State-of-the-art infrastructure for genetic, molecular, and imaging analyses is available not only to DZMB researchers but also to external users and collaboration partners.
Dr. Sahar Khodami
Leitung Metabarcoding und NGS Labor
DZMB
Our infrastructure
Metabarcoding and NGS Laboratory
Our unit focuses on advancing molecular biodiversity research through the integration of genomic approaches, natural history collections, and ecological applications. We aim to bridge classical taxonomy with cutting-edge molecular methods to better understand biodiversity patterns, evolutionary processes, and ecosystem responses to environmental change.
Marine ecosystems, particularly benthic fauna and zooplanktonic communities, remain among the least understood components of biodiversity due to their immense diversity, small organism size, and the global shortage of taxonomic expertise. We address these challenges by developing scalable molecular approaches that enable rapid, high-resolution characterization of biological communities across habitats—from coastal systems to the deep sea.
In this context, our work is structured around two complementary pillars. First, we develop and apply community-level molecular monitoring approaches, particularly DNA metabarcoding and environmental DNA (eDNA), to assess biodiversity change under natural and anthropogenic pressures. Second, we generate collection-linked molecular resources, including curated DNA barcode libraries and genomic datasets derived from both freshly collected and historical material. By integrating specimen-based barcoding into molecular workflows, we uncover cryptic diversity and resolve taxonomic ambiguities.
A central component of our research is the continuous refinement of laboratory and bioinformatic workflows. We optimize protocols for NGS library preparation and sequencing, and develop reproducible bioinformatic pipelines for processing high-throughput sequencing data, including trimming, filtering, and taxonomic assignment. Our work focuses on widely used genetic markers such as mitochondrial COI and the hypervariable regions of the 18S rRNA gene, while expanding into phylogenomic approaches using phylotranscriptomics to resolve deep evolutionary relationships and refine taxonomic frameworks across diverse marine taxa particularly crustaceans.
Beyond biodiversity assessment, we investigate population connectivity and evolutionary dynamics using genomic tools such as 2bRAD sequencing and mitogenomics. These approaches allow us to link patterns of genetic structures to ecological processes and to provide evidence for conservation and management strategies.
A key strength of our section lies in its integrative perspective. We combine molecular data with morphological expertise through close collaboration with taxonomists, ensuring high-quality reference frameworks for species identification, while actively contributing to methodological innovation.
Through this framework, our group develops robust, scalable, and future-oriented tools for biodiversity research. By embedding molecular approaches within collection-based research and collaborative networks, we support both fundamental science and applied monitoring, ultimately contributing to a better understanding and protection of marine ecosystems.
Head
2026
Kunze M., Khodami S., Ostmann A., Packmor J., George K.H. (2026) Redescription of Enhydrosoma sarsi (Scott, 1905) (Copepoda, Harpacticoida, Cletodidae T. Scott) from the western Baltic Sea (Germany) and remarks on the systematics of Enhydrosoma Boeck, 1873. Zootaxa, 5768 (3), 335–369. https://doi.org/10.11646/zootaxa.5768.3.2
