Abstract
ABSTRACTLeptospirillum ferriphilum plays a major role in acidic, metal-rich environments, where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of the type strain of this model species is available, limiting the possibilities to investigate the strategies and adaptations that Leptospirillum ferriphilum DSM 14647T (here referred to as Leptospirillum ferriphilumT) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilumT obtained by PacBio single-molecule real-time (SMRT) long-read sequencing for use as a high-quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, the oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as the substrate and those grown in bioleaching cultures containing chalcopyrite (CuFeS2). Adaptations of Leptospirillum ferriphilumT to growth on chalcopyrite included the possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated levels of RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, the expression and translation of genes responsible for chemotaxis and motility were enhanced.IMPORTANCE Leptospirillum ferriphilum is one of the most important iron oxidizers in the context of acidic and metal-rich environments during moderately thermophilic biomining. A high-quality circular genome of Leptospirillum ferriphilumT coupled with functional omics data provides new insights into its metabolic properties, such as the novel identification of genes for atmospheric nitrogen fixation, and represents an essential step for further accurate proteomic and transcriptomic investigation of this acidophile model species in the future. Additionally, light is shed on adaptation strategies of Leptospirillum ferriphilumT for growth on the copper mineral chalcopyrite. These data can be applied to deepen our understanding and optimization of bioleaching and biooxidation, techniques that present sustainable and environmentally friendly alternatives to many traditional methods for metal extraction.
Highlights
Leptospirillum ferriphilum plays a major role in acidic, metal-rich environments, where it represents one of the most prevalent iron oxidizers
Additional functional capabilities encoded in the L. ferriphilumT genome (Fig. 2) are detailed below, while expressed functions in Fe2ϩ-containing medium versus chalcopyrite bioleaching cultures were assessed by transcriptomic and proteomic analyses (Table 3 and Fig. 3)
The resulting values are given as transcripts per million base pairs (TPM) for RNA and label-free quantification (LFQ) intensities [25] for proteins, respectively
Summary
Leptospirillum ferriphilum plays a major role in acidic, metal-rich environments, where it represents one of the most prevalent iron oxidizers. Leptospirillum ferriphilum DSM 14647T (here referred to as Leptospirillum ferriphilumT) is an obligate aerobe that is capable of gaining energy only via ferrous iron (Fe2ϩ) oxidation [3] It has a pH optimum of 1.4 to 1.8, which requires the cells to maintain an internal, cytoplasmic pH close to neutral in the face of an ϳ104-fold proton gradient across the cytoplasmic membrane. The result of metal sulfide oxidation is an acidic solution typically containing high metal concentrations (reviewed in references 11 and 12) This requires acidophiles to have multiple chemical and biological metal resistance strategies, such as efflux pumps, metal sequestration methods, and the ability to reduce metal uptake via the inside positive membrane potential (reviewed in references 12 and 13). Knowledge of how the leptospirilli survive high metal concentrations and ROS is limited
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