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

Giantommaso Scarascia,Hong Cheng,Pei-Ying Hong,Moustapha Harb

doi:10.1186/s12866-017-0998-2

Abstract

BackgroundEstablishing 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.ResultsThe 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.ConclusionsOverall, 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.

Highlights

Establishing an optimal proportion of nitrifying microbial populations, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), complete nitrite oxidizers and ammonia-oxidizing archaea (AOA), is important for ensuring the efficiency of nitrification in water treatment systems
AOB abundance in biofilm reactor quantified by Hierarchical oligonucleotide primer extension (HOPE) throughout the operational phases The relative abundances of nitrifying bacterial populations quantified by the HOPE approach were collated for multivariate analysis on a multidimensional scaling plot (Fig. 2a)
Vector-based analysis showed an increase in the abundance of AOB in Phases E and D2 compared to the early operational phases

Summary

Introduction

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. Nitrification in the wastewater treatment process is generally performed in two consecutive steps. The first step is ammonia oxidation by either ammoniaoxidizing bacteria (AOB) or ammonia-oxidizing archaea (AOA), and the second step is nitrite oxidation by nitriteoxidizing bacteria (NOB). Representative AOB genera include Nitrosomonas and Nitrosospira while Nitrososphaera and Nitrosopumilus would account as two examples of AOA. Three members within the genus Nitrospira, namely Candidatus Nitrospira inopinata, Candidatus Nitrospira nitrosa and Candidatus Nitrospira nitrificans, were shown to perform complete nitrification in a single step and are referred to as comammox [1, 2].

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Conclusion