DNA metabarcoding on repeat: Sequencing data of marine macrobenthos are reproducible and robust across labs and protocols

TY - JOUR

T1 - DNA metabarcoding on repeat: Sequencing data of marine macrobenthos are reproducible and robust across labs and protocols

AU - Van den Bulcke, Laure

AU - De Backer, Annelies

AU - Wittoeck, Jan

AU - Beentjes, Kevin

AU - Maes, Sara

AU - Christodoulou, Magdalini

AU - Martinez Arbizu, Pedro

AU - Sapkota, Rumakanta

AU - Van der Hoorn, Berry

AU - Winding, Anne

AU - Hostens, Kris

AU - Derycke, Sofie

PY - 2023/6

Y1 - 2023/6

N2 - DNA metabarcoding can be used in marine environmental monitoring if results are reproducible between labs and robust against modifications to the lab protocol. In this interlaboratory study, we conducted a ring test where subsamples of blended macrobenthos samples were distributed to four laboratories located in Belgium, the Netherlands, Germany and Denmark. Samples were processed by a standardized lab protocol and by an adapted protocol, and the resulting datasets were analyzed with the same bioinformatics pipeline. Different biodiversity indicators were calculated. Our results show that bulkDNA metabarcoding of marine macrobenthos offers a highly reproducible assessment of alpha diversity patterns when using a standardized protocol, since comparable species numbers, Shannon indices and Inverse Simpson indices were found between laboratories. Especially high abundant species and species with large body sizes where shared between the laboratories. The need for using a standardized protocol to enhance comparability in alpha diversity between different studies was shown. Beta diversity patterns are less subjected to changes in the metabarcoding protocol and were almost identical between different laboratories, as the main clustering was always based on the macrobenthic community, independent of the used protocol or the laboratory that conducted the work. We conclude that DNA metabarcoding for marine environmental monitoring is an appropriate method when the aim is to study changes in community patterns and advocate its implementation in routine monitoring programs of national and European authorities, providing that a standardized protocol is implemented and/or a detailed description of the protocol is available.

AB - DNA metabarcoding can be used in marine environmental monitoring if results are reproducible between labs and robust against modifications to the lab protocol. In this interlaboratory study, we conducted a ring test where subsamples of blended macrobenthos samples were distributed to four laboratories located in Belgium, the Netherlands, Germany and Denmark. Samples were processed by a standardized lab protocol and by an adapted protocol, and the resulting datasets were analyzed with the same bioinformatics pipeline. Different biodiversity indicators were calculated. Our results show that bulkDNA metabarcoding of marine macrobenthos offers a highly reproducible assessment of alpha diversity patterns when using a standardized protocol, since comparable species numbers, Shannon indices and Inverse Simpson indices were found between laboratories. Especially high abundant species and species with large body sizes where shared between the laboratories. The need for using a standardized protocol to enhance comparability in alpha diversity between different studies was shown. Beta diversity patterns are less subjected to changes in the metabarcoding protocol and were almost identical between different laboratories, as the main clustering was always based on the macrobenthic community, independent of the used protocol or the laboratory that conducted the work. We conclude that DNA metabarcoding for marine environmental monitoring is an appropriate method when the aim is to study changes in community patterns and advocate its implementation in routine monitoring programs of national and European authorities, providing that a standardized protocol is implemented and/or a detailed description of the protocol is available.

KW - Marine environmental monitoring

KW - North Sea

KW - COI

KW - Standardized operational protocol

KW - Ring test

KW - Standard operating procedures (SOPS)

UR - http://www.scopus.com/inward/record.url?scp=85152602515&partnerID=8YFLogxK

U2 - 10.1016/j.ecolind.2023.110207

DO - 10.1016/j.ecolind.2023.110207

M3 - Journal article

SN - 1470-160X

VL - 150

JO - Ecological Indicators

JF - Ecological Indicators

M1 - 110207

ER -