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1. Global Distribution and Diversity of Haloarchaeal pL6-Family Plasmids.

Author

Dyall-Smith, Mike and Pfeiffer, Friedhelm

Subjects
*PLASMIDS, *SALT lakes, *HALOBACTERIUM, *ADENOSINE triphosphatase, *METAGENOMICS
Abstract

Australian isolates of Haloquadratum walsbyi, a square-shaped haloarchaeon, often harbor small cryptic plasmids of the pL6-family, approximately 6 kb in size, and five examples have been previously described. These plasmids exhibit a highly conserved gene arrangement and encode replicases similar to those of betapleolipoviruses. To assess their global distribution and recover more examples for analysis, fifteen additional plasmids were reconstructed from the metagenomes of seven hypersaline sites across four countries: Argentina, Australia, Puerto Rico, and Spain. Including the five previously described plasmids, the average plasmid size is 6002 bp, with an average G+C content of 52.5%. The tetramers GGCC and CTAG are either absent or significantly under-represented, except in the two plasmids with the highest %G+C. All plasmids share a similar arrangement of genes organized as outwardly facing replication and ATPase modules, but variations were observed in some core genes, such as F2, and some plasmids had acquired accessory genes. Two plasmids, pCOLO-c1 and pISLA-c6, shared 92.7% nt identity despite originating from Argentina and Spain, respectively. Numerous metagenomic CRISPR spacers matched sequences in the fifteen reconstructed plasmids, indicating frequent invasion of haloarchaea. Spacers could be assigned to haloarchaeal genera by mapping their associated direct repeats (DR), with half of these matching Haloquadratum. Finally, strand-specific metatranscriptome (RNA-seq) data could be used to demonstrate the active transcription of two pL6-family plasmids, including antisense transcripts. [ABSTRACT FROM AUTHOR]

Published
2024
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2. Proposed minimal standards for description of new taxa of the class Halobacteria

Author

Cui, Heng-Lin, primary, Hou, Jing, additional, Amoozegar, Mohammad Ali, additional, Dyall-Smith, Mike L., additional, de la Haba, Rafael R., additional, Minegishi, Hiroaki, additional, Montalvo-Rodriguez, Rafael, additional, Oren, Aharon, additional, Sanchez-Porro, Cristina, additional, Ventosa, Antonio, additional, and Vreeland, Russell H., additional

Published
2024
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4. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author

Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.

Published
2021
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5. Whole‐genome comparison between the type strain of Halobacterium salinarum (DSM 3754T) and the laboratory strains R1 and NRC‐1

Author

Pfeiffer, Friedhelm, Losensky, Gerald, Marchfelder, Anita, Habermann, Bianca, Dyall‐Smith, Mike, Pfeiffer, Friedhelm, Losensky, Gerald, Marchfelder, Anita, Habermann, Bianca, and Dyall‐Smith, Mike

Abstract

Halobacterium salinarum is an extremely halophilic archaeon that is widely distributed in hypersaline environments and was originally isolated as a spoilage organism of salted fish and hides. The type strain 91‐R6 (DSM 3754T) has seldom been studied and its genome sequence has only recently been determined by our group. The exact relationship between the type strain and two widely used model strains, NRC‐1 and R1, has not been described before. The genome of Hbt. salinarum strain 91‐R6 consists of a chromosome (2.17 Mb) and two large plasmids (148 and 102 kb, with 39,230 bp being duplicated). Cytosine residues are methylated (m4C) within CTAG motifs. The genomes of type and laboratory strains are closely related, their chromosomes sharing average nucleotide identity (ANIb) values of 98% and in silico DNA–DNA hybridization (DDH) values of 95%. The chromosomes are completely colinear, do not show genome rearrangement, and matching segments show <1% sequence difference. Among the strain‐specific sequences are three large chromosomal replacement regions (>10 kb). The well‐studied AT‐rich island (61 kb) of the laboratory strains is replaced by a distinct AT‐rich sequence (47 kb) in 91‐R6. Another large replacement (91‐R6: 78 kb, R1: 44 kb) codes for distinct homologs of proteins involved in motility and N‐glycosylation. Most (107 kb) of plasmid pHSAL1 (91‐R6) is very closely related to part of plasmid pHS3 (R1) and codes for essential genes (e.g. arginine‐tRNA ligase and the pyrimidine biosynthesis enzyme aspartate carbamoyltransferase). Part of pHS3 (42.5 kb total) is closely related to the largest strain‐specific sequence (164 kb) in the type strain chromosome. Genome sequencing unraveled the close relationship between the Hbt. salinarum type strain and two well‐studied laboratory strains at the DNA and protein levels. Although an independent isolate, the type strain shows a remarkably low evolutionary difference to the laboratory strains.

