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Communication

Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage

1
Microbial Ecology and Technology Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-higashi, Toyohira-ku, Sapporo 062-8517, Japan
2
Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
3
Technical Department, TechnoSuruga Laboratory Co. Ltd., 330 Nagasaki, Shimizu-ku, Shizuoka 424-0065, Japan
*
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(9), 1373; https://doi.org/10.3390/microorganisms8091373
Received: 9 August 2020 / Revised: 29 August 2020 / Accepted: 4 September 2020 / Published: 7 September 2020
(This article belongs to the Section Environmental Microbiology)
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. View Full-Text
Keywords: bacteria; filterable bacteria; phylogeny; novel lineage; genome; nitrogen cycling bacteria; filterable bacteria; phylogeny; novel lineage; genome; nitrogen cycling
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MDPI and ACS Style

Nakai, R.; Naganuma, T.; Tazato, N.; Morohoshi, S.; Koide, T. Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage. Microorganisms 2020, 8, 1373. https://doi.org/10.3390/microorganisms8091373

AMA Style

Nakai R, Naganuma T, Tazato N, Morohoshi S, Koide T. Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage. Microorganisms. 2020; 8(9):1373. https://doi.org/10.3390/microorganisms8091373

Chicago/Turabian Style

Nakai, Ryosuke, Takeshi Naganuma, Nozomi Tazato, Sho Morohoshi, and Tomomi Koide. 2020. "Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage" Microorganisms 8, no. 9: 1373. https://doi.org/10.3390/microorganisms8091373

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