Archaeal Richmond Mine acidophilic nanoorganisms
| ARMAN (uncultured acidophilic lineages) | |
|---|---|
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Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN) were first discovered in an extremely acidic mine located in northern California (Iron Mountain Mine) by Brett Baker in Jillian F. Banfield's laboratory at the University of California Berkeley. These novel groups of Archaea named ARMAN-1, ARMAN-2, and ARMAN-3 were missed by previous PCR-based surveys of the mine community because the ARMAN's have several mismatches with commonly used PCR primers for 16S rRNA genes. Baker et al detected them in a later study using shotgun sequencing of the community. The three groups represent three novel lineage within the Euryarchaeota, a subgroup of the Archaea. Their 16S rRNA genes differ by as much as 17% between the three groups. Prior to their discovery all of the Archaea shown to be associate with Iron Mountain belonged to the order Thermoplasmatales (eg. Ferroplasma spp.).
Examination of different sites in the mine using fluorescent probes specific to the ARMAN groups has revealed that they are always present in communities associated with acid mine drainage (AMD) that have pH < 1.5. They are usually found in low abundance (5-25%) in the community.
Using cryo-electron tomography an extensive 3D characterization of uncultivated ARMAN cells within mine biofilms has been done (Comolli et al. in press). This has revealed that they are right at the cell size predicted to be the lower limit for life, 0.009 µm3 and 0.04 µm3 (NRC Steering group). Furthermore, the cells contains on average ~92 ribosomes per cell. This is astoundingly little when you consider that the average E. coli cell grown in culture contains ~10,000 ribosomes.
Filtration of the mine samples and examination using microscopy has revealed that they are very small cells (~300nm in diameter), possibly the smallest yet described that are free living. The genomes of these are groups have been been sequenced at the DOE Joint Genome Institute during a 2006 community sequencing program (CSP). Draft assemblies of the genomes are complete and their lifestyle is becoming well understood.
References
- Brett J. Baker, Gene W. Tyson, Richard I. Webb, Judith Flanagan, Phil Hugenholtz and Jill F. Banfield (2006) Lineages of acidophilic Archaea revealed by community genomic analysis. Science. 314,1933-1935. Abstract
- Comolli, LR, Baker BJ, Downing, KH, Siegerist CE and Banfield JF (2008) Novel archaea have ultra-small cell size and few ribosomes, yet host multiple virus populations. ISME Journal, in press.
- NCBI CoreNucleotide ARMAN-1
- NCBI CoreNucleotide ARMAN-2