Published
2024

6. Halobacterium Hubeiense sp. nov., a Haloarchaeal Species Isolated from a Bore Core Drilled in Hubei Province, PR China

Author

Universidad de Sevilla. Departamento de Microbiología y Parasitología, Ministerio de Ciencia, Innovación y Universidades (MICINN). España, Junta de Andalucía, León León, María José, Sánchez-Porro Álvarez, Cristina, Ruiz de la Haba, Rafael, Pfeiffer, Friedhelm, Dyall-Smith, Mike, Oksanen, Hanna M., Ventosa Ucero, Antonio, Universidad de Sevilla. Departamento de Microbiología y Parasitología, Ministerio de Ciencia, Innovación y Universidades (MICINN). España, Junta de Andalucía, León León, María José, Sánchez-Porro Álvarez, Cristina, Ruiz de la Haba, Rafael, Pfeiffer, Friedhelm, Dyall-Smith, Mike, Oksanen, Hanna M., and Ventosa Ucero, Antonio

Abstract

Eight colonies of live microbes were isolated from an extensively surface-sterilized halite sample which had been retrieved from a depth of 2000 m from a salt mine in the Qianjiang Depression, Hubei Province, PR China. The eight colonies, obtained after 4 weeks of incubation, were named JI20-1T–JI20-8 and JI20-1T was selected as the type strain. The strains have been previously described, including a genomic analysis based on the complete genome for strain JI20-1T and draft genomes for the other strains. In that study, the name Halobacterium hubeiense was suggested, based on the location of the drilling site. Previous phylogenomic analysis showed that strain JI20-1T is most closely related to the Permian isolate Halobacterium noricense from Alpine rock salt. The orthologous average nucleotide identity (orthoANI) and digital DNA–DNA hybridization (dDDH) percentages between the eight strains are 100–99.6% and 99.8–96.4%, respectively. The orthoANI and dDDH values of these strains with respect to the type strains of species of the genus Halobacterium are 89.9–78.2% and 37.3–21.6%, respectively, supporting their placement in a novel extremely halophilic archaeal species. The phylogenomic tree based on the comparison of sequences of 632 core-orthologous proteins confirmed the novel species status for these haloarchaea. The polar lipid profile includes phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, and sulfated galactosyl man-nosyl galactosyl glucosyl diether, a profile compatible with that of Halobacterium noricense. Based on genomic, phenotypic, and chemotaxonomic characterization, we propose strain JI20-1T (=DSM 114402T = HAMBI 3616T) as the type strain of a novel species in the genus Halobacterium, with the name Halobacterium hubeiense sp. nov.

