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The unsung heroes of the Ribosomal Database Project (RDP) quietly raced past an important milestone sometime last August when they added the 100,000th 16S gene sequence to their rapidly growing collection. More sequences pour in, meaning the total soon could surpass 200,000, if it has not done so already. But the RDP, which is maintained by Center for Microbial Ecology at Michigan State University (MSU) in East Lansing, Mich., is more than the sum of its epic numbers. It is a treasure chest of data describing unexpected microbiological diversity, containing a richness that remains largely underappreciated and understudied.

            By several criteria, these numbers are impressive, and outright “staggering,” according to some of the scientists working in this area. For instance, try comparing these numbers to those being collected as part of microbial genomic sequencing efforts, a related field in which large datasets are talked about in similarly hyperbolic language. As of mid-November 2004, there were datasets for 168 completed and 2 incompletely sequenced genomes for 18 archaea and 150 bacteria available through the Comprehensive Microbial Resource (CMR) website that is maintained by the Institute for Genomic Research (TIGR) in Rockville, Md. Those are figures not to scoff at, reflecting plenty of hard labor. Nonetheless, such microbial genome sequence gathering seems only a drop in the biodiversity bucket when juxtaposed to the accumulating volumes of ribosomal gene sequences. But enough of unfairly comparing apples and oranges.

            Ribosomal sequencing deserves the attention and efforts it receives in large part because it “revolutionized taxonomy,” says microbiologist Karl Schleifer of Technische Universität München in Munich, Germany. Much of the credit for that revolution goes to Carl Woese of the University of Illinois (UI), Champaign-Urbana, and his collaborators. From comparative analyses of partial sequences of small subunit (SSU) rRNA molecules, Woese deduced that organisms could be divided into three domains: Bacteria, Archaea, and Eucarya.

            However, “not only taxonomists benefited from these studies, but also ecologists,” Schleifer continues. PCR amplification techniques now enable researchers to pluck small-subunit rRNA gene sequences from the environment without culturing individual species. “This was a major breakthrough in microbial ecology,” he says, noting how this approach enables ecologists to begin characterizing and classifying microbial species merely on the basis of their 16S rRNA gene sequences.

            “I recall writing a review in ASM News in the mid-1980s (ASM News, January 1985, p.4-12), just as the environmental stuff was dropping onto the table, and touting ‘some two dozen small-subunit rRNA sequences are now known,’ says Norm Pace of the University of Colorado, Boulder, a champion of this PCR-based, environmental sampling approach to microbial ecology.  “Now I am blown away not only by the number, but also the diversity.” He points out that these accumulating ribosomal gene sequences led microbiologists from knowing only about 12 phylogenetic divisions, all of which had representatives that could be cultured, to recognizing about 80 such divisions, of which a mere 20 have representatives that can be cultured.

            From such sequencing data, “we can build natural classes rather than classes based on subjective physical properties,” Pace continues. The approach “also gives us a metric rather than [relying] on a series of anecdotes. Our culture-based view of microbiology is horribly skewed The sequences don't tell us everything, but at least we know the ground plan, and we can know what's out there. I can't begin to say how profound that is.”

            This approach is not only profound but also practical, according to MSU microbiologist George Garrity, who is also editor in chief of Bergey's Manual. The 16S ribosomal gene sequence is now being used as a “digital object identifier” for microorganisms, thus serving as a key to “the history of a microorganism and a pointer to gaining access to all the other data about it,” he says. “It remains constant and serves as an anchor, even though the names and other taxonomic constraints may change. The 16S has become the contemporary equivalent of the Gram stain but is much richer, and it is the first thing we do. It's also the way Bergey's Manual is now structured.”

            However, not everything about the scope and content of the RDP collection is considered ideal. “If the data were collected in a more programmatic fashion, it would be far more meaningful,” UI's Woese says. Perhaps more importantly, the existence of RDP and its steady growth highlight what Woese calls a “travesty” in biology--namely, a failure to mount a concerted effort to “search for the bacteria and archaea that are the major players in the environment. We need a push to get complete accounts,” he says.

            This same kind of broad-based effort also should be followed in microbial genomic sequencing, instead of the current “haphazard” approach, Woese adds. “Sure, any genome will provide you some information, but only if you go out and look more broadly will you find something truly unusual.”  

 

Jeffrey L. Fox

Jeffrey L. Fox is the ASM News Current Topics and Features Editor.

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