Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA
Abstract Aqueous environmental DNA (eDNA) analysis has been applied to the monitoring of various ecosystems and taxa, and the characteristics of aqueous eDNA have been previously studied. In contrast, although sedimentary eDNA has been used to restore past information, the characteristics of sedimen...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2020-10-01
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| Series: | Environmental DNA |
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| Online Access: | https://doi.org/10.1002/edn3.75 |
| _version_ | 1818198975550849024 |
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| author | Masayuki K. Sakata Satoshi Yamamoto Ryo O. Gotoh Masaki Miya Hiroki Yamanaka Toshifumi Minamoto |
| author_facet | Masayuki K. Sakata Satoshi Yamamoto Ryo O. Gotoh Masaki Miya Hiroki Yamanaka Toshifumi Minamoto |
| author_sort | Masayuki K. Sakata |
| collection | DOAJ |
| description | Abstract Aqueous environmental DNA (eDNA) analysis has been applied to the monitoring of various ecosystems and taxa, and the characteristics of aqueous eDNA have been previously studied. In contrast, although sedimentary eDNA has been used to restore past information, the characteristics of sedimentary eDNA are not well understood. In this study, we compared the properties of sedimentary and aqueous eDNA of macro‐organisms. First, to clarify the preservation ability of sediments, we compared the difference in decay rates between aqueous and sedimentary eDNA using samples collected from a biotope (an artificial pond prepared with concrete). Next, to clarify the biological information retained in sedimentary eDNA both qualitatively and quantitatively, we compared eDNA concentrations between sediment and water samples collected simultaneously from a lake, and the fish species detected by eDNA metabarcoding were also compared. The results demonstrated the following: (a) the decay rate (decreased eDNA copy number divided by the initial eDNA copy number per unit time) of sedimentary eDNA (0.00033 ± 0.000049 [mean ± SE]/hr) was lower than that of aqueous eDNA (0.01863 ± 0.0011/hr); (b) sedimentary eDNA concentration of the mitochondrial marker of three fish species was higher than aqueous eDNA concentration for the same sample weight (12.5–1,456.9 times); and (c) the species composition obtained by metabarcoding was not significantly different between sediment and water; however, considering the lower decay rate of sedimentary eDNA, using both sample types may provide more comprehensive information of species distribution. Thus, sedimentary eDNA analysis will expand future biomonitoring and ecological studies by providing a difference in timescale. |
| first_indexed | 2024-12-12T02:14:25Z |
| format | Article |
| id | doaj.art-5ebca623be8442b1b773cf9a7697b666 |
| institution | Directory Open Access Journal |
| issn | 2637-4943 |
| language | English |
| last_indexed | 2024-12-12T02:14:25Z |
| publishDate | 2020-10-01 |
| publisher | Wiley |
| record_format | Article |
| series | Environmental DNA |
| spelling | doaj.art-5ebca623be8442b1b773cf9a7697b6662022-12-22T00:41:50ZengWileyEnvironmental DNA2637-49432020-10-012450551810.1002/edn3.75Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNAMasayuki K. Sakata0Satoshi Yamamoto1Ryo O. Gotoh2Masaki Miya3Hiroki Yamanaka4Toshifumi Minamoto5Graduate School of Human Development and Environment Kobe University Kobe JapanGraduate School of Human Development and Environment Kobe University Kobe JapanDepartment of Ecology and Environmental Sciences Natural History Museum and Institute Chiba JapanDepartment of Ecology and Environmental Sciences Natural History Museum and Institute Chiba JapanDepartment of Environmental Solution Technology Faculty of Science & Technology Ryukoku University Otsu JapanGraduate School of Human Development and Environment Kobe University Kobe JapanAbstract Aqueous environmental DNA (eDNA) analysis has been applied to the monitoring of various ecosystems and taxa, and the characteristics of aqueous eDNA have been previously studied. In contrast, although sedimentary eDNA has been used to restore past information, the characteristics of sedimentary eDNA are not well understood. In this study, we compared the properties of sedimentary and aqueous eDNA of macro‐organisms. First, to clarify the preservation ability of sediments, we compared the difference in decay rates between aqueous and sedimentary eDNA using samples collected from a biotope (an artificial pond prepared with concrete). Next, to clarify the biological information retained in sedimentary eDNA both qualitatively and quantitatively, we compared eDNA concentrations between sediment and water samples collected simultaneously from a lake, and the fish species detected by eDNA metabarcoding were also compared. The results demonstrated the following: (a) the decay rate (decreased eDNA copy number divided by the initial eDNA copy number per unit time) of sedimentary eDNA (0.00033 ± 0.000049 [mean ± SE]/hr) was lower than that of aqueous eDNA (0.01863 ± 0.0011/hr); (b) sedimentary eDNA concentration of the mitochondrial marker of three fish species was higher than aqueous eDNA concentration for the same sample weight (12.5–1,456.9 times); and (c) the species composition obtained by metabarcoding was not significantly different between sediment and water; however, considering the lower decay rate of sedimentary eDNA, using both sample types may provide more comprehensive information of species distribution. Thus, sedimentary eDNA analysis will expand future biomonitoring and ecological studies by providing a difference in timescale.https://doi.org/10.1002/edn3.75decay rateenvironmental DNAMiFish metabarcodingreal‐time PCRsedimentsedimentary eDNA |
| spellingShingle | Masayuki K. Sakata Satoshi Yamamoto Ryo O. Gotoh Masaki Miya Hiroki Yamanaka Toshifumi Minamoto Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA Environmental DNA decay rate environmental DNA MiFish metabarcoding real‐time PCR sediment sedimentary eDNA |
| title | Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA |
| title_full | Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA |
| title_fullStr | Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA |
| title_full_unstemmed | Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA |
| title_short | Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA |
| title_sort | sedimentary edna provides different information on timescale and fish species composition compared with aqueous edna |
| topic | decay rate environmental DNA MiFish metabarcoding real‐time PCR sediment sedimentary eDNA |
| url | https://doi.org/10.1002/edn3.75 |
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