A scanning electron micrograph (SEM) of a grouping of Vibrio vulnificus bacteria. Image: Centers for Disease Control |
Bacteria
are the most populous organisms on the planet: They thrive in almost every
known environment, adapting to different habitats by means of genetic
variations that provide the capabilities essential for survival. These genetic
innovations arise from what scientists believe is a random mutation and
exchange of genes and other bits of DNA among bacteria that sometimes confers
an advantage, and which then becomes an intrinsic part of the genome.
But
how an advantageous mutation spreads from a single bacterium to all the other
bacteria in a population is an open scientific question. Does the gene
containing an advantageous mutation pass from bacterium to bacterium, sweeping
through an entire population on its own? Or does a single individual obtain the
gene, then replicate its entire genome many times to form a new and
better-adapted population of identical clones? Conflicting evidence supports
both scenarios.
In
a paper appearing in Science, researchers in Massachusetts Institute of
Technology’s (MIT) Department of Civil and Environmental Engineering (CEE)
provide evidence that advantageous mutations can sweep through populations on
their own. The study reconciles the previously conflicting evidence by showing
that after these gene sweeps, recombination becomes less frequent between
bacterial strains from different populations, yielding a pattern of genetic
diversity resembling that of a clonal population.
This
indicates that the process of evolution in bacteria is very similar to that of
sexual eukaryotes—which do not pass their entire genome intact to their
progeny—and suggests a unified method of evolution for Earth’s two major life
forms: Prokaryotes and eukaryotes.
The
findings also get to the heart of another scientific question: how to delineate
species of bacteria—or determine if the term “species” even applies to
bacteria, which are typically identified as ecological populations and not
species. If all bacteria in a population are clones from a common ancestor, the
idea of species doesn’t apply. But if, as this new study shows, genes randomly
shared among individuals can bring about a new, ecologically specialized
population, use of the term may be warranted.
“We
found that the differentiation between populations was restricted to a few
small patches in the genome,” says Eric Alm, the Karl Van Tassel (1925) Career
Development Associate Professor of Civil and Environmental Engineering and
Biological Engineering and an associate member of the Broad Institute.
Professor
Martin Polz of CEE, co-principal investigator on the project, adds, “Similar
patterns have been observed in animals, but we didn’t expect to see it in
bacteria.”
The
process of ecological differentiation in bacteria, the researchers found, is
similar to that in malaria-transmitting mosquitoes: Some populations develop
resistance to antimalarial agents by means of a single gene sweep, while other
populations sharing the same habitat do not. The stickleback fish has also been
shown to follow this pattern of “sympatric speciation” in shared habitats.
“Even
though the sources of genetic diversity are quite different between bacteria
and sexual eukaryotes, the process by which adaptive diversity spreads and
triggers ecological differentiation seems very similar,” says first author
Jesse Shapiro PhD ’10, a postdoctoral researcher at Harvard
University who did his
graduate work in Alm’s laboratory at MIT.
The
researchers performed the work using 20 complete genomes of the bacterium
Vibrio cyclitrophicus that had recently diverged into two ecological
populations adapted to microhabitats containing different types of zooplankton,
phytoplankton, and suspended organic particles in seawater. In a previous study
based on just a few marker genes, they had predicted that these closely related
Vibrio populations were in the process of developing into two distinct habitat-associated
populations.
The
new study shows that the two populations were frequently mixed by genetic
recombination, remaining genetically distinct at just a handful of ecologically
adaptive genes, with an increasing trend toward gene-sharing within—rather than
between—habitats.
“This
is the most sophisticated paper on bacterial speciation to appear yet, all the
more so because it uses the dubious word ‘species’ only once, and that with
caution,” says W. Ford Doolittle, a professor emeritus of biochemistry at Dalhousie University
in Canada. “The genetic basis of ecological differentiation in bacteria—how genotype maps
to ecotype and what processes determine this mapping—is in my mind the biggest
issue in modern microbial ecology.”