The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

Jan Pawlowski; Mary Kelly-Quinn; Florian Altermatt; Laure Apothéloz-Perret-Gentil; Pedro Beja; Angela Boggero; Angel Borja; Agnès Bouchez; Tristan Cordier; Isabelle Domaizon; Maria Joao Feio; Ana Filipa Filipe; Riccardo Fornaroli; Wolfram Graf; Jelger Herder; Berry van der Hoorn; J. Iwan Jones; Marketa Sagova-Mareckova; Christian Moritz; Jose Barquín; Jeremy J. Piggott; Maurizio Pinna; Frederic Rimet; Buki Rinkevich; Carla Sousa-Santos; Valeria Specchia; Rosa Trobajo; Valentin Vasselon; Simon Vitecek; Jonas Zimmerman; Alexander Weigand; Florian Leese; Maria Kahlert

doi:10.1016/j.scitotenv.2018.05.002

The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

Jan Pawlowski, Mary Kelly-Quinn, Florian Altermatt, Laure Apothéloz-Perret-Gentil, Pedro Beja, Angela Boggero, Angel Borja, Agnès Bouchez, Tristan Cordier, Isabelle Domaizon, Maria Joao Feio, Ana Filipa Filipe, Riccardo Fornaroli, Wolfram Graf, Jelger Herder, Berry van der Hoorn, J. Iwan Jones, Marketa Sagova-Mareckova, Christian Moritz, Jose BarquínJeremy J. Piggott, Maurizio Pinna, Frederic Rimet, Buki Rinkevich, Carla Sousa-Santos, Valeria Specchia, Rosa Trobajo, Valentin Vasselon, Simon Vitecek, Jonas Zimmerman, Alexander Weigand, Florian Leese, Maria Kahlert

Research output: Contribution to journal › Article › peer-review

Abstract

The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.

Original language	English
Pages (from-to)	1295-1310
Number of pages	16
Journal	Science of the Total Environment
Volume	637-638
DOIs	https://doi.org/10.1016/j.scitotenv.2018.05.002
State	Published - 1 Oct 2018
Externally published	Yes

Bibliographical note

Funding Information:
This paper is a result of the COST Action CA15219 “Developing new genetic tools for bioassessment of aquatic ecosystems in Europe” (DNAqua-Net), funded by the European Union. JP has been supported by the Swiss National Sciences Foundation (grant 313003A_159709). MK has been supported by the Swedish Agency for Marine and Water Management (SwAM). FA has been supported by the Swiss National Science Foundation (grants PP00P3_150698 and 31003A_173074). PB was supported by EDP Biodiversity Chair and the ERA Chair in Environmental Metagenomics (EU Horizon 2020 research and innovation programme Grant agreement No 668981). AFF was supported by the FRESHING Project funded by FCT and COMPETE (PTDC/AAG-MAA/2261/2014—POCI-01-0145-FEDER-356 016824). JZ and FL have been supported by the German Federal Ministry for Education and Research (BMBF) Grant 01LI1501E and 01Li1501K for GBOL-2. MP and VS thank FFABR grants from Italian Ministry of University and Research (MIUR), and ImPrEco project funded by Interreg-ADRION 2014-2020 (CUP C69H18000250007). BR was supported by the Ministry of National Infrastructures, Energy and Water Resources, Israel. AB, FR and VV have been supported by the French Biodiversity Agency (AFB). MS-M has been supported by Ministry of Education, Youth and Sports of the Czech Republic, Grant No. LTC17075.

Publisher Copyright:
© 2018 Elsevier B.V.

Keywords

Bioassessment
Biomonitoring
Environmental DNA
Freshwater
Marine
Metabarcording

ASJC Scopus subject areas

Environmental Engineering
Environmental Chemistry
Waste Management and Disposal
Pollution

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10.1016/j.scitotenv.2018.05.002

Cite this

Pawlowski, J., Kelly-Quinn, M., Altermatt, F., Apothéloz-Perret-Gentil, L., Beja, P., Boggero, A., Borja, A., Bouchez, A., Cordier, T., Domaizon, I., Feio, M. J., Filipe, A. F., Fornaroli, R., Graf, W., Herder, J., van der Hoorn, B., Iwan Jones, J., Sagova-Mareckova, M., Moritz, C., ... Kahlert, M. (2018). The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. Science of the Total Environment, 637-638, 1295-1310. https://doi.org/10.1016/j.scitotenv.2018.05.002

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title = "The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems",

abstract = "The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.",

keywords = "Bioassessment, Biomonitoring, Environmental DNA, Freshwater, Marine, Metabarcording",

author = "Jan Pawlowski and Mary Kelly-Quinn and Florian Altermatt and Laure Apoth{\'e}loz-Perret-Gentil and Pedro Beja and Angela Boggero and Angel Borja and Agn{\`e}s Bouchez and Tristan Cordier and Isabelle Domaizon and Feio, {Maria Joao} and Filipe, {Ana Filipa} and Riccardo Fornaroli and Wolfram Graf and Jelger Herder and {van der Hoorn}, Berry and {Iwan Jones}, J. and Marketa Sagova-Mareckova and Christian Moritz and Jose Barqu{\'i}n and Piggott, {Jeremy J.} and Maurizio Pinna and Frederic Rimet and Buki Rinkevich and Carla Sousa-Santos and Valeria Specchia and Rosa Trobajo and Valentin Vasselon and Simon Vitecek and Jonas Zimmerman and Alexander Weigand and Florian Leese and Maria Kahlert",