Published
2024

7. Proposed Minimal Standards for Description of New Taxa of the Class Halobacteria

Author

Universidad de Sevilla. Departamento de Microbiología y Parasitología, National Natural Science Foundation of China, National Science and Tech- nology Fundamental Resources Investigation Program of China, Ministerio de Ciencia e Innovación (MICIN). España, Junta de Andalucía, Cui, Heng Lin, Hou, Jing, Amoozegar, Mohammad Ali, Dyall-Smith, Mike L., Ruiz de la Haba, Rafael, Minegishi, Hiroaki, Montalvo Rodríguez, Rafael, Oren, Aharon, Sánchez-Porro Álvarez, Cristina, Ventosa Ucero, Antonio, Vreeland, Russell H., Universidad de Sevilla. Departamento de Microbiología y Parasitología, National Natural Science Foundation of China, National Science and Tech- nology Fundamental Resources Investigation Program of China, Ministerio de Ciencia e Innovación (MICIN). España, Junta de Andalucía, Cui, Heng Lin, Hou, Jing, Amoozegar, Mohammad Ali, Dyall-Smith, Mike L., Ruiz de la Haba, Rafael, Minegishi, Hiroaki, Montalvo Rodríguez, Rafael, Oren, Aharon, Sánchez-Porro Álvarez, Cristina, Ventosa Ucero, Antonio, and Vreeland, Russell H.

Abstract

Halophilic archaea of the class Halobacteria are the most salt-requiring prokaryotes within the domain Archaea. In 1997, minimal standards for the description of new taxa in the order Halobacteriales were proposed. From then on, the taxonomy of the class Halobacteria provides an excellent example of how changing concepts on prokaryote taxonomy and the development of new methods were implemented. The last decades have witnessed a rapid expansion of the number of described taxa within the class Halobacteria coinciding with the era of genome sequencing development. The current members of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteria propose these revisions to the recommended minimal standards and encourage the use of advanced technologies in the taxonomic description of members of the Halobacteria. Most previously required and some recommended minimal standards for the description of new taxa in the class Halobacteria were retained in the present revision, but changes have been proposed in line with the new methodologies. In addition to the 16S rRNA gene, the rpoB′ gene is an important molecular marker for the identification of members of the Halobacteria. Phylogenomic analysis based on concatenated conserved, single-copy marker genes is required to infer the taxonomic status of new taxa. The overall genome relatedness indexes have proven to be determinative in the classification of the taxa within the class Halobacteria. Average nucleotide identity, digital DNA–DNA hybridization, and average amino acid identity values should be calculated for rigorous comparison among close relatives.

Published
2024

9. Iron starvation results in up-regulation of a probable Haloferax volcanii siderophore transporter.

Author

Sailer, Anna-Lena, Jevtic, Zivojin, Stoll, Britta, Wörtz, Julia, Sharma, Kundan, Urlaub, Henning, Dyall-Smith, Mike, Pfeiffer, Friedhelm, Marchfelder, Anita, and Lenz, Christof

Subjects
LIBRARY acquisitions, GROWTH disorders, MASS spectrometry, MOLECULAR docking, CELL morphology
Abstract

The response of the haloarchaeal model organism Haloferax volcanii to iron starvation was analyzed at the proteome level by data-independent acquisition mass spectrometry. Cells grown in minimal medium with normal iron levels were compared to those grown under low iron conditions, with samples being separated into membrane and cytoplasmic fractions in order to focus on import/export processes which are frequently associated with metal homeostasis. Iron starvation not only caused a severe retardation of growth but also altered the levels of many proteins. Using a comprehensive annotated spectral library and data-independent acquisition mass spectrometry (DIA-MS), we found that iron starvation resulted in significant changes to both the membrane and the soluble proteomes of Hfx. volcanii. The most affected protein is the RND family permease HVO_A0467, which is 44-fold enriched in cells grown under iron starvation. The gene HVO_A0467 can be deleted suggesting that it is not essential under standard conditions. Compared to wild type cells the deletion strain shows only slight changes in growth and cell morphologies show no differences. Molecular docking predictions indicated that HVO_A0467 may be an exporter of the siderophore schizokinen for which a potential biosynthesis cluster is encoded in the Hfx. volcanii genome. Together, these findings confirm the importance of iron for archaeal cells and suggest HVO_0467 as a siderophore exporter. [ABSTRACT FROM AUTHOR]

Published
2024
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13. ICTV Virus Taxonomy Profile: Sphaerolipoviridae 2023

Author

Demina, Tatiana A., Dyall-Smith, Mike, Jalasvuori, Matti, Du, Shishen, and Oksanen, Hanna M.

