Archaeal Extrachromosomal Genetic Elements

Wang, Haina; Peng, Nan; Shah, Samir A.; Huang, Li; She, Qunxin

doi:10.1128/mmbr.00042-14

Cited by 65 publications

(70 citation statements)

References 294 publications

(428 reference statements)

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“…Viral metagenomes indicated the predominance of a lytic lifestyle as suggested by the significant proportion of lys-like genes encoding for proteins involved in host cell lysis (López-López et al 2013;Schoenfeld et al 2008). This evidence is in contrast to the cultured thermophilic crenarchaeal viruses, most of which are non-lytic (Contursi et al 2006;Prangishvili 2013;Snyder et al 2015;Wang et al 2015b). The evidence of the replacement of cellular genes by non-orthologous viral genes (i.e.…”

Section: Yellowstone National Park Usamentioning

confidence: 85%

“…A common feature to these two sites is the predominance of the Lipothrixviridae (Prangishvili 2013;Snyder et al 2015;Wang et al 2015b) viral sequences, representing the 43.5 and 81.7%, respectively (Gudbergsdottir et al 2016). Despite the high abundance of contigs assigned to this family, the absence of a complete lipothrixviral genome in the metagenomes could indicate the presence of multiple related but not identical genomes of similar abundance.…”

Section: Phlegraean Fields Italymentioning

confidence: 99%

“…Conversely, the IS3-13 site is mostly populated by Ampullaviridae members and constitutes only a small percentage of all the viral sequences in the former sample. Furthermore, sequences referable to Bicaudoviridae one of the most widely represented crenarchaeal family in hot springs (Wang et al 2015b), are absent in IS2-5S metagenome (Prangishvili 2013;Snyder et al 2015). Interestingly, the longest contig in Is3-13 metagenome was assigned to a near complete Acidanius-bottle-shaped (ABV)-like genome (Haring et al 2005).…”

Section: Icelandmentioning

confidence: 99%

“…At present, one order and 10 families (Fuselloviridae, Bicaudaviridae, Ampullaviridae, Clavaviridae, Guttaviridae, Lipothrixviridae, Rudiviridae, Globuloviridae, Myoviridae, Siphoviridae) of archaeal viruses have been documented (Fusco et al 2015a, b;Prangishvili 2013;Snyder et al 2015;Wang et al 2015b). Until relatively recent times, the only methodology available to study these viruses was through the cultivation of their hosts (López-López et al 2013).…”

Section: Viral Metagenomicsmentioning

confidence: 99%

“…Common to both the sites are contigs assigned to the Rudiviridae family (Prangishvili 2013;Snyder et al 2015;Wang et al 2015b) and viral sequences assigned to Pyrobaculum spherical virus (PSV) (Haring et al 2004) and Thermoproteus tenax virus 1 (TTV1) (Neumann et al 1989) and accordingly the metagenomes also contain sequences assigned to their archaeal Pyrobaculum and Thermoproteus tenax hosts (Menzel et al 2015).…”

Section: Icelandmentioning

confidence: 99%

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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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