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Chapter 3 : Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology
Authors:
P. J. Maxfield1,
R. P. Evershed2
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Affiliations:
1: Organic Geochemistry Unit, Bristol Biogeochemistry Research Centre, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom;
2: Organic Geochemistry Unit, Bristol Biogeochemistry Research Centre, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
Content Type: Monograph
Publication Year:
2011
Category: Environmental Microbiology; Applied and Industrial Microbiology
Book DOI:
10.1128/9781555816896
Chapter DOI:
10.1128/9781555816896.ch3
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Abstract:
This chapter reviews the methodologies used to present stable isotopically labeled substrates to microbial communities present in a wide range of environmental materials, and also discusses the wet chemical and instrumental methods used to determine compound-specific δ13C values of individual phospholipid fatty acid (PLFA). The different ways in which the δ 13C values obtained can be used to assess a variety of properties and activities of microbial communities in the environment are discussed in this chapter. The most widely used labeling techniques for PLFA- stable isotope probing (SIP) utilize 13C-enriched gases as substrates. The PLFA-SIP approach significantly extends conventional PLFA profiling methods by identifying PLFAs diagnostic of specific functional groups through their enhanced 13C signatures derived from the assimilation of applied 13C-substrate(s). In this respect, the approach has key resonances with current trends in the way that environmental microbial communities are being considered in terms of the functioning and stability of ecosystems, especially in relation to the importance of ecosystem services in the context of sustainable environments. The relative ease of preparing PLFA fatty acid methyl esters (FAMEs), combined with the high sensitivity of the gas chromatography combustion-isotope ratio mass spectrometry (GC-C-IRMS) method, makes PLFA-SIP an extremely robust methodology, which allows very large numbers of environmental samples to be studied.
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
Figures
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology
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Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig01
FIGURE 1.
General structure of a phospholipid. Sn denotes the C number position on the glycerol backbone. R1 and R2 represent long hydrocarbon chains. × represents one of the various substituents listed in
Table 1
.
10.1128/9781555816896/f0038-01_thmb.gif
10.1128/9781555816896/f0038-01.gif
FIGURE 1.
General structure of a phospholipid. Sn denotes the C number position on the glycerol backbone. R1 and R2 represent long hydrocarbon chains. × represents one of the various substituents listed in Table 1 .
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig02
FIGURE 2.
Pictorial representation of a cross section through a cell membrane displaying the phospholipid bilayer with integral (a) and peripheral (b) membrane proteins.
10.1128/9781555816896/f0038-02_thmb.gif
10.1128/9781555816896/f0038-02.gif
FIGURE 2.
Pictorial representation of a cross section through a cell membrane displaying the phospholipid bilayer with integral (a) and peripheral (b) membrane proteins.
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig03
FIGURE 3.
13CO2 pulse labeling plant microcosm (adapted from
Nakano-Hylander and Olsson, 2007
).
10.1128/9781555816896/f0042-01_thmb.gif
10.1128/9781555816896/f0042-01.gif
FIGURE 3.
13CO2 pulse labeling plant microcosm (adapted from Nakano-Hylander and Olsson, 2007 ).
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig04
FIGURE 4.
Static flux chamber (a) and continuous-flow flux chamber (b).
10.1128/9781555816896/f0043-01_thmb.gif
10.1128/9781555816896/f0043-01.gif
FIGURE 4.
Static flux chamber (a) and continuous-flow flux chamber (b).
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig05
FIGURE 5.
Freshwater sediment core incubation setup (adapted from
Deines et al., 2007
).
10.1128/9781555816896/f0044-01_thmb.gif
10.1128/9781555816896/f0044-01.gif
FIGURE 5.
Freshwater sediment core incubation setup (adapted from Deines et al., 2007 ).
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig06
FIGURE 6.
Continuous-flow gas diffusion core incubator schematic.
10.1128/9781555816896/f0044-02_thmb.gif
10.1128/9781555816896/f0044-02.gif
FIGURE 6.
Continuous-flow gas diffusion core incubator schematic.
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig07
FIGURE 7.
Partial gas chromatogram of the PLFA fraction of Bronydd Mawr upland grassland soil following derivatization with BF3 methanol. Separation was achieved using a Varian Factor Four VF23 ms (high cyanopropyl modified methyl polysiloxane) fused silica column (60 m by 0.32 mm internal diameter [ID]; 0.15-mm film thickness). The carrier gas was hydrogen, and the oven temperature was programmed from 50°C (held for 2 min) to 100°C at 15°C min-1, from 100 to 220°C at 4°C min-1, and from 220 to 240°C (held for 5 min) at 15°C min-1. PLFA assignments: 1 = C19 alkane, 2 = 14:0, 3 = i15:0, 4 = a15:0, 5 = 15:0, 6 = i16:0, 7 = 16:0, 8 = 16:1ω11, 9 = br17:0, 10 = 16:1ω7, 11 = i17:0 & 16:1ω5, 12 = a17:0, 13 = 17:1ω8, 14 = 17:0, 15 = 18:0, 16 = cyc19:0, 17 = 18:1ω9c, 18 = 18:1ω7c, 19 = 18:1ω5, 20 = 18:2ω3,6 (
Maxfield et al., 2006
).
10.1128/9781555816896/f0048-01_thmb.gif
10.1128/9781555816896/f0048-01.gif
FIGURE 7.
