New phyllum

Thu May 2 00:03:24 EDT 2002

Just a few weeks ago we were intrigued to learn about a whole new insect order.
Today's NATURE (May 2, 2002) carries a paper describing a whole new PHYLUM.

To whet your interest, here is a general discussion paper about the discovery
(first few paragraphs only to spare slow readers or computers) followed by the
first few paragraphs of the actual description.

The organism  doesn't look like a butterfly, but not much is known about the
leps at Deep Sea Vents.

Mike Gochfeld
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Biodiversity: Something new under the sea

YAN BOUCHER AND W. FORD DOOLITTLE
Yan Boucher and W. Ford Doolittle are in the Department of Biochemistry and
Molecular Biology, Dalhousie University,
Halifax, Nova Scotia B3H 4H7, Canada.

e-mail: ford at is.dal.ca

The discovery, in an undersea hot vent, of an organism that does not fit into
any previously defined category of life marks
the creation of yet another group within the mysterious Archaea.

An exciting new creature has been discovered under the sea off Iceland, and it
is described by Huber et al. on page 63 of
this issue1. Although invisible to the naked eye, it is as worthy of our notice
as any coelacanth or other macroscopic
'living fossil', for three reasons. First, its discovery means that current
methods are still inadequate to reveal life's
true diversity. Second, it is either very primitive or extremely modified by
evolution. Finally, this newly identified
entity may represent a whole new group within the Archaea, the most recently
discovered and still most mysterious of life's
three domains (the others being the Eukaryota and Bacteria).

Much of life's diversity is microbial, but most microbes cannot be grown in
culture. How, then, can we discover anything
about such organisms? In particular, by what methods can we establish their
relatedness to those few microbes that we are
able to cultivate and study in the laboratory? The answer is the polymerase
chain reaction (PCR). This technique can be
used to amplify - make many copies of - DNA isolated directly from environmental
samples; the DNA can then be sequenced.
Comparing sequences with each other and with those stockpiled in databases gives
us a measure of true microbial diversity2.

Genes that code for the RNA component of ribosomal small subunits (SSU rRNA) are
the best targets for amplification,
sequencing and comparison. This is because ribosomes - cellular complexes of
rRNA and protein that are the site of
translation of the DNA code - are essential for the survival of any organism. So
all organisms carry at least one rRNA
gene, and rRNA gene sequences have changed relatively little during the
3-4-billion year history of life on Earth. They are
accepted by microbiologists as the common currency of microbial taxonomy.
Indeed, it was rRNA sequence analysis that led to
the initial discovery of the Archaea, a group now known on many grounds (lipid
biochemistry, and the fundamental
machineries of DNA replication, transcription and translation of RNA, for
instance) as being distinct from Bacteria.

Using PCR 'primers' to target specific regions of bacterial, archaeal or
eukaryotic SSU rRNA genes makes modern-day microbe
hunting even more selective and efficient. In this way, the number of known
major divisions within life's two prokaryotic
domains, Bacteria and Archaea, has doubled3, 4. And just last year, two groups
reported finding totally unknown, tiny
eukaryotes among the 'picoplankton' of the Pacific and along the Antarctic polar
front5, 6. (Prokaryotes are organisms that
have no intracellular organelles or nucleus; eukaryotes possess organelles and a
nucleus for their DNA.)

Satisfying as this has been, there is a lingering suspicion - or romantic hope,
depending on your disposition - that there
might be even weirder organisms hiding out there. Such organisms could be
especially primitive or wildly divergent
creatures that have drifted so far out of the biological mainstream that the
usual PCR primers don't recognize or amplify
their SSU rRNA genes. Huber et al.1 provide a stunning example of just such a
weird bug, something they call Nanoarchaeum
equitans (Fig. 1).....
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A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont

HARALD HUBER*, MICHAEL J. HOHN*, REINHARD RACHEL*, TANJA FUCHS**, VERENA C.
WIMMER* & KARL O. STETTER*

* Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg,
Universitätsstrasse 31, D-93053 Regensburg,
Germany
* Max Planck Institute for Medical Research, Department of Cell Physiology,
Jahnstrasse 29, 69120 Heidelberg, Germany
* Present address: AstraZeneca GmbH, Tinsdaler Weg 183, D-22876 Wedel, Germany.

Correspondence and requests for material should be addressed to K.O.S. (e-mail:
karl.stetter at biologie.uni-regensburg.de).
The 16S rRNA (ss rRNA) sequences for 'Nanoarchaeum equitans' and Ignicoccus sp.
were deposited at GenBank under accession
numbers AJ318041 and AJ318042, respectively.
According to small subunit ribosomal RNA (ss rRNA) sequence comparisons all
known Archaea belong to the phyla
Crenarchaeota, Euryarchaeota, and-indicated only by environmental DNA
sequences-to the 'Korarchaeota'1, 2. Here we report
the cultivation of a new nanosized hyperthermophilic archaeon from a submarine
hot vent. This archaeon cannot be attached
to one of these groups and therefore must represent an unknown phylum which we
name 'Nanoarchaeota' and species, which we
name 'Nanoarchaeum equitans'. Cells of 'N. equitans' are spherical, and only
about 400 nm in diameter. They grow attached
to the surface of a specific archaeal host, a new member of the genus
Ignicoccus3. The distribution of the 'Nanoarchaeota'
is so far unknown. Owing to their unusual ss rRNA sequence, members remained
undetectable by commonly used ecological
studies based on the polymerase chain reaction4. 'N. equitans' harbours the
smallest archaeal genome; it is only 0.5
megabases in size. This organism will provide insight into the evolution of
thermophily, of tiny genomes and of
interspecies communication.

Hyperthermophilic microorganisms with optimal growth temperatures above 80 °C
occur in both prokaryotic domains, the
Bacteria and Archaea. In phylogenetic trees based on ss rRNA they represent all
the short deep lineages, forming a cluster
around the root5. This feature and their ancient biotopes indicate that
hyperthermophiles are still primitive5. Within the
Archaea, hyperthermophilic members of the Crenarchaeota and the Euryarchaeota
have been cultivated, which exhibit unusual
cell morphologies such as disks, networks, 'golf clubs', irregular spheres, and
branched and irregular rods6. Variations in
cell volume by up to four orders of magnitude even within a pure culture were
observed (for example, Thermoproteales and
Desulfurococcales)6.

To investigate hot submarine vent microbial communities, we carried out
experiments to cultivate hyperthermophiles from
samples of originally hot rocks and gravel taken at the Kolbeinsey ridge, north
of Iceland7. By anaerobic incubation at 90
°C in the presence of S, H2 and CO2, a new autotrophic sulphur-reducing species
of the archaeal genus Ignicoccus3 could be
enriched. In contrast to known species, several large spherical Ignicoccus cells
were covered by very tiny cocci which
could be stained by DNA-specific fluorescence microscopy (DAPI)8. Few such tiny
cocci existed in the free state.

These tiny cocci could be physically isolated either by using 'optical
tweezers'9, 10 or by ultrafiltration (pore width,
0.45 µm). All attempts to grow them in pure culture employing various inorganic
and organic energy sources failed. However,
isolation of a combination of a tiny coccus attached to an Ignicoccus sphere
after incubation under enrichment conditions,
resulted in a defined coculture in which about half of the Ignicoccus cells
appeared to be colonized by the tiny cocci. The
final density of both the tiny cocci and the Ignicoccus cells was about 3  107
cells ml-1 resulting in about two tiny cocci
per Ignicoccus cell on average. The purified coculture was used in all further
investigations. Cloning of single Ignicoccus
cells gave rise to cultures which never contained tiny cocci.

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