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Genomic Characterization of Bacillus safensis Isolated from Mine Tailings in Peru and Evaluation of Its Cyanide-Degrading Enzyme CynD.

ABSTRACT: Understanding the biochemistry and metabolic pathways of cyanide degradation is necessary to improve the efficacy of cyanide bioremediation processes and industrial requirements. We have isolated and sequenced the genome of a cyanide-degrading Bacillus strain from water in contact with mine tailings from Lima, Peru. This strain was classified as Bacillus safensis based on 16S rRNA gene sequencing and core genome analyses and named B. safensis PER-URP-08. We searched for possible cyanide-degradation enzymes in the genome of this strain and identified a putative cyanide dihydratase (CynD) gene similar to a previously characterized CynD from Bacillus pumilus C1. Sequence analysis of CynD from B. safensis and B. pumilus allow us to identify C-terminal residues that differentiate both CynDs. We then cloned, expressed in Escherichia coli, and purified recombinant CynD from B. safensis PER-URP-08 (CynD_PER-URP-08) and showed that in contrast to CynD from B. pumilus C1, this recombinant CynD remains active at up to pH 9. We also showed that oligomerization of CynD_PER-URP-08 decreases as a function of increased pH. Finally, we demonstrated that transcripts of CynD_PER-URP-08 in B. safensis PER-URP-08 are strongly induced in the presence of cyanide. Our results suggest that the use of B. safensis PER-URP-08 and CynD_PER-URP-08 as potential tool for cyanide bioremediation warrants further investigation. IMPORTANCE Despite being of environmental concern around the world due to its toxicity, cyanide continues to be used in many important industrial processes. Thus, searching for cyanide bioremediation methods is a matter of societal concern and must be present on the political agenda of all governments. Here, we report the isolation, genome sequencing and characterization of cyanide degradation capacity of a bacterial strain isolated from an industrial mining site in Peru. We characterize a cyanide dehydratase (CynD) homolog from one of these bacteria, Bacillus safensis PER-URP-08.

SUBMITTER: Justo Arevalo S

PROVIDER: S-EPMC9317851 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The mechanism of bacterial adaption to manganese-polluted environments was explored using 50 manganese-tolerant strains of bacteria isolated from soil of the largest manganese mine in China. Efficiency of manganese removal by the isolated strains was investigated using atomic absorption spectrophotometry. Bacillus safensis strain ST7 was the most effective manganese-oxidizing bacteria among the tested isolates, achieving up to 82% removal at a Mn(II) concentration of 2,200 mg/L. Bacteria-mediated manganese oxide precipitates and high motility were observed, and the growth of strain ST7 was inhibited while its biofilm formation was promoted by the presence of Mn(II). In addition, strain ST7 could grow in the presence of high concentrations of Al(III), Cr(VI), and Fe(III). Genome-wide analysis of the gene expression profile of strain ST7 using the RNA-seq method revealed that 2,580 genes were differently expressed under Mn(II) exposure, and there were more downregulated genes (n = 2,021) than upregulated genes (n = 559) induced by Mn stress. KAAS analysis indicated that these differently expressed genes were mainly enriched in material metabolisms, cellular processes, organism systems, and genetic and environmental information processing pathways. A total of twenty-six genes from the transcriptome of strain ST7 were involved in lignocellulosic degradation. Furthermore, after 15 genes were knocked out by homologous recombination technology, it was observed that the transporters, multicopper oxidase, and proteins involved in sporulation and flagellogenesis contributed to the removal of Mn(II) in strain ST7. In summary, B. safensis ST7 adapted to Mn exposure by changing its metabolism, upregulating cation transporters, inhibiting sporulation and flagellogenesis, and activating an alternative stress-related sigB pathway. This bacterial strain could potentially be used to restore soil polluted by multiple heavy metals and is a candidate to support the consolidated bioprocessing community.

Project description:Copper mining, the central axis of Chile's economic development, produces a large number of tailings, which become a potential environmental risk. This study aims to evaluate the mechanical properties resulting from the making of Portland cement mixtures with tailings as aggregates so that they can be eventually used in paving stones for building inactive tailings dams. Tailings coming from two dams at a concentration plant located in Taltal (Chile) were used. Currently, Dam 1 is inactive, while Dam 2 is active. The tailings samples obtained from both dams were granulometrically characterized by sieving. In addition, pH, humidity, Eh, and mineralogical assays (sulfides, oxides, sulfates, carbonates, phosphates, and silicates) were measured. The fines content of the tailings from Dams 1 and 2 with a sieve size of N°200 ASTM were 76.2% and 29.6%, respectively. Therefore, owing to their high percentage of fines, they cannot be as used as concrete aggregates. Aggregates must contain a maximum percentage of fines so that mortars and concrete can meet Chilean standards. In this paper, to comply with a 7% and 15% fines content lower than 0.075 mm, tailings materials were mixed with conventional aggregates containing very little fines. In addition, a reference mixture was made with only tailings aggregates with and without a superplasticizer additive. To measure the mixtures of cement, aggregates, and tailings, bending and compression strength assays were made of the specimens after a 28-day curing, according to the Chilean standard. The results of the study show that the addition of only part of the tailings to the mixture increases bending strength by 26% and compression strength by 180% compared with the reference mortar, with a fines content lower than 0.075 mm in the 7% mixture, thus allowing paving stone manufacture with tailings materials. In addition, it was possible to increase the workability of the reference mixture by using superplasticizers as additives.

Dataset Information

Genomic Characterization of Bacillus safensis Isolated from Mine Tailings in Peru and Evaluation of Its Cyanide-Degrading Enzyme CynD.

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