Partial gas chromatogram of the PLFA fraction of Bronydd Mawr upland grassland soil following derivatization with BF3 methanol. Separation was achieved using a Varian Factor Four VF23 ms (high cyanopropyl modified methyl polysiloxane) fused silica column (60 m by 0.32 mm internal diameter [ID]; 0.15-mm film thickness). The carrier gas was hydrogen, and the oven temperature was programmed from 50°C (held for 2 min) to 100°C at 15°C min-1, from 100 to 220°C at 4°C min-1, and from 220 to 240°C (held for 5 min) at 15°C min-1. PLFA assignments: 1 = C19 alkane, 2 = 14:0, 3 = i15:0, 4 = a15:0, 5 = 15:0, 6 = i16:0, 7 = 16:0, 8 = 16:1ω11, 9 = br17:0, 10 = 16:1ω7, 11 = i17:0 & 16:1ω5, 12 = a17:0, 13 = 17:1ω8, 14 = 17:0, 15 = 18:0, 16 = cyc19:0, 17 = 18:1ω9c, 18 = 18:1ω7c, 19 = 18:1ω5, 20 = 18:2ω3,6 ( Maxfield et al., 2006 ).
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig08
FIGURE 8.
Partial gas chromatogram of the PLFA fraction of Bronydd Mawr upland grassland soil following derivatization with DMDS to separate and identify the unsaturated PLFAs. Separation was achieved with a Chrompack CPSIL5-CB (100% dimethyl polysiloxane) fused silica column (50 m by 0.32 mm ID; 0.12 mm film thickness). The carrier gas was hydrogen and the oven was programmed from 40°C (held for 2 min) to 150°C at 12°C min-1, then 150 to 260°C (held for 5 min) at 4°C min-1. PLFA assignments: 1 = i15:0, 2 = a15:0, 3 = i16:0, 4 = 16:0, 5 = br17:0, 6 = i17:0, 7 = a17:0, 8 = 17:0, 9 = 18:0, 10 = 19:0, 11 = cyc19:0, 12 = 18:1ω13, 13 = 15:1ω11, 14 = 16:1ω12, 15 = 18:1ω7, 16 = 16:1ω11 & 16:1ω9, 17 = 16:1ω7, 18 = 16:1ω5, 19 = 17:1ω8, 20 = 18:1ω9c, 21 = 18:1ω7c, 22 = 18:1ω5, 23 = 19:1ω6, 24 = 19:1ω7. All unsaturated compounds were analyzed as DMDS derivatives.
10.1128/9781555816896/f0049-01_thmb.gif
10.1128/9781555816896/f0049-01.gif
FIGURE 8.
Partial gas chromatogram of the PLFA fraction of Bronydd Mawr upland grassland soil following derivatization with DMDS to separate and identify the unsaturated PLFAs. Separation was achieved with a Chrompack CPSIL5-CB (100% dimethyl polysiloxane) fused silica column (50 m by 0.32 mm ID; 0.12 mm film thickness). The carrier gas was hydrogen and the oven was programmed from 40°C (held for 2 min) to 150°C at 12°C min-1, then 150 to 260°C (held for 5 min) at 4°C min-1. PLFA assignments: 1 = i15:0, 2 = a15:0, 3 = i16:0, 4 = 16:0, 5 = br17:0, 6 = i17:0, 7 = a17:0, 8 = 17:0, 9 = 18:0, 10 = 19:0, 11 = cyc19:0, 12 = 18:1ω13, 13 = 15:1ω11, 14 = 16:1ω12, 15 = 18:1ω7, 16 = 16:1ω11 & 16:1ω9, 17 = 16:1ω7, 18 = 16:1ω5, 19 = 17:1ω8, 20 = 18:1ω9c, 21 = 18:1ω7c, 22 = 18:1ω5, 23 = 19:1ω6, 24 = 19:1ω7. All unsaturated compounds were analyzed as DMDS derivatives.
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig09
FIGURE 9.
Mass spectra of monounsaturated C18 fatty acid DMDS derivatives (18:1ω7 and 18:1ω9) extracted from Bronydd Mawr upland grassland soil. The fragment ions denoted D, E, and F are used to determine the position of the double bonds in the original PLFA.
10.1128/9781555816896/f0050-01_thmb.gif
10.1128/9781555816896/f0050-01.gif
FIGURE 9.
Mass spectra of monounsaturated C18 fatty acid DMDS derivatives (18:1ω7 and 18:1ω9) extracted from Bronydd Mawr upland grassland soil. The fragment ions denoted D, E, and F are used to determine the position of the double bonds in the original PLFA.
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig10
FIGURE 10.
Mass spectra of picolinyl esters of (a) straight-chain 17:0 fatty acid and (b) 10Me16:0 fatty acid. Note loss of ion at m/z 262 in panel b, associated with branching at position 7 on the aliphatic C chain.
10.1128/9781555816896/f0052-01_thmb.gif
10.1128/9781555816896/f0052-01.gif
FIGURE 10.
Mass spectra of picolinyl esters of (a) straight-chain 17:0 fatty acid and (b) 10Me16:0 fatty acid. Note loss of ion at m/z 262 in panel b, associated with branching at position 7 on the aliphatic C chain.
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig11
FIGURE 11.
Origin of major fragment ions in the EI mass spectra of picolinyl esters of PLFAs methyl esters.
10.1128/9781555816896/f0052-02_thmb.gif
10.1128/9781555816896/f0052-02.gif
FIGURE 11.
