Talking about my f-f-fermentation
As part of my Summer Microbiology reading, I am presently working my way through The Enigma of Ferment, by Ulf Lagerkvist. The book is a short, very readable presentation of the historical origins of the field of Biochemistry culminating in the Nobel Prize winning work of Eduard Buchner.
I was intrigued while reading this book of the use of the term ferment, and it’s use as a noun instead of the way I had thought of it as a verb. I had always seen fermentation and ferment as an active process: the action and ability of microorganisms to convert one organic material into a novel product. Lagerkvist makes the argument through his presentation of historical figures that this concept grew fluidly from the work of alchemists in the 15th and 16th centuries, where transmutation of one compound to another was accomplished by the use of an object like the Philosopher’s Stone. Vitalism grew out of alchemy, and held that the process of biological transmutation required the presence of a living organism. The concept of vitalism was refuted by the work of Buchner, who as written about earlier on this blog, was able to extract the process of fermentation of sugar to alcohol from a living cell and carry it out in the absence of a living cell. This led to the development of Biochemistry as a discipline, where biological processes could be reduced to their individual components of substrates and products, and the enzymes that catalyze specific reactions.
So back to the idea of the ferment: according to Merriam Webster, the word ferment is indeed a noun, but is used to mean an organism such as yeast that carries out fermentation. This use goes back to the strong vitalist view of Louis Pasteur that it was the cell that carried out the fermentation process. Fermentation in this view was the process by which the yeast cell obtained the necessary nutrients for cellular growth, and would therefore be useless outside the cell. This concept was superseded by the idea that the cell could be removed from the process.
One of the first inklings that this could be true came about by the work in 1860 of the French chemist Marcelin Berthelot, who obtained a soluble extract from yeast that was capable of breaking down sucrose into a mixture of glucose and fructose (invert sugar) in a single step. The enzyme responsible for this action, now known as invertase, was fortuitously secreted by the yeast cell and could be easily collected from spent culture medium. Pasteur immediately argued that the chemical breakdown of sucrose could also be accomplished by a great many other methods, including treatment with simple acids, and the argument of vitalism continued to go back and forth even after the work of Buchner.
One of the to my mind fascinating aspects of the Golden Age of Microbiology in the latter half of the 19th century was the realization of the incredible diversity of microorganism. One aspect of this was the discovery that the mechanisms used by Homo sapiens to obtain nutrients (carbon for cellular structures from carbohydrates, energy for metabolic reactions and cellular work from organic carbon-containing compounds) represented a small portion of the diversity of ways that living systems can obtain carbon and energy. With this came the realization that fermentation (and ferments) were not limited to the breakdown of glucose to carbon dioxide and ethanol as accomplished by Saccharomyces cerevisiae. Indeed, many reactions were now found to be analogous to classical ethanol fermentation.
An early example of one of these reactions is the nitrification pathway, or the nitric ferment proposed by Sergei Winogradsky. Winogradsky’s key insight was that the breakdown of biological materials was a step-wise process, with certain organisms responsible for the degradation of macromolecules into ammonia, other organisms responsible for the conversion of ammonia into nitrites, and yet other organisms that converted nitrites into nitrates. As with the ethanol ferment, the nitric ferment was used as a mechanism for the obtaining of energy to drive cellular growth. We see now the use of the word ferment means something a bit different than it did before, and can now refer to the multitude of potential mechanisms that an ecosystem has available for the movement of compounds into and out of the biosphere.
What has happened to the use of this terminology? I think that it has been supplanted, as our understanding of the biochemistry within an ecosystem has grown. The term “ferment” is know used to refer to a specific energy generating pathway, in essence referring to the specific enzymes from that pathway, which since the work of Buchner can now be reconstituted in a test tube. For an indication of the importance of that insight, we have the ability to introduce completely novel biochemical pathways in genetically engineered microorganism, which is changing the face of modern medicine.