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.
Highlights
Methanogenesis, biogenic methane formation, is a metabolic trait found exclusively in certain members of the Archaea
The high degree of protein similarity that was deduced from the genomic sequence to other M. bourgensis strains (MS2T or MAB1), for example, those involved in energy metabolism, supports this notion
The Blf4 virus consists of an isometric icosahedral head and a non-contractile tail, which suggests that it belongs to the Siphoviridae virus family
Summary
Methanogenesis, biogenic methane formation, is a metabolic trait found exclusively in certain members of the Archaea. Cultivated methanogens are currently classified into seven orders, Methanococcales, Methanopyrales, Methanocellales, Methanobacteriales, Methanomassiliicoccales, Methanosarcinales, and Methanomicrobiales [6] Of the latter two, the genera Methanosarcina and Methanoculleus are abundant in biogas plants fed with energy crops [7,8], which indicates their crucial role in the process. In addition to defense mechanisms against foreign nucleic acids, such as restriction– modification (RM) systems, prokaryotes often have clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, which are the adaptive prokaryotic immunity They are present in most sequenced archaeal genomes (>90%). The virus belongs to the Siphoviridae, and is the first one described to infect a member of the Methanomicrobiales, expanding the repertoire of isolated viruses infecting methanogens
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