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Assessing Functions of Soil Microbes with Isotopic Measurements

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Microorganisms in Soils: Roles in Genesis and Functions

Part of the book series: Soil Biology ((SOILBIOL,volume 3))

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References

  • Abelson PH, Hoering TC (1961) Carbon isotope fractionation in formation of amino acids by photosynthetic organisms. Proc Natl Acad Sci USA 47: 623–632

    CAS  Google Scholar 

  • Abraham W-R, Hesse C, Pelz O (1998) Ratios of carbon isotopes in microbial lipids as an indicator of substrate usage. Appl Environ Microbiol 61:4202–4209

    Google Scholar 

  • Ågren GI, Bosatta E (1996) Theoretical ecosystem ecology. Cambridge Univ Press, Cambridge

    Google Scholar 

  • 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 31:1015–1020

    Article  CAS  Google Scholar 

  • Bago B, Pfeffer P, Shachar-Hill Y (2001) Could the urea cycle be translocating nitrogen in the arbuscular mycorrhizal symbiosis? New Phytol 149:4–8

    Article  CAS  Google Scholar 

  • Benner R, Fogel ML, Sprague EK, Hodson RE (1987) Depletion of 13C in lignin and its implications for stable carbon isotope studies. Nature 329:708–710

    CAS  Google Scholar 

  • Bigeleisen J (1965) Chemistry of isotopes. Science 147: 463–471

    CAS  Google Scholar 

  • Blair N, Leu A, Munoz E, Olsen J, Kwong E, Des Marais D (1985) Carbon isotopic fractionation in heterotrophic microbial metabolism. Appl Environ Microbiol 50:996–1001

    CAS  Google Scholar 

  • Boschker HTS, Middelburg JJ (2002) Stable isotopes and biomarkers in microbial ecology. FEMS Microbiol Ecol 40:85–95

    CAS  Google Scholar 

  • Bréas O, Guillou C, Reniero F, Wada E (2001) The global methane cycle: isotopes and mixing ratios, sources and sinks. Isotopes Environ Health Stud 37:257–379

    Google Scholar 

  • Brugnoli E, Farquhar GD (2000) Photosynthetic fractionation of carbon isotopes. In: Leegood RC, Sharkey TD, von Caemmerer S (eds) Photosynthesis: physiology and metabolism. Kluwer, Dordrecht, pp 399–434

    Google Scholar 

  • Bull ID, Parekh NR, Hall GH, Ineson P, Evershed RP (2000) Detection and classification of atmospheric methane oxidising bacteria in soil. Nature 405:175–178

    Article  CAS  Google Scholar 

  • Carlile MJ, Watkinson SC, Gooday GW (2001) The fungi, 2nd edn. Academic Press, Boston

    Google Scholar 

  • Cifuentes LA, Salata GG (2001) Significance of carbon isotope discrimination between bulk carbon and extracted phospholipid fatty acids in selected terrestrial and marine environments. Org Geochem 32: 613–621

    Article  CAS  Google Scholar 

  • Coffin RB, Fry B, Peterson BJ, Wright RT (1989) Carbon isotopic compositions of estuarine bacteria. Limnol Oceanogr 34:1305–1310

    CAS  Google Scholar 

  • Coffin R, Devereux R, Price W, Cifuentes L (1990) Analysis of stable isotopes of nucleic acids to trace sources of dissolved substrates used by estuarine bacteria. Appl Environ Microbiol 66:2012–2020

    Google Scholar 

  • Créach V, Bertru G, Mariotti A (1997) Natural isotopic composition of heterotrophic bacteria to determine the origin of bioavailable dissolved organic carbon. CR Acad Sci 320:339–347

    Google Scholar 

  • Currie WS, Nadelhoffer KJ (1999) Dynamic redistribution of isotopically labeled cohorts of nitrogen inputs in two temperate forests. Ecosystems 2:4–18

    Article  CAS  Google Scholar 

  • Dawson TE, Mambelli S, Plamboeck AH, Templer PH, Tu KP (2002) Stable isotopes in plant ecology. Annu Rev Ecol Syst 33:507–559

    Article  Google Scholar 

  • Day DA, Poole PS, Tyerman SD, Rosendahl L (2001) Ammonia and amino acid transport across symbiotic membranes in nitrogen-fixing legume nodules. Cell Mol Life Sci 58:61–71

    CAS  Google Scholar 

  • Ekblad A, Nyberg G, Högberg P (2002) 13C-discrimination during microbial respiration of added C3-, C4-and 13C-labelled sugars to a C3-forest soil. Oecologia 131:245–249

