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BioGeoChemistry of tidal flats (2001-2011)

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Prof. Dr. Heribert Cypionka 

Microbiological garden 

Picolay

Grundlagen der Mikrobiologie

Fermentation processes in tidal flat sediments
of the German Wadden Sea

Background

Tidal flat sediments are microbially active systems characterized by a high turnover of organic matter under anoxic conditions. A representative sampling site is the backbarrier area of "Spiekeroog", which is intensively studied within the frame of the research group "BioGeoChemistry of tidal flats". Until now investigations predominantly focused on sulfate reduction and methanogenesis, the terminal degradation steps. However, the initial fermentation processes remain poorly understood. The open questions are: What are the main pathways of the stepwise organic matter degradation? Which are the intermediate substances? Who are the microbial key-players involved?


First experiments

To get deeper insights into the course of fermentation, we have performed growth experiments that were monitored by microcalorimetry. This technique allows a highly sensitive detection of the heat production resulting from metabolic activities. Two peaks of activity were found in sediment-slurries amended with 10 mM glucose indicating at least two subsequent degradation steps. During the experiment, the active bacterial community compositions were analyzed by PCR-DGGE of 16S rRNA. The stimulated members were identified by combining microcalorimetry and RNA-based stable-isotope probing using 13C-glucose as sole carbon source. In addition, complex substrates such as intact cells of spirulina instead of glucose will be used to simulate natural conditions.

Team 

  • Jutta Graue
  • Sara Kleindienst
  • Bert Engelen
  • Heribert Cypionka

Related publications 

  • Graue J, Kleindienst S, Lueders T, Cypionka H, Engelen B (2012) Identifying fermenting bacteria in anoxic tidal-flat sediments by a combination of microcalorimetry and ribosome-based stable-isotope probing. FEMS Microbiol Ecol 81:78–87
  • Graue J, Engelen B, Cypionka H (2012) Degradation of cyanobacterial biomass in anoxic tidal-flat sediments: a microcosm study of metabolic processes and community changes. ISME J 6:660-669
  • Logemann J, Graue J, Köster J, Engelen B, Rullkötter J, Cypionka H (2011) A laboratory experiment of intact polar lipid degradation in sandy sediments. Biogeosciences 8:2547-2560

Activity and community composition of sulfate reducers
in tidal flat sediments

Background

Tidal flat sediments are characterised by a high input of organic matter. Most of it is rapidly remineralised in the upper few centimetres of the sediment by microorganisms employing a variety of electron acceptors. Thus, compared to open ocean sites tidal flat sediments show vertically compressed biogeochemical gradients and moreover, may harbour typical deep subsurface communities within a few meters depth (Wilms et al., 2006).

Dissimilatory sulfate reduction is the major terminal anaerobic degradation process accounting for up to half of the total organic carbon remineralisation in marine sediments (Jørgensen, 1982). So, sulfate-reducing (SRB) significantly contribute to biogeochemical processes, even though they do not belong to the most abundant bacterial groups in marine sediments (Böttcher et al., 2000; Llobet-Brossa et al., 2002).

Previous studies on tidal surface sediments in the German Wadden Sea have shown that highest sulfate reduction rates occur in near-surface layers where microbial activity is not limited by the availability of easily degradable electron donors. In contrast, deeper sediment layers are thought to be less active due to the increase in the recalcitrance of organic matter.

However, the dynamical structure of tidal flats allows for pore water transport between corresponding permeable sediment layers and may therefore lead to an influx of nutrients into greater depths (Billerbeck et al., 2006). So, our project addresses the question how this special environmental setting influences the activity and structure of the sulfate-reducing community.

Team 

  • Antje Gittel
  • Martin Könneke
  • Stephanie Reischke
  • Heribert Cypionka

Cooperations

  • Henrik Sass (Cardiff, Wales)
  • Marc Mußmann (MPI, Bremen)
  • Nicole Dubilier (MPI, Bremen)

Related publications 

  • Gittel, Antje (2007) Community, structure, activity and ecophysiology of sulfate-reducing bacteria in deep tidal flat sediments = Struktur, Aktivität und Ökophysiologie sulfatreduzierender Bakteriengemeinschaften in tiefen Sedimenten des Deutschen Wattenmeeres
  • Gittel A, Mußmann M, Sass H, Cypionka H, Könneke M (2008) Identity and abundance of active sulfate-reducing bacteria in deep tidal flat sediments determined by directed cultivation and CARD-FISH analysis. Environ Microbiol 10:2645-2658
  • Billerbeck, M., Werner, U., Polerecky, L., , Walpersdorf, E., de Beer, D. and Huettel, M. (2006) Surficial and deep pore water circularion governs spatial and temporal scales of nutrient recycling in intertidal sand flat sediment. Mar Ecol Prog Ser 326: 61-76.
  • Wilms, R., Köpke, B., Chang, T. S., Sass, H., Cypionka, H., and Engelen, B. (2006) Deep-biosphere related bacteria within the subsurface of tidal flat sediments. Environ Microbiol 8: 709-719.
  • Böttcher, M. E., Hespenheide, B., Llobett-Brossa. E., Beardsley, C. et al. (2000) The biogeochemistry, stable isotope geochemistry, and microbial community structure of a temperate intertidal mudfalt: an integrated study. Cont Shelf Res 20: 1749-1769.
  • Llobet-Brossa, E., Rabus, R., Böttcher, M. E., Könneke, M., Finke, N., Schramm, A., Meyer, R. L., Grötzschel, S., Rossello-Mora, R., and Amann, R. (2002) Community structure and activity of sulfate-reducing bacteria in an intertidal surface sediment: a multimethod approach. Aquat Microb Ecol 29: 211-226.
  • Fenchel, T., King, G. M., and Blackburn, T. (1998) Bacterial biogeochemistry: the ecophysiology of mineral cycling. 2nd edn. Acadamic press, San Diego.
  • Jørgensen, B. B. (1982) Mineralization of organic matter in the sea bed: the role of sulphate reduction. Nature 296: 643-645.

