Looking inside the box: Using Raman microspectroscopy to deconstruct microbial biomass stoichiometry one cell at a time

ISME Journal

Volumn 5, Issue 2, 2011, Pages 196-208

  Hall, Edward K ^a   Singer, Gabriel A ^a   Pölzl, Marvin ^a   Hämmerle, Ieda ^a   Schwarz, Christian ^a   Daims, Holger ^a   Maixner, Frank ^a,b   Battin, Tom J ^a  

^a UNIVERSITY OF VIENNA   (Austria)

^b INSTITUTE FOR RENEWABLE ENERGY   (Italy)

Author keywords

Ecological stoichiometry; macromolecular composition; Raman microspectroscopy; resource allocation

Indexed keywords

CARBOHYDRATE; NUCLEIC ACID; PROTEIN;

BACTERIUM; BIOMASS; HETEROGENEITY; MICROBIAL COMMUNITY; RAMAN SPECTROSCOPY; RECYCLING; RESOURCE ALLOCATION; STOICHIOMETRY;

ARTICLE; BIOMASS; CHEMISTRY; CHLAMYDIACEAE; DISCRIMINANT ANALYSIS; GROWTH, DEVELOPMENT AND AGING; MACROMOLECULE; PECTOBACTERIUM CAROTOVORUM; PRINCIPAL COMPONENT ANALYSIS; RAMAN SPECTROMETRY;

BIOMASS; CARBOHYDRATES; CHLAMYDIALES; DISCRIMINANT ANALYSIS; MACROMOLECULAR SUBSTANCES; NUCLEIC ACIDS; PECTOBACTERIUM CAROTOVORUM; PRINCIPAL COMPONENT ANALYSIS; PROTEINS; SPECTRUM ANALYSIS, RAMAN;

BACTERIA (MICROORGANISMS);

EID: 78751575599     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2010.115     Document Type: Article

References (39)

