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

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

doi:10.1038/ncomms12115

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.

Highlights

Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured
Nanoarchaeota has been a proposed archaeal lineage following the discovery and cultivation of Nanoarchaeum equitans, an ultra-small ectosymbiont residing on the marine hyperthermophilic crenarchaeote, Ignicoccus hospitalis[10]
Genomic and physiological features of N. equitans suggest a parasitic-type adaptation that explains its strict dependence on direct contact with its host[17,18,19,20,21]

Summary

Introduction

Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. 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. Genomic and physiological features of N. equitans (extensive fragmentation of protein and tRNA genes, massive loss of biosynthetic capabilities) suggest a parasitic-type adaptation that explains its strict dependence on direct contact with its host[17,18,19,20,21]. A better understanding of how Nanoarchaeota evolved to be dependent on direct interaction with other Archaea and how that relationship shaped the genomes and physiology of the interacting species clearly requires the isolation and detailed characterization of such novel symbiotic systems. We use single-cell genomics to infer physiological dependencies and adaptation to low-pH environments for the isolation and characterization of the first terrestrial Nanoarchaeota-host system, from an acidic hot spring in YNP

Methods

Results

Conclusion