Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria

Handle URI:
http://hdl.handle.net/10754/623627
Title:
Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria
Authors:
Scarascia, Giantommaso ( 0000-0003-3202-9871 ) ; Cheng, Hong ( 0000-0002-4943-9060 ) ; Harb, Moustapha ( 0000-0002-1566-987X ) ; Hong, Pei-Ying ( 0000-0002-4474-6600 )
Abstract:
Background: Establishing an optimal proportion of nitrifying microbial populations, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), complete nitrite oxidizers (comammox) and ammonia-oxidizing archaea (AOA), is important for ensuring the efficiency of nitrification in water treatment systems. Hierarchical oligonucleotide primer extension (HOPE), previously developed to rapidly quantify relative abundances of specific microbial groups of interest, was applied in this study to track the abundances of the important nitrifying bacterial populations. Results: The method was tested against biomass obtained from a laboratory-scale biofilm-based trickling reactor, and the findings were validated against those obtained by 16S rRNA gene-based amplicon sequencing. Our findings indicated a good correlation between the relative abundance of nitrifying bacterial populations obtained using both HOPE and amplicon sequencing. HOPE showed a significant increase in the relative abundance of AOB, specifically Nitrosomonas, with increasing ammonium content and shock loading (p < 0.001). In contrast, Nitrosospira remained stable in its relative abundance against the total community throughout the operational phases. There was a corresponding significant decrease in the relative abundance of NOB, specifically Nitrospira and those affiliated to comammox, during the shock loading. Based on the relative abundance of AOB and NOB (including commamox) obtained from HOPE, it was determined that the optimal ratio of AOB against NOB ranged from 0.2 to 2.5 during stable reactor performance. Conclusions: Overall, the HOPE method was developed and validated against 16S rRNA gene-based amplicon sequencing for the purpose of performing simultaneous monitoring of relative abundance of nitrifying populations. Quantitative measurements of these nitrifying populations obtained via HOPE would be indicative of reactor performance and nitrification functionality.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Water Desalination and Reuse Research Center (WDRC)
Citation:
Scarascia G, Cheng H, Harb M, Hong P-Y (2017) Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria. BMC Microbiology 17. Available: http://dx.doi.org/10.1186/s12866-017-0998-2.
Publisher:
Springer Nature
Journal:
BMC Microbiology
KAUST Grant Number:
FCC/1/1971–06-01
Issue Date:
4-Apr-2017
DOI:
10.1186/s12866-017-0998-2
Type:
Article
ISSN:
1471-2180
Sponsors:
This study was supported by funding from King Abdullah University of Science and Technology (KAUST Center Competitive Funding Program grant FCC/1/1971–06-01) awarded to P.-Y. Hong. The funders had no role in the study design, data collection, analysis and interpretation of the data, decision to publish, or preparation of the manuscript.
Additional Links:
http://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-017-0998-2
Appears in Collections:
Articles; Water Desalination and Reuse Research Center (WDRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorScarascia, Giantommasoen
dc.contributor.authorCheng, Hongen
dc.contributor.authorHarb, Moustaphaen
dc.contributor.authorHong, Pei-Yingen
dc.date.accessioned2017-05-17T07:41:38Z-
dc.date.available2017-05-17T07:41:38Z-
dc.date.issued2017-04-04en
dc.identifier.citationScarascia G, Cheng H, Harb M, Hong P-Y (2017) Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria. BMC Microbiology 17. Available: http://dx.doi.org/10.1186/s12866-017-0998-2.en
dc.identifier.issn1471-2180en
dc.identifier.doi10.1186/s12866-017-0998-2en
dc.identifier.urihttp://hdl.handle.net/10754/623627-
dc.description.abstractBackground: Establishing an optimal proportion of nitrifying microbial populations, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), complete nitrite oxidizers (comammox) and ammonia-oxidizing archaea (AOA), is important for ensuring the efficiency of nitrification in water treatment systems. Hierarchical oligonucleotide primer extension (HOPE), previously developed to rapidly quantify relative abundances of specific microbial groups of interest, was applied in this study to track the abundances of the important nitrifying bacterial populations. Results: The method was tested against biomass obtained from a laboratory-scale biofilm-based trickling reactor, and the findings were validated against those obtained by 16S rRNA gene-based amplicon sequencing. Our findings indicated a good correlation between the relative abundance of nitrifying bacterial populations obtained using both HOPE and amplicon sequencing. HOPE showed a significant increase in the relative abundance of AOB, specifically Nitrosomonas, with increasing ammonium content and shock loading (p < 0.001). In contrast, Nitrosospira remained stable in its relative abundance against the total community throughout the operational phases. There was a corresponding significant decrease in the relative abundance of NOB, specifically Nitrospira and those affiliated to comammox, during the shock loading. Based on the relative abundance of AOB and NOB (including commamox) obtained from HOPE, it was determined that the optimal ratio of AOB against NOB ranged from 0.2 to 2.5 during stable reactor performance. Conclusions: Overall, the HOPE method was developed and validated against 16S rRNA gene-based amplicon sequencing for the purpose of performing simultaneous monitoring of relative abundance of nitrifying populations. Quantitative measurements of these nitrifying populations obtained via HOPE would be indicative of reactor performance and nitrification functionality.en
dc.description.sponsorshipThis study was supported by funding from King Abdullah University of Science and Technology (KAUST Center Competitive Funding Program grant FCC/1/1971–06-01) awarded to P.-Y. Hong. The funders had no role in the study design, data collection, analysis and interpretation of the data, decision to publish, or preparation of the manuscript.en
dc.publisherSpringer Natureen
dc.relation.urlhttp://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-017-0998-2en
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subject16S rRNA gene-based amplicon sequencingen
dc.subjectAOB/NOB ratioen
dc.subjectQuantitative monitoringen
dc.subjectShock loading eventen
dc.subjectSingle nucleotide primer extensionen
dc.titleApplication of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteriaen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentWater Desalination and Reuse Research Center (WDRC)en
dc.identifier.journalBMC Microbiologyen
dc.eprint.versionPublisher's Version/PDFen
kaust.authorScarascia, Giantommasoen
kaust.authorCheng, Hongen
kaust.authorHarb, Moustaphaen
kaust.authorHong, Pei-Yingen
kaust.grant.numberFCC/1/1971–06-01en
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