MetSV, a novel archaeal lytic virus targeting Methanosarcina strains
Weidenbach K, Nickel L, Neve H, Alkhnbashi OS, Künzel S, Kupczok A, Bauersachs T, Cassidy L, Tholey A, Backofen R, Schmitz RA.
A novel archaeal lytic virus targeting species of the genus Methanosarcina was isolated using Methanosarcina mazei strain Gö1 as host. Due to its spherical morphology the virus was designated Methanosarcinaspherical virus (MetSV). Molecular analysis demonstrated that MetSV contains double stranded linear DNA with a genome size of 10,567 bp containing 22 open reading frames (ORFs) all oriented in the same direction. Functions were predicted for some of these ORFs, i. e. like DNA polymerase, ATPase, DNA-binding protein, as well as envelope (structural) protein. MetSV-derived spacers in CRISPR loci were detected in several published Methanosarcina draft genomes using bioinformatic tools, revealing the potential PAM motif (TTA/T). Transcription and expression of several predicted viral ORFs were validated by RT-PCR, PAGE analysis and LC-MS based proteomics. Analysis of core lipids by APCI mass spectrometry showed that MetSV and M. mazei both contain archaeol and glycerol dialkyl glycerol tetraether without cyclopentane moiety (GDGT-0). The MetSV host range is limited to Methanosarcina strains growing as single cells (M. mazei, M. bakeri and M. soligelidi). In contrast, strains growing as sarcina-like aggregates were apparently protected from infection. Heterogeneity related to morphology phases in M. mazei cultures allowed acquisition of resistance to MetSV after challenge by growing as sarcina-like aggregates. CRISPR/Cas mediated resistance was excluded since neither of the two CRISPR arrays showed MetSV-derived spacer acquisition. Based on these findings, we propose that changing the morphology from single cells to sarcina-like aggregates upon rearrangement of the envelope structure prevents infection and subsequent lysis by MetSV.IMPORTANCE Methanoarchaea are among the most abundant organisms on the planet since they are present in high numbers in major anaerobic environments. They convert various carbon sources e.g. acetate, methylamines or methanol to methane and carbon dioxide, thus they have a significant impact on the emission of major greenhouse gases. Today very little is known about viruses specifically infecting methanoarchaea, which most probably impact the abundance of methanoarchaea in microbial consortia. Here we characterize the first identified Methanosarcina infecting virus (MetSV) and show a mechanism for acquiring resistance against MetSV. Based on our results we propose that growth as sarcina-like aggregates prevents infection and subsequent lysis. These findings allow new insights into virus-host relationship in methanogenic community structures, their dynamics and their phase heterogeneity. Moreover, the availability of a specific virus provides new possibilities to deepen our knowledge on defence mechanisms of potential hosts and offers tools for genetic manipulation.