Stable isotope fingerprinting: A novel method for identifying plant, fungal, or bacterial origins of amino acids

Ecology

Volumn 90, Issue 12, 2009, Pages 3526-3535

  Larsen, Thomas ^a   Lee Taylor, D ^a   Leigh, Mary Beth ^a   O'Brien, Diane M ^a  

^a UNIVERSITY OF ALASKA FAIRBANKS   (United States)

Author keywords

13C; Alaska; Compound specific stable isotope analysis; Essential amino acids; Eukaryotes; Gas chromatography combustion isotope ratio mass spectrometry (GC C IRMS); Prokaryotes; USA

Indexed keywords

AMINO ACID; CARBON;

AMINO ACID; BACTERIUM; BOREAL FOREST; CARBON ISOTOPE; DISCRIMINANT ANALYSIS; DNA FINGERPRINTING; FOOD WEB; FUNGUS; GAS CHROMATOGRAPHY; MASS SPECTROMETRY; STABLE ISOTOPE;

ARTICLE; BACTERIUM; CHEMISTRY; CLASSIFICATION; DISCRIMINANT ANALYSIS; ELECTROSPRAY MASS SPECTROMETRY; FUNGUS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; METHODOLOGY; PLANT; SPECIES DIFFERENCE;

AMINO ACIDS; BACTERIA; CARBON ISOTOPES; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; DISCRIMINANT ANALYSIS; FUNGI; PLANTS; SPECIES SPECIFICITY; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION;

ANIMALIA; BACTERIA (MICROORGANISMS); EUKARYOTA; FUNGI; HEXAPODA; PROKARYOTA;

EID: 72949117710     PISSN: 00129658     EISSN: None     Source Type: Journal    
DOI: 10.1890/08-1695.1     Document Type: Article

References (51)

