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

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.

Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont,Desulfobulbus oralis

“…The whole-cell proteome and the soluble proteins released into the medium were fragmented and analyzed by bottom-up, two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS). A total of 1,628 proteins were detected, representing 70% of the predicted proteome (see Data Sets S1 and S6 in the supplemental material), which is similar to coverage that has been previously obtained on other organisms with reduced genomes (83,84). Considering that proteins containing multiple transmembrane domains are difficult to detect in tryptic digests (here we detected only 40% of the proteins predicted to contain more than 1 transmembrane domain) we conclude that a very large fraction of the D. oralis genetic potential (Ͼ80%) was expressed under the tested condition.…”

A Novel Type of Polyhedral Viruses Infecting Hyperthermophilic Archaea

“…In addition, ORF25-400 and ORF26-357 are homologous to each other and to the minor structural proteins conserved in all members of the family Rudiviridae (36) as well as in some members of the families Lipothrixviridae and Bicaudaviridae, all infecting members of the archaeal order Sulfolobales. Notably, whereas the N-terminal regions of ORF25-400 and ORF26-357 products showed highest similarity to the viral homologs, the central regions of the corresponding proteins were more similar to homologs encoded by "Candidatus Nanopusillus acidilobi," a symbiotic archaeon of the order Nanoarchaeota inhabiting terrestrial geothermal environments (37).…”

The multi-omics promise in context: from sequence to microbial isolate

“…This first isolated geothermal nanoarchaeon, proposed as "Candidatus Nanopusillus acidilobi" represents the smallest cultured organism to date (100-300 nm cell size), and available cultures now allow experimentation to reveal its particular metabolism and adaptation features. Many more ultra-small bacteria and archaea with similar ectosymbiotic or ectoparasitic lifestyles might await discovery and identification of their hosts, something that -apart from single cell genomics -is only feasible by direct cultivation (Delafont et al 2015;He et al 2015;Wurch et al 2016). We conclude that genomic information of microbes derived from low diversity environments can often be obtained relatively easily and that individual genome reconstructions are often feasible (Figure 3).…”

“…The nanoarchaeon's fragmented, extremely small genome lacked many essential biosynthetic pathways which indicated that the nanoarchaeon cannot live autonomously and hence depends on the presence of a crenarchaeal associate. Potential glycolysis and gluconeogenesis pathways, however, are retained in the nanoarchaeon, suggesting the use of peptides or complex sugars as energy source (Podar et al 2013;Wurch et al 2016). On this basis, Wurch et al (2016) established enrichment cultures containing yeast extract, casamino acids and sucrose or glycogen in anoxic Brock medium with low pH and 80-85 C and obtained stable communities with increasing relative abundance of nanoarchaeota, as monitored by qPCR.…”

“…Potential glycolysis and gluconeogenesis pathways, however, are retained in the nanoarchaeon, suggesting the use of peptides or complex sugars as energy source (Podar et al 2013;Wurch et al 2016). On this basis, Wurch et al (2016) established enrichment cultures containing yeast extract, casamino acids and sucrose or glycogen in anoxic Brock medium with low pH and 80-85 C and obtained stable communities with increasing relative abundance of nanoarchaeota, as monitored by qPCR. After two rounds of dilution to extinction, they transferred a single crenarchaeal cell carrying a nanoarchaeon into liquid medium using optical tweezers, thereby obtaining a pure co-culture of the crenarchaeon host (Acidilobus sp.…”