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Metagenomics: Sequences from the Environment [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2006.

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Metagenomics: Sequences from the Environment [Internet].

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Acid Mine Drainage Biofilm

This biofilm sequencing project was designed to explore the distribution and diversity of metabolic pathways in acidophilic biofilms (e.g., nitrogen fixation, sulfur oxidation, iron oxidation), in order to understand the mechanisms by which the microbes tolerate environmental extremes, and to evaluate how this might impact the geochemistry of the environment.

Data

WGS studyAADL00000000
ContigsAADL01000001-AADL01002534
ScaffoldsCH003520-CH004435
Trace data180,713 reads available from the Trace Archive
16S ribosomal RNANo 16S rRNA data available

A total of 76.2 million bp of DNA sequence was generated from 103,462 high quality trimmed reads.

Coverage average depth in raw shotgun data: 10X

85% of shotgun reads were combined into contigs greater then 2 kb with a combined length of 10.83 Mbp.

Isolation Source

Acidophilic biofilms are self-sustaining communities that grow in the deep subsurface and receive no significant inputs of fixed carbon or nitrogen from external sources. While some acid mine drainage is caused by the oxidization of rocks rich in sulfide minerals, this is a very slow process and most acid mine drainage is due directly to microbial activity.

This data was isolated underground from a pink biofilm microbial community growing on the surface of flowing acid mine drainage (AMD) in the five-way region (CG) of the Richmond mine at Iron Mountain, California 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 in pH 0.83, 42 degrees C, 317 mM Fe, 14 mM Zn, 4 mM Cu, and 2 mM As solution and was collected from a surface area of approximately 0.05 m2.

Genome Assembly

The 2455 contigs were subdivided into five sets of WGS scaffolds:

AssemblySequencesNotes
Leptospirillum sp. Group II '5-way CG' CH003520-CH003544Iron-oxidizing bacteria
Leptospirillum sp. Group IIICH003545-CH003921Iron-oxidizing bacteria
Ferroplasma acidarmanus Type ICH003922-CH004070Iron-oxidizing archaea
Ferroplasma sp. Type IICH004071-CH004104Iron-oxidizing archaea
Thermoplasmatales archaeon Gpl (G-plasma)CH004105-CH004435Archaea; facultatively anaerobic, thermoacidophilic, autotrophic or heterotrophic organisms

References

1.
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment Nature 428, 25-26 . [PubMed: 14961025]
2.
Ram RJ, Verberkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC 2nd, Shah M, Hettich RL, Banfield JF (2005) Community proteomics of a natural microbial biofilm Science 308, 1915-1920 . [PubMed: 15879173]
3.
Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM (2005) Comparative metagenomics of microbial communities Science 308, 554-557 . [PubMed: 15845853]
4.
Acid Mine Drainage Home Page at the University of California, Berkeley.

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Sequence Analysis

  • BLAST against these contigs.
  • Genome Project ID: 13696

Evolution

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