Gene sequences, most commonly those encoding rRNAs, provide a basis for estimating microbial phylogenetic diversity ( 5, 7, 14– 18) and generating taxonomic inventories of marine microbial populations ( 5, 7, 14– 18). Two inescapable conclusions emerge from these phylogenetic, genomic, and metagenomic analyses: ( i) microbes account for the majority of genetic and metabolic variation in the oceans and ( ii) the genetic diversity, community composition, relative abundance, and distribution of microbes in the sea remain undersampled and essentially uncharted. There is evidence of hitherto unrecognized physiological groups among the planktonic microbes ( 12, 13). Recurrent discoveries of novel genetic information suggest that cryptic “genetic reservoirs” reshape genomic architecture through lateral gene transfer processes ( 11). At the genomic level, comparisons of chromosomal size sequences from cultivars, marine microbial metagenomic analyses of bacterial artificial chromosomes ( 9), and shotgun small-insert libraries ( 10) reveal unanticipated levels of metabolic diversity and extensive horizontal gene transfer. There have been spectacular discoveries of previously unknown microorganisms, many of which have major impacts on oceanic processes ( 6– 8). With each new survey, this window on the microbial world increases in size. Direct interrogation of microbial genomes based on comparisons of orthologous gene sequences have shown that, in addition to enormous phylogenetic diversity, the complexity of microbial life (the number of different kinds or “species” of microbes) is at least 100 times greater than estimates based on cultivation-dependent surveys ( 5).
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