# Haloarchaea.com > for everything haloarchaeal ## Posts - [Black rust bandits: corrosive methanogens!](https://haloarchaea.com/2026/03/18/black-rust-bandits-corrosive-methanogens/): 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 […] - [pL6-family plasmids of Haloquadratum](https://haloarchaea.com/2025/02/03/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 […] - [A detective story using genomics to find the parent strain of Hbt. salinarum NRC-1 and R1](https://haloarchaea.com/2023/07/28/a-detective-story-using-genomics-to-find-the-parent-strain-of-hbt-salinarum-nrc-1-and-r1/): Many labs have worked with Halobacterium salinarum, and they either use the R1 strain or the NRC-1 strain. When the genomes of these two strains were reported in 2008 (Pfeiffer et al.), it showed they are so similar in sequence that they must have derived from the same isolate, but for various reasons it was not possible to identify that isolate. Here we used publicly available sequence data to hunt down the parent. See https://doi.org/10.1002/mbo3.1365. This is not a simple BLASTn comparison but rather a comprehensive analysis and includes a speculative outline of how the two strains ended up as […] - [Genome sequence of Hardyhisp2, a Gammapleolipovirus infecting Har. hispanica.](https://haloarchaea.com/2022/07/22/genome-sequence-of-hardyhisp2-a-gammapleolipovirus-infecting-har-hispanica/): Published in Microbial Resource Announcements in May, 2021 (doi: 10.1128/MRA.00226-21) this describes the genome of Hardyhisp2, a virus isolated in my lab way back in 1998! It came from a water sample of the hypersaline Lake Hardy, Victoria, Australia. As seen in the dot plot (above left) and genome map comparison (above right), the 16,133 bp linear dsDNA genome shows strong sequence similarity to the type species of gammapleolipovirus, His2. The most disparate gene appears to be the one encoding spike protein (VP1 spike), which is used by the virus for cell attachment, but both Hardyhisp2 and His2 infect the […] - [A novel halovirus, Hardycor1](https://haloarchaea.com/2021/01/29/halovirus-hardycor1/): In the second paper of the series, we describe the genome of a siphovirus that infects Halorubrum coriense. It was isolated from Lake Hardy way back in 1998, and the genome shows it is quite distinct from other reported caudoviruses of haloarchaea. The graphical abstract above shows a picture of Hardy Lake in the background, and a map of the Hardycor1 genome in the foreground. We also observed a number of active proviruses occurred in our stocks of this virus and other haloviruses, highlighting the dynamic nature of proviruses in haloarchaea. See the paper here, at doi.org/10.3390/genes12020149. - [Review: Cultivation of halophilic archaea (class Halobacteria)](https://haloarchaea.com/2021/01/12/review-cultivation-of-halophilic-archaea-class-halobacteria/): Wonderful review with Heng-Lin Cui on the cultivation of haloarchaea published in MLST at https://link.springer.com/article/10.1007%2Fs42995-020-00087-3. The supplementary table has an extensive list of media used. - [hypermotility in Haloferax](https://haloarchaea.com/2020/12/31/hypermotility-in-haloferax/) - [Two New HF1-like Haloviruses described](https://haloarchaea.com/2020/04/09/two-new-hf1-like-haloviruses-described/): Serpecor1 and Hardycor2 are tailed viruses infecting the haloarchaeon Halorubrum coriense, and were recovered from widely separated hypersaline lakes in Australia way back in the late 1990s. They are similar to HF1 and add to an expanding group of viruses within a newly proposed genus Haloferacalesvirus. Read all about them in Genes at https://www.mdpi.com/2073-4425/11/4/405 - [Transcription of Halovirus His2 and its host.](https://haloarchaea.com/2020/04/04/transcription-of-halovirus-his2-and-its-host/): Our microarray study of the transcription of the gammapleolipovirus His2 and its host Har. hispanica has just been published in MicrobiologyOpen. The direct link to it is https://doi.org/10.1002/mbo3.1016. Viral gene expression occurred in three main phases (early, middle, and late), and by 4.5 hr p.i. the majority of genes were actively transcribed. Eighty host genes were differentially regulated ≥twofold post-infection. - [Halobacterium salinarum (DSM 3754T) comparison to strains R1 and NRC‐1](https://haloarchaea.com/2019/12/04/halobacterium-salinarum-dsm-3754t-comparison-to-strains-r1-and-nrc%e2%80%901/): Friedhelm