Complete Genome Sequence of Ferriphaselus amnicola Strain OYT1, a Neutrophilic, Stalk-Forming, Iron-Oxidizing Bacterium.

Ferriphaselus amnicola is a freshwater, neutrophilic, iron-oxidizing bacterium that produces extracellular twisted-ribbon-like iron biominerals called stalks. Here, we report the 2.72-Mb closed genome sequence of F. amnicola strain OYT1, which was isolated from iron oxide deposits at a groundwater stream in Japan.

ANNOUNCEMENT

In the 1830s, a freshwater, stalk-forming, iron-oxidizing bacterium (FeOB), Gallionella ferruginea, was described (1), and it is one of the oldest records of a bacterial species. Several physiological and morphological characterizations of G. ferruginea have been reported since then (2, 3); however, G. ferruginea is not currently available in any culture collection. Previously, we isolated another stalk-forming FeOB strain, OYT1T (JCM 18545T=DSM 26810T), from a groundwater seep in Japan (4) and proposed the name Ferriphaselus amnicola gen. nov., sp. nov. (5). F. amnicola belongs to the class Betaproteobacteria and shows a 92.9% 16S rRNA gene sequence similar to that of G. ferruginea. The draft genome sequence (2.68 Mb, 23 contigs) of the strain was already determined by 454 pyrosequencing and Ion PGM sequencing, which indicated the presence of putative genes involved in carbon fixation, iron oxidation, and stalk formation (6). However, its complete genome has not been reported so far.

Here, we present the complete genome sequence of F. amnicola strain OYT1. The cultivation of the strain and the DNA extraction from the culture have been reported previously (6). In brief, F. amnicola strain OYT1 was cultured in a mineral medium with agarose-stabilized FeS as the Fe(II) source at pH 6.2 and 25°C. Using the same DNA extract, we resequenced its genome on a MiSeq platform (Illumina, USA) and on a MinION device (Oxford Nanopore Technologies [ONT], United Kingdom) with an R9.4 flow cell (ONT). Sequencing libraries were constructed using a QIAseq FX DNA library kit (Qiagen, Germany) for the Illumina sequencing and a rapid sequencing kit (SQK-RAD004, ONT) for the ONT sequencing. We obtained 9,621,832 Illumina paired-end short reads (mean length, 223 bp) with a total of 4,295,964,156 bp and 610,696 ONT long reads (mean length, 1,717 bp) with a total of 1,048,892,817 bp. De novo assembly of the genome using both the short and long reads was performed using Unicycler version 0.3.0b (7), resulting in a circular contig of 2,717,229 bp with a G+C content of 55.9%. Genome annotation was performed using Prokka version 1.12 (8) and the Rapid Annotations using Subsystems Technology (RAST) server version 2.0 (9), and the annotated genome was manually curated.

The genome contained 2,683 protein-coding regions (CDSs), 3 copies of rRNA gene operons (5S, 16S, and 23S), and 50 coding regions of tRNAs. In addition to the rRNA genes, 4 copies of CDSs for transposase (identical to each other, 1,026 bp) and 7 copies of CDSs for integrase (identical to each other, 1,515 bp) were encoded in the genome. These CDSs probably caused the previous failure of the finished genome assembly, which used only short reads (<400 bp) produced by 454 pyrosequencing and Ion PGM sequencing (6), as supported by the mapping of the previously reported contigs on the complete genome (Fig. 1) using Mauve version 2015-02-25 (10). The presence of these CDSs related to mobile genetic elements suggests that transposons and integrons have played a role in the evolution of the F. amnicola genome.

FIG 1

Comparison between the complete genome determined in this study and the previously reported draft genome of F. amnicola strain OYT1 (6). Three copies of the rRNA gene operon with 2 tRNAs and over 10 CDSs for transposase and integrase were detected in the genome. Colored regions of the complete genome represent the homologous regions to the previously reported contigs. Asterisks (*) indicate partial CDSs.

Data availability.

The complete genome sequence determined in the present study has been deposited in DDBJ/ENA/GenBank under the accession no. AP018738, which is linked to the BioProject accession no. PRJDB3480.