The microbial dark matter and “wanted list” in worldwide wastewater treatment plants
Abstract Background Wastewater treatment plants (WWTPs) are one of the largest biotechnology applications in the world and are of critical importance to modern urban societies. An accurate evaluation of the microbial dark matter (MDM, microorganisms whose genomes remain uncharacterized) proportions...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-03-01
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| Series: | Microbiome |
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| Online Access: | https://doi.org/10.1186/s40168-023-01503-3 |
| _version_ | 1797853671556382720 |
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| author | Yulin Zhang Yulin Wang Mingxi Tang Jizhong Zhou Tong Zhang |
| author_facet | Yulin Zhang Yulin Wang Mingxi Tang Jizhong Zhou Tong Zhang |
| author_sort | Yulin Zhang |
| collection | DOAJ |
| description | Abstract Background Wastewater treatment plants (WWTPs) are one of the largest biotechnology applications in the world and are of critical importance to modern urban societies. An accurate evaluation of the microbial dark matter (MDM, microorganisms whose genomes remain uncharacterized) proportions in WWTPs is of great value, while there is no such research yet. This study conducted a global meta-analysis of MDM in WWTPs with 317,542 prokaryotic genomes from the Genome Taxonomy Database and proposed a “wanted list” for priority targets in further investigations of activated sludge. Results Compared with the Earth Microbiome Project data, WWTPs had relatively lower genome-sequenced proportions of prokaryotes than other ecosystems, such as the animal related environments. Analysis showed that the median proportions of the genome-sequenced cells and taxa (100% identity and 100% coverage in 16S rRNA gene region) in WWTPs reached 56.3% and 34.5% for activated sludge, 48.6% and 28.5% for aerobic biofilm, and 48.3% and 28.5% for anaerobic digestion sludge, respectively. This result meant MDM had high proportions in WWTPs. Besides, all of the samples were occupied by a few predominant taxa, and the majority of the sequenced genomes were from pure cultures. The global-scale “wanted list” for activated sludge contained four phyla that have few representatives and 71 operational taxonomic units with the majority of them having no genome or isolate yet. Finally, several genome mining methods were verified to successfully recover genomes from activated sludge such as hybrid assembly of the second- and third-generation sequencing. Conclusions This work elucidated the proportion of MDM in WWTPs, defined the “wanted list” of activated sludge for future investigations, and certified potential genome recovery methods. The proposed methodology of this study can be applied to other ecosystems and improve understanding of ecosystem structure across diverse habitats. Video Abstract |
| first_indexed | 2024-04-09T19:54:27Z |
| format | Article |
| id | doaj.art-b0fdc6024d4e41f886c6c42715acc0d6 |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-04-09T19:54:27Z |
| publishDate | 2023-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-b0fdc6024d4e41f886c6c42715acc0d62023-04-03T05:34:08ZengBMCMicrobiome2049-26182023-03-0111111510.1186/s40168-023-01503-3The microbial dark matter and “wanted list” in worldwide wastewater treatment plantsYulin Zhang0Yulin Wang1Mingxi Tang2Jizhong Zhou3Tong Zhang4Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong KongEnvironmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong KongInstitute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of OklahomaEnvironmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong KongAbstract Background Wastewater treatment plants (WWTPs) are one of the largest biotechnology applications in the world and are of critical importance to modern urban societies. An accurate evaluation of the microbial dark matter (MDM, microorganisms whose genomes remain uncharacterized) proportions in WWTPs is of great value, while there is no such research yet. This study conducted a global meta-analysis of MDM in WWTPs with 317,542 prokaryotic genomes from the Genome Taxonomy Database and proposed a “wanted list” for priority targets in further investigations of activated sludge. Results Compared with the Earth Microbiome Project data, WWTPs had relatively lower genome-sequenced proportions of prokaryotes than other ecosystems, such as the animal related environments. Analysis showed that the median proportions of the genome-sequenced cells and taxa (100% identity and 100% coverage in 16S rRNA gene region) in WWTPs reached 56.3% and 34.5% for activated sludge, 48.6% and 28.5% for aerobic biofilm, and 48.3% and 28.5% for anaerobic digestion sludge, respectively. This result meant MDM had high proportions in WWTPs. Besides, all of the samples were occupied by a few predominant taxa, and the majority of the sequenced genomes were from pure cultures. The global-scale “wanted list” for activated sludge contained four phyla that have few representatives and 71 operational taxonomic units with the majority of them having no genome or isolate yet. Finally, several genome mining methods were verified to successfully recover genomes from activated sludge such as hybrid assembly of the second- and third-generation sequencing. Conclusions This work elucidated the proportion of MDM in WWTPs, defined the “wanted list” of activated sludge for future investigations, and certified potential genome recovery methods. The proposed methodology of this study can be applied to other ecosystems and improve understanding of ecosystem structure across diverse habitats. Video Abstracthttps://doi.org/10.1186/s40168-023-01503-3Wastewater treatment plantsActivated sludgeBiofilmAnaerobic digestion sludgeMicrobiomeMicrobial dark matter |
| spellingShingle | Yulin Zhang Yulin Wang Mingxi Tang Jizhong Zhou Tong Zhang The microbial dark matter and “wanted list” in worldwide wastewater treatment plants Microbiome Wastewater treatment plants Activated sludge Biofilm Anaerobic digestion sludge Microbiome Microbial dark matter |
| title | The microbial dark matter and “wanted list” in worldwide wastewater treatment plants |
| title_full | The microbial dark matter and “wanted list” in worldwide wastewater treatment plants |
| title_fullStr | The microbial dark matter and “wanted list” in worldwide wastewater treatment plants |
| title_full_unstemmed | The microbial dark matter and “wanted list” in worldwide wastewater treatment plants |
| title_short | The microbial dark matter and “wanted list” in worldwide wastewater treatment plants |
| title_sort | microbial dark matter and wanted list in worldwide wastewater treatment plants |
| topic | Wastewater treatment plants Activated sludge Biofilm Anaerobic digestion sludge Microbiome Microbial dark matter |
| url | https://doi.org/10.1186/s40168-023-01503-3 |
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