Revealing the Microbiome of Four Different Thermal Springs in Turkey with Environmental DNA Metabarcoding
One of the most significant challenges for detecting microbial life in thermal springs by conventional techniques such as culturing is these places’ physicochemical (temperature, heavy metal content, pH, etc.) conditions. Data from several studies suggest that high-throughput DNA sequencing technolo...
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| Format: | Article |
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MDPI AG
2022-06-01
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| Series: | Biology |
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| Online Access: | https://www.mdpi.com/2079-7737/11/7/998 |
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| author | Işılay Çelik Emre Keskin |
| author_facet | Işılay Çelik Emre Keskin |
| author_sort | Işılay Çelik |
| collection | DOAJ |
| description | One of the most significant challenges for detecting microbial life in thermal springs by conventional techniques such as culturing is these places’ physicochemical (temperature, heavy metal content, pH, etc.) conditions. Data from several studies suggest that high-throughput DNA sequencing technologies can be used to perform more accurate and detailed microbiome analyses. The primary aim of this paper was to determine the microbiome in the thermal source by metabarcoding environmental DNA isolated from four different sources and reveal the reflection of differences caused by temperature and chemical content on the microbiome. DNA was extracted from water filtered with enclosed filters and using the Illumina high-throughput sequencing platform, V3 and V4 regions of the 16S rRNA gene were sequenced. The results showed a correlation between physicochemical conditions and microorganism composition of four different thermal springs. Springs with extremely high temperature (89–90 °C) were dominated by hyperthermophiles such as <i>Hydrogenobacter</i> and <i>Thermus</i>, while a spring with a high temperature (52 °C) was dominated by thermophiles such as <i>Thermoanaerobaculum</i> and <i>Desulfurispora</i>, and a spring with a low temperature (26 °C) and high salinity was dominated by halophiles and sulfur-oxidizers such as <i>Hydrogenovibrio</i> and <i>Sulfirimonas</i>. With this research, we observed many manipulable steps according to the work of interest. This study sought to obtain data that will help decide the right gene region and choose the optimal bioinformatic pipeline. |
| first_indexed | 2024-03-09T03:41:24Z |
| format | Article |
| id | doaj.art-5b72303b1bb8452692708d6656fb1e95 |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-09T03:41:24Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-5b72303b1bb8452692708d6656fb1e952023-12-03T14:40:28ZengMDPI AGBiology2079-77372022-06-0111799810.3390/biology11070998Revealing the Microbiome of Four Different Thermal Springs in Turkey with Environmental DNA MetabarcodingIşılay Çelik0Emre Keskin1Biotechnology Institute, Ankara University, Ankara 06135, TurkeyEvolutionary Genetics Laboratory (eGL), Department of Fisheries and Aquaculture, Agricultural Faculty, Ankara University, Ankara 06135, TurkeyOne of the most significant challenges for detecting microbial life in thermal springs by conventional techniques such as culturing is these places’ physicochemical (temperature, heavy metal content, pH, etc.) conditions. Data from several studies suggest that high-throughput DNA sequencing technologies can be used to perform more accurate and detailed microbiome analyses. The primary aim of this paper was to determine the microbiome in the thermal source by metabarcoding environmental DNA isolated from four different sources and reveal the reflection of differences caused by temperature and chemical content on the microbiome. DNA was extracted from water filtered with enclosed filters and using the Illumina high-throughput sequencing platform, V3 and V4 regions of the 16S rRNA gene were sequenced. The results showed a correlation between physicochemical conditions and microorganism composition of four different thermal springs. Springs with extremely high temperature (89–90 °C) were dominated by hyperthermophiles such as <i>Hydrogenobacter</i> and <i>Thermus</i>, while a spring with a high temperature (52 °C) was dominated by thermophiles such as <i>Thermoanaerobaculum</i> and <i>Desulfurispora</i>, and a spring with a low temperature (26 °C) and high salinity was dominated by halophiles and sulfur-oxidizers such as <i>Hydrogenovibrio</i> and <i>Sulfirimonas</i>. With this research, we observed many manipulable steps according to the work of interest. This study sought to obtain data that will help decide the right gene region and choose the optimal bioinformatic pipeline.https://www.mdpi.com/2079-7737/11/7/998microbiomeenvironmental DNA (eDNA)metabarcodingthermal springhigh throughput sequencingextremophiles |
| spellingShingle | Işılay Çelik Emre Keskin Revealing the Microbiome of Four Different Thermal Springs in Turkey with Environmental DNA Metabarcoding Biology microbiome environmental DNA (eDNA) metabarcoding thermal spring high throughput sequencing extremophiles |
| title | Revealing the Microbiome of Four Different Thermal Springs in Turkey with Environmental DNA Metabarcoding |
| title_full | Revealing the Microbiome of Four Different Thermal Springs in Turkey with Environmental DNA Metabarcoding |
| title_fullStr | Revealing the Microbiome of Four Different Thermal Springs in Turkey with Environmental DNA Metabarcoding |
| title_full_unstemmed | Revealing the Microbiome of Four Different Thermal Springs in Turkey with Environmental DNA Metabarcoding |
| title_short | Revealing the Microbiome of Four Different Thermal Springs in Turkey with Environmental DNA Metabarcoding |
| title_sort | revealing the microbiome of four different thermal springs in turkey with environmental dna metabarcoding |
| topic | microbiome environmental DNA (eDNA) metabarcoding thermal spring high throughput sequencing extremophiles |
| url | https://www.mdpi.com/2079-7737/11/7/998 |
| work_keys_str_mv | AT isılaycelik revealingthemicrobiomeoffourdifferentthermalspringsinturkeywithenvironmentaldnametabarcoding AT emrekeskin revealingthemicrobiomeoffourdifferentthermalspringsinturkeywithenvironmentaldnametabarcoding |