Download MPIMM Research activities and assets

MPIMM Research activities and assets
Focus Biodiversity
Research objectives and points of emphasis
The Max Planck Institute investigates microbial processes and the diversity of the
involved bacteria in the marine environment and other aquatic habitats, and the role
of these bacteria in the global chemical cycles. The research activities are devoted to
topics that are relevant for our understanding of natural habitats and natural
processes. Natural activities of bacteria are usually part of a balanced system that
represents the normal case and, therefore, taken for granted. Only if the environment
is disturbed by human activities, for instance by water pollution, or by natural events
with high environmental impact, the importance of microbes for the balance of the
global cycles of the elements becomes obvious.
The sea is the largest biotope on our planet. The oceans not only harbor their own,
distinct communities of animals and plants, but also a great variety of
microorganisms that are adapted to this habitat. Living conditions in the sea,
however, are very diverse and are determined, for instance, by high concentrations of
mineral salts, extremely low nutrient concentrations in the open ocean, low
temperatures and high pressures in the deep ocean, high temperatures in
hydrothermal vent areas, or the natural transformations and reactivity of sulfur, iron
and manganese species in coastal sediments. Regardless of which marine site or
biotope we investigate, it always seems that several of the main microbial processes
are still inadequately understood, and that many of the microbial actors are unknown.
The MPI in Bremen dedicates most of its research activities to bacteria and bacterial
processes in sediments. Sediments are the sites with the most intense and diverse
transformation processes of organic and inorganic substances in the sea. The
accumulation of organic detritus in marine sediments, particularly in coastal zones,
upwelling areas or certain deep marine basins, causes high rates of respiratory oxygen
consumption by microbes and higher organisms. Such sediments are therefore anoxic
below an oxic surface layer that often has a thickness of a few millimeters or less.
The oxic zone, transition (suboxic) zone and anoxic zone in sediments harbor diverse
populations of microorganisms; many of those possess metabolic capabilities which
are not encountered in plants and animals. Bacterial activities in sediments
significantly influence the global cycles of elements, and have led to major
depositions of minerals over geological periods.
The anoxic zone of sediments harbors microorganisms that are mainly prokaryotic. A
particular feature among anaerobic prokaryotes is the use of inorganic electron
acceptors for respiratory processes that allow conservation of energy for growth
without free oxygen. Two quantitatively important anaerobic electron acceptors in the
marine environment are sulfate and, depending on the area, also ferric iron. Further
relevant electron acceptors are nitrate and manganese (IV). Of all reductive
processes, bacterial reduction of sulfate to sulfide has probably the strongest
influence on the biogeochemistry of marine sediments, due to the properties of the
product, sulfide. Sulfide serves as substrate for a diverse community of bacteria that
grow by oxidation of sulfide in the presence of oxygen or nitrate in the upper zone, or
also under anoxic conditions if light has access. Sulfide reacts also chemically
(abiologically) with iron minerals and oxygen. Deep in the sea floor, where inorganic
electron acceptors are exhausted, methane is formed as the terminal product of
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organic degradation processes. The methane may accumulate in the pore water or as
gas hydrates. However most of it is reoxidized as it diffuses up into the sulfate zone
or seeps up to the sediment surface where, together with hydrogen sulfide, it supports
rich communities of free-living or symbiotic bacteria.
Department of Biogeochemistry
Director: Prof. Dr. Bo Barker Jørgensen
- Group for Biogeochemistry
Head: Prof. Dr. Bo Barker Jørgensen
Pathways, regulations and interactions of marine microbial and geochemical
processes in sediments; ecology and physiology of cold-adapted bacteria and
bacteria from the carbon, nitrogen, sulfur and iron cycles.
- Group for Microsensors
Head: Dr. Dirk de Beer
High-resolution studies of chemical microenvironments and metabolic
processes by microsensors; development of electrochemical, fiber-optic and
other microsensors. Study of calcification.
- Group for Flux Studies
Head: Dr. Markus Hüttel
Physical transport processes in sediment and water; simulation in flume
systems. Measurement of biogeochemical processes on the sea floor by
automated benthic landers.
These groups will not deliver core assets to the proposed project and thus are
not described further. Some of their resources may nevertheless be utilized as
described further on.
Description of Departments mainly contributing to MARBEF
Department of Microbiology
Director: Prof. Dr. Friedrich Widdel
The Department of Microbiology investigates the physiology and diversity of aquatic
bacteria from the cycles of carbon, nitrogen, sulfur and iron. Investigations usually
include the isolation of bacteria and their study under defined conditions.
Characterization of enrichment and pure cultures is often combined with the analysis
of ribosomal nucleic acids, which is carried our in collaboration with the Department
of Molecular Ecology.
One major project is the study of the anaerobic degradation of long-lived natural
products such as hydrocarbons, mostly by denitrifying and sulfate-reducing bacteria.
Furthermore, the physiology of naturally abundant forms of sulfur-oxidizing and
sulfate-reducing bacteria is of interest.
The Department of Microbiology works on the physiology and metabolism of aquatic
bacteria; with increasing attention to gene-based and biochemical (enzymatic)
approaches. Knowledge and collaborations in the field of chemical (organic) analyses
are of increasing importance for the study of metabolic pathways.
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Department for Molecular Ecology
Director: Prof. Dr. Rudolf I. Amann
The Department of Molecular Ecology directs its work towards the use of molecular
biological techniques such as comparative sequence analysis and fluorescence-in-situhybridization (FISH) for the studies of the structure and function of microbial
communities and their dynamics with regard to biotic and abiotic changes in the
environment. The habitats that are under investigation in the Department are of
different complexity ranging from more defined systems like biofilms or symbiotic
associations to more complex systems as planctonic or benthic bacterial communities.
In the project REGX the whole genome of three different marine bacteria are
analysed. The project aims at the comprehensive understanding of molecular
mechanisms and regulatory networks correlated with the adaptation of bacteria to
environmental changes. This will be achieved with the use of bioinformatics and chip
technology.
Selection of major projects
In situ analysis of bacterial communities in sediments
Besides the biogeochemical and physical processes that can be measured at a large
and small scale, the bacteria that dominate the marine habitats and catalyse the
observed processes are of major interest. Since only a minor fraction of the
microscopically detectable bacterial community could be cultivated thus far, the
application of molecular methods based on conservative nucleic acid sequences is of
increasing importance for the study of bacteria in their natural habitat. These