1. Amann RI. (1995). In situ identification of micro-organisms by whole cell hybridization with rRNA-targeted nucleic acid probes. Molecular Microbial Ecology Manual Akkeman ADC, , van Elsas JD, de Bruigin FJ Kluwer Academic Publishers: Dortrecht, 1-15.
2. Anderson MJ. (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.
3. Bradford MM. (1976). A rapid and sensitive method for the quantification of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72: 248-254.
4. Cherif M, Loreau M. (2009).When microbes and consumers determine the limiting nutrient of autotrophs: a theoretical analysis. Proc R Soc Lond B 276: 487-497.
5. Cotner JB, Makino W, Biddanda BA. (2006). Temperature affects stoichiometry and biochemical composition of Escherichia coli. Microb Ecol 52: 26-33.
6. Danger M, Oumarou C, Benest D, Lacroix G. (2007). Bacteria can control stoichiometry and nutrient limitation of phytoplankton. Funct Ecol 21: 202-210.
7. Danger M, Daufresne T, Lucas F, Pissard S, Lacroix G. (2008). Does Liebig's law of the minimum scale up from species to communities. Oikos 117: 1741-1751.
8. Daniels L, Hanson RS, Phillips J. (2007). Total carbohydrates by phenol reaction. Methods for General and Molecular Microbiology Reddy CA, Beveridge TJ, Breznak JA et al. Chemical Analysis ASM Press:Washington, D.C.
9. De Gelder J, Willemse-Rix D, Scholtes MJ, Sanchez JI, Maquelln K, Vandenabeele P et al. (2008). Monitoring Poly(3-hydroxydutyrate) production in Cupriavidus necator DSM 428 (H16) with Raman Spectroscopy. Anal Chem 80: 2155-2160.
10. De Gelder J, De Gussem K, Vandenabelle P, De Vos P, Moens L. (2007). Methods for extracting biochemical information from bacterial Raman spectra: an explorative study on Cupriavidus metallidurans. Analytica Chimica Acta 585: 234-240.
11. Elser JJ, Dobberfuhl DR, Mackay NA, Schampel JH. (1996). Organism size, life history, and N:P stoichiometry. BioScience 46: 674-684.
12. Elser JJ, Acharya K, KyleM, Cotner JB, MakinoW, Markow TA et al. (2003). Growth rate-stoichiometry couplings in diverse biota. Ecol Lett 6: 936-943.
13. Goral J, Zichy V. (1990). Fourier transform Raman studies of materials and compounds of biological importance. Spectrochim Acta 46A: 253-275.
14. Gorokhova E, Dowling TE, Weider LJ, Crease TJ, Elser JJ. (2002). Functional and ecological significance of rDNA intergenic spacer variation in a clonal organism under divergent selection for production rate. Proc R Soc Lond B 269: 2373-2379.
15. Hall EK, Dzialowski AR, Stoxen SM, Cotner JB. (2009). The effect of temperature on the coupling between phosphorus and growth in lacustrine bacterioplankton communities. Limnol Oceanogr 54: 880-889.
16. Howard WFJ, Nelson WH, Sperry JF. (1980). A resonance Raman method for the rapid detection and identification of bacteria in water. App Spectrosc 34: 72-75.
17. Huang WE, Stoecker K, Griffiths R, Newbold L, Daims H, Whiteley AS et al. (2007a). Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ Microbiol 9: 1878-1889.
18. HuangWE, Bailey MJ, Thompson IP, Whiteley AS, Spiers AJ. (2007b). Single-cell Raman spectral profiles of Pseudomonas fluorescence SBW25 reflects in vitro and in planta metabolic history. Microb Ecol 53: 414-425.
19. Huang WE, Griffiths R, Thompson IP, Bailey MJ, Whiteley AS. (2004). Raman microscopic analysis of single microbial cells. Anal Chem 76: 4452-4458.
20. Keiblinger KM, Hall EK, Szukics U, Haemmerle I, Ellersdorfer G, Sterflinger K et al. (2010). The effect of resource quantity and resource stoichiometry on microbial carbon use efficiency. FEMS Microbiol Ecol. doi:10.1111/j.1574-6941.2010.00913.x.
21. Kim S, Kaplan LA, Hatcher PG. (2006). Biodegradable dissolved organic matter in a temperate and a tropical stream determined from ultra-high resolution mass spectrometry. Limnol Oceanogr 51: 1054-1063.
22. Klausmeier CA, Litchman E, Daufresne T, Levin SA. (2004). Optimal nitrogen-to-phosphorus stoichiometry of phytoplankton. Nature 429: 171-175.
23. Kornberg A, Rao NN, Ault-Riche D. (1999). Inorganic polyphosphate: a molecule of many functions. Annu Rev Biochem 68: 89-125.
24. Legendre L, Legendre P. (2003). Numerical Ecology. Elsevier Science: Amsterdam.
25. Lopez-Amores R, Comas J, Garcia MT, Vives-Rego J. (1998). Use of the 5-cyano-2,3-ditolyl tetrazolium chloride reduction test to asses respiring marine bacteria and grazing effects by flow cytometry during linear alkylbenzene sulfonate degradation. FEMS Microbiol Ecol 27: 33-42.
26. Makino W, Cotner JB. (2004). Elemental stoichiometry of a heterotrophic bacterial community in a freshwater lake: implications for growth and resource dependent variations. Aquat Microb Ecol 34: 33-41.
27. Makino W, Cotner JB, Sterner RW, Elser JJ. (2003). Are bacteria more like plants or animals? Growth rate and resource dependence of bacterial C:N:P stoichiometry. Funct Ecol 17: 121-130.
28. Manzoni S, Jackson RB, Trofymow JA, Porporato A. (2008). The global stoichiometry of nitrogen mineralization. Science 321: 684-686.
29. Maquelin K, Kirschner C, Choo-Smith LP, van den Braak N, Endtz HP, Naumann D et al. (2002). Identification of medically relevant microorganisms by virbrational spectroscopy. J Microbiol Methods 51: 255-271.
30. Norland S, Fagerbakke K, Heldel M. (1995). Light element analysis of individual bacteria by X-ray microanalysis. Appl Environ Microbiol 61: 1357-1362.
31. Pérombelon MCM. (1980). Ecology of the soft rot Erwinias. Ann Rev Phytopathol 18: 361-387.
32. R-Development-Core-Team (2005). R: A language and environment for statistical computing, R Foundation for statistical computing. R-Development-Core-Team: Vienna, Austria.
33. Sangwan P, Chen X, Hugenholtz P, Janssen PH. (2004). Chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia. Appl Environ Microbiol 70: 5875-5881.
34. Schinner F, Oḧlinger R, Kandeler E, Margesin R. (1993). Bodenbiologische Arbeitsmethoden. Springer Labor: Berlin, Germany.
35. Schlesner H. (1987). Verrucomicrobium spinosum gen. nov., sp. nov,: a fimbriated prosthecate bacterium. System Appl Microbiol 10: 54-56.
36. Schuster KC, Reese I, Urlaub E, Gapes JR, Lendl B. (2000). Multidimensional information on the chemical composition of single bacterial cells by confocal Raman microspectroscopy. Anal Chem 72: 5529-5534.
37. Sterner RW, Elser JJ. (2002). Ecological stoichiometry: The biology of the elements from the molecules to the biosphere. Princeton University Press: Princeton, New Jersey.
38. Tilman DG. (1982). Resource competition and community structure. Princeton University Press: Princeton.
39. Wagner M. (2009). Single cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging. Annu Rev Microbiol 63: 411-429.