MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

Abstract

Biological wastewater treatment and an increased focus on resource recovery is fundamental for environmental protection, human health, and sustainable development. Microbial communities are responsible for these processes, but our knowledge of their diversity and function is still poor, partly due to the lack of good reference databases and comprehensive global studies. Here, we sequenced more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 wastewater treatment plants (WWTPs) across the world and used the sequences to construct MiDAS 4, a full-length amplicon sequence variant resolved 16S rRNA gene reference database with a comprehensive taxonomy from the domain to species-level for all references. Using a study-independent amplicon dataset from the Global Water Microbiome Consortium project (269 WWTPs), we showed that the MiDAS 4 database provides much better coverage for bacteria in WWTPs worldwide compared to commonly applied universal references databases, and greatly improved the rate of genus and species-level classification. Hence, MiDAS 4 provides a unifying taxonomy for the majority of prokaryotic diversity in WWTPs globally, which can be used for linking microbial identities with their functions across studies. Taking advantage of MiDAS 4, we carried out an amplicon-based, global-scale microbial community profiling of activated sludge plants using two common sets of primers targeting the V1-V3 and V4 region of the 16S rRNA gene. We found that the V1-V3 primers were generally best suited for this ecosystem, and revealed how environmental conditions and biogeography shape the activated sludge microbiota. We also identified process-critical taxa (core and conditionally rare or abundant taxa), encompassing 966 genera and 1530 species. These represented approximately 80% and 50% of the accumulated read abundance, respectively, and represent targets for further investigations. Finally, we showed that for well-studied functional guilds, such as nitrifiers or polyphosphate accumulating organisms, the same genera were prevalent worldwide, with only a few abundant species in each genus.

The structure of microbial communities of activated sludge of large-scale wastewater treatment plants in the city of Moscow

“…The only cultured member of “Agitococcus lubricus group’, A. lubricus , is a lipolytic aerobic heterotroph found in freshwater bodies 86 . The relative abundance of this lineage reached 4% in WWTP2, while it was below 0.2% in all AS samples currently described in the MiDAS database 14 .…”

“…The taxonomic assignment of OTUs was performed by searching against the SILVA v.138 rRNA sequence database using the VSEARCH v. 2.14.1 algorithm 28 . The recently developed MiDAS 4 14 , a full-length 16S rRNA gene reference database for wastewater treatment systems, was used to taxonomically identify OTUs up to the species level in the same way.…”

“…Another large-scale initiative, the MiDAS project, analyzed samples (mostly AS) from 740 WWTPs using different types of treatment technologies, and represents the largest global sampling of WWTPs to date 13 , 14 . The resulting full-length 16S rRNA gene reference database, MiDAS 4, represent a comprehensive catalogue of bacteria in wastewater treatment systems and taxonomy from the domain to species level 14 . Although this study targeted WWTPs located in 425 cities, 31 countries on 6 continents, like the GWMC project, MiDAS mostly covered the same geographic regions.…”

Comparative Genomics of Members of the Genus Defluviicoccus With Insights Into Their Ecophysiological Importance

“…This situation highlights that much is still to be learned about Defluviicoccus systematics, shown by a recent global survey of activated sludge plants of many different configurations ( Dueholm et al, 2021 ) and based on 16S rRNA sequence data to consist of at least 18 putative new species. What is not yet clear is whether they all belong to the currently existing five clades, or additional clades are required to accommodate them.…”

AsCoM: An ecosystem-specific reference database for increased taxonomic resolution in soil microbial profiling

“…Full-length 16S rRNA gene sequencing was carried out as previously described [31] with the addition of an extra primer pair targeting archaeal 16S rRNA genes. Oligonucleotides used can be found in Table S1.…”