine stream Arch. Hydrobiol. 146 189–217

    Google Scholar 

  • M. Brunke T. Gonser (1997) ArticleTitleThe ecological significance of exchange processes between rivers and groundwaters Freshwat. Biol. 377 1–33

    Google Scholar 

  • M. Brunke A. Sukhodolov H. Fischer S. Wilczek C. Engelhardt M. Pusch (2002) ArticleTitleBenthic and hyporheic habitats of a large lowland river (ElbeGermany): influence of river engineering Verh. Internat. Verein. Limnol. 28 153–156

    Google Scholar 

  • P.A. Carling J.J. Williams E. Gölz A.D. Kelsey (2000) ArticleTitleThe morphodynamics of fluvial sand dunes in the River Rhinenear Mainz, Germany. II. Hydrodynamics and sediment transport Sedimentology 47 253–278

    Google Scholar 

  • K.R. Chappell R. Goulder (1994) ArticleTitleSeasonal variation of epilithic extracellular enzyme activity in three diverse headstreams Arch. Hydrobiol. 130 195–214

    Google Scholar 

  • R.J. Chrost (1991) Environmental control of the synthesis and activity of aquatic microbial ectoenzymes R.J. Chrost (Eds) Microbial Enzymes in Aquatic Environments Springer New York 42–50

    Google Scholar 

  • M. Church (2002) ArticleTitleGeomorphic thresholds in riverine landscapes Freshwat. Biol. 47 541–558

    Google Scholar 

  • Dahlke S. and Remde A. 1998. Denitrifikation. In: Vereinigung für Allgemeine und Angewandte Mikrobiologie (VAAM) (ed), Mikrobiologische Charakterisierung aquatischer Sedimente: Methodensammlung. R. Oldenbourg Verlag, München, pp. 122–140.

  • C.N. Dahm N.B. Grimm P. Marmonier H.M. Valett P. Vervier (1998) ArticleTitleNutrient dynamics at the interface between surface waters and groundwaters Freshwat. Biol. 40 427–451

    Google Scholar 

  • InstitutionalAuthorNameDEW (1985) Deutsche Einheitsverfahren zur Wasser-, Abwasser- und Schlammuntersuchung Verlag Chemie Weinheim

    Google Scholar 

  • A.H. Elliott N.H. Brooks (1997) ArticleTitleTransfer of nonsorbing solutes to a streambed with bed forms: theory Water Resour. Res. 33 123–136

    Google Scholar 

  • H. Fischer M. Pusch (1999) ArticleTitleUse of the [14C]leucine incorporation technique to measure bacterial production in river sediments and the epiphyton Appl. Environ. Microbiol. 65 4411–4418

    Google Scholar 

  • H. Fischer M. Pusch (2001) ArticleTitleComparison of bacterial production in sediments, epiphyton, and the pelagic zone of a lowland river Freshwat. Biol. 46 1335–1348

    Google Scholar 

  • H. Fischer A. Sukhodolov S. Wilczek C. Engelhardt (2003) ArticleTitleEffects of flow dynamics and sediment movement on microbial activity in a lowland river River Res. Appl. 19 473–482

    Google Scholar 

  • H. Fischer S.C. Wanner M. Pusch (2002) ArticleTitleBacterial abundance and production in river sediments as related to the biochemical composition of particulate organic matter (POM) Biogeochemistry 61 37–55 Occurrence Handle10.1023/A:1020298907014

    Article  Google Scholar 

  • S.G. Fisher N.B. Grimm E. Marti R.M. Holmes J.B. Jones (1998) ArticleTitleMaterial spiraling in stream corridors: a telescoping ecosystem model Ecosystems 1 19–34 Occurrence Handle10.1007/s100219900003

    Article  Google Scholar 

  • R. García-Ruiz S.N. Pattinson B.A. Whitton (1998) ArticleTitleDenitrification in river sediments: relationship between process rate and properties of water and sediment Freshwat. Biol. 39 467–476

    Google Scholar 

  • A. Gieseke U. Purkhold M. Wagner R. Amann A. Schramm (2001) ArticleTitleCommunity structure and activity dynamics of nitrifying bacteria in a phosphate-removing biofilm Appl. Environ. Microbiol. 67 1351–1362 Occurrence Handle10.1128/AEM.67.3.1351-1362.2001

