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Article: Genome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess

TitleGenome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess
Authors
KeywordsDenitrifying PAO
Denitrification
Enhanced biological phosphorus removal (EBPR)
Nitrous oxide
Metagenome-assembled genomes (MAGs)
Issue Date2019
PublisherPergamon. The Journal's web site is located at http://www.elsevier.com/locate/watres
Citation
Water Research, 2019, v. 155, p. 275-287 How to Cite?
AbstractDenitrification is the stepwise microbial reduction of nitrate or nitrite (NO2−) to nitrogen gas via the obligate intermediates nitric oxide (NO) and nitrous oxide (N2O). Substantial N2O accumulation has been reported in denitrifying enhanced biological phosphorus removal (EBPR) bioreactors enriched in denitrifying polyphosphate accumulating organisms (DPAOs), but little is known about underlying mechanisms for N2O generation, prevalence of complete versus truncated denitrification pathways, or the impact of NO2− feed on DPAO-enriched consortia. To address this knowledge gap, we employed genome-resolved metagenomics to investigate nitrogen transformation potential in a NO2− fed denitrifying EBPR bioreactor enriched in Candidatus Accumulibacter and prone to N2O accumulation. Our analysis yielded 41 near-complete metagenome-assembled genomes (MAGs), including two co-occurring Accumulibacter strains affiliated with clades IA and IC (the first published genome from this clade) and 39 non-PAO flanking bacterial genomes. The dominant Accumulibacter clade IA encoded genes for complete denitrification, while the lower abundance Accumulibacter clade IC harbored all denitrification genes except for a canonical respiratory NO reductase. Analysis of the 39 non-PAO MAGs revealed a high prevalence of taxa harboring an incomplete denitrification pathway. Of the 27 MAGs harboring capacity for at least one step in the denitrification pathway, 10 were putative N2O producers lacking N2O reductase, 16 were putative N2O reducers that lacked at least one upstream denitrification gene, and only one harbored a complete denitrification pathway. We also documented increasing abundance over the course of reactor operation of putative N2O producers. Our results suggest that the unusually high levels of N2O production observed in this Accumulibacter-enriched consortium are linked in part to the selection for non-PAO flanking microorganisms with truncated denitrification pathways.
Persistent Identifierhttp://hdl.handle.net/10722/293306
ISSN
2023 Impact Factor: 11.4
2023 SCImago Journal Rankings: 3.596
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorGao, H-
dc.contributor.authorMao, Y-
dc.contributor.authorZhao, X-
dc.contributor.authorLiu, WT-
dc.contributor.authorZhang, T-
dc.contributor.authorWells, G-
dc.date.accessioned2020-11-23T08:14:51Z-
dc.date.available2020-11-23T08:14:51Z-
dc.date.issued2019-
dc.identifier.citationWater Research, 2019, v. 155, p. 275-287-
dc.identifier.issn0043-1354-
dc.identifier.urihttp://hdl.handle.net/10722/293306-
dc.description.abstractDenitrification is the stepwise microbial reduction of nitrate or nitrite (NO2−) to nitrogen gas via the obligate intermediates nitric oxide (NO) and nitrous oxide (N2O). Substantial N2O accumulation has been reported in denitrifying enhanced biological phosphorus removal (EBPR) bioreactors enriched in denitrifying polyphosphate accumulating organisms (DPAOs), but little is known about underlying mechanisms for N2O generation, prevalence of complete versus truncated denitrification pathways, or the impact of NO2− feed on DPAO-enriched consortia. To address this knowledge gap, we employed genome-resolved metagenomics to investigate nitrogen transformation potential in a NO2− fed denitrifying EBPR bioreactor enriched in Candidatus Accumulibacter and prone to N2O accumulation. Our analysis yielded 41 near-complete metagenome-assembled genomes (MAGs), including two co-occurring Accumulibacter strains affiliated with clades IA and IC (the first published genome from this clade) and 39 non-PAO flanking bacterial genomes. The dominant Accumulibacter clade IA encoded genes for complete denitrification, while the lower abundance Accumulibacter clade IC harbored all denitrification genes except for a canonical respiratory NO reductase. Analysis of the 39 non-PAO MAGs revealed a high prevalence of taxa harboring an incomplete denitrification pathway. Of the 27 MAGs harboring capacity for at least one step in the denitrification pathway, 10 were putative N2O producers lacking N2O reductase, 16 were putative N2O reducers that lacked at least one upstream denitrification gene, and only one harbored a complete denitrification pathway. We also documented increasing abundance over the course of reactor operation of putative N2O producers. Our results suggest that the unusually high levels of N2O production observed in this Accumulibacter-enriched consortium are linked in part to the selection for non-PAO flanking microorganisms with truncated denitrification pathways.-
dc.languageeng-
dc.publisherPergamon. The Journal's web site is located at http://www.elsevier.com/locate/watres-
dc.relation.ispartofWater Research-
dc.subjectDenitrifying PAO-
dc.subjectDenitrification-
dc.subjectEnhanced biological phosphorus removal (EBPR)-
dc.subjectNitrous oxide-
dc.subjectMetagenome-assembled genomes (MAGs)-
dc.titleGenome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess-
dc.typeArticle-
dc.identifier.emailZhang, T: zhangt@hkucc.hku.hk-
dc.identifier.authorityZhang, T=rp00211-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1016/j.watres.2019.02.020-
dc.identifier.pmid30852315-
dc.identifier.scopuseid_2-s2.0-85062455249-
dc.identifier.hkuros319414-
dc.identifier.volume155-
dc.identifier.spage275-
dc.identifier.epage287-
dc.identifier.isiWOS:000464488500027-
dc.publisher.placeUnited Kingdom-
dc.identifier.issnl0043-1354-

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