Damm L., Khodami S., Rubel V., Molari M., Vink A., Stoeck T., Martinez Arbizu P. (2026) Community DNA outperforms eDNA metabarcoding for biodiversity assessments in the Clarion–Clipperton Fracture Zone. Metabarcoding and Metagenomics 10: e173793. https://doi.org/10.3897/mbmg.10.173793
Gwinner M., Haslob H., Neumann H., Schupp P.J., Khodami S., Bonthond G. (2026) Flatfish intestinal microbiota depend on various host traits, and vary with sediment type and bottom trawling effort. Scientific Reports 16, 632. https://doi.org/10.1038/s41598-025-34195-w
2025
Stratmann T., Simon-Lledó E., van der Meer M., Christodoulou M., Rossel S., Colaco A. (2025) Trophic ecology of Ophiuroidea and Asteroidea in the Clarion-Clipperton-Fracture Zone (Central Pacific), Deep Sea Research Part I: Oceanographic Research Papers 225, https://doi.org/10.1016/j.dsr.2025.104598
Blanco-Bercial L., Questel M.J., Batta-Lona P., Escribano R., Falkenhaug T., Hirai J., Huggett J., Martínez Arbizu P., Peijnenburg K., Suter L., Weydmann-Zwolicka A., Dubbeldam S., Duijm E., Ershova E., González C.E., Govender A., Groeneveld J., Khodami S., Kuczyński R., MacDonald A., Mioduchowska M., Polanowski A.M., Rodríguez-Pérez R., O’Brien T., Bucklin A. (2025) MetaZooGene Intercalibration Experiment (MZG-ICE): Metabarcoding marine zooplankton diversity of the global Ocean. Molecular Ecology Resources 26, 1: e70090. https://doi.org/10.1111/1755-0998.70090
Khodami S., Ostmann A., Packmor J., George K.H., Martínez Arbizu P. (2025) Baseline studies on meiofauna in the Baltic Sea before bottom-trawl fisheries exclusion II. A comparative study using multi-gene metabarcoding and morphology. Metabarcoding and Metagenomics 9: e169630. https://doi.org/10.3897/mbmg.9.169630
Bonk F., Khodami S., Brandt A., Martínez Arbizu P., Hadal copepods in and around: A metabarcoding Survey of meiofauna in the Aleutian trench and adjacent regions, Progress in Oceanography 239: 103596. https://doi.org/10.1016/j.pocean.2025.103596
Christodoulou M., Derycke S., Beentjes K.K., Hillewaert H., Laakmann S., Lundin K., Kamyab E., Khodami S., Maes S., Reiss H., Uhlir C., Van den Bulcke L., Van der Hoorn B., De Backer A., Martinez Arbizu P. (2025) A taxonomically reliable DNA barcode reference library for North Sea macrobenthos. Scientific Data 12, 1198. https://doi.org/10.1038/s41597-025-05500-z
Bernot J.P., Khodami S., Boyen J., de Troch M., Boxshall G.A., Martínez Arbizu P. (2025) Copepod phylogenomics supports Canuelloida as a valid order separate from Harpacticoida, Molecular Phylogenetics and Evolution 206, 108311. https://doi.org/10.1016/j.ympev.2025.108311
Neuhaus, J., deWilt M. E., Rossel S., et al. (2025) “High Connectivity at Abyssal Depths: Genomic and Proteomic Insights Into Population Structure of the Pan-Atlantic Deep-Sea Bivalve Ledella ultima (E. A. Smith, 1885).” Ecology and Evolution15, 8: e71903. https://doi.org/10.1002/ece3.71903
Wieschermann L., Kihara T.C. (2025) A new species of the genus Aphotopontius Humes, 1987 (Siphonostomatoida, Dirivultidae) from a vent field at the Southeast Indian Ridge, Plankton and Benthos Research 20, s120, https://doi.org/10.3800/pbr.20.s102
Kuru S., Martínez Arbizu P., Rossel S. (2025) Revealing high genetic divergence masked by low morphological variability in harpacticoid genus Leptastacus Scott T., 1906 (Copepoda, Harpacticoida, Leptastacidae) including the description of five new species. Marine Biodiversity 55:113. https://doi.org/10.1007/s12526-025-01583-4
Kniesz K., Hoffman L., Martínez Arbizu P., Kihara T.C. (2025) High genomic connectivity within Anatoma at hydrothermal vents along the Central and Southeast Indian Ridge. Scientific Report 15, 1971. https://doi.org/10.1038/s41598-025-85507-z
2024
