• [1]
    Parkes, R.J. (1987) Analysis of microbial communities within sediments using biomarkers. In: Ecology of Microbial Communities (Hetcher, M., Gray, R.T.G. and Jones, J.G., Eds.), pp. 147–177. Cambridge University Press, Cambridge.
  • [2]
    Tunlid, A. and White, D.C. (1992) Biochemical analysis of biomass, community structure, nutritional status, and metabolic activity of microbial communities in soil. In: Soil Biochemistry (Bollag, J.M. and Stotzky, G., Eds.), pp. 229–262. Marcel Dekker, New York.
  • [3]
    Hayes, J.M., Freeman, K.H., Popp, B.N., Hoham, C.H. (1990) Compound-specific isotope analysis: a novel tool for reconstruction of ancient biogeochemical processes. Org. Geochem. 16, 11151128.
  • [4]
    Brenna, J.T., Corso, T.N., Tobias, H.J., Caimi, R.J. (1997) High-precision continuous-flow isotope ratio mass spectrometry. Mass Spectrom. Rev. 16, 227258.
  • [5]
    Boschker, H.T.S., Nold, S.C., Wellsbury, P., Bos, D., de Graaf, W., Pel, R., Parkes, R.J., Cappenberg, T.E. (1998) Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature 392, 801805.
  • [6]
    Hinrichs, K.U., Hayes, J.M., Sylva, S.P., Brewer, P.G., Delong, E.F. (1999) Methane-consuming archaebacteria in marine sediments. Nature 398, 802805.
  • [7]
    Pelz, O., Tesar, M., Wittich, R.M., Moore, E.R.B., Timmis, K.N., Abraham, W.R. (1999) Towards elucidation of microbial community metabolic pathways: unravelling the network of carbon sharing in a pollutant-degrading bacterial consortium by immunocapture and isotopic ratio mass spectrometry. Environ. Microbiol. 1, 167174.
  • [8]
    Boschker, H.T.S., de Brouwer, J.F.C., Cappenberg, T.E. (1999) The contribution of macrophyte-derived organic matter to microbial biomass in salt-marsh sediments: Stable carbon isotope analysis of microbial biomarkers. Limnol. Oceanogr. 44, 309319.
  • [9]
    Middelburg, J.J., Barranguet, C., Boschker, H.T.S., Herman, P.M.J., Moens, T., Heip, C.H.R. (2000) The fate of intertidal microphytobenthos carbon: An in situ 13C-labeling study. Limnol. Oceanogr. 45, 12241234.
  • [10]
    Pelz, O., Chatzinotas, A., Andersen, N., Bernasconi, S.M., Hesse, C., Abraham, W.R., Zeyer, J. (2001) Use of isotopic and molecular techniques to link toluene degradation in denitrifying aquifer microcosms to specific microbial populations. Arch. Microbiol. 175, 270281.
  • [11]
    Hayes, J.M. (2001) Fractionation of carbon and hydrogen isotopes in biosynthetic processes. Rev. Mineral. Geochem. 43, 225277.
  • [12]
    Pelz, O., Cifuentes, L.A., Hammer, B.T., Kelley, C.A., Coffin, R.B. (1998) Tracing the assimilation of organic compounds using δ13C analysis of unique amino acids in the bacterial peptidoglycan cell wall. FEMS Microbiol. Ecol. 25, 229240.
  • [13]
    Hama, T., Hama, J. and Handa, N. (1993) 13C tracer methodology in microbial ecology with special reference to primary production processes in aquatic environments. In: Advances in Microbial Ecology, Vol. 13 (Jones, J.G., Ed.), pp. 39–83. Plenum, New York.
  • [14]
    Sun, M.Y., Aller, R.C., Lee, C., Wakeham, S.G. (1999) Enhanced degradation of algal lipids by benthic macrofaunal activity: Effect of Yoldia limatula. J. Mar. Res. 57, 775804.
  • [15]
    Moodley, L., Boschker, H.T.S., Middelburg, J.J., Pel, R., Herman, P.M.J., de Deckere, E., Heip, C.H.R. (2000) Ecological significance of benthic foraminifera: 13C labelling experiments. Mar. Ecol. Prog. Ser. 202, 289295.
