The ocean microbe within us

By Carl Zimmer | July 28, 2011 7:58 pm

Our cells are packed with various protein-stuffed sacs, each dedicated to carrying out essential tasks. One kind of organelle is peculiar, though. Mitochondria are jellybean-shaped structures whose jobs include making the fuel that our cells use to power everything they do. What makes mitochondria strange is that they carry their own DNA. It’s not a lot of DNA–just 37 genes–but mitochondria can make extra copies of it as they grow and divide. In other words, they act an awful lot like bacteria.

About a century ago, Russian biologists proposed that mitochondria actually started out as bacteria, which set up house in our single-celled ancestors. In the 1960s, University of Massachusetts biologist Lynn Margulis resurrected the idea, pointing to certain features in mitochondria, like their double membrane, found in bacteria but not in other organelles. In the 1970s, biologists began to invent the tools that allowed them to look at the DNA in mitochondria. As predicted, that DNA matched DNA from bacteria, not from animals.

Acquiring mitochondria over 2 billion years ago was a pivotal moment in our evolution. We are eukaryotes, as are trees, mushrooms, and amoebae. We all carry mitochondria (or organelles that started out as mitochondria). Once our eukaryotes acquired mitochondria, they could produce so much fuel that they could get very big. Eukaryote cells are much bigger than bacteria, and eukaryote cells have, on several occasions, stuck together to form multicellular bodies. You can thank your mitochondria for being more than a germ.

But what kind of bacteria did mitochondria come from? This is a lot harder to answer, because we know so little about the diversity of bacteria in the world. When scientists trace the origins of an organism, they compare it to other living things. In the case of birds, for example, scientists have compared them to other land vertebrates. In the big scheme of things, land vertebrates have never been particularly diverse. Scientists have a pretty good grasp of every group of land vertebrates that ever lived, and so they’ve been able to carefully compare birds to all of them. Birds did not evolve from frogs. They did not evolve from skunks. They evolved from feathered dinosaurs. There’s still plenty to learn about exactly which fossil dinosaur was the closest relative to the first birds. But in general terms, the origin of birds is pretty much settled.

When it comes time to compare mitochondria to bacteria, however, scientists face a much tougher challenge. Consider this: there are 5,000 species of mammals alive today. It’s big news when a mammalogist stumbles across a single new species of mammal. If you dig up a spoonful of dirt from your front yard, there may be 10,000 species of bacteria in it–many of which are new to science. If you’re anything like me, even your bellybutton is rife with exotic, undescribed bacteria.

This diversity makes comparisons difficult. It’s as if alien scientists wanted to figure out where humans came from, but they could only compare us to tulips and E. coli. Our DNA shows we are closer to tulips than E. coli, and so the alien scientists might be tempted to declare that we started out as flowers. If the alien scientists could compare the millions of eukaryote species that human scientists know about, however, they could see that plants and animals became multicellular on their own. We have no petals in our past.

Over the past twenty years, scientists have been finding bacteria that are closer and closer to mitochondria, and, in the process, they’ve been zeroing in on what the ancestors of mitochondria might have been like. Recently, J. Cameron Thrash at Oregon State University and his colleagues published a big new study of mitochondria and their relatives that brings them into even sharper focus. The open-access paper appears in the new journal Scientific Reports.

Initially, scientists recognized that mitochondria belonged to a big group of species called alphaproteobacteria. Then researchers sequenced a genome of Rickettsia, a group of alphaproteobacteria that cause diseases like typhus. They found a striking match between Rickettsia and mitochondria. Particularly intriguing was the fact that Rickettsia can only replicate inside eukaryote cells. One could imagine mitochondria starting out the same way, infecting some amoeba-like ancestor. Yet some researchers disputed this conclusion, arguing that the data wasn’t strong enough.

Then scientists went trawling for new bacteria in the oceans and, as they always do, found some surprises. They found new kinds of Rickettsia bobbing in the sea. This lineage of Rickettsia, called SAR11, does not need to infect a host to survive. Instead, this tiny microbe breathes oxygen and slurps up dissolved carbon.  Scientists now recognize SAR11 as one of the most successful lineages in all life: they make up 25% of all the bacteria in the ocean.

