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 (CandidatusMicrarchaeum 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 were originally thought to represent three unique lineages deeply branched within the Euryarchaeota, a subgroup of the Archaea. However, based on a more complete archaeal genomic tree, they were assigned to a new superphylum named DPANN.[2] The ARMAN groups now comprise deeply divergent phyla named Micrarchaeota and Parvarchaeota.[3] 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 associated with Iron Mountain belonged to the order Thermoplasmatales (e.g., Ferroplasma acidarmanus).
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,[4] another acid mine drainage site in extreme environments of Rio Tinto, southwestern Spain,[5] and at a weak-alkaline deep subsurface hot spring in Yunohama, Japan.[6]
Cell structure and ecologyedit
Using cryo-electron tomography, a 3D characterization of uncultivated ARMAN cells within mine biofilms[7] revealed that they are right at the cell size predicted[citation needed] to be the lower limit for life, 0.009 μm3 and 0.04 μm3. 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 [8]). The Thermoplasmatales cells appear to penetrate the cell wall to the cytoplasm of the ARMAN cells.[9] 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 proteomicsedit
The genomes of three ARMAN groups were sequenced at the DOE Joint Genome Institute during a 2006 Community Sequencing Program.[10] These three genomes were successfully binned from the community genomic data using ESOM or Emergent Self-Organizing Map clustering of tetranucleotide DNA signatures.[11]
The first draft of Candidatus Micrarchaeum acidiphilum ARMAN-2 is ≈1 Mb.[8] 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 small average gene lengths, similar to those seen in endosymbiotic and parasitic bacteria. This may be signature of their interspecies interactions with other Archaea in nature.[8] Furthermore, the branching of these groups near the Euryarchaea/Crenarchaea divide is reflected in them sharing many genetic aspects of both Crenarchaea and 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 genomes.
A novel type of tRNA splicing endonuclease, involved in the processing of tRNA, has been discovered in ARMAN groups 1 and 2.[12] The enzyme consists of two duplicated catalytic units and one structural unit encoded on a single gene, representing a novel three-unit architecture.
Referencesedit
^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. PMID 17185602. S2CID 26033384.
^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
^LR Comolli; KH Downing; BJ Baker; CE Siegerist; JF Banfield (2009). "Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon". ISME Journal. 3 (2): 159–167. doi:10.1038/ismej.2008.99. PMID 18946497.
Dr. Luis Comolli's home page with several images of ARMAN cells
2010 Univ. of California Berkeley press release 2010-05-27 at the Wayback Machine
2010 USA Today article about ARMAN
2010 MSNBC article about ARMAN
January 01, 1970
archaeal, richmond, mine, acidophilic, nanoorganisms, arman, redirects, here, other, uses, arman, disambiguation, this, article, technical, most, readers, understand, please, help, improve, make, understandable, experts, without, removing, technical, details, . ARMAN redirects here For other uses see Arman disambiguation This article may be too technical for most readers to understand Please help improve it to make it understandable to non experts without removing the technical details April 2018 Learn how and when to remove this message 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 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 were originally thought to represent three unique lineages deeply branched within the Euryarchaeota a subgroup of the Archaea However based on a more complete archaeal genomic tree they were assigned to a new superphylum named DPANN 2 The ARMAN groups now comprise deeply divergent phyla named Micrarchaeota and Parvarchaeota 3 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 associated with Iron Mountain belonged to the order Thermoplasmatales e g Ferroplasma acidarmanus ARMAN uncultured acidophilic lineages Scientific classification Domain Archaea Phylum Micrarchaeota Parvarchaeota Contents 1 Distribution 2 Cell structure and ecology 3 Genomics and proteomics 4 References 5 External linksDistribution editExamination 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 lt 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 4 another acid mine drainage site in extreme environments of Rio Tinto southwestern Spain 5 and at a weak alkaline deep subsurface hot spring in Yunohama Japan 6 Cell structure and ecology editUsing cryo electron tomography a 3D characterization of uncultivated ARMAN cells within mine biofilms 7 revealed that they are right at the cell size predicted citation needed to be the lower limit for life 0 009 mm3 and 0 04 mm3 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 8 The Thermoplasmatales cells appear to penetrate the cell wall to the cytoplasm of the ARMAN cells 9 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 editThe genomes of three ARMAN groups were sequenced at the DOE Joint Genome Institute during a 2006 Community Sequencing Program 10 These three genomes were successfully binned from the community genomic data using ESOM or Emergent Self Organizing Map clustering of tetranucleotide DNA signatures 11 The first draft of Candidatus Micrarchaeum acidiphilum ARMAN 2 is 1 Mb 8 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 small average gene lengths similar to those seen in endosymbiotic and parasitic bacteria This may be signature of their interspecies interactions with other Archaea in nature 8 Furthermore the branching of these groups near the Euryarchaea Crenarchaea divide is reflected in them sharing many genetic aspects of both Crenarchaea and 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 genomes A novel type of tRNA splicing endonuclease involved in the processing of tRNA has been discovered in ARMAN groups 1 and 2 12 The enzyme consists of two duplicated catalytic units and one structural unit encoded on a single gene representing a novel three unit architecture References edit 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 PMID 17185602 S2CID 26033384 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 Bibcode 2013Natur 499 431R doi 10 1038 nature12352 hdl 1912 6194 PMID 23851394 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 Rio 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 LR Comolli KH Downing BJ Baker CE Siegerist JF Banfield 2009 Three dimensional analysis of the structure and ecology of a novel ultra small archaeon ISME Journal 3 2 159 167 doi 10 1038 ismej 2008 99 PMID 18946497 a b c Baker et al 2010 Enigmatic ultrasmall uncultivated Archaea Proc Natl Acad Sci 107 19 8806 8811 Bibcode 2010PNAS 107 8806B doi 10 1073 pnas 0914470107 PMC 2889320 PMID 20421484 Sanders Robert 3 May 2010 Weird ultra small microbes turn up in acidic mine drainage Our Projects Dick et al Community wide analysis of microbial genome sequence signatures Archived 2014 07 15 at the Wayback Machine Genome Biology 10 R85 Fujishima et al 2011 A novel three unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity Nucleic Acids Res 39 22 9695 704 doi 10 1093 nar gkr692 PMC 3239211 PMID 21880595 NCBI CoreNucleotide ARMAN 1 NCBI CoreNucleotide ARMAN 2 NCBI Candidatus Micrarchaeum acidiphilum ARMAN 2 genome NCBI Candidatus Parvarchaeum acidiphilum ARMAN 4 genome NCBI Candidatus Parvarchaeum acidophilus ARMAN 5 genome 1 External links editASM Small Things Considered blog article JGI Community Sequencing Program 2006 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 Archived 2010 05 27 at the Wayback Machine 2010 USA Today article about ARMAN 2010 MSNBC article about ARMAN Retrieved from https en wikipedia org w index php title Archaeal Richmond Mine acidophilic nanoorganisms amp oldid 1220236009, wikipedia, wiki, book, books, 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