Characterization of Blf4, an Archaeal Lytic Virus Targeting a Member of the Methanomicrobiales

Abstract

Today, the number of known viruses infecting methanogenic archaea is limited. Here, we report on a novel lytic virus, designated Blf4, and its host strain Methanoculleus bourgensis E02.3, a methanogenic archaeon belonging to the Methanomicrobiales, both isolated from a commercial biogas plant in Germany. The virus consists of an icosahedral head 60 nm in diameter and a long non-contractile tail of 125 nm in length, which is consistent with the new isolate belonging to the Siphoviridae family. Electron microscopy revealed that Blf4 attaches to the vegetative cells of M. bourgensis E02.3 as well as to cellular appendages. Apart from M. bourgensis E02.3, none of the tested Methanoculleus strains were lysed by Blf4, indicating a narrow host range. The complete 37 kb dsDNA genome of Blf4 contains 63 open reading frames (ORFs), all organized in the same transcriptional direction. For most of the ORFs, potential functions were predicted. In addition, the genome of the host M. bourgensis E02.3 was sequenced and assembled, resulting in a 2.6 Mbp draft genome consisting of nine contigs. All genes required for a hydrogenotrophic lifestyle were predicted. A CRISPR/Cas system (type I-U) was identified with six spacers directed against Blf4, indicating that this defense system might not be very efficient in fending off invading Blf4 virus.

Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction

“…114, incorporate in their sequence integrated proviruses of the Siphoviridae family. While most Siphoviridae are bacteriophages, there’s evidence that some members of the family infect Archaea , including the methanogenic species Methanoculleus bourgensis and Methanobacterium formicicum [ 110 , 111 ]. These members of Siphoviridae are lytic, i.e., do not integrate in the host of the genome; the newly recovered genomes show the existence of lysogenic archaeal Siphoviridae as well.…”

Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing

“…Siphoviridae-like head-tailed viruses have already been reported for methanogenic digesters previously [29,33]. Moreover, a recent study on a Siphoviridae phage, designated Blf4 and isolated from a commercial biogas plant in Germany, also described that this phage infected methanogenic Archaea of the species Methanoculleus bourgensis [58]. Considering the relatively high abundance of Methanoculleus members in AD [19,59,60] and its metabolic relevance, Blf4 and Siphoviridae-like phages infecting members of the genus Methanoculleus genus might profoundly affect their host's abundance and, thus, the efficiency of the entire biogas process.…”

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

“…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.…”