Origin of major fragment ions in the EI mass spectra of picolinyl esters of PLFAs methyl esters.
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig12
FIGURE 12.
Generalized schematic of a GC-C-IRMS configured for determining δ13C values of individual compounds. Inset (a) details the optimized connection of the fused silica capillary to the combustion reactor. Mixtures of compounds are separated by GC; combusted online, generating CO2 and H2O; H2O is removed; and the CO2 is introduced into an MS equipped with a triple collector comprising three Faraday cups monitoring simultaneously m/z 44, 45, and 46, corresponding to 12C16O2, 13C16O2, and 12C18O16O, respectively. The output currents are amplified and integrated to allow calculation of δ13C values. Reference CO2 and FAs of known δ13C values are utilized to monitor instrument performance and standardize determinations.
10.1128/9781555816896/f0053-01_thmb.gif
10.1128/9781555816896/f0053-01.gif
FIGURE 12.
Generalized schematic of a GC-C-IRMS configured for determining δ13C values of individual compounds. Inset (a) details the optimized connection of the fused silica capillary to the combustion reactor. Mixtures of compounds are separated by GC; combusted online, generating CO2 and H2O; H2O is removed; and the CO2 is introduced into an MS equipped with a triple collector comprising three Faraday cups monitoring simultaneously m/z 44, 45, and 46, corresponding to 12C16O2, 13C16O2, and 12C18O16O, respectively. The output currents are amplified and integrated to allow calculation of δ13C values. Reference CO2 and FAs of known δ13C values are utilized to monitor instrument performance and standardize determinations.
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig13
FIGURE 13.
The m/z 44 ion current (below) and instantaneous ratio of m/z 45/44 ions (above) recorded for the PLFAs extracted from a soil following incubation with 13CH4.PLFA assignments: 1 = C19 alkane, 2 = 14:0, 3 = i15:0, 4 = a15:0, 5 = 15:0, 6 = i16:0, 7 = 16:0, 8 = 16:1ω11, 9 = br17:0, 10 = 16:1ω7, 11 = i17:0 and 16:1ω5, 12 = a17:0, 13 = 17:1ω8, 14 = 17:0, 15 = i18:0, 16 = 18:0, 17 = cyc19:0, 18 = 18:1ω9c, 19 = 18:1ω7c, 20 = 18:1ω5, 21 = 18:2ω3,6.
10.1128/9781555816896/f0054-01_thmb.gif
10.1128/9781555816896/f0054-01.gif
FIGURE 13.
The m/z 44 ion current (below) and instantaneous ratio of m/z 45/44 ions (above) recorded for the PLFAs extracted from a soil following incubation with 13CH4.PLFA assignments: 1 = C19 alkane, 2 = 14:0, 3 = i15:0, 4 = a15:0, 5 = 15:0, 6 = i16:0, 7 = 16:0, 8 = 16:1ω11, 9 = br17:0, 10 = 16:1ω7, 11 = i17:0 and 16:1ω5, 12 = a17:0, 13 = 17:1ω8, 14 = 17:0, 15 = i18:0, 16 = 18:0, 17 = cyc19:0, 18 = 18:1ω9c, 19 = 18:1ω7c, 20 = 18:1ω5, 21 = 18:2ω3,6.
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03eq01
Untitled
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10.1128/9781555816896/e0055-01.gif
Untitled
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03eq02
Untitled
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10.1128/9781555816896/e0056-01.gif
Untitled
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03eq03
Untitled
10.1128/9781555816896/e0056-02_thmb.gif
10.1128/9781555816896/e0056-02.gif
Untitled
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03eq04
Untitled
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10.1128/9781555816896/e0056-03.gif
Untitled
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03eq05
Untitled
10.1128/9781555816896/e0056-04_thmb.gif
10.1128/9781555816896/e0056-04.gif
Untitled
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03eq06
Untitled
10.1128/9781555816896/e0056-05_thmb.gif
10.1128/9781555816896/e0056-05.gif
Untitled
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig14
FIGURE 14.
Concentrations of the total extracted PLFAs and comparison of the 13C-label concentration incorporated into each PLFA as nanograms of 13C per gram of soil dry weight following 17 to 18 weeks incubation under 2 ppmv 13CH4 for Bronydd Mawr NCaPK, CaPK, and Nil-graze soils. Error bars represent ±1 standard deviation (Maxfield et al., 2008a).
10.1128/9781555816896/f0057-01_thmb.gif
10.1128/9781555816896/f0057-01.gif
FIGURE 14.
Concentrations of the total extracted PLFAs and comparison of the 13C-label concentration incorporated into each PLFA as nanograms of 13C per gram of soil dry weight following 17 to 18 weeks incubation under 2 ppmv 13CH4 for Bronydd Mawr NCaPK, CaPK, and Nil-graze soils. Error bars represent ±1 standard deviation (Maxfield et al., 2008a).
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig15
FIGURE 15.
Comparison of Tenerife Andisol 13C-labeled PLFA distributions with published PLFA compositions of pure cultures of methanotrophic bacteria (
Bowman et al., 1993
;
Dedysh, 2002
;
Bodelier et al., 2009
). The PLFA compositions employed were the mole percentages of the PLFAs of pure cultures and the labeled PLFAs extracted from the soils. A hierarchical tree was produced by cluster analysis performed with the R v2.8.1 statistical package. Bootstrap probabilities were based on 1,000 repetitions (
Maxfield et al., 2009
).
