Project Name Acid Mine Drainage Metagenome 
Domain (1) bacteria
Investigators (1)
Institution DOE Joint Genome Institute
Project Code CAM_PROJ_AcidMine
Project Type metagenome
Publications (1)


Samples of biofilms associated acid mine drainage were collected from the Richmond Mine, Iron Mountain, CA, from the 5-way (CG) and Ultra Back A (UBA) sites. Iron Mountain is located at 40 deg 40' 38.42'' N and 122 deg 31' 19.90'' W (elevation ~ 3,100 ft)..

5-Way (CG) Acid Mine Drainage Biofilm Metagenome

The Richmond mine at Iron Mountain, California, is an acid mine drainage (AMD) superfund site. AMD is a worldwide environmental problem that arises largely from microbial activity. Acid solutions form when rocks rich in sulfide minerals are oxidized upon exposure to air and water (acid rock drainage), but the rates of sulfide oxidation are typically slow and the sulfuric acid is rapidly neutralized by interaction with surrounding silicate minerals (hydrolysis reactions). Perhaps one of the most intriguing aspects of the AMD problem is that the majority of the AMD formed is due directly to microbial activity.

This project is a genome-based approach that enables culture-independent understanding of microbial activity relevant to geochemical processes that occur in AMD systems. The biofilm sequencing project was designed to explore the distribution and diversity of metabolic pathways in these communities (e.g., nitrogen fixation, sulfur oxidation, iron oxidation), in order to understand the mechanisms by which the microbes tolerate the environmental extremes, and to evaluate how these tolerance mechanisms impact the geochemistry of the environment .

This community sample was collected from a low-complexity microbial biofilm growing hundreds of feet underground within a pyrite (FeS2) ore body. This represents a self-contained biogeochemical system characterized by tight coupling between microbial iron oxidation and acidification due to pyrite dissolution. Samples of pink biofilm and associated acid mine drainage were collected from the Richmond Mine, Iron Mountain CA from the 5-way (CG) site in March 2002. Iron Mountain is located at 40 deg 40' 38.42'' N and 122 deg 31' 19.90'' W (Elevation ~ 3,100 ft). The 5-way biofilm was growing at pH 0.83 on the surface of 42 deg C AMD solution.

Random shotgun sequencing of this biofilm resulted in the first reconstruction of multiple genomes directly from an environmental sample.

UBA Acid Mine Drainage Biofilm Metagenome

Samples of pink biofilm and associated acid mine drainage were collected from the Richmond Mine, Iron Mountain, CA, from the Ultra Back A (UBA) site in June 2005. Iron Mountain is located at 40 deg 40' 38.42'' N and 122 deg 31' 19.90'' W (elevation ~ 3,100 ft). The UBA biofilm was subaerial, collected from the base of a ~2 m high pile of pyrite sediment over which pH 1.28, 38 deg C acid mine drainage solution was flowing.

The first version of this project has a partial genome of one Leptospirillum group II species that dominates this biofilm.


Name Code Organism CDS NT Pep
ACID_MINE_02 (5Way) Metagenomic Assembly JGI_AMD_5WAY_IRNMTN_ASM_20020301 ACID_MINE_02      
ACID_MINE_05 (UBA) Assembly of Leptospirillum sp. Group II JGI_AMD_UBA_IRNMTN_ASM_LeptoII ACID_MINE_05      


Sample Name PI Desc Cart
ACID_MINE_02 NA ACID_MINE_02 - 5-Way (CG) Acid Mine Drainage Biofilm
ACID_MINE_05 NA ACID_MINE_05 - UBA Acid Mine Drainage Biofilm