The rapid industrial development and modernized lifestyle have increased the metal extraction activities leading towards the depletion of high grade ore globally. Metals are cornerstone of rapidly developing human civilization. Our everyday lives in the modern society are surrounded by metals in the form of vehicles, electronic equipments, construction materials and many more. Therefore in recent past attempt are being made to extract metals from low grade ores and different wastes (i.e. mine tailings, industrial wastes, electrical and electronic waste etc.) to meet the growing demand. Metal extraction from low grade ores and wastes using microorganisms are gaining interest as traditional metallurgical technologies are inefficient in terms of cost, energy and environmental issues. Bioleaching has been successfully implemented for the extraction of certain valuable metals like copper, uranium, nickel, cobalt and zinc. Copper bioleaching from secondary sulfide ores is a well established process contributing towards 20-25% of copper production globally. Several acidophilic, iron and sulphur oxidizing chemolithotropic bacteria such as Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans, Leptospirillum ferrooxidans, Letospirillum ferriphilum etc. are able to extract valuable metals form low grade resources efficiently. Bioleaching study of several metals from low grade ores and wastes using acidophilic bacteria have obtained satisfactory results. However, it is associated with certain limitations such as microbial cell sensitivity towards pulp density, high metal concentration and lower pH. To address such issues, researchers are targeting to use the indigenous microbes/microbial consortia for metal extraction from respective ores. Several studies have reported about the microbial diversity in such harsh environmental conditions. Innate microbial consortium inhabiting the rock, soil, water and surface of living things in a particular ecological niche are known as indigenous microorganisms. These occur naturally in environment having an important role in various biogeochemical processes such as bioleaching, biodegradation, biocomposting, improving soil fertility, nitrogen fixation and many more.

Microbial consortia inhabiting the soil and water of the mining sites have a great ability of metal bioleaching from the respective ore. Researchers have a strong believe that indigenous microorganisms isolated from a mining site would efficiently recover metals from the respective ore as they had adapted to the mineralogy of the ore. Several researchers have studied the recovery of metal from low grade ores and wastes using indigenous microbial consortia. Three different Acidithiobacillus sp. isolated from sulfur springs of Ramsar, Iran were able to 100% uranium. Bacillus anthrasis MSB 2, Acinetobacter sp. MSB 5, Bacillus sp. MMR 1, and Lysinibacillus sp. MSB 11 isolated from low grade ores of Sanindipur manganese mine of Sundargarh, Odisha solubilises significant amount of manganese from the low grade ore. 77% of copper and 70.58% of zinc were recovered by a consortia of three indigenous acidophilic iron oxidizing bacteria Acidithiobacillus ferrooxidans strain AS2, Leptospirillum ferriphilum strain YSK, and Leptosirillum ferrooxidans strain L15 isolated from Baiyin copper mine stope, China. Five indigenous cyanogenic bacteria isolated from two e-waste burial sites in Iran were efficient in extracting copper. Leptospirillum ferriphilum strain isolated from Chitradurga mine drainage samples was capable of recovering 96.96% of zinc sphalerite concentrate of Dariba mines.

Identification and characterization of indigenous microorganisms from extreme mining environments is one of the important aspects of research in bioleaching. The developments of different OMIC technologies have enabled researchers to study the microbial diversity of extreme mining environment and their possible role in metal dissolution. Molecular techniques such as FISH (fluorescence insitu hybridization), DGGE (denaturing gradient gel electrophoresis), qRT-PCR, 16S rRNA sequence analysis, etc. are used for identification of more efficient bioleaching microbes inhabiting the extreme mining environment. Genomic sequencing of 16S rRNA gene is widely being used for the identification of bacterial isolates isolated from mining sites. Unculturable nature of some microbes as well as the enormous biodiversity provides hurdles in accurate assessment of microbial diversity of a particular ecological niche. Metagenomics provide a possible solution to the above mentioned problem. It involves high throughput sequencing of environmental samples such as soil, acid mine drainage, marine and sediment samples. Metagenomic data provides all genomic information of the culturable and unculturable microbial diversity of the area under study. This area of bioleaching research needs more attention.