10.1128/9781555816896/f0064-01_thmb.gif
10.1128/9781555816896/f0064-01.gif
FIGURE 15.
Comparison of Tenerife Andisol 13C-labeled PLFA distributions with published PLFA compositions of pure cultures of methanotrophic bacteria ( Bowman et al., 1993 ; Dedysh, 2002 ; Bodelier et al., 2009 ). The PLFA compositions employed were the mole percentages of the PLFAs of pure cultures and the labeled PLFAs extracted from the soils. A hierarchical tree was produced by cluster analysis performed with the R v2.8.1 statistical package. Bootstrap probabilities were based on 1,000 repetitions ( Maxfield et al., 2009 ).
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03fig16
FIGURE 16.
Landfill soil PLFA δ13C values following up to 27 days of incubation under 5,000 ppmv 13CH4 (1% enriched 13C) indicating primary (a), secondary (b), and tertiary (c) C assimilation (
Dildar, 2010
).
10.1128/9781555816896/f0066-01_thmb.gif
10.1128/9781555816896/f0066-01.gif
FIGURE 16.
Landfill soil PLFA δ13C values following up to 27 days of incubation under 5,000 ppmv 13CH4 (1% enriched 13C) indicating primary (a), secondary (b), and tertiary (c) C assimilation ( Dildar, 2010 ).
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
References
/content/book/10.1128/9781555816896.ch03
1.
Abraham, W.,, C. Hesse, and, O. Pelz. 1998. Ratios of carbon isotopes in microbial lipids as an indicator of substrate usage. Appl. Environ. Microbiol. 64 : 4202– 4209.
2.
Arao, T. 1999. In situ detection of changes in soil bacterial and fungal activities by measuring 13C incorporation into phospholipid fatty acids from 13C acetate. Soil Biol. Biochem. 31 : 1015– 1020.
3.
Balasooriya, W. K.,, K. Denef,, J. Peters,, N. E. C. Verhoest, and, P. Boeckx. 2008. Vegetation composition and soil microbial community structural changes along a wetland hydrological gradient. Hydrol. Earth System Sci. 12 : 277– 291.
4.
Barrie, A.,, J. Bricout, and, J. Koziet. 1984. Gas-chromatography—stable isotope ratio analysis at natural abundance levels. Biomed. Mass Spectrom. 11 : 439– 447.
5.
Bellinger, B. J.,, G. J. C. Underwood,, S. E. Ziegler, and, M. R. Gretz. 2009. Significance of diatom-derived polymers in carbon flow dynamics within estuarine biofilms determined through isotopic enrichment. Aquat. Microb. Ecol. 55 : 169– 187.
6.
Blumenberg, M.,, R. Seifert,, K. Nauhaus,, T. Pape, and, W. Michaelis. 2005. In vitro study of lipid biosynthesis in an anaerobically methane-oxidizing microbial mat. Appl. Environ. Microbiol. 71 : 4345– 4351.
7.
Bodelier, P. L. E.,, B. Gillisen,, M.-J. Hordijk,, K. Sinninghe Damste,, J. S. Rijpstra,, W. I. C. Geenevasen, and, P. F. Dunfield. 2009. A reanalysis of phospholipid fatty acids as ecological biomarkers for methanotrophic bacteria. ISME J. 3 : 606– 617.
8.
Boschker, H. T. S.,, S. C. Nold,, P. Wellsbury,, D. Bos,, W. de Graaf,, R. Pel,, R. J. Parkes, and, T. E. Cappenberg. 1998. Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature 392 : 801– 805.
9.
Bowman, J. P.,, L. I. Sly,, P. D. Nichols, and, A. C. Hayward. 1993. Revised taxonomy of the methanotrophs—description of Methylobacter gen-Nov, emendation of Methylococcus, validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the group-I methanotrophs. Int. J. Syst. Bacteriol. 43 : 735– 753.
10.
Bull, I. D.,, N. R. Parekh,, G. H. Hall,, P. Ineson, and, R. P. Evershed. 2000. Detection and classification of atmospheric methane oxidizing bacteria in soil. Nature 405 : 175– 178.
11.
Butler, T. J.,, D. Mellon,, J. Kim,, J. Litman, and, A. J. Orr-Ewing. 2009. Optical-feedback cavity ring-down spectroscopy measurements of extinction by aerosol particles. J. Phys. Chem. A 113 : 3963– 3972.
12.
Christie, W. W. 1989. Silver ion chromatography using solid-phase extraction columns packed with bonded-sulfonic acid phase. J. Lipid Res. 30 : 1471– 1473.
13.
Craig, H. 1957. Isotopic standards for carbon and oxygen and correction factors for mass spectrometric analysis of carbon dioxide. Geochim. Cosmochim. Acta 12 : 133– 149.
14.
Cook, P. L. M.,, B. Veuger,, S. Böer, and, J. J. Middelburg. 2007. Effect of nutrient availability on carbon and nitrogen incorporation and flows through benthic algae and bacteria in near-shore sandy sediment. Aquat. Microb. Ecol. 49 : 165– 180.
15.
Crossman, Z. M.,, F. Abraham, and, R. P. Evershed. 2004. Stable isotope pulse-chasing and compound specific stable carbon isotope analysis of phospholipid fatty acids to assess methane oxidizing bacterial populations in landfill cover soils. Environ. Sci. Technol. 38 : 1359– 1367.
16.
