Published online 28 November 2008 | Nature | doi:10.1038/news.2008.1265

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Terrestrial origin mooted for more microbes

More than two-thirds of bacteria may have descended from a land-dwelling ancestor.

BacteriaCould many bacteria have descended from a terrestrial ancestor?Punchstock

The majority of bacteria may have evolved on land from an early common ancestor, according to an analysis by two US scientists.

The relationships between different families of bacteria has long been contentious. Traditionally, phylogenetic trees that show how bacteria are related to each other have been based on two different techniques, each yielding different results. One tree is built by comparing the genes encoding ribosomal RNA, whereas the other method uses 20–40 core genes that are found in nearly every living organism.

Now, Blair Hedges at Pennsylvania State University and Fabia Battistuzzi, now at Arizona State University in Tempe, have found that the two methods yield similar trees once an intrinsic bias in the ribosomal RNA data is taken into account. Reporting in the journal Molecular Biology and Evolution1, the researchers say that the new charts suggest that 6,157 out of 9,740 prokaryotic species — including cyanobacteria, actinobacteria, bacilli and chloroflexi — share a common ancestor that was adapted to life on land.

"It seems that all of these groups had a terrestrial common ancestor three billion years ago," says Hedges.

RNA riddle

The key to the new research was the observation that, in bacteria from warm environments such as deep sea hydrothermal vents, the genes coding for ribosomal RNA contain more guanine and cytosine than adenine and thymine. That's not surprising because the bond formed in DNA between guanine and cytosine is less likely to break at high temperatures than the adenine–thymine bond, so there would be selective pressure for bacteria dwelling in high temperatures to use these more stable bonds in their DNA.

However, the two researchers realized that the guanine/cytosine bias could also account for the discrepancy between the ribosomal RNA and core gene trees, and applied a statistical correction to compensate for it. That produced two phylogenetic trees that were much more alike.

To test whether the trees they had produced from the genetic information were correct, Hedges and Battistuzzi decided to check their results against reality, examining the cellular characteristics of the microbes and their habitats.

They found that the classes they suggested had descended from a common land-based ancestor shared characteristics — such as tolerance to ultraviolet light, resistance to water loss, and the ability to form a protective spore during adverse conditions — that would have been crucial for surviving life on land.

Contentious clades

"I fully expected to see something like this but I am thrilled just the same," says geochemist Paul Knauth at Arizona State University. "I've long been arguing that the real action in early life was non-marine and that the reason we don't see it is because terrestrial environments are so rapidly eroded and quite rare in the rock record."

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But others are more cautious. "I like the idea behind the paper," says evolutionary biologist Jonathan Eisen of the University of California, Davis. "But many of the details are weird. The authors tend to cite papers that agree with their trees, but not those that don't agree."

Eisen says he is unsure how the researchers selected the habitats they compared. "They have, for example, left out hot springs as far as I can tell," he says. A key issue, he adds, is the sampling significance. "If a few clades are excluded — such as Gloeobacter [a type of cyanobacteria] — the hypothesis is not supported."

"I must admit I am rather unenthusiastic about the proposals," says molecular biologist Radhey Gupta at McMaster University in Ontario, Canada. There is evidence from earlier work that these bacteria are not descended from a single common ancestor, he says — for example, the endospores formed by the Firmicutes are very different from the spores produced by actinobacteria and cyanobacteria.

Hedges agrees that the terrestrial group has some marine members, but argues that the combined evidence points to a terrestrial ancestor for all. 

  • References

    1. Battistuzzi, F. and Hedges, S., Molecular Biology and Evolution, advance online publication doi:10.1093/molbev/msn247 (2008)
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