Viruses in acidic geothermal environments of the Kamchatka Peninsula

Bize, Ariane; Peng, Xu; Prokofeva, M. I.; MacLellan, Kirsty; Lucas, Soizick; Forterre, Patrick; Garrett, Roger A.; Bonch-Osmolovskaya, E. A.; Prangishvili, David

doi:10.1016/j.resmic.2008.04.009

Cited by 39 publications

(30 citation statements)

References 33 publications

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“…Until relatively recent times, the only methodology available to study these viruses was through the cultivation of their hosts (López-López et al 2013). By systematically applying this approach, our knowledge on viruses populating (hyper)thermal environments over the last 30 years has considerably expanded thanks to the pioneer work of Wolfram Zillig and, subsequently, of several groups in Europe and USA (Bize et al 2008;Dellas et al 2013Dellas et al , 2014Diemer and Stedman 2012;Haring et al 2005;Peng et al 2012;Prangishvili et al 2001Prangishvili et al , 2006Prangishvili and Rice et al 2001Rice et al , 2004Snyder et al 2011;Snyder and Young 2013;Zillig et al 1996). While enrichment cultures have been invaluable in the study of thermophilic viruses, contextual information, such as relative abundance, diversity, and distribution, was mainly unknown.…”

Section: Viral Metagenomicsmentioning

confidence: 99%

Metagenomics of microbial and viral life in terrestrial geothermal environments

Strazzulli

Fusco

Cobucci‐Ponzano

et al. 2017

Rev Environ Sci Biotechnol

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Geothermally heated regions of Earth, such as terrestrial volcanic areas (fumaroles, hot springs, and geysers) and deep-sea hydrothermal vents, represent a variety of different environments populated by extremophilic archaeal and bacterial microorganisms. Since most of these microbes thriving in such harsh biotopes, they are often recalcitrant to cultivation; therefore, ecological, physiological and phylogenetic studies of these microbial populations have been hampered for a long time. More recently, culture-independent methodologies coupled with the fast development of next generation sequencing technologies as well as with the continuous advances in computational biology, have allowed the production of large amounts of metagenomic data. Specifically, these approaches have assessed the phylogenetic composition and functional potential of microbial consortia thriving within these habitats, shedding light on how extreme physico-chemical conditions and biological interactions have shaped such microbial communities. Metagenomics allowed to better understand that the exposure to an extreme range of selective pressures in such severe environments, accounts for genomic flexibility and metabolic versatility of microbial and viral communities, and makes extreme-and hyper-thermophiles suitable for bioprospecting purposes, representing an interesting source for novel thermostable proteins that can be potentially used in several industrial processes.Keywords Hyperthermophiles Á Geothermal environments Á Microbial and viral metagenomics Á CRISPR Á Enzyme discovery BackgroundHot springs populated by extreme thermophiles (T opt : 65-79°C) and hyperthermophiles (T opt [ 80°C) (DeCastro et al. 2016) are very diverse and some of them show combinations of extreme chemo-physical conditions, such as temperature, acidic or alkaline pHs, high pressure, and high concentrations of salts and heavy metals (López-López et al. 2013). As with all studies of environmental microbiology, our understanding of the composition, functional and physiological dynamics, and evolution of extreme-and hyper-thermophilic microbial consortia has lagged A. Strazzulli Á M. Moracci Á P. Contursi

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Section: Viral Metagenomicsmentioning

confidence: 99%

Metagenomics of microbial and viral life in terrestrial geothermal environments

Strazzulli

Fusco

Cobucci‐Ponzano

et al. 2017

Rev Environ Sci Biotechnol

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“…These viruses are revealed as important players in carbon and energy cycling in the oceans and other natural environments and as major agents in the ecology and evolution of their cellular hosts (34,59,235). (iv) The isolation and characterization of new viruses have accelerated (22,207,294). This has been especially important for the archaeal viruses, where the discovery of new viruses and of new virus types had lagged behind bacteriophage discovery (205,213).…”

Section: Introductionmentioning

confidence: 99%

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

Krupovìč

Prangishvili

Hendrix

et al. 2011

Microbiol Mol Biol Rev

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216

176

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SUMMARY Prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet Earth with human beings (among others). However, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. An understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. The vast majority of characterized prokaryotic viruses belong to the order Caudovirales, double-stranded DNA (dsDNA) bacteriophages with tails. Consequently, these viruses have been studied (and reviewed) extensively from both genomic and functional perspectives. However, albeit numerous, tailed phages represent only a minor fraction of the prokaryotic virus diversity. Therefore, the knowledge which has been generated for this viral system does not offer a comprehensive view of the prokaryotic virosphere. In this review, we discuss all families of bacterial and archaeal viruses that contain more than one characterized member and for which evolutionary conclusions can be attempted by use of comparative genomic analysis. We focus on the molecular mechanisms of their genome evolution as well as on the relationships between different viral groups and plasmids. It becomes clear that evolutionary mechanisms shaping the genomes of prokaryotic viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the life cycle. We also point out that horizontal gene transfer is not equally prevalent in different virus families and is not uniformly unrestricted for diverse viral functions.

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“…While there have been few quantitative analyses of the relative abundance of different virus-like morphotypes in archaeal-rich environments, electron microscopy studies of samples from terrestrial hot springs suggest that spindles, filaments, rods and spheres predominate [8,9], while other morphotypes are much less common. Similarly, spindle-shaped and spherical virus-like particles (VLPs) dominate in hypersaline environments [6,10,11].…”

Section: Remarkable Diversitymentioning

confidence: 99%

Archaeal viruses—novel, diverse and enigmatic

Peng

Garrett

She

2012

Sci. China Life Sci.

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Recent research has revealed a remarkable diversity of viruses in archaeal-rich environments where spindles, spheres, filaments and rods are common, together with other exceptional morphotypes never recorded previously. Moreover, their double-stranded DNA genomes carry very few genes exhibiting homology to those of bacterial and eukaryal viruses. Studies on viral life cycles are still at a preliminary stage but important insights are being gained especially from microarray analyses of viral transcripts for a few model virus-host systems. Recently, evidence has been presented for some exceptional archaealnspecific mechanisms for extra-cellular morphological development of virions and for their cellular extrusion. Here we summarise some of the recent developments in this rapidly developing and exciting research area. virus morphotypes, diversity and evolution, life cycle, temporal regulation, cellular extrusion mechanism

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Viruses in acidic geothermal environments of the Kamchatka Peninsula

Cited by 39 publications

References 33 publications

Metagenomics of microbial and viral life in terrestrial geothermal environments

Metagenomics of microbial and viral life in terrestrial geothermal environments

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

Archaeal viruses—novel, diverse and enigmatic

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