Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage
Rhizobiales bacterium strain IZ6 is a novel filterable bacterium that was isolated from a suspension filtrate (<0.22 µm) of soil collected in Shimane Prefecture, western Japan. Additional closely related isolates were recovered from filterable fractions of terrestrial environmental samples collec...
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ftmdpi:oai:mdpi.com:/2076-2607/8/9/1373/ 2023-08-20T04:04:45+02:00 Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage Ryosuke Nakai Takeshi Naganuma Nozomi Tazato Sho Morohoshi Tomomi Koide agris 2020-09-07 application/pdf https://doi.org/10.3390/microorganisms8091373 EN eng Multidisciplinary Digital Publishing Institute Environmental Microbiology https://dx.doi.org/10.3390/microorganisms8091373 https://creativecommons.org/licenses/by/4.0/ Microorganisms; Volume 8; Issue 9; Pages: 1373 bacteria filterable bacteria phylogeny novel lineage genome nitrogen cycling Text 2020 ftmdpi https://doi.org/10.3390/microorganisms8091373 2023-08-01T00:03:38Z Rhizobiales bacterium strain IZ6 is a novel filterable bacterium that was isolated from a suspension filtrate (<0.22 µm) of soil collected in Shimane Prefecture, western Japan. Additional closely related isolates were recovered from filterable fractions of terrestrial environmental samples collected from other places in Japan; the Gobi Desert, north-central China; and Svalbard, Arctic Norway. These findings indicate a wide distribution of this lineage. This study reports the cell variation and genomic structure of IZ6. When cultured at lower temperatures (4 °C and 15 °C), this strain contained ultra-small cells and cell-like particles in the filtrate. PacBio sequencing revealed that this chromosome (3,114,641 bp) contained 3150 protein-coding, 51 tRNA, and three rRNA genes. IZ6 showed low 16S rRNA gene sequence identity (<97%) and low average nucleotide identity (<76%) with its closest known relative, Flaviflagellibacter deserti. Unlike the methylotrophic bacteria and nitrogen-fixing bacteria in related genera, there were no genes that encoded enzymes for one-carbon-compound utilization and nitrogen fixation in the IZ6 genome; the genes related to nitrate and nitrite reductase are retained and those related to the cell membrane function tend to be slightly enriched in the genome. This genomic information helps elucidate the eco-physiological function of a phenotypically heterogeneous and diverse Rhizobiales group. Text Arctic Svalbard MDPI Open Access Publishing Arctic Svalbard Norway Microorganisms 8 9 1373 |
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Open Polar |
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MDPI Open Access Publishing |
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English |
topic |
bacteria filterable bacteria phylogeny novel lineage genome nitrogen cycling |
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bacteria filterable bacteria phylogeny novel lineage genome nitrogen cycling Ryosuke Nakai Takeshi Naganuma Nozomi Tazato Sho Morohoshi Tomomi Koide Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage |
topic_facet |
bacteria filterable bacteria phylogeny novel lineage genome nitrogen cycling |
description |
Rhizobiales bacterium strain IZ6 is a novel filterable bacterium that was isolated from a suspension filtrate (<0.22 µm) of soil collected in Shimane Prefecture, western Japan. Additional closely related isolates were recovered from filterable fractions of terrestrial environmental samples collected from other places in Japan; the Gobi Desert, north-central China; and Svalbard, Arctic Norway. These findings indicate a wide distribution of this lineage. This study reports the cell variation and genomic structure of IZ6. When cultured at lower temperatures (4 °C and 15 °C), this strain contained ultra-small cells and cell-like particles in the filtrate. PacBio sequencing revealed that this chromosome (3,114,641 bp) contained 3150 protein-coding, 51 tRNA, and three rRNA genes. IZ6 showed low 16S rRNA gene sequence identity (<97%) and low average nucleotide identity (<76%) with its closest known relative, Flaviflagellibacter deserti. Unlike the methylotrophic bacteria and nitrogen-fixing bacteria in related genera, there were no genes that encoded enzymes for one-carbon-compound utilization and nitrogen fixation in the IZ6 genome; the genes related to nitrate and nitrite reductase are retained and those related to the cell membrane function tend to be slightly enriched in the genome. This genomic information helps elucidate the eco-physiological function of a phenotypically heterogeneous and diverse Rhizobiales group. |
format |
Text |
author |
Ryosuke Nakai Takeshi Naganuma Nozomi Tazato Sho Morohoshi Tomomi Koide |
author_facet |
Ryosuke Nakai Takeshi Naganuma Nozomi Tazato Sho Morohoshi Tomomi Koide |
author_sort |
Ryosuke Nakai |
title |
Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage |
title_short |
Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage |
title_full |
Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage |
title_fullStr |
Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage |
title_full_unstemmed |
Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage |
title_sort |
cell plasticity and genomic structure of a novel filterable rhizobiales bacterium that belongs to a widely distributed lineage |
publisher |
Multidisciplinary Digital Publishing Institute |
publishDate |
2020 |
url |
https://doi.org/10.3390/microorganisms8091373 |
op_coverage |
agris |
geographic |
Arctic Svalbard Norway |
geographic_facet |
Arctic Svalbard Norway |
genre |
Arctic Svalbard |
genre_facet |
Arctic Svalbard |
op_source |
Microorganisms; Volume 8; Issue 9; Pages: 1373 |
op_relation |
Environmental Microbiology https://dx.doi.org/10.3390/microorganisms8091373 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/microorganisms8091373 |
container_title |
Microorganisms |
container_volume |
8 |
container_issue |
9 |
container_start_page |
1373 |
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1774715124668432384 |