Integrated mobile genetic elements in Thaumarchaeota

Abstract

Summary To explore the diversity of mobile genetic elements (MGE) associated with archaea of the phylum Thaumarchaeota, we exploited the property of most MGE to integrate into the genomes of their hosts. Integrated MGE (iMGE) were identified in 20 thaumarchaeal genomes amounting to 2 Mbp of mobile thaumarchaeal DNA. These iMGE group into five major classes: (i) proviruses, (ii) casposons, (iii) insertion sequence‐like transposons, (iv) integrative‐conjugative elements and (v) cryptic integrated elements. The majority of the iMGE belong to the latter category and might represent novel families of viruses or plasmids. The identified proviruses are related to tailed viruses of the order Caudovirales and to tailless icosahedral viruses with the double jelly‐roll capsid proteins. The thaumarchaeal iMGE are all connected within a gene sharing network, highlighting pervasive gene exchange between MGE occupying the same ecological niche. The thaumarchaeal mobilome carries multiple auxiliary metabolic genes, including multicopper oxidases and ammonia monooxygenase subunit C (AmoC), and stress response genes, such as those for universal stress response proteins (UspA). Thus, iMGE might make important contributions to the fitness and adaptation of their hosts. We identified several iMGE carrying type I‐B CRISPR‐Cas systems and spacers matching other thaumarchaeal iMGE, suggesting antagonistic interactions between coexisting MGE and symbiotic relationships with the ir archaeal hosts.

The global distribution and evolutionary history of the pT26‐2 archaeal plasmid family

“…and and Table ). These proteins are also encoded by MGEs from other families in Thermococcales, such as the plasmid pTN3 (Gaudin et al ., ), the virus TPV1 (Gorlas et al ., ) and the integrated plasmid TKV1 (Fukui et al ., ) and by MGEs from other archaeal lineages (Krupovič et al ., ; Krupovic et al ., ). Moreover, one or several genes encoding MCM proteins are present in all archaeal genomes and correspond to chromosomal replicative helicases (Raymann et al ., ).…”

“…Finally, four plasmids of the pT26‐2 family present in Methanococcales encode a new family of distantly related MCM‐like proteins (Fig. and Table ), previously identified in bacteria (Mir‐Sanchis et al ., ) and Thaumarchaea (Krupovic et al ., ) MGEs. Notably, the bacterial MGEs also encode a serine recombinase downstream of the MCM‐like replication gene, responsible for the integration activity.…”

Spindle-shaped viruses infect marine ammonia-oxidizing thaumarchaea

“…In particular, the pPolB of NSVs is shared with several groups of archaeal viruses and nonviral mobile genetic elements, which, like NSV, have linear genomes with terminal inverted repeats. These include the haloarchaeal spindle-shaped (genus Salterprovirus) and pleomorphic (family Pleolipoviridae, genus Gammapleolipovirus) viruses His1 (41) and His2 (30), respectively; hyperthermophilic bottle-shaped (family Ampullaviridae) (25) and ellipsoid (family Ovaliviridae) (42) viruses; and casposons, which integrate into the genomes of diverse thaumarchaea (43,44).…”

Diverse viruses carrying genes for microbial extremotolerance in the Atacama Desert hyperarid soil

“…Notably, we also identified a putative thaumarchaeal virus matched to eight thaumarchaeal MAGs found across all three sampling sites. While recent studies have isolated a novel family of viruses infecting marine Thaumarchaeota(52), and a provirus in order Caudovirales in mesophilic soil Nitrososphaera viennensis(53,54), very little is known about lytic viruses infecting soil Thaumarchaeota, despite their ubiquity and abundance in many terrestrial ecosystems(55,56).The abundance and diversity of the viruses in the Atacama Desert soils are surprising considering that the microorganisms that inhabit these soils are low in both biodiversity and biomass. Typically, groups of viruses infecting the same host exchange genetic materials, forming genotypic clusters.…”