Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria
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 nitrificati...
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| Format: | Article |
| Language: | English |
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BMC
2017-04-01
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| Series: | BMC Microbiology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12866-017-0998-2 |
| _version_ | 1818905707912626176 |
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| author | Giantommaso Scarascia Hong Cheng Moustapha Harb Pei-Ying Hong |
| author_facet | Giantommaso Scarascia Hong Cheng Moustapha Harb Pei-Ying Hong |
| author_sort | Giantommaso Scarascia |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-19T21:27:37Z |
| format | Article |
| id | doaj.art-c842c0506bd342bd8d37a4bed99c0bb9 |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-12-19T21:27:37Z |
| publishDate | 2017-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj.art-c842c0506bd342bd8d37a4bed99c0bb92022-12-21T20:05:04ZengBMCBMC Microbiology1471-21802017-04-0117111610.1186/s12866-017-0998-2Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteriaGiantommaso Scarascia0Hong Cheng1Moustapha Harb2Pei-Ying Hong3Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC)Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC)Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC)Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC)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.http://link.springer.com/article/10.1186/s12866-017-0998-2Single nucleotide primer extensionQuantitative monitoring16S rRNA gene-based amplicon sequencingAOB/NOB ratioShock loading event |
| spellingShingle | Giantommaso Scarascia Hong Cheng Moustapha Harb Pei-Ying Hong Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria BMC Microbiology Single nucleotide primer extension Quantitative monitoring 16S rRNA gene-based amplicon sequencing AOB/NOB ratio Shock loading event |
| title | Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria |
| title_full | Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria |
| title_fullStr | Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria |
| title_full_unstemmed | Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria |
| title_short | Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria |
| title_sort | application of hierarchical oligonucleotide primer extension hope to assess relative abundances of ammonia and nitrite oxidizing bacteria |
| topic | Single nucleotide primer extension Quantitative monitoring 16S rRNA gene-based amplicon sequencing AOB/NOB ratio Shock loading event |
| url | http://link.springer.com/article/10.1186/s12866-017-0998-2 |
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