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

Microbiome
Jessica K JarettTanja Woyke

Abstract

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. 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 ...Continue Reading

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Jan 11, 2019·FEMS Microbiology Letters·Nina DombrowskiAnja Spang
Feb 16, 2019·Environmental Microbiology Reports·Emily St JohnAnna-Louise Reysenbach
May 3, 2019·The ISME Journal·Katrin SchwankAlexander J Probst
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Oct 6, 2020·Frontiers in Microbiology·Jacob P BeamRamunas Stepanauskas
Feb 13, 2019·Angewandte Chemie·Jackson K B Cahn, Jörn Piel

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Methods Mentioned

BETA
RNA-Seq
PCR
MDA
PCA
FACS
glycosylation

Software Mentioned

CheckM
superheat
PhyloBayesMPI
BLAST
IQ
align
SINA aligner
alluvial
co
R ggtree

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