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Title (Primary) Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses
Author Chen, S.-C.; Budhraja, R.; Adrian, L.; Calabrese, F.; Stryhanyuk, H.; Musat, N.; Richnow, H.-H.; Duan, G.-L.; Zhu, Y.-G.; Musat, F.
Journal ISME Journal
Year 2021
Department ISOBIO; UBT
Volume 15
Issue 12
Page From 3508
Page To 3521
Language englisch
Topic T7 Bioeconomy
Supplements https://static-content.springer.com/esm/art%3A10.1038%2Fs41396-021-01022-9/MediaObjects/41396_2021_1022_MOESM1_ESM.docx
UFZ wide themes ProVIS;
Abstract Most microorganisms in the biosphere remain uncultured and poorly characterized. Although the surge in genome sequences has enabled insights into the genetic and metabolic properties of uncultured microorganisms, their physiology and ecological roles cannot be determined without direct probing of their activities in natural habitats. Here we employed an experimental framework coupling genome reconstruction and activity assays to characterize the largely uncultured microorganisms responsible for aerobic biodegradation of biphenyl as a proxy for a large class of environmental pollutants, polychlorinated biphenyls. We used 13C-labeled biphenyl in contaminated soils and traced the flow of pollutant-derived carbon into active cells using single-cell analyses and protein–stable isotope probing. The detection of 13C-enriched proteins linked biphenyl biodegradation to the uncultured Alphaproteobacteria clade UBA11222, which we found to host a distinctive biphenyl dioxygenase gene widely retrieved from contaminated environments. The same approach indicated the capacity of Azoarcus species to oxidize biphenyl and suggested similar metabolic abilities for species of Rugosibacter. Biphenyl oxidation would thus represent formerly unrecognized ecological functions of both genera. The quantitative role of these microorganisms in pollutant degradation was resolved using single-cell-based uptake measurements. Our strategy advances our understanding of microbially mediated biodegradation processes and has general application potential for elucidating the ecological roles of uncultured microorganisms in their natural habitats.
Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=24692
Chen, S.-C., Budhraja, R., Adrian, L., Calabrese, F., Stryhanyuk, H., Musat, N., Richnow, H.-H., Duan, G.-L., Zhu, Y.-G., Musat, F. (2021):
Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses
ISME J. 15 (12), 3508 - 3521