  • [16]
    Hanson, J.R., Macalady, J.L., Harris, D., Scow, K.M. (1999) Linking toluene degradation with specific microbial populations in soil. Appl. Environ. Microbiol. 65, 54035408.
  • [17]
    Bull, I.D., Parekh, N.R., Hall, G.H., Ineson, P., Evershed, R.P. (2000) Detection and classification of atmospheric methane oxidizing bacteria in soil. Nature 405, 175178.
  • [18]
    Boschker, H.T.S., de Graaf, W., Koster, M., Meyer-Reil, L.A., Cappenberg, T.E. (2001) Bacterial populations and processes involved in acetate and propionate consumption in anoxic brackish sediment. FEMS Microbiol. Ecol. 35, 97103.
  • [19]
    De Rosa, M. and Gambacorta, A. (1994) Archeal lipids. In: Chemical Methods in Prokaryote Systematics (Goodfellow, M. and O'Donnell, A.G., Eds.), pp. 197–264. John Wiley and Sons, Chicester.
  • [20]
    Pelz, O., Hesse, C., Tesar, M., Coffin, R.B., Abraham, W.R. (1997) Development of methods to measure carbon isotope ratios of bacterial biomarkers in the environment. Isotop. Environ. Health Stud. 33, 131144.
  • [21]
    Arao, T. (1999) In situ detection of changes in soil bacterial and fungal activities by measuring 13C incorporation into soil phospholipid fatty acids from 13C acetate. Soil Biol. Biochem. 31, 10151020.
  • [22]
    Sun, M.Y. (2000) Mass spectrometric characterization of 13C-labeled lipid tracers and their degradation products in microcosm sediments. Org. Geochem. 31, 199209.
  • [23]
    Bidigare, R.R., Kennicutt, M.C., Keeney-Kennicutt, W.L., Macko, S.A. (1991) Isolation and purification of chlorophyll-a and chlorophyll-b for the determination of stable carbon and nitrogen isotope composition. Anal. Chem. 63, 130133.
  • [24]
    Macko, S.A., Fogel, M.L., Hare, P.E., Hoering, T.C. (1987) Isotopic fractionation of nitrogen and carbon synthesis of amino acids by microorganisms. Chem. Geol. 65, 7992.
  • [25]
    Lundberg, P., Ekblad, A., Nilsson, M. (2001) 13C NMR spectroscopy studies of forest soil microbial activity: glucose uptake and fatty acid biosynthesis. Soil Biol. Biochem. 33, 621632.
  • [26]
    Brinch-Iversen, J., King, G.M. (1990) Effects of substrate concentration, growth state, and oxygen availability on relationships among bacterial carbon, nitrogen and phospholipid phosphorus content. FEMS Microbiol. Ecol. 74, 345355.
  • [27]
    Peterson, B.J., Fry, B. (1987) Stable isotopes in ecosystem studies. Annu. Rev. Ecol. Syst. 18, 293320.
  • [28]
    Blair, N.E., Leu, A., Muñoz, E., Olsen, J., Kwong, E., des Marais, D.J. (1985) Carbon isotopic fractionation in heterotrophic microbial metabolism. Appl. Environ. Microbiol. 50, 9961001.
  • [29]
    Coffin, R.B., Velinsky, D.J., Devereux, R., Price, W.A., Cifuentes, L.A. (1990) Stable carbon isotope analysis of nucleic-acids to trace sources of dissolved substrates used by estuarine bacteria. Appl. Environ. Microbiol. 56, 20122020.
  • [30]
    Hullar, M.A.J., Fry, B., Peterson, B.J., Wright, R.T. (1996) Microbial utilization of estuarine dissolved organic carbon: A stable isotope tracer approach tested by mass balance. Appl. Environ. Microbiol. 62, 24892493.
  • [31]
    Abraham, W.R., Hesse, C., Pelz, O. (1998) Ratios of carbon isotopes in microbial lipids as an indicator of substrate usage. Appl. Environ. Microbiol. 64, 42024209.