    Google Scholar 

  • Emmerton KS, Callaghan TV, Jones HE, Leake JR, Michelsen A, Read DJ (2001) Assimilation and isotopic fractionation of nitrogen by mycorrhizal fungi. New Phytol 151:503–511

    CAS  Google Scholar 

  • Gaines GL III, Smith L, Neidle EL (1996) Novel nuclear magnetic resonance spectroscopy methods demonstrate preferential carbon source utilization by Acetinobacter calcoaceticus. J Bacteriol 178: 6833–6841

    CAS  Google Scholar 

  • Gebauer G, Dietrich P (1993) Nitrogen isotope ratios in different compartments of a mixed stand of spruce, larch and beech trees and of understorey vegetation including fungi. Isotopenpraxis 29:35–44

    CAS  Google Scholar 

  • Gleixner G, Danier H-J, Werner RA, Schmidt H-L (1993) Correlations between the 13C content of primary and secondary plant products in different cell compartments and that in decomposing basidiomycetes. Plant Physiol 102:1287–1290

    CAS  Google Scholar 

  • Handley LL, Raven JA (1992) The use of natural abundance of nitrogen isotopes in plant physiology and ecology. Plant Cell Environ 15: 965–985

    CAS  Google Scholar 

  • Hayes JM (2002) Fractionation of the isotopes of carbon and hydrogen in biosynthetic processes. In: Valley JW, Cole DR (eds) Stable isotope geochemistry. Mineralogical Society of America and the Geochemical Society, Washington, DC, pp 225–277

    Google Scholar 

  • Henn MR, Chapela IH (2000) Differential C isotope discrimination by fungi during decomposition of C3-and C4-derived sucrose. Appl Environ Microbiol 66:4180–4186

    Article  CAS  Google Scholar 

  • Henn MR, Chapela IH (2001) Ecophysiology of 13C and 15N isotopic fractionation in forest fungi and the roots of the saprotrophic-mycorrhizal divide. Oecologia 128:480–487

    Article  Google Scholar 

  • Hill SA, Waterhouse JS, Field EM, Switsur VR, ap Rees T (1995) Rapid recycling of triose phosphates in oak stem tissue. Plant Cell Environ 18:931–936

    CAS  Google Scholar 

  • Hobbie EA, Colpaert JV (2003) Nitrogen availability and colonization by mycorrhizal fungi correlate with nitrogen isotope patterns in plants. New Phytol 157:115–126

    Article  CAS  Google Scholar 

  • Hobbie EA, Colpaert JV (2004) Nitrogen availability and mycorrhizal colonization influence water use efficiency and carbon isotope patterns in Pinus sylvestris L. New Phytol (in press)

    Google Scholar 

  • Hobbie EA, Macko SA, Shugart HH (1999) Insights into nitrogen and carbon dynamics of ectomycorrhizal and saprotrophic fungi from isotopic evidence. Oecologia 118:353–360

    Article  Google Scholar 

  • Hobbie EA, Weber NS, Trappe JM (2001) Determining mycorrhizal or saprotrophic status of fungi from isotopic evidence: implications for element cycling and fungal evolution. New Phytol 150:601–610

    Article  CAS  Google Scholar 

  • Hobbie EA, Weber NS, Trappe JM, van Klinken GJ (2002) Using radiocarbon to determine mycorrhizal status in fungi. New Phytol 156: 129–136

    Article  Google Scholar 

  • Hobbie EA, Watrud LS, Maggard S, Shiroyama S, Rygiewicz PT (2003) Carbohydrate use by litter and soil fungi assessed through stable isotopes and BIOLOG® assays. Soil Biol Biochem 35:303–311

    Article  CAS  Google Scholar 

  • Hobbie EA, Sanchez FS, Rygiewicz PT (2004) Carbon use, nitrogen use, and isotopic fractionation of ectomycorrhizal and saprotrophic fungi in natural abundance and 13C-labelled cultures. Mycol Res 108:725–736

    Article  CAS  Google Scholar 

  • Hoefs J (1997) Stable isotope geochemistry, 4th edn. Springer, Berlin Heidelberg New York

    Google Scholar 

  • Högberg P (1990) 15N natural abundance as a possible marker of the ectomycorrhizal habit of trees in mixed African woodlands. New Phytol 115:483–486

    Google Scholar 

  • Högberg P (1997) 15N natural abundance in soil-plant systems. New Phytol 137:179–203

    Google Scholar 

  • Högberg P, Plamboeck AH, Taylor AFS, Fransson PMA (1999a) Natural 13C abundance reveals trophic status of fungi and host-origin of carbon in mycorrhizal fungi in mixed forests. Proc Natl Acad Sci USA 96:8534–8539

