Genome Research Challenges Previous Understanding of the Origin of Photosynthesis

Colorful chloroflexi-rich microbial mats grow in a Japanese onsen (hot-spring ba
Colorful chloroflexi-rich microbial mats grow in a Japanese onsen (hot-spring bath). Supposedly billions of years old, these photosynthetic bacteria actually evolved just 867 million years ago, according to the study’s co-first author Caltech’s Woodward Fischer. (Credit: Lewis Ward, Caltech)

–Written by Leah Sloan

Plant biologists at Lawrence Berkeley National Laboratory (Berkeley Lab), in collaboration with colleagues from the California Institute of Technology (Caltech), have reconstructed the evolutionary history of photosynthesis to provide new insight into the yet-unfolding story of its origins.

The most commonly studied form of photosynthesis is oxygenic photosynthesis, the method through which plants use sunlight to convert water to oxygen. However, further studies of anoxygenic photosynthesis, which does not produce oxygen, are crucial to understanding how early microbial metabolisms may have influenced the geochemical cycles of the planet.

"Photosynthesis supports the majority of life on our planet; however, we know very little about when this important metabolism evolved," explained Patrick Shih, a postdoctoral researcher in Berkeley Lab’s Environmental Genomics and Systems Biology Division and co-first author of a recent study in the Proceedings of the National Academy of Sciences titled, " Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi." Woodward Fischer, professor of geobiology at Caltech, is also co-first author of the study.

It is thought that anoxygenic photosynthesis evolved before oxygenic photosynthesis, playing a role in some of the earliest evidence for life on Earth, before the rise of atmospheric oxygen.

"It has been widely speculated that a special group of bacteria called Chloroflexi were the inventors of anoxygenic photosynthesis," Shih said. "We looked through the genomes of different Chloroflexi and used phylogenetics to show that this group could not have been one of the original inventors of photosynthesis."

Using a combination of comparative genomics and molecular clock analyses, researchers determined that phototrophic members of the Chloroflexi phylum evolved far too recently to have been the progenitors of oxygenic photosynthesis, a process that evolved about 2.3 billion years ago. In contrast, it was found that Chloroflexi did not predate the process at all, having evolved roughly 867 million years ago.

"We used phylogenetic methods to estimate when evolutionary events occurred, specifically molecular clock analyses. Molecular clocks are a way to look at the rate of molecular evolution of proteins, which then can enable us to make estimations as to when specific events occurred," Shih explained. "We used this method to understand when phototrophic members of the Chloroflexi phylum evolved. Chloroflexi have traditionally been thought to be one of the oldest phototrophic lineages that we know of. However, our molecular clock analysis reveals that this group is actually much younger than previously suggested."

This study is merely the starting point in determining the age and role of important microbial metabolisms and identifying the original inventors of phototrophy.

"We’ve shown that we can revisit some old questions that have been around for decades with new genomic and phylogenetic tools," Shih added. "This study addresses understanding the origin of photosynthesis and highlights how little we know about the history of the major metabolism that drives our planet."
The Joint BioEnergy Institute is supported by the U.S. Department of Energy, Office of Science (BER).