note = "Funding Information: This paper is a result of the COST Action CA15219 “Developing new genetic tools for bioassessment of aquatic ecosystems in Europe” (DNAqua-Net), funded by the European Union. JP has been supported by the Swiss National Sciences Foundation (grant 313003A_159709). MK has been supported by the Swedish Agency for Marine and Water Management (SwAM). FA has been supported by the Swiss National Science Foundation (grants PP00P3_150698 and 31003A_173074). PB was supported by EDP Biodiversity Chair and the ERA Chair in Environmental Metagenomics (EU Horizon 2020 research and innovation programme Grant agreement No 668981). AFF was supported by the FRESHING Project funded by FCT and COMPETE (PTDC/AAG-MAA/2261/2014—POCI-01-0145-FEDER-356 016824). JZ and FL have been supported by the German Federal Ministry for Education and Research (BMBF) Grant 01LI1501E and 01Li1501K for GBOL-2. MP and VS thank FFABR grants from Italian Ministry of University and Research (MIUR), and ImPrEco project funded by Interreg-ADRION 2014-2020 (CUP C69H18000250007). BR was supported by the Ministry of National Infrastructures, Energy and Water Resources, Israel. AB, FR and VV have been supported by the French Biodiversity Agency (AFB). MS-M has been supported by Ministry of Education, Youth and Sports of the Czech Republic, Grant No. LTC17075. Publisher Copyright: {\textcopyright} 2018 Elsevier B.V.",

year = "2018",

month = oct,

day = "1",

doi = "10.1016/j.scitotenv.2018.05.002",

language = "English",

volume = "637-638",

pages = "1295--1310",

journal = "Science of the Total Environment",

issn = "0048-9697",

publisher = "Elsevier",

}

Pawlowski, J, Kelly-Quinn, M, Altermatt, F, Apothéloz-Perret-Gentil, L, Beja, P, Boggero, A, Borja, A, Bouchez, A, Cordier, T, Domaizon, I, Feio, MJ, Filipe, AF, Fornaroli, R, Graf, W, Herder, J, van der Hoorn, B, Iwan Jones, J, Sagova-Mareckova, M, Moritz, C, Barquín, J, Piggott, JJ, Pinna, M, Rimet, F, Rinkevich, B, Sousa-Santos, C, Specchia, V, Trobajo, R, Vasselon, V, Vitecek, S, Zimmerman, J, Weigand, A, Leese, F & Kahlert, M 2018, 'The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems', Science of the Total Environment, vol. 637-638, pp. 1295-1310. https://doi.org/10.1016/j.scitotenv.2018.05.002

TY - JOUR

T1 - The future of biotic indices in the ecogenomic era

T2 - Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

AU - Pawlowski, Jan

AU - Kelly-Quinn, Mary

AU - Altermatt, Florian

AU - Apothéloz-Perret-Gentil, Laure

AU - Beja, Pedro

AU - Boggero, Angela

AU - Borja, Angel

AU - Bouchez, Agnès

AU - Cordier, Tristan

AU - Domaizon, Isabelle

AU - Feio, Maria Joao

AU - Filipe, Ana Filipa

AU - Fornaroli, Riccardo

AU - Graf, Wolfram

AU - Herder, Jelger

AU - van der Hoorn, Berry

AU - Iwan Jones, J.

AU - Sagova-Mareckova, Marketa

AU - Moritz, Christian

AU - Barquín, Jose

AU - Piggott, Jeremy J.

AU - Pinna, Maurizio

AU - Rimet, Frederic

AU - Rinkevich, Buki

AU - Sousa-Santos, Carla

AU - Specchia, Valeria

AU - Trobajo, Rosa

AU - Vasselon, Valentin

AU - Vitecek, Simon

AU - Zimmerman, Jonas

AU - Weigand, Alexander

AU - Leese, Florian

AU - Kahlert, Maria

N1 - Funding Information: This paper is a result of the COST Action CA15219 “Developing new genetic tools for bioassessment of aquatic ecosystems in Europe” (DNAqua-Net), funded by the European Union. JP has been supported by the Swiss National Sciences Foundation (grant 313003A_159709). MK has been supported by the Swedish Agency for Marine and Water Management (SwAM). FA has been supported by the Swiss National Science Foundation (grants PP00P3_150698 and 31003A_173074). PB was supported by EDP Biodiversity Chair and the ERA Chair in Environmental Metagenomics (EU Horizon 2020 research and innovation programme Grant agreement No 668981). AFF was supported by the FRESHING Project funded by FCT and COMPETE (PTDC/AAG-MAA/2261/2014—POCI-01-0145-FEDER-356 016824). JZ and FL have been supported by the German Federal Ministry for Education and Research (BMBF) Grant 01LI1501E and 01Li1501K for GBOL-2. MP and VS thank FFABR grants from Italian Ministry of University and Research (MIUR), and ImPrEco project funded by Interreg-ADRION 2014-2020 (CUP C69H18000250007). BR was supported by the Ministry of National Infrastructures, Energy and Water Resources, Israel. AB, FR and VV have been supported by the French Biodiversity Agency (AFB). MS-M has been supported by Ministry of Education, Youth and Sports of the Czech Republic, Grant No. LTC17075. Publisher Copyright: © 2018 Elsevier B.V.

PY - 2018/10/1

Y1 - 2018/10/1

N2 - The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.

AB - The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.

KW - Bioassessment

KW - Biomonitoring

KW - Environmental DNA

KW - Freshwater

KW - Marine

KW - Metabarcording

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U2 - 10.1016/j.scitotenv.2018.05.002

DO - 10.1016/j.scitotenv.2018.05.002

M3 - Article

C2 - 29801222

AN - SCOPUS:85047091292

SN - 0048-9697

VL - 637-638

SP - 1295

EP - 1310

JO - Science of the Total Environment

JF - Science of the Total Environment

ER -

The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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