Environmental Engineering Reference
In-Depth Information
THE PALEOME: LETTERS FROM
ANCIENT EARTH
Fumio Inagaki
1
and Kenneth H. Nealson
1,2
1
Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Subground Animalcule
Retrieval (SUGAR) Project, Extremobiosphere Research Center, 2-15 Natsushima-cho, Yokosuka
237-0061, Japan
2
Department of Earth Sciences, University of Southern California, 3651 Trousdale Pkwy, Los
Angeles, CA 90089-0740, USA
Abstract
Recent advances in molecular ecological techniques have led to the revelation
that sedimentary environments contain molecular signals in the form of DNA
sequences: signals that tend to be consistent with the in situ geochemical envi-
ronment. However, as one moves to more ancient environments, the correlation
of molecular signals with the in situ environment becomes more difficult. We
have called the pool of molecular information that can be obtained from such an-
cient environments the 'Paleome'. This concept is controversial, in part because
it demands that the molecular sequences be stable for long periods of time, and
in part because the interpretation of such sequences in a geochemical context is
often difficult, even for contemporary samples. We review results from a variety
of environments, discussing the potential explanations for each, and focusing on
the relationship of the molecular signals to the biological history of the sample.
In almost every case, while molecular signals were abundant, viable cells were
not cultivated. We posit here that the paleome is the genetic record of the bio-
logical past, a record that has been preserved on geologic timescales: a record
that may well provide us with insights into both the paleoenvironment and the
co-evolution of Earth and its biota.
Keywords:
Paleome, Subsurface biosphere, 16S rRNA gene, Extremophiles
1. INTRODUCTION
Recent progress using culture-independent molecular (sequence-based) ap-
proaches has revealed the presence of ubiquitous and often abundant prokary-
otes in many environments previously thought to be uninhabited. Because of
the ability of the polymerase chain reaction (PCR) to amplify small signals,
it is possible to interrogate very low levels of biomass in search of specific
sequence information. Furthermore, because of the power of statistical analysis
of the DNA sequences, it has been possible to define the remarkable systematic
(i.e. taxonomic and phylogenetic) diversities within the prokaryotic communi-
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