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Jan Macher

Jan Macher

I am a molecular ecologist with a strong interest in understanding biodiversity on different levels, from genes to ecosystems. I am especially interested in how biodiversity changes along ecological gradients.  In most of my projects I infer the diversity of species and communities by using genetic information obtained through barcoding, metabarcoding, metagenomics and metatranscriptomics.

Keywords

Molecular ecology, Metabarcoding, Metagenomics, Biomonitoring, Communities, Stress response, Ecological gradients

Dr. Jan- Niklas Macher

Researcher
Marine biodiversity

jan.macher@naturalis.nl
+31 (0)71 751 9600
https://twitter.com/jnmscie@JNMScience

Key
publications

  • Macher,  J.N., Prazeres, M., Taudien, S., Jompa, J., Sadekov, A., Renema, W. (2021). Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia. Plos one 16 (1), e0244616
  • Macher, J.N., Drakou, K., Papatheodoulou, A., van Der Hoorn, Vasquez, M. (2020) The mitochondrial genomes of 11 aquatic macroinvertebrate species from Cyprus. Metabarcoding and Metagenomics 4, e58259
  • Macher,  J.N., Speksnijder, A., Choo, L.Q., van Der Hoorn, B., Renema, W. (2019). Uncovering bacterial and functional diversity in macroinvertebrate mitochondrial-metagenomic datasets by differential centrifugation. Scientific reports 9 (1), 1-9
  • Macher, J. N., Vivancos, A., Piggott, J. J., Centeno, F. C., Matthaei, C. D., & Leese, F. (2018). Comparison of environmental DNA and bulk‐sample metabarcoding using highly degenerate cytochrome c oxidase I primers. Molecular ecology resources, 18(6), 1456-1468.
  • Macher, J. N., Zizka, V. M. A., Weigand, A. M., & Leese, F. (2018). A simple centrifugation protocol for metagenomic studies increases mitochondrial DNA yield by two orders of magnitude. Methods in Ecology and Evolution, 9(4), 1070-1074.
  • Weigand, A. M., & Macher, J. N. (2018). A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics, 2, e26869.
  • Macher, J. N., Salis, R. K., Blakemore, K. S., Tollrian, R., Matthaei, C. D., & Leese, F. (2016). Multiple-stressor effects on stream invertebrates: DNA barcoding reveals contrasting responses of cryptic mayfly species. Ecological Indicators, 61, 159-169.
  • Macher, J. N., Rozenberg, A., Pauls, S. U., Tollrian, R., Wagner, R., & Leese, F. (2015). Assessing the phylogeographic history of the montane caddisfly Thremma gallicum using mitochondrial and restriction‐site‐associated DNA (RAD) markers. Ecology and evolution, 5(3), 648-662.

All publications on GoogleScholar

Publications

2024

Journals SCI, peer-reviewed

Versteegen E., Macher J.N., Rowley S.J., Renema W. 2024. Changes in the Microbial Community Associated with the Large Benthic Foraminifera Cycloclypeus Carpenteri, Along a Depth Gradient.. Journal of Foraminiferal Research 54 (1) : 10 p. DOI https://doi.org/10.2113/gsjfr.54.1.65
2023

Journals SCI, peer-reviewed

Macher J-N., Coots N.L., Poh Y-P., Girard E.B., Langerak A., Muñoz-Gómez S.A., Sinha S.D., Jirsová D., Vos R., Wissels R., Gile G.H., Renema W., Wideman J.G. 2023. Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria).. MBIO 14 (2) : e0030223. DOI https://doi.org/10.1128/mbio.00302-23
Copilas-Ciocianu D., Sidagyte-Copilas E., Son M.O., Morhun H., Macher J.N., Arbaciauskas K. 2023. Genetic diversity of Ponto-Caspian amphipods throughout the invaded Baltic and native NW Black Sea donor ranges: does introduction mode matter?.. Hydrobiologia 850: 3061–3076. DOI https://doi.org/10.1007/s10750-023-05230-6
2022

