My dear friend Linc Sonenshein introduced me to Bacillus subtilis forty years ago when he was a graduate student with Salvador Luria. The remarkable capacity of B. subtilis to transform itself into a spore has been the focus of my research ever since. Before too long, Sonenshein and I focused on 168 and related strains, the E. coli K12 of the B. subtilis world. We did so for the reason that, thanks to the pioneering work of John Spizizen (with some magic from Charley Yanofsky and Norm Giles sprinkled in), strain 168 exhibited the remarkable capacity to take up DNA from its environment and recombine the DNA into its chromosome. This discovery of genetic competence opened the way to traditional and, eventually, molecular, genetics in B. subtilis and made the bacterium a premier model organism. At the same time, and what I did not realize until many years later, we also paid a price for using a strain that had been passaged many times in the laboratory.

Domestication has led to the production of long chains of sessile cells. Shown is a fluorescence micrograph taken by Dan Kearns of growing cells of laboratory B. subtilis. In addition to swimming cells (the green-colored singlets and doublets), the population contains many long chains of sessile cells. The cells were visualized with the vital membrane stain FM4-64 (red) and contained a fusion of the gene for the Green Fluorescence Protein (responsible for the green color) to a promoter under the control of a transcription factor that controls motility. Thus, only the motile cells in the image are green. Wild (undomesticated) strains, in comparison, produce relatively few chains of sessile cells.

      Ferdinand Cohn reported the discovery of B. subtilis in 1877. But the B. subtilis laboratory strains of today are a shadow of their former selves. Years and years of manipulation in the laboratory has robbed B. subtilis of much of its biology. On the one hand, laboratory strains can be transformed with DNA much more efficiently than undomesticated strains. On the other hand, laboratory strains are generally deficient in a variety of behaviors manifest in wild strains. Whereas wild strains are highly motile, have the capacity to swarm on surfaces, and form architecturally complex communities (biofilms), laboratory strains form long chains of sessile cells, fail to swarm, and form smooth colonies and thin pellicles. Indeed, studies with biofilms (in collaboration with Roberto Kolter) have changed our thinking about sporulation. We traditionally treated sporulation as largely a behavior of solitary cells, but recent work emphasizes the importance of studying spore formation in the context of multicellular communities (as has long been recognized in myxobacteria).

      Domestication has led to the production of long chains of sessile cells. Shown is a fluorescence micrograph taken by Dan Kearns of growing cells of laboratory B. subtilis. In addition to swimming cells (the green-colored singlets and doublets), the population contains many long chains of sessile cells. The cells were visualized with the vital membrane stain FM4-64 (red) and contained a fusion of the gene for the Green Fluorescence Protein (responsible for the green color) to a promoter under the control of a transcription factor that controls motility. Thus, only the motile cells in the image are green. Wild (undomesticated) strains, in comparison, produce relatively few chains of sessile cells.

      Source: Kearns, DB, R Losick. 2005. Cell population heterogeneity during growth of Bacillus subtilis. Genes & Development 19:3083-3094.

How did this happen? I suspect that it is the result of heavy mutagenesis along with generations of researchers who, without thinking about it, favored rare smooth colonies that stayed put on the agar plate over other more unruly ones.

      There are two lessons here that may be of general interest for those of us who consider small things. First, much biology may await discovery from revisiting the ancestral roots of popular laboratory strains. Second, this missing biology may hold the key to understanding the function of some of the myriad mysterious genes with which bacterial genomes are riddled. In short, back to the wild!

       Richard Losick is Harvard College Professor, Maria Moors Cabot Professor of Biology at Harvard University.

      September 15, 2008

       bit.ly/1M2m15Q

      #8

      by Elio

      Can you think of a place on Earth where there is free water but no microbes? (outside the bodies of other organisms or the lab)

      March 2, 2007

       bit.ly/1Gfpsdq

7

      The Tyranny of Phylogeny: An Exhortation

      by Elio

       Two archaea walk into a bar and the bartender says, “If you guys are going to start in with the jokes again, Woese is me.”

      —Fred Rosenberg

      There are days when I wish that the Woesian Three Domain scheme were wrong. Not that I would be happier if there were four or five or whatever number of domains. What would please me would be an escape from what I feel is an unnecessarily oppressive way of thinking, the seating of phylogeny (and its acolyte, genomics) alone at the head of the table. Why do I say this? Because as essential as phylogeny is to our understanding of the evolution of living organisms, equally vital is ecology to comprehend present day life. While it’s good to know where you come from, it’s equally important to know where you are and what you’re doing there. The Spanish philosopher Ortega y Gasset said it well: “Yo soy yo y mi circunstancia” (“I am I and my circumstance”).

A

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