Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics

Abstract

Diversity of viruses infecting non‐extremophilic archaea has been grossly understudied. This is particularly the case for viruses infecting methanogenic archaea, key players in the global carbon biogeochemical cycle. Only a dozen of methanogenic archaeal viruses have been isolated so far. In the present study, we implemented an original coupling between stable isotope probing and complementary shotgun metagenomic analyses to identify viruses of methanogens involved in the bioconversion of formate, which was used as the sole carbon source in batch anaerobic digestion microcosms. Under our experimental conditions, the microcosms were dominated by methanogens belonging to the order Methanobacteriales (Methanobacterium and Methanobrevibacter genera). Metagenomic analyses yielded several previously uncharacterized viral genomes, including a complete genome of a head‐tailed virus (class Caudoviricetes, proposed family Speroviridae, Methanobacterium host) and several near‐complete genomes of spindle‐shaped viruses. The two groups of viruses are predicted to infect methanogens of the Methanobacterium and Methanosarcina genera and represent two new virus families. The metagenomics results are in good agreement with the electron microscopy observations, which revealed the dominance of head‐tailed virus‐like particles and the presence of spindle‐shaped particles. The present study significantly expands the knowledge on the viral diversity of viruses of methanogens.

A global virome of methanogenic archaea highlights novel diversity and adaptations to the gut environment

“…1). Finally, we added 44 MGE sequences assigned to methanogenic hosts in the IMG/VR database 65 and 38 MGEs of methanogenic archaea from the NCBI database identi ed in previous studies 29,31,33,37,43,54,[77][78][79] ("known MGEs of methanogens", Fig. 1).…”

“…Methylarchaeales 18,19 ), in the Methanotecta (Methanonatronarchaeia 20 , Archaeoglobales 21 , Methanoliparales 16 , Metheno orentales 22 ), in the Diaforarchaea (Methanomassiliicoccales 23 ) and in the Acherontia (Nuwarchaeales_NM3 16 , Methanofastidiosa 24 ). Methanogenic archaea thrive in diverse arti cial and natural anoxic environments covering an extensive range of salinity and temperatures: freshwater and saline sediments 20,25,26 , peatlands 27 , terrestrial aquifers 28 , hydrothermal vents 29,30 , biogas reactors 31,32 , digesters [33][34][35][36][37] , wastewater treatment plants [38][39][40][41][42] , oil facilities 43 and coal seam 44 . Methanogens contribute to climate change through the production of a powerful greenhouse gas, participate in the complete degradation of organic matter in many anoxic environments through their interaction with fermentative bacteria, and are used in industry to transform biowaste into biogas.…”

Viral DNA SIP: the isotopic composition of virions is correlated with that of the substrate used for host growth

“…Stable Isotope Probing (SIP) (1) has been recently employed in viral ecology to identify viruses infecting hosts with specific metabolisms (e.g. (2-7)), such as ammonia oxidation (6), methane oxidation (3) or methanogenesis (7), and it is emerging as a promising approach. Indeed, since all viruses depend on a host for virion production, a link between the isotopic compositions of hosts and the virions they produce is expected.…”

“…By contrast, DNA SIP for the study of host-virus interactions has been directly applied to microbial communities (2)(3)(4)6), without being validated on simple biological models. Moreover, either the total DNA (3,6) or the cellular DNA (7) has been used, likely due to the difficulty of obtaining sufficient amounts of viral DNA. In principle, the application of SIP to viral DNA should be possible if enough material is obtained.…”

“…g . (2–7)), such as ammonia oxidation (6), methane oxidation (3) or methanogenesis (7), and it is emerging as a promising approach. Indeed, since all viruses depend on a host for virion production, a link between the isotopic compositions of hosts and the virions they produce is expected.…”