Reñé A., Timoneda N., Khodami S., López-García P., Martinez Arbizu P., Hoppenrath M. (2024) Morpho-molecular characterization of sand-dwelling dinoflagellate communities from the German Wadden Sea and insights into their spatiotemporal distribution. European Journal of Phycology, 59 (2), 196–217. https://doi.org/10.1080/09670262.2023.2279547
Neufeld M., Meyn K., Kihara T.C., Martinez Arbizu P., Kuhn T. (2024) First record of the giant anemone, Relicanthus daphneae, at active hydrothermal vent fields in the Indian Ocean. Journal of the Marine Biological Association of the United Kingdom 104, e122, 1–6. https://doi.org/10.1017/ S0025315424001127
Kapshyna I., Veit-Köhler G., Hoffman L., Khodami S. (2024) Impact of a coastal protection measure on sandy-beach meiofauna at Ahrenshoop (Baltic Sea, Germany): results from metabarcoding and morphological approaches are similar. Metabarcoding and Metagenomics 8: e127688. https://https://doi.org/10.3897/mbmg.8.127688
Sosa SOSA, Brandt A, Chen C, Engel L, Esquete P, Horton T, Jażdżewska AM, Johannsen N, Kaiser S, Kihara TC, Knauber H, Kniesz K, Landschoff J, Lörz AN, Machado FM, Martínez-Muñoz CA, Riehl T, Serpell-Stevens A, Sigwart JD, Tandberg AHS, Tato R, Tsuda M, Vončina K, Watanabe HK, Wenz C, Williams JD. (2024) Ocean Species Discoveries 1-12 – A primer for accelerating marine invertebrate taxonomy. Biodiversity Data Journal 12: e128431. https://doi.org/10.3897/BDJ.12.e128431
Stratmann T., Busch K., de Kluijver A., Kelly M., Mills S., Rossel S., Schupp P.J., (2024) Nutrient fluxes, oxygen consumption and fatty acid composition from deep-water demo- and hexactinellid sponges from New Zealand, Deep Sea Research Part I: Oceanographic Research Papers b 214, 104416, https://doi.org/10.1016/j.dsr.2024.104416
2023
Bonthond G., Beermann J., Gutow L., Neumann A., Barboza F., Desiderato A., Fofonova V., Helber S., Khodami S., Kraan C., Neumann H., Rohde S., Schupp P. (2023) Benthic microbial biogeographic trends in the North Sea are shaped by an interplay of environmental drivers and bottom trawling effort. ISME Communications 3, 132. https://doi.org/10.1038/s43705-023-00336-3
Eichsteller A., Martynov A., O’Hara T.D., Christodoulou M., Korshunova T., Bribiesca-Contreras G., Martinez Arbizu P. (2023) Ophiotholia (Echinodermata: Ophiuroidea): A little-known deep-sea genus present in polymetallic nodule fields with the description of a new species. Frontiers in Marine Science. 10:1056282. https://doi.org/10.3389/fmars.2023.1056282
Kaiser S., Christodoulou M., Janssen A., Kihara T.C., Mohrbeck I., Pasotti F., Schnurr S., Vink A., Martinez Arbizu P. (2023) Diversity, distribution and composition of abyssal benthic Isopoda in a region proposed for deep-seafloor mining of polymetallic nodules: a synthesis. Marine. Biodiversity. 53, 30. https://doi.org/10.1007/s12526-023-01335-2
Hablützel P.I., Arbizu Martínez P., Bilsen A., Christodoulou M., Delacauw S., Deneudt K., Khodami S., et al. (2023) DNA-based monitoring of non-Indigenous Species (NIS) Project: GEANS-Genetic tools for Ecosystem health Assessment in the North Sea region. [Technical report] https://doi.org/10.13140/RG.2.2.23641.53606
Derycke S., Beentjes K., Christodoulou M, Hansen J, Khodami S., Kröncke I., Martinez Arbizu P., et al. (2023) DNA-Based monitoring of soft sediments. Project: GEANS-Genetic tools for Ecosystem health Assessment in the North Sea region. [Technical report] https://doi.org/10.13140/RG.2.2.30352.42241
2022
Rossel S., Kaiser P., Bode-dalby M., Renz J., Laakmann S., Auel H., Hagen W., Arbizu P.M., Peters J. (2022) Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean. Molecular Ecology Resources. 23, 382–395. https://doi.org/10.1111/1755-0998.13714
