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

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

doi:10.1186/s40168-018-0539-8

Abstract

BackgroundNanoarchaeota 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.ResultsFrom 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.ConclusionsThis 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.

Highlights

Nanoarchaeota are obligate symbionts of other Archaea first discovered 16 years ago, yet little is known about this largely uncultivated taxon
Nanoarchaeota genome bins ranged from 28,158 bp to 549,214 bp in size (Table 1) and were clearly separated from putative host genome bins by Tetranucleotide frequencies (TNF) principal components analysis (PCA) in all co-sorted Single amplified genome (SAG) (Additional file 1: Figure S2)
In summary, we have demonstrated that Nanoarchaeota can be readily co-sorted with putative hosts in a high-throughput and culture-independent manner using single-cell genomics techniques, enabling us to perform a detailed genomic analysis

Summary

Introduction

Nanoarchaeota are obligate symbionts of other Archaea first discovered 16 years ago, yet little is known about this largely uncultivated taxon. Later surveys of 16S rRNA sequences revealed Nanoarchaeota living in diverse environments, including marine hydrothermal sediments, terrestrial hot springs in Asia, North America, and New Zealand [11,12,13,14,15], and mesophilic hypersaline environments [11]. Nanoarchaeota sequences were retrieved from cool photic regions of the Yellowstone Lake, the organisms likely originated from submerged thermal springs [15]. These environments span a variety of temperatures from 4 to greater than 100 °C, and pH values from 3.5 to 8.0, suggesting that Nanoarchaeota genomes may be diverse. N. equitans is currently the sole sequenced representative from a marine environment [3], and only two other genomes are available (Nanopusillus acidilobi and Nst1, “Nanobsidianus stetteri”), both from hot springs in Yellowstone National Park (YNP) [16, 17]

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Results

Conclusion