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taxonomic units, and (3) filling the dearth of reference strains and genomes needed to test
hypotheses generated via genomic and metagenomic approaches.
The sheer volume of data available at relatively low cost increasingly pushes
analytical challenges into the realm of computer science—one of the major challenges of the
next few years. Added to these computational challenges will be interfacing the omics data
with geochemical/geological data—two data sets that are fundamentally different in terms of
definition and quantification. Bringing the two fields together will ultimately allow each to
make predictions about the other: omics approaches open entirely new avenues for probing
geochemistry, while the geochemical community (organic and inorganic) can provide a rich
context in which to understand molecular geomicrobiology. Integrating these communities
has vast potential for transformative cross-disciplinary breakthroughs, including new
advances at very fine temporal scales.
Among the emerging research questions and opportunities empowered by new
computational, nanoscale, and DNA-based approaches are the following:
•
What regulates cellular and subcellular agents in complex environmental systems?
•
How does biodiversity relate to ecosystem function, stability, and resilience, and how
does it respond to environmental perturbation and specifically climate change?
•
What can the genetic record tell us about the history of life and its planetary habitat?
•
How can we integrate genomics and the geological record to probe the emergence of
metabolic processes and their impacts on the evolving geochemical states of Earth?
The deep-time record of past biotic turnovers and mass extinction events
associated with warm periods (many associated with massive outgassing of carbon
dioxide or methane), transient warmings, and major transitions between climate states
offer an under-tapped repository from which unique insight can be obtained regarding
patterns of ecosystem stress, the potential for ecological collapse, and mechanisms of
ecosystem recovery (NRC, 2011a). Such periods of crisis naturally resonate with
today's global warming and biotic crises. For example, the warm, low-pH, and low-
oxygen ocean that will come with global warming was first experienced in the
Phanerozoic and Proterozoic. It was linked to profound global climatic and biological
instability. At least some Phanerozoic mass extinctions appear to be associated with a
doubling to tripling of carbon dioxide concentrations that occurred over human
timescales. Examples include those at the end-Triassic (McElwain et al., 1999;
Schaller et al., 2011) or Cretaceous-Paleogene (Beerling et al., 2003) that were caused
by massive volcanic eruptions or bolide impacts. Hot, rapidly weathering soils in the
coming century have loose analogs in deglacial Permian paleosols (throughout the
Pangaean paleotropics) and in the postglacial phase of Proterozoic glaciation (i.e., in
the wake of the hypothesized “snowball Earth”).
The recovery from mass extinction is more than just recovery of taxonomic
diversity. The dynamics of recovery include coupled biological and geochemical
feedbacks. They also include evolutionary responses such as rapid bursts of
speciation in surviving clades, followed by increasing morphological disparity and
biotic provinciality. The patterns of these different diversity changes are not well
documented. However, they clearly have relevance to the present-day human-caused
biodiversity crisis that appears to be causing a mass extinction that may be
comparable in magnitude to the Big 5 of the Phaneozoic and perhaps larger in effect
than the PETM.
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