    Article  Google Scholar 

  • L.O. Hedin J.C. von Fischer N.E. Ostrom B.P. Kennedy M.G. Brown G.P. Robertson (1998) ArticleTitleThermodynamic constraints on nitrogen transformations and other biogeochemical processes at soil-stream interfaces Ecology 79 684–703

    Google Scholar 

  • S.R. Hinkle J.H. Duff F.J. Triska A. Laenen E.B. Gates K.E. Bencala D.A. Wentz S.R. Silva (2001) ArticleTitleLinking hyporheic flow and nitrogen cycling near the Willamette River - a large river in Oregon, USA J. Hydrol. 244 157–180 Occurrence Handle10.1016/S0022-1694(01)00335-3

    Article  Google Scholar 

  • H.-G. Hoppe (1993) Use of fluorogenic model substrates for extracellular enzyme activity (EEA) measurement of bacteria P.F. Kemp B.F. Sherr E.B. Sherr (Eds) Handbook of Methods in Aquatic Microbial Ecology Lewis Publishers Boca Raton 423–431

    Google Scholar 

  • L.A. Kaplan T.L. Bott (1989) ArticleTitleDiel fluctuations in bacterial activity on streambed substrata during vernal algal blooms: Effects of temperaturewater chemistry, and habitat Limnol. Oceanogr. 34 718–733

    Google Scholar 

  • L.A. Kaplan J.D. Newbold (2003) The role of monomers in stream ecosystem metabolism S.E.G. Findlay R.L. Sinsabaugh (Eds) Aquatic Ecosystems. Interactivity of Dissolved Organic Matter Academic Press San Diego 97–119

    Google Scholar 

  • D.L. Kirchman (1993) Leucine incorporation as a measure of biomass production by heterotrophic bacteria P.F. Kemp B.F. Sherr E.B. Sherr (Eds) Handbook of Methods in Aquatic Microbial Ecology Lewis Publishers Boca Raton 509–512

    Google Scholar 

  • E. Kristensen S.I. Ahmed A.H. Devol (1995) ArticleTitleAerobic and anaerobic decomposition of organic matter in marine sediment: which is fastest? Limnol. Oceanogr. 40 1430–1437

    Google Scholar 

  • S. Lefebvre P. Marmonier G. Pinay (2004) ArticleTitleStream regulation and nitrogen dynamics in sediment interstices: comparison of natural and straightened sectors of a third-order stream River Res. Applic. 20 499–512 Occurrence Handle10.1002/rra.765

    Article  Google Scholar 

  • J. Marxsen (2001) ArticleTitleBacterial production in different streambed habitats of an upland stream: sandy versus coarse gravelly sediments Arch. Hydrobiol. 152 543–565

    Google Scholar 

  • J. Marxsen D.M. Fiebig (1993) ArticleTitleUse of perfused cores for evaluating extracellular enzyme-activity in stream-bed sediments FEMS Microbiol. Ecol. 13 1–11

    Google Scholar 

  • Marxsen J., Tippmann P., Heininger P., Preuß G. and Remde A. 1998. Enzymaktivität. In: Vereinigung für Allgemeine und Angewandte Mikrobiologie (VAAM) (ed), Mikrobiologische Charakterisierung aquatischer Sedimente: Methodensammlung. R. Oldenbourg Verlag, München, pp. 87–114.

  • M.A. Moran W.M. Sheldon SuffixJr J.E. Sheldon (1999) ArticleTitleBiodegradation of riverine dissolved organic carbon in five estuaries of the southeastern United States Estuaries 22 55–64

    Google Scholar 

  • D. Patureau E. Zumstein J.P. Delgenes R. Moletta (2000) ArticleTitleAerobic denitrifiers from diverse natural and managed ecosystems Microb. Ecol. 39 145–152 Occurrence Handle10.1007/s002480000009

    Article  Google Scholar 

  • K.G. Porter Y.S. Feig (1980) ArticleTitleThe use of DAPI for identifying and counting aquatic microflora Limnol. Oceanogr. 25 943–948

