280
Views
12
CrossRef citations to date
0
Altmetric
Original Articles

Organic Carbon Degradation in Anoxic Organic-Rich Shelf Sediments: Biogeochemical Rates and Microbial Abundance

, , &
Pages 303-314 | Received 29 Jul 2009, Accepted 05 Oct 2009, Published online: 26 May 2010

REFERENCES

  • Albert , D B and Martens , C S . 1997 . Determination of low-molecular-weight organic acid concentrations in seawater and pore-water samples via HPLC . Mar Chem , 56 : 27 – 37 .
  • Alderkamp , A-C , Nejstgaard , J C , Verity , P G , Zirbel , M J , Sazhin , A F and Rijssel , M . 2006 . Dynamics in carbohydrate composition of Phaeocystis pouchetii colonies during spring blooms in mecocosm . J Sea Res , 55 : 169 – 181 .
  • Alderkamp , A-C , Rijssel , M and Bolhuis , H . 2007 . Characterization of marine bacteria and the activity of their enzyme systems involved in degradation of the algal storage glucan laminarin . FEMS Microbiol Ecol , 59 : 108 – 117 .
  • Alperin , M A , Martens , C S , Albert , D B , Suayah , I B , Benninger , L K , Blair , N E and Jahnke , R A . 1999 . Benthic fluxes and pore water concentration profiles of dissolved organic carbon in sediments from the North Carolina continental slope . Geochim Cosmochim Acta , 63 : 427 – 448 .
  • Amann , R I , Binder , B J , Olson , R J , Chisholm , S W , Devereux , R and Stahl , D A . 1990 . Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations . Appl Environ Microbiol , 56 : 1919 – 1925 .
  • Antranikian , G . 1992 . “ Microbial degradation of starch ” . In Microbial degradation of natural products , Edited by: Winkelmann , G . Vol. 2 , 28 – 50 . Weilheim : VCH .
  • Arnosti , C . 2004 . Speed bumps and barricades in the carbon cycle: substrate structural effects on carbon cycling . Mar Chem , 92 : 263 – 273 .
  • Arnosti , C . 2003 . Fluorescent derivatization of polysaccharides and carbohydrate-containing biopolymers for measurement of enzyme activities in complex media . J Chromatog B , 793 : 181 – 191 .
  • Arnosti , C . 1995 . Measurement of depth- and site-related differences in polysaccharide hydrolysis rates in marine sediments . Geochim Cosmochim Acta , 59 : 4247 – 4257 .
  • Arnosti , C , Finke , N , Larsen , O and Ghobrial , S . 2005 . Anoxic carbon degradation in Arctic sediments: Microbial transformations of complex substrates . Geochim Cosmochim Acta , 69 : 2309 – 2320 .
  • Arnosti , C and Holmer , M . 2003 . Carbon cycling in a continental margin sediment: contrasts between organic matter characteristics and remineralization rates and pathways . Estuar Coast Shelf Sci , 58 : 197 – 208 .
  • Arnosti , C and Holmer , M . 1999 . Carbohydrate dynamics and contributions to the carbon budget of an organic-rich coastal sediment . Geochim Cosmochim Acta , 63 : 393 – 403 .
  • Arnosti , C and Jørgensen , B B . 2006 . Organic carbon degradation in Arctic marine sediments, Svalbard: A comparison of initial and terminal steps . J Geomicrobiol , 23 : 551 – 563 .
  • Arnosti , C and Repeta , D J . 1994 . Extracellular enzyme activity in anaerobic bacterial cultures: Evidence of pullulanase activity among mesophilic marine bacteria . Appl Environ Microbiol , 60 : 840 – 846 .
  • Baty , A M III , Eastburn , C C , Diwu , Z , Techkarnjanaruk , S , Goodman , A E and Geesey , G G . 2000 . Differentiation of chitinase-active and non-chitinase-active subpopulations of a marine bacterium during chitin degradation . Appl Environ Microbiol , 66 : 3566 – 3573 .
  • Benner , R and Strom , M . 1993 . A critical-evaluation of the analytical blank associated with DOC measurements by high-temperature catalytic-oxidation . Mar Chem , 41 : 153 – 160 .
  • Bold , H C and Wynne , M J . 1985 . Introduction to the Algae , Englewood Cliffs, NJ : Prentice Hall .
  • Brüchert , V , Pérez , M E and Lange , C B . 2000 . Coupled primary production, benthic foraminiferal assemblage, and sulfur diagenesis in organic-rich sediments of the Benguela upwelling system . Mar Geol , 163 : 27 – 40 .
