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Center for Geomicrobiology, Aarhus University, 2007-2012
Bo Barker Jørgensen and Camilla Nissen Toftdal
Nils Risgaard-Petersen, Hans Røy, Kasper U. Kjeldsen, and Ian Marshall
Aarhus University, Department of Bioscience,
Center for Geomicrobiology ©
http://geomicrobiology.au.dk
2012
October 2012
Kathe Møgelvang and Juana Jacobsen, Graphics Group, AU Silkeborg
Nils Risgaard-Petersen
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978-87-92825-68-1
Rosendahl Schultz Grafisk A/S
The report is available in electronic format (pdf) at
http://geomicrobiology.au.dk
PHOTO: IODP-USIO
Welcome to the Center for Geomicrobiology . . . . . . . . . . . . . . . . . . .
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Research goals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Discovery of the deep biosphere . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Biodiversity of the deep biosphere . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Microbial processes in the seabed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Microbiology – one cell at a time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Life at the energetic limit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Harvesting energy with electricity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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The future of Geomicrobiology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Academic staff . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Instruments available at the Center for Geomicrobiology . . . . .
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Drilling and coring expeditions 2007-2012 . . . . . . . . . . . . . . . . . . . . . .
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Activities and special events at the Center . . . . . . . . . . . . . . . . . . . . . .
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Funding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
WELCOME
Head of the Center,
Bo Barker Jørgensen.
PHOTO: MORTEN BARKER
TO THE
CENTER FOR GEOMICROBIOLOGY
AT AARHUS UNIVERSITY
The Center for Geomicrobiology was founded in 2007 by Prof. Bo
Barker Jørgensen, director at the Max Planck Institute for Marine
Microbiology in Bremen. The Center was jointly funded for five
years by the German Max Planck Society, the Danish National
Research Foundation, and Aarhus University.
On October 1st, 2012, a new five-year funding period started for
the Center for Geomicrobiology, this time as a Center of Excellence under the Danish National Research Foundation. The Center
is organized under the Department of Bioscience and continues
a close cooperation with the Department’s Microbiology Group,
with the Max Planck Institute for Marine Microbiology, and with
many international research groups. The Center is located on
the beautiful campus of Aarhus University. The staff includes
the young and international group of coworkers from the earlier
Center, therefore the new Center starts out with a fully developed
scientific program.
The Center studies microbial life in the seabed with a particular
focus on the deep sub-seafloor biosphere. Our aim is to understand the predominant microbial life on our planet: communities
of microorganisms buried in the dark subsurface and subsisting
at the minimum energy flow that can sustain basic biological
processes. We use approaches and concepts from very different
disciplines, including molecular ecology, microbial physiology,
and geochemistry.
On the following pages we present the research field of the Center
and describe some of the highlights of our results from the first
five years, 2007-2012. I wish you enjoyable reading.
Bo Barker Jørgensen
Head of the Center for Geomicrobiology
Professor of Geomicrobiology at Aarhus University
CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
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Aarhus University campus.
PHOTO: POUL IB HENRIKSEN
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
RESEARCH GOALS
A large part of all bacteria and archaea on Earth live in the “deep
biosphere”. Their cellular energy flux is orders of magnitude below
anything studied in laboratory cultures so far. Thus, the prokaryotic
cells of the deep biosphere are essentially non-growing with
apparent mean generation times of hundreds to thousands of
years. In spite of their slow life, these microorganisms drive major
processes in the geosphere and control element cycles that affect
hydrocarbon reservoirs, ocean chemistry, and global climate on
geological time scales.
The Center for Geomicrobiology develops and applies new approaches to study microbial life under extreme energy limitation. It
is our goal to understand the genetic and physiological potential
of the marine deep biosphere and determine how it differs from
the much more active surface biosphere. This is a major challenge
as it is has generally not been possible to cultivate the organisms
in the laboratory.
Members of the Center join research expeditions to different
regions of the world oceans in order to obtain the precious sediment core material. In the laboratory we combine high-capacity
genomic sequence analyses with sensitive chemical and isotopic
techniques to search for the coupling between organisms and processes. We also apply new high-resolution techniques for singlecell studies in order to reveal the coupling between phylogenetic
identity and metabolic function of dominant microorganisms.
Results from our recent work have been exciting and surprising.
Further details of these results and a complete publication list can
be found on the Center’s website (www.geomicrobiology.au.dk).
Gravity coring of the seabed in Aarhus Bay.
