Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile

Issotta, Francisco; Galleguillos, Pedro A.; Moya-Beltrán, Ana; Davis-Belmar, Carol S.; Rautenbach, George; Covarrubias, Paulo C.; Acosta, Mauricio; Ossandon, Francisco J.; Contador, Yasna; Holmes, David S.; Marín-Eliantonio, Sabrina; Quatrini, Raquel; Demergasso, Cecilia

doi:10.1186/s40793-016-0142-1

Cited by 25 publications

(17 citation statements)

References 35 publications

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“…The Leptospirillum genus was chosen as a model system for this study because it is one of the most extreme bacterial acidophiles known with a growth pH range between 0.7 and 2.2 [47,48]. In addition, fluorescent in situ hybridization and "omic" studies highlight Leptospirillum as one of the main active taxa in extremely low pH natural and man-made acid mine drainage environments [49][50][51][52][53][54][55][56][57][58] and in commercial copper and gold biorecovery operations [47,59].…”

Section: Introductionmentioning

confidence: 99%

Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus

Vergara

Neira

González

et al. 2020

Genes

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Organisms that thrive in extremely acidic environments (≤pH 3.5) are of widespread importance in industrial applications, environmental issues, and evolutionary studies. Leptospirillum spp. constitute the only extremely acidophilic microbes in the phylogenetically deep-rooted bacterial phylum Nitrospirae. Leptospirilli are Gram-negative, obligatory chemolithoautotrophic, aerobic, ferrous iron oxidizers. This paper predicts genes that Leptospirilli use to survive at low pH and infers their evolutionary trajectory. Phylogenetic and other bioinformatic approaches suggest that these genes can be classified into (i) “first line of defense”, involved in the prevention of the entry of protons into the cell, and (ii) neutralization or expulsion of protons that enter the cell. The first line of defense includes potassium transporters, predicted to form an inside positive membrane potential, spermidines, hopanoids, and Slps (starvation-inducible outer membrane proteins). The “second line of defense“ includes proton pumps and enzymes that consume protons. Maximum parsimony, clustering methods, and gene alignments are used to infer the evolutionary trajectory that potentially enabled the ancestral Leptospirillum to transition from a postulated circum-neutral pH environment to an extremely acidic one. The hypothesized trajectory includes gene gains/loss events driven extensively by horizontal gene transfer, gene duplications, gene mutations, and genomic rearrangements.

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Section: Introductionmentioning

confidence: 99%

Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus

Vergara

Neira

González

et al. 2020

Genes

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“…Typical acidophile biomining strains are highly sensitive to anions and in particular chloride that have been demonstrated to inhibit ferrous iron oxidation by a Leptospirillum ferriphilum -dominated culture (Gahan et al, 2010) and the bioleaching ability of an undefined mixed acidophile consortium (Shiers et al, 2005). One exception is the salt tolerant industrial isolate, L. ferriphilum Sp-Cl and its genome sequence will aid in discovering adaptations to high salt concentrations in acidophiles (Issotta et al, 2016). The greater sensitivity to the membrane permeable anion chloride is due to its ability to cross the cell membrane.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2017

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Extremely acidophilic microorganisms (pH optima for growth of ≤3) are utilized for the extraction of metals from sulfide minerals in the industrial biotechnology of “biomining.” A long term goal for biomining has been development of microbial consortia able to withstand increased chloride concentrations for use in regions where freshwater is scarce. However, when challenged by elevated salt, acidophiles experience both osmotic stress and an acidification of the cytoplasm due to a collapse of the inside positive membrane potential, leading to an influx of protons. In this study, we tested the ability of the halotolerant acidophile Acidihalobacter prosperus to grow and catalyze sulfide mineral dissolution in elevated concentrations of salt and identified chloride tolerance mechanisms in Ac. prosperus as well as the chloride susceptible species, Acidithiobacillus ferrooxidans. Ac. prosperus had optimum iron oxidation at 20 g L−1 NaCl while At. ferrooxidans iron oxidation was inhibited in the presence of 6 g L−1 NaCl. The tolerance to chloride in Ac. prosperus was consistent with electron microscopy, determination of cell viability, and bioleaching capability. The Ac. prosperus proteomic response to elevated chloride concentrations included the production of osmotic stress regulators that potentially induced production of the compatible solute, ectoine uptake protein, and increased iron oxidation resulting in heightened electron flow to drive proton export by the F0F1 ATPase. In contrast, At. ferrooxidans responded to low levels of Cl− with a generalized stress response, decreased iron oxidation, and an increase in central carbon metabolism. One potential adaptation to high chloride in the Ac. prosperus Rus protein involved in ferrous iron oxidation was an increase in the negativity of the surface potential of Rus Form I (and Form II) that could help explain how it can be active under elevated chloride concentrations. These data have been used to create a model of chloride tolerance in the salt tolerant and susceptible species Ac. prosperus and At. ferrooxidans, respectively.

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“…Due to its extraordinary characteristics, Leptospirillum species have been used throughout the world in industrial bioleaching operations (Sand et al . 1992; Issotta et al . 2016).…”

Section: Resultsmentioning

confidence: 99%

Untapped microbial composition along a horizontal oxygen gradient in a Costa Rican volcanic influenced acid rock drainage system

Arce-Rodríguez

Puente-Sánchez

Avendaño³

et al. 2019

Preprint

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Based on the analysis of 16S rRNA gene metabarcoding, here we report the shift in the microbial community structure along a horizontal oxygen gradient (0.40-6.06 mg L−1) in a volcanic influenced acid rock drainage (VARD) environment, known as San Cayetano (Cartago, Costa Rica; pH =2.94-3.06, sulfate ~0.87-1.19 g L−1, iron ~35-61 mg L−1). This VARD is dominated by microorganisms involved in the geochemical cycling of iron, sulfur and nitrogen; however, the identity of the species changes with the oxygen gradient along the river course. The anoxic spring of San Cayetano is dominated by a putative anaerobic sulfate-reducing Deltaproteobacterium as well as sulfur-oxidizing bacteria (such as Acidithiobacillus or Sulfobacillus), which favor the process of dissolution of sulfide minerals and oxidation of H2S. In oxic conditions, aerobic iron-oxidizers (Leptospirillum, Acidithrix, Ferritrophicum, Ferrovum) and heterotrophic bacteria (Burkholderiaceae Betaproteobacterium, Trichococcus, Acidocella) were identified among others. Thermoplasmatales archaea closely related to environmental phylotypes found in other ARD/AMD niches were also found throughout the entire ecosystem. This work describes the changes in bacterial diversity, and possible metabolic activities occurring along a horizontal oxygen gradient in a volcanic influenced acid rock drainage system.

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Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile

Cited by 25 publications

References 35 publications

Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus

Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus

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

Untapped microbial composition along a horizontal oxygen gradient in a Costa Rican volcanic influenced acid rock drainage system

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