Metabarcoding

Reiter

Info

We are a young innovative research team working on DNA metabarcoding methods to understand ecosystem dynamics and biodiversity decline.

DNA metabarcoding allows the identification of thousands of specimens often on species level, by sequencing a small standardized gene fragment. Unlike with DNA barcoding this is done on the whole community, allowing for a more rapid assessment of biodiversity.

Our research projects focus on:

Biomonitoring of terrestrial and aquatic ecosystems
Community structure and ecosystem change
DNA metabarcoding methods development
Bioinformatics
Large scale laboratory processing
Diet & gut content analyses
Host-parasite interactions
Mitogenomics and 'PCR-free' methods

We are always looking for talented and ambitious students, working with us on existing research projects.

Staff

Scientist, permanent position

Dr. Sarah Bourlat

Head of metabarcoding section, Deputy ombudsperson for good scientific practice

Tel: +49 228 9122-353

Fax: +49 228 9122-212

E-Mail: s.bourlat [at] leibniz-zfmk.de

Technical or laboratory assistant

Ashley Nicole Fulgham-Scott

Technical Assistant Metabarcoding

E-Mail: nicolefulghamscott [at] gmail.com

Dr. Kathrin Langen

Molecular Biology

Tel: +49 228 9122-354

Fax: +49 228 9122-295

E-Mail: k.langen [at] leibniz-zfmk.de

Scientist, third-party funded

Dr. Carolina Corrales Duque

BGE project

Tel: +49 228 9122-420

Fax: +49 228 9122-212

E-Mail: c.corrales [at] leibniz-lib.de

Postdoc

Leighton Thomas, PhD

AMMOD project

E-Mail: l.thomas [at] leibniz-lib.de

Ph.D. student

Dr. Ameli Kirse

Post-doc

Tel: +49 228 9122-453

Fax: +49 228 9122-212

E-Mail: A.Kirse [at] leibniz-zfmk.de

MSc or Diploma Candidate

Felix Pleiss

MSc student

Fax: +49 228 9122-212

E-Mail: felixpleiss [at] rub.de

Alumni

Former staff members

Dr. Vera G. Fonseca

Former Head of Metabarcoding Section

E-Mail: v.fonseca [at] leibniz-zfmk.de

Projects

2022

BioMonitor4CAP

The EU project "BioMonitor4CAP" develops a modern biodiversity monitoring system for a result-based and effective agricultural policy and transformation.

Project lead:

Prof. Dr. Christoph Scherber

Funding:

European Union

BGE - Biodiversity Genomics Europe

Project lead:

Astrid Böhne

Funding:

European Union

2021

Hybrid swarm evolution in minnows

In biodiversity research, little is known so far about how hybridizations of a native and a non-native species can lead to the evolution of an invasive hybrid. A group of researchers led by Dr Madlen Stange is now studying this aspect in a project at the Zoological Research Museum Alexander Koenig – Leibniz Institute for Animal Biodiversity (ZFMK). The group is investigating the spread of Phoxinus, an ecologically important schooling fish, in the River Sieg, a 155 km tributary of the River Rhine.

Project lead:

Dr. Madlen Stange

Funding:

Leibniz Association

BALIN: Insect conservation at railway stations

The project is located in the field of action of light pollution of the German Federal Government's insect protection action programme.

Project lead:

Prof. Dr. Christoph Scherber

2020

GBOL III: Dark Taxa

The BMBF-funded GBOL, the German Barcode of Life initiative, has been run successfully over the last eight years. It delivered an operative DNA barcode reference library for German animals, fungi and plants. However, a significant proportion of insect taxa has so far been excluded from GBOL and merely all biodiversity research, because no or only very insufficient expertise and information are available that allow to get a grip on them. They are called “Dark Taxa”.

Project lead:

Dr. Ralph S. Peters

Funding:

Federal Ministry of Education and Research

2019

AMMOD: A "Weatherstation" counting species diversity

A "Weatherstation" counting species diversity (AMMOD = Automated Multisensor Station for Monitoring of Species Diversity).

Project lead:

Prof. Dr. J. Wolfgang Wägele

Funding:

Federal Ministry of Education and Research

DINA – Diversity of Insects in Nature Protected Areas

In collaboration with the German NABU the ZFMK has been an active partner to initiate a large joint project to understand drivers of insect decline, the DINA project (2019-2022). The goal of the project is to assess and monitor the insect fauna in 21 selected Nature-protected areas using a Malaise trap transect approach. A particular goal of this project is to demonstrate the power of metabarcoding for the rapid and efficient assessment of the insect fauna relying on the GBOL database. Additionally to the insect fauna, landscape parameters including anthropogenic influence will be recorded.

