Viruses in ancient ice wedges in the Central Yakutia, Siberia (original) (raw)
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Glacier ice archives fifteen-thousand-year-old viruses
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Frontiers in Microbiology, 2015
Bellas CM, Anesio AM and Barker G (2015) Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions. Front. Microbiol. 6:656. Microbial communities in glacial ecosystems are diverse, active, and subjected to strong viral pressures and infection rates. In this study we analyse putative virus genomes assembled from three dsDNA viromes from cryoconite hole ecosystems of Svalbard and the Greenland Ice Sheet to assess the potential hosts and functional role viruses play in these habitats. We assembled 208 million reads from the virus-size fraction and developed a procedure to select genuine virus scaffolds from cellular contamination. Our curated virus library contained 546 scaffolds up to 230 Kb in length, 54 of which were circular virus consensus genomes. Analysis of virus marker genes revealed a wide range of viruses had been assembled, including bacteriophages, cyanophages, nucleocytoplasmic large DNA viruses and a virophage, with putative hosts identified as Cyanobacteria, Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes, eukaryotic algae and amoebae. Whole genome comparisons revealed the majority of circular genome scaffolds (CGS) formed 12 novel groups, two of which contained multiple phage members with plasmid-like properties, including a group of phage-plasmids possessing plasmid-like partition genes and toxin-antitoxin addiction modules to ensure their replication and a satellite phage-plasmid group. Surprisingly we also assembled a phage that not only encoded plasmid partition genes, but a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas adaptive bacterial immune system. One of the spacers was an exact match for another phage in our virome, indicating that in a novel use of the system, the lysogen was potentially capable of conferring immunity on its bacterial host against other phage. Together these results suggest that highly novel and diverse groups of viruses are present in glacial environments, some of which utilize very unusual life strategies and genes to control their replication and maintain a long-term relationship with their hosts.
Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch
Proceedings of the National Academy of Sciences, 2014
Viruses preserved in ancient materials provide snapshots of past viral diversity and a means to trace viral evolution through time. Here, we use a metagenomics approach to identify filterable and nuclease-resistant nucleic acids preserved in 700-y-old caribou feces frozen in a permanent ice patch. We were able to recover and characterize two viruses in replicated experiments performed in two different laboratories: a small circular DNA viral genome (ancient caribou feces associated virus, or aCFV) and a partial RNA viral genome (Ancient Northwest Territories cripavirus, or aNCV). Phylogenetic analysis identifies aCFV as distantly related to the plant-infecting geminiviruses and the fungi-infecting Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 and aNCV as within the insect-infecting Cripavirus genus. We hypothesize that these viruses originate from plant material ingested by caribou or from flying insects and that their preservation can be attributed to protection within viral capsids maintained at cold temperatures. To investigate the tropism of aCFV, we used the geminiviral reverse genetic system and introduced a multimeric clone into the laboratory model plant Nicotiana benthamiana. Evidence for infectivity came from the detection of viral DNA in newly emerged leaves and the precise excision of the viral genome from the multimeric clones in inoculated leaves. Our findings indicate that viral genomes may in some circumstances be protected from degradation for centuries.
Paleovirology: Blessing or Curse of Ancient Viruses - A Review
Agricultural Reviews, 2019
Ancient virus genomes preserved as fossils and carried by host within their genome. Although viral genomes evolve rapidly, their rate of change slows to the same pace as that of the host’s DNA after insertion, making it possible to study viral DNA sequences that are many millions of years old. Paleovirology is the study of viral fossil records typically over prehistoric or geological timescales and the effects that these agents have had on the evolution of their hosts. Viruses sometimes heritably integrate into the genomes of their hosts, resulting in genomic features known as endogenous viral elements (EVEs). Using EVEs, the field of paleovirology investigates the long term evolution of viruses and their impact on hosts. One of the fruitful outcomes of high throughput genomics is the widespread availability of whole genome data, offering the unprecedented opportunity to investigate EVEs at a large scale. This review, highlights the utility of antiviral gene evolution for the study ...
