Research Themes


The Joint Research Group on Deep-Sea Ecology and Technology, headed by Prof. Antje Boetius, is co-funded by the Alfred Wegener Institute Helmholtz Center for Polar and Marine Research and the Max-Planck-Institute for Marine Microbiology. We combine the expertise of the MPI branch (former Microbial Habitat Group, 2003-2010) in marine microbial ecology and biogeochemistry, the development of new molecular, biological and in situ analytical methods, with the expertise of the AWI branch (former Deep-Sea Research group, 1999-2008) in studying polar environments, pursuing long-term environmental observations, and sampling in the deep sea.

The main goals of the HGF-MPG Deep-Sea Ecology and Technology group are (1) to obtain “true” quantitative insight to ecosystem structure, dynamics and biogeochemical fluxes based on in situ measurements (2) to show the effects of global change on deep-sea ecosystems and including variations in microbial to macrofaunal biodiversity on relevant spatial and temporal scales, and (3) to unravel the functioning of key microorganisms in specific deep-sea environment. To quantify transport and reactions in submarine and subglacial deep-sea ecosystems we develop and improve in situ instruments and describe habitats with a variety of geochemical methods. To study the inhabiting (micro)fauna and to describe their functions we use state of the art molecular approaches.

Here we report mostly the MPI-centered research, more information for the AWI-centered research is here.

Functional diversity of marine microbiomes

Scientists: Antje Boetius (main PI), Christina Bienhold, Pier Luigi Buttigieg, Verena Carvalho, Eduard Fadeev, *Mar Fernandez-Mendez, Cedric Hahn, *Christiane Hassenrück, *Katy Hoffmann, Marianne Jacob, *Gerdhard Jessen, *Viola Krukenberg, Rafael Laso-Pérez, Massimiliano Molari, *Pierre Offre, Claudia Pala, *Alban Ramette, Josephine Rapp, Pamela Rossel, *Emil Ruff, Halina Tegetmeyer, *Tobias Vonnahme, Gunter Wegener; Laboratory support: Jakob Barz, Susanne Menger, Wiebke Stiens, Erika Weiz-Bersch; Technical Support: Volker Asendorf, Axel Nordhausen, Fabian Schramm

*former members of the group

Describing microbial diversity and its drivers in complex natural environments represents a cornerstone of modern microbial ecology. Similar questions and approaches drive this research in different fields ranging from extreme deep-sea habitats to the human microbiome. The technological revolution of the field by fast new sequencing techniques has also transformed concepts of microbial diversity and community turnover at different spatial and temporal scales. We develop data pipelines and expert knowledge systems to provide a statistical resource to analyze datasets of increasing complexity and size. The aim is to resolve the identity and metabolism of taxa defining the core microbiome of marine environments. We investigate microbial life in polar environments, deep-sea floor and trenches, anoxic basins, mud volcanoes, gas and oil seeps, hydrothermal vents, food falls, manganese nodules, and coral reefs. These habitats are characterized by different biological, geological, and physical conditions, showing substantial temporal and spatial variations. Combining ‘omics approaches with experimental and field work enables the characterization of the ecological roles of several uncultivated microbial groups as well as the interplay between microorganisms and their energy sources.

Main recent achievements include:

