Journal article Open Access
Susanne Krause; Sabrina Gfrerer; Carsten Reuse; Nina Dombrowski; Laura Villanueva; Boyke Bunk; Thomas R. Neu; Ute Kuhlicke; Kerstin Schmidt-Hohagen; Reinhard Rachel; Anja Spang; Johannes Gescher
Micrarchaeota is a distinctive lineage assigned to the DPANN archaea, which includes poorly characterised microorganisms with reduced genomes that likely depend on interactions with hosts for growth and survival. Here, we report the enrichment of a stable co-culture of a member of the Micrarchaeota (Ca. Micrarchaeum harzensis) together with its Thermoplasmatales host (Ca. Scheffleriplasma hospitalis), as well as the isolation of the latter. We show that symbiont-host interactions depend on biofilm formation as evidenced by growth experiments, comparative transcriptomic analyses and electron microscopy. In addition, genomic, metabolomic, extracellular polymeric substances and lipid content analyses indicate that the Micrarchaeon symbiont relies on the acquisition of metabolites from its host. Our study of the cell biology and physiology of a Micrarchaeon and its host adds to our limited knowledge of archaeal symbioses.
# Description of contents of this directory
Contains the protein files used for the annotations and to extract certain proteins for phylogenetic analyses.
This folder contains the full workflow to annotate the genomes of interest and a jupyter lab book (python3) used for parsing the data.
Additionally, this folder contains:
Contains all files generated for the phylogenies of certain lipid genes.
These files are provided for the archaea only and the universal analysis (see Methods of the main paper for details).
Each folder contains:
## 4_raw data_ARMAN lipids
Lipid extracts were analyzed by UHPLC–atmospheric pressure chemical ionization (APCI) MS for archaeal core lipids, including archaeol (diether, C20 isoprenoid chains) and glycerol dialkyl glycerol tetraether (GDGTs, tetraether, C40 side chain), according to Hopmans et al., 2016 (Organic geochemistry 93:1-6), with some modifications. Briefly, the analysis was performed on an Agilent 1260 UHPLC coupled to a 6130 quadrupole MSD in selected ion monitoring (SIM) mode.
Files provided here are raw data files out of these analyses: Ca. Scheffleriplasma hospitalis Bligh&Dyer total lipid extract (U1808198) analysis includes the core lipid analysis of those present in the culture; Ca. Scheffleriplasma hospitalis Bligh&Dyer total lipid extract after acid hydrolysis (U1809068) includes the intact polar-lipid-derived core lipids plus the core lipids of the previous analysis run. Run U1809060 corresponds to the run of the Bligh&Dyer total lipid extract of the co-culture of Ca. Micrarchaeum harzensis and Ca. Scheffleriplasma hospitalis, including the present core lipids. Run U1809066, corresponds to the run of the Bligh&Dyer total lipid extract after acid hydrolysis of the co-culture of Ca. Micrarchaeum harzensis and Ca. Scheffleriplasma hospitalis, including the the intact polar-lipid-derived core lipids plus the core lipids of the previous analysis run.
- Comment for Version 2: We forgot to upload files in a subfolder in 3_Phylogenies and provide them now in this updated version.
- Comment for Version 3: Added some new data (4_raw data_ARMAN lipids)
4_raw data_ARMAN lipids.zip
|All versions||This version|
|Data volume||7.4 GB||1.6 GB|