Schulz Frederik

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Schulz
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Frederik
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  • Article
    Ancestral absence of electron transport chains in Patescibacteria and DPANN
    (Frontiers Media, 2020-08-17) Beam, Jacob P. ; Becraft, Eric D. ; Brown, Julia M. ; Schulz, Frederik ; Jarett, Jessica K. ; Bezuidt, Oliver ; Poulton, Nicole J. ; Clark, Kayla ; Dunfield, Peter F. ; Ravin, Nikolai V. ; Spear, John R. ; Hedlund, Brian P. ; Kormas, Konstantinos Ar. ; Sievert, Stefan M. ; Elshahed, Mostafa S. ; Barton, Hazel A. ; Stott, Matthew B. ; Eisen, Jonathan A. ; Moser, Duane P. ; Onstott, Tullis C. ; Woyke, Tanja ; Stepanauskas, Ramunas
    Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell–cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.
  • Article
    Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free-living relative
    (Wiley, 2023-11-27) Espada-Hinojosa, Salvador ; Karthauser, Clarissa ; Srivastava, Abhishek ; Schuster, Lukas ; Winter, Teresa ; de Oliveira, Andre Luiz ; Schulz, Frederik ; Horn, Matthias ; Sievert, Stefan ; Bright, Monika
    Thiotrophic symbioses between sulphur-oxidizing bacteria and various unicellular and metazoan eukaryotes are widespread in reducing marine environments. The giant colonial ciliate Zoothamnium niveum, however, is the only host of thioautotrophic symbionts that has been cultivated along with its symbiont, the vertically transmitted ectosymbiont Candidatus Thiobius zoothamnicola (short Thiobius). Because theoretical predictions posit a smaller genome in vertically transmitted endosymbionts compared to free-living relatives, we investigated whether this is true also for an ectosymbiont. We used metagenomics to recover the high-quality draft genome of this bacterial symbiont. For comparison we have also sequenced a closely related free-living cultured but not formally described strain Milos ODIII6 (short ODIII6). We then performed comparative genomics to assess the functional capabilities at gene, metabolic pathway and trait level. 16S rRNA gene trees and average amino acid identity confirmed the close phylogenetic relationship of both bacteria. Indeed, Thiobius has about a third smaller genome than its free-living relative ODIII6, with reduced metabolic capabilities and fewer functional traits. The functional capabilities of Thiobius were a subset of those of the more versatile ODIII6, which possessed additional genes for oxygen, sulphur and hydrogen utilization and for the acquisition of phosphorus illustrating features that may be adaptive for the unstable environmental conditions at hydrothermal vents. In contrast, Thiobius possesses genes potentially enabling it to utilize lactate and acetate heterotrophically, compounds that may be provided as byproducts by the host. The present study illustrates the effect of strict host-dependence of a bacterial ectosymbiont on genome evolution and host adaptation.