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fragments of archaeal 16S rRNA genes, and used this material to investigate
the vertical community structure of the Archaea in this environment, using a
combination of molecular ecological techniques [14]. The T-RFLP fingerprint
analysis showed that the archaeal community structure was clearly shifted
at a point of 4 mbsf (Fig. 1). The phylogenetic analysis of clone libraries
indicated that the archaeal community structures in shallow sediments were
mainly composed of the members belonging to the Marine Crenarchaeota
Group I (MGI) as they are called (Fig.1), a phylotype known to be the most
abundant Crenarchaeota in marine benthic environments [8, 11, 25, 50]. These
data are consistent with the notion of a continuous population of Crenarchaeota
in ocean bottom waters and shallow sediments.
In contrast, the deeper core horizons below 4.8 mbsf were dominated by ex-
tremophilic Archaea. In the pelagic clay samples at depths of 4.8 and 5.8 mbsf,
the archaeal 16S rRNA gene clone libraries were predominantly composed of
sequences related to the genus
Thermococcus
and the Deep-Sea Hydrothermal
Vent Euryarchaeotic (DHVE) Group. Both the
Thermococcus
group (known
as hyperthermophilic fermenters) and the DHVE are ubiquitous inhabitants
of hydrothermal vent environments [44]. At a depth range from 7.8 to 12.8
mbsf, in addition to
Thermococcus
, we found sequences related to the extreme
halophilic Archaea in the genus
Haloarcula
(Fig. 1).
Haloarcula
species are
known to be long-term survivors in various hyper-saline environments such
as salt lakes, salt mines, salt firms, and salt deposits [24], with reports of 16S
rRNA gene fragments detected from inside of a crystal halite formed over
200 million years ago [35]. These organisms are ubiquitously distributed in
marine environments as well, with
Haloarcula
DNA reported from a deep-sea
hydrothermal vent chimney structure obtained from the Manus Basin, Papua
New Guinea [45]. In addition, the 16S rRNA fragments related to the genera
Sulfolobus
and
Sulfurisphaera
were found to be present in the deeper part of
the piston core sediment (Fig. 1). These organisms are common in terrestrial
acidic geothermal environments and characterized to be extreme thermophilic
acidophiles; this was the first report of DNA of the order
Sulfolobales
from the
marine environment. Attempts to cultivate these extremophilic Archaea from
the marine sediments have so far yielded no growth. The DGGE analysis of
the archaeal 16S rRNA using a different primer set from that used to establish
the clone library showed almost the same results from the T-RFLP and clone
library analyses (Fig. 1F).
These data pose a fundamental question related to the origin of the various
cell types. A tempting hypothesis that we entertain here is that these unex-
pected DNA sequences represent paleomes of buried archaeal cells that were
transferred from another terrains and preserved to the present time. Since the
predicted growth characteristics of detected cells do not match the in situ cold,
low-organic subseafloor environment and most of detected cells are known to
