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This is a protocol from: Stedman,K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6:The isolation of viruses infecting Archaea.Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7 Please see the published manuscript for additional information.

This is a protocol from: Stedman,K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6:The isolation of viruses infecting Archaea.Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7 Please see the published manuscript for additional information.

These are protocols from: Stedman,K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6:The isolation of viruses infecting Archaea.Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7 Please see the published manuscript for additional information.

This is a protocol from: Stedman,K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6:The isolation of viruses infecting Archaea.Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7 Please see the published manuscript for additional information.

This protocol is based on Schleper et al. (1992) as modified by Stedman et al. (2003). This is a protocol from: Stedman,K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6:The isolation of viruses infecting Archaea.Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7 Please see the published manuscript for additional information.

This protocol is based on Schleper et al. (1992) as modified by Stedman et al. (2003). This is a protocol from: Stedman,K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6:The isolation of viruses infecting Archaea.Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7 Please see the published manuscript for additional information.

This is a protocol from: Stedman,K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6:The isolation of viruses infecting Archaea.Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7 Please see the published manuscript for additional information.

The following methods are basically method “A” of Zillig et al. (1994) and were described recently in detail by Prangishvili (2006). These methods consist of enrichment cultures followed by host isolation and screening for virus production in both these isolates and enrichment cultures. These techniques are very similar to those used for bacteriophages, with the major exception being the extreme growth conditions (80˚C, pH 3). This is a protocol from: Stedman, K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6: The isolation of viruses infecting Archaea. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7 Please see the published manuscript for additional information.

Members of the haloarchaeal genera Halosarcina and Halogeometricum (family Halobacteriaceae) are closely related to each other and show 96.6-98 % 16S rRNA gene sequence similarity. This is higher than the accepted threshold value (95 %) to separate two genera, and a taxonomic study using a polyphasic approach of all four members of the two genera was conducted to clarify their relationships. Polar lipid profiles indicated that Halogeometricum rufum RO1-4(T), Halosarcina pallida BZ256(T) and Halosarcina limi RO1-6(T) are related more to each other than to Halogeometricum borinquense CGMCC 1.6168(T). Phylogenetic analyses using the sequences of three different genes (16S rRNA gene, rpoB' and EF-2) strongly supported the monophyly of these four species, showing that they formed a distinct clade, separate from the related genera Halopelagius, Halobellus, Haloquadratum, Haloferax and Halogranum. The results indicate that the four species should be assigned to the same genus, and it is proposed that Halosarcina pallida and Halosarcina limi be transferred to the genus Halogeometricum as Halogeometricum pallidum comb. nov. (type strain, BZ256(T) = KCTC 4017(T) = JCM 14848(T)) and Halogeometricum limi comb. nov. (type strain, RO1-6(T) = CGMCC 1.8711(T) = JCM 16054(T)).

BackgroundHaloquadratum walsbyi commonly dominates the microbial flora of hypersaline waters. Its cells are extremely fragile squares requiring >14%(w/v) salt for growth, properties that should limit its dispersal and promote geographical isolation and divergence. To assess this, the genome sequences of two isolates recovered from sites at near maximum distance on Earth, were compared.Principal findingsBoth chromosomes are 3.1 MB in size, and 84% of each sequence was highly similar to the other (98.6% identity), comprising the core sequence. ORFs of this shared sequence were completely synteneic (conserved in genomic orientation and order), without inversion or rearrangement. Strain-specific insertions/deletions could be precisely mapped, often allowing the genetic events to be inferred. Many inferred deletions were associated with short direct repeats (4-20 bp). Deletion-coupled insertions are frequent, producing different sequences at identical positions. In cases where the inserted and deleted sequences are homologous, this leads to variant genes in a common synteneic background (as already described by others). Cas/CRISPR systems are present in C23(T) but have been lost in HBSQ001 except for a few spacer remnants. Numerous types of mobile genetic elements occur in both strains, most of which appear to be active, and with some specifically targetting others. Strain C23(T) carries two ∼6 kb plasmids that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters commonly found in haloarchaea.ConclusionsDeletion-coupled insertions show that Hqr. walsbyi evolves by uptake and precise integration of foreign DNA, probably originating from close relatives. Change is also driven by mobile genetic elements but these do not by themselves explain the atypically low gene coding density found in this species. The remarkable genome conservation despite the presence of active systems for genome rearrangement implies both an efficient global dispersal system, and a high selective fitness for this species.