PHOTO: BO BARKER JØRGENSEN
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
DISCOVERY OF THE DEEP BIOSPHERE
Microscopic counting of microbial cells in deep sediment cores
from the world’s oceans has shown that microorganisms are present almost everywhere. The subsurface world is widely inhabited
by at least two of the three domains of life, namely the bacteria
and the archaea. This is revealed by analyses of DNA or of intact
membrane lipids. The discovery of microorganisms in several million year old sedimentary deposits, and even in basement rock,
has profoundly changed our perspective on the limits of living
organisms. It is now apparent that processes in the geosphere
may provide a driving force for life and that, vice versa, the subsurface biosphere has a large impact on geological processes.
The biological degradation of organic carbon in the deep subsurface has a large-scale impact on carbon preservation in the
seabed with consequences for the chemistry of the ocean and
atmosphere. We aim to understand the microbiology behind
these slow processes and how they differ from the highly active
surface of the sea floor.
The Center for Geomicrobiology collaborates internationally in
studies of the deep biosphere through expeditions in the world
oceans. Since 2007, members of the Center have participated in
six expeditions of the Integrated Ocean Drilling Program (IODP)
in the Pacific and the Atlantic Ocean. On board the US drilling
vessel, JOIDES Resolution, the Center has engaged in research
on arctic sediments of the Bering Sea, on ocean crust and sediment of the Northeast Pacific and the mid-Atlantic ridge, and
on the nutrient-starved South Pacific. On board the Japanese
drilling vessel, Chikyu, the Center has joined drilling to more than
2 kilometer deep coal beds off Japan.
The Japanese drilling vessel, Chikyu.
PHOTO: UNIVERSITY OF MISSOURI
Key publications
The Center also works intensively with marine sediments at our
doorstep. In Aarhus Bay a ten meter thick mud deposit has accumulated during the past 8,000 years following the last ice age.
Our new methods and hypotheses are first tested in Aarhus Bay
sediment where fresh core material can be repeatedly sampled.
10
Log cell numbers (cm–3)
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The microbial community size
drops steeply with increasing
depth and age of the seabed.
At the sediment surface, with an
age of a hundred years, there
are a billion cells per cm3. In
more than ten-million-year-old
subsurface sediments numbers
drop to a million and even to a
few thousand per cm3.
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Baltic Sea, (Parkes RJ, unpubl.)
Peru Shelf, IODP 1227
Peru Shelf, IODP 1230
East Pacific, IODP 1225
Peru Basin, IODP 1231
South Pacific gyre, SPG-2
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3
1
2
3
4
5
Log age (years)
GRAPH: BO BARKER JØRGENSEN
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Jørgensen, B.B. (2012). Shrinking majority of the deep
biosphere. Proceedings of
the National Academy of
Science, USA, 109: 1597615977.
Orcutt, B., Sylvan, J.B., Knab,
N.J. & Edwards, K.J. (2011).
Microbial ecology of the
dark ocean above, at, and
below the seafloor. Microbiology and Molecular Biology Reviews 75: 361-422.
Jørgensen, B.B. & Boetius, A.
(2007). Feast and Famine
– microbial life in the deepsea bed. Nature Review
Microbiology 5: 770-781.
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Cutting a gravity core liner on the deck.
PHOTO: BO BARKER JØRGENSEN
CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
BIODIVERSITY OF THE DEEP BIOSPHERE
Very basic questions remain open about the identity of microorganisms in the deep biosphere. Who are they and from where did
they originate? Are the deeply buried communities relicts of a time
when the sediment was originally deposited or are they selected
by the current environmental conditions in the subsurface? Is there
a unique microbial biosphere deep down in the seabed or do
the organisms mix genetically with the surface world?
To answer these questions we have extracted community DNA
from distinct biogeochemical zones in marine sediments. We have
analyzed hundreds of thousands of gene sequences of important
marker genes for specific physiological types of organisms such
as sulfate-reducing bacteria or methane-producing archaea.
This allows us to compare the diversity of microbial species in the
different biogeochemical zones in the seabed. The results show
that even well-known physiological types belong to unknown
phylogenetic groups that may even be deeply branching in the
tree of life. This is, for example, the case for the sulfate-reducing
microorganisms in subsurface sediment.
