The evolutionary diversification of cyanobacteria: molecular-phylogenetic and paleontological perspectives

Abstract

Cyanobacteria have played a significant role in Earth history as primary producers and the ultimate source of atmospheric oxygen. To date, however, how and when the group diversified has remained unclear. Here, we combine molecular phylogenetic and paleontological studies to elucidate the pattern and timing of early cyanobacterial diversification. 16S rRNA, rbcL, and hetR genes were sequenced from 20 cyanobacterial strains distributed among 16 genera, with particular care taken to represent the known diversity of filamentous taxa. Unlike most other bacteria, some filamentous cyanobacteria evolved a degree of cell differentiation, producing both specialized cells for nitrogen fixation (heterocysts) and resting cells able to endure environmental stress (akinetes). Phylogenetic analyses support the hypothesis that cyanobacteria capable of cell differentiation are monophyletic, and the geological record provides both upper and lower bounds on the origin of this clade. Fossil akinetes have been identified in 1,650- to 1,400-mega-annum (Ma) cherts from Siberia, China, and Australia, and what may be the earliest known akinetes are preserved in approximately 2,100-Ma chert from West Africa. Geochemical evidence suggests that oxygen first reached levels that would compromise nitrogen fixation (and hence select for heterocyst differentiation) 2,450-2,320 Ma. Integrating phylogenetic analyses and geological data, we suggest that the clade of cyanobacteria marked by cell differentiation diverged once between 2,450 and 2,100 Ma, providing an internal bacterial calibration point for studies of molecular evolution in early organisms.

Fig. 1.

The phylogenetic relationships of cyanobacteria inferred from 16S rRNA (A), rbcL (B), and hetR (C) nucleotide sequences; trees were constructed by the ML method (19). Roman numerals denote cyanobacterial subsections I–V; sequences obtained in this study are indicated in boldface. Numbers at each branch point are the bootstrap values (22) for percentages of 1,000 replicate trees calculated by NJ (20) (Upper) and MP (21) (Lower) methods; only values >50% are shown. Arrowheads mark the deepest roots determined by using Agrobacterium and Prochlorococcus as outgroups for 16S rRNA and rbcL, respectively. N, nonheterocystous cyanobacteria known to fix nitrogen; -, cyanobacteria for which nitrogen fixation has been tested but not detected.

Fig. 2.

Modern cyanobacterial akinetes and Archaeoellipsoides fossils. (A) Three-month-old culture of living A. cylindrica grown in a medium without combined nitrogen. A, akinete; H, heterocyst; V, vegetative cells. (B–D) Shown are Archaeoellipsoides fossils from 1,500-Ma Billyakh Group, northern Siberia (B); 1,650-Ma McArthur Group, northern Australia (C); and 2,100-Ma Franceville Group, Gabon (D). (Scale bars, 10 μm.)

Fig. 3.

The geochemical record of atmospheric oxygen as it relates to nitrogen fixation and the evolution of heterocystous cyanobacteria. The curve presents an estimate of atmospheric P_O2 through time, as constrained by paleosol (42) and S isotopic (43, 44, 46) data. Numbers in Right indicate the P_O2 level at which in vitro nitrogenase activity is inhibited in nonheterocystous Plectonema and heterocystous Anabaena (34) (A), and P_O2 or [O₂] optima for in vivo nitrogenase activity of Plectonema (36) (B), nonheterocystous Gloeothece (37) (C), Trichodesmium (38) (D), and Anabaena (39) (E). F indicates the intracellular [O₂] of Anabaena heterocysts. The [O₂] (the left vertical axis) corresponds to P_O2 (right axis) when [O₂] is 250 μM in air-saturated water. PAL, present atmospheric level.