{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T02:53:13Z","timestamp":1790650393679,"version":"4.1.0"},"reference-count":43,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2021,2,17]],"date-time":"2021-02-17T00:00:00Z","timestamp":1613520000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP15H05712"],"award-info":[{"award-number":["JP15H05712"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001700","name":"Ministry of Education, Culture, Sports, Science and Technology","doi-asserted-by":"publisher","award":["ArCS"],"award-info":[{"award-number":["ArCS"]}],"id":[{"id":"10.13039\/501100001700","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001700","name":"Ministry of Education, Culture, Sports, Science and Technology","doi-asserted-by":"publisher","award":["ArCSII"],"award-info":[{"award-number":["ArCSII"]}],"id":[{"id":"10.13039\/501100001700","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Plankton samples have been routinely collected and preserved in formalin in many laboratories and museums for more than 100 years. Recently, attention has turned to use DNA information from formalin-fixed samples to examine changes in plankton diversity over time. However, no molecular ecological studies have evaluated the impact of formalin fixation on the genetic composition of the plankton community structure. Here, we developed a method for extracting DNA from archived formalin-preserved plankton samples to determine their community structure by a DNA metabarcoding approach. We found that a lysis solution consisting of borate-NaOH buffer (pH 11) with SDS and proteinase K effectively cleaved the cross-link formed by formalin fixation. DNA was extracted from samples preserved for decades in formalin, and the diatom community of the extracted DNA was in good agreement with the microscopy analysis. Furthermore, we stored a plankton sample for 1.5 years and demonstrated that 18S rRNA gene community structures did not change significantly from non-formalin-fixed, time-zero samples. These results indicate that our method can be used to describe the original community structure of plankton archived in formalin for years. Our approach will be useful for examining the long-term variation of plankton diversity by metabarcoding analysis of 18S rRNA gene community structure.<\/jats:p>","DOI":"10.1371\/journal.pone.0245936","type":"journal-article","created":{"date-parts":[[2021,2,17]],"date-time":"2021-02-17T13:46:58Z","timestamp":1613569618000},"page":"e0245936","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":21,"title":["A DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5160-3472","authenticated-orcid":true,"given":"Takuhei","family":"Shiozaki","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fumihiro","family":"Itoh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuu","family":"Hirose","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonaotaro","family":"Onodera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akira","family":"Kuwata","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naomi","family":"Harada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,2,17]]},"reference":[{"key":"pone.0245936.ref001","doi-asserted-by":"crossref","first-page":"1961","DOI":"10.1016\/S0002-9440(10)64472-0","article-title":"Effect of fixatives and tissue processing on the content and integrity of nucleic acids","volume":"161","author":"M Srinivasan","year":"2002","journal-title":"American Journal of Pathology"},{"key":"pone.0245936.ref002","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1078\/1439-6092-00071","article-title":"DNA, PCR and formalinized animal tissue\u2014a short review and protocols","volume":"3","author":"C Schander","year":"2003","journal-title":"Organisms Diversity & Evolution"},{"key":"pone.0245936.ref003","doi-asserted-by":"crossref","first-page":"eabc5654","DOI":"10.1126\/science.abc5654","article-title":"Using paleo-archives to safeguard biodiversity under climate change","volume":"369","author":"DA Fordham","year":"2020","journal-title":"Science"},{"key":"pone.0245936.ref004","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/0006-291X(85)90390-0","article-title":"Purification of DNA from Formaldehyde Fixed and Paraffin Embedded Human-Tissue","volume":"130","author":"SE Goelz","year":"1985","journal-title":"Biochemical and Biophysical Research Communications"},{"key":"pone.0245936.ref005","doi-asserted-by":"crossref","first-page":"e537","DOI":"10.1371\/journal.pone.0000537","article-title":"The Isolation of Nucleic Acids from Fixed, Paraffin-Embedded Tissues-Which Methods Are Useful When?","volume":"2","author":"MTP Gilbert","year":"2007","journal-title":"Plos One"},{"key":"pone.0245936.ref006","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1016\/j.ab.2013.04.006","article-title":"Comparison of protocols for DNA extraction from long-term preserved formalin fixed tissues","volume":"439","author":"S Paireder","year":"2013","journal-title":"Analytical Biochemistry"},{"key":"pone.0245936.ref007","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1016\/j.ympev.2003.11.002","article-title":"MtDNA sequencing from zooplankton after long-term preservation in buffered formalin","volume":"30","author":"A Bucklin","year":"2004","journal-title":"Molecular Phylogenetics and Evolution"},{"key":"pone.0245936.ref008","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/j.mimet.2008.02.001","article-title":"Development and validation of a molecular technique for the analysis of archived formalin-preserved phytoplankton samples permits retrospective assessment of Emiliania huxleyi communities","volume":"73","author":"SJ Ripley","year":"2008","journal-title":"Journal of Microbiological Methods"},{"key":"pone.0245936.ref009","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1111\/1755-0998.12655","article-title":"Phylogenomics using formalin-fixed and 100+year-old intractable natural history specimens","volume":"17","author":"S Ruane","year":"2017","journal-title":"Molecular Ecology Resources"},{"key":"pone.0245936.ref010","unstructured":"United Nations Educational Scientific and Cultural Organization (UNESCO) (1994) Protocols for the Joint Global Ocean Flux Study (JGOFS) Core Measurements. 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