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Prokaryotes
are organisms that lack a membrane-bound nucleus, and they
consist of two very different groups of microorganisms,
Bacteria and Archaea. They are ubiquitous and immensely
important in all global elemental cycles as well as all
biological systems in general. The focus of our research
is the marine environment. In that environment, like many
others, the diversity of naturally-occurring prokaryotes
is poorly known. It has only been in the last decade or
so, with the advent of molecular biological techniques in
this field, that we have the ability to say what kinds of
bacteria and archaea live in seawater. We have been using
such techniques, originally pioneered by Norman Pace and
his colleagues, to study naturally-occurring marine
microbes by means of 16S rRNA gene sequences. This
approach has provided a valuable and extremely broad
phylogenetic framework of classification, and has the huge
benefit that it can be done without culturing the
organisms. The results are in the form of sequence data,
and interpretation within the context of a large existing
database is via phylogenetic analysis computer programs.
In
our study, we obtained seawater from numerous locations
around the world (see map link), collected the organisms
on a filter, extracted their DNA, amplified partial 16S
rRNA genes, cloned those PCR products, sequenced them, and
analyzed the sequences phylogenetically. Detailed
scientific protocols can be found in our research
publications (e.g. Fuhrman, J.A., and A.A. Davis.1997.
Widespread Archaea and novel Bacteria from the deep sea as
shown by 16S rRNA gene sequences. Mar. Ecol. Prog. Ser.
150: 275-285). This research has discovered the existence
of numerous groups of organisms that were previously
unknown. Perhaps the most exciting discovery was that
archaea are common in the deep sea (Fuhrman, J.A., K.
McCallum, and A.A. Davis. 1992. Novel major
archaebacterial group from marine plankton. Nature 356:
148-149). Previously, the archaea were thought to include
only “extremophiles” such as hyperthermophiles,
halophiles, and methanogens. We have also found numerous
novel types of bacteria by this approach.
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Phylogenetic
trees that include the various sequences we have obtained
from seawater samples around the world can be accessed by
the accompanying links. There is also a key to clone
identifiers. All sequences are available from GenBank.
Examination of the trees shows that many groups, such as
the SAR 11 cluster, are globally distributed, with some
distinct subgroups in warmer surface waters and others in
deeper and polar waters. However, not all of the samples
had members of the SAR 11 cluster. The cyanobacteria are
ubiquitous in warm surface waters, but not found in polar
areas. All the cyanobacterial clones, with the exception
of a few clones from near Singapore, wererelated to
cultivated marine Prochlorococcus and Synechococcus.
Numerous other themes are evident in the data.
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Global Survey of Marine Prokaryotes