The extraction of DNA is fundamental to studies of community
composition. Some of the DNA may not reside in living cells,
however, but be free or adsorbed DNA that remains from microorganisms that lived there in the past. During the last years we
have developed a DNA extraction method to separate cellular
DNA (iDNA) and extracellular, fossil DNA (eDNA). We can now
recover and PCR-amplify bacterial and archaeal DNA in the
sub-seafloor and have applied our methods to low-biomass,
sub-seafloor environments, such as the central South Pacific, the
Bering Sea, and the Northeast Pacific. The new eDNA extraction
protocol will be used in future research to examine the potential
for marine sub-seafloor sediments as a genetic archive of past
environmental change.
Chemical analyses of samples of
sediment pore water.
PHOTO: NILS RISGAARD-PETERSEN
Key publications
Sampling for microbiology
through windows in the core liner.
PHOTO: NILS RISGAARD-PETERSEN
Lever, M. (2012). Acetogenesis
in the Energy-Starved Deep
Biosphere – A Paradox?
Frontiers in Microbiology 2:
1-18.
Tarpgaard, I.H., Røy, H. & Jørgensen, B.B. (2011). Concurrent low- and high-affinity
sulfate reduction kinetics in
marine sediment. Geochimica et Cosmochimica Acta
75: 2997-3010.
Lloyd, K., Teske, A. & Alperin,
M.J. (2011). Environmental
evidence for net methane
production and oxidation in
putative ANaerobic MEthanotrophic (ANME) archaea.
Environmental Microbiology
13: 2548-2564.
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
MICROBIAL PROCESSES IN THE SEABED
A fresh 10-m long sediment core section is retrieved on the drill ship.
PHOTO: IODP-TAMU
In deep sediments we calculate the ongoing microbiological
processes from transport-reaction modeling based on analyzed
pore water chemistry. In more active sediments the processes are
determined from laboratory experiments using radioisotopes or
stable isotopes as tracers. For example, we have developed the
experimental method for measuring respiratory sulfate reduction
to extreme sensitivity so that the reduction of less than a millionth
of the sulfate can be determined.
From our studies of sulfate reduction rates in the seabed we have
recognized a universal power law of mineralization rates versus
age for organic carbon buried over thousands to millions of years.
The power law shows that microbial respiration decreases by
about two orders of magnitude for each order of magnitude
increase in depth or age in the seabed. This relation appears to
be inherent to organic matter degradation, independent of the
terminal pathway of mineralization in the microbial food chain.
We used this power law to model very deep oxygen respiration
in the central North Pacific. The most striking feature of this and
other “desert” areas of the ocean gyres is that oxygen penetrates
tens of meters through the sediment column and even into the
basaltic ocean crust. We could show that the deep oxygen
penetration is controlled primarily by low sedimentation rate
rather than by low influx of organic matter. In 86-million-yearold sediment the oxygen was still being used for respiration at
rates of 1 μM O2 per 1000 years and was turning over on a time
scale of 40,000 years.
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
Shipboard gas chromatographic
analysis of methane.
PHOTO: BO BARKER JØRGENSEN
0
Key publications
Røy, H., Kallmeyer, J., Adhikari,
R.R., Pockalny, R., Jørgensen,
B.B. & D’Hondt, S. (2012).
Aerobic microbial respiration in 86-million-year-old
deep-sea red clay. Science
336: 922-925.
Wehrmann, L.M., RisgaardPetersen, N., Schrum, H.N.,
Walsh, E.A., Huh, Y., Ikehara,
M., Pierre, C., D’Hondt, S.,
Ferdelman, T.G., Ravelo,
A.C., Takahashi, K., Zarikian,
C.A. & The Integrated
Ocean Drilling Program Expedition 323 Scientific Party
(2011). Coupled organic and
inorganic carbon cycling in
the deep subseafloor sediment of the northeastern
Bering Sea Slope (IODP Exp.
323). Chemical Geology
284: 251-261.
5
Depth (m)
10
15
15
20
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Oxygen penetration to
more than 30 m depth
in the seabed of the
central North Pacific. In
the 86-million-year-old
sediment oxygen is turned
over once in 40,000 years.
FROM RØY ET AL., SCIENCE, 2012.
