Sediment Core DNA-Metabarcoding and Chitinous Remain Identification: Integrating Complementary Methods to Characterise Chironomidae Biodiversity in Lake Sediment Archives.
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| Titel: | Sediment Core DNA-Metabarcoding and Chitinous Remain Identification: Integrating Complementary Methods to Characterise Chironomidae Biodiversity in Lake Sediment Archives. |
|---|---|
| Autoren: | Blattner LA; Department of Environmental Sciences, Geoecology, University of Basel, Basel, Switzerland.; Natural History Museum Basel, Basel, Switzerland., Lapellegerie P; Department of Environmental Sciences, Geoecology, University of Basel, Basel, Switzerland., Courtney-Mustaphi C; Department of Environmental Sciences, Geoecology, University of Basel, Basel, Switzerland., Heiri O; Department of Environmental Sciences, Geoecology, University of Basel, Basel, Switzerland. |
| Quelle: | Molecular ecology resources [Mol Ecol Resour] 2025 Jan; Vol. 25 (1), pp. e14035. Date of Electronic Publication: 2024 Oct 21. |
| Publikationsart: | Journal Article; Evaluation Study |
| Sprache: | English |
| Info zur Zeitschrift: | Publisher: Blackwell Country of Publication: England NLM ID: 101465604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1755-0998 (Electronic) Linking ISSN: 1755098X NLM ISO Abbreviation: Mol Ecol Resour Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: Oxford, England : Blackwell |
| MeSH-Schlagworte: | Chironomidae*/genetics , Chironomidae*/classification , Lakes* , DNA Barcoding, Taxonomic*/methods , Geologic Sediments*/chemistry , Biodiversity*, Animals ; Switzerland ; Larva/genetics ; Larva/classification ; DNA/genetics ; DNA/chemistry ; Chitin ; Metagenomics/methods |
| Abstract: | Chironomidae, so-called non-biting midges, are considered key bioindicators of aquatic ecosystem variability. Data derived from morphologically identifying their chitinous remains in sediments document chironomid larvae assemblages, which are studied to reconstruct ecosystem changes over time. Recent developments in sedimentary DNA (sedDNA) research have demonstrated that molecular techniques are suitable for determining past and present occurrences of organisms. Nevertheless, sedDNA records documenting alterations in chironomid assemblages remain largely unexplored. To close this gap, we examined the applicability of sedDNA metabarcoding to identify Chironomidae assemblages in lake sediments by sampling and processing three 21-35 cm long sediment cores from Lake Sempach in Switzerland. With a focus on developing analytical approaches, we compared an invertebrate-universal (FWH) and a newly designed Chironomidae-specific metabarcoding primer set (CH) to assess their performance in detecting Chironomidae DNA. We isolated and identified chitinous larval remains and compared the morphotype assemblages with the data derived from sedDNA metabarcoding. Results showed a good overall agreement of the morphotype assemblage-specific clustering among the chitinous remains and the metabarcoding datasets. Both methods indicated higher chironomid assemblage similarity between the two littoral cores in contrast to the deep lake core. Moreover, we observed a pronounced primer bias effect resulting in more Chironomidae detections with the CH primer combination compared to the FWH combination. Overall, we conclude that sedDNA metabarcoding can supplement traditional remain identifications and potentially provide independent reconstructions of past chironomid assemblage changes. Furthermore, it has the potential of more efficient workflows, better sample standardisation and species-level resolution datasets. (© 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd.) |
