Mapping ecologically important virus-host interactions in geographically diverse solar salterns with metagenomics
- Published
- Accepted
- Subject Areas
- Bioinformatics, Computational Biology, Ecology, Genomics, Microbiology
- Keywords
- CRISPR, hypersaline ecosystems, metagenomics, microbial ecology, halophiles, viral shunt, bioinformatics, extremophiles, environmental genomics, viruses
- Copyright
- © 2016 Moller et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2016. Mapping ecologically important virus-host interactions in geographically diverse solar salterns with metagenomics. PeerJ Preprints 4:e2106v1 https://doi.org/10.7287/peerj.preprints.2106v1
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 and related them to carbon cycling. 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 most dihydroxyacetone kinase genes affiliate to Halorubrum and Haloquadratum while most glycerol-3-phosphate dehydrogenase genes affiliate to Salinibacter. We identified CRISPR spacers in the metagenomes with two different methods and found more spacers in the Halobacteriaceae-dominated IC21 and C34 salterns compared with the Haloquadratum-dominated SS19, SS33, and SS37 salterns, suggesting low CRISPR diversity and possibly a high rate of CRISPR loss in the Haloquadratum-dominated salterns. After CRISPR detection, spacers were aligned against haloviral genomes to map virus to host. While most alignments linked viruses to Haloquadratum walsbyi, there were clusters of interactions with less abundant Haloarcula and Haloferax. Further examination of the dimer and codon usage differences between paired viruses and their hosts and detection of cas genes in the salterns confirmed both the plausibility of virus-host interactions and the possibility of CRISPR activity. Taken together, our studies suggest CRISPR loss in archaeal hosts controls the level of virus proliferation and the nutrient turnover viruses induce in these environments.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Percentage of reads mapping to reference library in taxonomic profiling steps (MetaPhyler)
Percentage of reads mapping to reference library in functional profiling steps (ShotMAP)
Number of CRISPR spacers detected by de novo and reference guided methods, normalized by millions of reads in each metagenome
Network of virus-host interactions generated from Haloquadratum walsbyi strain C23 spacer alignments against the haloviral genome library used in this study
Viruses are marked in blue, while spacers are in orange.
Measures of the number of contig BLAST hits to cas genes extracted from three different halobacterial orders (Halobacteriales, Haloferacales, and Natrialbales)
Taxonomic affiliation of all BLAST hits of cas genes against contigs (not only best hits)
Additional information about the Santa Pola, Isla Cristina, and Cahuil solar saltern metagenomes provided in the NCBI Sequence Read Archive (SRA) and associated genome announcements
Site names (as listed in the Figures) are listed in bold. NCBI SRA accession numbers (SRX for experiment and SRR for run) are included in the table.
Additional information about the Chula Vista saltern metagenomes obtained from the iMicrobe Collaborative and combined into three metagenomes based on salt concentration
Site names (as listed in the Figures) are in bold. The datasets can be found at this web address: http://data.imicrobe.us/project/view/58.
The library of haloviral genomes examined
The library included 326 contigs more than 500 bp in length assembled from Chula Vista metaviromes (http://data.imicrobe.us/project/view/58) and the following haloviral genomes obtained from NCBI GenBank.
Alignments of combined Santa Pola CRISPR direct repeats identified with Crass against a library of taxonomically annotated direct repeat sequences obtained from CRISPRdb
Query sequences used for reference-guided CRISPR search and associated archaeal hosts
Summary of CRISPR virus-host pairings in Cahuil (C34) metagenome
CRISPR spacers were detected with the reference-guided method.
Summary of CRISPR virus-host pairings in SS13 metagenome
CRISPR spacers were detected with the reference-guided method.
Summary of CRISPR virus-host pairings in SS19 metagenome
CRISPR spacers were detected with the reference-guided method.
Summary of CRISPR virus-host pairings in IC21 metagenome
CRISPR spacers were detected with the reference-guided method.
Summary of CRISPR virus-host pairings in SS33 metagenome
CRISPR spacers were detected with the reference-guided method.
Summary of CRISPR virus-host pairings in SS37 metagenome
CRISPR spacers were detected with the reference-guided method.
The library of cas genes identified in Halobacteriales genomes that were used in cas operon detection
The library was aligned against Newbler contigs assembled from the Cahuil/C34, combined Chula Vista, and combined Santa Pola/Isla Cristina metagenomes.
The library of cas genes identified in Haloferacales genomes that were used in cas operon detection
The library was aligned against Newbler contigs assembled from the Cahuil/C34, combined Chula Vista, and combined Santa Pola/Isla Cristina metagenomes.
The library of cas genes identified in Natrialbales genomes that were used in cas operon detection
The library was aligned against Newbler contigs assembled from the Cahuil/C34, combined Chula Vista, and combined Santa Pola/Isla Cristina metagenomes.