Subjects
taxonomy, virukset, sphaerolipoviridae, systematiikka (biologia), ICTV report
Abstract

Members of the family Sphaerolipoviridae have non-enveloped tailless icosahedral virions with a protein-rich internal lipid membrane. The genome is a linear double-stranded DNA of about 30 kbp with inverted terminal repeats and terminal proteins. The capsid has a pseudo triangulation T=28 dextro symmetry and is built of two major capsid protein types. Spike complexes decorate fivefold vertices. Sphaerolipoviruses have a narrow host range and a lytic life cycle, infecting haloarchaea in the class Halobacteria (phylum Euryarchaeota). This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Sphaerolipoviridae, which is available at ictv.global/report/sphaerolipoviridae. peerReviewed

Published
2023

14. ICTV Virus Taxonomy Profile : Sphaerolipoviridae 2023

Author

Demina, Tatiana, Dyall-Smith, Mike, Jalasvuori, Matti, Du, Shishen, Oksanen, Hanna M, Department of Microbiology, Helsinki Institute of Sustainability Science (HELSUS), Molecular and Integrative Biosciences Research Programme, and Molecular Principles of Viruses

Subjects
Sphaerolipoviridae, 11832 Microbiology and virology, ICTV Report, Taxonomy
Published
2023

15. ICTV Virus Taxonomy Profile : Simuloviridae 2023

Author

Liu, Ying, Du, Shishen, Chen, Xiangdong, Dyall-Smith, Mike, Jalasvuori, Matti, and Oksanen, Hanna M.

Subjects
taxonomy, virukset, systematiikka (biologia), simuloviridae, ICTV report
Abstract

The family Simuloviridae includes tailless icosahedral viruses with an internal lipid membrane. The capsid is constructed from two major capsid proteins, both with a single jelly-roll fold. The genome is a circular dsDNA molecule of 16–19 kb. All members infect halophilic archaea in the class Halobacteria (phylum Euryarchaeota) and are temperate viruses, their proviruses residing in host cells as extrachromosomal episomes. Once the lytic life cycle is triggered, production of virions causes cell lysis. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Simuloviridae, which is available at ictv.global/report/simuloviridae. peerReviewed

Published
2023

22. What levels of soil Mn2+ can pulse and legume crops tolerate when grown in rotation with paddy rice?

Author

Haque, K. M. Shamsul, Howitt, Julia A., Dyall-Smith, Mike, Weston, Leslie A., and Eberbach, Philip L.

Subjects
MUNG bean, CROP rotation, PADDY fields, LEGUMES, FAVA bean, WETLAND soils, SOILS, CROP growth
Abstract

Elevated concentrations of manganese (Mn2+) can persist after drainage in soil following wetland rice production, leading to toxicity in subsequent legume crops. To evaluate Mn2+ concentration causing adverse impacts on crop establishment and growth, a controlled environment experiment using hydroponics was designed. Germination and growth of field pea, faba bean and mung bean were evaluated over 21 d with an increase in Mn2+ (0 − 50 mg Mn2+L−1). Germination of all crops was impacted significantly with an increase in concentration of Mn2+. Leaf chlorophyll content as well as all plant growth parameters assessed (dry weight, height) were negatively impacted (p < 0.05) by increasing concentrations of Mn2+. Field peas and faba beans proved more sensitive to Mn2+ than did mung beans at concentrations of 5 − 10 mg L−1. Field pea and faba bean specifically exhibited reduced height (30 − 60% and 4 − 41%, respectively), root length (12 − 30% and 20 − 25%, respectively), and shoot weight (41 − 69% and 47 − 81%, respectively). Mung bean was less impacted in terms of plant height with 23% reduction at 25 mg Mn2+ L−1 and shoot dry weight reduced by 48% at 50 mg Mn2+ L−1. Total chlorophyll content of mung bean was severely affected (86% reduction at 50 mg Mn2+ L−1), with field pea least impacted. Our findings suggest that significant Mn2+ toxicity could potentially occur in terms of legume germination and overall growth if legume crops are sown into post-rice soils with ≥5 mg Mn2+L−1. Soil Mn2+ level must be considered when developing cropping strategies following flooded rice. [ABSTRACT FROM AUTHOR]

