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C-DEBI research focuses and integrates across four broad
research themes:
- Activity in the deep subseafloor biosphere:
function & rates of global biogeochemical processes;
- Extent of life: biomes and the degree
of connectivity (biogeography & dispersal);
- Limits of life: extremes and norms of
carbon, energy, nutrient, temperature, pressure, pH;
- Evolution and survival: adaptation, enrichment,
and repair.
Research Theme I. Activity in the deep subseafloor biosphere:
function & rates of global biogeochemical processes.
Subseafloor microbial processes exert fundamental influence
on the biogeochemistry of the ocean and atmosphere. For example,
sulfate reduction coupled to metal sulfide (e.g., pyrite)
precipitation in sediments is a major sink of sulfate from
the world ocean and potentially a significant source of ocean
alkalinity on geological timescales (ka to Ma) [Schlesinger
1997]. Oxidation of organic carbon leads to a major source
of dissolved inorganic carbon (DIC) to the ocean. Because
the geographic distribution of organic carbon degradation
as well as sulfate reduction and sulfide precipitation is
poorly quantified, the global effect of these coupled processes
is not well known. As another example, waterrock weathering
reactions in the ocean crust impose significant negative feedback
on atmospheric CO2, accounting
for ~30% of the silicate-drawdown globally [Dessert et al.
2003]. Microbes are known to promote these reactions in the
laboratory [Edwards et al. 2004], and at the seafloor [Edwards
et al. 2003], but the degree to which they influence these
processes in situ in the subseafloor remains unknown.
Through targeted support of research aiming to quantify geographic
distributions of subseafloor sedimentary respiration, rates
and magnitude of microbial crustal alteration, energy sources
and carbon flow, C-DEBI will enable robust analyses linking
subseafloor processes to global scales and biogeochemical
cycles.
> See the report from the Activity
Theme Team Meeting held August 19-21, 2012 at the Portofino Hotel in Redondo Beach, California. [PDF]
Research Theme II. Extent of life: biomes and the degree of
connectivity (biogeography and dispersal).
We are now aware of the basic fact that there is a deep subseafloor
biosphere—intraterrestrial microbes that appear to represent
a significant biosphere in sediments (e.g., [D'Hondt et al.
2004]) and rock (e.g., [Fisk et al. 1998]) below the bottom
of the ocean. How microbes are transported and dispersed in
the deep subseafloor biosphere—the biogeography of microbes—is
an open and intriguing problem. Questions concerning biogeography
speak to the most fundamental problems in microbiology (e.g.,
as discussed in [O'Malley 2007, de Wit and Bouvier 2006]),
and date at least back to the Baas-Becking hypothesis that
'everything is everywhere, but, the environment selects' [Baas
Becking 1934]. The variety of dispersal mechanisms for microbes
to deep subseafloor habitats, and the vast spatial- and time-scales
we consider, presents opportunities to address fundamental
questions in this field.
As discussed above, it is well documented that tremendous
volumes of seawater infiltrate the crust and hence, seawater
is likely a source of inoculum "seeding" subseafloor
biomes. The transport time for fluid to travel through different
crustal aquifers varies enormously, as do the physical and
chemical conditions of these fluids and any microbiology they
carry [Bach et al. 2004]. Deep sea sediments remain in exchange
with seawater at their top and bottom layers via the overlying
water column and deep crustal aquifers. What microbes take
seed and why? What are the most significant physical and chemical
controls of these colonization processes? How similar or different
are the resulting crustal and sedimentary ecosystems from
deep subseafloor ecosystems and from each other? We expect
that geochemical and physical site parameters will shape the
patterns of archaeal and bacterial community compositions.
Questions relating to biogeography are a cornerstone component
of C-DEBI, because it is only through inter-project comparisons
that true headway in comparing these ecosystems may be made.
Each site and project is an island in and of itself, but when
compared with this disparate set of habitats, will coalesce
as a global model for biogeography of microbes below the ocean
floor.
