Metagenomic Analysis Reveals the Presence of Heavy Metal Response Genes from Cyanobacteria Thriving in Balatoc Mines, Benguet Province, Philippines

Libertine Rose S. Sanchez¹ and Ernelea P Cao^1,2

¹Institute of Biology (IB), College of Science (CS)
University of the Philippines (UP) Diliman, Quezon City 1101 Philippines
¹Natural Sciences Research Institute (NSRI), CS, UP Diliman, Quezon City 1101 Philippines

*Corresponding Author: lssanchez@up.edu.ph

 

ABSTRACT

Tailing ponds of mining sites heavily contaminated with metals is a serious problem in many parts of the world. Metagenomic sequencing and bioinformatics analysis of water samples from the Balatoc mine tailings – an abandoned mining site in Itogon, Benguet, Philippines – revealed microbial communities, particularly cyanobacteria consortia that implied their ability to survive in metal-stressed environments. Thus, their presence can be further investigated for applications in bioremediation. Surface water samples were collected from three sampling points in the Balatoc mine tailings. Physicochemical properties of the samples were also determined. Genomic DNA was extracted from all water samples and subjected to shotgun sequencing using Illumina NextSeq2500 2 x 150 paired ends. Thirty-eight (38) Gbases raw reads obtained from three data sets showed similar microbial assemblages using St. Petersburg genome assembler (SPAdes v3.10.1). Taxonomic assignments to contigs using CLAssfier based on reduced K-mers (CLARK) revealed the relative abundance of 97% Bacteria and 3% Archaea. All sampling sites were found to have relatively the same physicochemical properties. The abandoned Balatoc tailing site exhibited high temperature (31.50 ˚C), alkaline pH (8.42), and elevated levels of copper (Cu2+) (1.53 mg/L) and zinc (Zn2+) (0.077 mg/L). A CLARK v1.2.5 custom database of cyanobacteria was also used to determine the classification, taxonomic assignment, as well as the estimation of percentage relative abundance of the cyanobacteria. Taxonomic assignments of all metadata revealed a dominant cyanobacterium, classified as Leptolyngbya sp., which comprises about 3% of the assembled contigs. Prokka v1.12 was used for annotation and protein-coding sequences (CDS) were evaluated for gene ontology (GO) using the evolutionary genealogy of genes-Non-supervised Orthologous Groups (eggNOG) Mapper v4.5. The genes conferring stress-response to metal ions Cu2+, Zn2+, lead (Pb2+), and cadmium (Cd2+) are reported to be involved in efflux/transport functions and heavy metal resistance that can be major attributes of Leptolyngbya sp. for survival to extreme metal conditions.