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Life in the Deep Biosphere
Amy Mayer
When rock meets water in the dark.
The drill ship JOIDES Resolution is equipped with state-of-the-art science labs.
Photograph: John Beck, Senior Imaging Specialist, Integrated Ocean
Drilling Program.
W
hen the fourth phase of international scientific ocean drilling gets under way next year, one of
the initiatives of the 10-year program
will be “Biosphere Frontiers.” This
component marks a coming-of-age of
sorts for microbiology as a partner in
ocean-drilling research.
Microbiologists are already hard at
work. From September to November
2011, Katrina Edwards, biology professor
at the University of Southern California
and director of the National Science
Foundation–funded Center for Dark
Energy Biosphere Investigations, co-led
“Expedition 336: Mid-Atlantic Ridge
Microbiology,” a trip that took her team
to a site called North Pond. The cruise
may represent the type of prime billing
that the life sciences can expect.
Originally, biologists’ work complemented that of geoscientists in the scientific ocean-drilling community. But
the shift to marquee status for the life
sciences reflects developments made
during the past 45 years.
First glimmers of microbial life
In the beginning, the ocean-drilling
community focused primarily on geologic questions, from paleoclimate
records to hydrogeology or geochemistry, but there was always a glimmer
of interest in the possibility of life deep
beneath the seafloor. Steven D’Hondt,
professor of oceanography at the
University of Rhode Island, said that
as far back as the 1920s, two petroleum scientists conducted studies of
bacteria found in the fluids produced
from drilling oil wells. D’Hondt cited
that research as the first inkling of
deep microbial life but cautioned that,
at the time, it was hardly mainstream
science. When scientific drilling got
underway—both the ocean-going work
and continental drilling—­geochemists
looking at ­methane production and
sulfate reduction “showed in some
cases [that] those processes were going
on hundreds of meters below the
seafloor,” he said.
That led microbiologists to realize
that if fluids were circulating through
a vast underground aquifer, chemical
reactions between seawater and rock
could likely sustain life there, according to Jim Cowen, a research professor
at the University of Hawaii at Manoa.
“It just screamed out that there had to
be some kind of microbial community
there to exploit the energy involved in
this water–rock reaction,” he said.
Geomicrobiologists were invited to
participate in drilling expeditions, and
BioScience 62: 453–457. © 2012 Mayer. ISSN 0006-3568, electronic ISSN 1525-3244. All rights reserved. doi:10.1525/bio.2012.62.5.4
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The drill team onboard the JOIDES Resolution prepares a CORK (circulation
obviation retrofit kit) for the derrick lift and its eventual placement deep
below the seafloor. Photograph: William Crawford, Senior Imaging Specialist,
Integrated Ocean Drilling Program.
in the 1980s and 1990s, researchers
in the United States, England, and
Switzerland began looking more seriously at the prospects of exploring
subseafloor life. They started with sediment cores recovered by the JOIDES
Resolution, or JR (JOIDES stands for
Joint Oceanographic Institutions for
Deep Earth Sampling). It is the flagship drilling platform of the Integrated
Ocean Drilling Program (IODP), which
officially becomes the International
Ocean Discovery Program in 2013.
Scientific ocean drilling began with the
Deep Sea Drilling Program (1968–1983),
which was followed by the Ocean
Drilling Program (1983–2003), and
then the IODP (2003–2013). The JR
and other drilling platforms, operated
by Japanese and European managers,
have allowed scores of scientists from
around the world—including the 24
member countries of the IODP—to
Box 1. Ocean drilling and the search for extraterrestrial life.
The microbial environment deep beneath the seafloor may provide a window into how organisms could survive in places beyond Earth.
The lack of light and the likelihood that microbes rely on chemosynthesis for survival may give the deep-ocean biosphere some commonalities with extraterrestrial environments where there is no surface water but there is subsurface water.
