Use of Cellular CRISPR (Clusters of Regularly Interspaced Short Palindromic Repeats) Spacer-Based Microarrays for Detection of Viruses in Environmental Samples

• Published in: Applied and Environmental Microbiology 2010-11, Vol.76 (21), p.7251-7258
• Main Authors: Snyder, Jamie C, Bateson, Mary M, Lavin, Matthew, Young, Mark J
• Format: Article
• Language: English
• Subjects: Archaeal Viruses - genetics; Biological and medical sciences; DNA probes; Environment; Environmental Microbiology; Fundamental and applied biological sciences. Psychology; Genomics; High temperature; Hot Springs - virology; Interspersed Repetitive Sequences - genetics; Inverted Repeat Sequences - genetics; Metagenomics - methods; Methods; Microbiology; Multigene Family - genetics; Oligonucleotide Array Sequence Analysis - instrumentation; Oligonucleotide Array Sequence Analysis - methods; Sulfolobus solfataricus - virology; Temperature effects; Viral infections; Viruses; Viruses - genetics
• ISSN: 0099-2240; 1098-5336; 1098-6596
• DOI: 10.1128/aem.01109-10

It is currently difficult to detect unknown viruses in any given environment. The recent discovery of CRISPR (clusters of regularly interspaced short palindromic repeats) loci within bacterial and archaeal cellular genomes may provide an alternative approach to detect new viruses. It has been shown that the spacer sequences between the direct repeat units of the CRISPR loci are often derived from viruses and likely function as guide sequences to protect the cell from viral infection. The spacer sequences within the CRISPR loci may therefore serve as a record of the viruses that have replicated within the cell. We have cataloged the CRISPR spacer sequences from cellular metagenomic data from high-temperature (>80°C), acidic (pH < 4) hot spring environments located in Yellowstone National Park (YNP). We designed a microarray platform utilizing these CRISPR spacer sequences as potential probes to detect viruses present in YNP hot spring environments. We show that this microarray approach can detect viral sequences directly from virus-enriched environmental samples, detecting new viruses which have not been previously characterized. We further demonstrated that this microarray approach can be used to examine temporal changes in viral populations within the environment. Our results demonstrate that CRISPR spacer sequence-based microarrays will be useful tools for detecting and monitoring viruses from diverse environmental samples.