  • Brüchert , V , Currie , B , Peard , K R , Lass , U , Endler , R , Dübecke , A , Julies , E , Leipe , T and Zitzmann , S . 2006 . “ Shelf anoxia in the Namibian coastal upwelling system. Biogeochemical and physical control on shelf anoxia and water column hydrogen sulphide in the Benguela coastal upwelling system off Namibia ” . In and present water column anoxia , NATO Science Series Edited by: Neretin , L , Jørgensen , B B and Murray , J . 161 – 193 . Kluwer Springer .
  • Brüchert , V , Jørgensen , B B , Neumann , K , Riechmann , D , Schlösser , M and Schulz , H . 2003 . Regulation of bacterial sulfate reduction and hydrogen sulfide fluxes in the central Namibian coastal upwelling zone . Geochim Cosmochim Acta , 67 : 4505 – 4518 .
  • Burdige , D J , Skoog , A and Gardner , K . 2000 . Dissolved and particulate carbohydrates in contrasting marine sediments . Geochim Cosmochim Acta , 64 : 1029 – 1041 .
  • Burdige , D J . 2007 . Preservation of organic matter in marine sediments: Controls, mechanisms, and an imbalance in sediment organic carbon budgets . Chem Rev , 107 : 467 – 485 .
  • Carr , M E . 2002 . Estimation of potential productivity in Eastern boundary currents using remote sensing . Deep Sea Res , 49 : 59 – 80 .
  • Chaplin , M F and Kennedy , J F . 1986 . Carbohydrate analysis: A practical approach , IRL Press .
  • Clark , D P . 1989 . The fermentation pathways of Escherichia-Coli . FEMS Microbiol Rev , 63 : 223 – 234 .
  • Eilers , H , Pernthaler , J , Glockner , F O and Amann , R . 2000 . Culturability and in situ abundance of pelagic bacteria from the North Sea . Appl Environ Microbiol , 66 : 3044 – 3051 .
  • Fuchs , B M , Spring , S , Teeling , H , Quast , C , Wulf , J , Schattenhofer , M , Yan , S , Ferriera , S , Johnson , J , Glöckner , F O and Amann , R . 2007 . Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis . PNAS , 104 : 2891 – 2896 .
  • Fuchs , B M , Zubkov , M V , Sahm , K , Burkill , P H and Amann , R . 2000 . Changes in community composition during dilution cultures of marine bacterioplankton as assessed by flow cytometric and molecular biological techniques . Appl Environ Microbiol , 2 : 191 – 201 .
  • Hoehler , T M , Alperin , M J , Albert , D B and Martens , C S . 1998 . Thermodynamic control on hydrogen concentrations in anoxic sediments . Geochim Cosmochim Acta , 62 : 1745 – 1756 .
  • Hoppe , H G , Arnosti , C and Herndl , G F . 2002 . “ Ecological significance of bacterial enzymes in the marine environment ” . In Enzymes in the Environment. Activity, Ecology and Applications , Edited by: Burns , R G and Dick , R P . 73 – 108 . Marcel Dekker, Inc. .
  • Inthorn , M , Wagner , T , Scheeder , G and Zabel , M . 2006 . Lateral transport controls distribution, quality and burial of organic matter along continental slopes in high-productive areas . Geology , 34 : 205 – 208 .
  • Jahnke , R A . 1990 . Early diagenesis and recycling of biogenic debris at the seafloor, Santa Monica Basin, California . J Mar Res , 48 : 413 – 436 .
  • Jørgensen , B B . 1978 . A comparison of methods for the quantification of bacterial sulfate reduction in coastal marine sediments . J Geomicrobiol , 1 : 11 – 27 .
  • Kallmeyer , J , Ferdelman , T G , Weber , A , Fossing , H and Jørgensen , B B . 2004 . A cold chromium distillation procedure for radiolabeled sulfide applied to sulfate reduction measurements . Limnol Oceanogr Meth , 2 : 171 – 180 .
  • Kirchman , D L . 2002 . The ecology of Cytophaga-Flavobacteria in aquatic environments . FEMS Microbiol Ecol , 39 : 91 – 100 .
  • Manz , W , Eisenbrecher , M , Neu , T R and Szewzyk , U . 1998 . Abundance and spatial organization of Gram-negative sulfate-reducing bacteria in activated sludge investigated by in situ probing with specific 16S rRNA targeted oligonucleotides . FEMS Microbiol Ecol , 25 : 43 – 61 .
  • Manz , W , Amann , R , Ludwig , W , Wagner , M and Schleifer , K H . 1992 . Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria: problems and solutions . Syst Appl Microbiol , 15 : 593 – 600 .