1. Abelson, P. H., and T. C. Hoering. 1961. Carbon isotope fractionation in formation of amino acids by photosynthetic organisms. Proceedings of the National Academy of Sciences (USA) 47: 623-632.
2. Abraham, W. R., and C. Hesse. 2003. Isotope fractionations in the biosynthesis of cell components by different fungi: a basis for environmental carbon flux studies. Fems Microbiology Ecology 46: 121-128.
3. Baumann, P.,N.A.Moran, and L. Baumann. 2006. Bacteriocyte-associated endosymbionts of insects. Pages 403-438 in M. Dworkin, S. Falkow, E. Rosenberg, K. H. Schleifer, and E. Stackebrandt, editors. The Prokaryotes. Springer, New York, New York, USA.
4. Blair, N., A. Leu, E. Munoz, J. Olsen, E. Kwong, and D. Desmarais. 1985. Carbon isotopic fractionation in heterotrophic microbial-metabolism. Applied and Environmental Microbiology 50: 996-1001.
5. Brundrett, M. 2004. Diversity and classification of mycorrhizal associations. Biological Reviews 79: 473-495.
6. Chahartaghi, M., R. Langel, S. Scheu, and L. Ruess. 2005. Feeding guilds in Collembola based on nitrogen stable isotope ratios. Soil Biology and Biochemistry 37: 1718-1725.
7. Chalot, M., D. Blaudez, and A. Brun. 2006. Ammonia: a candidate for nitrogen transfer at the mycorrhizal interface. Trends in Plant Science 11: 263-266.
8. Cole, M. A., and G. H. Elkan. 1973. Transmissible resistance to penicillin-G, neomycin, and chloramphenicol in Rhizobium japonicum. Antimicrobial Agents and Chemotherapy 4: 248-253.
9. Fantle, M. S., A. I. Dittel, S. M. Schwalm, C. E. Epifanio, and M. L. Fogel. 1999. A food web analysis of the juvenile blue crab Callinectes sapidus using stable isotopes in whole animals and individual amino acids. Oecologia 120: 416-426.
10. Fogel, M. L., and N. Tuross. 1999. Transformation of plant biochemicals to geological macromolecules during early diagenesis. Oecologia 120: 336-346.
11. Gietzen, D. W., S. Hao, and T. G. Anthony. 2007. Mechanisms of food intake repression in indispensable amino acid deficiency. Annual Review of Nutrition 27: 63-78.
12. Hagelstein, P., B. Sieve, M. Klein, H. Jans, and G. Schultz. 1997. Leucine synthesis in chloroplasts: leucine/isoleucine aminotransferase and valine aminotransferase are different enzymes in spinach chloroplasts. Journal of Plant Physiology 150: 23-30.
13. Hare, P. E., M. L. Fogel, T. W. Stafford, A. D. Mitchell, and T. C. Hoering. 1991. The isotopic composition of carbon and nitrogen in individual amino acids isolated from modern and fossil proteins. Journal of Archaeological Science 18: 277-292.
14. 13 C contents of sedimentary organic compounds: principles and evidence. Marine Geology 113: 111-125.
15. Hayes, J. M. 2001. Fractionation of the isotopes of carbon and hydrogen isotopes in biosynthetic processes. Pages 225-277 in J. W. Valley and D. R. Cole, editors. Reviews in mineralogy and geochemistry 43. Stable isotope geochemistry. Mineral-ogical Society of America, Washington, D.C., USA.
16. Hudson, A. O., C. Bless, P. Macedo, S. P. Chatterjee, B. K. Singh, C. Gilvarg, and T. Leustek. 2005. Biosynthesis of lysine in plants: evidence for a variant of the known bacterial pathways. Biochimica et Biophysica Acta, General Subjects 1721: 27-36.
17. Hudson, A. O., B. K. Singh, T. Leustek, and C. Gilvarg. 2006. An LL-diaminopimelate aminotransferase defines a novel variant of the lysine biosynthesis pathway in plants. Plant Physiology 140: 292-301.
18. Janson, E. M., J. O. Stireman, M. S. Singer, and P. Abbot. 2008. Phytophagous insect-microbe mutualisms and adaptive evolutionary diversification. Evolution 62: 997-1012.
19. Keseler, I. M., J. Collado-Vides, S. Gama-Castro, J. Ingraham, S. Paley, I. T. Paulsen, M. Peralta-Gil, and P. D. Karp. 2005. EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Research 33: D334-D337.
20. Kielland, K., J. McFarland, and K. Olson. 2006. Amino acid uptake in deciduous and coniferous taiga ecosystems. Plant and Soil 288: 297-307.
21. Kohlhaw, G. B. 2003. Leucine biosynthesis in fungi: entering metabolism through the back door. Microbiology and Molecular Biology Reviews 67: 1-15.
22. Kosuge, T., and T. Hoshino. 1999. The alpha-aminoadipate pathway for lysine biosynthesis is widely distributed among Thermus strains. Journal of Bioscience and Bioengineering 88: 672-675.
23. Larsen, T., A. Gorissen, P. H. Krogh, M. Ventura, and J. Magid. 2007. Assimilation dynamics of soil carbon and nitrogen by wheat roots and Collembola. Plant and Soil 295: 253-264.
24. Lehninger, A. L. 1975. Biochemistry. Worth, New York, New York, USA.
25. Macko, S. A., M. L. Fogel, P. E. Hare, and T. C. Hoering. 1987. Isotopic fractionation of nitrogen and carbon in the synthesis of amino-acids by microorganisms. Chemical Geology 65: 79-92.
