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

Ryosuke Nakai,Nozomi Tazato,Tomomi Koide,Takeshi Naganuma,Sho Morohoshi

doi:10.3390/microorganisms8091373

Abstract

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.

Highlights

Filter sterilization using a small pore size filter is commonly used in various scientific fields, and medical and industrial processes
The filterable bacteria cultivated to date include ultra-small bacteria, miniaturized ultramicrocells induced by external factors, and slender filamentous bacteria with small cell widths [13]
During the course of mining filterable bacteria, we isolated a novel Rhizobiales bacterium, strain IZ6, from a suspension filtrate of soils collected in Shimane Prefecture, western Japan [14]

Summary

Introduction

Filter sterilization using a small pore size filter (approximately 0.2 μm) is commonly used in various scientific fields, and medical and industrial processes. During the course of mining filterable bacteria, we isolated a novel Rhizobiales bacterium, strain IZ6, from a suspension filtrate of soils collected in Shimane Prefecture, western Japan [14]. This strain was distantly related to members of known genera with low 16S rRNA gene sequence similarities (

Test for Cell Morphological Change and Filterability

Phylogenetic and Comparative Genomic Analyses

Temperature-Induced Cell Morphological Change

Genome Structure and Phylogenetic Relationships