Poster

  • Poster VAAM Jena 2006
  • Poster ISME Vienna 2006

Links

  • Biogeochemistry of Tidal flats (DFG research group)

Methanogenesis in the subsurface of a sandy intertidal sediment

Methane concentrations in the water column in the back barrier tidal flat of the island of Spiekeroog were found to be twenty times higher than in the open ocean. However, sources and sinks of methane in tidal flats are rarely investigated so far. As high methane concentrations are not exclusively introduced by fresh water input, it is assumed that the major source is microbial methane production within the sediments. Methane can be produced under anoxic conditions by different groups of methanogenic archaea from acetate, hydrogen and carbon dioxide or methylated compounds. Most of these microorganisms compete for the available substrates with sulfate reducing bacteria. Previous molecularbiological surveys of an adjacent tidal flat from the same area indicated a succession of different physiological groups of methanogenic archaea along the depth profile (Wilms et al. 2007). While metyhlotrophic methanogenes were found within the entire sediment column, putitative hydrogenotrophic methanogenes were only detected in sediment layers where sulfate was depleted.

Team 

  • Yvonne Hilker
  • Sara Kleindienst
  • Bert Engelen
  • Heribert Cypionka

Cooperations 

  • Kerstin Bischof (MPI Bremen)
  • Rudi Amann (MPI Bremen)

Related publications 

  • Wilms R, Sass H, Köpke B, Cypionka H, Engelen B (2007) Methane and sulfate profiles within the subsurface of a tidal flat are reflected by the distribution of sulfate-reducing bacteria and methanogenic archaea. FEMS Microbiol Ecol 59:611–621
  • Wilms R, Sass H, Köpke B, Köster J, Cypionka H, Engelen B (2006) Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediment along a vertical profile of several meters. Appl Environ Microbiol 72:2756-2764
  • Köpke B, Wilms R, Engelen B, Cypionka H, Sass H (2005) Microbial diversity in coastal subsurface sediments - a cultivation approach using various electron acceptors and substrate gradients. Appl Environ Microbiol 71:7819-7830

Microbial diversity and activities within the subsurface of tidal-flat sediments

Tidal flats are young and dynamic ecosystems showing intense microbial activities with a variety of metabolic processes occuring along the depth profile of the sediment column. To understand the function and composition of microbial communities within the sediment subsurface, we have used a combination of geochemical, microbiological and molecular biological techniques. This polyphasic approach was applied to sediment cores from different locations of a German tidal flat area from the sediment surface down to a depth of 5.5 m. The molecular biological investigation by DGGE analysis revealed that different compartments of the sediment columns were characterized by specific microbial communities. In total, 113 DGGE bands were sequenced. The upper sandy layers were dominated by various Proteobacteria. Below this zone, a dramatical shift with depth was observed. Here the Proteobacteria were replaced by the Chloroflexus group, a typical deep subsurface phylum. A slightly different shift was also detected by the cultivation approach. In total, 112 pure cultures were isolated, that could be grouped into 53 different operational taxonomical units (OTU). In the deeper mud-dominated sediment layers almost exclusively endospore-forming bacteria were detected. To link the information of who is there with geochemical profiles, the abundance of sulfate reducers and methanogens was determined by quantitative PCR. Additionally, exoenzyme activities and sulfate reduction rates were measured.

Team 

  • Beate Köpke
  • Reinhard Wilms
  • Bert Engelen
  • Heribert Cypionka

Related publications

 

  • Köpke, Beate (2007) Dissertation: "Verteilung, Zusammensetzung und Aktivitäten mikrobieller Gemeinschaften in Wattsedimenten von der Oberfläche bis in mehrere Meter Tiefe"
  • Wilms, Reinhard (2006) Dissertation: "Molekularbiologische Erfassung und Charakterisierung der mikrobiellen Gemeinschaften im Rückseitenwatt der Insel Spiekeroog"
  • Köpke B, Wilms R, Engelen B, Cypionka H, Sass H (2005) Microbial diversity in coastal subsurface sediments - a cultivation approach using various electron acceptors and substrate gradients. Appl Environ Microbiol 71:7819-7830
  • Wilms R, Sass H, Köpke B, Cypionka H, Engelen B (2007) Methane and sulfate profiles within the subsurface of a tidal flat are reflected by the distribution of sulfate-reducing bacteria and methanogenic archaea. FEMS Microbiol Ecol 59:611–621
  • Wilms R, Sass H, Köpke B, Köster J, Cypionka H, Engelen B (2006) Specific bacterial, archaeal, and eukaryotic communities in tidal-flat sediment along a vertical profile of several meters. Appl Environ Microbiol 72:2756-2764
  • Wilms R, Köpke B, Sass H, Chang TS, Cypionka H, Engelen B (2006) Deep biosphere-related bacteria within the subsurface of tidal flat sediments. Environ Microbiol 8:709-719
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