  • [32]
    Creach, V., Lucas, F., Deleu, C., Bertru, G., Mariotti, A. (1999) Combination of biomolecular and stable isotope techniques to determine the origin of organic matter used by bacterial communities: application to sediment. J. Microbiol. Methods 38, 4352.
  • [33]
    Boschker, H.T.S., Wielemaker, A., Schaub, B.E.M., Holmer, M. (2000) Limited coupling of macrophyte production and bacterial carbon cycling in the sediments of Zostera spp. meadows. Mar. Ecol. Prog. Ser. 203, 181189.
  • [34]
    Holmer, M., Andersen, F.O., Nielsen, S.L., Boschker, H.T.S. (2001) The importance of mineralization based on sulfate reduction for nutrient regeneration in tropical seagrass sediments. Aquat. Bot. 71, 117.
  • [35]
    Canuel, E.A., Freeman, K.H., Wakeham, S.G. (1997) Isotopic compositions of lipid biomarker compounds in estuarine plants and surface sediments. Limnol. Oceanogr. 42, 15701583.
  • [36]
    Cifuentes, L.A., Salata, G.G. (2001) Significance of carbon isotope discrimination between bulk carbon and extracted phospholipid fatty acids in selected terrestrial and marine environments. Org. Geochem. 32, 613621.
  • [37]
    Summons, R.E., Jahnke, L.L., Roksandic, Z. (1994) Carbon isotopic fractionation in lipids from methanotrophic bacteria: Relevance for interpretation of the geochemical record of biomarkers. Geochim. Cosmochim. Acta 58, 28532863.
  • [38]
    Jahnke, L.L., Summons, R.E., Hope, J.M., des Marais, D.J. (1999) Carbon isotopic fractionation in lipids from methanotrophic bacteria II: The effects of physiology and environmental parameters on the biosynthesis and isotopic signatures of biomarkers. Geochim. Cosmochim. Acta 63, 7993.
  • [39]
    Jahnke, L.L., Summons, R.E., Dowling, L.M., Zahiralis, K.D. (1995) Identification of methanotrophic lipid biomarkers in cold-seep mussel gills: Chemical and isotopic analysis. Appl. Environ. Microbiol. 61, 576582.
  • [40]
    van der Meer, M.T.J., Schouten, S., de Leeuw, J.W., Ward, D.M. (2000) Autotrophy of green non-sulphur bacteria in hot spring microbial mats: biological explanations for isotopically heavy organic carbon in the geological record. Environ. Microbiol. 2, 428435.
  • [41]
    Elvert, M., Suess, E., Whiticar, M.J. (1999) Anaerobic methane oxidation associated with marine gas hydrates: Superlight C-isotopes from saturated and unsaturated C-20 and C-25 irregular isoprenoids. Naturwissenschaften 86, 295300.
  • [42]
    Thiel, V., Peckmann, J., Seifert, R., Wehrung, P., Reitner, J., Michaelis, W. (1999) Highly isotopically depleted isoprenoids: Molecular markers for ancient methane venting. Geochim. Cosmochim. Acta 63, 39593966.
  • [43]
    Pancost, R.D., Sinninghe Damsté, J.S., de Lint, S., van der Maarel, M.J.E.C., Gottschal, J.C. (2000) Biomarker evidence for widespread anaerobic methane oxidation in Mediterranean sediments by a consortium of methanogenic archaea and bacteria. Appl. Environ. Microbiol. 66, 11261132.
  • [44]
    Orphan, V.J., Hinrichs, K.U., Ussler, W., Paull, C.K., Taylor, L.T., Sylva, S.P., Hayes, J.M., Delong, E.F. (2001) Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl. Environ. Microbiol. 67, 19221934.
  • [45]
    Boetius, A., Ravenschlag, K., Schubert, C.J., Rickert, D., Widdel, F., Gieseke, A., Amann, R., Jorgensen, B.B., Witte, U., Pfannkuche, O. (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407, 623626.
  • [46]
    Orphan, V.J., House, C.H., Hinrichs, K.U., McKeegan, K.D., Delong, E.F. (2001) Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293, 484487.
  • [47]
    Pancost, R.D., Hopmans, E.C., Sinninghe Damsté, J.S. (2001) Archaeal lipids in Mediterranean cold seeps: Molecular proxies for anaerobic methane oxidation. Geochim. Cosmochim. Acta 65, 16111627.
