Complete Genome Sequence of Leptospirillum ferrooxidans Strain C2-3, Isolated from a Fresh Volcanic Ash Deposit on the Island of Miyake, Japan

Abstract

A diazotrophic, acidophilic, iron-oxidizing bacterium, Leptospirillum ferrooxidans , known to be difficult to cultivate, was isolated from a fresh volcanic ash deposit on the island of Miyake, Japan. Here, we report the complete genome sequence of a cultured strain, C2-3.

New Group in the Leptospirillum Clade: Cultivation-Independent Community Genomics, Proteomics, and Transcriptomics of the New Species “Leptospirillum Group IV UBA BS”

“…The genomic assemblies were manually curated to verify the existence of paralogous nifZ genes, which share only 39% sequence identity. This duplication is not part of the L. ferrooxidans Nif operon (14,19).…”

“…The genes encoding hydrogenase maturation proteins HypBFCDE are located in a cluster with a nickel transporter. Hydrogenases have not yet been reported for the Leptospirillum spp., but the recently deposited genome of a Leptospirillum ferrooxidans isolate contains a single cluster of hydrogenase and maturation genes (19), which share an average 66% amino acid identity with the Leptospirillum group IV UBA BS orthologs.…”

“…Based on isolate characterization studies, all are iron-oxidizing chemoautotrophs, and two groups (groups I and III) are reported to be capable of nitrogen fixation (9,14). Near-complete genomes for Leptospirillum rubarum (UBA type), "Leptospirillum group II 5wayCG" type, and L. ferrodiazotrophum have been recovered from community genomic data sets (15)(16)(17), and the complete genomes of L. ferrooxidans and L. ferriphilum isolates are now available (18,19). Much research has focused on floating biofilms sampled from the Richmond Mine at Iron Mountain, California; the biofilms are microns to hundred microns thick and are typically dominated by Leptospirillum group II (20,21).…”

The Family Nitrospiraceae

“…Many conjugal transfer proteins from this region are significantly similar to homologous proteins on a large extrachromosomal plasmid ($250 kb), which was assembled from the same AMD metagenome and may be associated with Leptospirillum (Goltsman et al 2009). No evidence for plasmids was found in strain ML-04, and plasmids were not reported for strain C2-3 either (Mi et al 2011;Fujimura et al 2012a). However, two plasmids (28 and 29 kb) were isolated from L. ferrooxidans ATCC 49879 and sequenced (Coram et al 2005).…”

“…rubarum'' was introduced to distinguish it from L. ferriphilum (also group II). More recently, the genomes of L. ferriphilum strain ML-04 (group II), isolated from acidic water near a hot spring in China, and L. ferrooxidans strain C2-3 (group I), isolated from a volcanic ash deposit in Japan, were completely sequenced (Mi et al 2011;Fujimura et al 2012a). The genome of strain ML-04 is 2,406,157 bp and the genome of strain C2-3 is 2,559,538 bp long; these genome sizes are similar to those of environmental (AMD) draft genomes from group II (Tyson et al 2004;Goltsman et al 2009).…”