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For the first time a single experimental approach, 16 S ribosomal RNA sequence characterization, has been used to develop an overview of phylogenetic relationships in the bacterial world. The technique permits the tracing of relationships back to the common ancestor of all extant life. This first glimpse of bacterial phylogeny reveals a world whose roots appear to span more than 3 billion years. A deep phylogenetic split exists among the bacteria, which necessitates their division into two major lines of descent, the archaebacteria and the true bacteria (or eubacteria). It is a general finding that the most ancient bacterial phenotypes are anaerobic, and that aerobic phenotypes have arisen a number of times. Photosynthetic phenotypes are also extremely ancient. Many nonphotosynthetic groups appear to have arisen from photosynthetic ancestry, which is reason to question the generally held belief that the first bacteria were anaerobic heterotrophs. The two ultimate lines of bacterial descent are no more closely related to one another than either is to the cytoplasmic aspect of the eukaryotic cell. However, in that the eukaryotic cell is a phylogenetic chimera, it itself cannot be seen as a line of descent comparable to the two bacterial lines—although some of its individual parts can be so viewed. In this way, the chloroplast and perhaps the mitochondrion are each eubacterial, and at least one ribosomal protein is archaebacterial. A third line of descent that is neither eubacterial nor archaebacterial is represented in the 18 S ribosomal RNA.

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We report here the sequences of oligonucleotides released by T1-ribonuclease digestion of the 16S ribosomal RNA's (rRNA's) of unicellular cyanobacteria Agmenellum quadruplicatum (strain BG-1) and Synechococcus 7502. We compare them with sequences previously obtained for the 16S RNA's of six other cyanobacteria and two chloroplasts, and conclude that: (i) Synechocystis-like unicells form a discrete cluster which also (and surprisingly) includes Agmenelium quadruplicatum, usually considered to be a Synechococcus; (ii) filamentous cyanobacteria of the genera Nostoc and Fischerella arose from within the Synechocystis group; (iii) phylogenetic diversity (and hence presumably evolutionary antiquity) within the Synechococcus group is very great; and (iv) red algal chloroplasts are of definite cyanobacterial origin, while Euglena chloroplasts are of separate and quite possibly noncyanobacterial origin. We also present the results of a computer-aided search among the 10 oligonucleotide 'catalogues' for families of related but nonidentical sequences. Examination of these families reinforces the above conclusions.