  • [48]
    Cottrell, M.T., Kirchman, D.L. (2000) Natural assemblages of marine proteobacteria and members of the Cytophaga–Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl. Environ. Microbiol. 66, 16921697.
  • [49]
    Nold, S.C., Boschker, H.T.S., Pel, R., Laanbroek, H.J. (1999) Ammonium addition inhibits 13C-methane incorporation into methanotroph membrane lipids in a freshwater sediment. FEMS Microbiol. Ecol. 29, 8189.
  • [50]
    Crossman, Z.M., McNamara, N., Parekh, N., Ineson, P., Evershed, R.P. (2001) A new method for identifying the origins of simple and complex hopanoids in sedimentary materials using stable isotope labelling with 13C-CH4 and compound specific stable isotope analyses. Org. Geochem. 32, 359364.
  • [51]
    Roslev, P., Iversen, N. (1999) Radioactive fingerprinting of microorganisms that oxidize atmospheric methane in different soils. Appl. Environ. Microbiol. 65, 40644070.
  • [52]
    Bodelier, P.L.E., Roslev, P., Henckel, T., Frenzel, P. (2000) Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots. Nature 403, 421424.
  • [53]
    Pel, R., Oldenhuis, R., Brand, W., Vos, A., Gottschal, J.C., Zwart, K.B. (1997) Stable-isotope analysis of a combined nitrification–denitrification sustained by thermophilic methanotrophs under low-oxygen conditions. Appl. Environ. Microbiol. 63, 474481.
  • [54]
    Shin, K.H., Hama, T., Yoshie, N., Noriki, S., Tsunogai, S. (2000) Dynamics of fatty acids in newly biosynthesized phytoplankton cells and seston during a spring bloom off the west coast of Hokkaido Island, Japan. Mar. Chem. 70, 243256.
  • [55]
    Hamanaka, J., Sawada, K., Tanoue, E. (2000) Production rates of C-37 alkenones determined by 13C-labeling technique in the euphotic zone of Sagami Bay, Japan. Org. Geochem. 31, 10951102.
  • [56]
    Holben, W.E., Ostrom, P.H. (2000) Monitoring bacterial transport by stable isotope enrichment of cells. Appl. Environ. Microbiol. 66, 49354939.
  • [57]
    Lytle, C.A., Fuller, M.E., Gan, Y.D.M., Peacock, A., DeFlaun, M.F., Onstott, T.C., White, D.C. (2001) Utility of high performance liquid chromatography/electrospray/mass spectrometry of polar lipids in specifically Per-13C labeled Gram-negative bacteria DA001 as a tracer for acceleration of bioremediation in the subsurface. J. Microbiol. Methods 44, 271281.
  • [58]
    Lollar, B.S., Slater, G.F., Sleep, B., Witt, M., Klecka, G.M., Harkness, M., Spivack, J. (2001) Stable carbon isotope evidence for intrinsic bioremediation of tetrachloroethene and trichloroethene at Area 6, Dover Air Force Base. Environ. Sci. Technol. 35, 261269.
  • [59]
    Smith, D.J., Underwood, G.J.C. (1998) Exopolymer production by intertidal epipelic diatoms. Limnol. Oceanogr. 43, 15781591.
  • [60]
    Goto, N., Mitamura, O., Terai, H. (2001) Biodegradation of photosynthetically produced extracellular organic carbon from intertidal benthic algae. J. Exp. Mar. Biol. Ecol. 257, 7386.
  • [61]
    Blair, N.E., Levin, L.A., DeMaster, D.J., Plaia, G. (1996) The short-term fate of fresh algal carbon in continental slope sediments. Limnol. Oceanogr. 41, 12081219.
  • [62]
    Radajewski, S., Ineson, P., Parekh, N.R., Murrell, J.C. (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403, 646649.
  • [63]
    Harvey, H.R., McManus, G.B. (1991) Marine ciliates as a widespread source of tetrahymanol and hopan-3-β-ol in sediments. Geochim. Cosmochim. Acta 55, 33873390.