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This study optimized a conventional soil DNA extraction protocol to improve DNA yield and purity from tropical swamp peat. The optimized protocol produced fourfold higher DNA concentration, improved integrity, reduced variability, and increased bacterial and archaeal 16S rRNA and mcrA abundances. Agarose electrophoresis also indicated potential co-extraction of RNA.",{"@graph":69,"@context":122},[70,84,105],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":40,"@type":76,"position":81},"https://docshare.wps.com/document/research-report/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/an-effective-dna-extraction-protocol-optimized-for-tropical-swamp-peat-samples/446624/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/an-effective-dna-extraction-protocol-optimized-for-tropical-swamp-peat-samples/446624.png","ImageObject",300,407,{"name":92,"@type":93},"McGucket","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-04","2026-09-29",true,{"@type":102,"interactionType":103,"userInteractionCount":19},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"Why are conventional DNA extraction kits often ineffective for tropical peat soils?","Question",{"text":112,"@type":113},"High organic matter content, low pH, and PCR inhibitors reduce DNA yield and purity, limiting reliable molecular analyses.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"What improvements did the optimized protocol achieve compared with the conventional protocol?",{"text":117,"@type":113},"The optimized protocol increased DNA concentration about fourfold, improved purity and integrity, and reduced the coefficient of variation across replicates.",{"name":119,"@type":110,"acceptedAnswer":120},"Which molecular markers showed higher detection after optimization?",{"text":121,"@type":113},"qPCR revealed significantly higher abundances of bacterial and archaeal 16S rRNA genes and the mcrA gene, supporting better characterization of microbial communities.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},446624,1790749893,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":133,"doc_module":4,"category_id":39,"category_name":40,"doc_title":65,"doc_description":67,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":19,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":139,"language":140,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":67,"update_tm":144,"read_time":41},1236954412713,"https://us-avatar.wpscdn.com/davatar_29158cc5080c5b710cf443261637dec0","| Environmental Microbiology | Methods and Protocols  \nAn effective DNA extraction protocol optimized for tropical swamp peat samples  \nJúlia Brandão Gontijo,1,2 Gabriel Valverde Firmino,1 Jéssica Adriele Mandro,1 André Luiz Miranda Reis,3 Wanderlei Bieluczyk,1,4 Júlio César Feitosa Fernandes,3 Plínio Barbosa de Camargo,4 Jorge Luiz Mazza Rodrigues,2,5 Siu Mui Tsai,1 Pablo Vidal-Torrado3  \nAUTHOR AFFILIATIONS See affiliation list on p. 10.  \nABSTRACT Peatlands are waterlogged ecosystems that store large amounts of carbon, harbor highly specialized endemic biodiversity, and play a crucial role in climate regulation. However, the microbial communities of tropical peatlands, particularly in the Atlantic Forest, remain largely unexplored. Molecular tools are essential for characterizing these communities, yet conventional DNA extraction kits are often ineffective for peat soils, likely due to their high organic matter content, low pH, and the presence of PCR inhibitors. This study aimed to optimize a conventional soil DNA extraction protocol to enhance DNA yield and purity from tropical peat soils, ensuring more reliable molecular analyses. The optimized protocol resulted in a four-times increase in DNA concentration compared to the conventional protocol and improved DNA purity. Agarose gel electrophoresis confirmed higher DNA integrity and also revealed the presence of RNA in samples subjected to the optimized protocol, indicating its potential for co-extraction of DNA and RNA. Quantitative PCR (qPCR) analysis showed significantly higher abundances of bacterial and archaeal 16S rRNA genes, as well as the mcrA gene, in optimized compared to conventional protocol, with statistically significant differences across soil profiles and depths. Furthermore, the optimized protocol yielded a lower coefficient of variation among replicates, enhancing reproducibility and consistency in microbial quantification. These findings demonstrate that the optimized protocol effectively extracts high-quality DNA from tropical peat soils, addressing common challenges associated with commercial kits. Its implementation can support improved future research on microbial-driven biogeochemical processes in tropical peatlands, particularly in the context of greenhouse gas emissions and climate change.  \nIMPORTANCE Tropical peatlands play a central role in carbon storage and greenhouse gas dynamics, yet their microbial communities remain largely unexplored due to analytical challenges. High organic matter content, low pH, and PCR inhibitors commonly limit the efficiency of molecular tools in these environments. This study presentsan optimized DNA extraction protocol that improves yield, purity, and reproducibility across peat profiles. The protocol enhanced the detection of microbial marker genes, such as bacterial and archaeal 16S rRNA and mcrA, and showed potential for co-extraction of RNA, expanding possibilities for future multi-omic approaches. This methodological advance enables more accurate and consistent microbial analyses in tropical peat soils, contributing to a better understanding of microbial roles in biogeochemical cyclesand climate-related processes.  \nKEYWORDS DNA extraction, microbial communities, 16S rRNA, mcrA, tropical peatlands  \nP eatlands are wetland ecosystems that cover approximately 2.84% of the Earth’s  \nsurface and are composed primarily of peat, a unique soil layer formed from partially  \nEditor Jing Han, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China  \nAddress correspondence to Júlia Brandão Gontijo, [jbgontijo@ucdavis.edu](jbgontijo@ucdavis.edu).  \nJúlia Brandão Gontijo and Gabriel Valverde Firmino contributed equally to this article. Author order reflects leadership in manuscript coordination.  \nThe authors declare no conflict of interest.  \nto highly decomposed organic matter. These ecosystems store vast carbon reserves, serving as critical carbon sinks by sequestering between 142 and 288 gigatons of c","cbCaitrTixf6wpuL","https://ap.wps.com/l/cbCaitrTixf6wpuL","pdf",7266227,12,"English","# Abstract\n## Importance\n## Background on peatlands and microbiota\n## DNA extraction challenges in peat soils\n## Study aims and optimization outcomes","[{\"question\":\"Why are conventional DNA extraction kits often ineffective for tropical peat soils?\",\"answer\":\"High organic matter content, low pH, and PCR inhibitors reduce DNA yield and purity, limiting reliable molecular analyses.\"},{\"question\":\"What improvements did the optimized protocol achieve compared with the conventional protocol?\",\"answer\":\"The optimized protocol increased DNA concentration about fourfold, improved purity and integrity, and reduced the coefficient of variation across replicates.\"},{\"question\":\"Which molecular markers showed higher detection after optimization?\",\"answer\":\"qPCR revealed significantly higher abundances of bacterial and archaeal 16S rRNA genes and the mcrA gene, supporting better characterization of microbial communities.\"}]","An effective DNA extraction protocol optimized for tropical swamp peat samples | PDF",1790716327]