Evaluation of lake sedimentary ancient DNA metabarcoding to assess fungal biodiversity in Arctic paleoecosystems
Abstract Fungi are crucial organisms in most ecosystems as they exert ecological key functions and are closely associated with land plants. Fungal community changes may, therefore, help reveal biodiversity changes in past ecosystems. Lake sediments contain the DNA of organisms in the catchment area,...
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ftdoajarticles:oai:doaj.org/article:553a78bc3c1d45bb94b257b8e1adf992 2023-05-15T15:12:45+02:00 Evaluation of lake sedimentary ancient DNA metabarcoding to assess fungal biodiversity in Arctic paleoecosystems Peter Andreas Seeber Barbara vonHippel Hårvard Kauserud Ulrike Löber Kathleen Rosmarie Stoof‐Leichsenring Ulrike Herzschuh Laura S. Epp 2022-09-01T00:00:00Z https://doi.org/10.1002/edn3.315 https://doaj.org/article/553a78bc3c1d45bb94b257b8e1adf992 EN eng Wiley https://doi.org/10.1002/edn3.315 https://doaj.org/toc/2637-4943 2637-4943 doi:10.1002/edn3.315 https://doaj.org/article/553a78bc3c1d45bb94b257b8e1adf992 Environmental DNA, Vol 4, Iss 5, Pp 1150-1163 (2022) fungi in silico PCR ITS lake sediment metabarcoding sedimentary ancient DNA Environmental sciences GE1-350 Microbial ecology QR100-130 article 2022 ftdoajarticles https://doi.org/10.1002/edn3.315 2022-12-30T21:05:32Z Abstract Fungi are crucial organisms in most ecosystems as they exert ecological key functions and are closely associated with land plants. Fungal community changes may, therefore, help reveal biodiversity changes in past ecosystems. Lake sediments contain the DNA of organisms in the catchment area, which allows reconstructing past biodiversity by using metabarcoding of ancient sedimentary DNA. We re‐evaluated various commonly used metabarcoding primers, and we developed a novel PCR primer combination for fungal metabarcoding to produce a short amplicon, thus accounting for amplification bias due to the degradation of ancient DNA. In silico PCRs showed higher diversity using this new primer combination, compared with previously established fungal metabarcoding primers. We analyzed data from sediment cores from four artic and one boreal lake in Siberia. These cores had been stored for 2–22 years after coring; we, therefore, examined the degradation effects of ancient DNA and storage time‐related bias affecting fungal communities. Amplicon lengths showed considerable variation within and between the major divisions of fungi, for example, amplicons of Basidiomycota were significantly longer than those of Mucoromycota; however, we observed no significant effect of sample age on amplicon length and GC content, suggesting the robustness of our results. We also found no indication of post‐coring fungal growth during storage regarding the proportions of common mold taxa, which would otherwise distort conclusions on past fungal communities. Terrestrial soil fungi, including mycorrhizal fungi and saprotrophs, were predominant in all lakes, whereas typical aquatic taxa were only represented to a negligible extent, which supports the use of lake sedimentary ancient DNA for reconstructing terrestrial communities. Article in Journal/Newspaper Arctic Siberia Directory of Open Access Journals: DOAJ Articles Arctic Boreal Lake ENVELOPE(-127.670,-127.670,58.802,58.802) Environmental DNA 4 5 1150 1163 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
fungi in silico PCR ITS lake sediment metabarcoding sedimentary ancient DNA Environmental sciences GE1-350 Microbial ecology QR100-130 |
spellingShingle |
fungi in silico PCR ITS lake sediment metabarcoding sedimentary ancient DNA Environmental sciences GE1-350 Microbial ecology QR100-130 Peter Andreas Seeber Barbara vonHippel Hårvard Kauserud Ulrike Löber Kathleen Rosmarie Stoof‐Leichsenring Ulrike Herzschuh Laura S. Epp Evaluation of lake sedimentary ancient DNA metabarcoding to assess fungal biodiversity in Arctic paleoecosystems |