  • Bienhold et al. (2016) identified core bacterial taxa in a global survey of marine seafloor environments
  • Ruff et al. (2015) identified core taxa and key members of functional groups in cold seep environments 
  • Rossel et al. (2016) performed high-resolution molecular profiles of dissolved organic matter (DOM) from sediment porewaters of the deep Eurasian basins in relation to environmental parameters
  • Hoffmann et al. (2017) identified patterns in deep-sea microbial communities in response to natural nutrient inputs
  • Fernández-Méndez et al. (2016) identified microbial nitrogen fixation potential in the nitrogen-limited Central Arctic Ocean 
  • Schöttner et al. (2013) identified the complex host-microbe diversity and co-evolutionary patterns in cold water coral reef sponges
  • Furthermore, we continuously test and re-evaluate the in-depth analyses of classical vs. NGS tools to explore microbial diversity in natural environments. Different generations of molecular techniques may be complementarily used to meaningfully describe microbial diversity and its drivers
  • Also, we permanently optimize our statistical toolbox (interactive guide and software package) to obtain more transparent and reproducible analytical procedures in our field
Network graph of 23 methane seeps based on occurrence of ANME
Network of occurrence of anaerobic methane-oxidizing euryarchaea (ANME) at 23 methane seeps. Gray lines connect ANME operational taxonomic units (OTUs), represented as colored circles, to the seeps where they occurred. The ten most abundant ANME OTUs accounted for 85% of all ANME 16S rRNA sequences retrieved in the global dataset and had a cosmopolitan distribution. The majority of the ANME diversity was rare and locally restricted. Ruff et al. (2015) PNAS 112:4019.

Geosphere-biosphere interactions and anaerobic hydrocarbon degradation in extreme environments

Scientists: Gunter Wegener (main PI), Antje Boetius, *Viola Krukenberg, Rafael Laso-Pérez, Massimiliano Molari, Pamela Rossel, *Emil Ruff, *Alban Ramette, *Tobias Vonnahme, Frank Wenzhöfer; Laboratory support: Jakob Barz, Mirja Meiners, Susanne Menger; Technical support: Fabian Schramm, Axel Nordhausen

* former members of the group

Extreme environments are defined by one or more physicochemical parameters, such as e.g. extremely high or low temperature, salinity, pH, and energy availability, at which life operates close to its known limits. Cold seeps and hot vents habitats represent extreme environment at which cold or hot fluids from the subsurface are emitted to the seafloor that are enriched in reduced compounds such as methane, short- and long-chain hydrocarbons, and hydrogen. We aim at a functional understanding on the variety the microorganisms that harvest the energy from these fluids and are the basis of completely light-independent ecosystems in the deep oceans. Therefore we visit hot vents in the Gulf of Mexico (Campeche Hydrocarbon field), the Gulf of California (Guaymas Basin), and the Arctic Ocean (Gakkel Ridge). Other types of extreme environments studied by international collaborations are deep-sea trenches, mud volcanoes, and CO2 vents. Currently we study the distribution and genomes of microorganisms in the plumes of vents and in hydrocarbon-rich sediments. Therefore, we use  a variety of in situ technologies such as benthic chambers, multisensory modules, and camera platforms, operated from remotely operated vehicles such as ROV Quest (MARUM, Bremen), or as autonomous lander systems. In the home laboratories we cultivate specific microbial groups thriving on energy-rich components in the geofluids, such as methane, short-chain hydrocarbons, and hydrogen, and study their physiology in experiments by using a variety of molecular approaches, including metagenomics, metatranscriptomics, and in situ hybridization.

Main recent achievements include:

  • Wegener et al. (2015) identified nanowires and cytochromes that enable direct electron transfer from the ANME to their partner bacteria
  • Krukenberg et al. (2016) isolated HotSeep-1, the partner bacterium in thermophilic AOM and other hydrocarbon degrading consortia
  • Laso-Perez et al. (2016) identified the process of butane and propane activation via alkyl-CoM formation, analogous to the oxidation of methane, in some archaeal-bacterial consortia
  • Pop-Ristova et al. (2015) investigated the development of wood falls into chemosynthetic habitats
  • Boetius and Wenzhöfer (2013) quantified the efficiency of the benthic filter for methane at continental margins worldwide
  • Furthermore, we continuously study how in situ temperature variations shape the microbial diversity in the Guaymas Basin sediments
  • Also, we permanently develop novel stable isotope probing-based approaches to quantify microbial productivity, carbon fixation, and transformation under extreme environmental conditions


nanowires in AOM consortia
Species interaction in AOM aggregates of methane-oxidizing ANME-1 archaea (A) and partner bacteria (H). The intercellular space between the partners is filled with nanowire-like structures (arrows) that apparently enable direct electron transfer. Wegener et al. (2015) Nature 526: 587-590.

