Integrated Omic Analyses Provide Evidence that a “<italic toggle="yes">Candidatus</italic> Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions

ABSTRACT The ability of “Candidatus Accumulibacter phosphatis” to grow and remove phosphorus from wastewater under cycling anaerobic and aerobic conditions has also been investigated as a metabolism that could lead to simultaneous removal of nitrogen and phosphorus by a single organism. However, alt...

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Autores principales:	Pamela Y. Camejo, Ben O. Oyserman, Katherine D. McMahon, Daniel R. Noguera
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	Accumulibacter RNA sequencing denitrification metagenomics transcriptional regulation Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/0860aea0948b4576b9d173274a1fc247
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spelling	oai:doaj.org-article:0860aea0948b4576b9d173274a1fc2472021-12-02T18:15:45ZIntegrated Omic Analyses Provide Evidence that a “<italic toggle="yes">Candidatus</italic> Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions10.1128/mSystems.00193-182379-5077https://doaj.org/article/0860aea0948b4576b9d173274a1fc2472019-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00193-18https://doaj.org/toc/2379-5077ABSTRACT The ability of “Candidatus Accumulibacter phosphatis” to grow and remove phosphorus from wastewater under cycling anaerobic and aerobic conditions has also been investigated as a metabolism that could lead to simultaneous removal of nitrogen and phosphorus by a single organism. However, although phosphorus removal under cyclic anaerobic and anoxic conditions has been demonstrated, clarifying the role of “Ca. Accumulibacter phosphatis” in this process has been challenging, since (i) experimental research describes contradictory findings, (ii) none of the published “Ca. Accumulibacter phosphatis” genomes show the existence of a complete respiratory pathway for denitrification, and (iii) some genomes lacking a complete respiratory pathway have genes for assimilatory nitrate reduction. In this study, we used an integrated omics analysis to elucidate the physiology of a “Ca. Accumulibacter phosphatis” strain enriched in a reactor operated under cyclic anaerobic and microaerobic conditions. The reactor’s performance suggested the ability of the enriched “Ca. Accumulibacter phosphatis” strain (clade IC) to simultaneously use oxygen and nitrate as electron acceptors under microaerobic conditions. A draft genome of this organism was assembled from metagenomic reads (“Ca. Accumulibacter phosphatis” UW-LDO-IC) and used as a reference to examine transcript abundance throughout one reactor cycle. The genome of UW-LDO-IC revealed the presence of a full pathway for respiratory denitrification. The observed transcript abundance patterns showed evidence of coregulation of the denitrifying genes along with a cbb3 cytochrome, which has been characterized as having high affinity for oxygen. Furthermore, we identified an FNR-like binding motif upstream of the coregulated genes, suggesting transcription-level regulation of both denitrifying and respiratory pathways in UW-LDO-IC. Taking the results together, the omics analysis provides strong evidence that “Ca. Accumulibacter phosphatis” UW-LDO-IC uses oxygen and nitrate simultaneously as electron acceptors under microaerobic conditions. IMPORTANCE “Candidatus Accumulibacter phosphatis” is widely found in full-scale wastewater treatment plants, where it has been identified as the key organism for biological removal of phosphorus. Since aeration can account for 50% of the energy use during wastewater treatment, microaerobic conditions for wastewater treatment have emerged as a cost-effective alternative to conventional biological nutrient removal processes. Our report provides strong genomics-based evidence not only that “Ca. Accumulibacter phosphatis” is the main organism contributing to phosphorus removal under microaerobic conditions but also that this organism simultaneously respires nitrate and oxygen in this environment, consequently removing nitrogen and phosphorus from the wastewater. Such activity could be harnessed in innovative designs for cost-effective and energy-efficient optimization of wastewater treatment systems.Pamela Y. CamejoBen O. OysermanKatherine D. McMahonDaniel R. NogueraAmerican Society for MicrobiologyarticleAccumulibacterRNA sequencingdenitrificationmetagenomicstranscriptional regulationMicrobiologyQR1-502ENmSystems, Vol 4, Iss 1 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Accumulibacter RNA sequencing denitrification metagenomics transcriptional regulation Microbiology QR1-502