topic_facet |
fungi in silico PCR ITS lake sediment metabarcoding sedimentary ancient DNA Environmental sciences GE1-350 Microbial ecology QR100-130 |
description |
Abstract Fungi are crucial organisms in most ecosystems as they exert ecological key functions and are closely associated with land plants. Fungal community changes may, therefore, help reveal biodiversity changes in past ecosystems. Lake sediments contain the DNA of organisms in the catchment area, which allows reconstructing past biodiversity by using metabarcoding of ancient sedimentary DNA. We re‐evaluated various commonly used metabarcoding primers, and we developed a novel PCR primer combination for fungal metabarcoding to produce a short amplicon, thus accounting for amplification bias due to the degradation of ancient DNA. In silico PCRs showed higher diversity using this new primer combination, compared with previously established fungal metabarcoding primers. We analyzed data from sediment cores from four artic and one boreal lake in Siberia. These cores had been stored for 2–22 years after coring; we, therefore, examined the degradation effects of ancient DNA and storage time‐related bias affecting fungal communities. Amplicon lengths showed considerable variation within and between the major divisions of fungi, for example, amplicons of Basidiomycota were significantly longer than those of Mucoromycota; however, we observed no significant effect of sample age on amplicon length and GC content, suggesting the robustness of our results. We also found no indication of post‐coring fungal growth during storage regarding the proportions of common mold taxa, which would otherwise distort conclusions on past fungal communities. Terrestrial soil fungi, including mycorrhizal fungi and saprotrophs, were predominant in all lakes, whereas typical aquatic taxa were only represented to a negligible extent, which supports the use of lake sedimentary ancient DNA for reconstructing terrestrial communities. |
format |
Article in Journal/Newspaper |
author |
Peter Andreas Seeber Barbara vonHippel Hårvard Kauserud Ulrike Löber Kathleen Rosmarie Stoof‐Leichsenring Ulrike Herzschuh Laura S. Epp |
author_facet |
Peter Andreas Seeber Barbara vonHippel Hårvard Kauserud Ulrike Löber Kathleen Rosmarie Stoof‐Leichsenring Ulrike Herzschuh Laura S. Epp |
author_sort |
Peter Andreas Seeber |
title |
Evaluation of lake sedimentary ancient DNA metabarcoding to assess fungal biodiversity in Arctic paleoecosystems |
title_short |
Evaluation of lake sedimentary ancient DNA metabarcoding to assess fungal biodiversity in Arctic paleoecosystems |
title_full |
Evaluation of lake sedimentary ancient DNA metabarcoding to assess fungal biodiversity in Arctic paleoecosystems |
title_fullStr |
Evaluation of lake sedimentary ancient DNA metabarcoding to assess fungal biodiversity in Arctic paleoecosystems |
title_full_unstemmed |
Evaluation of lake sedimentary ancient DNA metabarcoding to assess fungal biodiversity in Arctic paleoecosystems |
title_sort |
evaluation of lake sedimentary ancient dna metabarcoding to assess fungal biodiversity in arctic paleoecosystems |
publisher |
Wiley |
publishDate |
2022 |
url |
https://doi.org/10.1002/edn3.315 https://doaj.org/article/553a78bc3c1d45bb94b257b8e1adf992 |
long_lat |
ENVELOPE(-127.670,-127.670,58.802,58.802) |
geographic |
Arctic Boreal Lake |
geographic_facet |
Arctic Boreal Lake |
genre |
Arctic Siberia |
genre_facet |
Arctic Siberia |
op_source |
Environmental DNA, Vol 4, Iss 5, Pp 1150-1163 (2022) |
op_relation |
https://doi.org/10.1002/edn3.315 https://doaj.org/toc/2637-4943 2637-4943 doi:10.1002/edn3.315 https://doaj.org/article/553a78bc3c1d45bb94b257b8e1adf992 |
op_doi |
https://doi.org/10.1002/edn3.315 |
container_title |
Environmental DNA |
container_volume |
4 |
container_issue |
5 |
container_start_page |
1150 |
op_container_end_page |
1163 |
_version_ |
1766343387124858880 |