Rhodopseudomonas palustris

by Sean Gibbons

For most of history, to the extent that anyone considered the question, it was assumed that all organisms ultimately got their energy from carbon. Carbon seems an unglamorous foodstuff, but it is what protein, carbohydrates and fats are all ultimately built of. Carbon is the stuff of apple pie, meatballs, or grass. Plants, although they don’t eat other organisms, produce sugars made out of carbon to use as energy. Even our cars run on carbon; it long seemed an inescapable foodstuff.  However, during the same era that Jack the Ripper roamed London and Sitting Bull eluded the U.S. Calvary, Sergei Winogradsky began to uncover a world of other kinds of  “food:” energy sources no one had remotely anticipated, revealing the very Earth and sky to be edible.

In his youth, Winogradsky did not imagine he would study biology. He thought himself an artist. But not everyone agreed. In the fall of 1877, at the age of 21, Winogradsky flunked out of music school.  His German music professor thought he lacked the “spiritual flame” of an artist1. Fortunately, he had a backup career, science! He enrolled at St. Petersburg University where he studied science. Even in science, Winogradsky did not quite fit in. This would prove his great strength. He fit nowhere, but was passionate about everything.

Winogradsky read about art; he read about economics; he read about microbiology. As he did, he began to integrate the perspectives from these fields, quilting together what had so long been separate. He began to see nature as both a sort of evolved art and as a living economy, where matter and energy were exchanged and transformed among and between organisms. Winogradsky’s friends looked outside and saw birds and squirrels. He looked outside and saw nature’s wheeling and dealing. In order to understand this economy, he combined new microbiology techniques (recently developed by Louis Pasteur) with microbial field ecology (gathering muck from the environment and culturing it in the lab) and thermodynamics (theory involving how energy is transformed from one form to another). He sewed patches of different fields together. Here was his art. Here was his great spirit!

As his quilt expanded, Winogradsky would make many important discoveries, among the greatest of these would be uncovering the diverse diets of microbes. Winogradsky showed that some microbes (lithotrophs) could eat rocks; they sustain themselves by crunching up energy-rich inorganic molecules locked in stone, formed in the Earth’s crust. He isolated nitrifying bacteria that get their energy by converting ammonia into nitrate. He showed that organisms that derived energy from rocks, ammonia or other inorganic (without carbon) compounds could use that energy to turn the carbon dioxide gas in the air into solid carbon in their bodies (autotrophs).  The discovery of rock and nitrogen eaters led to revelations about how microbes affect the world around us; they degrade rocks; they alter elemental cycles; they reshape the Earth and the sky and connect all species on Earth as they do so2.

Winogradsky’s discoveries were scattered among many species of microorganisms. You can find many of the species he studied on your body, in your house or at the very least in your backyard. Yet no single bacterium embodied all of the exotic diets that Winogradsky described. Then, after Winogradsky’s death, came Rhodopseudomonas palustris.  R. palustris is a purple nonsulfur bacterium. It is most often found in lake or ocean sediments and wastewater treatment sludge, but it also resides in the more familiar places, like backyards and mud puddles. R. palustris is a microbial “Jack of All Trades.” In the presence of oxygen, it grows on both organic and inorganic compounds. In the absence of oxygen, it uses sunlight as an energy source and eats whatever is available. As a result of this and other flexibilities, R. palustris can gobble tough woody plant materials and pollutants, mop up exotic metals, belch hydrogen, synthesize complicated fat molecules called hopanoids that can be detected in the fossil record, and finely tune its gene expression to the tiniest of changes in environmental conditions3. With less than a quarter of the number of genes found in the human genome, the single-celled R. palustris runs circles around us humans. Most of what it can do, we, simply put, cannot.

Whereas Winogradsky got by on a patchwork of ideas, R. palustris lives on a patchwork of sustenance, wherever it happens to land in the microbial universe. If alive today, Winogradsky would have loved to study how such versatility arises and persists during the course of evolution. We invite you to participate by exploring the microbial ecosystems that exist in your own backyards. Start by building your own Winogradsky Column (named after one of Dr. Winogradsky’s famous experiments). The linked video above shows you how to set it up.  After allowing the column to incubate in a window for several weeks, you’ll be able to observe many of the rock-eaters and phototrophs that Winogradsky first described back in the 19th century.  If you’re lucky, you’ll find R. palustris there, sunbathing near the top of the sediment layer, munching away at organic acids. You could also find it, recent research shows, on your own body — even inside your belly buttons4. Winogradsky would have loved this (I think so anyway) — a species living on him capable of nearly anything, much like Winogradsky himself.

References

  1. Ackert, L.T.  The “Cycle of Life” in Ecology: Sergei Vinogradskii’s Soil Microbiology, 1885-1940. Journal of the History of Biology 40, 109-145, (2007).
  2. Falkowski, P. G., Fenchel, T. & Delong, E. F. The Microbial Engines That Drive Earth’s Biogeochemical Cycles. Science 320, 1034-1039, doi:10.1126/science.1153213 (2008).
  3. Larimer, F. W. et al. Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat. Biotechnol. 22, 55-61 (2004).
  4. Hulcr, J. et al. A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable. PLoS One 7, e47712, doi:10.1371/journal.pone.0047712 (2012).

About the Author

Sean Gibbons is an EPA STAR Graduate Fellow in the Biophysical Sciences Graduate Program at the University of Chicago, a research associate at the Institute for Genomics and Systems Biology at Argonne National Laboratory, and a data analyst for the Earth Microbiome Project. He’s interested in using tools and techniques from different scientific disciplines to address questions in molecular systems ecology and evolution. His current research, advised by Jack Gilbert and Maureen Coleman, focuses on the application of complex systems theory to the assembly of microbial communities under varying regimes of disturbance. Sean has published on a number of topics, including cellular thermodynamics, physiology, ecology, systems biology, and French/English poetry translation.