25
25
36
38
40
42
30
0
50
100
O2 (µmol L–1)
150
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
MICROBIOLOGY – ONE CELL AT A TIME
In the deep biosphere, the metabolic rate per cell is very much
lower than the resting metabolic rate in a laboratory culture. It is not
realistic to explore the natural life of the microorganisms by culturing them in the laboratory, and therefore we develop new methods that are independent of cultivation. In 2010 we succeeded
in isolating single microbial cells from the seabed by using laser
microdissection (LMD) microscopy and by fluorescence-assisted
cell sorting (FACS) in collaboration with the Bigelow Laboratory for
Ocean Sciences, USA. We have since been able to amplify the
genomes of a large number of single cells and determine a large
part of their entire genome sequence information. By analyzing
the genetic code in single bacterial cells we can simultaneously
determine the identity of the microorganisms and the metabolic
processes for which they have the genetic potential.
More than half of the cells belong to groups of bacteria or archaea
that are so far known only from marker genes in environmental
DNA. Their metabolic capabilities and ecological function are
completely unknown. We have thus caught representatives from
groups of archaea that are among the most abundant organisms in the world. By sequencing and analyzing the cells’ genetic
code we have investigated for which enzymes the genes code.
Our surprising finding is that archaea in the seabed are capable
of decomposing complex refractory organic compounds and
therefore have a very different function in the marine ecosystem
than previously anticipated. We now assume that they subsist by
fermenting organic compounds, and that they have a type of
metabolism that we normally ascribe to bacteria.
Laser microdissection microscrope.
PHOTO: BO BARKER JØRGENSEN
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
LIFE AT THE ENERGETIC LIMIT
Even though so many prokaryotes reside in the deep biosphere,
the energy flux available to them from buried organic carbon is
less than one percent of the photosynthetically fixed carbon on
the surface of our planet. With increasing depth and age of marine
sediments, microbial cells become increasingly energy limited. At
several hundred meters below the sea floor population sizes are
still large but the energy flux and the theoretical growth rate of
the bacteria are orders of magnitude below anything we know
from cultivated microorganisms. One of the greatest enigmas is
how these vast communities can subsist under conditions that
provide only marginal energy for cell growth and division and
seem to barely enable the maintenance of basic cell functions.
We have determined the mean metabolic rate of microbial cells
from measurements of their bulk activity in the sediment divided
by their cell numbers. From this we have estimated the turnover
rate of their biomass and thereby calculated their generation
1 hour
10–2
1 week
10–4
1 year
10–6
100 years
10–8
10,000 years
–5
0
5
10
15
20
25
Temperature (°C)
Turnover of cell carbon and corresponding generation time in
microbial communities from surface environments (blue, e.g. lakes
and soils) and sub-surface environments (red, e.g. young and old
marine sediments) at different temperatures.
FROM JØRGENSEN, PNAS, 2012
Such extremely slow life is difficult to reconcile with our laboratory
knowledge of microbial growth and maintenance metabolism.
Importantly, we could confirm these controversial results by a
completely independent approach that uses the slow interconversion between the mirror images of common amino acids
as a molecular clock. By determining the ratio between these L
and D mirror images in sediment amino acids, their age can be
estimated and used to estimate the turnover of amino acids in
the microbial community.
Key publications
Turnover time
Metabolic rate (g C g–1 cell C h–1)
100
time. We have done such calculations specifically for sulfate
reducing microorganisms in marine sediments and discovered
a systematic variation where generation times range from one
year near the seafloor to a thousand years deep beneath the
seafloor. In comparison, laboratory cultures of these bacteria
have generation times of days, that is 100,000 times shorter than
in the deep biosphere.
Lomstein, B.Aa., Langerhuus,
A.T., D’Hondt, S., Jørgensen,
B.B. & Spivack, A. (2012).
Endospore abundance, microbial growth and necromass turnover in deep subseafloor sediment. Nature
484: 101-104.
Jørgensen, B.B. (2011). Deep
subseafloor microbial cells
on physiological standby,
Proceedings of the National
Academy of Science, USA,
108: 18193-18194.
Hubert, C., Loy, A., Nickel,
M., Arnosti, C., Baranyi, C.,
Brüchert, V., Ferdelman,
T., Finster, K., Christensen,
F.M., Rosa de Rezende, J.
Vandieken, V. & Jørgensen,
B.B. (2009). A constant flux
of diverse thermophilic
bacteria into the cold arctic
seabed. Science 325: 15411544.
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
Experiments on the electric
conductance by cable bacteria
in a core of marine sediment.
PHOTO: NILS RISGAARD-PETERSEN
“Cable bacteria” grow as filaments up
through a fractured sediment column of
2-cm width.
