Viral community composition of hypersaline lakes
Despite their widespread distribution and remarkable antiquity no RNA viruses definitively associated with the domain Archaea have been identified. In contrast, 17 families of DNA viruses are known to infect archaea. In an attempt to uncover more of the elusive archaeal virosphere, we investigated t...
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ftpubmed:oai:pubmedcentral.nih.gov:10492444 2023-10-09T21:47:08+02:00 Viral community composition of hypersaline lakes Le Lay, Callum Hamm, Joshua N Williams, Timothy J Shi, Mang Cavicchioli, Ricardo Holmes, Edward C 2023-08-30 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10492444/ http://www.ncbi.nlm.nih.gov/pubmed/37692898 https://doi.org/10.1093/ve/vead057 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10492444/ http://www.ncbi.nlm.nih.gov/pubmed/37692898 http://dx.doi.org/10.1093/ve/vead057 © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Virus Evol Research Article Text 2023 ftpubmed https://doi.org/10.1093/ve/vead057 2023-09-17T00:45:02Z Despite their widespread distribution and remarkable antiquity no RNA viruses definitively associated with the domain Archaea have been identified. In contrast, 17 families of DNA viruses are known to infect archaea. In an attempt to uncover more of the elusive archaeal virosphere, we investigated the metatranscriptomes of hypersaline lakes that are a rich source of archaea. We sequenced RNA extracted from water filter samples of Lake Tyrrell (Victoria, Australia) and cultures seeded from four lakes in Antarctica. To identify highly divergent viruses in these data, we employed a variety of search tools, including Hidden Markov models (HMMs) and position-specific scoring matrices (PSSMs). From this, we identified 12 highly divergent, RNA virus-like candidate sequences from the virus phyla Artverviricota, Duplornaviricota, Kitrinoviricota, Negarnaviricota, and Pisuviricota, including those with similarity to the RNA-dependent RNA polymerase (RdRp). An additional analysis with an artificial intelligence (AI)-based approach that utilises both sequence and structural information identified seven putative and highly divergent RdRp sequences of uncertain phylogenetic position. A sequence matching the Pisuviricota from Deep Lake in Antarctica had the strongest RNA virus signal. Analyses of the dinucleotide representation of the virus-like candidates in comparison to that of potential host species were in some cases compatible with an association to archaeal or bacterial hosts. Notably, however, the use of archaeal CRISPR spacers as a BLAST database failed to detect any RNA viruses. We also described DNA viruses from the families Pleolipoviridae, Sphaerolipoviridae, Halspiviridae, and the class Caudoviricetes. Although we were unable to provide definitive evidence the existence of an RNA virus of archaea in these hypersaline lakes, this study lays the foundations for further investigations of highly divergent RNA viruses in natural environments. Text Antarc* Antarctica PubMed Central (PMC) Tyrrell ENVELOPE(-69.512,-69.512,-69.634,-69.634) Four Lakes ENVELOPE(-126.826,-126.826,54.858,54.858) Virus Evolution 9 2 |
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Research Article Le Lay, Callum Hamm, Joshua N Williams, Timothy J Shi, Mang Cavicchioli, Ricardo Holmes, Edward C Viral community composition of hypersaline lakes |
topic_facet |
Research Article |
description |
Despite their widespread distribution and remarkable antiquity no RNA viruses definitively associated with the domain Archaea have been identified. In contrast, 17 families of DNA viruses are known to infect archaea. In an attempt to uncover more of the elusive archaeal virosphere, we investigated the metatranscriptomes of hypersaline lakes that are a rich source of archaea. We sequenced RNA extracted from water filter samples of Lake Tyrrell (Victoria, Australia) and cultures seeded from four lakes in Antarctica. To identify highly divergent viruses in these data, we employed a variety of search tools, including Hidden Markov models (HMMs) and position-specific scoring matrices (PSSMs). From this, we identified 12 highly divergent, RNA virus-like candidate sequences from the virus phyla Artverviricota, Duplornaviricota, Kitrinoviricota, Negarnaviricota, and Pisuviricota, including those with similarity to the RNA-dependent RNA polymerase (RdRp). An additional analysis with an artificial intelligence (AI)-based approach that utilises both sequence and structural information identified seven putative and highly divergent RdRp sequences of uncertain phylogenetic position. A sequence matching the Pisuviricota from Deep Lake in Antarctica had the strongest RNA virus signal. Analyses of the dinucleotide representation of the virus-like candidates in comparison to that of potential host species were in some cases compatible with an association to archaeal or bacterial hosts. Notably, however, the use of archaeal CRISPR spacers as a BLAST database failed to detect any RNA viruses. We also described DNA viruses from the families Pleolipoviridae, Sphaerolipoviridae, Halspiviridae, and the class Caudoviricetes. Although we were unable to provide definitive evidence the existence of an RNA virus of archaea in these hypersaline lakes, this study lays the foundations for further investigations of highly divergent RNA viruses in natural environments. |
format |
Text |
author |
Le Lay, Callum Hamm, Joshua N Williams, Timothy J Shi, Mang Cavicchioli, Ricardo Holmes, Edward C |
author_facet |
Le Lay, Callum Hamm, Joshua N Williams, Timothy J Shi, Mang Cavicchioli, Ricardo Holmes, Edward C |
author_sort |
Le Lay, Callum |
title |
Viral community composition of hypersaline lakes |
title_short |
Viral community composition of hypersaline lakes |
title_full |
Viral community composition of hypersaline lakes |
title_fullStr |
Viral community composition of hypersaline lakes |
title_full_unstemmed |
Viral community composition of hypersaline lakes |
title_sort |
viral community composition of hypersaline lakes |
publisher |
Oxford University Press |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10492444/ http://www.ncbi.nlm.nih.gov/pubmed/37692898 https://doi.org/10.1093/ve/vead057 |
long_lat |
ENVELOPE(-69.512,-69.512,-69.634,-69.634) ENVELOPE(-126.826,-126.826,54.858,54.858) |
geographic |
Tyrrell Four Lakes |
geographic_facet |
Tyrrell Four Lakes |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_source |
Virus Evol |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10492444/ http://www.ncbi.nlm.nih.gov/pubmed/37692898 http://dx.doi.org/10.1093/ve/vead057 |
op_rights |
© The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
op_doi |
https://doi.org/10.1093/ve/vead057 |
container_title |
Virus Evolution |
container_volume |
9 |
container_issue |
2 |
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1779309934991638528 |