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 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.

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-situ-hybridization (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. sulfate-reducing 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 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 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

• 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 radio-label 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.

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)