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Friday, June 06, 2014

March of the Microbes

It can be hard to convey to non-biologists, who may think of germs as pests (an unseen, unclean residue to be neutralized with disinfectants), the grandeur and miraculous intricacy of microbial life. After more than three billion years of evolution, microbes are still, numerically speaking, the principal inhabitants of this planet; most of life on earth is invisible to the naked eye. But sightings of microbial life are all around us if we know where to look. In March of the Microbes: Sighting the Unseen (2010, Harvard University Press), Professor John L. Ingraham shows those of us with eyes to see just how and where to look.

It's impossible for me to come at this book with anything approaching objectivity, because I know the author well: I was Dr. Ingraham's student at U.C. Davis in the 1970s and did my graduate studies under his kind, insightful direction. And it was thanks largely to him that I developed what has turned out to be a deep, abiding, lifelong appreciation for the stunning ingeniousness (for there's no other way to put it) of microbial life.

The Ingraham lab, in those days, specialized in the study of pyrimidine metabolic pathways in Salmonella, but Dr. Ingraham's interests were broad and his understanding of microbial ecology impressively deep. Before undertaking some of the first studies of cold-sensitive mutants of bacteria, Ingraham had made important contributions to the understanding of fusel oil production by enologically important yeasts. But Ingraham was and is also an avid naturalist, as likely to identify a particular oak species as to diagnose the fungal disease causing its slow death. Serve him rainbow trout and he'll likely comment on the multiple layers of guanine crystals in the fish's shimmering scales before reminding you (as he does on page 24 of March of the Microbes) that the lack of a "fishy" smell in rainbow trout is due to the absence of trimethyl amine oxide, an osmolyte that would otherwise be converted by bacteria to oh-so-smelly trimethyl amine (TMA).

Go with Ingraham on a walk in the woods and he's sure to point out (as on p. 76 of MoM) that the age of a lichen on a boulder can be estimated from its size, based on its half-millimeter-a-year growth rate; and don't be surprised if he can name the particular cyanobacterium that gives the lichen its greenish hue. You'll forgive him, of course, when he uproots a small plant to show you the Rhizobium-fostered nodules on its roots, nodules that (when sliced open with a pocket knife) are red inside, crimson with the plant hemoglobin (p. 118) that only a symbiotically infected legume can produce. If you're worried about the safety of drinking water from that nearby mountain stream, he'll explain that you'd have to drink 250 gallons of such water before you're likely to imbibe a cell of Giardia (p. 298).

Reading March of the Microbes, I felt like I was on an extended nature walk with a world-class naturalist, except that this "walk" knows no physical bounds, for it extends from Sierra Nevada ski slopes, where slope operators mix dry powder made of Pseudomonas syringae cells (sold as Snomax) into the snow-machine slurry to facilitate ice-crystal nucleation (p. 263), all the way to miles-deep thermal chimneys on the ocean floor, where Pyrolobus furnarii grows in total darkness at 3000-psi pressure and 113-degree-Celsius temperatures (p.186); and from there to the inside of the 22-gallon rumen of a cow (p. 80), then to the 200-microliter hindgut of the termite, where, again (as in the cow), microbes do the vital work of digesting cellulose, something no higher life form can do.

The interconnectedness of life on earth is a recurring theme in March of the Microbes, as is the sheer adaptability of microbial life. We learn that only microbes can harness molecular nitrogen directly from the atmosphere; only microbes can return it. Only microbes can respire hydrogen sulfide and nitrate to sulfuric acid and nitrite, carving out caverns (such as the famous Carlsbad Caverns) in total darkness. Only microbes can utilize cellulose as a carbon source. Only microbes can survive temperatures well below freezing or significantly above boiling, or live through prolonged exposure to concentrated radiation in a nuclear reactor. Microbes are responsible for the world's great sulfur deposits; the calcium carbonate in the white cliffs of Dover; the 100-meter-thick diatomaceous earth pits in Clark County, Nevada; the massive saltpeter deposits (formed by decomposition of guano) in the coastal ranges of Chile's Atacama Desert. Only Archaea (prokaryotic extremophiles that were once thought to be bacteria) can make methane. And only a bacterium (Alcaligenes eutrophus, for example; there are others) can store 80 percent of its body weight as plastic (polyhydroxybutyrate).

Most bacteria are harmless to humans and other life forms, but March of the Microbes doesn't shy away from pointing out the exceptions. We learn about the (fungal) origins and history of potato blight, the history of syphilis and smallpox (one being a gift of the New World to the Old; the other, vice versa); the curious mode of action of botulism poisoning, and tetanus; the bacterial origins of peptic ulcers; the recent rise of the oddly pathogenic E. coli O157:H7; and the many intricate and interesting ways in which antibiotic resistant bacteria develop drug resistance. An entire chapter is devoted to viruses, which are rather harshly (but deservedly, some would say) villified, despite their contribution to evolution.

If one organism is glaringly absent from March of the Microbes, it would be (drum roll, please) Amoeba proteus, the prototype of the "lowly amoeba," which of course is not so lowly when you consider that the amoeba genome contains 100  times the DNA of a human genome. The freshwater amoeba is, conceptually at least, the progenitor of the modern-day phagocyte (white blood cell); many consider it the "nursery" organism on which Mycobacteria and other pathogens practiced and perfected their anti-phagocytic skills before adapting to warm-blooded animals.

Aside from the lack of an amoeba sighting, March of the Microbes lacks for very little, combining (as it does) refreshingly edifying bits of natural history and ecology with the occasional dash of epidemiology and immunology, plus just the right amount of common-sense chemistry, to provide a deeply satisfying view into the astonishingly diverse, always-full-of -surprises microbial world. It's the kind of book you wish you could never reach the end of, a 306-page Aha moment; a delight from start to finish.

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