Interactions of members of the Candidate Phyla Radiation (CPR) with prokaryotic and eukaryotic hosts in a WWTP

Current projects

Members of the Candidate Phyla Radiation (CPR) represent a significant fraction (>15%) of the total bacterial diversity of Earth. Almost all members of the CPR are uncultured and their reduced genomes encode very limited biosynthetic capabilities, strongly suggesting a lifestyle that depends on other organisms. For two members of the CPR life as an intracellular symbiont of a protist and as an obligate epibiont of a bacterium has been demonstrated, but for most other CPR members nothing is known about partners and type of metabolic interactions. While many studies on CPR were performed in difficult to sample subsurface systems, my group has detected via metagenomics in a wastewater treatment plant (wwtp) six described CPR phyla as well as a novel CPR phylum. Using metatranscriptomics, we could demonstrate that these CPR are active, rendering this plant ideal for in-depth studies of CPR microbes.

Aims: Test the hypothesis that the different CPR members in the wwtp are metabolically dependent on specific prokaryotic and eukaryotic partners and live as epibionts or intracellular symbionts of their hosts. Identification of hosts, analysis of host range, and insights into type of metabolic interactions.

Approach: As many CPR members are ultrasmall specific FISH-based visualization will be combined with super-resolution fluorescence microscopy, scanning-, transmission-, and cryo-electron microscopy. After visualization of the CPR members, their microbial or eukaryotic interaction partners will be identified by FISH, too. Subsequently, host cells (with attached CPR cells) will be sorted after fixation-free FISH via FACS or micromanipulation and genomic information of both partners will be obtained. Finally, ultra-deep metatranscriptomic data from the wwtp will be mapped onto these genomes.

Relevance: Urgently needed insights into the biology of CPR in a highly active and easily accessible system.

Student: Huifeng Hu

Faculty: Wagner (PI), Horn, Rattei

Funding: FWF project MAINTAIN



Selected Publications:

Anantharaman, K., Brown, C. T., Hug, L. A., Sharon, I., Castelle, C. J., Probst, A. J., Thomas, B. C., Singh, A., Wilkins, M. J., Karaoz, U., Brodie, E. L., Williams, K. H., Hubbard, S. S. & Banfield, J. F. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat. Commun. 7, 13219 (2016).

Brown, C. T., Hug, L. A., Thomas, B. C., Sharon, I., Castelle, C. J., Singh, A., Wilkins, M. J., Wrighton, K. C., Williams, K. H. & Banfield, J. F. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523, 208–211 (2015).

Hug, L. A., Baker, B. J., Anantharaman, K., Brown, C. T., Probst, A. J., Castelle, C. J., Butterfield, C. N., Hernsdorf, A. W., Amano, Y., Ise, K., Suzuki, Y., Dudek, N., Relman, D. A., Finstad, K. M., Amundson, R., Thomas, B. C. & Banfield, J. F. A new view of the tree of life. Nat Microbiol 1, 16048 (2016).

Gong, J., Qing, Y., Guo, X. & Warren, A. ‘Candidatus Sonnebornia yantaiensis’, a member of candidate division OD1, as intracellular bacteria of the ciliated protist Paramecium bursaria (Ciliophora, Oligohymenophorea). Syst. Appl. Microbiol. 37, 35–41 (2014).

He, X., McLean, J. S., Edlund, A., Yooseph, S., Hall, A. P., Liu, S.-Y., Dorrestein, P. C., Esquenazi, E., Hunter, R. C., Cheng, G., Nelson, K. E., Lux, R. & Shi, W. Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proc. Natl. Acad. Sci. U. S. A. 112, 244–249 (2015).