Chapter 8 : Stable Isotope Probing and Plants

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in

Stable Isotope Probing and Plants, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555816896/9781555815370_Chap08-1.gif /docserver/preview/fulltext/10.1128/9781555816896/9781555815370_Chap08-2.gif


This chapter summarizes the applications of stable isotope probing (SIP) technology in plant-soil systems and presents an overview of the progress achieved in the understanding of the plant-soil microbe interactions and their role in ecosystem functioning. The applications of phospholipid fatty acids-based SIP (PLFA-SIP) and then the applications of DNA- and RNA-based SIP in upland soils and flooded rice field soils, respectively, are described. Several studies have exploited PLFA-SIP technology to determine the plant-microbe interactions driven by rhizosphere carbon flow. In these studies, the living plants, either in the field or laboratory, are exposed to C-labeled CO, and the microbial PLFAs are collected from rhizosphere soil. After pulse-labeling of rice plants with CO in a microcosm, soil samples were divided into rhizosphere and bulk soil, and the bulk soil samples were further partitioned vertically into upper layer and lower layer and horizontally into five layers with an increasing distance from roots. A study performed on grassland soil and on peatland soil, targeted mainly the root symbiont's arbuscular mycorrhizal (AM) fungi and the bacteria possibly associated with them. RNA-SIP revealed that AM fungi were labeled with C immediately after plant assimilation, suggesting that AM fungi preferentially used assimilates provided by plants rather than previously fixed carbon. Combining SIP with techniques such as metatranscriptomics, pyrosequencing, and community systems biology, promises a better and deeper understanding of plant-microbe interactions.

Citation: Lu Y, Conrad R. 2011. Stable Isotope Probing and Plants, p 151-163. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch8

Key Concept Ranking

Microbial Ecology
Restriction Fragment Length Polymorphism
Denaturing Gradient Gel Electrophoresis
Restriction Fragment Length Polymorphism
Denaturing Gradient Gel Electrophoresis
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of FIGURE 1

Generalized flow chart for SIP protocol in plant-soil system. (a) C isotopic labeling, which is usually conducted by CO feeding to plants; (b) RNA/DNA/PLFA fractionation, which can be completed by either density gradient centrifugation or gas chromatography in case of PLFA-SIP; (c) microbial identification by the analysis of biomarkers such as 16S rRNA genes and phospholipid fatty acids.

Citation: Lu Y, Conrad R. 2011. Stable Isotope Probing and Plants, p 151-163. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2

Isotope dilution and cross-feeding can occur in plant-soil systems. met1 and met2 represent different types of metabolites derived from decomposition of root exudates and turnover of microbial biomass. mic1, mic2, mic3, and mic4 represent different groups of microorganisms in soil. Isotope dilution is indicated by the different size and boldface of the numbers in C.