Scanning electron microscope image of
cable bacteria (in false blue color) in a
marine sediment. Bacteria are ca 2 μm wide.
PHOTO: NILS RISGAARD-PETERSEN
IMAGE: MINGDONG DONG, JIE SONG, AND NILS RISGAARD-PETERSEN
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
HARVESTING ENERGY WITH ELECTRICITY
Our research on biogeochemical processes in the surface layers of
marine sediments have revealed that electric currents can couple spatially separated biogeochemical processes, such as oxygen reduction
at the sediment surface and hydrogen sulphide oxidation in anoxic
layers several centimeters below. This spatial separation of microbial
processes has a major impact on the geochemistry of the sediment.
It induces pH extremes that accelerate mineral dissolution or precipitation by mechanisms that have not previously been known to exist.
In a collaborative project we discovered that sulfate-reducing bacteria of the genus Desulfubulbus in the sediment form unique “electric
cables” that mediate electron conduction. These organisms are highly
abundant in sediments with bioelectric properties. The rod-shaped
bacteria form cm-long filaments composed of many hundreds of
individual cells and each cell is joined to its neighbors with multiple
longitudinal fibers. Electrostatic force microscopy suggests that these
fibers have metallic conductive properties. We use both metabolic
and nano-science approaches to understand this electron conduction
that is completely new for biology.
Cable bacteria are picked from marine sediment for microbiological analysis.
PHOTO: CAMILLA NISSEN TOFTDAL
Key publications
Pfeffer, C., Larsen, S., Song, J.,
Dong, M., Besenbacher, F.,
Meyer, R.L., Kjeldsen, K.U.,
Schreiber, L., Gorby, Y.A.,
El-Naggar, M.Y., Leung, K.M.,
Schramm, A., RisgaardPetersen, N., & Nielsen, L.P.
(2012). Filamentous bacteria
transport electrons over
centimetre distances. Nature,
doi:10.1038/nature11586
Risgaard-Petersen, N., Revil,
A., Meister, P. & Nielsen,
L.P. (2012). Sulfur, iron-, and
calcium cycling associated
with natural electric currents
running through marine
sediment. GeochimicaetCosmochimicaActa92: 1–13.
Nielsen, L.P., RisgaardPetersen, N., Fossing, H.,
Christensen, P.B. & Sayama,
M. (2010). Electric currents
couple spatially separated
biogeochemical processes
in marine sediment. Nature
463: 1071–1074.
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
THE FUTURE
OF GEOMICROBIOLOGY
The new Center for Geomicrobiology, funded for
2012-2017, will build on the research described on
the preceding pages and will also take up new challenges. The Center will focus on the most promising
research directions such as bioenergetics, biodiversity,
bioelectricity, single-cell genomics, and several aspects
of microbial physiology and sediment biogeochemistry.
Exploring the life of the deep underground is an ambitious endeavor. Yet, the development of the necessary
techniques is progressing rapidly and the prospects for
future methodological and conceptual breakthroughs
are great. The Center will continue to engage in IODPbased research. In 2013, Bo Barker Jørgensen will be
the co-chief on a drilling expedition in the Baltic Sea
under the European Consortium for Ocean Drilling
(ECORD) (http://www.eso.ecord.org/expeditions/347/).
This expedition will sample the past 140,000 years of
glacial and interglacial climate history and will provide
a unique opportunity to test how past climate affects
the deep biosphere even today.
Deep biosphere research in the Center will be exemplary of the interdisciplinary approach to marine Geomicrobiology. We believe that the results may break
new ground in our basic understanding of microbial
energy metabolism and the biological controls in the
marine environment.
CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
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PHOTO: IODP-USIO
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
ACADEMIC STAFF
Bo Barker Jørgensen
Head of Center, Professor, Dr.
