Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods

Research output: Contribution to journalJournal articlepeer-review

Standard

Toward global integration of biodiversity big data : a harmonized metabarcode data generation module for terrestrial arthropods. / Arribas, Paula; Andújar, Carmelo; Bohmann, Kristine; deWaard, Jeremy R.; Economo, Evan P.; Elbrecht, Vasco; Geisen, Stefan; Goberna, Marta; Krehenwinkel, Henrik; Novotny, Vojtech; Zinger, Lucie; Creedy, Thomas J.; Meramveliotakis, Emmanouil; Noguerales, Víctor; Overcast, Isaac; Morlon, Hélène; Papadopoulou, Anna; Vogler, Alfried P.; Emerson, Brent C.

In: GigaScience, Vol. 11, giac065, 2022.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Arribas, P, Andújar, C, Bohmann, K, deWaard, JR, Economo, EP, Elbrecht, V, Geisen, S, Goberna, M, Krehenwinkel, H, Novotny, V, Zinger, L, Creedy, TJ, Meramveliotakis, E, Noguerales, V, Overcast, I, Morlon, H, Papadopoulou, A, Vogler, AP & Emerson, BC 2022, 'Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods', GigaScience, vol. 11, giac065. https://doi.org/10.1093/gigascience/giac065

APA

Arribas, P., Andújar, C., Bohmann, K., deWaard, J. R., Economo, E. P., Elbrecht, V., Geisen, S., Goberna, M., Krehenwinkel, H., Novotny, V., Zinger, L., Creedy, T. J., Meramveliotakis, E., Noguerales, V., Overcast, I., Morlon, H., Papadopoulou, A., Vogler, A. P., & Emerson, B. C. (2022). Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods. GigaScience, 11, [giac065]. https://doi.org/10.1093/gigascience/giac065

Vancouver

Arribas P, Andújar C, Bohmann K, deWaard JR, Economo EP, Elbrecht V et al. Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods. GigaScience. 2022;11. giac065. https://doi.org/10.1093/gigascience/giac065

Author

Arribas, Paula ; Andújar, Carmelo ; Bohmann, Kristine ; deWaard, Jeremy R. ; Economo, Evan P. ; Elbrecht, Vasco ; Geisen, Stefan ; Goberna, Marta ; Krehenwinkel, Henrik ; Novotny, Vojtech ; Zinger, Lucie ; Creedy, Thomas J. ; Meramveliotakis, Emmanouil ; Noguerales, Víctor ; Overcast, Isaac ; Morlon, Hélène ; Papadopoulou, Anna ; Vogler, Alfried P. ; Emerson, Brent C. / Toward global integration of biodiversity big data : a harmonized metabarcode data generation module for terrestrial arthropods. In: GigaScience. 2022 ; Vol. 11.

Bibtex

@article{c4cef759cc0348f1877063bb5df02c3f,
title = "Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods",
abstract = "Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity,with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale synthesesmay be compromised if metabarcoding workflows differ from each other. There are ongoing efforts to improve standardization for the reporting of inventory data. However, harmonization at the stage of generating metabarcode data has yet to be addressed. A modular framework for harmonized data generation offers a pathway to navigate the complex structure of terrestrial metazoan biodiversity. Here, through our collective expertise as practitioners,method developers, and researchers leading metabarcoding initiatives to inventory terrestrial biodiversity, we seek to initiate a harmonized framework for metabarcode data generation, with a terrestrial arthropod module. We develop an initial set of submodules covering the 5 main steps of metabarcode data generation: (i) sample acquisition; (ii) sample processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, and sequencing; and (v) DNA sequence and metadata deposition, providing a backbone for a terrestrial arthropod module. To achieve this, we (i) identified key points for harmonization, (ii) reviewed the current state of the art, and (iii) distilled existing knowledge within submodules, thus promoting best practice by providing guidelines and recommendations to reduce the universe of methodological options.We advocate the adoption and further development of the terrestrial arthropodmodule.We further encourage the development of modules for other biodiversity fractions as an essential step toward large-scale biodiversity synthesis through harmonization. ",
keywords = "arthropods, biodiversity big data integration, biodiversity inventory, comparability, data generation, harmonization, metabarcoding, modular structure, reproducibility",
author = "Paula Arribas and Carmelo And{\'u}jar and Kristine Bohmann and deWaard, {Jeremy R.} and Economo, {Evan P.} and Vasco Elbrecht and Stefan Geisen and Marta Goberna and Henrik Krehenwinkel and Vojtech Novotny and Lucie Zinger and Creedy, {Thomas J.} and Emmanouil Meramveliotakis and V{\'i}ctor Noguerales and Isaac Overcast and H{\'e}l{\`e}ne Morlon and Anna Papadopoulou and Vogler, {Alfried P.} and Emerson, {Brent C.}",
note = "Publisher Copyright: {\textcopyright} The Author(s) 2022.",
year = "2022",
doi = "10.1093/gigascience/giac065",
language = "English",
volume = "11",
journal = "GigaScience",
issn = "2047-217X",
publisher = "Oxford Academic",

