Unraveling the critical growth factors for stable cultivation of (nano-sized) Micrarchaeota

Abstract

Micrarchaeota are members of the archaeal DPANN superphylum. These so far poorly characterized archaea have been found to have reduced genomes and likely depend on interactions with host organisms for growth and survival. Here we report on the enrichment of the first stable co-culture of a member of the Micrarchaeota together with its host, as well as the isolation of the latter. Electron microscopic analysis suggest that growth is dependent on the physical interaction of the two organisms within a biofilm. The interaction seems to be ensured by the necessity to grow in form of a biofilm. Furthermore, transcriptomic analyses indicate a shift towards biofilm formation of the host as a result of co-cultivation. Finally, genomic, metabolomic, extracellular polymeric substance (EPSs) and lipid content analyses reveal that the Micrarchaeon symbiont relies on the acquisition of metabolites from its host and thereby provide first insights into the basis of symbiont-host interactions.

Acidophilic Micrarchaeon Seems to Maintain a Slightly Alkaline Cytosolic pH

“…Membranes consisting of archaeal tetraetherlipids have been reported to be highly impermeable for protons [5,[64][65][66][67]. With a caldarchaeol content of 97 % the cell membrane of A_DKE is predominantly composed of such lipids [17]. Furthermore, in T. acidophilum HO-62 a correlation between acid tolerance and elevated levels of surface glycosylation has been found [68].…”

“…A_DKE possesses only one gene (icd2, Micr_00902) annotated to be encoding a putative NADP-dependent IDH, which is actively expressed, according to available transcriptomic data [17]. In silico analyses of its amino acid sequence allowed the calculation of a theoretical molecular weight and isoelectric point (pI) of 45.05 kDa and 5.82, respectively, as well as the discovery of a highly conserved isocitrate/isopropylmalate dehydrogenase domain (Pfam: PF00180.20), almost spanning the entire length of the sequence (Thr23-Leu402).…”

“…Micrarchaeum harzensis A_DKE" and "Ca. Scheffleriplasma hospitalis B_DKE" [17] via oligonucleotide primers 1 & 2 (see Table 1). The latter introduced a 6x His-tag encoding sequence to the 5'-end, as well as complementary overlaps to the target vector pBAD202 (Invitrogen, Carlsbad, CA, USA).…”

“…Common characteristics of known members of this phylum are small-sized, circular genomes and an overall limited metabolic potential [13][14][15][16][17]. Thus, Micrarchaeota are assumed to be dependent on a symbiotic relationship with host organisms of the order Thermoplasmatales [15,18,19].…”

“…To our best knowledge, the only acidophilic Micrarchaeon currently cultivated under laboratory conditions is "Candidatus Micrarchaeum harzensis A_DKE" in co-culture with its putative host "Ca. Scheffleriplasma hospitalis B_DKE" [17]. The culture was enriched from acid mine drainage biofilms originating from the abandoned pyrite mine "Drei Kronen und Ehrt" in the Harz Mountains (Germany) [18,20].…”