Microbial life at the energetic limits
Alice Thoft Langerhuus
Postdoc, PhD
Microbial growth and turnover time
in deep sub-seafloor sediments
Hans Røy
Scientist, PhD
Slow microbial food webs
of the deep subsurface
Regina Schauer
Postdoc, PhD
Electric currents and cable bacteria
in marine sediment
Nils Risgaard-Petersen
Senior Scientist, PhD
Electric currents and cable bacteria
in marine sediments
Ian Marshall
Postdoc, PhD
Physiological adaptations to conditions
of extreme energy limitation
Dorthe Groth Petersen
Postdoc, PhD
Diversity, abundance and activity of nitrifiers
in oxic gyre sediments
Clemens Glombitza
Postdoc, PhD
Energy and carbon fluxes
in sub-seafloor sediments
Kasper Urup Kjeldsen
Scientist, PhD
Identity and ecophysiology of sulfate reducers
in marine sediments
Bente Lomstein
Associate Professor
Bacterial activity and endospore formation
in deep sub-seafloor sediments
Mark Alexander Lever
Postdoc, PhD
Controls on microbial carbon cycling pathways
in marine sediment and basalt
Andreas Schramm
Associate Professor
Genome evolution and ecology
of sub-seafloor microbes
Lars Schreiber
Postdoc, PhD
Single-cell genomics, metagenomics,
and gene expression in marine sediments
Lars Peter Nielsen
Professor
Electric currents and cable bacteria
in marine sediments
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
PHD-STUDENTS
VISITING
SCIENTISTS
TECHNICAL AND
ADMINISTRATIVE
STAFF
Hyunsoo Na
Chao Peng
Jeanette Pedersen
Irene Harder Tarpgaard
Katy Hoffmann
Trine Bech Søgaard
Xihan Chen
Stefan Braun
Karina Bomholt Henriksen
Christian Pfeffer
Marion Jaussi
Susanne Nielsen
Andrea Torti
Sissel Rønning
Camilla Nissen Toftdal
FORMER
ACADEMIC
STAFF
Signe Høgslund
Antje Vossmeyer
Sabine Flury
Elisa Piña Ochoa
Britta Gribsholt
Laura Lapham
Andrew Steen
Karen Lloyd
Beth Orcutt
Julia Rosa de Rezende
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
INSTRUMENTS
AVAILABLE AT THE CENTER FOR GEOMICROBIOLOGY
Loading an autosampler
with N2 samples for
isotope measurements.
PHOTO: NILS RISGAARD-PETERSEN
Isotope ratio mass spectrometer from Sercon. The system is equipped
with the GLS-system for preparation of solid, liquid and gaseous samples. At present the system is configured for analysis of the isotopic
composition of solid and gaseous N compounds.
PHOTO: NILS RISGAARD-PETERSEN
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
Geochemistry analyses
Molecular biology analyses
• Several HPLC instruments are available with conductivity detectors for ion chromatography and with fluorescence detector for derivatized biomarker molecules.
• Two gas chromatographs (SRI Instruments and Peak
Laboratories) are used mostly for measuring methane
(Flame Ionization Detector) and hydrogen (Reducing
Gas Detector).
• A specially designed, two-dimensional ion chromatograph and mass spectrometer (IC-IC-MS) instrument
(Dionex) is available for separating and quantifying very
low concentrations of anionic compounds. The method
was developed by Dionex at the request of the CfG to
measure acetate and other volatile fatty acids in marine pore water.
• Two isotope ratio mass spectrometers (IR-MS) (Sercon
20-22 and Thermo Delta V) are equipped with gas samplers and elemental analyzers for resolving the natural
isotopic composition of carbon, nitrogen and other isotopes in solids, liquids and gases.
• Gravity corer for up to 12-m long sediment cores.
• Manheim press for sampling of pore water.
• Standard PCR (Verity) and qPCR (Roche Light Cycler and
Agilent) thermal cyclers are used for detecting and quantifying microbial taxonomic and functional marker genes from
environmental DNA extracts.
• Concentrations of DNA and RNA isolated from environmental samples are determined with a Bioanalyzer (Agilent).
• An Ion Torrent Personal Genome Machine (Life Technologies) can sequence entire microbial genomes within hours.
• A six core, 48 GB ram Fujitsu R570 computer is used for analyzing genomic sequences and for numerical modeling.
• Laser microdissection (Leica) and laser tweezer (Zeiss) microscopes are used for physically isolating single microbial
cells from environmental samples.
• An ultracentrifuge (Beckman-Coulter) is used for DNAbased stable isotope probing using 13C- labeled substrates
to trace metabolic pathways
HPLC instrument for the sensitive chemical analysis of microbial cell
components.
With a laser tweezer microscope
we can catch individual cells in
a focused laser beam and move
them into thin capillaries for subsequent analyses.