}

RIS

TY - JOUR

T1 - Toward global integration of biodiversity big data

T2 - a harmonized metabarcode data generation module for terrestrial arthropods

AU - Arribas, Paula

AU - Andújar, Carmelo

AU - Bohmann, Kristine

AU - deWaard, Jeremy R.

AU - Economo, Evan P.

AU - Elbrecht, Vasco

AU - Geisen, Stefan

AU - Goberna, Marta

AU - Krehenwinkel, Henrik

AU - Novotny, Vojtech

AU - Zinger, Lucie

AU - Creedy, Thomas J.

AU - Meramveliotakis, Emmanouil

AU - Noguerales, Víctor

AU - Overcast, Isaac

AU - Morlon, Hélène

AU - Papadopoulou, Anna

AU - Vogler, Alfried P.

AU - Emerson, Brent C.

N1 - Publisher Copyright: © The Author(s) 2022.

PY - 2022

Y1 - 2022

N2 - Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity,with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale synthesesmay be compromised if metabarcoding workflows differ from each other. There are ongoing efforts to improve standardization for the reporting of inventory data. However, harmonization at the stage of generating metabarcode data has yet to be addressed. A modular framework for harmonized data generation offers a pathway to navigate the complex structure of terrestrial metazoan biodiversity. Here, through our collective expertise as practitioners,method developers, and researchers leading metabarcoding initiatives to inventory terrestrial biodiversity, we seek to initiate a harmonized framework for metabarcode data generation, with a terrestrial arthropod module. We develop an initial set of submodules covering the 5 main steps of metabarcode data generation: (i) sample acquisition; (ii) sample processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, and sequencing; and (v) DNA sequence and metadata deposition, providing a backbone for a terrestrial arthropod module. To achieve this, we (i) identified key points for harmonization, (ii) reviewed the current state of the art, and (iii) distilled existing knowledge within submodules, thus promoting best practice by providing guidelines and recommendations to reduce the universe of methodological options.We advocate the adoption and further development of the terrestrial arthropodmodule.We further encourage the development of modules for other biodiversity fractions as an essential step toward large-scale biodiversity synthesis through harmonization.

AB - Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity,with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale synthesesmay be compromised if metabarcoding workflows differ from each other. There are ongoing efforts to improve standardization for the reporting of inventory data. However, harmonization at the stage of generating metabarcode data has yet to be addressed. A modular framework for harmonized data generation offers a pathway to navigate the complex structure of terrestrial metazoan biodiversity. Here, through our collective expertise as practitioners,method developers, and researchers leading metabarcoding initiatives to inventory terrestrial biodiversity, we seek to initiate a harmonized framework for metabarcode data generation, with a terrestrial arthropod module. We develop an initial set of submodules covering the 5 main steps of metabarcode data generation: (i) sample acquisition; (ii) sample processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, and sequencing; and (v) DNA sequence and metadata deposition, providing a backbone for a terrestrial arthropod module. To achieve this, we (i) identified key points for harmonization, (ii) reviewed the current state of the art, and (iii) distilled existing knowledge within submodules, thus promoting best practice by providing guidelines and recommendations to reduce the universe of methodological options.We advocate the adoption and further development of the terrestrial arthropodmodule.We further encourage the development of modules for other biodiversity fractions as an essential step toward large-scale biodiversity synthesis through harmonization.

KW - arthropods

KW - biodiversity big data integration

KW - biodiversity inventory

KW - comparability

KW - data generation

KW - harmonization

KW - metabarcoding

KW - modular structure

KW - reproducibility

U2 - 10.1093/gigascience/giac065

DO - 10.1093/gigascience/giac065

M3 - Journal article

C2 - 35852418

AN - SCOPUS:85134557257

VL - 11

JO - GigaScience

JF - GigaScience

SN - 2047-217X

M1 - giac065

ER -

ID: 319886184