Complete genome of Leptospirillum ferriphilum ML-04 provides insight into its physiology and environmental adaptation

Abstract

Leptospirillum ferriphilum has been identified as the dominant, moderately thermophilic, bioleaching microorganism in bioleaching processes. It is an acidic and chemolithoautrophic bacterium that gains electrons from ferrous iron oxidation for energy production and cell growth. Genetic information about this microorganism has been limited until now, which has hindered its further exploration. In this study, the complete genome of L. ferripilum ML-04 is sequenced and annotated. The bacterium has a single circular chromosome of 2,406,157 bp containing 2,471 coding sequences (CDS), 2 rRNA operons, 48 tRNA genes, a large number of mobile genetic elements and 2 genomic islands. In silico analysis shows L. ferriphilum ML-04 fixes carbon through a reductive citric acid (rTCA) cycle, and obtains nitrogen through ammonium assimilation. The genes related to "cell envelope biogenesis, outer membrane" (6.9%) and "DNA replication, recombination and repair" (5.6%) are abundant, and a large number of genes related to heavy metal detoxification, oxidative and acidic stress defense, and signal transduction pathways were detected. The genomic plasticity, plentiful cell envelope components, inorganic element metabolic abilities and stress response mechanisms found the base for this organism's survival in the bioleaching niche.

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

“…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).…”

Experiences and Future Challenges of Bioleaching Research in South Korea

“…Microorganism(s) Parameters Leaching (%) [105] T. ferrooxidans Proteomic analysis - [106] A. ferrooxidans Gene expression - [107] A. caldus Electrotransformation Cu: 92 [108] L. ferriphilum Genome -Findings related to protein and gene expression studies have been published in biotechnology related journals. Hu et al [105] conducted a proteomic analysis of T. ferrooxidans comparing the bacterial growth on elemental sulfur with that in Fe(II).…”

“…They claimed to be the first research team to achieve the electrotransformation of this biomining species. One year later, the Chinese team Mi et al [108] sequenced and annotated the complete genome of L. ferriphilum in the Journal of Microbiology. They studied the genes responsible for iron oxidation, pH and metal tolerance, as well as carbon fixation.…”

The Family Nitrospiraceae

“…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).…”