Biomarkers microbial

A range of biomarkers (biological markers) have been developed for the detection of microorganisms using both their genetic (DNA and RNA) and biochemical components. Most methods have originated from studies on pure isolates and have been adapted to identify and quantify either the total or a sub.set of the microbial biomass in a sample. In these methods,. specific taxonomic or pheno-... 

The previous biomarkers relate to phenotypic assessments of microbial diversity and most will probably measure a restricted part of the total microbial pool, since not alt markers will be expressed uniformly by every cell. In contrast, methods involving the detection of nucleic acids may be directly applicable to all microorganisms provided that the complete extraction of DNA (lysis of cells) or permea-bilization of cells can be achieved. 

TABLE 4.1 Examples of Microbial Biomarkers and Potential Source Organisms (Volkman, 1986 Ourisson et al., 1987 Ratledge and Wilkinson, 1988 Mayer et al., 1989 Conte et al., 1994 Jeffrey et al.,... 

The biomarker molecules are particularly resistant to microbial attack, and thus the ratio of other hydrocarbon components to the biomarker will decrease as the crude oil is biodegraded (Wang et al., 1994). In the case of an ongoing oil discharge into the soil, this ratio will be highest nearest the source and will decrease with increasing distance from the source. Thus, the ratio may be used to locate the source of the contaminant (Whittaker et al., 1995). 

The hopane series are the natural product biomarkers elucidated initially as attributable to bacteria.The 17a(H),2ip(H)-hopanes ranging from C27 to C35 (no C28) were encountered in numerous ancient sediments and petroleums, and diagenesis and maturation of the microbial precursors (e.g. bacteriohopanepolyol and diploptene, Fig. 4) were elucidated. The diagenesis of diploptene in contemporary sediments proceeds by double bond migration from via to... 

The example of a total extract composition of a tropical soil from the Amazon, Brazil, shows mycose as the major compound, numerous other monosaccharides, lipid components such as fatty acids and fatty alcohols, and natural product biomarkers (Fig. 9a). The mycose and elevated levels of the other saccharides reflect the efficient fungal/microbial degradation of plant detritus in the tropics. This can be compared to the saccharides in the soil from an almond orchard in California, where glucose and mycose are the main sugars with lipids, sterols and triterpenoids (Fig. 9b, ). 

The branched f -alkane series are biomarkers because of the locale of their occurrence and the presence of only alternate pseudohomologs (even- or odd-carbon numbers only). Their inferred origin is from probable microbial precursors of unknown species, where methylation and ethylation, diethylation, butylation and ethylation occurred during biosynthesis... 

Signature lipid biomarkers (SLB), or fatty acid profiling, is another molecular approach that has become widely used to study microbial communities (White and Ringelberg 1998) because, like nucleic acid methods, it is not dependent on the growth or morphology of organisms but relies on the direct... 

White, D. C. and Ringelberg, D. B. (1998). Signature lipid biomarker analysis, in Techniques in Microbial Ecology (R. S. Burlage, R. M. Atlas, D. A. Stahl, G. Geesey, and G. S. Sayler, Eds.). Oxford Oxford University Press, 255-272. 

Boschker, H.T.S., de Brower, I.F.C., and Cappenberg, T.E. (1999) The contribution of macrophyte-derived organic matter to microbial biomass in salt-marsh sediments Stable carbon isotope analysis of microbial biomarkers. Limnol. Oceanogr. 44, 309-319. 

Boschker, H. T. S., andMiddelburg, J.J. (2002). Stable isotopes and biomarkers in microbial ecology. FEMS Microbiol. Ecol. 40, 85—95. 

Figure 21 Comparison of vertical distribution of biomarker and microbial abundances in oceanic water columns, (a) Contour plots of concentration (ngL ) of hexadecanoic acid, (b) Crenarcheol at various depths in the water column and distances from shore on a northwest-to-southeast transect off Oman in the Arabian Sea (after Sinninghe Damste et al, 2002). Hexadecanoic acid serves as a biomarker proxy for eukaryotic and bacterial biomass and clearly shows the expected surface maximum, with concentrations dropping off steeply with increasing water depth. In contrast, crenarcheol, a molecular biomarker for planktonic crenarcheota, shows two maxima with one near 50 m and the other —500 m. (c) Vertical distributions of microbial concentrations in the North Pacific subtropical gyre bacteria (solid squares) and planktonic crenarcheota (open squares). Effectively, there are two microbial domains which were determined using a DAPI nucleic acid stain (after Karner et al., 2001). These data show the increasing proportion of planktonic archea in deep waters, with the result that at depths greater than 2,000 m, the crenarcheota are as abundant...

Rather interestingly, the oldest usable biomarkers in carbonaceous shales date from the Neoarchean. Molecular fossils extracted from 2.5 Ga to 2.7 Ga shales of the Fortescue and Hamersley groups in the Pilbara Craton, Western Australia, indicate that the photic zone of the water column in the areas where these shales were deposited was probably weakly oxygenated, and that cyanobacteria were part of the microbial biota (Brocks et al., 1999, 2002 Summons et al., 1999). The similarity of the timing of the rise in the range of in sediments and the earliest evidence for the presence of cyanobacteria may, however, be coincidental, because to date no sediments older than 2.7 Ga have been found that contain usable biomarker molecules (Brocks, personal communication, 2002). 

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