“Learning more about our subseafloor community may tell us more about what to look for on some of these other planets,” said Jim
Cowen, a research professor at the University of Hawaii at Manoa. “We learn as well about [the] fundamental limits of life.” How slowly
can organisms metabolize? How little energy can sustain them? Insight gleaned from the habitat deep below the ocean could suggest
what might eventually be found on Mars or on Jupiter’s moon Europa (for more information, see the Web sites listed in box 2).
That’s one reason Penelope Boston follows microbiology work from the IODP. Boston is a professor in the Department of Earth
and Environmental Sciences at the New Mexico Institute of Mining and Technology and associate director of the National Cave and
Karst Research Institute.
“Most of us in the extremophile biology community keep an eye on other communities than (just) the ones we work on,” Boston
said. The caves where she works, like the deep biosphere, have extreme temperatures and “exotic chemistry.” She said that recent research
indicates evolutionary links between microbes found in extreme terrestrial environments and those found in the deep biosphere.
Boston is interested in how these microbes make a living. Research on that could influence a future mission to Europa or to Saturn’s
rings.
“The ocean is a direct analog for places like that,” she said, “and it’s an indirect analog for Mars.” Boston said that work from
­different environments and conducted by different people informs her research.
“It’s good cross-fertilization,” she said. Research has illuminated the incredible biodiversity of microbial life on Earth, yet genetic
work on microbes from widely varying environments identifies “these curves of relatedness,” Boston said.
Katrina Edwards, a biology professor at the University of Southern California and director of the Center for Dark Energy Biosphere
Investigations, said that some of the closest relatives to microbes found near the Juan de Fuca Ridge flank in the north Pacific are organisms that were found in deep mines in South Africa. They all live in the “very deep subsurface,” she said, “but in very different realms.”
What may be shared in their evolutionary paths, and why they’re found in such different places today, remains a mystery.
“Trying to chase these things down scientifically is very, very difficult,” Boston said. Using data-mining techniques and other tools,
Boston hopes to connect biological evolution to geological history.
“My whole career, I’ve been flamboyantly interdisciplinary,” she said, adding that working across fields has become easier, and it
is something increasingly important to the scientific ocean-drilling community, which, through the International Ocean Discovery
Program, has named biosphere frontiers as one of the four foci of its next decade.
“To me, this is the most fun part,” said Boston. “I have one foot firmly in geoscience and one foot firmly in bioscience… and I have
a few other feet.”
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study sediment cores and rocks
extracted from beneath the seafloor.
In 1998, an article was published in
the Proceedings of the National Academy
of Sciences (PNAS) in which microbiologist William Whitman and his
colleagues presented a mathematically
derived estimate of prokaryote life in
the deep-ocean biosphere. That article
raised awareness about the scope of
such an environment.
In the PNAS article, Whitman and
colleagues suggested that up to onethird of the Earth’s biomass carbons
could be buried deep beneath the ocean.
“So that kind of took people a few
steps back,” Edwards said. Researchers
began with basic questions: Could this
possibly be true, and are the organisms alive? Since then, other scientists
have revised that original one-third
figure downward. Still, the interest
in deep-ocean microbiology continues
to grow. Microbiologists use existing
IODP infrastructure and technology,
especially in situ observatories developed for hydrology and geochemistry.
The opportunities for biological studies have grown and improved significantly over the past decade. In 2002,
D’Hondt led the Ocean Drilling Program’s first expedition dedicated to
subsurface life. He then sailed again as
a cochief scientist in 2010 on a South
Pacific Gyre expedition, beginning the
first studies of that vast region’s deep
subseafloor ecosystem. Other biologists, including those who study karst
and caves and are engaged in the search
for extraterrestrial life, are interested
in developments in deep-ocean biosphere research. (See box 1.)