    Google Scholar 

  • Högberg P, Högberg MN, Quist ME, Ekblad A, Näsholm T (1999b) Nitrogen isotope fractionation during nitrogen uptake by ectomycorrhizal and non-mycorrhizal Pinus sylvestris. New Phytol 142:569–576

    Google Scholar 

  • Ingram LO, Calder JA, van Baalen C, Plucker FE, Parker PL (1973) Role of reduced exogenous organic compounds in the physiology of the blue-green bacteria (algae): photoheterotrophic growth of a “heterotrophic” blue-green bacterium. J Bacteriol 114:695–700

    CAS  Google Scholar 

  • Jennings DH (1995) The physiology of fungal nutrition. Cambridge Univ Press, Cambridge

    Google Scholar 

  • Johnsen AR, Winding A, Karlson U, Roslev P (2002) Linking of microorganisms to phenanthrene metabolism in soil by analysis of 13C-labeled cell lipids. Appl Environ Microbiol 68:6106–6113

    CAS  Google Scholar 

  • Jones TH, Bradford MA (2001) Assessing the functional implications of soil biodiversity in ecosystems. Ecol Res 16:845–858

    Article  Google Scholar 

  • Kohzu A, Yoshioka T, Ando T, Takahashi M, Koba K, Wada E (1999) Natural 13C and 15N abundance of field-collected fungi and their ecological implications. New Phytol 144:323–330

    Article  Google Scholar 

  • Kohzu A, Tateishi T, Yamada A, Koba K, Wada E (2000) Nitrogen isotope fractionation during nitrogen transport from ectomycorrhizal fungi, Suillus granulatus, to the host plant, Pinus densiflora. Soil Sci Plant Nutr 46:733–739

    Google Scholar 

  • Lekkerkerk L, Lundkvist H, Ågren GI, Ekbohm G, Bosatta E (1990) Decomposition of heterogeneous substrates: an experimental investigation of a hypothesis on substrate and microbial properties. Soil Biol Biochem 22:161–167

    Article  CAS  Google Scholar 

  • Li C, Aber J, Stange F, Butterbach-Bahl K, Papen H (2000) A process-oriented model of N2O and NO emissions from forest soils. 1. Model development. J Geophys Res 105:4369–4384

    CAS  Google Scholar 

  • Lichtfouse E, Berthier G, Houot S, Barriuso E, Bergheaud V, Vallaeys T (1995) Stable carbon isotope evidence for the microbial origin of C14-C18 n-alkanoic acids in soils. Org Geochem 23:849–852

    CAS  Google Scholar 

  • Lilleskov EA, Hobbie EA, Fahey TJ (2002) Ectomycorrhizal fungal taxa differing in response to nitrogen deposition also differ in pure culture organic nitrogen use and natural abundance of nitrogen isotopes. New Phytol 154:219–231

    Article  CAS  Google Scholar 

  • Lundberg P, Ekblad A, Nilsson M (2001) C-13 NMR spectroscopy studies of forest soil microbial activity: glucose uptake and fatty acid biosynthesis. Soil Biol Biochem 33:621–632

    Article  CAS  Google Scholar 

  • Luo Y, Sternberg L (1994) Alterations in δ13C values of seedling cellulose associated with respiration during germination. Phytochemistry 35:877–880

    CAS  Google Scholar 

  • MacGregor BJ, Brüchert V, Fleischer S, Amann R (2002) Isolation of small-subunit rRNA for stable isotopic characterization. Environ Microbiol 4:451–464

    Article  CAS  Google Scholar 

  • Macko SA, Estep MLF (1984) Microbial alteration of stable nitrogen and carbon isotopic compositions of organic matter. Org Geochem 6: 787–790

    Article  CAS  Google Scholar 

  • Monson KD, Hayes JM (1982) Carbon isotopic fractionation in the biosynthesis of bacterial fatty acids. Ozonolysis of unsaturated fatty acids as a means of determining the intramolecular distribution of carbon isotopes. Geochim Cosmochim Acta 46:139–149

    Article  CAS  Google Scholar 

  • Moore JC, de Ruiter PC, Hunt HW, Coleman DC, Freckman DW (1996) Microcosms and soil ecology: critical linkages between field studies and modelling food webs. Ecology 77:694–705

    Google Scholar 

  • Nakano A, Takahashi K, Kimura M (1999) The carbon origin of arbuscular mycorrhizal fungi estimated from δ13C values of individual spores. Mycorrhiza 9:141–147