Viral dynamics in cryoconite holes on a high Arctic glacier (Svalbard)
Journal of Geophysical Research, 2007
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The first known virus isolates from Antarctic sea ice have complex infection patterns
FEMS microbiology ecology, 2018
Viruses are recognized as important actors in ocean ecology and biogeochemical cycles, but many details are not yet understood. We participated in a winter expedition to the Weddell Sea, Antarctica, to isolate viruses and to measure virus-like particle abundance (flow cytometry) in sea ice. We isolated 59 bacterial strains and the first four Antarctic sea-ice viruses known (PANV1, PANV2, OANV1 and OANV2), which grow in bacterial hosts belonging to the typical sea-ice genera Paraglaciecola and Octadecabacter. The viruses were specific for bacteria at the strain level, although OANV1 was able to infect strains from two different classes. Both PANV1 and PANV2 infected 11/15 isolated Paraglaciecola strains that had almost identical 16S rRNA gene sequences, but the plating efficiencies differed among the strains, whereas OANV1 infected 3/7 Octadecabacter and 1/15 Paraglaciecola strains and OANV2 1/7 Octadecabacter strains. All the phages were cold-active and able to infect their original...
Paleovirology: The Study of Endogenous Viral Elements
Viruses sometimes heritably integrate into the genomes of their hosts, resulting in genomic features known as endogenous viral elements (EVEs). Using EVEs, the field of paleovirology investigates the long-term evolution of viruses and their impact on hosts. One of the fruitful outcomes of high throughput genomics is the widespread availability of whole genome data, offering the unprecedented opportunity to investigate EVEs at a large scale. In this chapter, we review the consequent surge in paleovirology research that can be traced to landmark work performed over half a century ago. We describe general principles of EVE biology and the main methodological techniques used to study them. We show how EVEs can only be understood within an evolutionary framework and we outline a generalized workflow for conducting paleovirology studies. We review exemplar paleovirological discoveries from each of the main viral groups, highlighting a range of approaches to paleovirology. We also discuss the major implications that certain discoveries and insights from paleovirology could have on our understanding of both virus and genome evolution. Finally, we consider the current limitations and potential pitfalls in paleovirology, and anticipate the possible future directions of this exciting and rapidly growing field.
Detection of tomato mosaic tobamovirus RNA in ancient glacial ice
Polar Biology, 1999
Tomato mosaic tobamovirus is a very stable plant virus with a wide host range, which has been detected in plants, soil, water, and clouds. Because of its stability and prevalence in the environment, we hypothesized that it might be preserved in ancient ice. We detected tomato mosaic tobamovirus RNA by reverse-transcription polymerase chain reaction ampli®cation in glacial ice subcores <500 to approximately 140,000 years old from drill sites in Greenland. Subcores that contained multiple tomato mosaic tobamovirus genotypes suggest diverse atmospheric origins of the virus, whereas those containing tomato mosaic tobamovirus sequences nearly identical to contemporary ones suggest that recent tomato mosaic tobamovirus populations have an extended age structure. Detection of tomato mosaic tobamovirus in ice raises the possibilities that stable viruses of humans and other hosts might be preserved there, and that entrapped ancient viable viruses may be continually or intermittently released into the modern environment.
Paleovirology - ghosts and gifts of viruses past
Current opinion in virology, 2011
The emerging field of paleovirology aims to study the evolutionary age and impact of ancient viruses (paleoviruses) on host biology. Despite a historical emphasis on retroviruses, paleoviral 'fossils' have recently been uncovered from a broad swathe of viruses. These viral imprints have upended long-held notions of the age and mutation rate of viruses. While 'direct' paleovirology relies on the insertion of viral genes in animal genomes, examination of adaptive changes in host genes that occurred in response to paleoviral infections provides a complementary strategy for making 'indirect' paleovirological inferences. Finally, viruses have also impacted host biology by providing genes hosts have domesticated for their own purpose.