    Google Scholar 

  • M. Pusch D. Fiebig I. Brettar H. Eisenmann B.K. Ellis L.A. Kaplan M.A. Lock M.W. Naegeli W. Traunspurger (1998) ArticleTitleThe role of micro-organisms in the ecological connectivity of running waters Freshwat. Biol. 40 453–495

    Google Scholar 

  • P.A. Raymond J.E. Bauer (2001) ArticleTitleRiverine export of aged terrestrial organic matter to the North Atlantic Ocean Nature 409 497–500 Occurrence Handle10.1038/35054034

    Article  Google Scholar 

  • W.B. Richardson E.A. Strauss L.A. Bartsch E.M. Monroe J.C. Cavanaugh L. Vingum D.M. Soballe (2004) ArticleTitleDenitrification in the Upper Mississippi River: rates, controls, and contribution to nitrate flux Can. J. Fish. Aquat. Sci. 61 1102–1112 Occurrence Handle10.1139/f04-062

    Article  Google Scholar 

  • A. Romaní J. Marxsen (2002) ArticleTitleExtracellular enzymatic activities in epilithic biofilms of the Breitenbach: microhabitat differences Arch. Hydrobiol. 155 541–555

    Google Scholar 

  • J.C. Rutherford G.J. Latimer R.K. Smith (1993) ArticleTitleBedform mobility and benthic oxygen uptake Wat. Res. 27 1545–1558 Occurrence Handle10.1016/0043-1354(93)90099-4

    Article  Google Scholar 

  • W. Sauer A. Schmidt (2001) ArticleTitleDie Bedeutung suspendierten Sandes für die Sohlhöhenentwicklung der Elbe Wasserwirtschaft 91 443–449

    Google Scholar 

  • S.P. Seitzinger L.P. Nielsen J. Caffrey P.B. Christensen (1993) ArticleTitleDenitrification measurements in aquatic sediments: a comparison of three methods Biogeochemistry 23 147–167 Occurrence Handle10.1007/BF00023750

    Article  Google Scholar 

  • S.P. Seitzinger R.V. Styles E.W. Boyer R.B. Alexander B. Gillen R.W. Howarth B. Mayer N. van Breemen (2002) ArticleTitleNitrogen retention in rivers: model development and application to watersheds in the northeastern USA Biogeochemistry 57 IssueID58 99–237

    Google Scholar 

  • R.W. Sheibley J.H. Duff A.P. Jackman F.J. Triska (2003) ArticleTitleInorganic nitrogen transformations in the bed of the Shingobee RiverMinnesota: Integrating hydrologic and biological processes using sediment perfusion cores Limnol. Oceanogr. 48 1129–1140 Occurrence Handle10.4319/lo.2003.48.3.1129

    Article  Google Scholar 

  • M. Simon F. Azam (1989) ArticleTitleProtein content and protein synthesis rates of planktonic marine bacteria Mar. Ecol. Prog. Ser. 51 201–213

    Google Scholar 

  • R.L. Sinsabaugh S. Findlay (1995) ArticleTitleMicrobial production, enzyme activity, and carbon turnover in surface sediments of the Hudson River Estuary Microbial Ecol. 30 127–141 Occurrence Handle10.1007/BF00172569

    Article  Google Scholar 

  • R.L. Sinsabaugh A.E. Linkins (1988) ArticleTitleExoenzyme activity associated with lotic epilithon Freshwat. Biol. 20 249–261

    Google Scholar 

  • W.V. Sobczak S. Findlay S. Dye (2003) ArticleTitleRelationships between DOC bioavailability and nitrate removal in a mountain stream: an experimental approach Biogeochemistry 62 309–327 Occurrence Handle10.1023/A:1021192631423

    Article  Google Scholar 

  • J. Sørensen (1978) ArticleTitleDenitrification rates in a marine sediment as measured by the acetylene inhibition technique Appl. Environ. Microbiol. 36 139–143

    Google Scholar 

  • J.A. Stanford J.V. Ward (1993) ArticleTitleAn ecosystem perspective of alluvial rivers: connectivity and the hyporheic corridor J. N. Am. Benthol. Soc. 12 48–60

