Methanosaeta and " Candidatus Velamenicoccus archaeovorus"

• Published in: Applied and environmental microbiology 2022-04, Vol.88 (7), p.e0240721-e0240721
• Main Authors: Kizina, Jana, Jordan, Sebastian F A, Martens, Gerrit Alexander, Lonsing, Almud, Probian, Christina, Kolovou, Androniki, Santarella-Mellwig, Rachel, Rhiel, Erhard, Littmann, Sten, Markert, Stephanie, Stüber, Kurt, Richter, Michael, Schweder, Thomas, Harder, Jens
• Format: Article
• Language: English
• Subjects: Archaea; Archaea - metabolism; Bacteria - genetics; Candidate species; Cell culture; Centrifugation; Conservation; Deoxyribonucleic acid; Depolymerization; DNA; Energy conservation; Environmental Microbiology; Fermentation; Ferredoxin; Ferredoxins - metabolism; Filaments; Fluorescence; Fluorescence in situ hybridization; Genomes; Glycolysis; In Situ Hybridization, Fluorescence; Limonene; Macromolecules; Metabolism; Metagenomics; Methanosaeta; Methanosarcinaceae - metabolism; Microscopy; NAD; New species; Nucleic acids; Oxidoreductase; Oxidoreductases - metabolism; Phylogeny; Predation; Pyruvic acid; Pyruvic Acid - metabolism; RNA, Ribosomal, 16S - genetics; rRNA; Scanning electron microscopy; Sugars - metabolism; Transmission electron microscopy
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/aem.02407-21

The phylum " Omnitrophica" (candidate division OP3) is 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 epibiotic cells. In this study, we enriched OP3 cells by double density gradient centrifugation and obtained the first closed genome of an apparently clonal OP3 cell population by applying metagenomics and PCR for gap closure. Filaments of acetoclastic , the largest morphotype in the culture community, contained empty cells, cells devoid of rRNA or of both rRNA and DNA, and dead cells according to transmission electron microscopy (TEM), thin-section TEM, scanning electron microscopy (SEM), catalyzed reporter deposition-fluorescence hybridization (CARD-FISH), and LIVE/DEAD imaging. OP3 LiM cells were ultramicrobacteria (200 to 300 nm in diameter) and showed two physiological stages in CARD-FISH fluorescence signals: strong signals of OP3 LiM cells attached to and to indicated many rRNA molecules and an active metabolism, 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 and 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. Our study demonstrated a predatory metabolism for OP3 LiM cells, and therefore, we propose the name " Velamenicoccus archaeovorus" gen. nov., sp. nov., for OP3 LiM. Epibiotic bacteria are known to live on and off bacterial cells. Here, we describe the ultramicrobacterial anaerobic epibiont OP3 LiM living on and . We detected sick and dead cells of the filamentous archaeon in slowly growing methanogenic cultures. OP3 LiM lives as a sugar fermenter, likely on polysaccharides from outer membranes, and has the genomic potential to live as a syntroph. The predatory lifestyle of OP3 LiM was supported by its genome, the first closed genome for the phylum " Omnitrophica," and by images of cell-to-cell contact with prey cells. We propose naming OP3 LiM " Velamenicoccus archaeovorus." Its metabolic vers