Mike Dyall-Smith’s Haloblog – for all things haloarchaeal

  • Black rust bandits: corrosive methanogens!

    genome comparison of Mcc. maripaludis strains

    In a recently published study of a metal corrosive strain of Methanococcus maripaludis (FEMS Microbes; Kleinbub et al., 2025) the genes involved in this process and the functions of their proteins were examined. What was surprising to me was how unstable the corrosion-related genes are in the host! Even when grown under conditions that strongly select functional metal corrosion it was estimated that only a third of cells in a population retained the genes. If grown on hydrogen, where electrons from iron are not needed, then all cells in a population lose the corrosion genes –  entirely. Gone. The mechanism of gene loss itself is clear, as they are all found in a small genetic “island” (the MIC island seen at about 8 o’clock on the figure) that is flanked by 221 bp direct repeats. Homologous recombination between the repeats then leaves just one repeat copy and no intervening genes. But how do cells ever get these genes back when they need them? That remains an open question.

  • pL6-family plasmids of Haloquadratum

    In two earlier studies of Haloquadratum walsbyi [1,2], Australian isolates were often found to harbor small cryptic plasmids of the pL6-family, approximately 6 kb in size (see diagram above). Only five examples of these plasmids had been previously described but they are peculiar because they show no homology to other haloarchaeal plasmids yet display a highly conserved gene arrangement. Intriguingly, they encode a replicase very similar to those found in betapleolipoviruses. In the current study [3], fifteen additional plasmids were reconstructed by mining the metagenomes of  hypersaline sites in four countries: Argentina, Australia, Puerto Rico, and Spain. Overall, the average plasmid size was 6002 bp, and the gene arrangement remained well conserved. Many metagenomic CRISPR spacers were found to match sequences in the fifteen reconstructed plasmids, indicating frequent invasion of haloarchaea. A surprise finding was that strand-specific metatranscriptome (RNA-seq) data from other published studies could be used to map transcripts produced by two plasmids, confirming the active transcription of coding sequences and also high levels of counter-transcripts. It remains unclear whether these fascinating, highly conserved plasmids are viruses or perhaps virus satellites, but they are widespread and probably extend beyond Haloquadratum.