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Many new microbial lineages have recently been discovered in the course of ribosomal RNA-based environmental surveys (1). Although the recognition of such extensive diversity has been exhilarating, it also raises large questions about the nature, activities, and ecological significance of all this newly recognized microbial life. What are the specific biological properties of environmentally abundant but previously unrecognized microbial groups? Are these new microbes significantly different from commonly cultivated laboratory strains? Do ubiquitous, newly recognized microbial species significantly impact their surrounding environment, and if so, how? In this issue of PNAS, the work of Ingalls et al. (2) illustrates one powerful approach for addressing such questions. These authors, led by Ann Pearson of Harvard University, used compound-specific isotope analyses (3) to track the flow of organic and inorganic carbon into the lipids of naturally occurring Archaea in deep ocean waters. Their results extend and confirm the notion that one group of marine Archaea, the Crenarchaea, are autotrophic and derive their carbon from CO2. Ingalls et al. (2) convincingly demonstrate that CO2 is a main carbon source for deep-sea Crenarchaea, indicating one major biogeochemical role for Archaea in the sea. Archaea have a dramatically different lipid composition compared with other cellular life. Although Bacteria and Eucarya possess mainly ester-linked fatty acids in their lipids, archaeal cell membranes are composed predominantly of ether-linked isoprenoid core lipids (structure I, for example, in Fig. 1 B). Some Archaea biosynthesize lipid bilayers composed of 20-carbon isoprenoid units, individually linked to a single glycerol backbone by an ether bond—these form conventional lipid bilayers. Other archaeal lipids include 40-carbon isoprenoids that are ether-linked at either end of their carbon chain to glycerol, thereby spanning the entire membrane in a tetraether monolayer (structure I in Fig. 1 B). These unique lipids provide specific biomarkers that …

Archaeal mysteries of the deep revealed