The Loom

A Feast of Bugs

In the past few months, the New York Times science section has been putting together some special packages of articles, and this week’s bundle is on the topic of evolution. You can read John Noble Wilford on hominids, Nicholas Wade on recent human evolution, Carol Kaesuk Yoon on the evolution of animal development, and more. No animals for me, thanks–I got the microbes. Which is just fine with me. It’s a world of evolution I get all to myself.

In my article, I take a look at experiments in which scientists watch microbes evolve, testing out hypotheses about natural selection and other processes. I was already quite familiar with experiments on E. coli, which I learned about during the research for my next book on that particularly lovable species. But it was fascinating to get better acquainted with some of the many other experiments being carried out on other microbes, such as the soil predator Myxococcus xanthus. While E. coli may be good for studying a lot of features of biology, even I must admit that other species sometimes are the better pick. If you want to know how cooperation and cheating evolve, it only makes sense to look at microbes that actually hunt in packs, share their kills, and sacrifice their own lives so that their fellow M. xanthus can become spores and survive in times of famine. (The picture on the left is a spore-forming mound.)

In the article, I focused mainly on basic questions in biology. Does evolution repeat itself, for example? How does biodiversity emerge? But these experiments are also meaningful to bio-engineers who manipulate microbes to churn out useful molecules like insulin or ethanol. Bernhard Palsson of UC San Diego ran an experiment in which E. coli adapted to a diet of glycerol. He was able to pinpoint all the mutations that natural selection favored in that process (something that hasn’t been done before). Some of the genes they struck came as a complete surprise to him. He had no idea they could be important for breaking down glycerol. “We would never have had this knowledge by any other way,” he told me. “This revolution is going to be a discovery tool.”

Here are a few of the key papers on which I based the article…

Richard Lenski’s long-term experiments: take your pick of pdfs from his web site.

E. coli adapts to heat

Palsson’s glycerol experiment

Social evolution in M. xanthus: abstract, pdf

Diversification of Pseudomonas fluorescens


  1. #1 Jonathan Eisen
    June 26, 2007

    Nice article. Just an aside here really. Rich Lenski is my personal scientific hero. Here are some reasons

    1. Not only did a brief conversation with him save me from immense trouble during my PhD research (I was working on “Adaptive Mutation” and heading down a big hole and he convinced me it was not a place I wanted to be as a student. That conversation, which happened at a conference (we were not at the same institution), made me rethink my research project and shift to this new fangled area that was just starting up – genomics.

    2. The 18 year E. coli experiment still strikes me as one of the greatest ideas in modern evolutionary biology.

    3. He seems to train and/or attract an incredible collection of students and post docs. Now that I am a Professor at a University, I dream of ending up with his record in this area.

    Well, I could go on and on, but do not want to seem too much like a groupie. But if anyone out there wants some good diversions, read some of Lenski’s papers that are linked above.

  2. #2 Alan Kellogg
    June 26, 2007

    My infamously atrocious memory is living down to its reputation again, but last I looked ol’ Myxococcus xanthus isn’t a Protist, Plant, Animal, or even Fungus. The group M. xanthus belongs to has been given a kingdom of its own.

    You did note the multi-nucleus cells members of the kingdom have.

  3. #3 Eivind Eklund
    June 26, 2007

    Typo in the article, diet of glycerol is spelled “diet of glyerol”. Apart from that: Fun post (as usual)

  4. #4 CCP
    June 26, 2007

    I was going to recommend in particular Lenski’s collaborations with Al Bennett on adaptation to temperature regimes–then I read the NYT article and saw that Carl already did so.

    Anybody doing this kind of thing with a sexually reproducing critter?

  5. #5 Jim Hu
    June 26, 2007

    Alan Kellog:

    M. xanthus on NCBI taxonomy

    The Protists, Plants, Animals, and Fungi are all eukaryotes. M. xanthus (aka myxo to those in the field) a eubacterium, like E. coli. It’s one of the delta proteobacteria, E. coli is in the gamma proteobacteria.

    Wikipedia has a brief overview of the evolution of the idea of kingdoms

  6. #6 David B. Benson
    June 26, 2007

    And this adaptation appears to be immediately industrially useful, re: glycerol reduction…

  7. #7 Alan Kellogg
    June 26, 2007


    Not so. I suspect somebody got the acellular slime molds mixed up with another group. I’m putting together a post on what I’ve found, but for now I can relate the following…

    Cellular and acellular slime molds haven’t been put into a group, or even assigned a group of their own. For now they’re grouped with the protists under a phylum level classification. Thus we’re talking about a pair of phyla classified directly under a eukaryotic kingdom (possibly a sub-domain)

    The third slime mold group is now part of the chromatist kingdom, one of those odd little groups that pop up every now and then. The chromatists also include the brown algae, which includes kelp from Southern California.

    As to slime molds being eubacteria, you need to remember that bacteria don’t have a nucleus. They may have nucleus elements, but they don’t have a proper nucleus. Slime molds, regardless of kingdom, have a nucleus. The acellular slime molds during parts of their life cycle have multiple nuclei for the single cell that is the plasmodium. In some species thousands of nuclei.

    On an unrelated topic, in my search for slime mold information I found some on rhodophyta, red algae. The rhodophyta are one of the sub-kingdoms of the plantae kingdom, the other being green plants. So, yes, there are red-leafed plants.

  8. #8 Jonathan Eisen
    June 27, 2007

    OK Can someone back up here and help explain the debate going on here. In Kellog’s earlier comment he says

    “My infamously atrocious memory is living down to its reputation again, but last I looked ol’ Myxococcus xanthus isn’t a Protist, Plant, Animal, or even Fungus.”

    Huh? M. xanthus is a bacteria – a delta proteobacteria to be more specific – that happens to have some cool phenotypic and social behavioral properties. But there is no doubt it is a bacteria.

  9. #9 Alan Kellogg
    June 27, 2007

    Gigablast search results

    What I get for not paying attention.

  10. #10 Alan Kellogg
    June 27, 2007

    A follow up here.

    In the bacerium and the eubaryote we see a remarkable example of convergent evolution. Both form mases of protoplasm that glide about slurping up the neighbors. I’m not up on the exact mechanics and chemistry, but I wouldn’t be surprised if they used similar solutions to similar problems. However, I would be very surprised if they used similar genes for the job.

    In the case of the bacterium we get a look at how our ideas regarding bacterial cooperation have been shown wrong. Bacteria are, in some cases, of engaging in cooperative behavior. Even of forming multi-celled organisms with distinctive tissue types. Fruiting bodies in the case of M. xanthus, membrane producing cells in the case of encysting bacterias such as Streptococcus. Were eukaryotes to disappear would the world see bacterial plantae and metazoans arise?

  11. #11 Jonathan Eisen
    June 29, 2007

    I too would be surprised if they used the same genes. In fact, I wrote something related to this a few years ago when a paper in Nature on the S. pombe genome (which was overall a great paper), made a big error when trying to identify genes associated with multicellularity in eukaryotes. They compared genomes of multicellular euks. to single celled euks and found that the multi celled species did not share many genes in common. They concluded that multicellularity must be due to changes in gene expression not due to invention of new genes. The problem — they included milticelled plants and animals in their comparison but did not account for the fact that these species evolved their multicellularity separately.

    In my News and Views in Nature , I pointed out this mistake. To me, this was a lesson in “phylogenomics” in that to make sense out of genome data, they needed to better understand the phylogeny of the species being studied.

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