PHOTO: NILS RISGAARD-PETERSEN
PHOTO: CAMILLA NISSEN TOFTDAL
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
DRILLING AND CORING EXPEDITIONS
2007-2012
The Center for Geomicrobiology has participated in international
drilling and coring expeditions in the world oceans as well as in
local waters:
SOURCE: EARTHOBSERVATORY.NASA.GOV
MS Farm, Svalbard, 2009
RV Knorr, Equatorial Pacific, 2009
RV Meteor, Argentine Basin, 2009
DV Joides Resolution, Bering Sea, 2009
RV Atlantis and Alvin, Guaymas Basin, 2008+2009
RV Merian, Baltic Sea, 2010
DV Joides Resolution, Juan de Fuca Ridge Flank, 2010
DV Joides Resolution, South Pacific Gyre, 2010
DV Joides Resolution, North Pond, 2011
RV Dana, North Atlantic, 2012
DV Chikyu, Kumano Sea, 2012
DV Chikyu, Shimokita Coal Bed, 2012
CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
23
ACTIVITIES AND SPECIAL EVENTS
AT THE CENTER
Education
Scientists of the Center participate as teachers in university courses
on microbiology, molecular ecology, biogeochemistry, and modeling. The PhD students participate in these same courses as
teaching assistants. The Center scientists furthermore supervise
and train PhD students who obtain their degree at the Graduate
School of Science and Technology, Aarhus University.
Workshops
The first PhD degree at the Center to Julia Rosa de Rezende, Brazil,
summer 2012. The Center mug is a symbol of “many happy returns”.
The Center has organized two international workshops on “Life
under Extreme Energy Limitation”. An international group of 5070 scientists met to give presentations and discuss this central
research theme for three days (www.microenergy2012.org). The
Center was also engaged in the International Symposium for
Microbial Ecology in Copenhagen, August 2012, with over 2000
participants.
Break-out group during a workshop at Aarhus University on “Life under
Extreme Energy Limitation”.
Honors
Head of the Center, Bo Barker Jørgensen, was elected Fellow
of the American Academy of Microbiology, 2009, and Fellow of
the European Academy of Microbiology, 2009. He received the
German Environmental Prize 2009 of the Deutsche Bundesstiftung Umwelt and the Jim Tiedje Award 2010 of the International
Society for Microbial Ecology.
Bo Barker Jørgensen receives the German Environmental Prize 2009
from the President, Horst Köhler.
PHOTO: DBU
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CENTER FOR GEOMICROBIOLOGY, AARHUS UNIVERSITY, 2007-2012
Everyday life at the Center
• Monday morning seminars with the Microbiology Research
Group: We present and discuss new results.
• Tuesday morning discussion meetings at the Center: We discuss projects, theories, results and new ideas.
• Seminar series with invited speakers jointly with the Microbiology Research Group.
• Journal Club for PhD students jointly with the Microbiology
Research Group.
Group photo from Retreat in Rønbjerg, August 2012.
Social life at the Center
• Annual Retreat at Rønbjerg Marine Research Station
• Welcome and farewell parties, Danish julefrokost and
German Oktoberfest etc.
• Lunch and coffee breaks in the Center’s lunch-room during
the day.
Traditional “Easter egg rolling contest” in the park of Aarhus University
campus.
FUNDING
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Danish National Research Foundation, Center for Geomicrobiology, 2007-2012
German Max Planck Society, Center for Geomicrobiology, 2007-2012
AGSoS/ GSST, PhD stipends and screening grants, 2007-2012
Marie Curie Actions Intra European Fellowship, 2008-2009
STENO fellowship, 2007-2010
FP7 BONUS program (EU and FNU), Baltic Gas, 2009-2011
FP7 Actions, Deep Sea and Sub-Seafloor Frontiers, 2010-2012
Universities Denmark (guest researcher), 2011
Swiss National Science Foundation postdoctoral fellowship, 2010-2011
Sloan Foundation (research project), 2010-2011
FNU postdoctoral fellowship, 2010-2012
Villum Kann Rasmussen block stipend, 2010-2012
Marie Curie Actions Intra European Fellowship, 2010-2012
EU, Leonardo da Vinci Scholarship, 2012.
AU Ideas (research project), 2012
ERC Advanced Grant, COULOMBUS, 2012-2017
ERC Advanced Grant, MICROENERGY, 2012-2017
Danish National Research Foundation, Center for Geomicrobiology, 2012-2017
Center for Geomicrobiology
Department of Bioscience, Aarhus University
Ny Munkegade 114, DK-8000 Aarhus C
Denmark
Phone: +45 87156556
Email: [email protected]
http://geomicrobiology.au.dk
ISBN: 978-87-92825-68-1