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Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics

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 g...

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Autores principales: Moller, Abraham G., Liang, Chun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5228507/
https://www.ncbi.nlm.nih.gov/pubmed/28097058
http://dx.doi.org/10.7717/peerj.2844
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author Moller, Abraham G.
Liang, Chun
author_facet Moller, Abraham G.
Liang, Chun
author_sort Moller, Abraham G.
collection PubMed
description 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.
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spelling pubmed-52285072017-01-17 Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics Moller, Abraham G. Liang, Chun PeerJ Bioinformatics 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. PeerJ Inc. 2017-01-10 /pmc/articles/PMC5228507/ /pubmed/28097058 http://dx.doi.org/10.7717/peerj.2844 Text en ©2017 Moller and Liang http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , 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) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Moller, Abraham G.
Liang, Chun
Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics
title Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics
title_full Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics
title_fullStr Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics
title_full_unstemmed Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics
title_short Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics
title_sort determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5228507/
https://www.ncbi.nlm.nih.gov/pubmed/28097058
http://dx.doi.org/10.7717/peerj.2844
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