  • Mayer , L M . 1989 . Extracellular proteolytic enzyme activity in sediments of an intertidal mudflat . Limnol Oceanogr , 34 : 973 – 981 .
  • Musat , N , Werner , U , Knittel , K , Kolb , S , Dodenhof , T , van Beusekom , J EE , de Beer , D , Dubilier , N and Amann , R . 2006 . Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea . Syst Appl Microbiol , 29 : 333 – 348 .
  • Mussmann , M , Schulz , H N , Strotmann , B , Kjaer , T , Nielsen , L P , Rosselló-Mora , R A , Amann , R and Jørgensen , B B . 2003 . Phylogeny and distribution of nitrate-storing Beggiatoa spp. in coastal marine sediments . Environ Microbiol , 5 : 523 – 533 .
  • Pallud , C and van Cappellen , P . 2006 . Kinetics of microbial sulfate reduction in estuarine sediments . Geochim Cosmochim Acta , 70 : 1148 – 1162 .
  • Parkes , R J , Gibson , G R , Mueller-Harvey , I , Buckingham , W J and Herbert , R A . 1989 . Determination of the substrates for sulphate-reducing bacteria within marine and estuarine sediments with different rates of sulphate reduction . J Microbiol , 135 : 175 – 187 .
  • Parkes , R J , Cragg , B A , Banning , N , Brock , F , Webster , G , Fry , J C , Hornibrook , E , Pancost , R D , Kelly , S , Knab , N , Jørgensen , B B , Rina , J and Weightman , A J . 2007 . Biogeochemistry and diversity of methane cycling in subsurface marine sediments (Skaggerak, Denmark) . Environ Microbiol , 9 : 1146 – 1161 .
  • Pernthaler , A , Prenthaler , J and Amann , R . 2002 . Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria . Appl Environ Microbiol , 68 : 3094 – 3101 .
  • Porter , K G and Feig , Y S . 1980 . The use of DAPI for identifying and counting aquatic microflora . Limnol Oceanogr , 25 : 943 – 948 .
  • Reeburgh , W S . 1967 . An improved interstitial water sampler . Limnol Oceanogr , 12 : 163
  • Rosselló-Mora , R , Thamdrup , B , Schafer , H , Weller , R and Amann , R . 1999 . The response of the microbial community of marine sediments to organic carbon input under anaerobic conditions . Syst Appl Microbiol , 22 : 237 – 248 .
  • Sahm , K , Knoblauch , C and Amann , R . 1999 . Phylogenetic affiliation and quantification of psychrophilic sulfate-reducing isolates in marine arctic sediments . Appl Environ Microbiol , 65 : 3976 – 3981 .
  • Simon , M , Glöckner , F O and Amann , R . 1999 . Different community structure and temperature optima of heterotrophic picoplankton in various regions of the Southern Ocean . Aquat Microb Ecol , 18 : 275 – 284 .
  • Sørensen , J , Christensen , D and Jørgensen , B B . 1981 . Volatile fatty acids and hydrogen as substrates for sulfate-reducing bacteria in anaerobic marine sediment . Appl Environ Microbiol , 42 : 5 – 11 .
  • Stahl , D A and Amann , R . 1991 . “ Development and application of nucleic acid probes in bacterial systematics ” . In Nucleic Acid Techniques in Bacterial Systematics , Edited by: Stackebrandt , E and Goodfellow , M . 205 – 248 . New York : John Wiley & Sons Ltd .
  • Struck , U , Altenbach , A V , Emeis , E C , Alheit , J , Eichner , C and Schneider , R . 2002 . Changes in the upwelling rates of nitrate preserved in the δ15N-signature of sediments and fish scales from the diatomaceous mud belt of Namibia . Geobios , 35 : 3 – 11 .
  • Wainwright , M . 1981 . Assay and properties of alginate lyase and 1,3-b-glucanase in intertidal sands . Plant Soil , 59 : 83 – 89 .
  • Wallner , G , Amann , R and Beisker , W . 1993 . Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms . Cytometry , 14 : 136 – 143 .
  • Weller , R , Glöckner , F O and Amann , R . 2000 . 16S rRNA-targeted oligonucleotide probes for the in situ detection of members of the phylum Cytophaga-Flavobacterium-Bacteroides . System Appl Microbiol , 23 : 107 – 114 .
  • Ziervogel , K , Karlsson , E and Arnosti , C . 2007 . Surface associations of enzymes and organic matter: Consequences for hydrolytic activity and organic matter remineralization in marine systems . Mar Chem , 104 : 241 – 252 .

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.