eDNA Replicates, Polymerase and Amplicon Size Impact Inference of Richness Across Habitats
ABSTRACT Environmental DNA‐based monitoring has been increasingly used in the last decade to monitor biodiversity in aquatic and terrestrial systems. Molecular‐based surveys now allow quick and reliable production of baseline knowledge of species community composition on a large scale, allowing a be...
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2025-05-01
|
| Series: | Environmental DNA |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/edn3.70095 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849420169737142272 |
|---|---|
| author | Jarl Andreas Anmarkrud Fabricio dosAnjos Santa Rosa Lisbeth Thorbek Audun Schrøder‐Nielsen Silvana Melo Sviggum Jonathan Stuart Ready Hugo J. deBoer Quentin Mauvisseau |
| author_facet | Jarl Andreas Anmarkrud Fabricio dosAnjos Santa Rosa Lisbeth Thorbek Audun Schrøder‐Nielsen Silvana Melo Sviggum Jonathan Stuart Ready Hugo J. deBoer Quentin Mauvisseau |
| author_sort | Jarl Andreas Anmarkrud |
| collection | DOAJ |
| description | ABSTRACT Environmental DNA‐based monitoring has been increasingly used in the last decade to monitor biodiversity in aquatic and terrestrial systems. Molecular‐based surveys now allow quick and reliable production of baseline knowledge of species community composition on a large scale, allowing a better understanding of ecosystem function and mitigation of stressors linked to anthropogenic activities. Despite this, technical hurdles often remain, and the impact of replicates, PCR polymerases, and amplicon size on the recovered species richness is still poorly understood. Here, we conducted a large controlled experiment, with bulk samples collected from terrestrial, marine, and freshwater environments to assess the impact of natural and technical replicates, PCR polymerases with different degrees of fidelity or proofreading activity, as well as amplicon size on species richness recovery across habitats. In this study, we consistently found variations in sample species richness depending on PCR polymerase choice. We further demonstrate the dissimilar impacts between natural and technical replicates on species richness recovery and the necessity of increasing natural replications in eDNA‐based surveys. We highlight the benefits and limitations of replication strategies, polymerase choice, and amplicon size across terrestrial, marine, and freshwater habitats, and provide recommendations to increase the reliability of future eDNA‐based metabarcoding studies. |
| format | Article |
| id | doaj-art-a0ac8e931ed44336b7a3fc0527b1f5f0 |
| institution | Kabale University |
| issn | 2637-4943 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Wiley |
| record_format | Article |
| series | Environmental DNA |
| spelling | doaj-art-a0ac8e931ed44336b7a3fc0527b1f5f02025-08-20T03:31:49ZengWileyEnvironmental DNA2637-49432025-05-0173n/an/a10.1002/edn3.70095eDNA Replicates, Polymerase and Amplicon Size Impact Inference of Richness Across HabitatsJarl Andreas Anmarkrud0Fabricio dosAnjos Santa Rosa1Lisbeth Thorbek2Audun Schrøder‐Nielsen3Silvana Melo Sviggum4Jonathan Stuart Ready5Hugo J. deBoer6Quentin Mauvisseau7Natural History Museum University of Oslo Oslo NorwayGroup for Integrated Biological Investigation, Center for Advanced Studies of Biodiversity Federal University of Pará Belém BrazilNatural History Museum University of Oslo Oslo NorwayNatural History Museum University of Oslo Oslo NorwayNatural History Museum University of Oslo Oslo NorwayGroup for Integrated Biological Investigation, Center for Advanced Studies of Biodiversity Federal University of Pará Belém BrazilNatural History Museum University of Oslo Oslo NorwayNatural History Museum University of Oslo Oslo NorwayABSTRACT Environmental DNA‐based monitoring has been increasingly used in the last decade to monitor biodiversity in aquatic and terrestrial systems. Molecular‐based surveys now allow quick and reliable production of baseline knowledge of species community composition on a large scale, allowing a better understanding of ecosystem function and mitigation of stressors linked to anthropogenic activities. Despite this, technical hurdles often remain, and the impact of replicates, PCR polymerases, and amplicon size on the recovered species richness is still poorly understood. Here, we conducted a large controlled experiment, with bulk samples collected from terrestrial, marine, and freshwater environments to assess the impact of natural and technical replicates, PCR polymerases with different degrees of fidelity or proofreading activity, as well as amplicon size on species richness recovery across habitats. In this study, we consistently found variations in sample species richness depending on PCR polymerase choice. We further demonstrate the dissimilar impacts between natural and technical replicates on species richness recovery and the necessity of increasing natural replications in eDNA‐based surveys. We highlight the benefits and limitations of replication strategies, polymerase choice, and amplicon size across terrestrial, marine, and freshwater habitats, and provide recommendations to increase the reliability of future eDNA‐based metabarcoding studies.https://doi.org/10.1002/edn3.70095amplicon sizeeDNA metabarcodingenvironmentspolymerasereplicatesrichness |
| spellingShingle | Jarl Andreas Anmarkrud Fabricio dosAnjos Santa Rosa Lisbeth Thorbek Audun Schrøder‐Nielsen Silvana Melo Sviggum Jonathan Stuart Ready Hugo J. deBoer Quentin Mauvisseau eDNA Replicates, Polymerase and Amplicon Size Impact Inference of Richness Across Habitats Environmental DNA amplicon size eDNA metabarcoding environments polymerase replicates richness |
| title | eDNA Replicates, Polymerase and Amplicon Size Impact Inference of Richness Across Habitats |
| title_full | eDNA Replicates, Polymerase and Amplicon Size Impact Inference of Richness Across Habitats |
| title_fullStr | eDNA Replicates, Polymerase and Amplicon Size Impact Inference of Richness Across Habitats |
| title_full_unstemmed | eDNA Replicates, Polymerase and Amplicon Size Impact Inference of Richness Across Habitats |
| title_short | eDNA Replicates, Polymerase and Amplicon Size Impact Inference of Richness Across Habitats |
| title_sort | edna replicates polymerase and amplicon size impact inference of richness across habitats |
| topic | amplicon size eDNA metabarcoding environments polymerase replicates richness |
| url | https://doi.org/10.1002/edn3.70095 |
| work_keys_str_mv | AT jarlandreasanmarkrud ednareplicatespolymeraseandampliconsizeimpactinferenceofrichnessacrosshabitats AT fabriciodosanjossantarosa ednareplicatespolymeraseandampliconsizeimpactinferenceofrichnessacrosshabitats AT lisbeththorbek ednareplicatespolymeraseandampliconsizeimpactinferenceofrichnessacrosshabitats AT audunschrødernielsen ednareplicatespolymeraseandampliconsizeimpactinferenceofrichnessacrosshabitats AT silvanamelosviggum ednareplicatespolymeraseandampliconsizeimpactinferenceofrichnessacrosshabitats AT jonathanstuartready ednareplicatespolymeraseandampliconsizeimpactinferenceofrichnessacrosshabitats AT hugojdeboer ednareplicatespolymeraseandampliconsizeimpactinferenceofrichnessacrosshabitats AT quentinmauvisseau ednareplicatespolymeraseandampliconsizeimpactinferenceofrichnessacrosshabitats |