ArticleEnvironmental microbiome2025
Microbial community characterization in Red Sea-derived samples using a field-deployable DNA extraction system and nanopore sequencing.
Article in Environmental microbiome, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Lignocellulose-mediated selection of potential halophilic PET-degrading enzymes from mangrove soil.Nature communications · 2026Article
- Discovering PETases: An Interlink Between Engineering Enzymes and Microbiomes.Environmental microbiology · 2026Review
- The Coral Probiotics Village: An Underwater Laboratory to Tackle the Coral Reefs Crisis.Ecology and evolution · 2025Article
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27 authors.
Funding
Abstract
backgroundIn this study, xTitan, a field-deployable, automated, and versatile nucleic acid extraction system was employed to characterize microbial communities in Red Sea-derived samples, including coral colonies, mangrove sediments, and seawater. The use of the xTitan in the field was intended to minimize sample transport bias, obtaining data that may be closer to "ground truth" for microbial diversity. The observed microbial communities from DNA extracted in the field using the xTitan system were compared to DNA extractions performed in a laboratory setting using both xTitan and a standard commercial kit (Qiagen) after approximately 24 h of sample transfer and storage.
resultsMicrobial community analyses conducted on DNA extracted using the xTitan system and the Qiagen kit yielded similar alpha diversity metric values, with a trend toward higher diversity observed in most samples extracted with the xTitan. The microbial community structure in samples from a Pocillopora verrucosa colony, mangrove sediments, and seawater was affected by the DNA extraction system. In the P. verrucosa colony, 16S rRNA gene sequences affiliated to Endozoicomonas acroporae were preferentially abundant when DNA was extracted in the field with the xTitan system rather than in the lab. In mangrove sediments, significant differences (P-value < 0.05) in beta diversity and functional gene profiles were observed when comparing in-field to in-lab xTitan DNA extracts. In seawater, a pronounced decrease in the relative abundance of cyanobacterial populations was observed when DNA was extracted with both methods after samples were transported to the lab on ice. In addition, hundreds of species in mangrove-associated samples were differentially abundant when DNA was extracted on-site with the xTitan system compared to in-lab extractions. Balneolaceae was one of the most abundant taxa in mangrove sediments and several genera from this family were detected in all replicates across all DNA extraction systems.
conclusionsThe usability of different field-deployable instruments for microbial community characterization in marine-derived samples was demonstrated. Moreover, differences in beta diversity were observed when DNA was extracted in-field versus in-lab using the xTitan system, particularly for mangrove-associated samples. These results highlight the value of on-site nucleic acid extraction for enhancing the detection of microbial taxa that can be sensitive to cold storage. This study enabled the testing of the xTitan on Red Sea-derived samples, generating comprehensive information on the effects of DNA extraction systems and transportation of samples on coral and mangrove-associated microbiomes.
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