A n exciting new creature has been dis- covered under the sea off Iceland, and it is described by Huber et al. on page 63 of this issue 1 . Although invisible to the naked eye, it is as worthy of our notice as any coela- canth or other macroscopic ‘living fossil’, for three reasons. First, its discovery means that current methods are still inadequate to reveal life’s true diversity. Second, it is either very primitive or extremely modified by evolution. Finally, this newly identified entity may represent a whole new group within the Archaea, the most recently dis- covered and still most mysterious of life’s three domains (the others being the Eukaryota and Bacteria). Much of life’s diversity is microbial, but most microbes cannot be grown in culture. How, then, can we discover anything about such organisms? In particular, by what methods can we establish their relatedness to those few microbes that we are able to culti- vate and study in the laboratory? The answer is the polymerase chain reaction (PCR). This technique can be used to amplify — make many copies of — DNA isolated directly from environmental samples; the DNA can then be sequenced. Comparing sequences with each other and with those stockpiled in databases gives us a measure of true micro- bial diversity 2 . Genes that code for the RNA component of ribosomal small subunits (SSU rRNA) are the best targets for amplification, sequenc- ing and comparison. This is because ribo- somes — cellular complexes of rRNA and protein that are the site of translation of the DNA code — are essential for the survival of any organism. So all organisms carry at least one rRNA gene, and rRNA gene sequences have changed relatively little during the 3–4-billion year history of life on Earth. They are accepted by microbiologists as the com- mon currency of microbial taxonomy. Indeed, it was rRNA sequence analysis that led to the initial discovery of the Archaea, a group now known on many grounds (lipid biochemistry, and the fundamental machin- eries of DNA replication, transcription and translation of RNA, for instance) as being distinct from Bacteria. Using PCR ‘primers’ to target specific regions of bacterial, archaeal or eukaryotic SSU rRNA genes makes modern-day microbe hunting even more selective and efficient. In this way, the number of known major divisions within life’s two prokaryotic domains, Bacteria and Archaea, has dou- bled 3,4 . And just last year, two groups reported finding totally unknown, tiny eukaryotes among the ‘picoplankton’ of the Pacific and along the Antarctic polar front 5,6 . (Prokary- otes are organisms that have no intracellular organelles or nucleus; eukaryotes possess organelles and a nucleus for their DNA.) Satisfying as this has been, there is a lin- gering suspicion — or romantic hope, depending on your disposition — that there might be even weirder organisms hiding out there. Such organisms could be especially primitive or wildly divergent creatures that have drifted so far out of the biological mainstream that the usual PCR primers don’t recognize or amplify their SSU rRNA genes. Huber et al. 1 provide a stunning exam- ple of just such a weird bug, something they call Nanoarchaeum equitans (Fig. 1). Nanoarchaeum was discovered as small (400-nm) spherical structures attached to the cells of a much larger organism, a new species of the archaeal genus Ignicoccus taken from rock and gravel near a hot submarine vent north of Iceland 7 . Specific in situ stain- ing procedures showed that these tiny cells contain DNA. Although several SSU rRNA- specific primers were used, only one sort of SSU rRNA could be amplified by PCR from the mixed culture. However, two kinds of SSU rRNA genes could be detected by South- ern blot hybridization, a method that is less specific than PCR and which can be used to detect (but not amplify) most rRNA genes, no matter how unusual. One type of SSU rRNA gene comes from Ignicoccus ; the other could be shown to be localized to the tiny Nanoarchaeum cells. Sequencing suggests that this second gene is a true, functional SSU rRNA gene, the product of which could form a normal RNA secondary structure. And although the gene’s sequence is in general closer to those of archaeal than bacterial SSU rRNA genes, it is very divergent; only specially redesigned PCR primers could detect it. Cells of Nanoarchaeum can be purified from mixed cultures, and the total length of the DNA molecules they contain is roughly 500 kilobases. This is possibly the smallest- known prokaryotic cellular genome. It lies in the range for species of Mycoplasma, bacterial parasites that hold the current record as minimalists among the known organisms that can grow outside other cells. So far, Nanoarchaeum has not been grown NATURE | VOL 417 | 2 MAY2002 | www.nature.com 27 news and views Something new under the sea Yan Boucher and W. Ford Doolittle Figure 1 The little picture for microbe hunters. The main image is a fluorescence micrograph, taken after DNA-specific staining, which shows the newly discovered Nanoarchaeum equitans attached to its host, Ignicoccus. The two organisms are shown again in the inset, an electron micrograph. Scale bars are 5 Ȗm and 1 Ȗm, respectively. The investigations of ribosomal RNA gene sequences carried out by Huber et al. 1 show N. equitans to be a decidedly weird member of the Archaea. M. HOHN & K. STETTER/R. RACHEL & K. STETTER The discovery, in an undersea hot vent, of an organism that does not fit into any previously defined category of life marks the creation of yet another group within the mysterious Archaea. © 2002 Macmillan Magazines Ltd