Rossel S., Uhlenkott K., Peters J., Vink A., Martínez Arbizu P. (2022) Evaluating species richness using proteomic fingerprinting and DNA barcoding—a case study on meiobenthic copepods from the Clarion Clipperton Fracture Zone, Marine Biodiversity 52 (6), https://doi.org/10.1007/s12526-022-01307-y
Ralf T., Christodoulou M., Pogonoski J., Weddehage T., Vink A., Martinez Arbizu P. (2022) An application of morphological analysis and DNA barcoding to identify Ipnops from the Clarion-Clipperton Zone (CCZ) as I. meadi Nielsen, 1966 with notes on other species of the genus (Aulopiformes: Ipnopidae), Marine Biodiversity 52, https://doi.org/10.1007/s12526-022-01320-1
Hoffmann, L., Kniesz K., Martinez Arbizu, P., Kihara T.C. (2022) Abyssal vent field habitats along plate margins in the Central Indian Ocean yield new species in the genus Anatoma (Vetigastropoda: Anatomidae) European Journal of Taxonomy 826:135-162. https://doi.org/10.5852/ejt.2022.826.1841
Rossel S., Kaiser P., Bode-dalby M., Renz J., Laakmann S., Auel H., Hagen W., Martínez Arbizu P., Peters J. (2022) Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean. Molecular Ecology Resources 23, 2, https://doi.org/10.1111/1755-0998.13714
Christodoulou M., Grave S., Vink A., Martinez Arbizu P. (2022) Taxonomic assessment of deep-sea decapod crustaceans collected from polymetallic nodule fields of the East Pacific Ocean using an integrative approach, Marine Biodiversity 52, https://doi.org/10.1007/s12526-022-01284-2
Kniesz K., Jażdżewska A.M., Martínez Arbizu P., Kihara T.C. (2022) DNA Barcoding of Scavenging Amphipod Communities at Active and Inactive Hydrothermal Vents in the Indian Ocean. Frontiers in Marine Science. 8:752360. https://doi.org/10.3389/fmars.2021.752360
Korfhage S., Rossel S., Brix S., Mcfadden C.S., Martínez Abizu P. (2022) Species delimitation of Hexacorallia and Octocorallia around Iceland using nuclear and mitochondrial DNA and proteome fingerprinting, Frontiers in Marine Science, Deep-Sea Environments and Ecology 9. https://doi.org/10.3389/fmars.2022.838201
Sánchez N., González Casarrubios A., Cepeda D., Khodami S., Pardos F., Vink A., Martinez Arbizu P. (2022) Diversity and distribution of Kinorhyncha in abyssal polymetallic nodule areas of the Clarion-Clipperton Fracture Zone and the Peru Basin, East Pacific Ocean, with the description of three new species and notes on their intraspecific variation. Marine Biodiversity 52. https://link.springer.com/article/10.1007/s12526-022-01279-z
Paulus E., Brix E., Siebert A., Martinez Arbizu P., Rossel S., Peters J., Svavarsson J., Schwentner M. (2022) A complex pattern of recent speciation and hybridization in a deep-sea benthic isopod species-complex around Iceland revealed by DNA barcoding, ddRAD and proteomics. Molecular Ecology 31:313-330, https://doi.org/10.1111/mec.16234
2021
Jazdzewska A., Horton T., Hendrycks E., Mamos T., Driskell A., Brix S., Martinez Arbizu P. (2021) Pandora’s box in the deep sea –intraspecific diversity patterns and distribution of two congeneric scavenging amphipods. Frontiers in Marine Science, Sec. Deep-Sea Environments and Ecology. https://doi.org/10.3389/fmars.2021.750180
Rent J., Marksaseva E.L., Laakmann S., Rossel S., Martinez Arbizu P., Peters J. (2021) Molecular Ecology Resources; Proteomic fingerprinting facilitates biodiversity assessments in understudied ecosystems: a case study on integrated taxonomy of deep-sea copepods. Molecular Ecology Resources 21, 6, https://doi.org/10.1111/1755-0998.13405
Demidow O., Kihara T.C., Martinez Arbizu P., Clark P.F. (2021) The megalopal stage of the hydrothermal vent crab Austinograea rodriguezensis Tsuchida & Hashimoto, 2002 (Decapoda: Bythograeidae): a morphological description based on CLSM images. Zootaxa 5040(3):365-387, https://doi.org/10.11646/ZOOTAXA.5040.3.3