molecular approaches include, for instance, sequence analysis of 16S rRNA genes
retrieved from natural communities and 16S rRNA-targeted in situ hybridization.
Similar studies of functional genes of specific physiological types of microorganisms
reveal their actual metabolic activity. The technically advanced methods in this area
of research include the use of flow cytometry and confocal laser scanning
microscopy. Examples of bacteria recently studied by molecular approaches are giant
sulfur-oxidizing bacteria, communities from the Wadden Sea and the Arctic Ocean,
and in hydrocarbon-degrading enrichment cultures.
Anaerobic bacterial degradation of hydrocarbons
It is well-known that terminal degraders in the anaerobic "food chain", e.g. sulfatereducing and denitrifying bacteria, degrade fermentation products such as fatty acids
from the primary breakdown of biopolymers. We have, however, only little
knowledge about the fate of chemically and biochemically less reactive substances,
such as hydrocarbons, under anoxic conditions. Hydrocarbons are constituents of
many living organisms, and high amounts are present in sediment deposits or are
released into the environment via crude oil or oil products. One direction of
microbiological research is to investigate the fate and reactions of saturated
hydrocarbons (alkanes), aromatic hydrocarbons and alkenoic terpenes in cultures and
natural communities of anaerobic bacteria.
Anaerobic oxidation of methane
Methane is the main product of organic carbon degradation deep within the seafloor.
As it ascends towards the sediment surface it becomes oxidized by sulfate to carbon
dioxide. The biogeochemistry and microbiology of anaerobic methane oxidation at
gas hydrate sites, cold seeps and other sediment environments is the topic of a new
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research program which involves all research groups of the institute. Initial results
show that syntrophic aggregates of archaea and sulfate reducing bacteria are
responsible for the process in some sediments with high methane partial pressure. At
methane seeps these microbial consortia establish dense communities that form large
carbonate structures, well-known throughout the geological record. Research at the
MPI integrates field studies of methane fluxes and turnover with laboratory
cultivation and molecular characterization of the organisms involved.
Microbial mats and photosynthesis
Microbial mats and biofilms represent a wide-spread, densely populated form of
bacterial communities, and are characterized by steep concentration gradients of
oxygen, other electron acceptors and reduced compounds. These gradients are the
result of the intense bacterial activities; vice versa, the gradients shape the
composition and physical structure of the bacterial community. With the combined
use of microsensors, molecular methods based on 16S rRNA genes and traditional
cultivation of a number of species, the metabolic activities (e.g. in relation to oil
degradation) and the organismic structure of cyanobacterial mats and biofilms are
studied.
Many marine invertebrates, often those having carbonate skeletons, live in symbiosis
with phototrophic algae from which they gain organic carbon substrates. The
processes of photosynthesis, respiration and calcification are studied in corals and in
planktonic and benthic foraminifera by the use of microsensors and by other
approaches.
Bacterial symbionts of chemolithoautotrophic invertebrates
Symbioses between bacteria and eukaryotes are widespread in marine environments, a
demonstration of their ecological and evolutionary success. Sulfide-oxidizing bacteria
occur as ecto- and endosymbionts in a great range of marine hosts from protozoans to
invertebrates, in habitats that range from hydrothermal vents to shallow coastal
waters. Using both molecular and biogeochemical techniques, such as 16S rRNA
sequence analysis and in situ hybridization as well as microsensor and radiotracer
measurements, we are gaining a better understanding of the remarkable phylogenetic
and physiological diversity of these associations. This combination of approaches has
been decisive in describing a unique association in a gutless marine worm that harbors
both sulfide-oxidizing and sulfate-reducing bacteria as endosymbionts.
Future developments and goals of the institute
Since its establishment in 1992, the institute has been pursuing a multidisciplinary,
integrated approach to develop the functional understanding of the microbial world in
the sea from process studies in oceanic habitats to research on the level of cells and
cellular structures. This overall approach has not only lead to the discovery of hitherto
unknown processes, microorganisms, and functions, but also to the recognition of
new, unexplored fields of research in marine biology. The integrated research concept
of the past will, therefore, also be a foundation for the future of the institute. At the
same time, this research concept also offers students and young scientists an
orientation and multidisciplinary training in the interconnected fields of marine
microbiology.
The Department of Molecular Ecology has obtained substantial additional resources.
These will be used for a further upgrade of instrumentation for molecular studies of
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the diversity and composition of marine microorganisms. We will continue to broaden
our focus by studying not only single genes but also entire genomes. It will be
necessary to create a solid bioinformatic basis for marine microbial genomics.
The Department of Microbiology will continue its work on the physiology and
metabolism of aquatic bacteria; increasing attention will be paid to gene-based and
biochemical (enzymatic) approaches, as they have been already implanted in a
number of projects. Also, knowledge and collaborations in the field of chemical
(organic) analyses will be of increasing importance for the study of metabolic
pathways.
A focus of the Microsensor Group will be benthic photosynthesis and its coupling to
calcification in shallow coastal zones. Marine calcification rates are currently
decreasing probably due to the ongoing global climate change, both directly by
increased CO2 and indirectly by seawater warming. We hypothesize that oceanic
calcification is a potential atmospheric CO2 modifier.
The establishment of habitat-orientated research in combination with microbiological
and molecular investigations in one institute has stimulated "cross fertilization"
between the different disciplines and laboratories. The tools of molecular biology,
microsensor studies, and cultivation-based microbiology are now being regularly
used.
Ties to the University of Bremen have traditionally been strong. With the backing of
the University of Bremen, the Alfred Wegener Institute for Polar and Marine
Research, the International University of Bremen, and the Center for Tropical Marine
Ecology, the MPI is establishing an active international Ph.D. program with a
thematic focus on the diversity and function of prokaryotic and unicellular eukaryotic
marine microorganisms (MarMic).
Research facilities and equipment
General
A total of 34 laboratories including several laboratories licensed for work with
open radioactive material, for work with recombinant DNA (S1 and S2
classification) and for work with infectious material
Library (100 Scientific Journals (prints), access to 6000 electronic journals, 3500
books;)
Machine and Electronic workshops, storage rooms and working hall for landers
and other marine research field equipment
Microbiology
 2 Anaerobic cabinets, and equipment for anaerobic isolation and cultivation

