The overall goal of our project is to understand the impact of phages for biogeochemical cycling, microbial abundance and diversity in the marine subsurface. The integration of the viral component into the biogeochemical model for subsurface sediments of the South Pacific Gyre (SPG) is essential to understand the recycling of labile organic matter within this habitat. Thus, our aim is to identify if viral lysis could provide these compounds to this extremely nutrient-depleted habitat. We hypothesise that viruses might be one controling factor for the abundance and diversity of indigenous microorganisms.
First, viral counts were determined on SPG sediments to calculate their distribution within the subsurface. Our results indicate that the number of viruses always exceeded those of prokaryotic cells with an increasing virus-to-cell ratio with depth.
In our cultivation-based approach, we have started to isolate subseafloor microorganisms from the SPG to identify prophages within their genomes. Sediment samples that were recovered from various sites and sediment horizons were directly transferred into three different media onboard the JOIDES Resolution. Two media containing a mix of several monomers as substrates were used to target either aerobic or anaerobic heterotrophs. For the enrichment of autotrophs, cultures were set up in artifical seawater medium (without any organic substrate) and flushed with hydrogen/carbon dioxide.
Due to the slow growth of indigenous microorganisms, we have now obtained the first isolates from a limited number of oxic enrichments from site U1371 (3.7 mbsf, 122 mbsf, 127 mbsf). Those are affiliated to Nocardioides basaltis (99% 16S rRNA sim.), Halomonas aquamarina (100%), Erythrobacter vulgaris (99%), Pseudoaltoromonas sp. (99%), Alteromonas sp. (100%), and Dietzia sp. (100%). Their presence was already detected by molecular screening of the cultures by DGGE. When the process of strain purification is completed, we will start to induce the prophages within their genomes. The morphologic and phylogenetic diversity of these phages will be analysed in detail. Concerning our culture collection, we will then identify if the percentage of infected cells that are under severe starvation is different to those isolated from "high activity sites".
The diversity of viruses within the SPG sediments will be analysed by applying a novel approach using whole genome amplification. This technique is required to enhance the amount of viral DNA in sediments with an extremly low abundance of viruses. Subsequently, other molecular down stream applications such as RAPD-PCR will be used to analyse virus diversity patterns of the different sites.
Franziska Preuss (PhD student)
Lisa Marie Moskwa (Master student)
Engelen B, Engelhardt T, Cypionka H (2014) Phagen in Sedimenten der marinen
tiefen Biosphäre. Biospektrum 04.14:380-382, DOI: 10.1007/s12268-014-0451-0
Engelhardt T, Kallmeyer J, Cypionka H, Engelen B (2014) High virus-to-cell ratios indicate on-going production of viruses in deep subsurface sediments. ISME J 8:1503–1509
Engelhardt T, Sahlberg M, Cypionka H, Engelen B (2013) Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments. ISME J 7:199-209
Engelhardt T, Sahlberg M, Cypionka H, Engelen B (2011) Induction of prophages from deep-subseafloor bacteria Environm Microbiol Rep 3:459–465