The Paleomicrobiology group has profound experiences with the study of microbial processes in marine sediments. Our studies have been focused on the subsurface of tidal-flat sediments, surficial deep-sea sediments and the marine deep-biosphere.We have developed novel cultivation techniques for environmental bacteria and successfully applied them to different habitats with cultivation efficiencies of up to 3% of total cell counts. These cultivation approaches are always accompanied by molecular techniques to verify that indigenous microorganisms were isolated. During the last years, we extended our studies on benthic viruses, especially from the deep-biosphere. Here, we took advantage of the fact that many phages follow a lysogenic life mode and integrate their DNA into the genome of the bacterial host. Thus, a culture collection from a given habitat also represents an archive of its viral diversity.
Microbial community structures and biogeochemical processes in young and active Wadden Sea sediments were investigated within the DFG Research Group 'BioGeoChemistry of Tidal Flats'. In one interdisciplinary study (Beck et al., 2011), we have analyzed the imprint of past and present environmental conditions on the microbiology and biogeochemistry of two 20 meter long sediment cores exhibiting different sedimentation histories (glacial and interglacial periods). Even in this highly active system, the paleoenvironmental imprint was detectable but superimposed by modern processes. In general, the results of our Wadden Sea research have indicated surprising similarities between the subsurface of tidal-flat sediments and the deep biosphere (Wilms et al., 2006, Engelen & Cypionka, 2009).
Studies on the German North Sea coast are now continued in a subproject of the research unit: Assessment of ground- and porewater-derived nutrient fluxes into the German North Sea – Is there a ‘Barrier Island Mass Effect (BIME)’? Here, we mainly perform microbial community analyses using next generation sequencing to investigate microbial diversity in sandy beaches and the underlying subterranean estuary. By using Illumina sequencing of the 16S rRNA genes and transcripts on samples obtained at the same stations at different time points during the year, we aim to get a detailed understanding of microbial community dynamics on a spatial and seasonal scale. By comparing samples taken from areas influenced by SGD with samples lacking this influence, we will be able to see adaptations of the microbial community to freshwater influence and changing nutrient and redox conditions.
This research is embeded in the Collaborative Research Centre "Roseobacter" that runs since 2011 and will continue until 2022. In the first two phases of this CRC, we have gained deeper insights into the biogeography of Roseobacter-affiliated bacteria in marine sediments. Large datasets of 16S rRNA transcripts were obtained from extended research cruises and were extracted from a dataset comprising globally distributed samples from different sediment horizons of various oceanic regions. The vast amount of sequences that were assigned to “unknown” roseobacters was highly challenging concerning an exact definition of benthic core-taxa and the identification of environmental settings that trigger their distribution. This is now performed in the currently running synthesis phase of the project. Besides that, the metabolic potential of benthic roseobacters will mainly be inferred from genome analyses of our isolates and subsequent growth experiments to verify the genomic information. Additionally, we will investigate organosulfur cycling in coastal sediments in a collaborative experiment on North Sea samples.
In a new part of the project, we will focus on the role of roseophages for benthic roseobacters. Using the genomic information of our benthic isolates to identify the presence of prophages, we will perform phage-induction experiments to determine characteristic parameters for phage-host interactions and to obtain the genomes of free phages. Furthermore, we will go back to the environment, to detect roseophage-specific signatures in the metagenomes constructed from Pacific sediments and to quantify their distribution in original sediment samples by qPCR using phage-specific primers.
We have obtained a large collection of pure cultures from ODP Leg 201 to the equatorial Pacific and Peru margin in 2002. The composition of the culture collection was described in the article of (D'Hondt et al., 2004) and their physiological properties were published by (Batzke et al., 2007). Our most frequently isolated microorganism was affiliated to Rhizobium radiobacter (ca. 40 strains), which we already identified as highly abundant in ancient Mediterranean sapropels (Süß et al., 2006). In a second project, samples from the Juan de Fuca Ridge (IODP Exp. 301) were analyzed with biogeochemical, microbiological and molecular methods. The geoscientific goal of the project was to understand the role of hydrothermal fluids as a driving force for the deep biosphere (Engelen et al., 2008). New strains of sulfate reducers were investigated with respect to physiological properties such as autotrophic growth (Fichtel et al., 2012).
To access phages originating from the marine deep-biosphere, we treated our bacterial isolates from ODP Leg 201 with phage-induction agents (Engelhardt et al., 2011). We could show that all R. radiobacter-affiliated isolates were infected and could thus reveal the presence of a distinct phage-host association in a microbial deep-biosphere population. The viral impact on the deep-biosphere was elucidated by comparing virus-to-cell ratios and viral decay rates within a comprehensive set of subsurface sediments. Those were recovered from North Sea tidal-flats, the Equatorial Pacific and Peru margin (ODP Leg 201), the Bering Sea (IODP Expedition 323) and the South Pacific Gyre (IODP Expedition 329). We showed that viruses outnumber prokaryotic cells in all subsurface sediments. High virus-to-cell ratios indicate an ongoing production of viruses in the deep-biosphere (Engelhardt et al., 2014).
In this subproject of the graduate school ECOMOL, we will test the hypothesis that benthic microbial community structures and DOM compositions are linked by viral lysis. Next generation sequencing of ribosomal RNA is currently applied to a selection of sediment samples from research cruises of RV Sonne in 2016 and 2017. The results will be correlated to molecular DOM data also collected during both cruises.