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

Dueholm, Morten Kam Dahl ; Andersen, Kasper Skytte ; Korntved, Anne Kirstine C. ; Rudkjøbing, Vibeke ; Alves, Madalena ; Bajón-Fernández, Yadira ; Batstone, Damien ; Butler, Caitlyn ; Cruz, Mercedes Cecilia and Davidsson, Åsa LU orcid , et al. (2024) In Nature Communications 15(1).
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,... (More)

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.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Nature Communications
volume
15
issue
1
article number
5361
publisher
Nature Publishing Group
external identifiers
  • pmid:38918384
  • scopus:85196834155
ISSN
2041-1723
DOI
10.1038/s41467-024-49641-y
language
English
LU publication?
yes
id
7f4a67c8-ae60-49b5-8587-3c8657532f8b
date added to LUP
2024-07-03 14:24:35
date last changed
2024-09-11 22:05:21
@article{7f4a67c8-ae60-49b5-8587-3c8657532f8b,
  abstract     = {{<p>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.</p>}},
  author       = {{Dueholm, Morten Kam Dahl and Andersen, Kasper Skytte and Korntved, Anne Kirstine C. and Rudkjøbing, Vibeke and Alves, Madalena and Bajón-Fernández, Yadira and Batstone, Damien and Butler, Caitlyn and Cruz, Mercedes Cecilia and Davidsson, Åsa and Erijman, Leonardo and Holliger, Christof and Koch, Konrad and Kreuzinger, Norbert and Lee, Changsoo and Lyberatos, Gerasimos and Mutnuri, Srikanth and O’Flaherty, Vincent and Oleskowicz-Popiel, Piotr and Pokorna, Dana and Rajal, Veronica and Recktenwald, Michael and Rodríguez, Jorge and Saikaly, Pascal E. and Tooker, Nick and Vierheilig, Julia and De Vrieze, Jo and Wurzbacher, Christian and Nielsen, Per Halkjær}},
  issn         = {{2041-1723}},
  language     = {{eng}},
  number       = {{1}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Nature Communications}},
  title        = {{MiDAS 5 : Global diversity of bacteria and archaea in anaerobic digesters}},
  url          = {{http://dx.doi.org/10.1038/s41467-024-49641-y}},
  doi          = {{10.1038/s41467-024-49641-y}},
  volume       = {{15}},
  year         = {{2024}},
}