aFatty acids are described as follows. The number of carbons in the chain is followed by a colon, then by the number of unsaturations. w precedes the number of C atoms between the terminal double bond and the methyl end of the molecule. c, cis (most common form, omitted in most cases); t, trans; i, iso methyl branching (second C from the methyl end); a, anteiso methyl branching (third C from the methyl end); Me, follows position of methyl branching; cy, cyclopropane ring.

^Adapted from Vestal and White (1989).

and can be analyzed by: (1) colorimetric analysis of the phosphate after hydrolysis, (2) colorimetric analysis or gas chromatography (GC) after esterification, (3) capillary GC, and (4) GC-mass spectrometry or triple-quadruple mass spectrometry. The mass profile on mass spectrometry yields information on phospholipid classes present and on their relative intensities. Fragmentation spectra can provide the empirical formulas. The phosphatidic mass profiles can be compared by constructing a dendrogram to determine similarity indices of phospholipids from isolated organisms. The type of phospholipid fatty acid group also supplies information; bacteria contain odd-chain methyl-branched and cyclopropane fatty acids.

The odd-number and branched-chain fatty acids are produced by gram-positive (G+) bacteria, whereas the even-number, straight-chain and cyclopropyl fatty acids tend to be derived from G~ bacteria (Table 3.5). The straight-chain fatty acids, although of limited taxonomic value, can be used as indicators of microbial biomass. Unsaturation is associated with anaerobiosis, e.g., 18:1; 11C is found in anaerobic bacteria as well as in most G~ aerobes. The fatty acids 18:2w6 account for 43% of the total fatty acids of 47 species of soil fungi. The fatty acids of arbuscular mycor-rhizal fungi (AMF) offer special opportunities for identification and quantification; 16:1 w5 is found in the AMF genus Glomus and 20:1 w9 in the Gigaspora species. These fatty acids make it possible to differentiate non-AMF and provide an infection index for plant roots. 14C and 13C labeling and measurement of the tracer in fatty acids such as those in the AMF allow in situ determinations of turnover rates of the mycorrhizal symbionts by GC/MS. The ratios of cyclopropyl/ monoenoic precursors and total saturated/total monounsaturated fatty acids are applied as indicators of microbial stress in soils (Fierer et al., 2003). Recently, the fatty acid composition of soil animals was also used as indicator of animal diets in belowground systems (Ruess et al., 2004).

TABLE 3.5 Marker Fatty Acids in the Phospholipid Fraction of Several Groups of Organisms

Fatty acid


16:1m9, 15:0, i15:0 Cyl5:l 16:0, 18:3w3 il6:0 16:1u5

16:1u7, l6:lu7t l6:lul3t cyl7:0, cyl9:0 17:1u6, il7:lw7 18:1u7 18:1w9

l8:lull, 26:0 18:2u6

l8:3w3, l8:3w6 20:lu9

Eubacteria in general, cyanobacteria, actinomycetes



Gram-positive bacteria Cyanobacteria, AM fungi (e.g., Glomus) Eubacterial aerobes Green algae

Eubacterial anaerobes, gram-negative bacteria Sulfate-reducing eubacteria, actinomycetes Eubacterial aerobes, gram-negative bacteria Fungi, green algae, higher plants, gram-positive bacteria Higher plants

Eukaryotes, cyanobacteria, fungi Fungi, green algae, higher plants AM fungi (e.g., Gigasporea rosea) Protozoa

Barophyllica, psychrophilic eubacteria

While PLFA profiling is a well-established method in soil ecology, phospholipid ether lipid (PLEL) analyses for the characterization of Archaea is a rather new approach (Gattinger et al., 2003). PLEL-derived isoprenoid side chains are measured by GC/MS and provide a broad picture of the archaeal community in a mixed soil extract, because lipids identified in isolates belonging to the Subkingdom Eury- and Crenarchaeota are covered. Monomethyl-branched alka-nes dominate and account for 43% of the total identified ether-linked hydrocarbons, followed by straight-chain (unbranched) and isoprenoid hydrocarbons, which account for 34.6 and 15.5%, respectively.

The quinone profile, which is represented as a molar fraction of each quinone type in a soil, is a simple and useful tool to analyze population dynamics in soils; the total amount of quinones can be used as an indicator of microbial biomass (Fujie et al., 1998). Quinones are essential components in the electron transport systems of most organisms and are present in the membranes of mitochondria and chloro-plasts. Isoprenoid quinones are chemically composed of benzoquinone (or naph-thoquinone) and an isoprenoid side chain (Fig. 3.1). There are two major groups of quinones in soils: ubiquinones (1-methyl-2-isoprenyl-3,4-dimethoxypara-benzoquinone) and menaquinones (1-isoprenyl-2-methylnaphthoquinone). The nomenclature of bacterial quinones is as follows: the abbreviation for the type of quinone (ubiquinone, Q; menaquinone, MK) followed by a dash and the number of isoprene units in its side chain and the number of hydrogen atoms in the

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