Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-09-17

AUTHORS

Jessica K. Jarett, Stephen Nayfach, Mircea Podar, William Inskeep, Natalia N. Ivanova, Jacob Munson-McGee, Frederik Schulz, Mark Young, Zackary J. Jay, Jacob P. Beam, Nikos C. Kyrpides, Rex R. Malmstrom, Ramunas Stepanauskas, Tanja Woyke

ABSTRACT

BACKGROUND: Nanoarchaeota are obligate symbionts of other Archaea first discovered 16 years ago, yet little is known about this largely uncultivated taxon. While Nanoarchaeota diversity has been detected in a variety of habitats using 16S rRNA gene surveys, genome sequences have been available for only three Nanoarchaeota and their hosts. The host range and adaptation of Nanoarchaeota to a wide range of environmental conditions has thus largely remained elusive. Single-cell genomics is an ideal approach to address these questions as Nanoarchaeota can be isolated while still attached to putative hosts, enabling the exploration of cell-cell interactions and fine-scale genomic diversity. RESULTS: From 22 single amplified genomes (SAGs) from three hot springs in Yellowstone National Park, we derived a genome-based phylogeny of the phylum Nanoarchaeota, linking it to global 16S rRNA gene diversity. By exploiting sequencing of co-sorted tightly attached cells, we associated Nanoarchaeota with 6 novel putative hosts, 2 of which were found in multiple SAGs, and showed that the same host species may associate with multiple species of Nanoarchaeota. Comparison of single nucleotide polymorphisms (SNPs) within a population of Nanoarchaeota SAGs indicated that Nanoarchaeota attached to a single host cell in situ are likely clonal. In addition to an overall pattern of purifying selection, we found significantly higher densities of non-synonymous SNPs in hypothetical cell surface proteins, as compared to other functional categories. Genes implicated in interactions in other obligate microbe-microbe symbioses, including those encoding a cytochrome bd-I ubiquinol oxidase and a FlaJ/TadC homologue possibly involved in type IV pili production, also had relatively high densities of non-synonymous SNPs. CONCLUSIONS: This population genetics study of Nanoarchaeota greatly expands the known potential host range of the phylum and hints at what genes may be involved in adaptation to diverse environments or different hosts. We provide the first evidence that Nanoarchaeota cells attached to the same host cell are clonal and propose a hypothesis for how clonality may occur despite diverse symbiont populations. More... »

PAGES

161

References to SciGraph publications

  • 2013-04-22. Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park in BIOLOGY DIRECT
  • 2017-08-16. Microbial diversity in acidic thermal pools in the Uzon Caldera, Kamchatka in ANTONIE VAN LEEUWENHOEK
  • 2014-11-17. Fast and sensitive protein alignment using DIAMOND in NATURE METHODS
  • 2002-01-22. Phototrophic consortia: model systems for symbiotic interrelations between prokaryotes in ARCHIVES OF MICROBIOLOGY
  • 2013-12-08. Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures in NATURE GENETICS
  • 2017-10-31. The trajectory of microbial single-cell sequencing in NATURE METHODS
  • 2017-07-05. ‘ARMAN’ archaea depend on association with euryarchaeal host in culture and in situ in NATURE COMMUNICATIONS
  • 2018-02-21. A virus or more in (nearly) every cell: ubiquitous networks of virus–host interactions in extreme environments in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2013-11-22. Genomic analysis reveals key aspects of prokaryotic symbiosis in the phototrophic consortium “Chlorochromatium aggregatum” in GENOME BIOLOGY
  • 2017-06-23. Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2017-07-21. Uncultivated microbes in need of their own taxonomy in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2002-05. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont in NATURE
  • 2016-01-08. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2008-11-10. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans in GENOME BIOLOGY
  • 2008-07-12. Ignicoccus hospitalis and Nanoarchaeum equitans: ultrastructure, cell–cell interaction, and 3D reconstruction from serial sections of freeze-substituted cells and by electron cryotomography in ARCHIVES OF MICROBIOLOGY
  • 2014-04-10. Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics in NATURE PROTOCOLS
  • 2011-11-08. Extreme genome reduction in symbiotic bacteria in NATURE REVIEWS MICROBIOLOGY
  • 2017-05-08. ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates in NATURE METHODS
  • 2014-11-05. Untargeted metabolomics studies employing NMR and LC–MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis in METABOLOMICS
  • 2015-06-15. Unusual biology across a group comprising more than 15% of domain Bacteria in NATURE
  • 2013-07-14. Insights into the phylogeny and coding potential of microbial dark matter in NATURE
  • 2002-11. Genome evolution in bacterial endosymbionts of insects in NATURE REVIEWS GENETICS
  • 2002-06-28. Estimating Population Size and Transmission Bottlenecks in Maternally Transmitted Endosymbiotic Bacteria in MICROBIAL ECOLOGY
  • 2016-12-27. Microbial diversity and autotrophic activity in Kamchatka hot springs in EXTREMOPHILES
  • 2002-09-03. Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia in NATURE GENETICS
  • 2012-07-18. RNA processing in the minimal organism Nanoarchaeum equitans in GENOME BIOLOGY
  • 2008-06-14. Nanoarchaeal 16S rRNA gene sequences are widely dispersed in hyperthermophilic and mesophilic halophilic environments in EXTREMOPHILES
  • 2017-08-01. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea in NATURE BIOTECHNOLOGY
  • 2014-07-11. Life on the edge: functional genomic response of Ignicoccus hospitalis to the presence of Nanoarchaeum equitans in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2006-02-10. Asymmetrical Evolution of Cytochrome bd Subunits in JOURNAL OF MOLECULAR EVOLUTION
  • 2017-04-03. Retroelement guided protein diversification abounds in vast lineages of bacteria and archaea in NATURE MICROBIOLOGY
  • 2015-02-27. Diverse uncultivated ultra-small bacterial cells in groundwater in NATURE COMMUNICATIONS
  • 2016-07-05. Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment in NATURE COMMUNICATIONS
  • 2017-08-04. The growing tree of Archaea: new perspectives on their diversity, evolution and ecology in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s40168-018-0539-8

    DOI

    http://dx.doi.org/10.1186/s40168-018-0539-8

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1107066840

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30223889


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