Revealing the Microbiome of Four Different Thermal Springs in Turkey with Environmental DNA Metabarcoding

Abstract

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 Hydrogenobacter and Thermus, while a spring with a high temperature (52 °C) was dominated by thermophiles such as Thermoanaerobaculum and Desulfurispora, and a spring with a low temperature (26 °C) and high salinity was dominated by halophiles and sulfur-oxidizers such as Hydrogenovibrio and Sulfirimonas. 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.

Microbiome characterization of alpine water springs for human consumption reveals site- and usage-specific microbial signatures

“…Therefore the knowledge of spatial and temporal community dynamics is fundamental for both conservation issues and for the management of the ecosystem services provided by the water springs. Most studies, however, focused on a relatively small scale, describing the microbial diversity in springs along a transect or within a single hydrographic basin (e.g., Pedron et al, 2019 ; Yan et al, 2020 ; Çelik and Keskin, 2022 ). The studies that focused on a large scale are indeed very few (e.g., Power et al, 2018 ; Li and Ma, 2019 ; Yan et al, 2021 ), and the ones accounting also for temporal variation are even less.…”

Effect of biofloc technology in Farfantepenaeus aztecus culture: The optimization of dietary protein level on growth performance, digestive enzyme activity, non‐specific immune response, and intestinal microbiota

“…The primer set offering the highest efficacy was selected for use in the experiment (Çelik & Keskin, 2022). PCR was performed with a primary heating step for 2 min at 94°C, followed by 35 cycles of denaturation for 1 min at 94°C, annealing for 45 s at 53°C, and extension for 25 s at 72°C, then followed by a final extension step for 5 min at 72°C.…”

“…The primer set offering the highest efficacy was selected for use in the experiment (Çelik & Keskin, 2022). PCR was performed with a primary heating step for 2 min at 94 C, followed by 35 cycles of denaturation for 1 min at 94 C, annealing for 45 s at 53 C, and extension for 25 s at 72 C, then followed by a final extension step for 5 min at 72 C. Each 10 μL reaction mixture contained 2 μL of 5Â Promega Colorless GoTaq Flexi buffer, 0.5 μL DNA, 1.5 μL of 25 mM MgCl 2 , 0.8 μL of 3.2 μM dNTP, 0.5 μL of each primer (5 pmol/mL), 0.05 μL of Taq DNA polymerase, and sterile water to a final volume of 10 μL.…”

Hydrobiome of Thermal Waters: Potential Use in Dermocosmetics

“…Microbial biodiversity has also been investigated in several thermal springs in Italy [41][42][43][44][45], France [46], Iceland [47,48], Hungary [49], Czech Republic [50], Croatia [51], Turkey [52], Armenia [53], and Russia [54,55]. In the eastern countries, other geothermal aquifers have been studied: Trans-Himalayan plateau [56], Pakistan [57,58], Tibet [59], China [60], India [61], Thailand [62], and Japan [63,64].…”