    Google Scholar 

  • R.G. Storey R.R. Fulthorpe D.D. Williams (1999) ArticleTitlePerspectives and predictions on the microbial ecology of the hyporheic zone Freshwat. Biol. 41 119–130

    Google Scholar 

  • E.A. Strauss G.A. Lamberti (2000) ArticleTitleRegulation of nitrification in aquatic sediments by organic carbon Limnol. Oceanogr. 45 1854–1859 Occurrence Handle10.4319/lo.2000.45.8.1854

    Article  Google Scholar 

  • J.H. Thorp M.D. Delong (2002) ArticleTitleDominance of autochthonous autotrophic carbon in food webs of heterotrophic rivers Oikos 96 543–550 Occurrence Handle10.1034/j.1600-0706.2002.960315.x

    Article  Google Scholar 

  • J.M. Tiedje (1988) Ecology of denitrification and dissimilatory nitrate reduction to ammonium A.J.M. Zehnder (Eds) Biology of anaerobic bacteria Wiley New York 179–244

    Google Scholar 

  • C.R. Townsend (1996) ArticleTitleConcepts in river ecology: pattern and process in the catchment hierarchy Arch. Hydrobiol. Suppl. 113 IssueIDLarge Rivers 10 3–21

    Google Scholar 

  • R.L. Vannote G.W. Minshall K.W. Cummins J.R. Sedell C.E. Cushing (1980) ArticleTitleThe river continuum concept Can. J. Fish. Aquat. Sci. 37 130–137 Occurrence Handle10.1139/f80-017

    Article  Google Scholar 

  • P. Vervier M. Dobson G. Pinay (1993) ArticleTitleRole of interaction zones between surface and ground waters in DOC transport and processing: considerations for river restoration Freshwat. Biol. 29 275–284

    Google Scholar 

  • J.V. Ward (1989) ArticleTitleThe four-dimensional nature of lotic ecosystems J. N. Am. Benthol. Soc. 8 2–8

    Google Scholar 

  • J.V. Ward K. Tockner U. Uehlinger F. Malard (2001) ArticleTitleUnderstanding natural patterns and processes in river corridors as the basis for effective river restoration Regul. Rivers: Res. Manage. 17 311–323

    Google Scholar 

  • J.R. Webster J.L. Meyer (1997) ArticleTitleOrganic matter budgets for streams: a synthesis J. N. Am. Benthol. Soc. 16 141–161

    Google Scholar 

  • S. Wilczek H. Fischer M. Brunke M.T. Pusch (2004) ArticleTitleMicrobial activity within a subaqueous dune in a large lowland river (ElbeGermany) Aquat. Microb. Ecol. 36 83–97

    Google Scholar 

  • Wilczek S., Fischer H. and Pusch M.T. in press. Regulation and seasonal dynamics of extracellular enzyme activities in the sediments of a large lowland river. Microb. Ecol. (in press).

  • Wolff C. and Remde A. 1998. Autotrophe Nitrifikation. In: Vereinigung für Allgemeine und Angewandte Mikrobiologie (ed), Mikrobiologische Charakterisierung aquatischer Sedimente: Methodensammlung. R. Oldenbourg Verlag, München, pp. 156–170.

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Authors and Affiliations

  1. Institute of Freshwater Ecology and Inland Fisheries, Muggelseedamm 301, 12587, Berlin, Germany

    Helmut Fischer, Sabine Wilzcek & Martin T Pusch

  2. Federal Institute of Hydrology, Am Mainzer Tor 1, Koblenz, 56068, Germany

    Helmut Fischer

  3. Institute of Microbiology, Dresden University of Technology, Mommsenstr. 13, 01062, Dresden, Germany

    Frank Kloep

  4. Boehringer Ingelheim Pharma, Binger Str. 173, 55216, Ingelheim, Germany

    Frank Kloep

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  1. Helmut Fischer
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  4. Martin T Pusch
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Correspondence to Helmut Fischer.

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Fischer, H., Kloep, F., Wilzcek, S. et al. A River's Liver – Microbial Processes within the Hyporheic Zone of a Large Lowland River. Biogeochemistry 76, 349–371 (2005). https://doi.org/10.1007/s10533-005-6896-y

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