CORK technology
Fundamental to the infrastructure
that allows for this work is the JR, the
massive ship that Cowen, D’Hondt,
and Edwards have all sailed on. The
JR stretches 143 meters (m) long and
has six levels, several of which are
outfitted with state-of-the-art science
labs. The fundamental tool of the ship
is the drill, which requires a derrick
that stands 62 m above the water line
and can send up to 8000 m of drill
pipe boring down through the ocean
www.biosciencemag.org and into the seafloor. During a twomonth cruise, a science party with
specific interest in the expedition’s
drilling location receives the columns
of mud and rocks as they come on
board and immediately begins documentation, sampling, and shipboard
analysis. A crew of technicians—most
of them master’s- or PhD-level scientists themselves—assists the shipboard
science party. Other crews prepare the
meals and tend to the housekeeping on
the ship. That frees up the scientists to
work 12 hours a day, seven days a week,
during the expedition. In all, it’s a polyglot, multi­national floating adventure.
The researchers gather data from
deep beneath the ocean by installing
CORK (circulation obviation retrofit
kit) observatories into the boreholes.
Fluids flow through CORKs, and when
the CORKs are recovered, scientists
gain perspective on the hydrogeology
and geochemistry of the location. The
first microbiologically relevant data
came up from a CORK deployed on
the flanks of the Juan de Fuca Ridge,
a chain of seamounts in the north
Pacific, during the late 1990s. Cowen
said that the highly fractured crust
and the robust water circulation there
supported the hypothesis of a deepsea biosphere. “CORK observatories
provide a beautifully controlled access
to these fluids,” he said.
In the original design, the fluids rose
up through the center of a steel pipe.
The flow was terrific, and the results,
Cowen said, were fantastic, “although,
Fast fluid samplers wait to be lowered
into a borehole, shortly after assembly
in the Core Lab. Photograph: William
Crawford, Senior Imaging Specialist,
Integrated Ocean Drilling Program.
Members of the Expedition 336 shipboard science party pose for a photograph
moments before a completed CORK (circulation obviation retrofit kit) is
lowered into the sea. From left, Beth Orcutt, a microbiologist from Aarhus
Universitet, Denmark; Samuel Hulme, an inorganic geochemist at Moss
Landing Marine Laboratories, California; Keir Becker, a hydrogeologist with the
University of Miami, Florida; Geoffrey Wheat, an inorganic geochemist at the
University of Alaska Fairbanks. Photograph: William Crawford, Senior Imaging
Specialist, Integrated Ocean Drilling Program.
May 2012 / Vol. 62 No. 5 • BioScience 455
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as we were writing the papers, we were
concerned about the potential for contamination.” A wet iron pipe can rust,
turning the CORK casing itself into a
potential substrate on which microbes
can grow or derive energy. Still, CORKs
installed in the subseafloor constantly
sample and conduct experiments.
“The amount of information and
the quality of information is basically
accelerating,” Cowen said. “I think
we’re at a really exciting time.”
Like Cowen and D’Hondt, Edwards
is interested in understanding the
water–rock interactions that are mediated by microbes. Edwards hopes to
better understand the significance of
these processes when they happen in
the deep-ocean biosphere. “[Judging]
by its vast size, it must be playing an
important role, but it’s the one we
know the least about,” she said.
The rock–water interactions likely
explain how microbes survive in the
deep ocean and why they seem to be
more abundant at hydrothermal vents,
which are akin to hot springs on the
seafloor. Chemosynthesis—the process of creating energy from chemical
reactions—may replace photosynthesis in the lives of these organisms, and
the microbes may find the chemistry
they need for food at the vents.
On board the JR last fall, parked
at North Pond and actively sending
experiments down into holes, Edwards
and her colleagues hoped to shed light
on the nature of microbial communities harbored in young ridge flanks,
the role of these communities in ocean
crust alteration, and the origin of deepseated microbial communities.
Life at sea
North Pond differs in many ways from
Juan de Fuca. The Juan de Fuca Ridge
was buried in sediment during the
last glaciation, and thermal insulation there means much warmer, more
sluggish fluid movement. That leads
to depletion of oxygen through the
reactions that occur between rocks and
water. It is a warm, anoxic, sluggish
hydrothermal environment. In contrast, North Pond has water gushing
in through outcrops and then gushing
456 BioScience • May 2012 / Vol. 62 No. 5
out again, Edwards said. It is a very
open, oxic, cool environment.
