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

Scarascia, Giantommaso; Cheng, Hong; Harb, Moustapha; Hong, Pei‐Ying

doi:10.1186/s12866-017-0998-2

Cited by 9 publications

(6 citation statements)

References 43 publications

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“…The abundance of each nitrifying and anammox target detected by each specific primer, relative to the abundances of targets detected by 1390Rm_II, could be determined in accordance with the fluorescence of individual primer fragments accordingly. The specific details regarding the HOPE experiment and capillary DNA sequencer, as well as data processing, have been described previously. , …”

Section: Methodsmentioning

confidence: 99%

Comammox Nitrospira Species Dominate in an Efficient Partial Nitrification–Anammox Bioreactor for Treating Ammonium at Low Loadings

Shao

2021

Environ. Sci. Technol.

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Bacteria capable of complete ammonia oxidation (comammox) are widespread and contribute to nitrification in wastewater treatment facilities. However, their roles in partial nitrification–anaerobic ammonium oxidation (anammox) systems remain unclear. In this study, a bench-scale bioreactor with continuous stirring was operated for more than 1000 days with limited oxygen supply to achieve efficient nitrogen removal (70.1 ± 2.7%) at a low ammonium loading of 35.2 mg-N/L/day. High-throughput amplicon sequencing analysis of the comammox ammonia monooxygenase subunit A (amoA) gene revealed seven sequence types from two clusters in clade A of comammox Nitrospira. Quantitative polymerase chain reaction analyses suggested that the comammox species dominated the ammonia-oxidizing community, with an abundance as high as 89.2 ± 7.9% in total prokaryotic amoA copies. Multiple linear regression further revealed the substantial contribution of the comammox Nitrospira to ammonia oxidation in the bioreactor. The investigation with bioreactor and batch experiments consistently showed that activities of comammox Nitrospira were inhibited by free ammonia far more severely than other ammonia-oxidizing microbes. Overall, this study provided new insight into the ecology of comammox Nitrospira under hypoxic conditions and suggested comammox-associated partial nitrification–anammox as a potential method for treating low-strength ammonium-containing wastewater.

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Section: Methodsmentioning

confidence: 99%

Comammox Nitrospira Species Dominate in an Efficient Partial Nitrification–Anammox Bioreactor for Treating Ammonium at Low Loadings

Shao

2021

Environ. Sci. Technol.

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“…However, further studies using the FISH technique should employ bigger number of probes even considering the ammonia-oxidizing archaea, or bacteria of the Nitrospira genus that conduct the two steps of the nitrification process (Scarascia, Cheng, Harb, & Hong, 2017;VanKessel et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

Variability of the nitrifying bacteria in the biofilm and water column of a recirculating aquaculture system for tilapia ( Oreochromis niloticus ) production

et al. 2019

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The aim of this study was to evaluate variability of nitrifying bacterial community in the biofilm and in the water of a recirculating aquaculture systems (RAS) in a tilapia farming in order to determine if nitrification process is dependent, or not, of nitrifying bacteria abundance. Biofilm and water samples were collected periodically for 30 days and analysed with the fluorescent in situ hybridization (FISH) technique, used to quantify ammonia‐oxidizing bacteria (AOB) and nitrite‐oxidizing bacteria (NOB). Ammonia presented the peak in the first week, while the nitrite's maximum was recorded in the second week. Nitrate increased steadily, indicating nitrification activity. Total bacterial abundance in biofilm increased continuously, while in water, it did not change significantly. In the biofilm, number of AOB was high at beginning, decreased after few days and increased again following augment of ammonia. Number of NOB also showed an increase in abundance in biofilm following the increment of nitrite and nitrate. In water, AOB and NOB did not show major variability. Relative abundance of nitrifying bacteria represented more than 30% of total bacteria in biofilm at beginning of the experiment. Their contribution decreased to >3% in last days. It indicates that nitrifying bacteria are biofilm colonizers, and that their activity seems to be directly related to the concentration of nitrogen compounds. However, contribution of nitrifying bacteria did not vary much along the time. We may conclude that the biofilm‐nitrifying bacteria plays major role in nitrification process in RAS and that the activity of these organisms is dependent of their abundance in response to the concentration of nitrogen compounds.

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“…Extracted RNA was reverse transcribed into first-strand complementary DNA (cDNA) using the Invitrogen SuperScript TM First-Strand Synthesis System (Thermo Fisher Scientific, Carlsbad, CA). The cDNA was then used as template to amplify for 16S rRNA genes with primer pair 515F (5′- Illumina overhang- GTG YCA GCM GCC GCG GTA A-3′) and 907R (5′- Illumina overhang- CCC CGY CAA TTC MTT TRA GT-3′) based on the procedure described earlier (Scarascia et al, 2017 ). Purified amplicons were submitted to KAUST Genomic Core lab for amplicon sequencing on Illumina MiSeq platform.…”

Section: Methodsmentioning

confidence: 99%

Bacteriophage Infectivity Against Pseudomonas aeruginosa in Saline Conditions

et al. 2018

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Pseudomonas aeruginosa is a ubiquitous member of marine biofilm, and reduces thiosulfate to produce toxic hydrogen sulfide gas. In this study, lytic bacteriophages were isolated and applied to inhibit the growth of P. aeruginosa in planktonic mode at different temperature, pH, and salinity. Bacteriophages showed optimal infectivity at a multiplicity of infection of 10 in saline conditions, and demonstrated lytic abilities over all tested temperature (25, 30, 37, and 45°C) and pH 6–9. Planktonic P. aeruginosa exhibited significantly longer lag phase and lower specific growth rates upon exposure to bacteriophages. Bacteriophages were subsequently applied to P. aeruginosa-enriched biofilm and were determined to lower the relative abundance of Pseudomonas-related taxa from 0.17 to 5.58% in controls to 0.01–0.61% in treated microbial communities. The relative abundance of Alphaproteobacteria, Pseudoalteromonas, and Planococcaceae decreased, possibly due to the phage-induced disruption of the biofilm matrix. Lastly, when applied to mitigate biofouling of ultrafiltration membranes, bacteriophages were determined to reduce the transmembrane pressure increase by 18% when utilized alone, and by 49% when used in combination with citric acid. The combined treatment was more effective compared with the citric acid treatment alone, which reported ca. 30% transmembrane pressure reduction. Collectively, the findings demonstrated that bacteriophages can be used as a biocidal agent to mitigate undesirable P. aeruginosa-associated problems in seawater applications.

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

Cited by 9 publications

References 43 publications

Comammox Nitrospira Species Dominate in an Efficient Partial Nitrification–Anammox Bioreactor for Treating Ammonium at Low Loadings

Comammox Nitrospira Species Dominate in an Efficient Partial Nitrification–Anammox Bioreactor for Treating Ammonium at Low Loadings

Variability of the nitrifying bacteria in the biofilm and water column of a recirculating aquaculture system for tilapia ( Oreochromis niloticus ) production

Bacteriophage Infectivity Against Pseudomonas aeruginosa in Saline Conditions

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