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16. ICTV Virus Taxonomy Profile: Thaspiviridae 2021

Author

Kim, Jong-Geol, Gazi, Khaled, Krupovic, Mart, Rhee, Sung-Keun, Report Consortium, Ictv, Wonkwang University, Chungbuk National University, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], Production of this Profile, the ICTV Report, and associated resources was funded by a grant from the Wellcome Trust (WT108418AIA) and the National Research Foundation of Korea (NRF) grants funded by the Ministry of Science, ICT & Future Planning (2021R1A2C3004015)., Members of the ICTV Report Consortium are Stuart G. Siddell, Elliot J. Lefkowitz, Sead Sabanadzovic, Peter Simmonds, F. Murilo Zerbini, Donald B. Smith, Richard J. Orton and Mart Krupovic, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), and Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0303 health sciences, Thaumarchaeota, biology, Phylum, viruses, 030302 biochemistry & molecular biology, Nitrosopumilus, Fuselloviridae, Thaspiviridae, biology.organism_classification, Virology, Virus, 3. Good health, 03 medical and health sciences, taxonomy, Viral replication, Lytic cycle, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, ICTV Report, Virus classification, 030304 developmental biology
Abstract

Members of the family Thaspiviridae have linear dsDNA genomes of 27 to 29 kbp and are the first viruses known to infect mesophilic ammonia-oxidizing archaea of the phylum Thaumarchaeota. The spindle-shaped virions of Nitrosopumilus spindle-shaped virus 1 possess short tails at one pole and measure 64±3 nm in diameter and 112±6 nm in length. This morphology is similar to that of members of the families Fuselloviridae and Halspiviridae. Virus replication is not lytic but leads to growth inhibition of the host. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Thaspiviridae, which is available at ictv.global/report/thaspiviridae.

Published
2021

24. A Unique Benthic Microbial Community Underlying the Phaeocystis antarctica-Dominated Amundsen Sea Polynya, Antarctica: A Proxy for Assessing the Impact of Global Changes

Author

Cho, Hyeyoun, primary, Hwang, Chung Yeon, additional, Kim, Jong-Geol, additional, Kang, Sanghoon, additional, Knittel, Katrin, additional, Choi, Ayeon, additional, Kim, Sung-Han, additional, Rhee, Sung-Keun, additional, Yang, Eun Jin, additional, Lee, SangHoon, additional, and Hyun, Jung-Ho, additional

Published
2020
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27. A hydrophobic ammonia-oxidizing archaeon of the Nitrosocosmicus clade isolated from coal tar-contaminated sediment

Author

Jung, Man-Young, Kim, Jong-Geol, Sinninghe Damsté, Jaap S, Rijpstra, W Irene C, Madsen, Eugene L, Kim, So-Jeong, Hong, Heeji, Si, Ok-Ja, Kerou, Melina, Schleper, Christa, Rhee, Sung-Keun, and non-UU output of UU-AW members

Abstract

A wide diversity of ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota exists and plays a key role in the N cycle in a variety of habitats. In this study, we isolated and characterized an ammonia-oxidizing archaeon, strain MY3, from a coal tar-contaminated sediment. Phylogenetically, strain MY3 falls in clade 'Nitrosocosmicus' of the thaumarchaeotal group I.1b. The cells of strain MY3 are large 'walnut-like' cocci, divide by binary fission along a central cingulum, and form aggregates. Strain MY3 is mesophilic and neutrophilic. An assay of (13) C-bicarbonate incorporation into archaeal membrane lipids indicated that strain MY3 is capable of autotrophy. In contrast to some other AOA, TCA cycle intermediates, i.e. pruvate, oxaloacetate and α-ketoglutarate, did not affect the growth rates and yields of strain MY3. The attachment of cells of strain MY3 to XAD-7 hydrophobic beads and to the adsorbent vermiculite demonstrated the potential of strain MY3 to form biofilms. The cell surface was confirmed to be hydrophobic by the extraction of strain MY3 from an aqueous medium with p-xylene. Our finding of a strong potential for surface attachment by strain MY3 may reflect an adaptation to the selective pressures in hydrophobic terrestrial environments.

Published
2016

34. A hydrophobic ammonia-oxidizing archaeon of the Nitrosocosmicus clade isolated from coal tar-contaminated sediment

Author

non-UU output of UU-AW members, Jung, Man-Young, Kim, Jong-Geol, Sinninghe Damsté, Jaap S, Rijpstra, W Irene C, Madsen, Eugene L, Kim, So-Jeong, Hong, Heeji, Si, Ok-Ja, Kerou, Melina, Schleper, Christa, Rhee, Sung-Keun, non-UU output of UU-AW members, Jung, Man-Young, Kim, Jong-Geol, Sinninghe Damsté, Jaap S, Rijpstra, W Irene C, Madsen, Eugene L, Kim, So-Jeong, Hong, Heeji, Si, Ok-Ja, Kerou, Melina, Schleper, Christa, and Rhee, Sung-Keun

Published
2016

35. Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea

Author

non-UU output of UU-AW members, Kim, Jong-Geol, Park, Soo-Je, Sinninghe Damsté, Jaap S., Schouten, Stefan, Rijpstra, W. Irene C., Jung, Man-Young, Kim, So-Jeong, Gwak, Joo-Han, Hong, Heeji, Si, Ok-Ja, Lee, Sanghoon, Madsen, Eugene L., Rhee, Sung-Keun, non-UU output of UU-AW members, Kim, Jong-Geol, Park, Soo-Je, Sinninghe Damsté, Jaap S., Schouten, Stefan, Rijpstra, W. Irene C., Jung, Man-Young, Kim, So-Jeong, Gwak, Joo-Han, Hong, Heeji, Si, Ok-Ja, Lee, Sanghoon, Madsen, Eugene L., and Rhee, Sung-Keun

Published
2016

38. Comparative genomic analysis of <italic>Geosporobacter ferrireducens</italic> and its versatility of anaerobic energy metabolism.

Author

Jung, Man-Young, Kim, So-Jeong, Kim, Jong-Geol, Hong, Heeji, Gwak, Joo-Han, Park, Soo-Je, Kim, Yang-Hoon, and Rhee, Sung-Keun

Abstract

Members of the family Clostridiaceae within phylum Firmicutes are ubiquitous in various iron-reducing environments. However, genomic data on iron-reducing bacteria of the family Clostridiaceae, particularly regarding their environmental distribution, are limited. Here, we report the analysis and comparison of the genomic properties of Geosporobacter ferrireducens IRF9, a strict anaerobe that ferments sugars and degrades toluene under iron-reducing conditions, with those of the closely related species, Geosporobacter subterraneus DSM 17957. Putative alkyl succinate synthase-encoding genes were observed in the genome of strain IRF9 instead of the typical benzyl succinate synthase-encoding genes. Canonical genes associated with iron reduction were not observed in either genome. The genomes of strains IRF9 and DMS 17957 harbored genes for acetogenesis, that encode two types of Rnf complexes mediating the translocation of H+ and Na+ ions, respectively. Strain IRF9 harbored two different types of ATPases (Na+-dependent F-type ATPase and H+-dependent V-type ATPase), which enable full exploitation of ion gradients. The versatile energy conservation potential of strain IRF9 promotes its survival in various environmental conditions. [ABSTRACT FROM AUTHOR]

Published
2018
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