Comparison of PCR Primers for Analyzing Denitrifying Microorganisms in the Hyporheic Zone
In this study, the specific amplifications of six denitrification-associated genes using PCR(Polymerase Chain Reaction) primer sets were compared. Thereafter, the PCR primer sets that were determined to be suitable for each denitrification-associated gene were used to test samples from sixteen aqueo...
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doaj-7294f4223b8646f9baae61d12f887b482020-11-25T03:07:16ZengMDPI AGApplied Sciences2076-34172020-06-01104172417210.3390/app10124172Comparison of PCR Primers for Analyzing Denitrifying Microorganisms in the Hyporheic ZoneHeejung Kim0Department of Geology, College of Natural Sciences, Kangwon National University, Chuncheon 24341, KoreaIn this study, the specific amplifications of six denitrification-associated genes using PCR(Polymerase Chain Reaction) primer sets were compared. Thereafter, the PCR primer sets that were determined to be suitable for each denitrification-associated gene were used to test samples from sixteen aqueous environments (three from groundwater, three from stream water, and ten from hyporheic zone water). The specific amplification was determined using PCR primer sets for denitrification-associated genes and nucleic acids from eleven types of strains. <i>NosZ</i> was the most frequently amplified gene from the nucleic acid of type, with a specific band seen in all eleven strains. The specific band amplification and PCR time of the strains were analyzed to select one PCR primer set for each gene. The selected PCR primer sets were used to analyze sixteen samples from the aqueous environments in which denitrifying microorganisms were expected to be present. Specific bands of <i>narG</i>, <i>nirS</i>, and <i>nosZ</i> were most frequently observed in the hyporheic water samples. The results showed that microorganisms containing <i>nirG</i> (involved in the reduction of nitrate to nitrite), <i>nirS</i> (involved in the reduction of nitrite to nitric oxide), and <i>nosZ</i> (involved in the reduction of nitrous oxide to nitrogen gas) were the most abundant in the hyporheic zone samples used in this study.https://www.mdpi.com/2076-3417/10/12/4172hyporheic zonedenitrification-associated genepolymerase chain reactionnitrogen cycle |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Heejung Kim |
spellingShingle |
Heejung Kim Comparison of PCR Primers for Analyzing Denitrifying Microorganisms in the Hyporheic Zone Applied Sciences hyporheic zone denitrification-associated gene polymerase chain reaction nitrogen cycle |
author_facet |
Heejung Kim |
author_sort |
Heejung Kim |
title |
Comparison of PCR Primers for Analyzing Denitrifying Microorganisms in the Hyporheic Zone |
title_short |
Comparison of PCR Primers for Analyzing Denitrifying Microorganisms in the Hyporheic Zone |
title_full |
Comparison of PCR Primers for Analyzing Denitrifying Microorganisms in the Hyporheic Zone |
title_fullStr |
Comparison of PCR Primers for Analyzing Denitrifying Microorganisms in the Hyporheic Zone |
title_full_unstemmed |
Comparison of PCR Primers for Analyzing Denitrifying Microorganisms in the Hyporheic Zone |
title_sort |
comparison of pcr primers for analyzing denitrifying microorganisms in the hyporheic zone |
publisher |
MDPI AG |
series |
Applied Sciences |
issn |
2076-3417 |
publishDate |
2020-06-01 |
description |
In this study, the specific amplifications of six denitrification-associated genes using PCR(Polymerase Chain Reaction) primer sets were compared. Thereafter, the PCR primer sets that were determined to be suitable for each denitrification-associated gene were used to test samples from sixteen aqueous environments (three from groundwater, three from stream water, and ten from hyporheic zone water). The specific amplification was determined using PCR primer sets for denitrification-associated genes and nucleic acids from eleven types of strains. <i>NosZ</i> was the most frequently amplified gene from the nucleic acid of type, with a specific band seen in all eleven strains. The specific band amplification and PCR time of the strains were analyzed to select one PCR primer set for each gene. The selected PCR primer sets were used to analyze sixteen samples from the aqueous environments in which denitrifying microorganisms were expected to be present. Specific bands of <i>narG</i>, <i>nirS</i>, and <i>nosZ</i> were most frequently observed in the hyporheic water samples. The results showed that microorganisms containing <i>nirG</i> (involved in the reduction of nitrate to nitrite), <i>nirS</i> (involved in the reduction of nitrite to nitric oxide), and <i>nosZ</i> (involved in the reduction of nitrous oxide to nitrogen gas) were the most abundant in the hyporheic zone samples used in this study. |
topic |
hyporheic zone denitrification-associated gene polymerase chain reaction nitrogen cycle |
url |
https://www.mdpi.com/2076-3417/10/12/4172 |
work_keys_str_mv |
AT heejungkim comparisonofpcrprimersforanalyzingdenitrifyingmicroorganismsinthehyporheiczone |
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1724671544624414720 |