“We predict [that] the bugs we are
going to find there are going to be different [from those at Juan de Fuca],”
Edwards said. “They should be different because it’s a very different climate,
if you will, for the microbes.”
Edwards said North Pond has long
attracted the interest of researchers.
“This site abides perfectly by the ‘Goldilocks [principle].’ Everything about
it is just right, perfectly plain and average—globally speaking—in terms of
geology, hydrogeology, geophysics, and
we predict, microbiology,” she wrote
on her “Return to North Pond” blog
two weeks before heading out to sea.
And, Cowen said, from the crude
beginning, CORK technology has
ad­vanced in ways that significantly
improve biological experiments. New
CORKs, he said, use continuous stainless steel or Tefzel (ethylene tetrafluroethylene—a fluorocarbon) tubing that
runs the entire length of the CORK.
Tubings run from each horizontal level
to the seafloor so samples can be collected from multiple discreet depths.
The CORK casings, Cowen said, are also
coated either with epoxy or, in the case
of a deployment at North Pond, with
fiberglass, in the areas where experiments take place. These improvements,
he said, have led to systems that are
“much more inert, much more biology
friendly.”
“We [now have] the ability to collect samples that are vastly improved
with regard to contamination,” Cowen
said.
Throughout the expedition, Edwards
and her cochief scientist, Wolfgang
Bach, who is a petrologist, oversaw
the science party, helped troubleshoot
unexpected developments, and made
key decisions about how to sample
the cores as soon as they came onto
the ship’s deck. Edwards wrote about
the adventure for Scientific ­American’s
“Expeditions” blog. On 20 September,
just a few days out from Barbados,
where she boarded the ship, Edwards
wrote about launching the first operation—unlatching an existing CORK
and then “logging” the hole it was in.
This is an operation I’m very excited
about, because of a new tool we’ve
developed that will allow us to detect
microbial life in situ within the borehole. This has never been done before!
What we want to do is to identify
hotspots of microbial activity and
understand from a quantitative standpoint how abundant these microbes
Microbiologist Katrina Edwards
and biogeochemist Heath Mills
sample material from a CORK
(circulation obviation retrofit kit)
as it is retrieved from the seafloor.
Photograph: William Crawford,
Senior Imaging Specialist, Integrated
Ocean Drilling Program.
Assistant Lab Officer Tim Bronk,
a member of the ship’s technical crew,
carries harvested core samples as
they come in from the rig floor to the
Core Receiving Area. Photograph:
William Crawford, Senior Imaging
Specialist, Integrated Ocean Drilling
Program.
Box 2. Related Web sites.
www.darkenergybiosphere.org
http://blogs.scientificamerican.com/
expeditions/2011/08/30/introducingexpedition-336-at-north-pond
http://joidesresolution.org
http://iodp.tamu.edu
www.biosciencemag.org
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are as a function of depth. Then, we
would try to relate these hotspots
of bioload to geological, geochemical, and hydrological parameters in
order to begin to develop predicting
indicators.
The new tool that she is referring to
is the DEBI-t (for dark energy ­biosphere
investigative tool), which goes “down on
a wire-line into a borehole and scans
the sides, looking for life using a deep
ultraviolet technology—­spectroscopy,
essentially,” Edwards said.
Although some of the at-sea challenges involve keeping sophisticated
technologies such as the DEBI-t working and troubleshooting them when
things go wrong, others include more
basic scientific practices, such as the
ongoing and perennial challenge of
limiting the contamination of samples. Edwards blogged about that on
3 October.
[The] samples that are recovered
are first carefully rinsed with sterile seawater to remove contamination, and then [they] are sampled
in specialized sterile microbiological
boxes using flame-sterilized chisels
of various sizes. We then split [the]
samples, using these chisels and a
rock hammer. It is crude work for
microbiology, but there just isn’t any
other way to do it. Some samples get
further crushed using a sterile rock
crusher for starting microbial cultures
or doing incubations—[for example,]
shipboard biogeochemical assays.
