Refinement of the “Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration
ABSTRACTMembers of the “Candidatus Accumulibacter” genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 “Ca. Accumulibacter” species, whic...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2024-03-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/msystems.01188-23 |
| _version_ | 1797257178464124928 |
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| author | Rachel D. Stewart Kevin S. Myers Carly Amstadt Matt Seib Katherine D. McMahon Daniel R. Noguera |
| author_facet | Rachel D. Stewart Kevin S. Myers Carly Amstadt Matt Seib Katherine D. McMahon Daniel R. Noguera |
| author_sort | Rachel D. Stewart |
| collection | DOAJ |
| description | ABSTRACTMembers of the “Candidatus Accumulibacter” genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 “Ca. Accumulibacter” species, which have been proposed based on the phylogenetic divergence of the polyphosphate kinase 1 (ppk1) gene and genome-scale comparisons of metagenome-assembled genomes (MAGs). Phylogenetic classification based on the 16S rRNA genetic marker has been difficult to attain because most “Ca. Accumulibacter” MAGs are incomplete and often do not include the rRNA operon. Here, we investigate the “Ca. Accumulibacter” diversity in pilot-scale treatment trains performing BNR under low dissolved oxygen (DO) conditions using genome-resolved metagenomics. Using long-read sequencing, we recovered medium- and high-quality MAGs for 5 of the 18 “Ca. Accumulibacter” species, all with rRNA operons assembled, which allowed a reassessment of the 16S rRNA-based phylogeny of this genus and an analysis of phylogeny based on the 23S rRNA gene. In addition, we recovered a cluster of MAGs that based on 16S rRNA, 23S rRNA, ppk1, and genome-scale phylogenetic analyses do not belong to any of the currently recognized “Ca. Accumulibacter” species for which we propose the new species designation “Ca. Accumulibacter jenkinsii” sp. nov. Relative abundance evaluations of the genus across all pilot plant operations revealed that regardless of the operational mode, “Ca. A. necessarius” and “Ca. A. propinquus” accounted for more than 40% of the “Ca. Accumulibacter” community, whereas the newly proposed “Ca. A. jenkinsii” accounted for about 5% of the “Ca. Accumulibacter” community.IMPORTANCEOne of the main drivers of energy use and operational costs in activated sludge processes is the amount of oxygen provided to enable biological phosphorus and nitrogen removal. Wastewater treatment facilities are increasingly considering reduced aeration to decrease energy consumption, and whereas successful BNR has been demonstrated in systems with minimal aeration, an adequate understanding of the microbial communities that facilitate nutrient removal under these conditions is still lacking. In this study, we used genome-resolved metagenomics to evaluate the diversity of the “Candidatus Accumulibacter” genus in pilot-scale plants operating with minimal aeration. We identified the “Ca. Accumulibacter” species enriched under these conditions, including one novel species for which we propose “Ca. Accumulibacter jenkinsii” sp. nov. as its designation. Furthermore, the MAGs obtained for five additional “Ca. Accumulibacter” species further refine the phylogeny of the “Ca. Accumulibacter” genus and provide new insight into its diversity within unconventional biological nutrient removal systems. |
| first_indexed | 2024-04-24T22:33:31Z |
| format | Article |
| id | doaj.art-416d6673f5ed406a9f86c7f5c97bbba4 |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-04-24T22:33:31Z |
| publishDate | 2024-03-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-416d6673f5ed406a9f86c7f5c97bbba42024-03-19T13:01:37ZengAmerican Society for MicrobiologymSystems2379-50772024-03-019310.1128/msystems.01188-23Refinement of the “Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aerationRachel D. Stewart0Kevin S. Myers1Carly Amstadt2Matt Seib3Katherine D. McMahon4Daniel R. Noguera5Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USAWisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USADepartment of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USAMadison Metropolitan Sewerage District, Madison, Wisconsin, USADepartment of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USADepartment of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USAABSTRACTMembers of the “Candidatus Accumulibacter” genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 “Ca. Accumulibacter” species, which have been proposed based on the phylogenetic divergence of the polyphosphate kinase 1 (ppk1) gene and genome-scale comparisons of metagenome-assembled genomes (MAGs). Phylogenetic classification based on the 16S rRNA genetic marker has been difficult to attain because most “Ca. Accumulibacter” MAGs are incomplete and often do not include the rRNA operon. Here, we investigate the “Ca. Accumulibacter” diversity in pilot-scale treatment trains performing BNR under low dissolved oxygen (DO) conditions using genome-resolved metagenomics. Using long-read sequencing, we recovered medium- and high-quality MAGs for 5 of the 18 “Ca. Accumulibacter” species, all with rRNA operons assembled, which allowed a reassessment of the 16S rRNA-based phylogeny of this genus and an analysis of phylogeny based on the 23S rRNA gene. In addition, we recovered a cluster of MAGs that based on 16S rRNA, 23S rRNA, ppk1, and genome-scale phylogenetic analyses do not belong to any of the currently recognized “Ca. Accumulibacter” species for which we propose the new species designation “Ca. Accumulibacter jenkinsii” sp. nov. Relative abundance evaluations of the genus across all pilot plant operations revealed that regardless of the operational mode, “Ca. A. necessarius” and “Ca. A. propinquus” accounted for more than 40% of the “Ca. Accumulibacter” community, whereas the newly proposed “Ca. A. jenkinsii” accounted for about 5% of the “Ca. Accumulibacter” community.IMPORTANCEOne of the main drivers of energy use and operational costs in activated sludge processes is the amount of oxygen provided to enable biological phosphorus and nitrogen removal. Wastewater treatment facilities are increasingly considering reduced aeration to decrease energy consumption, and whereas successful BNR has been demonstrated in systems with minimal aeration, an adequate understanding of the microbial communities that facilitate nutrient removal under these conditions is still lacking. In this study, we used genome-resolved metagenomics to evaluate the diversity of the “Candidatus Accumulibacter” genus in pilot-scale plants operating with minimal aeration. We identified the “Ca. Accumulibacter” species enriched under these conditions, including one novel species for which we propose “Ca. Accumulibacter jenkinsii” sp. nov. as its designation. Furthermore, the MAGs obtained for five additional “Ca. Accumulibacter” species further refine the phylogeny of the “Ca. Accumulibacter” genus and provide new insight into its diversity within unconventional biological nutrient removal systems.https://journals.asm.org/doi/10.1128/msystems.01188-23Accumulibacterphylogenybiological nutrient removalenhanced biological phosphorus removal |
| spellingShingle | Rachel D. Stewart Kevin S. Myers Carly Amstadt Matt Seib Katherine D. McMahon Daniel R. Noguera Refinement of the “Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration mSystems Accumulibacter phylogeny biological nutrient removal enhanced biological phosphorus removal |
| title | Refinement of the “Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration |
| title_full | Refinement of the “Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration |
| title_fullStr | Refinement of the “Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration |
| title_full_unstemmed | Refinement of the “Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration |
| title_short | Refinement of the “Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration |
| title_sort | refinement of the candidatus accumulibacter genus based on metagenomic analysis of biological nutrient removal bnr pilot scale plants operated with reduced aeration |
| topic | Accumulibacter phylogeny biological nutrient removal enhanced biological phosphorus removal |
| url | https://journals.asm.org/doi/10.1128/msystems.01188-23 |
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