Genome studies of a soil bacterium, a potential candidate for removing arsenic from contaminated water

Worldwide various human activities such as mining, chemical industries, use of arsenic-based pesticides, and natural occurrences result in contamination of soil and water with heavy metals and cause severe environmental and health problems. Millions of people are exposed to directly or indirectly to the toxic metals including arsenic (As). Long-term exposure to As leads to several skin diseases, such as hyper- and hypo-pigmentation, hyperkeratosis and melanosis, as well as gangrene, skin cancer, lung cancer and bladder cancer. Poisoning occurs through drinking of contaminated water and/or consumption of foods produced on cultivated lands irrigated with As-contaminated water. It is therefore important to develop efficient, yet affordable technologies to remove As from water by any means. Use of microorganisms such as bacteria is one of the possibilities. In fact, the bacteria have developed several metabolic processes and strategies to convert As to various forms including respiratory arsenate reduction, cytoplasmic arsenate reduction and arsenite methylation. Furthermore, certain bacteria have developed the necessary genetic components that make the bacteria resistant to As toxicity, allowing them to survive and grow in an As contaminated environment where other organisms can hardly exist.

This report concerns a bacterial strain, Lysinibacillus sphaericus B1-CDA as potential candidate for removal of heavy metals from the contaminated sources. The strain was isolated from a cultivated land in the Chuadanga district of Bangladesh, where soil, sediment, and ground water were contaminated with As for many years. The genetic composition and evolutionary history of this bacterium were investigated by using massively parallel sequencing and comparative analysis with other known Lysinibacillus genomes. The summary of the genome with nucleotide content and gene count levels are presented in Table 1. All genes of B1-CDA predicted to be involved in its resistance to As and/or other heavy metals were annotated. Annotation of all genes predicted to be metal responsive was manually curated, with a particular focus on genes responsive to As. The presence of As responsive genes was verified by PCR in vitro conditions. PCR amplification confirmed that B1-CDA is harboring acr3, arsR, arsB and arsC arsenic responsive genes.

Table 1. Summary of the genome of B1-CDA with nucleotide content and gene count levels

Table 1. Summary of the genome of B1-CDA with nucleotide content and gene count levels

Based on results obtained by using several bioinformatics tools it was confirmed that L. sphaericus B1-CDA contains many specific metal resistant genes, such as arsenic, nickel, cobalt, iron, manganese, chromium, cadmium, lead and zinc. These results also revealed that B1-CDA genome consists of many proteins that catalyze binding and transport of metal ions. Therefore, the findings in this study may be useful in bioremediation of the toxic metals from the polluted environment. This study also demonstrates that it is possible to speed up molecular biology research by using bioinformatics tools.



Comparative genome analysis of Lysinibacillus B1-CDA, a bacterium that accumulates arsenics.
Rahman A, Nahar N, Nawani NN, Jass J, Ghosh S, Olsson B, Mandal A
Genomics. 2015 Sep 24


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