Published
2023
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25. ICTV Virus Taxonomy Profile: Pleolipoviridae 2022

Author

Liu, Ying, Dyall-Smith, Mike, Oksanen, Hanna M, Molecular and Integrative Biosciences Research Programme, Faculty Common Matters (Faculty of Biology and Environmental Sciences), and Molecular Principles of Viruses

Subjects
11832 Microbiology and virology, archaeal virus, virus taxonomy, virus species, virus evolution
Published
2022

29. Cellular and Genomic Properties of Haloferax gibbonsii LR2-5, the Host of Euryarchaeal Virus HFTV1

Author

Tittes, Colin, Schwarzer, Sabine, Pfeiffer, Friedhelm, Dyall-Smith, Mike, Rodriguez-Franco, Marta, Oksanen, Hanna M, Quax, Tessa E. F., Molecular and Integrative Biosciences Research Programme, and Molecular Microbiology

Subjects
type-IV pili, 11832 Microbiology and virology, Whole Genome Sequencing, type IV pili, euryarchaea, archaellum, 1182 Biochemistry, cell and molecular biology, archaeal virus, N-glycosylation, Microbiology, haloarchaea, Original Research, S-layer
Abstract

Hypersaline environments are the source of many viruses infecting different species of halophilic euryarchaea. Information on infection mechanisms of archaeal viruses is scarce, due to the lack of genetically accessible virus-host models. Recently, a new archaeal siphovirus, Haloferax tailed virus 1 (HFTV1), was isolated together with its host belonging to the genus Haloferax, but it is not infectious on the widely used model euryarcheon Haloferax volcanii. To gain more insight into the biology of HFTV1 host strain LR2-5, we studied characteristics that might play a role in its virus susceptibility: growth-dependent motility, surface layer, filamentous surface structures, and cell shape. Its genome sequence showed that LR2-5 is a new strain of Haloferax gibbonsii. LR2-5 lacks obvious viral defense systems, such as CRISPR-Cas, and the composition of its cell surface is different from Hfx. volcanii, which might explain the different viral host range. This work provides first deep insights into the relationship between the host of halovirus HFTV1 and other members of the genus Haloferax. Given the close relationship to the genetically accessible Hfx. volcanii, LR2-5 has high potential as a new model for virus-host studies in euryarchaea.

Published
2021

30. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author

Sub Bioinformatics, Theoretical Biology and Bioinformatics, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Sub Bioinformatics, Theoretical Biology and Bioinformatics, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtboke, Ipek, Brister, J. Rodney, Lood, Cedric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Lobocka, Malgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, Francois, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.

Published
2021

31. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., UCL - SST/ELI/ELIM - Applied Microbiology, Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung-Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.

Abstract

In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).

