Quantitative comparisons ofin situ microbial biodiversity by signature biomarker analysis

Microscopic examinations have convinced microbial ecologists that the culturable microbes recovered from environmental samples represent a tiny proportion of the extant microbiota. Methods for recovery and enzymatic amplification of nucleic acids from environmental samples have shown that a huge diversity existsin situ, far exceeding any expectations which were based on direct microscopy. It is now theoretically possible to extract, amplify and sequence all the nucleic acids from a community and thereby gain a comprehensive measure of the diversity as well as some insights into the phylogeny of the various elements within this community. Unfortunately, this analysis becomes economically prohibitive if applied to the multitude of niches in a single biome let alone to a diverse set of environments. It is also difficult to utilize PCR amplification on nucleic acids from some biomes because of coextracting enzymatic inhibitors. Signature biomarker analysis which potentially combines gene probe and lipid analysis on the same sample, can serve as a complement to massive environmental genome analysis in providing quantitative comparisons between microniches in the biome under study. This analysis can also give indications of the magnitude of differences in biodiversity in the blome as well as provide insight into the phenotypic activities of each community in a rapid and cost-effective manner. Applications of signature lipid biomarker analysis to define quantitatively the microbial viable biomass of portions of an Eastern USA deciduous forest, are presented.     

Comparison of Isocitrate Dehydrogenase Activity, Pyruvate Kinase Activity, and Polyphenol Content in Physiologically Different Pine Callus Tissue

During the growth of callus tissue of slash pine (Pinus elliottil Engelm.) several physiologically different types of tissue can be observed, often within the same culture. Different tissues were selected, based on color appearance, and used to determine isocitrate dehydrogenase and pyruvate kinase activity, and total polyphenol content. Isocitrate dehydrogenase and pyruvate kinase activity in yellow tissue was 3- to 5-fold greater than in brown tissue, whereas the polyphenol content in yellow tissue was approximately 5-fold less than in brown tissue. Dark brown callus, which also contained large amounts of polyphenols, did not have detectable enzyme activity. The differences in optimal concentrations of substrate and cofactors for the isocitrate dehydrogenase and pyruvate kinase reactions in yellow and brown tissues were very minor and therefore cannot account for the 3- to 5-fold difference in enzyme activity between these tissues. Also, the addition of brown or dark-brown tissue extract to the yellow tissue extract did not inhibit isocitrate dehydrogenase or pyruvate kinase activity in the yellow tissue extract.