| References: | Genome. 2018 Nov;61(11):787-796. (PMID: 30365909) Commun Biol. 2020 Apr 7;3(1):169. (PMID: 32265485) Mol Biol Evol. 2013 Apr;30(4):772-80. (PMID: 23329690) Nat Commun. 2022 Nov 4;13(1):6559. (PMID: 36333301) Glob Chang Biol. 2020 Mar;26(3):1155-1169. (PMID: 31596997) Bioinformatics. 2016 Oct 1;32(19):3047-8. (PMID: 27312411) PLoS One. 2016 Oct 5;11(10):e0163962. (PMID: 27706213) PeerJ. 2016 Oct 18;4:e2584. (PMID: 27781170) Nat Commun. 2014;5:3211. (PMID: 24487920) PLoS Genet. 2010 Feb 12;6(2):e1000834. (PMID: 20168995) FEMS Microbiol Ecol. 2012 Jul;81(1):111-23. (PMID: 22329626) Bioinformatics. 2019 Feb 1;35(3):526-528. (PMID: 30016406) PLoS One. 2015 Sep 25;10(9):e0138993. (PMID: 26406595) Biol Rev Camb Philos Soc. 2012 May;87(2):430-56. (PMID: 22032243) PLoS One. 2015 Jul 08;10(7):e0130324. (PMID: 26154168) PeerJ. 2019 Oct 7;7:e7745. (PMID: 31608170) Mol Ecol Resour. 2023 May;23(4):742-755. (PMID: 36478393) Bioinformatics. 2021 Dec 22;38(1):267-269. (PMID: 34244702) Nat Commun. 2014 Sep 11;5:4914. (PMID: 25208610) Mol Ecol Resour. 2022 May;22(4):1231-1246. (PMID: 34551203) Sci Adv. 2018 May 09;4(5):eaar4292. (PMID: 29750197) Data Brief. 2020 Apr 18;30:105553. (PMID: 32346576) Environ Sci Pollut Res Int. 2023 Feb;30(7):17039-17050. (PMID: 36622608) Bioinformatics. 2011 Aug 15;27(16):2194-200. (PMID: 21700674) Front Microbiol. 2022 May 09;13:864630. (PMID: 35615497) |
| Contributed Indexing: | Keywords: Chironomidae; Paleolimnology; SedDNA; lake sediments; morphogroups |
| Substance Nomenclature: | 9007-49-2 (DNA) 1398-61-4 (Chitin) |
| Entry Date(s): | Date Created: 20241022 Date Completed: 20241215 Latest Revision: 20250104 |
| Update Code: | 20250114 |
| PubMed Central ID: | PMC11646301 |
| DOI: | 10.1111/1755-0998.14035 |
| PMID: | 39434565 |
| Datenbank: | MEDLINE |
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| Items | – Name: Title Label: Title Group: Ti Data: Sediment Core DNA-Metabarcoding and Chitinous Remain Identification: Integrating Complementary Methods to Characterise Chironomidae Biodiversity in Lake Sediment Archives. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AU" term="%22Blattner+LA%22">Blattner LA</searchLink>; Department of Environmental Sciences, Geoecology, University of Basel, Basel, Switzerland.; Natural History Museum Basel, Basel, Switzerland.<br /><searchLink fieldCode="AU" term="%22Lapellegerie+P%22">Lapellegerie P</searchLink>; Department of Environmental Sciences, Geoecology, University of Basel, Basel, Switzerland.<br /><searchLink fieldCode="AU" term="%22Courtney-Mustaphi+C%22">Courtney-Mustaphi C</searchLink>; Department of Environmental Sciences, Geoecology, University of Basel, Basel, Switzerland.<br /><searchLink fieldCode="AU" term="%22Heiri+O%22">Heiri O</searchLink>; Department of Environmental Sciences, Geoecology, University of Basel, Basel, Switzerland. – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22101465604%22">Molecular ecology resources</searchLink> [Mol Ecol Resour] 2025 Jan; Vol. 25 (1), pp. e14035. <i>Date of Electronic Publication: </i>2024 Oct 21. – Name: TypePub Label: Publication Type Group: TypPub Data: Journal Article; Evaluation Study – Name: Language Label: Language Group: Lang Data: English – Name: TitleSource Label: Journal Info Group: Src Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22Blackwell%22">Blackwell </searchLink><i>Country of Publication: </i>England <i>NLM ID: </i>101465604 <i>Publication Model: </i>Print-Electronic <i>Cited Medium: </i>Internet <i>ISSN: </i>1755-0998 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%221755098X%22">1755098X </searchLink><i>NLM ISO Abbreviation: </i>Mol Ecol Resour <i>Subsets: </i>MEDLINE – Name: PublisherInfo Label: Imprint Name(s) Group: PubInfo Data: <i>Original Publication</i>: Oxford, England : Blackwell – Name: SubjectMESH Label: MeSH Terms Group: Su Data: <searchLink fieldCode="MM" term="%22Chironomidae%22">Chironomidae*</searchLink>/<searchLink fieldCode="MM" term="%22Chironomidae+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Chironomidae%22">Chironomidae*</searchLink>/<searchLink fieldCode="MM" term="%22Chironomidae+classification%22">classification</searchLink> <br /><searchLink fieldCode="MM" term="%22Lakes%22">Lakes*</searchLink> <br /><searchLink fieldCode="MM" term="%22DNA+Barcoding%2C+Taxonomic%22">DNA Barcoding, Taxonomic*</searchLink>/<searchLink fieldCode="MM" term="%22DNA+Barcoding%2C+Taxonomic+methods%22">methods</searchLink> <br /><searchLink fieldCode="MM" term="%22Geologic+Sediments%22">Geologic Sediments*</searchLink>/<searchLink