Crossman, Z. M.,, P. Ineson, and, R. P. Evershed. 2005. The use of C labelling of bacterial lipids in the characterisation of ambient methane-oxidising bacteria in soils. Org. Geochem. 36 : 769– 778.
17.
Crossman, Z. M.,, N. Mcnamara,, N. Parekh,, P. Ineson, and, R. P. Evershed. 2001. A new method for identifying the origins of simple and complex hopanoids in sedimentary materials using stable isotope labelling with 13CH 4 and compound specific stable isotope analyses. Org. Geochem. 32 : 359– 364.
18.
Crossman, Z. M.,, Z. Wang,, P. Ineson,, R. P. Evershed. 2006. Investigation of the effect of ammonium sulfate on populations of ambient methane oxidising bacteria by 13C-labelling and GC/C/IRMS analysis of phospholipid fatty acids. Soil Biol. Biochem. 38 : 983– 990.
19.
Dedysh, S. N. 2002. Methanotrophic bacteria of acidic Sphagnum peat bogs. Microbiology 71 : 638– 650.
20.
Deines, P.,, P. L. Bodelier, and, G. Eller. 2007. Methane-derived carbon flows through methane-oxidizing bacteria to higher trophic levels in aquatic systems. Environ. Microbiol. 9 : 1126– 1134.
21.
Dickson, L. 2009. Tracing trophic relationships of insects in cow dung using molecular and stable isotope approaches. PhD Thesis, University of Bristol
22.
Dickson, L.,, I. D. Bull,, P. J. Gates, and, R. P. Evershed. 2009. A simple modification of a silicic acid lipid fractionation protocol to eliminate free fatty acids from glycolipid and phospholipid fractions. J. Microbiol. Methods 78 : 249– 254.
23.
Dildar, N. 2010. The fate of methanotrophically fixed carbon in a landfill cap soil. PhD Thesis, University of Bristol, Bristol, UK.
24.
Dowling, N. J.,, F. Widdel, and, D. C. White. 1986. Phospholipid ester-linked fatty acid biomarkers of acetate-oxidizing sulphate-reducers and other sulphide-forming bacteria. Microbiology 132 : 1815– 1825.
25.
Ekblad, A., and, P. Hogberg. 2000. Analysis of δ 13C of CO 2 distinguishes between microbial respiration of added C4-sucrose and other soil respiration in a C3-ecosystem. Plant Soil 219 : 197– 209.
26.
Evershed, R. P. 1992. Mass spectrometry of lipids, P. 263–308. In R. J. Hamilton and, S. Hamilton (ed.), Lipid Analysis: A Practical Approach. IRL Press, Oxford, UK.
27.
Evershed, R. P.,, Z. M. Crossman,, I. D. Bull,, H. R. 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. Opin. Biotechnol. 17 : 72– 82.
28.
Evrard, V.,, P. L. M. Cook,, B. Veuger,, M. Huettel, and, J. J. Middelburg. 2008. Tracing carbon and nitrogen incorporation and pathways in the microbial community of a photic subtidal sand. Aquat. Microb. Ecol. 53 : 257– 269.
29.
Feisthauer, S.,, L. Y. Wick,, M. Kästner,, S. R. Kaschabek,, M., Schlömann, and, H. H. Richnow. 2008. Differences of heterotrophic 13CO 2 assimilation by Pseudomonas knackmussii strain B13 and Rhodococcus opacus 1CP and potential impact on biomarker stable isotope probing. Environ. Microbiol. 10 : 1641– 1651.
30.
Frostegård, Å., and, E. Bååth,. 1996. The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil. Biol. Fertil. Soils 22 : 59– 65.
31.
Frostegård, Å.,, A. Tunlid, and, E. Bååth,. 1991. microbial biomass measured as total lipid phosphate in soils of different organic content. J. Microbiol Methods 14 : 151– 163.
32.
Hanson, J. R.,, J. L. Macalady,, D. Harris, and, K. M. Scow. 1999. Linking toluene degradation with specific microbial populations in soil. Appl. Environ. Microbiol. 65 : 5403– 5408.
33.
Harvey, D. J. 1984. Picolinyl derivatives for the structural determination of fatty acids by mass spectrometry: applications to polyenoic acids, hydroxy acids, di-acids and related compounds. Biol. Mass Spectrom. 11 : 340– 347.
34.
Harwood, J. L., and, N. J. Russell. 1984. Lipids in Plants and Microbes. George Allen & Unwin Ltd., London, UK.
35.
Kindler, R.,, A. Miltner,, H. Richnow, and, M. Kastner. 2006. Fate of gram-negative bacterial biomass in soil—mineralization and contribution to SOM. Soil Biol. Biochem. 38 : 2860– 2870.
36.
Kindler, R.,, A. Miltner,, M. Thullner,, H. Richnow, and, M. Kastner. 2009. Fate of bacterial biomass derived fatty acids in soil and their contribution to soil organic matter. Org. Geochem. 40 : 29– 37.
37.
Knief, C.,, S. Kolb,, P. L. Bodelier,, A. Lipski, and, P. F. Dunfield. 2006. The active methanotrophic community in hydromorphic soils changes in response to changing methane concentration. Environ. Microbiol. 8 : 321– 333.
38.
Knief, C.,, A. Lipski, and, P. F. Dunfield . 2003. Diversity and activity of methanotrophic bacteria in different upland soils. Appl. Environ. Microbiol. 69 : 6703– 6714.
39.