spellingShingle	Accumulibacter RNA sequencing denitrification metagenomics transcriptional regulation Microbiology QR1-502 Pamela Y. Camejo Ben O. Oyserman Katherine D. McMahon Daniel R. Noguera Integrated Omic Analyses Provide Evidence that a “<italic toggle="yes">Candidatus</italic> Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions
description	ABSTRACT The ability of “Candidatus Accumulibacter phosphatis” to grow and remove phosphorus from wastewater under cycling anaerobic and aerobic conditions has also been investigated as a metabolism that could lead to simultaneous removal of nitrogen and phosphorus by a single organism. However, although phosphorus removal under cyclic anaerobic and anoxic conditions has been demonstrated, clarifying the role of “Ca. Accumulibacter phosphatis” in this process has been challenging, since (i) experimental research describes contradictory findings, (ii) none of the published “Ca. Accumulibacter phosphatis” genomes show the existence of a complete respiratory pathway for denitrification, and (iii) some genomes lacking a complete respiratory pathway have genes for assimilatory nitrate reduction. In this study, we used an integrated omics analysis to elucidate the physiology of a “Ca. Accumulibacter phosphatis” strain enriched in a reactor operated under cyclic anaerobic and microaerobic conditions. The reactor’s performance suggested the ability of the enriched “Ca. Accumulibacter phosphatis” strain (clade IC) to simultaneously use oxygen and nitrate as electron acceptors under microaerobic conditions. A draft genome of this organism was assembled from metagenomic reads (“Ca. Accumulibacter phosphatis” UW-LDO-IC) and used as a reference to examine transcript abundance throughout one reactor cycle. The genome of UW-LDO-IC revealed the presence of a full pathway for respiratory denitrification. The observed transcript abundance patterns showed evidence of coregulation of the denitrifying genes along with a cbb3 cytochrome, which has been characterized as having high affinity for oxygen. Furthermore, we identified an FNR-like binding motif upstream of the coregulated genes, suggesting transcription-level regulation of both denitrifying and respiratory pathways in UW-LDO-IC. Taking the results together, the omics analysis provides strong evidence that “Ca. Accumulibacter phosphatis” UW-LDO-IC uses oxygen and nitrate simultaneously as electron acceptors under microaerobic conditions. IMPORTANCE “Candidatus Accumulibacter phosphatis” is widely found in full-scale wastewater treatment plants, where it has been identified as the key organism for biological removal of phosphorus. Since aeration can account for 50% of the energy use during wastewater treatment, microaerobic conditions for wastewater treatment have emerged as a cost-effective alternative to conventional biological nutrient removal processes. Our report provides strong genomics-based evidence not only that “Ca. Accumulibacter phosphatis” is the main organism contributing to phosphorus removal under microaerobic conditions but also that this organism simultaneously respires nitrate and oxygen in this environment, consequently removing nitrogen and phosphorus from the wastewater. Such activity could be harnessed in innovative designs for cost-effective and energy-efficient optimization of wastewater treatment systems.
format	article
author	Pamela Y. Camejo Ben O. Oyserman Katherine D. McMahon Daniel R. Noguera
author_facet	Pamela Y. Camejo Ben O. Oyserman Katherine D. McMahon Daniel R. Noguera
author_sort	Pamela Y. Camejo
title	Integrated Omic Analyses Provide Evidence that a “<italic toggle="yes">Candidatus</italic> Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions
title_short	Integrated Omic Analyses Provide Evidence that a “<italic toggle="yes">Candidatus</italic> Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions
title_full	Integrated Omic Analyses Provide Evidence that a “<italic toggle="yes">Candidatus</italic> Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions
title_fullStr	Integrated Omic Analyses Provide Evidence that a “<italic toggle="yes">Candidatus</italic> Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions
title_full_unstemmed	Integrated Omic Analyses Provide Evidence that a “<italic toggle="yes">Candidatus</italic> Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions
title_sort	integrated omic analyses provide evidence that a “<italic toggle="yes">candidatus</italic> accumulibacter phosphatis” strain performs denitrification under microaerobic conditions
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/0860aea0948b4576b9d173274a1fc247
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Integrated Omic Analyses Provide Evidence that a “<italic toggle="yes">Candidatus</italic> Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions

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