> The latest workshop was a joint Extent Theme Team and Guaymas Drilling Proposal Workshop with sponsorship from the IODP U.S. Science Support Program at the Consortium for Ocean Leadership. The workshop was held February 27 - March 1, 2013 at the Wrigley Marine Science Center on Catalina Island, California. [Workshop Report PDF, 8.4 MB] [Guaymas Basin IODP Pre-proposal PDF, 9.4 MB]
> See the report from the Sediment
Microbiology DEBI RCN Meeting held March 6-9, 2011 at the Carolina Inn and the
University of North Carolina, Chapel Hill. [DEBI RCN Meeting Website]
Research Theme III. Limits of life: extremes and norms of
carbon, energy, nutrient, temperature, pressure, pH.
What are the factors that fundamentally limit the existence
and diversity of life within seafloor sediments and ocean
crust? High temperature is probably a critical limitation
in many areas, although the impact of temperature on the distribution
of life is likely to be convolved with other factors. For
example, survival at high temperatures may depend on the capacity
of organisms to repair the damage caused by thermal degradation
of cellular components [Shock and Holland 2007], so it may
be possible for microbes to exist at higher temperatures in
environments that supply more metabolic energy than in those
where the supply is less. Most seafloor sediments exhibit
low thermal gradients (1-30°C per km), but the highest
temperature documented for microbial activity to date (~122°C)
[Takai et al. 2008] is exceeded at shallow depths at certain
sediment-covered mid-ocean ridges such as the Juan de Fuca,
Okinawa Trough, and Guaymas Basin. Drilling along a temperature
gradient in deeply buried, organic rich sediments, such as
at Guaymas Basin (where the availability of organic C should
not be a limiting factor) will enable questions relating to
the thermal limit of life in deeply buried sediments to be
addressed empirically.
Low availability of electron donors may limit the distribution
of life in the subseafloor within marine sediments. In sediments,
buried organic matter from the surface photosynthetic world
is the principal source of electron donors (e.g., [D'Hondt
et al. 2004, Blair et al. 2007]). Within the South Pacific
Gyre, where the burial rate of organic matter is two orders
of magnitude lower than in other regions that have previously
been explored for life in subseafloor sediments, analyses
of shallow cores obtained as part of an NSF-sponsored site
survey cruise in 2007 revealed that only 10^3–10^4 cells/m^3
survive in shallow sediments [Kallmeyer et al. 2007]. If low
organic matter availability ultimately sets a limit to life
in marine sediments, active cells may be absent from the deeper
sediment column in the South Pacific Gyre.
Different factors are likely to define the ultimate limitation
to life in the igneous ocean crust and in marine sediments.
Sources of metabolic energy may not be a limiting factor in
the ocean crust, as reactions between the reduced ocean crust
and circulating fluids may supply chemical energy to support
primary carbon fixation in situ (e.g., [Bach and
Edwards 2003]). One proposed hypothesis is that microbes may
be active throughout the upper ocean crust wherever there
is active hydrology with temperatures below ~120°C, until
the crust undergoes subduction in ocean trenches. In one study
supporting this idea, textural and isotopic evidence suggested
that microorganisms are active in ocean crust aged over 1000
Ma [Banerjee and Muehlenbachs 2003]. However, another study
that examined textural features thought to be attributable
to microbial activity suggested that the features were established
early in the history of the crust (~<10 Ma) and then changed
little afterwards [Furnes et al. 2001]. Evidence for the timing
of oxidative alteration of the ocean crust, which may support
chemosynthetic biological activity, also indicates that most
alteration appears to occur early and then slows or ceases
as the crust ages [Bach and Edwards 2003]. Thus, an alternative
hypothesis is that life may be most active early in crustal
evolution, and fades out well before subduction. The C-DEBI
related projects and field sites, which span nearly the entire
age range of ocean crustal rock, will allow these conflicting
possibilities to be directly and explicitly tested.