Knowles, T. D. J.,, D. R. Chadwick,, R. Bol, and, R. P. Evershed. 2010. Tracing the rate and extent of N and C flow from 13C, 15N-glycine and glutamate into individual de novo synthesized soil amino acids. Org. Geochem. doi: 10.1016/j. Orggeochem.2010.09.003.
40.
Kramer, C., and, G. Gleixner. 2008. Soil organic matter in soil depth profiles: distinct carbon preferences of microbial groups during carbon transformation. Soil Biol. Biochem. 40 : 425– 433.
41.
Leckrone, K. J., and, J. M. Hayes. 1998. Water-induced errors in continuous-flow carbon isotope ratio mass spectrometry. Anal. Chem. 70 : 2737– 2744.
42.
Lechevalier, H., and, M. P. Lechevalier. 1988. Chemotaxonomic use of lipids—an overview, P. 869–902. In C. Ratledge and, S. G. Wilkinson (ed.), Microbial Lipids, vol. 1. Academic Press Ltd, London, UK.
43.
Lerch, T.,, M. Dignac,, N. Nunan,, G. Bardoux,, E. Barriuso, and, A. Mariotti. 2009. Dynamics of soil microbial populations involved in 2,4- d biodegradation revealed by FAME-based Stable Isotope Probing. Soil Biol. Biochem. 41 : 77– 85.
44.
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 : 179– 186.
45.
Lueders, T.,, R. Kindler,, A. Miltner,, M. W. Friedrich, and, M. Kaestner. 2006. Identification of bacterial micropredators distinctively active in a soil microbial food web. Appl. Environ. Microbiol. 72 : 5342– 5348.
46.
Malosso, E.,, L. English,, D. W. Hopkins, and, A. G. O'Donnell. 2004. Use of 13C-labelled plant materials and ergosterol, PLFA and NLFA analyses to investigate organic matter decomposition in Antarctic soil. Soil Biol. Biochem. 36 : 165– 175.
47.
Matthews, D. E., and, J. M. Hayes. 1978. Isotoperatio-monitoring gas chromatography-mass spectrometry. Anal. Chem. 50 : 1465– 1473.
48.
Mauclaire, L.,, O. Pelz,, M. Thullner,, W. R. Abraham, and, J. Zeyer. 2003. Assimilation of toluene along a bacteria-protist food chain determined by 13C-enrichment of biomarker fatty acids. J. Microbiol. Methods 55 : 635– 649.
49.
Maxfield, P. J.,, E. Brennand,, D. S. Poulson, and, R. P. Evershed. 2009. Impact of agricultural practices and land use change in the Rothamsted Classical Experiment on high affinity methanotrophic bacterial populations. Euro. J. Soil Sci., in press.
50.
Maxfield, P. J.,, E. R. C. Hornibrook, and, R. P. Evershed. 2006. Estimating high-affinity methanotrophic bacterial biomass, growth, and turnover in soil by phospholipid fatty acid 13C labeling. Appl. Environ. Microbiol. 72 : 3901– 3907.
51.
Maxfield, P. J.,, E. R. C. Hornibrook, and, R. P. Evershed. 2008a. Acute impact of agriculture on high-affinity methanotrophic bacterial populations. Environ. Microbiol. 10 : 1917– 1924.
52.
Maxfield, P. J.,, E. R. C. Hornibrook, and, R. P. Evershed. 2008b. Physical and biological controls on the in situ kinetic isotope effect associated with oxidation of atmospheric CH 4 in mineral soils. Environ. Sci. Technol. 42 : 7824– 7830.
53.
Maxfield, P. J.,, E. R. C. Hornibrook, and, R. P. Evershed. 2009. Substantial high-affinity methanotroph populations in andisols affect high rates of atmospheric methane oxidation. Environ. Microbiol. Reports 1 : 450– 456.
54.
Menyailo, O. V.,, B. A. Hungate,, W. Abraham, and, R. Conrad. 2008. Changing land use reduces soil CH 4 uptake by altering biomass and activity but not composition of high-affinity methanotrophs. Global Change Biol. 14 : 2405– 2419.
55.
Merritt, D. A.,, W. A. Brand, and, J. M. Hayes. 1994. Isotope-ratio-monitoring gas chromatography-mass spectrometry: methods for isotopic calibration. Org. Geochem. 21 : 573– 583.
56.
Merritt, D. A.,, K. H. Freeman,, M. P. Ricci,, S. A. Studley, and, J. M. Hayes. 1995. Performance and optimisation of a combustion interface for isotope ratio monitoring gas chromatography/mass spectrometry. Anal. Chem. 67 : 2461– 2473.
57.
Merritt, D. A., and, J. M. Hayes. 1994. Factors controlling precision and accuracy in isotoperatio monitoring mass spectrometry. Anal. Chem. 66 : 2336– 2347.
58.
Middelburg, J. J.,, C. Barranguet,, H. T. S. Boschker,, P. M. J. Herman,, T. Moens, and, C. H. R. Heip. 2000. The fate of intertidal microphytobenthos carbon: an in situ C 13 labeling study. Limnol. Oceanogr. 45 : 1224– 1234.
59.
Miltner, A.,, R. Kindler,, H. Knicker,, H. Richnow, and, M. Kästner. 2009. Fate of microbial biomassderived amino acids in soil and their contribution to soil organic matter. Org. Geochem. 40 : 978– 985.
60.