fieldCode="MM" term="%22Geologic+Sediments+chemistry%22">chemistry</searchLink> <br /><searchLink fieldCode="MM" term="%22Biodiversity%22">Biodiversity*</searchLink><br /><searchLink fieldCode="MH" term="%22Animals%22">Animals</searchLink> ; <searchLink fieldCode="MH" term="%22Switzerland%22">Switzerland</searchLink> ; <searchLink fieldCode="MH" term="%22Larva%22">Larva</searchLink>/<searchLink fieldCode="MH" term="%22Larva+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Larva%22">Larva</searchLink>/<searchLink fieldCode="MH" term="%22Larva+classification%22">classification</searchLink> ; <searchLink fieldCode="MH" term="%22DNA%22">DNA</searchLink>/<searchLink fieldCode="MH" term="%22DNA+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22DNA%22">DNA</searchLink>/<searchLink fieldCode="MH" term="%22DNA+chemistry%22">chemistry</searchLink> ; <searchLink fieldCode="MH" term="%22Chitin%22">Chitin</searchLink> ; <searchLink fieldCode="MH" term="%22Metagenomics%22">Metagenomics</searchLink>/<searchLink fieldCode="MH" term="%22Metagenomics+methods%22">methods</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Chironomidae, so-called non-biting midges, are considered key bioindicators of aquatic ecosystem variability. Data derived from morphologically identifying their chitinous remains in sediments document chironomid larvae assemblages, which are studied to reconstruct ecosystem changes over time. Recent developments in sedimentary DNA (sedDNA) research have demonstrated that molecular techniques are suitable for determining past and present occurrences of organisms. Nevertheless, sedDNA records documenting alterations in chironomid assemblages remain largely unexplored. To close this gap, we examined the applicability of sedDNA metabarcoding to identify Chironomidae assemblages in lake sediments by sampling and processing three 21-35 cm long sediment cores from Lake Sempach in Switzerland. With a focus on developing analytical approaches, we compared an invertebrate-universal (FWH) and a newly designed Chironomidae-specific metabarcoding primer set (CH) to assess their performance in detecting Chironomidae DNA. We isolated and identified chitinous larval remains and compared the morphotype assemblages with the data derived from sedDNA metabarcoding. Results showed a good overall agreement of the morphotype assemblage-specific clustering among the chitinous remains and the metabarcoding datasets. Both methods indicated higher chironomid assemblage similarity between the two littoral cores in contrast to the deep lake core. Moreover, we observed a pronounced primer bias effect resulting in more Chironomidae detections with the CH primer combination compared to the FWH combination. Overall, we conclude that sedDNA metabarcoding can supplement traditional remain identifications and potentially provide independent reconstructions of past chironomid assemblage changes. Furthermore, it has the potential of more efficient workflows, better sample standardisation and species-level resolution datasets.<br /> (© 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd.) – Name: Ref Label: References Group: RefInfo Data: Genome. 2018 Nov;61(11):787-796. (PMID: <searchLink fieldCode="PM" term="%2230365909%22">30365909)</searchLink><br />Commun Biol. 2020 Apr 7;3(1):169. (PMID: <searchLink fieldCode="PM" term="%2232265485%22">32265485)</searchLink><br />Mol Biol Evol. 2013 Apr;30(4):772-80. (PMID: <searchLink fieldCode="PM" term="%2223329690%22">23329690)</searchLink><br />Nat Commun. 2022 Nov 4;13(1):6559. (PMID: <searchLink fieldCode="PM" term="%2236333301%22">36333301)</searchLink><br />Glob Chang Biol. 2020 Mar;26(3):1155-1169. (PMID: <searchLink fieldCode="PM" term="%2231596997%22">31596997)</searchLink><br />Bioinformatics. 2016 Oct 1;32(19):3047-8. (PMID: <searchLink fieldCode="PM" term="%2227312411%22">27312411)</searchLink><br />PLoS One. 2016 Oct 5;11(10):e0163962. (PMID: <searchLink fieldCode="PM" term="%2227706213%22">27706213)</searchLink><br />PeerJ. 2016 Oct 18;4:e2584. (PMID: <searchLink fieldCode="PM" term="%2227781170%22">27781170)</searchLink><br />Nat Commun. 2014;5:3211. (PMID: <searchLink fieldCode="PM" term="%2224487920%22">24487920)</searchLink><br />PLoS Genet. 