Global change effects on microbial communities and functions

Scientists: Christina Bienhold (main PI), Antje Boetius, *Ulrike Braeckmann, Pier Luigi Buttigieg, *Christiane Hassenrück, *Katy Hoffmann, Marianne Jacob, Felix Janssen, *Gerdhard Jessen, *Mar Fernández-Méndez, Massimiliano Molari, *Pierre Offre, Josephine Rapp, *Alban Ramette, *Tobias Vonnahme, Frank Wenzhöfer; Laboratory support: Martina Alisch, Jana Bäger, Jakob Barz, Rafael Stiens, Wiebke Stiens, Erika Weiz-Bersch; Technical support: Axel Nordhausen, Volker Asendorf

* former members of the group

Oceanic ecosystems experience various environmental pressures, many of which are a consequence of human activities, such as anthropogenic carbon dioxide emissions, loss of sea ice by warming, pollution by hydrocarbons, and declining oxygen concentrations by eutrophication. Effects of such activities can already be recognized in remote polar and deep-sea environments. Our work aims at studying and quantifying the role of microorganisms in global change effects and feedback mechanisms to better understand future changes in marine ecosystems, which is one of the aspects of the ERC AdvG project Abyss. Furthermore, we contribute to the establishment of baselines for ecosystem status, which are largely missing in remote ocean ecosystems. In addition to fieldwork and laboratory studies, we carry out long-term observations, especially at the LTER site HAUSGARTEN in Fram Strait, which is one of the few biogeochemical deep-sea observatories on Earth.

Main recent achievements include:

  • Boetius et al. (2013) describe massive export of algal biomass from the sea ice to the seafloor as a result of sudden warming, causing fast reactions in the entire ecosystem from ocean productivity to export fluxes to the deep sea
  • Boetius et al. (2015) review current knowledge about bacterial diversity across sea ice, pelagic, and benthic ecosystems in the central Arctic Eurasian basin and present fundamental links between the dynamics in microbiomes and the rapidly changing cryosphere 
  • Jacob et al. (2013), Soltwedel et al. (2015) and Buttigieg and Ramette (2015) revealed that interannual variations in ocean surface temperatures and sea ice cover st the LTER site HAUSGARTEN (Fram Strait) and in the Central Arctic are reflected in benthic community structure and changes in the deposition of organic matter
  • Hassenrück et al. (2015, 2016) studied the effects of changing CO2 concentrations on benthic communities at natural CO2 vents, as analogues to ocean acidification, and showed that high CO2 levels cause diversity shifts, suggesting a coping mechanism for community resilience
  • Purser et al. (2016) revealed the association of deepsea octopods breeding with manganese crusts and nodules in the Pacific Ocean
  • Jessen et al. (2017) identified responses in microbial activity and community diversity to fluctuating hypoxia, and quantified the consequences for carbon burial 
  • Furthermore, we conduct continuous autonomous monitoring of oxygen dynamics at high spatial and temporal resolutions to better understand the effects of temporal hypoxia on ecosystems. We can show that short-term variations in oxygen fluxes have significant effects on benthic ecosystems, including differences in the preservation of organic matter, as well as the composition and diversity of bacterial communities.
  • Also, we study the long-term effects of large-scale disturbances and re-colonization by an experimental setup (DISCOL)  located in the South Pacific Ocean, simulating deep-sea mining on benthic communities. Initial observations suggest that mining can disturb seafloor communities for decades by disrupting the active surface layer.
Melosira arctica algae falls in Central Arctic
Observations during the record ice melt in the Central Arctic in 2012: Sea ice algal falls recovered from the seafloor on a multicorer (top left), with holothurians feeding on them (4100 m water depth; right), and the algae under the microscope (Melosira arctica; bottom left). Adapted from Boetius et al. (2013) Science 339: 1430-1432.

