MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants
AuthorsDueholm, Morten Kam Dahl
Andersen, Kasper Skytte
Chua, Adeline Seak May
Curtis, Thomas P.
Garcia-Chaves, Maria Carolina
Gu, April Z.
Pillai, Suraj Babu
Reis, Maria A.M.
van Loosdrecht, Mark
Nielsen, Per H.
Nielsen, Per Halkjær
KAUST DepartmentEnvironmental Science and Engineering Program
Water Desalination and Reuse Research Center (WDRC)
Permanent link to this recordhttp://hdl.handle.net/10754/678568
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AbstractMicrobial communities are responsible for biological wastewater treatment, but our knowledge of their diversity and function is still poor. Here, we sequence more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 wastewater treatment plants (WWTPs) across the world and use the sequences to construct the ‘MiDAS 4’ database. MiDAS 4 is an amplicon sequence variant resolved, full-length 16S rRNA gene reference database with a comprehensive taxonomy from domain to species level for all sequences. We use an independent dataset (269 WWTPs) to show that MiDAS 4, compared to commonly used universal reference databases, provides a better coverage for WWTP bacteria and an improved rate of genus and species level classification. Taking advantage of MiDAS 4, we carry out an amplicon-based, global-scale microbial community profiling of activated sludge plants using two common sets of primers targeting regions of the 16S rRNA gene, revealing how environmental conditions and biogeography shape the activated sludge microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 966 genera and 1530 species that represent approximately 80% and 50% of the accumulated read abundance, respectively. Finally, we show that for well-studied functional guilds, such as nitrifiers or polyphosphate-accumulating organisms, the same genera are prevalent worldwide, with only a few abundant species in each genus.
CitationDueholm, M. K. D., Nierychlo, M., Andersen, K. S., Rudkjøbing, V., Knutsson, S., Arriaga, S., Bakke, R., Boon, N., Bux, F., Christensson, M., Chua, A. S. M., Curtis, T. P., Cytryn, E., Erijman, L., Etchebehere, C., Fatta-Kassinos, D., Frigon, D., Garcia-Chaves, M. C., … Gu, A. Z. (2022). MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-29438-7
SponsorsThe project has been funded by the Danish Research Council (grant 6111-00617 A, P.H.N.) and the Villum Foundation (Dark Matter and grant 13351, P.H.N.). We thank all the involved WWTPs for providing samples and plant metadata.
PublisherSpringer Science and Business Media LLC
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