Microcosm by Carl Zimmer

Along with the spiders came beetles, butterflies, and even a monitor lizard. Some of the arriving species swam to the islands, some flew, and some simply drifted on the wind.
    These species did not take hold on Krakatau in a random scramble. Rugged pioneers came first and later gave way to other species. The savanna surrendered to forests. Coconut and fig trees grew. Orchids, fig wasps, and other delicate species could now move onto the islands. Early settlers such as zebra doves could no longer find a place in the food web and vanished. Even now, more than 120 years after the eruption, Krakatau is not finished with its transformation. In the future it may be ready to receive bamboo, which will revolutionize its ecosystem yet again.
    The history of Krakatau followed ecological rules that guide life wherever new habitats appear. Volcanic eruptions wipe islands clean. Landslides clear mountainsides. As glaciers melt, shorelines bounce out of the sea.
    And babies are born. To microbes, a newborn child is a Krakatau ready to be colonized. Its body starts out almost completely germ free, and in its first few days
E. coli
and other species of bacteria infect it. They establish a new ecosystem, which will mature and survive within the child through its entire life. And it will develop over time according to its own ecological rules.
    There is much more to
E. coli’
s life than can be seen in a petri dish. Its pampered existence in the laboratory makes very few demands on it. Out of the 4,288 genes scientists have identified in
E. coli
K-12, only 303 appear to be essential for its growth in a laboratory. That does not mean the other 3,985 genes are all useless. Many help
E. coli
survive in the crowded ecosystem of the human gut, where a thousand species of microbes compete for food.
    A scientist studying
E. coli
in a flask may completely overlook some of its essential strategies for surviving in the real world. For all the work that has gone into
E. coli
over the past century, for example, microbiologists often fail to acknowledge just how social a creature it is. To survive,
E. coli
work together. The bacteria communicate and cooperate. Billions of them join together to build microbial cities. They wage wars together against their enemies.
    In the real world there is no single way of being an
E. coli. E. coli
K-12 is just one of many strains that live in warm-blooded animals and have many strategies for surviving. Some are harmless gut grazers. Others shield us from infections. And still others kill millions of people a year. To know
E. coli
by K-12 alone is a bit like knowing the family
Canidae
from a Pomeranian dozing on a silk pillow. Outside there are dingoes and bat-eared foxes, red wolves and black-backed jackals.
    FINDING A HOME
    E. coli
is a pioneer. Long before most other microbes have moved into a human host, it has established a healthy colony.
E. coli
may infect a baby during the messy business of childbirth, hitch along on the fingertips of a doctor, or make its leap as mother nurses child. It rides waves of peristalsis into the stomach, where it must survive an acid bath. As the swarms of protons in hydrochloric acid seep into it,
E. coli
builds extra pumps that can flush most of them out. It does not try to behave like a normal microbe in the stomach; instead, it enters what one scientist has called “a Zen-like physiology.” Except for the proteins it needs to defend against stomach acid,
E. coli
simply stops making proteins altogether.
    After two hours in this acid Zen,
E. coli
is driven out of the stomach and into the intestines. Its pumps continue driving out its extra protons until its interior gets back its negative charge. Its biological batteries power up once more, and it can now begin to make new proteins and repair old ones. It returns to the everyday business of living.
E. coli
has not yet reached its new home, though—it must first travel through the small intestine and into the large one. The distance