Thiel R., Knebelsberger T., KiharaI T.C., Gerdes K. (2021) Description and DNA barcoding of a new eelpout Pachycara angeloi sp. nov. (Perciformes: Zoarcidae) from deep-sea hydrothermal vent fields in the Indian Ocean. Zootaxa 4980(1):99-112, https://doi.org/10.11646/zootaxa.4980.1.6
Kaiser S., Kihara T.C., Brix S., Mohrbeck I., Janssen A., Jennings R. (2021) Species boundaries and phylogeographic patterns in new species of Nannoniscus (Janiroidea: Nannoniscidae) from the equatorial Pacific nodule province inferred from mtDNA and morphology. Zoological Journal of the Linnean Society 193(3), https://doi.org/10.1093/zoolinnean/zlaa174
Degenhardt J., Khodami S., Milke F., Waska H., Engelen B., Martinez Arbizu P. (2021) The Three Domains of Life Within the Discharge Area of a Shallow Subterranean Estuary at a High Energy Beach. Frontiers in Environmental Science. 9. 642098. https://doi.org/10.3389/fenvs.2021.642098
Mohrbeck I., Horton T., Jażdżewska A., Martínez Arbizu P. (2021) DNA-barcoding and Cryptic Diversity of Deep-Sea Scavenging Amphipods in the Clarion-Clipperton Zone (Eastern Equatorial Pacific). Marine Biodiversity, 51, 26. https://doi.org/10.1007/s12526-021-01170-3
Jażdżewska A.M., Brandt A., Martinez Arbizu P., Vink A. (2021) Exploring the diversity of the deep sea – four new species of the amphipod genus Oedicerina described using morphological and molecular methods. Zoological Journal of the Linnean Society 194(1), https://doi.org/10.1093/zoolinnean/zlab032
2020 72. Rossel S., Barco A., Kloppmann M., Martínez Arbizu P., Huwer B., Knebelsberger T. (2020) Rapid species level identification of fish eggs by proteome fingerprinting using MALDi-TOF MS“.Journal of Proteomics https://doi.org/10.1016/j.jprot.2020.103993
Brix S., Osborn K.J., Kaiser S., Truskey S.B., Schnurr S.M., Brenke N., Malyutina M., Martínez Arbizu P. (2020) Adult life strategy affects distribution patterns in abyssal isopods – implications for conservation in Pacific nodule areas. Biogeosciences 17(23), https://doi.org/10.5194/bg-17-6163-2020
Rahlff J., Khodami S., Voskuhl L., Humphreys M., Stolle C., Martínez-Arbizu P., Wurl, O., Ribas-Ribas M. (2021) Short-term responses to ocean acidification: effects on relative abundance of eukaryotic plankton from the tropical Timor Sea. Marine Ecology Progress Series. 658. 59-74. https://doi.org/10.3354/meps13561
Steinert G., Busch K., Bayer K., Kodami S., Martinez Arbizu P., Kelly M., Mills S., Erpenbeck D., Dohrmann M., Wörheide G., Hentschel U., Schupp P.J. (2020) Compositional and Quantitative Insights Into Bacterial and Archaeal Communities of South Pacific Deep-Sea Sponges (Demospongiae and Hexactinellida). Frontiers in microbiology. https://doi.org/10.3389/fmicb.2020.00716
Christodoulou M., O’hara T., Hugall A., Khodami S., Rodrigues C.F., Hilario A., Vink A., Martinez Arbizu P. (2020) Unexpected high abyssal ophiuroid diversity in polymetallic nodule fields of the northeast Pacific Ocean and implications for conservation. Biogeosciences, 17, 1-32. https://doi.org/10.5194/bg-17-1-2020
Mercado-Salas N., Khodami S., Martínez Arbizu P. (2021) Copepods and ostracods associated with bromeliads in the Yucatán Peninsula, Mexico. PLOS ONE. 16. https://doi.org/10.1371/journal.pone.0248863
Khodami S., Mercado-Salas N., Martínez Arbizu P. (2020) Genus level molecular phylogeny of Aegisthidae Giesbrecht, 1893 (Copepoda: Harpacticoida) reveals morphological adaptations to deep-sea and pelagic habitats. BMC Evolutionary Biology. 20. 36. https://doi.org/10.1186/s12862-020-1594-x
