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 Jill Banfield's laboratory at the University of California Berkeley. These novel groups of Archaea named ARMAN-1, ARMAN-2 (Candidatus Micrarchaeum acidiphilum ARMAN-2 ), and ARMAN-3 were missed by previous PCR-based surveys of the mine community because the ARMANs have several mismatches with commonly used PCR primers for 16S rRNA genes. Baker et al.[1] detected them in a later study using shotgun sequencing of the community. The three groups represent three novel lineages 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 acidarmanus).
Distribution
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), at Iron Mountain in northern California, that have pH < 1.5. They are usually found in low abundance (5-25%) in the community. More recently, closely related organisms have been detected in an acidic boreal mire or bog in Finland [2].
Cell structure and Ecology
Using cryo-electron tomography an extensive 3D characterization of uncultivated ARMAN cells within mine biofilms has been done (Comolli et al.[3]). 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). They also found that despite their unusually small cell size it is common to find more than one type of virus attached to the cells while in the biofilms. Furthermore, the cells contain on average ~92 ribosomes per cell. By comparison, E.coli's ribosome density is roughly 2-8 times greater, given ~10,000 ribosomes in a 0.5-0.6 µm3 cell volume.
Genomics and proteomics
The genomes of three ARMAN groups have been sequenced at the DOE Joint Genome Institute during a 2006 Community Sequencing Program (CSP). These three genomes were successfully binned from the community genomic data using ESOM or Emergent Self-Organizing Map clustering of tetra-nucleotide DNA signatures (Dick et al. 2009[4]). The first draft of Candidatus Micrarchaeum acidiphilum ARMAN-2 has been released and is ~1 Mb (5 scaffolds, Baker et al.. in prep. Additionally, this has enabled the characterization of these lineages using shotgun community proteomics.
References
- ^ Baker, Brett J. "Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis". Science. 314 (5807): 1933–1935. doi:10.1126/science.1132690.
{{cite journal}}: Cite has empty unknown parameter:|month=(help); Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ Juottonen et al. Seasonality of rDNA- and rRNA-derived archaeal communities and methanogenic potential in a boreal mire, ISME Journal 24 July 2008; doi:10.1038/ismej.2008.66
- ^ Commolli, LR et al. Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon, ISME Journal 3, 159-167.
- ^ Dick et al. Community-wide analysis of microbial genome sequence signatures. Genome Biology 10:R85
- NCBI CoreNucleotide ARMAN-1
- NCBI CoreNucleotide ARMAN-2
- NCBI Candidatus Micrarchaeum acidiphilum ARMAN-2 genome