Published
2021

32. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV:update of taxonomy changes in 2021

Author

Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, Adriaenssens, Evelien M., Krupovic, Mart, Turner, Dann, Morozova, Vera, Dyall-Smith, Mike, Oksanen, Hanna M., Edwards, Rob, Dutilh, Bas E., Lehman, Susan M., Reyes, Alejandro, Baquero, Diana P., Sullivan, Matthew B., Uchiyama, Jumpei, Nakavuma, Jesca, Barylski, Jakub, Young, Mark J., Du, Shishen, Alfenas-Zerbini, Poliane, Kushkina, Alla, Kropinski, Andrew M., Kurtböke, Ipek, Brister, J. Rodney, Lood, Cédric, Sarkar, B. L., Yigang, Tong, Liu, Ying, Huang, Li, Wittmann, Johannes, Chanishvili, Nina, van Zyl, Leonardo J., Rumnieks, Janis, Mochizuki, Tomohiro, Jalasvuori, Matti, Aziz, Ramy K., Łobocka, Małgorzata, Stedman, Kenneth M., Shkoporov, Andrey N., Gillis, Annika, Peng, Xu, Enault, François, Knezevic, Petar, Lavigne, Rob, Rhee, Sung Keun, Cvirkaite-Krupovic, Virginija, Moraru, Cristina, Moreno Switt, Andrea I., Poranen, Minna M., Millard, Andrew, Prangishvili, David, and Adriaenssens, Evelien M.

Abstract

In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).

Published
2021

39. Haloviruses HF1 and HF2: evidence for a recent and large recombination event

Author

Tang, Sen-Lin, Nuttall, Stewart, and Dyall-Smith, Mike

Subjects
Genomes -- Research, Bacterial genetics -- Research, Prokaryotes -- Research, Prokaryotes -- Genetic aspects, Biological sciences
Abstract

Haloviruses HF1 and HF2 were isolated from the same saltern pond and are adapted to hypersaline conditions, where they infect a broad range of haloarchaeal species. The HF2 genome has previously been reported. The complete sequence of the HF1 genome has now been determined, mainly by PCR and primer walking. It was 75,898 bp in length and was 94.4% identical to the HF2 genome but about 1.8 kb shorter. A total of 117 open reading frames and five tRNA-like genes were predicted, and their database matches and characteristics were similar to those found in HF2. A comparison of the predicted restriction digest patterns based on nucleotide sequence with the observed restriction digest patterns of viral DNA showed that, unlike the case for HF2, some packaged HF1 DNA had cohesive termini. Except for a single base change, HF1 and HF2 were identical in sequence over the first 48 kb, a region that includes the early and middle genes. The remaining 28 kb of HF1 showed many differences from HF2, and the similarity of the two genomes over this late gene region was 87%. The abrupt shift in sequence similarity around 48 kb suggests a recent recombination event between either HF1 or HF2 and another HF-like halovirus that has swapped most of the right-end 28 kb. This example indicates there is a high level of recombination among viruses that live in this extreme environment.

Published
2004

49. Supplementary Tables for 'Whole-genome comparison between the type strain of Halobacterium salinarum (DSM 3754T) and the laboratory strains R1 and NRC-1'

Author

Pfeiffer, Friedhelm, Losensky, Gerald, Marchfelder, Anita, Habermann, Bianca, and Dyall-Smith, Mike

Subjects
Halobacterium salinarum
Abstract

The genome of the Halobacterium salinarum type strain (strain 91-R6) was compared to that of the laboratory strains R1 and NRC-1. Protein-coding genes were extensively correlated, mainly between strains 91-R6 and R1. Table S1 lists correlated proteins encoded on the chromosomes. Table S2 lists correlated proteins which are encoded on plasmids in at least one of the strains. Table S3 lists strain-specific proteins encoded on the chromosome of strain 91-R6. Table S4 lists strain-specific proteins encoded on the chromosome of strain R1. Table S5 lists strain-specific proteins encoded on plasmids of strain 91-R6. Table S6 lists strain-specific proteins encoded on plasmids of strain R1. Table S7 lists strain-specific proteins from strain NRC-1., These tables are associated with the published manuscript Pfeiffer et al, Microbiologyopen (2019), 8: e974 ""Whole-genome comparison between the type strain of Halobacterium salinarum (DSM 3754T) and the laboratory strains R1 and NRC-1" (DOI: 10.1002/mbo3.974 ; PubMed: 31797576)

Published
2019
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