> See the report from the Limits2Life
Theme Team Meeting held May 17-18, 2011 at the Portofino Hotel in Redondo Beach, California. [PDF]
Research Theme IV. Evolution and survival: adaptation, enrichment,
and repair.
The question of persistence of life from the perspective
of metabolic processes and growth can be distilled to the
concept of survival at the edge of bioenergetics and redox
processes [Hoehler et al. 2007]. The metabolic rates proposed
for subsurface microbes are up to six orders of magnitude
below respiration rates observed in microbial cultures and
in environmental microbes in surface sediments [D'Hondt et
al. 2002] and challenge our current understanding of the functioning
of life (i.e. having enough energy to maintain charge potential
across a cell membrane). Observations of living cells [Schippers
et al. 2005] with intact polar membrane lipids [Lipp et al.
2008] lead to the inference that subseafloor sedimentary microbes
must persist at extremely low rates of activity per cell.
Additionally, studies have shown that the subseafloor hosts
extremely unique microbial communities that are distinct from
surface habitats [Lipp et al. 2008, Sørensen and Teske
2006, Biddle et al. 2008]. Why are these microbial groups
so prevalent in the subsurface? Are there distinct adaptations
that are common to the subseafloor biosphere?
Since most subsurface microbes are recalcitrant to cultivation,
answers to questions about their adaptation, evolution and
survival need to be answered through genetic analysis. Genetic-based
studies of deep subseafloor biosphere to date have used targeted
polymerase-chain reaction (PCR) based approaches to examine
phylogenetic genes (e.g., [Teske 2005]) and on occasion, ribosomal
sequencing and analysis has been performed [Sørensen
and Teske 2006]. More rarely, PCR based approaches for looking
at functional genes encoding for important biogeochemical
processes (methane, iron, etc.) have been targeted (e.g.,
[Schippers and Neretin 2006, Webster et al. 2006]). However,
research concerning questions about survival and evolution
in the subseafloor has not yet emerged among the core foci
in subseafloor biosphere studies, nor have research approaches
that take a broader-scale view of the genetic content of microbes
buried beneath the seafloor. We envision Theme IV studies
will embrace a compare-and-contrast approach across our C-DEBI
field projects examining the total gene content of the deep
subseafloor biosphere using metagenomics-based approaches
(e.g., [Handelsman 2004]). The term "metagenomics"
includes a variety of whole-genome approaches such as shot-gun
sequencing, i.e., [Venter et al. 2004], vector-based library
tools [Beja et al. 2000], whole-genome amplifications [Dean
et al. 2001] and other specialized methods.
Our first-glimpse at use of metagenomics in the deep subseafloor
biosphere illustrates its potential power for evolutionary
questions. As part of the initial "census" of life
in subseafloor sediments [1], it has emerged that globally,
cell abundances decrease logarithmically with depth [Parkes
et al. 2000]. A consequence of this decrease is that with
depth, microbes become increasingly isolated from each other,
owing to the fact that chemical exchange in sediments is dictated
by diffusion, which operates slowly over long length scales.
Hence, we may hypothesize that an evolutionary consequence
of this increasing isolation may be the loss of genes for
functions such as chemotaxis and quorum sensing, which may
not be needed as cells become isolated. Indeed, metagenomics
surveys of sediments from the Peru Margin do show that genes
for chemotaxis decrease with depth [Biddle et al. 2008], hinting
that further metagenomics surveys and cross-comparisons may
yield exciting new insights on microbial evolution on Earth.
Through project integration with C-DEBI, we will be able to
integrate and compare these finding with metagenomics surveys
at other sites, and in distinct biomes.
> The latest workshop was held February 28 - March 1, 2013, at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. [Workshop Report PDF]
> See the report from the Evolution
Theme Team Meeting held April 20-22, 2011 at the Wrigley Marine
Science Center on Catalina Island, California. [PDF]
> Who are the theme
team leaders?
> Discuss research theme topics in our C-DEBI
Discussion Forum!
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