Edwards said that the members of
a shipboard science party are selected
for their areas of expertise, and that
means that everyone closely identifies as a microbiologist or a sedimentologist or a paleontologist, and so
forth. But, even so, they must work
together as a team, and she said that
the geologists have wholly embraced
biologists as part of the ocean-drilling
community.
Life at sea can be trying, and Edwards
wrote about some hurdles that they
confronted and some incredible acts of
technological and engineering ­prowess.
She and her colleagues will have the
raw material for countless studies, and
after an exclusive period, the material
that they recovered will be available to
www.biosciencemag.org others. All scientists with a legitimate
interest can request access to any cores
from past ocean-drilling expeditions.
Although many more groups around
the world are studying the deep biosphere than ever before, D’Hondt said
that there is really only one way to join
in the fun.
“The only practical, day-to-day, yearafter-year way to get samples is to be
part of IODP or one of its predecessors,” he said—or, beginning next year,
its successor, the International Ocean
Discovery Program. All of the cores
recovered from the JR and IODP’s
other platforms get housed in repositories in College Station, Texas; ­Bremen,
Germany; or Kochi, Japan.
The at-sea hurdles were no match
for the determination and ingenuity
of the shipboard crews, Edwards said
in an interview once she was back on
terra firma. “Overall, we managed to
tackle all the problems that were tackleable, and we had some really unexpected great things that we discovered,
and we’re very pleased,” she said.
As for the DEBI-t, she added, “it
worked beautifully.”
Future work
IODP’s embrace of the deep biosphere
represents a convergence of scientific
questions, infrastructure, and technology that “provide[s] this kind of
movement that you just can’t stop,”
Cowen said. Everyone is aware of the
magnitude of the deep-sea microbial environment. The drilling infrastructure exists to go explore it, and
funders or naysayers can no longer
argue that this environment cannot
be studied.
For now, the Expedition 336 ­scientists
are busy working with the cores that
they recovered during the cruise. Their
studies will eventually become part
of the voluminous legacy of ­deep-sea
research. Since 1968, the ocean-­drilling
programs have provided the raw material for over 26,000 peer-reviewed
scientific articles, over 400 of those
published in Science, Nature, or Nature
Geoscience. And some day, a microbe
recovered from the deep biosphere
could become the inspiration for a new
University of Southern California
graduate student Amanda Haddad
works onboard the JOIDES Resolution
as a member of the shipboard science
party of Expedition 336 in the
mid-Atlantic. Photograph: William
Crawford, Senior Imaging Specialist,
Integrated Ocean Drilling Program.
antibiotic or anticancer drug. David
Rowley, an associate professor in the
Department of ­Biomedical and Pharmaceutical Sciences at the University of
Rhode Island, has a lab full of microbe
strains amassed from IODP samples.
His colleagues D’Hondt and David
Smith, also at the University of Rhode
Island, connected Rowley with access
to microbes from the deep biosphere.
Now Rowley and his lab are studying
these microorganisms for their production of novel molecules that may
provide unexpected or improved properties for treating human diseases.
“We’re highly excited by what we’ve
seen so far,” Rowley said. “It looks
­promising.” Rowley adds that, prior
to his work with IODP, his search
for marine microbes with potential medicinal uses was limited by the
instrumentation available to recover
them—typically, sampling coastal
waters or those only hundreds of meters
deep. The drill ship opens the door to a
whole new realm of potential.
“For me, this is a really exciting new
opportunity to be able to explore part
of the globe that has been previously
inaccessible,” Rowley said. “That’s a
scientific opportunity that I just can’t
pass up.”
Amy Mayer ([email protected]),
a freelance science writer in Massachusetts,
sailed through the Panama Canal on board
the JOIDES Resolution in June 2011.
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