Moore-Kucera, J., and, R. P. Dick. 2008. Application of 13C-labeled litter and root materials for in situ decomposition studies using phospholipid fatty acids. Soil Biol. Biochem. 40 : 2485– 2493.
61.
Mottram, H. R., and, R. P. Evershed. 2003. Practical considerations in the gas chromatography/combustion/isotope ratio monitoring mass spectrometry of 13C-enriched compounds: detection limits and carryover effects. Rapid Commun. Mass Spectrom. 17 : 2669– 2674.
62.
Nakano-Hylander, A., and, P. Olsson. 2007. Carbon allocation in mycelia of arbuscular mycorrhizal fungi during colonisation of plant seedlings. Soil Biol. Biochem. 39 : 1450– 1458.
63.
Nold, S. C.,, H. T. S. Boschker,, R. Pel, and, H. J. Laanbroek. 1999. Ammonium addition inhibits C 13-methane incorporation into methanotroph membrane lipids in a freshwater sediment. FEMS Microbiol. Ecol. 29 : 81– 89.
64.
Nottingham, A. T.,, H. Griffiths,, P. M. Chamberlain,, A. W. Stott, and, E. V. J. Tanner. 2009. Soil priming by sugar and leaf-litter substrates: a link to microbial groups. Appl. Soil Ecol. 42 : 183– 190.
65.
Ostle, N.,, P. Ineson,, D. Benham, and, D. Sleep. 2000. Carbon assimilation and turnover in grassland vegetation using an in situ 13CO 2 pulse labelling system. Rapid Commun. Mass Spectrom. 14 : 1345– 1350.
66.
Pelz, O.,, A. Chatzinotas,, A. Zarda-Hess,, W. R. Abraham, and, J. Zeyer. 2001. Tracing toluene-assimilating sulfate-reducing bacteria using C-13-incorporation in fatty acids and whole-cell hybridization. FEMS Microbiol. Ecol. 38 : 123– 131.
67.
Pombo, S. A.,, J. Kleikemper,, M. H. Schroth, and, J. Zeyer. 2005. Field-scale isotopic labelling of phospholipid fatty acids from acetate degrading sulfate-reducing bacteria. FEMS Microbiol. Ecol. 51 : 197– 201.
68.
Pombo, S. A.,, O. Pelz,, M. H. Schroth, and, J. Zeyer. 2002. Field-scale 13C-labeling of phospholipid fatty acids (PLFA) and dissolved inorganic cabon: tracing acetate assimilation and mineralisation in a petroleum hydrocarbon-contaminated aquifer. FEMS Microbiol Ecol. 41 : 259– 267.
69.
Raghoebarsing, A. A.,, A. J. Smolders,, M. C. Schmid,, W. I. Rijpstra,, M. Wolters-Arts,, J. Derksen,, M. S. M. Jetten,, S. Schouten,, J. S. Sinninghe Damste,, L. P. M. Lamers,, J. G. M. Roelofs,, H. J. M. Op den Camp, and, M. Strous. 2005. Methanotrophic symbionts provide carbon for photosynthesis in peat bogs. Nature 436 : 1153– 1156.
70.
Ricci, M. P.,, D. A. Merritt,, K. H. Freeman, and, J. M. Hayes. 1994. Acquisition and processing of data for isotope-ratio-monitoring mass spectrometry. Org. Geochem. 21 : 561– 571.
71.
Rieley, G. 1994. Derivatization of organic-compounds prior to gas-chromatographic combustion-isotope ratio mass-spectrometric analysis—identification of isotope fractionation processes. Analyst 119 : 915– 919.
72.
Rinnan, R., and, E. Bååth. 2009. Differential utilization of carbon substrates by bacteria and fungi in tundra soil. Appl. Environ. Microbiol. 75 : 3611– 3620.
73.
Rubino, M.,, J. A. J. Dungait,, R. P. Evershed,, T. Bertolini,, P. De Angelis,, A. D'Onofrio,, A. Lagomarsino,, C. Lubritto,, A. Merola,, F. Terrasi, and, M. F. Cotrufo. 2010. Carbon input belowground is the major C flux contributing to leaf litter mass loss: evidences from a 13C labelled-leaf litter experiment. Soil Biol. Biochem. 42 : 1009– 1016.
74.
Sessions, A.,, L. L. Jahnke,, A. Schimmelmann, and, J. M. Hayes. 2002. Hydrogen isotope fractionation in lipids of the methane-oxidizing bacterium Methylococcus capsulatus. Geochim. Cosmochim. Acta 66 : 3955– 3969.
75.
Shrestha, M.,, W. R. Abraham,, P. M. Shrestha,, M. Noll, and, R. Conrad. 2008. Activity and composition of methanotrophic bacterial communities in planted rice soil studied by flux measurements, analyses of pmoA gene and stable isotope probing of phospholipid fatty acids. Environ. Microbiol. 10 : 400– 412.
76.
Singh, B. K., and, K. Tate. 2007. Biochemical and molecular characterization of methanotrophs in soil from a pristine New Zealand beech forest. FEMS Microbiol. Lett. 275 : 89– 97.
77.
Singh, B. K.,, K. R. Tate,, G. Kolipaka,, C. B. Hedley,, C. A. Macdonald,, P. Millard, and, J. C. Murrell. 2007. Effect of afforestation and reforestation of pastures on the activity and population dynamics of methanotrophic bacteria. Appl. Environ. Microbiol. 73 : 5153– 5161.
78.
