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...
Published in: | Microorganisms |
---|---|
Main Authors: | , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
MDPI AG
2020
|
Subjects: | |
Online Access: | https://doi.org/10.3390/microorganisms8091373 https://doaj.org/article/6f1490903f9d42cf9cbc5607fdfa16b5 |
id |
ftdoajarticles:oai:doaj.org/article:6f1490903f9d42cf9cbc5607fdfa16b5 |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:6f1490903f9d42cf9cbc5607fdfa16b5 2023-05-15T15:08:18+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 2020-09-01T00:00:00Z https://doi.org/10.3390/microorganisms8091373 https://doaj.org/article/6f1490903f9d42cf9cbc5607fdfa16b5 EN eng MDPI AG https://www.mdpi.com/2076-2607/8/9/1373 https://doaj.org/toc/2076-2607 doi:10.3390/microorganisms8091373 2076-2607 https://doaj.org/article/6f1490903f9d42cf9cbc5607fdfa16b5 Microorganisms, Vol 8, Iss 1373, p 1373 (2020) bacteria filterable bacteria phylogeny novel lineage genome nitrogen cycling Biology (General) QH301-705.5 article 2020 ftdoajarticles https://doi.org/10.3390/microorganisms8091373 2022-12-31T04:45:43Z 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. Article in Journal/Newspaper Arctic Svalbard Directory of Open Access Journals: DOAJ Articles Arctic Norway Svalbard Microorganisms 8 9 1373 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
bacteria filterable bacteria phylogeny novel lineage genome nitrogen cycling Biology (General) QH301-705.5 |
spellingShingle |
bacteria filterable bacteria phylogeny novel lineage genome nitrogen cycling Biology (General) QH301-705.5 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 Biology (General) QH301-705.5 |
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 |
Article in Journal/Newspaper |
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 |
MDPI AG |
publishDate |
2020 |
url |
https://doi.org/10.3390/microorganisms8091373 https://doaj.org/article/6f1490903f9d42cf9cbc5607fdfa16b5 |
geographic |
Arctic Norway Svalbard |
geographic_facet |
Arctic Norway Svalbard |
genre |
Arctic Svalbard |
genre_facet |
Arctic Svalbard |
op_source |
Microorganisms, Vol 8, Iss 1373, p 1373 (2020) |
op_relation |
https://www.mdpi.com/2076-2607/8/9/1373 https://doaj.org/toc/2076-2607 doi:10.3390/microorganisms8091373 2076-2607 https://doaj.org/article/6f1490903f9d42cf9cbc5607fdfa16b5 |
op_doi |
https://doi.org/10.3390/microorganisms8091373 |
container_title |
Microorganisms |
container_volume |
8 |
container_issue |
9 |
container_start_page |
1373 |
_version_ |
1766339681751924736 |