PXD025008

PXD025008 is an original dataset announced via ProteomeXchange.

Title	Methanosaeta and Candidatus Vampirococcus archaeovorus
Description	The Candidatus phylum Omnitrophica (candidate division OP3) occurs ubiquitous in anaerobic habitats, but is currently characterized only by draft genomes from metagenomes and single cells. We had visualized cells of the phylotype OP3 LiM in methanogenic cultures on limonene as small epibiontic cells. In this study, we enriched OP3 cells by double density centrifugation and obtained the first closed genome of an apparently clonal OP3 cell population applying metagenomics and PCR for gap closure. Filaments of acetoclastic Methanosaeta, the largest morphotype in limonene enrichment cultures, contained empty cells, dead cells and cells devoid of rRNA or both rRNA and DNA according to TEM, thin-section TEM, SEM, CARD-FISH and Live/Dead images. OP3 LiM cells were ultramicrobacteria (200-300 nm in diameter) and showed two physiological stages in CARD-FISH fluorescence signals: strong signals indicated many rRNA molecules and an active metabolism of OP3 LiM cells attached to Bacteria and to Archaea, whereas free-living OP3 cells had weak signals. Metaproteomics revealed that OP3 LiM lives with highly expressed secreted proteins involved in depolymerization and uptake of macromolecules, an active glycolysis and energy conservation by the utilization of pyruvate via a pyruvate:ferredoxin oxidoreductase and an RNF complex (Ferredoxin:NAD oxidoreductase). Besides sugar fermentation, a nucleotidyl transferase may contribute to energy conservation by phosphorolysis, the phosphate-dependent depolymerization of nucleic acids. Thin section TEM showed distinctive structures of predation that had been previously observed for “Vampirococcus”. Our study demonstrated a predatory metabolism for OP3 LiM cells and we propose as name for OP3 LiM Candidatus Vampirococcus archaeovorus gen. nov., sp. nov..
HostingRepository	PRIDE
AnnounceDate	2022-03-14
AnnouncementXML	Submission_2022-04-06_01:27:35.669.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD025008
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Stephanie Markert
SpeciesList	scientific name: unclassified Candidatus Omnitrophica; NCBI TaxID: 1047005;
ModificationList	monohydroxylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-25 08:58:46	ID requested
1	2022-03-14 05:05:03	announced
⏵ 2	2022-04-06 01:27:36	announced	2022-04-06: Updated publication reference for PubMed record(s): 35311510.

Kizina J, Jordan SFA, Martens GA, Lonsing A, Probian C, Kolovou A, Santarella-Mellwig R, Rhiel E, Littmann S, Markert S, St, ü, ber K, Richter M, Schweder T, Harder J, Velamenicoccus archaeovorus". Appl Environ Microbiol, 88(7):e0240721(2022) [pubmed]

submitter keyword: Omnitrophica, predatory bacteria, LPS, methanogenic enrichment culture, candidate division OP3, limonene

Stephanie Markert
contact affiliation	Universität Greifswald Institut für Pharmazie, AG Pharmazeutische Biotechnologie Greifswald, Germany
contact email	stephanie.markert@uni-greifswald.de
lab head
Stephanie Markert
contact affiliation	University of Greifswald
contact email	stephanie.markert@uni-greifswald.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/03/PXD025008

PRIDE project URI

• PRIDE
  1. PXD025008
     1. Label: PRIDE project
     2. Name: Methanosaeta and Candidatus Vampirococcus archaeovorus