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

MARC21 XML Export

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    <subfield code="a">EM, enrichments, metagenomics,, DPANN, archaea</subfield>
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    <subfield code="u">Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany</subfield>
    <subfield code="a">Sabrina Gfrerer</subfield>
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    <subfield code="u">Bioinformatics &amp; Biochemistry, Technische Universität Braunschweig</subfield>
    <subfield code="a">Carsten Reuse</subfield>
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  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands</subfield>
    <subfield code="a">Nina Dombrowski</subfield>
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    <subfield code="u">Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands</subfield>
    <subfield code="a">Laura Villanueva</subfield>
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    <subfield code="u">Leibniz Institute DSMZ, Braunschweig, Germany</subfield>
    <subfield code="a">Boyke Bunk</subfield>
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    <subfield code="u">Helmholtz-Centre for Environmental Research UFZ, Magdeburg, Germany</subfield>
    <subfield code="a">Thomas R. Neu</subfield>
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    <subfield code="u">Helmholtz-Centre for Environmental Research UFZ, Magdeburg, Germany</subfield>
    <subfield code="a">Ute Kuhlicke</subfield>
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    <subfield code="u">Bioinformatics &amp; Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany</subfield>
    <subfield code="a">Kerstin Schmidt-Hohagen</subfield>
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    <subfield code="u">Center for Electron Microscopy, University of Regensburg, Regensburg, Germany</subfield>
    <subfield code="a">Reinhard Rachel</subfield>
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    <subfield code="u">Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands</subfield>
    <subfield code="a">Anja Spang</subfield>
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    <subfield code="u">Department of Applied Biology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany</subfield>
    <subfield code="a">Johannes Gescher</subfield>
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    <subfield code="c">2021-04-28</subfield>
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    <subfield code="u">Department of Applied Biology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany</subfield>
    <subfield code="a">Susanne Krause</subfield>
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  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">Cultivation and characterization of a stable Micrarchaeon-Thermoplasmatales coculture</subfield>
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    <subfield code="u">https://creativecommons.org/licenses/by/4.0/legalcode</subfield>
    <subfield code="a">Creative Commons Attribution 4.0 International</subfield>
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    <subfield code="a">&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;
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    <subfield code="a">10.5281/zenodo.4725435</subfield>
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    <subfield code="a">10.5281/zenodo.4725436</subfield>
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