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ToolsLiu, Dong, Zhang, Yunhui, Shi, Hai, Guo, Zihua, Rowley, Gary, Todd, Jonathan D. and Zhang, Xiao-Hua (2025) DSMG-Chip: A high-throughput degenerate qPCR chip for profiling microbial DMSP and related organic sulfur metabolic genes in diverse environments. Environmental Science & Technology, 59 (45). pp. 24416-24429. ISSN 0013-936X
Full text not available from this repository. (Request a copy)Abstract
The organosulfur cycle involves active microbial transformations of dimethylsulfoniopropionate (DMSP) to yield the climate active gas dimethyl sulfide (DMS) and other compounds. The lack of rapid and accurate methods to quantify the DMSP metabolic potential hinders a deeper understanding of this cycling. We developed a high-throughput qPCR (HT-qPCR) chip, DSMG-chip, to quantify the absolute abundance of DMSP and related organic sulfur metabolic genes. DSMG-chip contains 42 degenerate primer sets targeting 27 organosulfur metabolic genes, with the 16S rRNA gene as a reference, allowing for the detection of 41 environmental samples simultaneously. In silico analysis indicated that the DSMG-chip possesses broad taxonomic coverage (1.4–91.3%, spanning 12 phyla and 275 genera) and high specificity (44.4–100%, mean: 85.34%). Validation experiments using conventional PCR, qPCR, and HT-qPCR confirmed the primers’ strict specificity, robust amplification efficiency (0.677 to 0.997, mean: 0.771), and excellent accuracy, correlating well with conventional qPCR (Pearson’s r = 0.914). Finally, application of the DSMG-chip accurately reflected variations in DMSP metabolism across diverse seawater and sediment samples, highlighting the active microbial DMSP cycling in Pacific Ocean (section P) seawater and the contribution of the methanethiol (MeSH) methylation pathway (via mddA) in sediments. Our findings provide a powerful, novel tool for studying the organosulfur cycle.
| Item Type: | Article |
|---|---|
| Additional Information: | Data Availability: The Primer Design Database is deposited on GitHub at [https://github.com/zerooooooooooooooo/DSMG-Chip]. The amplicon sequencing data from the validation of primer specificity experiments are available on NCBI under the BioProject ID [PRJNA1300291]. Funding information: This study was funded by the National Natural Science Foundation of China (32370118 and 42376101), the S & T Innovation Project of Qingdao Marine Science and Technology Center (2022QNLM030004-3), and the Fundamental Research Funds for the Central Universities (202172002 and 202541011). JDT was funded by Natural Environmental Research Council, UK, (NE/P012671) and Leverhulme trust (RPG-2020-413) grants. |
| Uncontrolled Keywords: | dms,dsmg-chip,high-throughput qpcr,microbial cycling,organic sulfur cycling,chemistry(all),environmental chemistry ,/dk/atira/pure/subjectarea/asjc/1600 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| UEA Research Groups: | Faculty of Science > Research Groups > Molecular Microbiology Faculty of Medicine and Health Sciences > Research Groups > Pathogen Biology Group Faculty of Science > Research Groups > Wolfson Centre for Advanced Environmental Microbiology |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 18 Dec 2025 13:30 |
| Last Modified: | 18 Dec 2025 13:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/101465 |
| DOI: | 10.1021/acs.est.5c10820 |
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