26. Marx, A., K. Striegel, A. A. deGraaf, H. Sahm, and L. Eggeling. 1997. Response of the central metabolism of Corynebacterium glutamicum to different flux burdens. Biotechnology and Bioengineering 56: 168-180.
27. Marx, D. 1969. The influence of ectotrophic mycorrhizal fungi on the resistance of pine roots to pathogenic infections. I. Antagonism of mycorrhizal fungi to root pathogenic fungi and soil bacteria. Phytopathology 59: 153-163.
28. McCarthy, M. D., R. Benner, C. Lee, J. I. Hedges, and M. L. Fogel. 2004. Amino acid carbon isotopic fractionation patterns in oceanic dissolved organic matter: An unaltered photoautotrophic source for dissolved organic nitrogen in the ocean? Marine Chemistry 92: 123-134.
29. Meier-Augenstein, W. 1999. Applied gas chromatography coupled to isotope ratio mass spectrometry. Journal of Chromatography A 842: 351-371.
30. 13C depletion in lipids. Journal of Biological Chemistry 262: 8159-8164.
31. Moran, N. A., and P. Baumann. 2000. Bacterial endosymbionts in animals. Current Opinion in Microbiology 3: 270-275.
32. Näsholm, T., A. Ekblad, A. Nordin, R. Giesler, M. Högberg, and P. Högberg. 1998. Boreal forest plants take up organic nitrogen. Nature 392: 914-916.
33. Nishida, H., and M. Nishiyama. 2000. What is characteristic of fungal lysine synthesis through the α-aminoadipate pathway? Journal of Molecular Evolution 51: 299-302.
34. O'Brien, D. M., C. L. Boggs, and M. L. Fogel. 2003. Pollen feeding in the butterfly Heliconius charitonia: isotopic evidence for essential amino acid transfer from pollen to eggs. Proceedings of the Royal Society B 270: 2631-2636.
35. O'Brien, D. M., C. L. Boggs, and M. L. Fogel. 2005. The amino acids used in reproduction by butterflies: a comparative study of dietary sources using compound-specific stable isotope analysis. Physiological and Biochemical Zoology 78: 819-827.
36. O'Brien, D. M., M. L. Fogel, and C. L. Boggs. 2002. Renewable and nonrenewable resources: amino acid turnover and allocation to reproduction in Lepidoptera. Proceedings of the National Academy of Sciences (USA) 99: 4413-4418.
37. O'Brien, D. M., K.-J. Min, T. Larsen, and M. Tatar. 2008. Use of stable isotopes to examine how dietary restriction extends Drosophila lifespan. Current Biology 18: R155-R156.
38. Phillips, D. L. 2001. Mixing models in analyses of diet using multiple stable isotopes: a critique. Oecologia 127: 166-170.
39. Phillips, D. L., and J. W. Gregg. 2003. Source partitioning using stable isotopes: coping with too many sources. Oecologia 136: 261-269.
40. Read, D. J., and J. Perez-Moreno. 2003. Mycorrhizas and nutrient cycling in ecosystems - a journey towards relevance? New Phytologist 157: 475-492.
41. Robbins, C. T. 1993. Wildlife feeding and nutrition. Second edition. Academic Press, San Diego, California, USA. Schloss, P. D., and J. Handelsman. 2006. Toward a census of bacteria in soil. PLoS Computational Biology 2: 786-793.
42. Scott, J. H., D. M. O'Brien, D. Emerson, H. Sun, G. D. McDonald, A. Salgado, and M. L. Fogel. 2006. An examination of the carbon isotope effects associated with amino acid biosynthesis. Astrobiology 6: 867-880.
43. Silfer, J. A., M. H. Engel, S. A. Macko, and E. J. Jumeau. 1991. Stable carbon isotope analysis of amino acid enantiomers by conventional isotope ratio mass spectrometry and combined gas chromatography/isotope ratio mass spectrometry. Analytical Chemistry 63: 370-374.
44. Stephanopoulos, G. N., A. A. Aristidou, and J. Nielsen. 1998. Metabolic engineering: principles and methodologies. Academic Press, San Diego, California, USA.
45. Taylor, D. L., M. G. Booth, J. W. McFarland, I. C. Herriott, N. J. Lennon, C. Nusbaum, and T. G. Marr. 2008. Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach. Molecular Ecology Resources 8: 742-752.
46. Van Berkum, P. 1990. Evidence for a third uptake hydrogenase phenotype among the soybean bradyrhizobia. Applied and Environmental Microbiology 56: 3835-3841.
47. Vauterin, M., V. Frankard, and M. Jacobs. 2000. Functional rescue of a bacterial dapA auxotroph with a plant cDNA library selects for mutant clones encoding a feedback-insensitive dihydrodipicolinate synthase. Plant Journal 21: 239-248.
48. Venables, W. N., and B. D. Ripley. 2002. Modern applied statistics with S-Plus. Fourth edition. Springer-Verlag, New York, New York, USA.
49. Walsh, K., and D. E. Koshland. 1985. Branch point control by the phosphorylation state of isocitrate dehydrogenase: a quantitative examination of fluxes during a regulatory transition. Journal of Biological Chemistry 260: 8430-8437.
50. Wernegreen, J. J. 2002. Genome evolution in bacterial endo-symbionts of insects. Nature Reviews: Genetics 3: 850-861.
51. 13Cin proteins and amino acids. Dissertation. University of Texas, Austin, Texas, USA.