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

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dc.contributor.author Scarascia, Giantommaso
dc.contributor.author Cheng, Hong
dc.contributor.author Harb, Moustapha
dc.contributor.author Hong, Pei-Ying
dc.date.accessioned 2019-03-08T14:57:40Z
dc.date.available 2019-03-08T14:57:40Z
dc.date.copyright 2017 en_US
dc.identifier.issn 1471-2180 en_US
dc.identifier.uri http://hdl.handle.net/10725/10156
dc.description.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. en_US
dc.language.iso en en_US
dc.title Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria en_US
dc.type Article en_US
dc.description.version Published en_US
dc.author.school SOE en_US
dc.author.idnumber 201806912 en_US
dc.author.department Civil Engineering en_US
dc.description.embargo N/A en_US
dc.relation.journal BMC Microbiology en_US
dc.journal.volume 17 en_US
dc.journal.issue 1 en_US
dc.article.pages 1-16 en_US
dc.keywords Single nucleotide primer extension en_US
dc.keywords Quantitative monitoring en_US
dc.keywords 16S rRNA gene-based amplicon sequencing en_US
dc.keywords AOB/NOB ratio en_US
dc.keywords Shock loading event en_US
dc.identifier.doi https://doi.org/10.1186/s12866-017-0998-2 en_US
dc.identifier.ctation 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(1), 1-26. en_US
dc.author.email moustapha.harb@lau.edu.lb en_US
dc.identifier.tou http://libraries.lau.edu.lb/research/laur/terms-of-use/articles.php en_US
dc.identifier.url https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-017-0998-2 en_US
dc.orcid.id https://orcid.org/0000-0002-1566-987X en_US
dc.author.affiliation Lebanese American University en_US


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