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

Abstract

Leptospirillum spp. are widespread members of acidophilic microbial communities that catalyze ferrous iron oxidation, thereby increasing sulfide mineral dissolution rates. These bacteria play important roles in environmental acidification and are harnessed for bioleaching-based metal recovery. Known members of the Leptospirillum clade of the Nitrospira phylum are Leptospirillum ferrooxidans (group I), Leptospirillum ferriphilum and "Leptospirillum rubarum" (group II), and Leptospirillum ferrodiazotrophum (group III). In the Richmond Mine acid mine drainage (AMD) system, biofilm formation is initiated by L. rubarum; L. ferrodiazotrophum appears in later developmental stages. Here we used community metagenomic data from unusual, thick floating biofilms to identify distinguishing metabolic traits in a rare and uncultivated community member, the new species "Leptospirillum group IV UBA BS." These biofilms typically also contain a variety of Archaea, Actinobacteria, and a few other Leptospirillum spp. The Leptospirillum group IV UBA BS species shares 98% 16S rRNA sequence identity and 70% average amino acid identity between orthologs with its closest relative, L. ferrodiazotrophum. The presence of nitrogen fixation and reverse tricarboxylic acid (TCA) cycle proteins suggest an autotrophic metabolism similar to that of L. ferrodiazotrophum, while hydrogenase proteins suggest anaerobic metabolism. Community transcriptomic and proteomic analyses demonstrate expression of a multicopper oxidase unique to this species, as well as hydrogenases and core metabolic genes. Results suggest that the Leptospirillum group IV UBA BS species might play important roles in carbon fixation, nitrogen fixation, hydrogen metabolism, and iron oxidation in some acidic environments.

Metabolic diversity and adaptive mechanisms of iron‐ and/or sulfur‐oxidizing autotrophic acidophiles in extremely acidic environments

“…Genes for the respiratory [NiFe]‐hydrogenase ( hydAB ), a [NiFe]‐hydrogenase large subunit ( hoxH ), and the hydrogenase maturation protein were found in Leptospirillum group IV (Goltsman et al ., ). However, previous results revealed that strains belonging to L. ferriphilum and L. ferrodiazotrophum did not grow on hydrogen, indicating that ferrous iron was used as the sole electron donor in these acidophiles (Hedrich and Johnson, ).…”

“…Genomic analyses revealed that A. ferrooxidans, A. ferrivorans, and members of groups I, III, and IV of the Leptospirillum genus harbor several genes encoding the nitrogenase complex (Table 2) (Levic an et al, 2008;Goltsman et al, 2013). However, A. thiooxidans and A. caldus, both of which lack genes encoding the nitrogenase complex, carry genes associated with the Fig.…”

“…Metabolic diversity and adaptive mechanisms 745 V C 2016 Society for Applied Microbiology and John Wiley & Sons Ltd,Environmental Microbiology Reports,8,[738][739][740][741][742][743][744][745][746][747][748][749][750][751] Genes for the respiratory [NiFe]-hydrogenase (hydAB), a [NiFe]-hydrogenase large subunit (hoxH), and the hydrogenase maturation protein were found in Leptospirillum group IV (Goltsman et al, 2013). However, previous results revealed that strains belonging to L. ferriphilum and L. ferrodiazotrophum did not grow on hydrogen, indicating that ferrous iron was used as the sole electron donor in these acidophiles (Hedrich and Johnson, 2013).…”

“…The genus Acidithiobacillus includes at least four species: A. ferrooxidans, A. thiooxidans, A. caldus, and A. ferrivorans. To date, Leptospirillum spp., an iron oxidizer abundant in various acidophilic microbial communities, includes four recognized groups: group I (L. ferrooxidans), group II (L. ferriphilum and L. rubarum), group III (L. ferrodiazotrophum), and group IV, a novel member (Goltsman et al, 2013). The availability of the genome sequences for these iron and/or sulfur oxidizers belonging to the genera Acidithiobacillus and Leptospirillum is rapidly increasing because of the development of highthroughput sequencing and bioinformatics-based approaches.…”

Multiple Osmotic Stress Responses in Acidihalobacter prosperus Result in Tolerance to Chloride Ions

“…As a result, many acidophile studies have utilized “omics” techniques, including proteomics to investigate not only whole communities (Belnap et al, 2011; Mueller et al, 2011; Goltsman et al, 2013) but also specific responses in a single species (Baker-Austin et al, 2010; Mykytczuk et al, 2011; Potrykus et al, 2011; Mangold et al, 2013). In this study, iron oxidation and biomining studies along with a proteomic strategy are used to investigate the differing responses to chloride by the salt susceptible and tolerant acidophiles At.…”