Singh, B. K.,, K. R. Tate,, D. J. Ross,, J. Singh,, J. Dando,, N. Thomas,, P. Millard, and, J. C. Murrell. 2009. Soil methane oxidation and methanotroph responses to afforestation of pastures with Pinus radiata stands. Soil Biol. Biochem. 41 : 2196– 2205.
79.
Tate, K.,, D. Ross,, S. Saggar,, C. Hedley,, J. Dando,, B. Singh, and, S. M. Lambie. 2007. Methane uptake in soils from Pinus radiata plantations, a reverting shrubland and adjacent pastures: effects of land-use change, and soil texture, water and mineral nitrogen. Soil Biol. Biochem. 39 : 1437– 1449.
80.
Treonis, A. 2004. Identification of groups of met-abolically-active rhizosphere microorganisms by stable isotope probing of PLFAs. Soil Biol. Biochem. 36 : 533– 537.
81.
Van Oevelen, D.,, J. J. Middelburg,, K. Soetaert, and, L. Moodley. 2006. The fate of bacterial carbon in an intertidal sediment: Modelling an in situ isotope tracer experiment. Limnol. Oceanogr. 51 : 1302– 1314.
82.
Vestal, J. R., and, D. C. White. 1989. Lipid analysis in microbial ecology—quantitative approaches to the study of microbial communities. Bioscience 39 : 535– 541.
83.
Veuger, B., and, J. J. Middelburg. 2007. Incorporation of nitrogen from amino acids and urea by benthic microbes: role of bacteria versus algae and coupled incorporation of carbon. Aquat. Microb. Ecol. 48 : 35– 46.
84.
Veuger, B.,, D. Van Oevelen,, H. T. S. Boschker, and, J. J. Middelburg. 2006. Fate of peptidoglycan in an intertidal sediment: An in situ 13C-labeling study. Limnol. Oceanogr. 51 : 1572– 1580.
85.
Waldrop, M. P., and, M. K. Firestone. 2004. Microbial community utilization of recalcitrant and simple carbon compounds: impact of oak-woodland plant communities. Oecologia 138 : 275– 284.
86.
Ward, S. E.,, R. D. Bardgett,, N. P. McNamara, and, N. J. Ostle. 2009. Plant functional group identity influences short-term peatland ecosystem carbon flux: evidence from a plant removal experiment. Functional Ecol. 23 : 454– 462.
87.
Webster, G.,, L. C. Watt,, J. Rinna,, J. C. Fry,, R. P. Evershed,, R. J. Parkes, and, A. J. Weightman. 2006. A comparison of stable-isotope probing of DNA and phospholipid fatty acids to study prokaryotic functional diversity in sulfate-reducing marine sediment enrichment slurries. Environ. Microbiol. 8 : 1575– 1589.
88.
White, D. C.,, W. M. Davis,, J. S. Nickels,, J. D. King, and, R. J. Bobbie. 1979. Determination of the sedimentary microbial biomass by extractable lipid phosphate. Oecologia 40 : 51– 62.
89.
Williams, M. A.,, D. D. Myrold, and, P. J. Bottomley. 2006. Carbon flow from 13C-labeled straw and root residues into the phospholipid fatty acids of a soil microbial community under field conditions. Soil Biol. Biochem. 38 : 759– 768.
90.
Wu, W. X.,, W. Liu,, H. H. Lu,, Y. X. Chen,, D. Medha, and, T. Janice. 2009. Use of 13C labeling to assess carbon partitioning in transgenic and nontransgenic (parental) rice and their rhizosphere soil microbial communities. FEMS Microbiol. Ecol. 67 : 93– 102.
91.
Xu, Y. P.,, M. P. Cooke,, H. M. Talbot, and, M. J. Simpson. 2009. Bacteriohopanepolyol signatures of bacterial populations in Western Canadian soils. Org. Geochem. 40 : 79– 86.
92.
Zelles, L. 1999. Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol. Fertil. Soil 29 : 111– 129.
93.
Zhang, X.,, H. He, and, W. Amelung. 2007. A GC/MS method for the assessment of 15N and 13C incorporation into soil amino acid enantiomers. Soil Biol. Biochem. 39 : 2785– 2796.
94.
Ziegler, S. E.,, P. M. White,, D. C. Wolf, and, G. J. Thoma. 2005. Tracking the fate and recycling of 13C-labeled glucose in soil. Soil Science 170 : 767– 778.
Tables
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology
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Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03tab01
TABLE 1
The structure and distribution of major phospholipids
a
TABLE 1
The structure and distribution of major phospholipids a
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03tab02
TABLE 2
Nomenclature of some naturally occurring fatty acids
TABLE 2
Nomenclature of some naturally occurring fatty acids
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03tab03
TABLE 3
Classes of PLFAs associated with particular taxonomic or functional groups of microorganisms
a
TABLE 3
Classes of PLFAs associated with particular taxonomic or functional groups of microorganisms a
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3
/content/10.1128/9781555816896.ch03.ch03tab04
TABLE 4
Summary of PLFA 13C-labeling studies of environmental microbial communities
TABLE 4
Summary of PLFA 13C-labeling studies of environmental microbial communities
Citation:
Maxfield P, Evershed R.
2011.
Phospholipid Fatty Acid Stable Isotope Probing Techniques in Microbial Ecology,
p 37-71.
In
Murrell J, Whiteley A (ed),
Stable Isotope Probing and Related Technologies.
ASM Press, Washington, DC.
doi: 10.1128/9781555816896.ch3