Environmental Engineering Reference
In-Depth Information
ties. Our own work has utilized these approaches to investigate the microbial
populations found in a variety of sedimentary and subsurface environments
in both modern and ancient terrains. As a general rule, in the more ancient
samples, the correlation between the microbial community and the present-day
in situ geochemical environment is more difficult to establish. Many reasons
may account for these discrepancies, including re-growth, deposition and stor-
age of organisms from other ecosystems, as well as storage (i.e. preservation
or degradation) of ancient relict DNA. We have called the composite nucleic
acid signals from such ancient environments the paleome [20] to connote the
idea that it may in some cases provide a taxonomic and phylogenetic window
to the past microbial community that inhabited the environment under study.
Here we review the results of community analyses of several environments and
discuss these in terms of their possible role(s) as ancient molecular signals, or
paleomes.
2. PALEOMES IN LOW-TEMPERATURE
SUBSEAFLOOR ENVIRONMENTS
2.1 Extremophiles in Cold Marine Sediments at the West
Philippine Basin
On the basis of the estimates of the prokaryotic biomass in core sediments
obtained by the Ocean Drilling Program (ODP), the marine subsurface sed-
iment is proposed to be the largest reservoir of biomass on Earth (Whitman
et al., 1998). Marine sediments consistently harbor more than 10
5
prokaryotic
cells/cm
3
even at a depth close to 1,000 m below the seafloor (mbsf) [39].
Perhaps the most intensively studied part of the marine subsurface, with regard
to the phylogenetic diversity and distribution of the prokaryotic communities
are the sediments at the continental margin associated with methane hydrates.
Despite these efforts, however, only a few sediment samples at a few depths
have been examined, and the role(s) of the microbiota in either formation or
degradation of these important deposits remain elusive.
The situation with regard to subsurface sediments in the open Pacific, the
locus of our studies, is even less well defined. In October 1999, we collected
a 14 m piston core from the center of the West Philippine Basin at a water
depth of 5719 m. The core was mainly composed of diatom ooze at the top,
with pelagic clay beneath, and a magnetostratigraphic age of approximately
2.5 million years. Such sediments serve to demonstrate a major conundrum
of sediment microbiology: surely microbes will be found, but are they merely
today's microbes processing yesterday's nutrients, or are they a snapshot of the
environmental conditions of the past?
With this question in mind, we extracted bulk DNA from the innermost part
of the core samples collected at 14 different depth horizons, amplified the DNA