Citation: Lu Y, Conrad R. 2011. Stable Isotope Probing and Plants, p 151-163. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Berg, G.,, L. Eberl, and, A. Hartmann, 2005. The rhizosphere as a reservoir for opportunistic human pathogenic bacteria. Environ. Microbiol. 71:42034213.
2. Bressan, M.,, M.-A. Roncato,, F. Bellvert,, G. Comte,, F. Z. Haichar,, W. Achouak, and, O. Berge. 2009. Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots. ISME J. 3:12431257.
3. Butler, J. L.,, M. A. Williams,, P. J. Bottomley, and, D. D. Myrold. 2003. Microbial community dynamics associated with rhizosphere carbon flow. Appl Environ. Microbiol. 69:67936800.
4. Bolton, H.,, J. K. Fredrickson, and, L. F. Elliott. 1993. Microbial ecology of the rhizosphere, p. 27–63. In F. B. Metting (ed.), Soil Microbial Ecology. Marcel Dekker, New York, NY.
5. Chin, K. J.,, T. Lueders,, M. W. Friedrich,, M. Klose, and, R. Conrad. 2004. Archaeal community structure and pathway of methane formation on rice roots. Microb. Ecol. 47:5967.
6. Choudhury, A. T. M. A., and, I. R. Kennedy. 2004. Prospects and potentials for systems of biological nitrogen fixation in sustainable rice production. Biol. Fert. Soils 39:219227.
7. Dannenberg, S., and, R. Conrad, 1999. Effect of rice plants on methane production and rhizospheric metabolism in paddy soil. Biogeochemistry 45:5371.
8. Denef, K.,, D. Roobroeck,, M. C. W. M. Wadu,, P. Lootens, and, P. Boeckx. 2009. Microbial community composition and rhizodepositcarbon assimilation in differently managed temperate grassland soils. Soil Biol. Biochem. 41:144153.
9. Erkel, C.,, M. Kube,, R. Reinhardt, and, W. Liesack. 2006. Genome of rice cluster I archaea—the key methane producers in the rice rhizosphere. Science 313:370372.
10. Evershed, R. P.,, Z. M. Crossman,, I. D. Bull,, H. Mottram,, J. A. J. Dungait,, P. J. Maxfield, and, E. L. Brennand. 2006. 13C-Labelling of lipids to investigate microbial communities in the environment. Curr. Opinion Biotech. 17:7282.
11. Griffiths, R. I.,, A. S. Whiteley,, A. G. O’Donnell, and, M. J. Bailey. 2003. Physiological and community responses of established grassland bacterial populations to water stress. Appl. Environ. Microbiol. 69:69616968.
12. Griffiths, R. I.,, M. Manefield,, M. J. Bailey,, A. S. Whiteley,, N. Ostle,, N. McNamara, and, A. G. O’Donnell. 2004. 13CO2 pulse labelling of plants in tandem with stable isotope probing: methodological considerations for examining microbial function in the rhizosphere. J. Microbiol. Methods 58:119129.
13. Haichar, F. Z.,, C. Marol,, O. Berge,, J. I. Rangel-Castro,, J. Prosser,, J. Balesdent,, T. Heulin, and, W. Achouak. 2008. Plant host habitat and root exudates shape soil bacterial community structure. ISME J. 2:12211230.
14. Halkier, B. A., and, J. Gershenzon. 2006. Biology and biochemistry of glucosinolates. Annu. Rev. Plant Biol. 57:303333.
15. IpCC. 2007. Summary for Policymakers. In: Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, Cambridge, United Kingdom.
16. Keith, H.,, J. M. Oades, and, J. K. Martin. 1986. Input of carbon to soil from wheat plants. Soil Biol. Biochem. 18:445449.
17. Kuzyakov, K. 2002. Review: factors affecting rhizosphere priming effects. J. Plant Nutr. Soil Sci. 165:382396.
18. Kuzyakov, K., and, G. Domanski, 2000. Carbon input by plants into the soil. Review. J. Plant Nutr. Soil Sci. 163:421431.
19. Lu, Y.,, W.-R. Abraham, and, R. Conrad. 2007. Spatial variation of active microbiota in the rice rhizosphere revealed by in situ stable isotope probing of phospholipid fatty acids. Environ. Microbiol. 9:474481.
20. Lu, Y., and, R. Conrad, 2005. In situ stable isotope probing of methanogenic archaea in the rice rhizo-sphere. Science 309:10881090.
21. Lu, Y.,, T. Lueders,, M. W. Friedrich, and, R. Conrad. 2005. Detecting active methanogenic populations on rice roots using stable isotope probing. Environ. Microbiol. 7:326336.
22. Lu, Y.,, J. Murase,, A. Watanabe,, A. Sugimoto, and, M. Kimura. 2004. Linking microbial community dynamics to rhizosphere carbon flow in a wetland rice soil. FEMS Microbiol. Ecol. 48:179186.
23. Lu, Y.,, D. Rosencrantz,, W. Liesack,, R. Conrad, 2006. Structure and activity of bacterial community inhabiting rice roots and the rhizosphere. Environ. Microbiol. 8:13511360.
24. Lu, Y.,, R. Wassmann,, H. U. Neue, and, C. Huang. 2000a. Dynamics of dissolved organic carbon and methane emissions in a flooded rice soil. Soil Sci. Soc. Am. J. 64:20112017.
