April 28, 2021 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

DataCite XML Export

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  <identifier identifierType="DOI">10.5281/zenodo.6090434</identifier>
  <creators>
    <creator>
      <creatorName>Susanne Krause</creatorName>
      <affiliation>Department of Applied Biology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Sabrina Gfrerer</creatorName>
      <affiliation>Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Carsten Reuse</creatorName>
      <affiliation>Bioinformatics &amp; Biochemistry, Technische Universität Braunschweig</affiliation>
    </creator>
    <creator>
      <creatorName>Nina Dombrowski</creatorName>
      <affiliation>Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands</affiliation>
    </creator>
    <creator>
      <creatorName>Laura Villanueva</creatorName>
      <affiliation>Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands</affiliation>
    </creator>
    <creator>
      <creatorName>Boyke Bunk</creatorName>
      <affiliation>Leibniz Institute DSMZ, Braunschweig, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Thomas R. Neu</creatorName>
      <affiliation>Helmholtz-Centre for Environmental Research UFZ, Magdeburg, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Ute Kuhlicke</creatorName>
      <affiliation>Helmholtz-Centre for Environmental Research UFZ, Magdeburg, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Kerstin Schmidt-Hohagen</creatorName>
      <affiliation>Bioinformatics &amp; Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Reinhard Rachel</creatorName>
      <affiliation>Center for Electron Microscopy, University of Regensburg, Regensburg, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Anja Spang</creatorName>
      <affiliation>Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands</affiliation>
    </creator>
    <creator>
      <creatorName>Johannes Gescher</creatorName>
      <affiliation>Department of Applied Biology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Cultivation and characterization of a stable Micrarchaeon-Thermoplasmatales coculture</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <subjects>
    <subject>EM, enrichments, metagenomics,, DPANN, archaea</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2021-04-28</date>
  </dates>
  <resourceType resourceTypeGeneral="JournalArticle"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/6090434</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.4725435</relatedIdentifier>
  </relatedIdentifiers>
  <version>v3</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;strong&gt;# Abstract&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;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 (&lt;em&gt;Ca.&lt;/em&gt; Micrarchaeum harzensis) together with its &lt;em&gt;Thermoplasmatales&lt;/em&gt; host (&lt;em&gt;Ca.&lt;/em&gt; 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.&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;# Description of contents of this directory&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;## 1_Genomes.tar.gz&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Contains the protein files used for the annotations and to extract certain proteins for phylogenetic analyses.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&lt;br&gt;
&lt;strong&gt;## 2_Annotations.tar.gz&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;This folder contains the full workflow to annotate the genomes of interest and a jupyter lab book (python3) used for parsing the data.&lt;br&gt;
Additionally, this folder contains:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;0_Dependencies: Any custom scripts used as well as databases and mapping files (only provided if databases were modified)&lt;/li&gt;
	&lt;li&gt;1_Input: Output of the annotation workflow as well as any mapping file required by the python3 script to further parse the data&lt;/li&gt;
	&lt;li&gt;2_Output: Parsed annotation table&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;br&gt;
&lt;strong&gt;## 3_Phylogenies.tar.gz&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Contains all files generated for the phylogenies of certain lipid genes.&lt;br&gt;
These files are provided for the archaea only and the universal analysis (see Methods of the main paper for details).&lt;/p&gt;

&lt;p&gt;Each folder&amp;nbsp;contains:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;required scripts and mapping files&lt;/li&gt;
	&lt;li&gt;raw sequences (protein, faa), separate for each lipid gene of interest. These come in individual versions:
	&lt;ul&gt;
		&lt;li&gt;&amp;nbsp;&amp;nbsp; &amp;nbsp;indiv: sequences for all arcogs&lt;/li&gt;
		&lt;li&gt;&amp;nbsp;&amp;nbsp; &amp;nbsp;final: sequences for arcogs and if several arcogs were assigned to the same COG, these arCOGs were combined into one file. If arCOGs were combined, this is listed in the provided overview table in the main directory.&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
	&lt;li&gt;aligned sequences&lt;/li&gt;
	&lt;li&gt;aligned and trimmed sequences&lt;/li&gt;
	&lt;li&gt;output from IQ-TREE&lt;/li&gt;
	&lt;li&gt;PDFs for each individual tree&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;## 4_raw data_ARMAN lipids&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Lipid extracts were analyzed by UHPLC&amp;ndash;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.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;Files provided here are raw data files out of these analyses: Ca. Scheffleriplasma hospitalis Bligh&amp;amp;Dyer total lipid extract (U1808198) analysis includes the core lipid analysis of those present in the culture; Ca. Scheffleriplasma hospitalis Bligh&amp;amp;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&amp;amp;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&amp;amp;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.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;- Comment for Version 2: We forgot to upload files in a subfolder in 3_Phylogenies and provide them now in this updated version.&lt;/p&gt;

&lt;p&gt;- Comment for Version 3: Added some new data (&lt;strong&gt;4_raw data_ARMAN lipids&lt;/strong&gt;)&lt;/p&gt;</description>
  </descriptions>
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