2010 Feb 12;6(2):e1000834. (PMID: <searchLink fieldCode="PM" term="%2220168995%22">20168995)</searchLink><br />FEMS Microbiol Ecol. 2012 Jul;81(1):111-23. (PMID: <searchLink fieldCode="PM" term="%2222329626%22">22329626)</searchLink><br />Bioinformatics. 2019 Feb 1;35(3):526-528. (PMID: <searchLink fieldCode="PM" term="%2230016406%22">30016406)</searchLink><br />PLoS One. 2015 Sep 25;10(9):e0138993. (PMID: <searchLink fieldCode="PM" term="%2226406595%22">26406595)</searchLink><br />Biol Rev Camb Philos Soc. 2012 May;87(2):430-56. (PMID: <searchLink fieldCode="PM" term="%2222032243%22">22032243)</searchLink><br />PLoS One. 2015 Jul 08;10(7):e0130324. (PMID: <searchLink fieldCode="PM" term="%2226154168%22">26154168)</searchLink><br />PeerJ. 2019 Oct 7;7:e7745. (PMID: <searchLink fieldCode="PM" term="%2231608170%22">31608170)</searchLink><br />Mol Ecol Resour. 2023 May;23(4):742-755. (PMID: <searchLink fieldCode="PM" term="%2236478393%22">36478393)</searchLink><br />Bioinformatics. 2021 Dec 22;38(1):267-269. (PMID: <searchLink fieldCode="PM" term="%2234244702%22">34244702)</searchLink><br />Nat Commun. 2014 Sep 11;5:4914. (PMID: <searchLink fieldCode="PM" term="%2225208610%22">25208610)</searchLink><br />Mol Ecol Resour. 2022 May;22(4):1231-1246. (PMID: <searchLink fieldCode="PM" term="%2234551203%22">34551203)</searchLink><br />Sci Adv. 2018 May 09;4(5):eaar4292. (PMID: <searchLink fieldCode="PM" term="%2229750197%22">29750197)</searchLink><br />Data Brief. 2020 Apr 18;30:105553. (PMID: <searchLink fieldCode="PM" term="%2232346576%22">32346576)</searchLink><br />Environ Sci Pollut Res Int. 2023 Feb;30(7):17039-17050. (PMID: <searchLink fieldCode="PM" term="%2236622608%22">36622608)</searchLink><br />Bioinformatics. 2011 Aug 15;27(16):2194-200. (PMID: <searchLink fieldCode="PM" term="%2221700674%22">21700674)</searchLink><br />Front Microbiol. 2022 May 09;13:864630. (PMID: <searchLink fieldCode="PM" term="%2235615497%22">35615497)</searchLink> – Name: SubjectMinor Label: Contributed Indexing Group: Data: <i>Keywords: </i>Chironomidae; Paleolimnology; SedDNA; lake sediments; morphogroups – Name: NumberCAS Label: Substance Nomenclature Group: ID Data: 9007-49-2 (DNA)<br />1398-61-4 (Chitin) – Name: DateEntry Label: Entry Date(s) Group: Date Data: <i>Date Created: </i>20241022 <i>Date Completed: </i>20241215 <i>Latest Revision: </i>20250104 – Name: DateUpdate Label: Update Code Group: Date Data: 20250114 – Name: PubmedCentralID Label: PubMed Central ID Group: ID Data: PMC11646301 – Name: DOI Label: DOI Group: ID Data: 10.1111/1755-0998.14035 – Name: AN Label: PMID Group: ID Data: 39434565 |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1111/1755-0998.14035 Languages: – Code: eng Text: English PhysicalDescription: Pagination: StartPage: e14035 Subjects: – SubjectFull: Animals Type: general – SubjectFull: Switzerland Type: general – SubjectFull: Larva genetics Type: general – SubjectFull: Larva classification Type: general – SubjectFull: DNA genetics Type: general – SubjectFull: DNA chemistry Type: general – SubjectFull: Chitin Type: general – SubjectFull: Metagenomics methods Type: general – SubjectFull: Chironomidae genetics Type: general – SubjectFull: Chironomidae classification Type: general – SubjectFull: Lakes Type: general – SubjectFull: DNA Barcoding, Taxonomic methods Type: general – SubjectFull: Geologic Sediments chemistry Type: general – SubjectFull: Biodiversity Type: general Titles: – TitleFull: Sediment Core DNA-Metabarcoding and Chitinous Remain Identification: Integrating Complementary Methods to Characterise Chironomidae Biodiversity in Lake Sediment Archives. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Blattner LA – PersonEntity: Name: NameFull: Lapellegerie P – PersonEntity: Name: NameFull: Courtney-Mustaphi C – PersonEntity: Name: NameFull: Heiri O IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Text: 2025 Jan Type: published Y: 2025 Identifiers: – Type: issn-electronic Value: 1755-0998 Numbering: – Type: volume Value: 25 – Type: issue Value: 1 Titles: – TitleFull: Molecular ecology resources Type: main |
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