Thrash and his colleague did a massive comparison of SAR11 and other  bacteria, analyzing over 60 entire genomes. They concluded that SAR11 are more closely related to mitochondria than other bacteria, including other Rickettsia.

It’s possible, they argue, that our mitochondria did not start out as typhus-like pathogens. Instead, we might look to SAR11 for some clues. SAR11 bacteria breathe oxygen–a capacity that mitochondria gave to our ancestors. SAR11 bacteria also have extremely small genomes–probably because the bacteria were living on a meager food supply and so natural selection favored individual microbes with few genes. It’s likely that once mitochondria became established in our cells they lost many genes that they no longer needed. But this new research hints that they were already tiny, lean bacteria when they took their first step inward.

I can remember first learning of the history of mitochondria, and marveling that we are the offspring of a collective, of a cell that became a home for bacteria, which gave it a new breath of life. Now I will marvel again when I look out at the ocean and realize how, until recently, we didn’t know that our bacterial residents are cousins to an inconceivable number of microbes in the sea.

[Image: Wellcome Images]

[Update–Changed Giardia to E. coli. Dang polytomies]

CATEGORIZED UNDER: Evolution, The Tangled Bank, Top posts

Comments (12)

  1. Rich

    Our DNA shows we are closer to tulips than Giardia, and so the alien scientists might be tempted to declare that we started out as flowers.

    I’m not sure that we have resolved the branching order of the eukaryotic supergroups to the level of resolution to make such a distinction.

    [CZ: Good point. I’ll change it to E. coli]

  2. fer

    is amazing how the secondary endosymbiosis has left its signature in the topography of plastid membranes like in dinoflagellates and cryptophytes

  3. amphiox

    It’s as if alien scientists wanted to figure out where humans came from, but they could only compare us to tulips and E. coli. Our DNA shows we are closer to tulips than E. coli, and so the alien scientists might be tempted to declare that we started out as flowers.

    Or perhaps, they’ll conclude that flowers started out like us! (The presence of a second endosymbiotic event in the tulip would support this hypothesis).

    They could point to couch potatoes and sunbathers as transitional forms.

  4. G Roelofs

    Is there any chance an early strain of mitochondria might have reversed course and struck off on its own again, ultimately leading to a SAR11-like bacterium rather than the other way around? Two billion years is a very, very long time… However suggestive the present-day similarities are, a whole lot might have transpired to get us here.

    [CZ: It’s possible, but to make a case for that hypothesis you’d need some evidence–such as showing that all of SAR11 bacteria are more closely related to the mitochondria found in some eukaryotes than others.]

  5. hs

    Is there supposed to be a link to the actual 60 genome study? Maybe I’m missing it?

    [CZ: The link is in the post. Here it is again.]

  6. Matt Gruner

    Presumably the mitochondrial genome is smaller than it was when the first bacteria were endocytosed since a number of genes essential for its function have been moved to the nucleus. The discovery of SAR11 may offer the opportunity to do a rare type of experiment in biology, re-run history and see how it turns out (with some help from molecular biology to speed things along). To what extent does the organization of the mitochondrial (and nuclear) genome represent optimal situations imposed by physical constraints versus neutral changes?

  7. David B. Benson

    Matt Gruner — I don’t think there are optima, only local improvements over prior forms.

  8. Dave in Calif

    Couch potatoes and sun bathers as transitional forms, now that’s funny!

  9. Martin

    You say, “SAR11 bacteria also have extremely small genomes–probably because the bacteria were living on a meager food supply and so natural selection favored individual microbes with few genes.”

    But wouldn’t a meager food supply favor a large genome, because the organism would have to manufacture many required nutrients. I would think that a small genome would be favored only for organisms living in a nutrient-rich environment, where they could just absorb needed nutrients and wouldn’t need the genes to manufacture them.

  10. Hellchylde

    And nobody mentioned that mitochondria allso allow us to use the Force… jus sayin

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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.

About Carl Zimmer

Carl Zimmer writes about science regularly for The New York Times and magazines such as DISCOVER, which also hosts his blog, The LoomHe is the author of 12 books, the most recent of which is Science Ink: Tattoos of the Science Obsessed.

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