High pressure microbiology equipment

Chemical analysis of metabolites through:


5 HPLC for biodegradation products

5 GC for permanent gases, hydrocarbons
Polyphasic taxonomic description tools and equipment
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
Cultures of marine and fresh water strains, capable of anaerobic transformation of
hydrocarbons, including methane
Molecular Ecology
Molecular biological and bioinformatics infrastructure for diversity analysis:

PCR and gel electrophoresis

robotic clone screening system

in-house sequencing and sequence assemblage facility

dedicated servers and 9 workstations for phylogenetic analysis and probe
design (ARB software)
 largest available database of 16S rDNA sequences (>30.000);
 local (internet-independent) access to Genbank database
 Genomic information on several microbial strains of functional and
physiological ecological interest (e.g. Pirellula sp #1, Desulfotalea and
Desulfobacterium genomes, annotated in Pedant and Gen DB)
Facilities for quantitative evaluation of community structure:
 6 Epifluorescence microscopes,
 Flow cytometers with laser excitation. The instrument is used for counting and
sorting of bacterial cells in natural communities according to cell sizes or to
optical signals from distinctive fluorescent stains. Usually, cells are
fluorescently labeled by specific, 16S rRNA-targeted oligonucleotide probing
 Confocal laser scanning electron microscope. The microscope is particularly
used for imaging of bacteria in natural communities after hybridization with
fluorescent oligonucleotide probes

