Diversity and functionality of groundwater viral communities

Li Deng1, Judith Feichtmayer1, Rene Kallies2, Christian Drosten3, Christian Griebler4
1 Institut für Grundwasserökologie, Helmholtz Zentrum München
2 Department für Mikrobiologie, Helmholtz Zentrum für Umweltforschung Leipzig
3 Institut für Virologie, Universität Bonn
4 Institute für Grundwasserökologie, Helmholtz Zentrum München

P 6.1 in Grundwasserbiologie


Viruses are the most abundant and diverse biological entities on the planet and their impact is global. They affect microbial hosts through mortality, re-mineralization of nutrients, and horizontal gene transfer. Phages can even drive the evolutionary trajectory of the Earth’s fundamental biogeochemical processes by encoding “host” genes that are expressed during infection and confer a direct fitness advantage for the phage.


While viral communities in surface freshwaters and marine systems received considerable attention in the recent past, our knowledge about viruses, others than pathogens, in groundwaters is almost zero. Sampling pristine as well as organically contaminated groundwater from different sites in Germany, we aim to shed light into the viral diversity and functionality.


Viral particles were concentrated from large amounts of groundwater (tens of cubicmeters) via nanofiltration. Viral communities were then investigated by means of viral tagging, metagenomic pyrosequencing, and protein cluster (PC) analysis. We build a PC datasets using viral metagenomes from freshwater and groundwater habitats, in conjunction with the marine viral GOS and POV data set to minimize the bias when analyzing the groundwater viral metagenoms.


Viruses in groundwater were dominated by dsDNA bacteriophages of the families of Myoviridae, Podoviridae and Siphoviridae. The dominance of tailed-morphology Myoviridae in our groundwater sample was confirmed by Transmission Electron Microscopy (TEM). Comparison of the groundwater viral metagenomes with different metagenomes from a variety of other aquatic environments (marine and freshwater) revealed that the freshwater viral consortia were more close to each other than to marine consortia. However, no significant difference between freshwater (including groundwater) and marine viral assemblies could be found, which is likely due to the insufficient sample size of the current database. The cluster richness of each virome, deduced from PCs, was significantly different between the groundwater environments from others, with the highest diversity being observed in groundwater. Mapping metabolic pathways from viral metagenome data obtained from groundwater of an organically polluted site revealed that viruses in this system carry bacterial functional genes related to biodegradation of the site-specific contaminants. Current research is directed to the functional role of viral communities in groundwater ecosystems.