Despite the best efforts of Walt Disney and Elton John, it
is the tree of life, not the circle, that remains the primary way that
organisms are classified and by which their evolutionary relationships
are depicted. The tree was initially made by categorizing life forms
with similar features into groups; this method distinguished not only
amphibians from reptiles but also protists from amoeba.
Genetic data expanded the tree by allowing us to use
similarities in genetic sequences—we didn’t have to actually see
anything in order to determine how everyone is related to each other.
Now, genomic studies have expanded the tree still further, allowing us
to place species we can’t even grow in the lab onto their proper branch.
It is hardly news that most life on Earth is unicellular. But the newest tree of life, published in Nature Microbiology,
reveals that most of life's diversity is bacterial and that much of it
belongs to a recently discovered branch of especially tiny bacteria that
no one has ever grown or seen under a microscope. All we have is their
DNA, mixed in with the DNA of everything else that inhabits the same
ecosystem.
To classify organisms genetically, scientists have placed
them in the appropriate “bins,” often by looking at the sequence of a
specific gene (one that encodes the small subunit ribosomal RNA). This
gene is required to make proteins, so all cells have it. The sequence
of species’ rRNA gene is unique, like a fingerprint, so it has provided a
tidy classification system. But these rRNA genes are still similar
enough between species to be recognizable—or so it was thought.
In order to fish out a gene, scientists need to hook onto it
using a complementary sequence, known as a primer. But these new
bacteria, identified by the lab of Jillian Banfield at UC Berkeley, have
rRNA genes that don’t interact with any previously used primers. That
rendered them pretty much undetectable by genetic methods.
The new tree is made with genomic data in which researchers get all
of the DNA of an organism rather than trying to fish out one or a few
particular predetermined sequences. Dr. Banfield and her lab looked at
thousands of genomes from the three traditional branches of
life—Bacteria, Archaea, and Eukarya—to make their new tree. They were
overwhelmed by the preponderance of life forms that have never been
cultivated in a laboratory setting.
These bacteria are tinier than any we've studied to date; they fit
through filters with holes that are only 0.1 microns in size. And their
genomes reflect that, as they are about five times smaller than E. coli's.
They lack genes for basic metabolic processes, like making amino acids,
DNA and RNA nucleotides, respiration, and the Krebs cycle, used to
generate energy from food. The researchers infer that they must
be symbionts with a partner supplying all of their required materials.
It’s not clear if they were always that way or if they had their own
metabolic capabilities once upon a time and lost them after establishing
symbiosis with more complex life forms.
Eukarya, including all multicellular life, such as ladybugs and
sunflowers and starfish and panda bears and us, comprise only a tiny
fraction of the tree, which makes sense as we only developed a
billion-and-a-half years into the whole evolutionary process. Ever since
then, we’ve been swimming in a sea of bacteria. This tree just gives us
a new way to visualize that fact.
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