25. Lu, Y.,, R. Wassmann,, H. U. Neue, and, C. Huang. 2000b. Dissolved organic carbon and methane emissions from a rice paddy fertilized with ammonium and nitrate. J. Environ. Qual. 29:17331740.
26. Lu, Y.,, A. Watanabe, and, M. Kimura, 2002. Contribution of plant-derived carbon to soil microbial biomass dynamics in a paddy rice microcosm. Biol. Fert. Soils 36:136142.
27. Lynch, J. M., and, J. M. Whipps. 1990. Substrate flow in the rhizosphere. Plant Soil 129:110.
28. Manefield, M.,, A. S. Whiteley,, R. I. Griffiths, and, M. J. Bailey. 2002a. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl. Environ. Microbiol. 68:53675373.
29. Manefield, M.,, A. S. Whiteley,, N. Ostle,, P. Ineson, and, M. J. Bailey. 2002b. Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function. Rapid Commun. Mass Spectrom. 16:21792183.
30. Meharg, A. 1994. A critical review of labelling techniques used to quality rhizosphere carbon-flow. Plant Soil 166:5562.
31. Minoda, T., and, M. Kimura, 1994. Contribution of photosynthesized carbon to the methane emitted from paddy fields. Geophy. Res. Let. 21:20072010.
32. Minoda, T.,, M. Kimura, and, E. Wada, 1996. Photosynthates as dominant source of CH4 and CO2 in soil water and CH4 emitted to the atmosphere from paddy fields. J. Geophys. Res. 101:2109121097.
33. Neufeld, J. D.,, M. Wagner, and, J. C. Murrell. 2007. Who eats what, where and when? Isotope labeling experiments are coming of age. ISME J. 1:103110.
34. Paterson, E.,, T. Gebbing,, C. Abel,, A. Sim, and, G. Telfer. 2007. Rhizodeposition shapes rhizosphere microbial community structure in organic soil. New Phytol. 173:600610.
35. Prosser, J. I.,, J. I. Rangel-Castro, and, K. Killham. 2006. Studying plant-microbe interactions using stable isotope technologies. Current Opinion Biotechnol. 17:98102.
36. Qiu, Q.,, R. Conrad, and, Y. Lu, 2009. Cross feeding of methane carbon among bacteria on rice roots revealed by DNA-stable isotope probing. Environ. Microbiol. Reports 1:355361.
37. Qiu, Q.,, M. Noll,, W.-R. Abraham,, Y. Lu, and, R. Conrad. 2008. Applying stable isotope probing of phospholipid fatty acids and rRNA in a Chinese rice field to study activity and composition of the methanotrophic bacterial communities in situ. ISME J. 2:602614.
38. Rangel-Castro, J. I.,, J. I. Prosser,, K. Killham,, G. W. Nicol,, A. Meharg,, N. Ostle,, I. C. Anderson,, C. M. Scrimgeour, and, P. Ineson. 2005b. Stable isotope probing analysis of the influence of liming on root exudates utilization by soil microorganisms. Environ. Microbiol. 7:828838.
39. Radajewski, S.,, P. Ineson,, N. R. Parekh, and, J. C. Murrell. 2000. Stable-isotope probing as a tool in microbial ecology. Nature 403:646649.
40. Rasche, F.,, T. Lueders,, M. Schloter,, S. Schaefer,, F. Buegger,, A. Gattinger,, R. C. Hood-Nowotny, and, A. Sessitsch. 2009. DNA-based stable isotope probing enables the identification of active bacterial endophytes in potatoes. New Phytol. 181:802807.
41. Sakai, S.,, H. Imachi,, S. Hanada,, A. Ohashi,, H. Harada, and, Y. Kamagata. 2008. Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage ‘Rice Cluster I’, and proposal of the new archaeal order Methanocellales ord. nov. Int. J. Syst. Evol. Microbiol. 58:929936.
42. Singh, B. K.,, P. Millard,, A. S. Whiteley, and, J. C. Murrell. 2004. Unravelling rhizosphere–microbial interactions: opportunities and limitations. Trends Microbiol. 12:386393.
43. Sturz, A. V. 1995. The role of endophytic bacteria during seed piece decay and potato tuberization. Plant Soil 175:257263.
44. Treonis, A. M.,, N. J. Ostle,, A. W. Stott,, R. Primrose,, S. J. Grayston, and, P. Ineson. 2004. Identification of groups of metabolically-active rhizosphere microorganisms by stable isotope probing of PLFAs. Soil Biol. Biochem. 36:533537.
45. Vandenkoornhuyse, P.,, S. Mahe,, P. Ineson,, P. Staddon,, N. Ostle,, J.-B. Cliquet,, A.-J. Francez,, A. H. Fitter, and, J. P. W. Young. 2007. Active root-inhabiting microbes identified by rapid incorporation of plant-derived carbon into RNA. PNAS 104:1697016975.
46. Wardle, D. A.,, R. D. Bardgett,, J. N. Klironomos,, H. Setala,, W. H. van der Putten, and, D. H. Wall. 2004. Ecological linkages between aboveground and belowground biota. Science 304:16291633.
47. Wu, L.,, K. Ma,, Q. Li,, X. Ke, and, Y. Lu. 2009. Composition of archaeal community in a paddy field as affected by rice cultivar and N fertilizer. Microb. Ecol. 58:819826.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error