Detection of microeukaryotes and their viruses in groundwater from a uranium contaminated site

Background/Question/Methods
Environmental contamination by radionuclides such as uranium, plutonium, and cesium can have severe impacts on aquatic (e.g., groundwater, sediment) microbiological communities. However, very little work has been done to look at how this type of contamination affects microeukaryotes (fungi and protists) and their viral pathogens in the subsurface. These organisms are important links between trophic levels within microbial communities: Fungi, the breakdown of organic matter through decay and disease, and the transport of nutrients by mycorrhizal members; protists the movement of nutrients upward in the food chain by grazing on bacteria and other organisms; and the release of nutrients by viruses as infected hosts die. Groundwater samples were collected and filtered from 15 monitoring wells at the Oak Ridge Integrated Field Research Center site representing a range of uranium contamination levels (0.001 to 55.286 mg/L). DNA from the samples was labeled and analyzed on a functional gene microarray (GeoChip 5.0) containing 11,416 probes, covering ~26,000 sequences of both functional (involved in biogeochemical cycling) and phylogenetic genes from fungi and protists and 1051 probes, covering ~1800 sequences from viral families known to infect these organisms.

Results/Conclusions
Between 1479 and 3532 probes from microeukaryotes and their viruses were detected per sample. Detected viral probes included proteins involved with viral structural (capsid), host recognition, and replication. Eukaryotic sequences included functional genes such as chitinases, laccases, and zinc transporters as well as  phylogenetic markers (e.g., actin, heat shock protein 90 (hsp90)). The Mantel analysis showed uranium concentration and pH were found to be important environmental factors for microeukaryotes (rM =  0.722, p = 0.002), while dissolved organic carbon (DOC) and sulfide were found to be important environmental factors for viruses that infect these microorganisms (rM = 0.551, p = 0.001). It was also found that, when probes were available, sequences for either the host or other closely related organisms of the fungal and protistian viruses detected were also found to be present. This study demonstrates the ability of functional gene arrays to study both microeukaryotes and their viruses in contaminated environments.