Abstract
Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we explored virus-host interactions in geographically diverse salterns. Using taxonomic profiling, we identified hosts such as archaeal Haloquadratum, Halorubrum, and Haloarcula and bacterial Salinibacter, and we found that community composition related to not only salinity but also local environmental dynamics. Characterizing glycerol metabolism genes in these metagenomes suggested Halorubrum and Haloquadratum possess most dihydroxyacetone kinase genes while Salinibacter possesses most glycerol-3-phosphate dehydrogenase genes. Using two different methods, we detected fewer CRISPR spacers in Haloquadratum-dominated compared with Halobacteriaceae-dominated saltern metagenomes. After CRISPR detection, spacers were aligned against haloviral genomes to map virus to host. While most alignments for each saltern metagenome linked viruses to Haloquadratum walsbyi, there were also alignments indicating interactions with the low abundance taxa Haloarcula and Haloferax. Further examination of the dinucleotide and trinucleotide usage differences between paired viruses and their hosts confirmed viruses and hosts had similar nucleotide usage signatures. Detection of cas genes in the salterns supported the possibility of CRISPR activity. Taken together, our studies suggest similar virus-host interactions exist in different solar salterns and that the glycerol metabolism gene dihydroxyacetone kinase is associated with Haloquadratum and Halorubrum.
Highlights
Viruses, the most abundant entities on the planet, are critical for maintaining global biogeochemical cycles (Suttle, 2007; Rohwer, Prangishvili & Lindell, 2009)
This study showed that Clustered regularly interspaced short palindromic repeat (CRISPR) in the lake were remarkably dynamic over time, it indicated a number of viruses could be mapped to saltern microbes with CRISPR spacers (Emerson et al, 2013)
These taxonomic profiles and clustering results further guided our analyses of host CRISPR arrays, as we used taxonomy to guide our searches for CRISPR spacers
Summary
The most abundant entities on the planet, are critical for maintaining global biogeochemical cycles (Suttle, 2007; Rohwer, Prangishvili & Lindell, 2009). Many viruses infect and lyse microbial hosts, releasing stored nutrients back into the ecosystem through a mechanism called the viral shunt (Suttle, 2007; Weitz & Wilhelm, 2012). This relationship suggests viral-microbial interactions are important for environmental nutrient cycling. Acting as an adaptive immune system against viral infection, CRISPRs incorporate short spacers cleaved from viral DNA into host genomes, providing a record of past infections and associations between viruses and prokaryotic hosts (Sorek, Kunin & Hugenholtz, 2008)
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