Pfeiffer, Gerald Losensky, Anita Marchfelder, Bianca Habermann and Mike Dyall‐Smith Finally the paper was online today in MicrobiologyOpen at (https://onlinelibrary.wiley.com/doi/full/10.1002/mbo3.974). It is a detailed description of the genome of Hbt. salinarum strain 91‐R6 (DSM 3754), which is the type strain of the genus. We have compared it to the two well-studied laboratory strains R1 and NRC-1, which were sequenced many years ago. The type strain has only rarely been studied, and as Aharon Oren said in 2012, “it is to be regretted that no genomic information is available for the nomenclatural type” – but now it is available for […] - [Genome of the type strain of Hbt. salinarum](https://haloarchaea.com/2019/07/13/genome-of-the-type-strain-of-hbt-salinarum/): In 2012, Aharon Oren wrote a review on the family Halobacteriaceae, where he pointed out with some surprise that the “type species of the type genus of the family and the order” had not yet been sequenced. This was despite the genomes of strains R1 and NRC-1 having been reported years previously. I am happy to say that today this deficit has been remedied, as described in our recent publication in Microbial Resource Announcements, and sequence submissions to Genbank, under accessions  CP038631 (chromosome), CP038632 (pHSAL1), and CP038633 (pHSAL2). Assembly of these replicons was not a straightforward task, as there were very large repeats, and […] - [ChaoS9 - a novel halovirus](https://haloarchaea.com/2019/03/10/chaos9-a-novel-halovirus/): The paper describing this new virus is now published and can be found at: https://www.mdpi.com/2073-4425/10/3/194 - [Halovirus phiH1](https://haloarchaea.com/2018/10/18/hello-world/): The genome sequence of the classic model halovirus phiH1 has just been published as part of a special thematic issue of Genes. Get the paper here.  There is more to this story (click ‘read more’). - [PL6-like plasmids of Haloquadratum](https://haloarchaea.com/2018/10/15/the-pl6-like-plasmid-paper/): This study describes the recovery of new Haloquadratum waslbyi isolates and focuses on a family of small plasmids that they commonly carry, which appear to be either haloviruses or at least very closely related to haloviruses. Go to the paper here. Read more about this project (click ‘read more’). ## Pages - [Publications (last 6 years)](https://haloarchaea.com/blog/publications/): Kleinbub S, Braymer JJ, Pfeiffer F, Dyall-Smith M, Spirgath K, Alfaro- Espinoza G, Koerdt A. From genes to Black Rust: genomic insights into corrosive methanogens. FEMS Microbes. 2025 Nov 17;6:xtaf018. doi: 10.1093/femsmc/xtaf018. PMID: 41333139; PMCID: PMC12667266. Dyall-Smith M. Archaeal symbioses all the way down. Nat Microbiol. 2025 Nov;10(11):2651-2652. doi: 10.1038/s41564-025-02158-6. PMID: 41116033. Di Cianni N, Bolsinger S, Brendel J, Raabe M, König S, Mitchell L, Bischler T, Gräfenhan T, Read C, Erdmann S, Allers T, Walther P, Urlaub H, Dyall-Smith M, Pfeiffer F, Marchfelder A. Provirus deletion from Haloferax volcanii affects motility, stress resistance, and CRISPR RNA expression. Microlife. 2025 […] - [Halohandbook](https://haloarchaea.com/blog/halohandbook/): The now outdated Halohandbook can still be downloaded from HERE. I recently (Feb, 2025) made a slight revision to correct the description of halovirus His2, remove some typographical errors, and add links to the pages of the table of contents. Since 2021, there is a new resource being developed, Archaea.bio (https://archaea.bio/), that has included the Halohandbook in its archive, and should provide updated and expanded protocols repository for methods relating to haloarchaea.   - [Blog](https://haloarchaea.com/blog/) - [About](https://haloarchaea.com/about/): You might be an artist who would like to introduce yourself and your work here or maybe you’re a business with a mission to describe. - [Home](https://haloarchaea.com/home/): This page has no content - [Bioinformatics Resources](https://haloarchaea.com/bioinformatics/): GALAXY: GENE, GENOME COMPARISON and ANNOTATION MICROBIAL GROWTH MEMBRANE TOPOLOGY, SIGNAL SEQUENCES, ETC. PLASMIDS PROTEIN STRUCTURE SEARCH ENGINES. TREES and PHYLOGENY VIRUS GENES, VIRUS DEFENCE GENES and ANNOTATIONS   ## Optional - [Agent (MCP protocol)](websites-agents.hostinger.com/haloarchaea.com/mcp) [comment]: # (Generated by Hostinger Tools Plugin)