MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters

Morten Kam Dahl Dueholm (), Kasper Skytte Andersen, Anne-Kirstine C. Korntved, Vibeke Rudkjøbing, Madalena Alves, Yadira Bajón-Fernández, Damien Batstone, Caitlyn Butler, Mercedes Cecilia Cruz, Åsa Davidsson, Leonardo Erijman, Christof Holliger, Konrad Koch, Norbert Kreuzinger, Changsoo Lee, Gerasimos Lyberatos, Srikanth Mutnuri, Vincent O’Flaherty, Piotr Oleskowicz-Popiel, Dana Pokorna, Veronica Rajal, Michael Recktenwald, Jorge Rodríguez, Pascal E. Saikaly, Nick Tooker, Julia Vierheilig, Jo Vrieze, Christian Wurzbacher and Per Halkjær Nielsen ()
Additional contact information
Morten Kam Dahl Dueholm: Aalborg University
Kasper Skytte Andersen: Aalborg University
Anne-Kirstine C. Korntved: Aalborg University
Vibeke Rudkjøbing: Aalborg University
Madalena Alves: University of Minho
Yadira Bajón-Fernández: Cranfield University
Damien Batstone: The University of Queensland
Caitlyn Butler: University of Massachusetts Amherst
Mercedes Cecilia Cruz: Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
Åsa Davidsson: Lund University
Leonardo Erijman: University of Buenos Aires
Christof Holliger: Ecole Polytechnique Fédérale de Lausanne (EPFL)
Konrad Koch: Technical University of Munich (TUM)
Norbert Kreuzinger: TU Wien
Changsoo Lee: Ulsan National Institute of Science and Technology (UNIST)
Gerasimos Lyberatos: National Technical University of Athens
Srikanth Mutnuri: Birla Institute of Technology and Science (BITS-Pilani)
Vincent O’Flaherty: University of Galway
Piotr Oleskowicz-Popiel: Poznan University of Technology
Dana Pokorna: University of Chemistry and Technology Prague
Veronica Rajal: Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
Michael Recktenwald: Espoo R&D Center
Jorge Rodríguez: Khalifa University
Pascal E. Saikaly: King Abdullah University of Science and Technology (KAUST)
Nick Tooker: University of Massachusetts Amherst
Julia Vierheilig: TU Wien
Jo Vrieze: Ghent University
Christian Wurzbacher: Technical University of Munich (TUM)
Per Halkjær Nielsen: Aalborg University

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: Abstract Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84–99% and 18–61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.

Date: 2024
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DOI: 10.1038/s41467-024-49641-y

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