Viral activity in subsurface sediments
Microbial Ecology and Applied Microbiology
Oceanography
Virology
Final Report Abstract
The oceanic crust is a large interconnected aquifer with intense fluid circulation. Diffusive flow of fluids from the crust aquifer transports nutrients and electron acceptors to the overlaying sediments. This effect is pronounced near oceanic ridges. At the Juan de Fuca ridge (IODP 301), a geochemical zonation is established and results in three compartments of an upper and lower sulfate zone and a sulfate-minimum zone that spreads in between. Microbial communities in the upper sediments have access to relatively young sources of organic carbon and sulfate as main terminal electron acceptor. For the lower sulfate zone, the available organic carbon is recalcitrant, however, the introduction of nutrients from the crust fluid has been shown to support microbial activity. Viruses are active parts of deeply buried microbial communities with diverse virus-host interactions. Viral genomes can be integrated into the host cell genomes (provirus) and may be induced to eventually lyse the host cell. Viral-mediated cell lysis results in carbon turnover by providing bioavailable organic carbon (viral shunt). This project aimed to quantify the viral shunt in a cultivation-based approach and get an estimate of the viral impact on deeply buried microbial communities. We started to develop a PCR-based detection system for viruses associated with Desulfovibrio indonesiensis strains for later use in growth experiments and sediment samples. We performed whole genome sequencing and genome analysis of three strains. As described, the virus host system turned out to be very complex and we decided to use a counting method for total virus counts for the growth experiments. We established a method for counting SYBR-Green-stained viruses by flow cytometry. The method was successfully applied for virus counting in cultures and surface sediments. The cultivation-based experiments were performed to quantify and the release of organic carbon via the viral shunt of autotrophically grown cultures. High background of organic carbon led to unexpected difficulties with the chemical analyseswhich could not finished within the funding period. However, the experiments to quantify the viral shunt are still part of the ongoing research in the work group. In the frame of the project, the genome analysis revealed interesting and unique insights into the virushost interaction in Desulfovibrio indonesiensis. Therefore, the genomic approach was followed with a higher focus. The numerous provirus and spacers gives evidence for a high frequency of virus-host interactions. The analysis of sequence information from CRISPR-spacers showed that all strains shared some part of their early viral infection history. Thus, it became apparent that the three strains had a common ancestor and got separate in the frame of the burial process. The presence of unique proviruses in strain P23 provided additional support for an individual infection history. Furthermore, some proviruses carried “auxiliary genes” which encode for beneficial metabolic functions to support the host cell, e.g. arsenate resistance for strain P23. Accordingly, viral infections and integration of proviruses might be a burden for the host cell, but might also be a fitness factor that increases survivability. These results indicate that Desulfovibrio indonesiensis strains were prone to numerous viral attacks and survived the long burial process, partly due to their successful defense against viruses by using CRISPR systems and conceivably by viral encoded fitness factors. The growth experiments showed the proviruses are still functional and to cause a continuous lysis of the host cells. Thus, viruses potentially contribute to the maintenance of a labile organic carbon pool for deeply buried microbial communities.
Publications
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(2017) Virus dynamics are influenced by season, tides and advective transport in intertidal, permeable sediments. Front Microbiol 8:2526
Vandieken V, Sabelhaus L, Engelhardt T
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(2018) Draft genome sequences of six Vibrio diazotrophicus strains isolated from deep subsurface sediments of the Baltic Sea. Genome Announcements 6:e00081-18
Castillo D, Vandieken V, Engelen B, Engelhardt T, Middelboe M
