The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems
Jan Pawlowski
(1)
,
Mary Kelly-Quinn
(2)
,
Florian Altermatt
(3, 4)
,
Laure Apothéloz-Perret-Gentil
(1)
,
Pedro Beja
(5, 6)
,
Angela Boggero
(7, 8)
,
Angel Borja
(9)
,
Agnes Bouchez
(10)
,
Tristan Cordier
(1)
,
Isabelle Domaizon
(10)
,
Maria João Feio
(11)
,
Ana Filipa Filipe
(5, 6)
,
Riccardo Fornaroli
(12)
,
Wolfram Graf
(13)
,
Jelger Herder
(14)
,
Berry van Der Hoorn
(15)
,
J. Iwan Jones
(16)
,
Marketa Sagova-Mareckova
(17)
,
Christian Moritz
(18)
,
Jose Barquin
(19)
,
Jeremy J. Piggott
(20, 21)
,
Maurizio Pinna
(22)
,
Frédéric Rimet
(10)
,
Buki Rinkevich
(23)
,
Carla Sousa-Santos
(24)
,
Valeria Specchia
(22)
,
Rosa Trobajo
(25)
,
Valentin Vasselon
(10)
,
Simon Vitecek
(26, 27, 28)
,
Jonas Zimmerman
(29)
,
Alexander Weigand
(30, 31)
,
Florian Leese
(30)
,
Maria Kahlert
(32)
1
UNIGE -
Université de Genève = University of Geneva
2 School of Biology and Environmental Science
3 Department of Aquatic Ecology
4 UZH - Universität Zürich [Zürich] = University of Zurich
5 Universidade do Porto = University of Porto
6 ULISBOA - Universidade de Lisboa = University of Lisbon
7 LifeWatch Italy
8 CNR - National Research Council of Italy | Consiglio Nazionale delle Ricerche
9 Marine Research Division,
10 CARRTEL - Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques
11 Universidade de Coimbra
12 UNIMI - Università degli Studi di Milano = University of Milan
13 Institute of Hydrobiology
14 RAVON
15 National Biodiversity Centre
16 QMUL - Queen Mary University of London
17 Crop research institute
18 ARGE Limnologie
19 Universidad de Cantabria [Santander]
20 University of Dublin
21 Department of Zoology
22 Università del Salento
23 IOLR - Israel Oceanographic and Limnological Research
24 Instituto Superior de Psicologia Aplicada
25 IRTA - Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology
26 University of Vienna [Vienna]
27 Senckenberg Research Institute
28 Senckenberg Museum [Frankfurt]
29 FU - Free University of Berlin
30 Universität Duisburg-Essen = University of Duisburg-Essen [Essen]
31 MNHN - Muséum national d'Histoire naturelle
32 SLU - Swedish University of Agricultural Sciences = Sveriges lantbruksuniversitet
2 School of Biology and Environmental Science
3 Department of Aquatic Ecology
4 UZH - Universität Zürich [Zürich] = University of Zurich
5 Universidade do Porto = University of Porto
6 ULISBOA - Universidade de Lisboa = University of Lisbon
7 LifeWatch Italy
8 CNR - National Research Council of Italy | Consiglio Nazionale delle Ricerche
9 Marine Research Division,
10 CARRTEL - Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques
11 Universidade de Coimbra
12 UNIMI - Università degli Studi di Milano = University of Milan
13 Institute of Hydrobiology
14 RAVON
15 National Biodiversity Centre
16 QMUL - Queen Mary University of London
17 Crop research institute
18 ARGE Limnologie
19 Universidad de Cantabria [Santander]
20 University of Dublin
21 Department of Zoology
22 Università del Salento
23 IOLR - Israel Oceanographic and Limnological Research
24 Instituto Superior de Psicologia Aplicada
25 IRTA - Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology
26 University of Vienna [Vienna]
27 Senckenberg Research Institute
28 Senckenberg Museum [Frankfurt]
29 FU - Free University of Berlin
30 Universität Duisburg-Essen = University of Duisburg-Essen [Essen]
31 MNHN - Muséum national d'Histoire naturelle
32 SLU - Swedish University of Agricultural Sciences = Sveriges lantbruksuniversitet
Jan Pawlowski
- Fonction : Auteur
- PersonId : 764498
- ORCID : 0000-0003-2421-388X
Florian Altermatt
- Fonction : Auteur
- PersonId : 780856
- ORCID : 0000-0002-4831-6958
Agnes Bouchez
- Fonction : Auteur
- PersonId : 737113
- IdHAL : agnes-bouchez
- ORCID : 0000-0001-8802-6966
- IdRef : 034094660
Tristan Cordier
- Fonction : Auteur
- PersonId : 778544
- ORCID : 0000-0001-7398-4790
Isabelle Domaizon
- Fonction : Auteur
- PersonId : 736724
- IdHAL : isabelle-domaizon
- ORCID : 0000-0001-9785-3082
- IdRef : 118288725
Frédéric Rimet
- Fonction : Auteur
- PersonId : 1204987
Valentin Vasselon
- Fonction : Auteur
- PersonId : 20047
- IdHAL : valentin-vasselon
- ORCID : 0000-0001-5038-7918
- IdRef : 253127432
Florian Leese
- Fonction : Auteur
- PersonId : 769328
- ORCID : 0000-0002-5465-913X
Maria Kahlert
- Fonction : Auteur
- PersonId : 780207
- ORCID : 0000-0001-9643-4281
Résumé
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.