    Article  Google Scholar 

  • Pelz O, Cifuentes LA, Hammer BT, Kelley CA, Coffin RB (1998) Tracing the assimilation of organic compounds using δ13C analysis of unique amino acids in the bacterial peptidoglycan cell wall. FEMS Microbiol Ecol 25:229–240

    CAS  Google Scholar 

  • Peterson B, Fry B, Deegan L, Hershey A (1993) The trophic significance of epilithic algal production in a fertilized tundra river ecosystem. Limnol Oceanogr 38:872–878

    Google Scholar 

  • Pfeffer PE, Douds DD, Bécard G, Shachar-Hill Y (1999) Carbon uptake and the metabolism and transport of lipids in an arbuscular mycorrhiza. Plant Physiol 120:587–598

    Article  CAS  Google Scholar 

  • Pfeffer PE, Bago B, Shachar-Hill Y (2001) Exploring mycorrhizal function with NMR spectroscopy. New Phytol 150:534–553

    Article  Google Scholar 

  • Portais J-C, Delort A-M (2002) Carbohydrate cycling in micro-organisms: what can 13CNMR tell us? FEMS Microbiol Rev 26:375–402

    Article  CAS  Google Scholar 

  • Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646–649

    CAS  Google Scholar 

  • Rees GN, Rainey FA, Harfoot CG (1994) Characterization of a novel obligate anaerobe that ferments agar. Arch Microbiol 162:395–400

    Article  CAS  Google Scholar 

  • Ryan MC, Aravena R (1994) Combining 13C natural abundance and fumigation-extraction methods to investigate soil microbial biomass turnover. Soil Biol Biochem 26:1583–1585

    Article  CAS  Google Scholar 

  • Šantrůcková H, Bird MI, Lloyd J (2000) Microbial processes and carbon-isotope fractionation in tropical and temperate grassland soils. Funct Ecol 14:108–114

    Google Scholar 

  • Schmidt S, Stewart GR (1997) Waterlogging and fire impacts on nitrogen availability and utilization in a subtropical wet heathland (wallum). Plant Cell Environ 20:1231–1241

    Article  Google Scholar 

  • Silfer JA, Engel MH, Macko SA (1992) Kinetic fractionation of stable carbon and nitrogen isotopes during peptide bond hydrolysis: experimental evidence and geochemical implications. Chem Geol 101:211–221

    Article  CAS  Google Scholar 

  • Smith SE, Smith FA (1990) Structure and function of the interfaces in biotrophic symbioses as they relate to nutrient transport. New Phytol 114:1–38

    CAS  Google Scholar 

  • Staddon PL, Robinson D, Graves JD, Fitter AH (1999) The δ13C signature of the external phase of a Glomus mycorrhizal fungus: determination and implications. Soil Biol Biochem 31: 1067–1070

    Article  CAS  Google Scholar 

  • Taylor AFS, Högbom L, Högberg M, Lyon AJE, Näsholm T, Högberg P (1997) Natural 15N abundance in fruit bodies of ectomycorrhizal fungi from boreal forests. New Phytol 136:713–720

    Article  Google Scholar 

  • Werner RA, Schmidt H-L (2002) The in vivo nitrogen isotope discrimination among organic plant compounds. Phytochemistry 61:465–484

    Article  CAS  Google Scholar 

  • Whiticar MJ (1999) Carbon and hydrogen isotope systematics of bacterial formation and oxidation of methane. Chem Geol 161:291–314

    Article  CAS  Google Scholar 

  • Will OH, Tieszen LL, Kellen M, Gerlach T (1986) Stable carbon isotope discrimination in the smut fungus Ustilago violacea. Exp Mycol 10:83–88

    CAS  Google Scholar 

  • Will OH, Tieszen LL, Gerlach T, Kellen M (1989) Alteration of carbon isotope ratios by eight Ustilago species on defined media. Bot Gaz 150:152–157

    CAS  Google Scholar 

  • Zhang CL, Ye Q, Reysenbach A-L, Götz D, Peacock A, White DC, Horita J, Cole DR, Fong J, Pratt L, Fang J, Huang Y (2002) Carbon isotopic fractionations associated with thermophilic bacteria Thermotoga maritima and Persephonella marina. Environ Microbiol 4:58–64

    CAS  Google Scholar 

  • Zyakun AM (1996) Stable carbon isotope discrimination by heterotrophic microorganisms. Appl Biochem Microbiol 32:153–159

    Google Scholar 

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Hobbie, E.A. (2005). Assessing Functions of Soil Microbes with Isotopic Measurements. In: Varma, A., Buscot, F. (eds) Microorganisms in Soils: Roles in Genesis and Functions. Soil Biology, vol 3. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-26609-7_18

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