Enigmatic, ultrasmall, uncultivated Archaea

Journal Article · Fri Jan 01 00:00:00 EST 2010 · Proceedings of the National Academy of Sciences

DOI:https://doi.org/10.1073/pnas.0914470107· OSTI ID:981811

Baker, Brett J. ^[1]; Comolli, Luis ^[2]; Dick, Gregory J. ^[1]; Hauser, Loren John ^[3]; Hyatt, Philip Douglas ^[3]; Dill, Brian ^[3]; Land, Miriam L ^[3]; Verberkmoes, Nathan C ^[3]; Banfield, Jillian F. ^[1]

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1. University of California, Berkeley
2. Lawrence Berkeley National Laboratory (LBNL)
3. ORNL

Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge-particularly for Archaea-that occur at relatively low abundance and in extreme environments. Ultrasmall cells (<500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected in a variety of acidic ecosystems. We reconstructed composite, near-complete similar to 1-Mb genomes for three lineages, referred to as ARMAN (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples and a biofilm filtrate. Genes of two lineages are among the smallest yet described, enabling a 10% higher coding density than found genomes of the same size, and there are noncontiguous genes. No biological function could be inferred for up to 45% of genes and no more than 63% of the predicted proteins could be assigned to a revised set of archaeal clusters of orthologous groups. Some core metabolic genes are more common in Crenarchaeota than Euryarchaeota, up to 21% of genes have the highest sequence identity to bacterial genes, and 12 belong to clusters of orthologous groups that were previously exclusive to bacteria. A small subset of 3D cryo-electron tomographic reconstructions clearly show penetration of the ARMAN cell wall and cytoplasmic membranes by protuberances extended from cells of the archaeal order Thermoplasmatales. Interspecies interactions, the presence of a unique internal tubular organelle [Comolli, et al. (2009) ISME J 3: 159-167], and many genes previously only affiliated with Crenarchaea or Bacteria indicate extensive unique physiology in organisms that branched close to the time that Cren- and Euryarchaeotal lineages diverged.

• Research Organization: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: Work for Others (WFO)
• DOE Contract Number: DE-AC05-00OR22725
• OSTI ID: 981811
• Journal Information: Proceedings of the National Academy of Sciences, Vol. 107, Issue 19; ISSN 0027-8424
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
ABUNDANCE
BACTERIA
BIOLOGICAL FUNCTIONS
CELL CONSTITUENTS
CELL WALL
ECOSYSTEMS
GENES
MEMBRANES
MICROORGANISMS
PHYSIOLOGY
PROTEINS
ACID-MINE DRAINAGE
NANOARCHAEUM-EQUITANS
GENOMIC ANALYSIS
IGNICOCCUS-HOSPITALIS
MICROBIAL COMMUNITIES
REVEALS
RECONSTRUCTION
PROKARYOTES
EUKARYOTES