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. 2016 Jul 5:7:12115.
doi: 10.1038/ncomms12115.

Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment

Louie Wurch  1   2 , Richard J Giannone  1 , Bernard S Belisle  1   2 , Carolyn Swift  1   2 , Sagar Utturkar  1 , Robert L Hettich  1   2 , Anna-Louise Reysenbach  3 , Mircea Podar  1   2
Affiliations

Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment

Louie Wurch et al. Nat Commun. .

Abstract

Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. However, cultivation is important for characterizing an organism's physiology and testing its genome-encoded potential. Here we use single-cell genomics to infer cultivation conditions for the isolation of an ectosymbiotic Nanoarchaeota ('Nanopusillus acidilobi') and its host (Acidilobus, a crenarchaeote) from a terrestrial geothermal environment. The cells of 'Nanopusillus' are among the smallest known cellular organisms (100-300 nm). They appear to have a complete genetic information processing machinery, but lack almost all primary biosynthetic functions as well as respiration and ATP synthesis. Genomic and proteomic comparison with its distant relative, the marine Nanoarchaeum equitans illustrate an ancient, common evolutionary history of adaptation of the Nanoarchaeota to ectosymbiosis, so far unique among the Archaea.

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Figures

Figure 1
Figure 1. Environment sampling for Nanoarchaeota cultivation.
(a) Cistern Spring pool in YNP. The arrow points to the sampled site for the Nanoarchaeota enrichments. (b) Fluorescence in situ hybridization (FISH) of a N. acidilobi–Acidilobus sp. 7A co-culture using Nanoarchaeota (green) and Crenarchaeota (orange) probes. The dotted arrow points to a free Nanoarchaeota cell. On the right is the same field imaged for DNA staining with DAPI.
Figure 2
Figure 2. Scanning electron micrographs of N. acidilobi on Acidilobus sp. 7A cells in co-culture.
The arrow points to the place of contact between two cells that reveals membrane stretching. Scale bars, 200 nm.
Figure 3
Figure 3. Maximum likelihood phylogeny of selected Archaea based on small subunit (SSU) rRNA.
Bootstrap support is indicated for selected groups at the nodes (* if <50). The three Nanoarchaeota-host systems are highlighted using blue, green and red colour.
Figure 4
Figure 4. Time course growth of Acidilobus sp. 7A in pure culture and in co-culture with Nanopusillus acidilobi.
Error bars (s.d.) are based on three culture replicates.
Figure 5
Figure 5. Immunofluorescence staining of co-cultures of N.acidilobi, Acidilobus sp. 7A and A. saccharovorans.
(a) N.acidilobi–Acidilobus sp. 7A co-culture. (b) N.acidilobi–Acidilobus sp. 7A–A. saccharovorans co-cultures. Blue corresponds to staining of the cell nucleoid DNA by DAPI (the only staining for A. saccharovorans). (c) Fluorescein-lectin (WGA, ConA and DBA) staining of N.acidilobi–Acidilobus sp. 7A co-cultures, counterstained with the DNA-binding dyes Syto62 (red) or DAPI (blue).
Figure 6
Figure 6. Circos-based genome alignments.
N. acidilobi–Nst1 (a), N. acidilobi–N. equitans (b) and Acidilobus sp. 7A–A. saccharovorans (c). Connecting line indicate pairs of orthologues between the genomes, the colour being scaled to % amino-acid identity levels. The outer ring histograms (a,c) show relative abundance of individual encoded proteins based on mass spectrometry proteomics.
Figure 7
Figure 7. Metabolic reconstruction of N. acidilobi–Acidilobus sp. 7A based on genomic sequences.
Proteome relative abundance data (based on protein spectral abundance) is colour-scaled for selected individual proteins in N. acidilobi or represented combined for functional COG categories (blue spheres) or specific metabolic processes or protein complexes (red spheres), with corresponding relative abundance.
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References

    1. Brown C. T. et al. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523, 208–211 (2015). - PubMed
    1. Rinke C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013). - PubMed
    1. Wrighton K. C. et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 337, 1661–1665 (2012). - PubMed
    1. Castelle C. J. et al. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr. Biol. 25, 690–701 (2015). - PubMed
    1. Comolli L. R. & Banfield J. F. Inter-species interconnections in acid mine drainage microbial communities. Front. Microbiol. 5, 367 (2014). - PMC - PubMed

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