quantitative PCR; and microarray spotter and reader
Biogeochemistry including Microsensor and Flux group
Infrastructure for in situ activity measurements
 Laboratory facilities for construction and application of microsensors
 in situ oxygen micro-imaging
 radioactivity laboratory (microautoradiography and bulk activity
measurements)
 high resolution autoradiography mapper (beta imager) for quantification of radiolabel distribution. Separate visualization of 2 different isotopes, i.e. double
labeling, possible. Measurement of uptake (growth or accumulation) profiles and
in transport studies
 Flume with Laser-Doppler-anemometer (LDA) and particle-image-velocimeter
(PIV) and aquarium section, upper level with full daylight
 Isotope mass spectrometer for C, N, and S, equipped with gas chromatograph.
 Automated, free-falling benthic landers for in situ measurements on the sea floor.
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Involvement in EU Projects
1. Past EU Projects
(MPIMM as partner, only)
Aegean Fluxes - Hydrothermal Fluxes and Biological Production in the Aegean Sea.
Subproject: Distribution and diversity of (Eu)bacteria at a marine hydrothermal vent
system located on Milos, Greece, MAS3-0021; (MAST CT-95-0021); Jan Kuever
(Lead Univ. Bangor)
MICRO-MARE - Development of MICROsensors for Use in the MARine
Environment, MAS3-0029 , MAS3-CT95-0029, Michael Kühl (Lead NERI)
MICRO-FLOW - A novel MICROsensor for Measurement of Liquid FLOW and
Diffusivity, MAS3-0078, Michael Kühl (Lead Univ. Aarhus)
BASIC - Applied and Systematic Investigations of Cyanobacteria
BIO4-0256, Ferran Garcia-Pichel/Rudi Amann (Lead Inst. Pasteur)
DeepBUG - Deep Bacteria Under Ground - Development and Assessment of New
Techniques and Approaches for Detecting Sub-Seafloor Bacteria and their Interaction
with Geosphere Processes,
EVK3-1999-00088; EVK3-CT-1999-00017, Bo B. Joergensen (Lead Univ. Bristol)
C/T-NET- Rapid Global Change during the Cenomanian/Turonian Oceanic Anoxic
Event, RTN1-1999-00286, HPRN-CT-1999-00055, Michael Böttcher (Lead NIOZ)
MATBIOPOL - Role of Microbial Mats in Bioremediation of Hydrocarbon Polluted
Coastal Zones, EVK2-1999-00043; EVK3-CT-1999-00010, Friedrich Widdel (Lead
Univ. Pau)
2. Running projects
BASICS - BActerial SIngle-Cell Approaches to the Relationship between Diversity
and Function in the Sea, EVK3-2001-00194, EVK3-CT-2002-00078, Jakob
Pernthaler (Lead ICM Barcelona)
BIOFLOW – Flume Facility Co-operation Network for Biological Benthic Boundary
Layer Research, EVR1-2001-00021; EVR1-CT-2001-20008,
Markus
Hüttel
(Lead NIOO)
COSA - COastal SAnds as Biocatalytical Filters, EVK3-2001-00183, EVK3-CT2002-0076, Markus Hüttel
METROL - - METhane Fluxes in Ocean Margin Sediments: Microbiological and
Geochemical ContROL, EVK3-2001-00206; EVK3-CT-2002-00080, Bo B
Joergensen
NAME – Nitrate from Aquifers and Influences on Carbon Cycling in Marine
Ecosystems, EVK2-2001-00004, EVK3-CT 2001-00066, Gaute Lavik (Lead Lead TU
Denmark)
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TREAD - Transport REActions and Dynamics of Heavy Metals in Contaminated
Marine Sediments, EVK3-001-00210; EVK3-CT-2002-00081, Ole Larsen
LIST - Larvae In Situ Tracking, MEIF-CT-2003-501323, Nicole Dubilier
COBO - Integrating new technologies for the study of benthic ecosystem response to
human activity: towards a Coastal Ocean Benthic Observatory , GOCE-CT-2003505564, Ursula Witte, Lead SAMS)
MARBEF - Marine Biodiversity and Ecosystem Functioning, GOCE-CT-2003505446, Friedrich Widdel (Lead NIOO)
MOMARNET - Longterm MOnitoring of the Mid-Atlantic Ridge: an Observatory
Approach, MRTN-CT-2004-50502, Nicole Dubilier (Lead Institut de Physique du
Globe de Paris)
MARINE GENOMICS - Marine Genomics Europe - Implementation of highthroughput genomic approaches to investigate the functioning of marine ecosystems
and the biology of marine organisms, GOCE-CT-2004-505403, Rudolf Amann (Lead
CNRS Roscoff)
HERMES - Global Ocean Margin Changes, The European Deep Ocean Margin from
Tromsoe to the Black Sea, Antje Boetius (Lead Southampton Oceanography Centre)
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