Project lead:

Dr. Livia Schäffler

Funding:

Federal Ministry of Education and Research

End biodiversity loss through improved tracking of threatened invertebrates

In today’s biodiversity crisis, there is an urgent need to monitor terrestrial and aquatic species in their natural habitats, especially those that may be endangered, invasive or elusive. Traditional species observation methods, based on acoustic or observational surveys are inefficient, costly and time consuming. On the other hand, DNA is continuously deposited in the environment from natural processes and this environmental DNA (eDNA) allows us to detect species and reconstruct their communities with a high level of sensitivity.

Project lead:

Dr. Sarah Bourlat

Integrative Analysis of the influence of pesticides and land use on biodiversity in Germany (INPEDIV)

The interdisciplinary joint project INPEDIV is funded for 3 years by the Leibniz Competition (March 2019 – February 2022). The aim of this study is to investigate consequences of organic and conventional farming for biodiversity in protected areas. By use of traditional methods and new technologies, we will examine agricultural land use effects on a broad range of plant and animal taxa across trophic levels at study sites in the Rhineland and in Brandenburg.

Project lead:

Dr. Livia Schäffler

Funding:

Leibniz Association

2017

GGBC: Assessment, Monitoring and Management of Caucasian Biodiversity

A Georgian-German initiative to explore and barcode the biodiversity of the Caucasus area

Project lead:

Prof. Dr. Bernhard Misof

Funding:

Federal Ministry of Education and Research

2011

GBOL- German Barcode of Life

"German Barcode of Life" ( GBOL ) is a project sponsored by the BMBF and includes the creation of inventories for the gentic characterization of the animals, fungi and plants of germany, using DNA-Barcodes.

Project lead:

Prof. Dr. J. Wolfgang Wägele

Funding:

Federal Ministry of Education and Research

Publications

Published in

2018

Zizka, V., Leese, F., Peinert, B., Geiger, M.F. (2018): DNA metabarcoding from sample fixative as a quick and voucher-preserving biodiversity assessment method.- Genome (na) doi.org/10.1139/gen-2018-0048

[read more]

Links:

Genome journal

2017

Lammers, F., Janke, A., Rückle, C., Zizka, V., Nilsson M.A. (2017): Screening for the ancient polar bear mitochondrial genome reveals low integration of mitochondrial pseidogenes (numts) in bears. - Mitochondrial DNA Part B 2 (1): 251-254.

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Batista, F. M., Fonseca, V. G., Ruano, F., Boudry, P. (2017): Asynchrony in settlement time between the closely related oysters Crassostrea angulata and C. gigas in Ria Formosa lagoon (Portugal). - Marine Biology 164:110. https://doi.org/10.1007/s00227-017-3145-6

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Fonseca, V. G., Frederic, S., Vause, B. J., Gaspar, J., Creer, S., Power, D. M., Peck, L. S., et. al. (2017): Revealing higher than expected meiofaunal diversity in Antarctic sediments: a metabarcoding approach. Scientific Reports 7: 6094. https://doi.org/10.1038/s41598-017-06687-x

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Haenel, Q., Holovachov, O., Jondelius, U., Sundberg, P., Bourlat S. J. (2017): NGS-based biodiversity and community structure analysis of meiofaunal eukaryotes in shell sand from Hållö island, Smögen, and soft mud from Gullmarn Fjord, Sweden. - Biodiversity Data Journal 5: e12731. https://doi.org/10.3897/BDJ.5.e12731

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Holovachov, O., Haenel, Q., Bourlat, S. J., Jondelius, U. (2017): Taxonomy assignment approach determines the efficiency of identification of OTUs in marine nematodes. Royal Society Open Science 4 (8): 170315. https://dx.doi.org/10.1098/rsos.170315

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Jakubavičiūtė, E., Bergström, U., Eklöf, J. S., Haenel, Q., Bourlat, S. J. (2017): DNA metabarcoding reveals diverse diet of the three-spined stickleback in a coastal ecosystem. - PLoS ONE 12(10): e0186929. https://doi.org/10.1371/journal. pone.0186929

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Langen, K., Bakker, T. C. M., Baldauf, S. A., Shrestha, J., Thünken T. (2017b): Effects of ageing and inbreeding on the reproductive traits in a cichlid fish I: the male perspective. - Biological Journal of the Linnean Society 120:752-761. https://doi.org/10.1093/biolinnean/blw002

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Langen, K., Bakker, T. C. M., Baldauf, S. A., Shrestha, J., Thünken, T. (2017a): Effects of ageing and inbreeding on the reproductive traits in a cichlid fish II: the female perspective. - Biological Journal of the Linnean Society 120:762-770. https://doi.org/10.1093/biolinnean/blw003

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Potter, C., Tang, C. Q., Fonseca, V. G., Lallias, D., Gaspar, J. M., Thomas, K., Creer, S. (2017): De novo species delimitation in metabarcoding datasets using ecology and phylogeny. - PeerJ Preprints 5:e3121v1. https://doi.org/10.7287/peerj.preprints.3121v1

[read more]

2016

Bourlat, S. J. (2016): Marine Genomics - Methods and protocols. Methods in Molecular Biology Series (1452). - Springer (New York). 264 pp.