Journals SCI, peer-reviewed

Macher​ J-N., Bloska D.M., Holzmann M., Girard E.B., Pawlowski J., Renema W. 2022. Mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding of Foraminifera communities using taxon- specific primers.. PeerJ – the Journal of Life & Environmental Sciences 10 (3) : e13952. DOI https://doi.org/10.7717/peerj.13952
Girard E.B., Langerak A., Jompa J., Wangensteen O.S., Macher J-N., Renema W. 2022. Mitochondrial Cytochrome Oxidase Subunit 1: A Promising Molecular Marker for Species Identification in Foraminifera.. Frontiers in Marine Science DOI https://doi.org/10.3389/fmars.2022.809659
Girard E.B., Macher J-N., Jompa J., Renema W. 2022. COI metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies.. Ecology and Evolution 12 (11) : e9549. DOI https://doi.org/10.1002/ece3.9549
2021

Journals SCI, peer-reviewed

Macher J.N.,Prazeres M., Taudien S., Jompa J.,Sadekov A., Renema W. 2021. Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia. PLoS ONE 16 (1) : e0244616. DOI https://doi.org/10.1371/journal.pone.0244616
Rotter A., Gaudêncio S.P., Klun K., Macher J.-N., Thomas O.P., Deniz I., Edwards C., Grigalionyte-Bembič E., Ljubešić Z., Robbens J., Varese G.C., Vasquez M.I. 2021. A new tool for faster construction of marine biotechnology collaborative networks. Frontiers in Marine Science 8: 685164. DOI https://doi.org/10.3389/fmars.2021.685164
Macher J.-N., Wideman J.G., Girard E.B., Langerak A., Duijm E., Jompa J., Sadekov A., Vos R., Wissels R., Renema W. 2021. First report of mitochondrial COI in foraminifera and implications for DNA barcoding.. Scientific Reports 11: 22165. DOI https://doi.org/10.1038/s41598-021-01589-5
Gielings R., Fais M., Fontaneto D., Creer S., Costa F.O., Renema W., Macher J.-N. 2021. DNA Metabarcoding Methods for the Study of Marine Benthic Meiofauna: A Review.. Frontiers in Marine Science 8: 730063. DOI https://doi.org/10.3389/fmars.2021.730063
2020

Journals SCI, peer-reviewed

Macher J.-N.,Drakou K., Papatheodoulou A., Hoorn B. van der, Vasquez M. 2020. The mitochondrial genomes of 11 aquatic macroinvertebrate species from Cyprus. Metabarcoding and metagenomics 4: e58259. DOI https://doi.org/10.3897/mbmg.4.58259
Hempel C.A., Peinert B., Beermann A.J., Elbrecht V., Macher J.N., Macher T.H., Jacobs G., Leese F. 2020. Using environmental DNA to monitor the reintroduction success of the Rhine sculpin (Cottus rhenanus) in a restored stream. Frontiers in Ecology and Evolution 8: 81. DOI https://doi.org/10.3389/fevo.2020.00081
2019

Journals SCI, peer-reviewed

Weigand H., Beermann A., Čiampor F., Costa F., Csabai Z., Duarte S., Geiger M., Grabowski M., Rimet F., Rulik B., Strand M., Szucsich N., Weigand A., Willassen E., Wyler S., Bouchez A., Borja A., Čiamporová-Zat'ovičová Z., Ferreira S., Dijkstra K., Eisendle U., Freyhof J., Gadawski P., Graf W., Haegerbaeumer A., Hoorn B van der., Japoshvili B., Keresztes L., Keskin E., Leese F., Macher J., Mamos T., Paz G., Pešić V., Pfannkuchen D., Pfannkuchen M., Price B., Rinkevich B., Teixeira M., Várbíró G., Ekrem T. 2019. DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work. Science of the Total Environment 678: 499-524. DOI https://doi.org/10.1101/576553
Macher J-N., Speksnijder A., Choo L.Q., Hoorn B. van der, Renema W. 2019. Uncovering bacterial and functional diversity in macroinvertebrate mitochondrial-metagenomic datasets by differential centrifugation. Scientific Reports 9: 10257. DOI https://doi.org/10.1038/s41598-019-46717-4
2018

Journals non-SCI, peer-reviewed

Weigand A.M., Macher J.-N. 2018. A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics 2: e26869. Pensoft. DOI https://doi.org/10.3897/mbmg.2.26869

Journals SCI, peer-reviewed

Macher J.N., Vivancos A., Piggott J.J., Centeno F.C., Matthaei C.D., Leese F. 2018. Comparison of environmental DNA and bulk‐sample metabarcoding using highly degenerate cytochrome c oxidase I primers. Molecular Ecology Resources 18 (6) : 1456-1468. DOI https://doi.org/10.1111/1755-0998.12940