Method developments: In situ technologies for microbial habitat studies

Scientists: Frank Wenzhöfer (main PI), Antje Boetius, *Daphne Donis, *Janine Felden, Ralf Hoffmann, Felix Janssen; Lab support: Martina Alisch, Mirja Meiners, Rafael Stiens, Erika Weiz-Bersch; Technical support: Volker Asendorf, Michael Hofbauer, Karin Hohmann, Axel Nordhausen, Fabian Schramm, and the MPI workshops

*former members of the group

Investigations of deep-sea ecosystems and their organisms, as well as related biogeochemical processes rely on the constant development of technology that enables in situ analyses and observations directly at the seafloor. Many processes occur at temporal and spatial scales that cannot be effectively studied after sample retrieval due to depressurization and warming, or the mortality of deep-sea animals. Thus, assessments of biological, geological, physical, and chemical processes in deep waters, as well as long-term observations of deep-sea ecosystems, require the design and development of new technology, especially with regard to energy supply, sensor configuration, and data communication. Innovative robotic technologies have become key to study ocean processes and changes in space and time. We have substantially improved the use of chemical and biological sensor systems and underwater platforms for deep-sea research, biogeochemistry and microbial ecology. We can equip diverse underwater platforms (e.g. ROVs, AUVs, crawler, submersibles, autonomous lander, towed and moored systems) with sensors and cameras for coverage at a wide range of temporal and spatial scales. The technological developments enable us to study the deep seafloor of a variety of extreme habitats, like the Central Arctic, deep trenches, CO2 seeps and vents including under-ice ecosystems of polar regions. In the ice-covered Central Arctic we used newly developed moored benthic lander systems to quantify export of organic material to the deep seafloor, measuring the total benthic community respiration in situ by benthic chamber and microprofiler.

Furthermore, we assist in long-term strategies to investigate the seasonal variation at the deep-sea floor. For example, a long-term microprofiler has been deployed at HAUSGARTEN in 2013 for one year. The system consists of an optical oxygen sensor array, which runs vertical profiles across the sediment-water interface every week moving a swinging arm horizontally between each vertical profile during its 12-month deployment.

Main recent achievements with technical aspects include:

  • Testing the sensitivity of eddy sensing systems for benthic flux measurements in the deep sea (Donis et al. 2015, 2016)
  • Miniaturization of payload systems (sensor and incubation systems) for biogeochemical process studies operated by ROVs (Pop-Ristova et al. 2015, 2017)
  • Operations of sea ice ROVs and tethered HROV in ice-covered environments - sea ice, vents, and seamounts in the Central Arctic (Katlein et al. 2015a, 2015b)
  • Design of hadal sampling, incubation, and measuring lander-systems (Wenzhöfer et al. 2016)
  • Development and deployments of a towed bathymetry camera system equipped with sonar and camera systems (OFOBS Ocean Floor Observation Bathymetry System), increasing surveyed regions from 3 m camera views to >30 m paths (Purser et al. 2016)
  • Furthermore, we continuously develop integrated payload systems (multi-sensor and -sampling systems) for ROV, AUV, towed instrument (OFOS) and crawler operations (e.g. EU-Eurofleets), and validate sensor systems for measurements at extreme conditions and for long-term applications (e.g. EU ITN-SenseNet).
  • Also, we continuously development under-ice deep-sea benthic lander system, construct instrument systems for biogeochemical studies in and directly under sea ice, design a combined chemical and optical observation system to explore deep-sea environments online, and optimize pipelines to annotate, archive and provide deep-sea photos and videos.
Technologies developed in the HGF MPG Research Group
Developing methods for the study of Arctic ecosystems and biogeochemical processes. Left: 3D profiler on a lander to be deployed under ice. Right: SenseNet field campaign Baltic Sea (Hel, Poland).
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