Archaeal Richmond Mine acidophilic nanoorganisms
Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) were first
discovered in an extremely acidic mine located in northern California
(Richmond Mine at Iron Mountain) by Brett Baker in Jill Banfield's
laboratory at the University of California Berkeley. These novel
groups of archaea named ARMAN-1, ARMAN-2 (
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. detected them in a later study using shotgun sequencing of the
community. The three groups were originally thought to represent three
unique lineages deeply branched within the Euryarchaeota, a subgroup
of the Archaea. However, this has been revised, based on more complete
archaeal genomic tree, that they belong to a super phylum named
DPANN. The ARMAN groups now comprise deeply divergent phyla named
Micrarchaeota and Parvarchaeota. Their 16S rRNA genes differ by as
much as 17% between the three groups. Prior to their discovery all of
Archaea shown to be associated with Iron Mountain belonged to the
Thermoplasmatales (e.g., Ferroplasma acidarmanus).
2 Cell structure and ecology
3 Genomics and proteomics
5 External links
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. Recently,
closely related organisms have been detected in an acidic boreal mire
or bog in Finland, another acid mine drainage site in extreme
environments of Rio Tinto, southwestern Spain and from weak
alkaline deep subsurface hot spring in Yunohama, Japan.
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. 2009). 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,
whereas the average
E. coli cell grown in culture contains ≈10,000
ribosomes. This suggests that for ARMAN cells a much more limited
number of metabolites are present in a given cell. It raises questions
about what the minimal requirements are for a living cell.
3D reconstructions of ARMAN cells in the environment has revealed that
a small number of them attach to other
Archaea of the order
Thermoplasmatales (Baker et al. 2010 ). The
appear to penetrate the cell wall to the cytoplasm of the ARMAN
cells. The nature of this interaction hasn't been determined. It
could be some sort of parasitic or symbiotic interaction. It is
possible that ARMAN is getting some sort of metabolite that it is not
able to produce on its own.
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).
The first draft of
Micrarchaeum acidiphilum ARMAN-2 is ≈1
Mb (3 scaffolds, Baker et al.). PNAS 2010. The ARMAN-2 has recently
been closed using 454 and Solexa sequencing of other biofilms to close
the gaps and is being prepared for submission to NCBI. The genomes of
ARMAN-4 and ARMAN-5 (roughly 1 Mb as well) have unusually average
genes sizes, similar to those seen in endosymbiotic and parasitic
bacteria. This may be signature of their inter-species interactions
Archaea in nature (Baker et al. 2010 ). Furthermore, the
branching of these groups near the Euryarchaea/
Crenarchaea divide is
reflected in them sharing many genetic aspects of both
Euryarchaea. Specifically they have many genes that had previously
only been identified in Crenarchaea. It is difficult to elucidate many
of the commonly known metabolic pathways in ARMAN due to the unusually
high number of unique genes that have been identified in their
A novel type of tRNA splicing endonuclease, involved in the processing
of tRNA, has been discovered in ARMAN groups 1 and 2 (Fujishima et al.
2011). The enzyme consists of two duplicated catalytic units and
one structural unit encoded on a single gene, representing a novel
^ Baker, Brett J.; et al. (2006). "Lineages of Acidophilic Archaea
Revealed by Community Genomic Analysis". Science. 314 (5807):
1933–1935. Bibcode:2006Sci...314.1933B. doi:10.1126/science.1132690.
^ Rinke, C; Schwientek, P; Sczyrba, A; Ivanova, NN; Anderson, IJ;
Cheng, JF; Darling, A; Malfatti, S; Swan, BK; Gies, EA; Dodsworth, JA;
Hedlund, BP; Tsiamis, G; Sievert, SM; Liu, WT; Eisen, JA; Hallam, SJ;
Kyrpides, NC; Stepanauskas, R; Rubin, EM; Hugenholtz, P; Woyke, T
(2013). "Insights into the phylogeny and coding potential of microbial
dark matter". Nature. 499 (7459): 431–437.
^ Castelle, CJ; Wrighton, KC; Thomas, BC; Hug, LA; Brown, CT; Wilkins,
MJ; Frischkorn, KR; Tringe, SG; Singh, A; Markillie, LM; Taylor, RC;
Williams, KH; Banfield, JF (2015). "Genomic Expansion of Domain
Archaea Highlights Roles for Organisms from New Phyla in Anaerobic
Carbon Cycling". Current Biology. 25 (6): 690–701.
doi:10.1016/j.cub.2015.01.014. PMID 25702576.
^ Juottonen et al. Seasonality of rDNA- and rRNA-derived archaeal
communities and methanogenic potential in a boreal mire, ISME Journal
24 July 2008
^ Amaral-Zettler et al. Microbial community structure across the tree
of life in the extreme Río Tinto, ISME Journal 2010
^ Murakami et al. Metatranscriptomic analysis of microbes in an
ocean-front deep subsurface hot spring reveals novel small RNAs and
type-specific tRNA degradation, Appl Environ Microbiol 2011
^ Commolli, LR et al. Three-dimensional analysis of the structure and
ecology of a novel, ultra-small archaeon, ISME Journal 3, 159–167.
^ a b c Baker; et al. (2010). "Enigmatic, ultrasmall, uncultivated
Archaea". Proc. Natl. Acad. Sci. 107 (19): 8806–8811.
PMC 2889320 . PMID 20421484.
^ Sanders, Robert (3 May 2010). "Weird, ultra-small microbes turn up
in acidic mine drainage".
^ Dick et al. Community-wide analysis of microbial genome sequence
signatures. Genome Biology 10:R85
^ Fujishima; et al. "A novel three-unit tRNA splicing endonuclease
found in ultrasmall
Archaea possesses broad substrate specificity".
Nucleic Acids Res.
NCBI CoreNucleotide ARMAN-1
NCBI CoreNucleotide ARMAN-2
Micrarchaeum acidiphilum ARMAN-2 genome
Candidatus Parvarchaeum acidiphilum ARMAN-4 genome
Candidatus Parvarchaeum acidophilus ARMAN-5 genome
ASM Small Things Considered blog article
JGI Community Sequencing Program
University of California Berkeley
University of California Berkeley Press Release
Dr. Luis Comolli's home page with several images of ARMAN cells
2010 Univ. of California Berkeley press release
2010 USA Today article about ARMAN
2010 MSNBC article about ARMAN
Thermophile / Hyperthermophile
Abiogenic petroleum origin
Acidophiles in acid mine drainage