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Bourlat, S. J., Haenel, Q., Finnman, J., Leray, M. (2016): Preparation of amplicon libraries for metabarcoding of marine eukaryotes using Illumina MiSeq: the dual- PCR method. In: Bourlat, S. J. (ed.): Marine Genomics - Methods and protocols. - Springer (New York). pp. 197-208. https://doi.org/10.1007/978-1-4939-3774-5_13

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Fonseca, V. G. & Lallias, D. (2016): Metabarcoding marine sediments: preparation of amplicon libraries. In: Bourlat, S. J. (ed.): Marine Genomics - Methods and protocols. - Springer (New York). pp. 183-196. https://doi.org/10.1007/978-1-4939-3774-5_12

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Hardisty, H., Bacall, F., Beard, N., Balcazar-Vargas, M. P., Balech, B., Barcza, Z., Bourlat, S. J., et al. (2016): BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology. - BMC Ecology 16:49. https://doi.org/10.1186/s12898-016-0103-y

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Leese, F., Altermatt, F., Bouchez, A., Torbjørn, E., Hering, D., Meissner, K., …, Fonseca, V. G., et al. (2016): DNAqua-Net: developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe. - Research Ideas and Outcomes 2: e11321. https://doi.org/10.3897/rio.2.e11321

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Leray, M., Haenel, Q., Bourlat, S.J. (2016): Preparation of amplicon libraries for metabarcoding of marine eukaryotes using Illumina MiSeq: the adaptor ligation method. In: Bourlat, S. J. (ed.): Marine Genomics - Methods and protocols. - Springer (New York). pp. 209-218. https://doi.org/10.1007/978-1-4939-3774-5_14

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2015

Astrin, J.J., Fonseca, V., Geiger, M.F., Grobe, P., Rulik, B., Wägele, W. Lessons from the first phase of the German Barcode of Life initiative (2012–2015) In: Scientific abstracts from the 6th International Barcode of Life Conference / Résumés scientifiques du 6e congrès international Barcode of Life. Genome 58(5): 190.

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Schwarzer, J., Lamboj, A., Langen, K., Misof, B., & Schliewen, U. K. (2015). Phylogeny and age of chromidotilapiine cichlids (Teleostei: Cichlidae). Hydrobiologia, 748(1), 185-199.

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2011

Langen, K., Schwarzer, J., Kullmann, H., Bakker, T. C., & Thünken, T. (2011). Microsatellite support for active inbreeding in a cichlid fish. PLoS One, 6(9), e24689.

[read more]

Contact person

Dr. Sarah Bourlat

Head of metabarcoding section

Deputy ombudsperson for good scientific practice

Metabarcoding

+49 228 9122-353

+49 228 9122-212

s.bourlat [at] leibniz-zfmk.de

Metabarcoding

Reiter

Scientist, permanent position

Technical or laboratory assistant

Scientist, third-party funded

Postdoc

Ph.D. student

MSc or Diploma Candidate

Former staff members

2022

BioMonitor4CAP

BGE - Biodiversity Genomics Europe

2021

Hybrid swarm evolution in minnows

BALIN: Insect conservation at railway stations

2020

GBOL III: Dark Taxa

2019

AMMOD: A "Weatherstation" counting species diversity

DINA – Diversity of Insects in Nature Protected Areas

End biodiversity loss through improved tracking of threatened invertebrates

Integrative Analysis of the influence of pesticides and land use on biodiversity in Germany (INPEDIV)

2017

GGBC: Assessment, Monitoring and Management of Caucasian Biodiversity

2011

GBOL- German Barcode of Life

2018

2017

2016

2015

2011

Pages

Contact person

THE LIB

Research

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Metabarcoding

Reiter

Scientist, permanent position

Technical or laboratory assistant

Scientist, third-party funded

Postdoc

Ph.D. student

MSc or Diploma Candidate

Former staff members

2022

2021

2020

2019

2017

2011

Pages

2018

2017

2016

2015

2011

Pages

Contact person