Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Environmental Science and Engineering Program
Water Desalination and Reuse Research Center (WDRC)
KAUST Grant NumberFCC/1/1971–06-01
Online Publication Date2017-04-04
Print Publication Date2017-12
Permanent link to this recordhttp://hdl.handle.net/10754/623627
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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.
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.
SponsorsThis 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.
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