2019
Rossel S., Khodami S., Martínez Arbizu P. (2019) Comparison of Rapid Biodiversity Assessment of Meiobenthos Using MALDI-TOF MS and Metabarcoding. Frontiers in Marine Science 6:659. https://doi.org/10.3389/fmars.2019.00659
Christodoulou M., O’hara T., Hugall A.F., Martinez Arbizu P. (2019) Dark Ophiuroid Biodiversity in a Prospective Abyssal Mine Field. Current Biology 29, 1-4. https://doi.org/10.1016/j.cub.2019.09.012
Rossel S., Martínez Arbizu P. (2019) Revealing higher than expected diversity of Harpacticoida (Crustacea: Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding. Scientific Reports. https://doi.org/10.1038/s41598-019-45718-7
Khodami S., Mercado-salas N.F., Tang D., Martinez Arbizu P. (2019) Molecular evidence for the retention of the Thaumatopsyllidae in the order Cyclopoida (Copepoda) and establishment of four suborders and two families within the Cyclopoida. Molecular Phylogenetics and Evolution, 138:43-52. https://doi.org/10.1016/j.ympev.2019.05.01
Holst S., Heins A., Laakmann S. (2019) Morphological and molecular diagnostic species characters of Staurozoa (Cnidaria) collected on the coast of Helgoland (German Bight, North Sea). 10013/epic.4f95b184-bb12-44fe-943d-b0f989f1bf93
Laakmann S., Markhaseva E.L., Renz J. (2019) Do molecular phylogenies unravel the relationships among the evolutionary young “Brafordian” families (Copepoda; Calanoida)? Molecular Phylogenetics and Evolution, 130: 330-345. https://doi.org/10.1016/j.ympev.2018.10.028
Holst, S., Laakmann, S. (2019) First record of the stalked jellyfish Haliclystus tenuis Kishinouye, 1910 (Cnidaria: Staurozoa) in Atlantic waters. Marine Biodiversity 49, 1061–1066. https://doi.org/10.1007/s12526-018-0888-3
2018
Mercado-Salas N.F., Mercado-Salas N.F., Khodami S., Kihara T.C., Elías-Gutiérrez M., Arbizu P.M. (2018) Genetic structure and distributional patterns of the genus Mastigodiaptomus (Copepoda) in Mexico, with the description of a new species from the Yucatan Peninsula. Arthropod Systematics & Phylogeny 76(3): 487-507. https://doi.org/10.3897/asp.76.e31965
Christodoulou M., Cristina Kihara T. (2018) Lectotype designation and distribution updates on the freshwater shrimp species Atyaephyra stankoi Karaman 1972. Zootaxa 4531 (1): 123–133. https://doi.org/10.11646/zootaxa.4531.1.7
Renz J., Markhaseva E.L., Laakmann S. (2018) The phylogeny of Ryocalanoidea (Copepoda, Calanoida) based on morphology and a multi-gene analysis with a description of new ryocalanoidean species. Zoological Journal of the Linnean Society, 1-33 . https://doi.org/10.1093/zoolinnean/zly069
Rossel S., Martinez Arbizu P. (2018) Effects of Sample Fixation on Specimen Identification in Biodiversity Assemblies Based on Proteomic Data (MALDI-TOF). Frontiers in Marine Science 5:149. https://doi.org/10.3389/fmars.2018.00149
Mercado-Salas N., Martínez Arbizu P., Khodami S. (2018) Convergent evolution of mouthparts morphology between Siphonostomatoida and a new genus of deep-sea Aegisthidae Giesbrecht, 1893 (Copepoda: Harpacticoida). Arthropod Systematics and Phylogeny 76(3). 487-507. https://doi.org/10.1007/s12526-018-0932-3
Günther B., Knebelsberger T., Neumann H., Laakmann S., Martinez Arbizu P. (2018) Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes. Scientific Reports 8, 14822. https://doi.org/10.1038/s41598-018-32917-x
Mertens K.N., Carbonell-Moore M.C., Pospelova V., Head M.J., Highfield A., Schroeder D., Gu H., Andree K.B., Fernandez M., Yamaguchi A., Takano Y., Matsuoka K., Nézan E., Bilien G., Okolodkov Y., Koike K., Hoppenrath M., Pfaff M., Pitcher G., Al-Muftah A., Rochon A., Lim P.T., Leaw C.P., Lim Z.F., Ellegaard M., 2018. Pentaplacodinium saltonense gen. et sp. nov. (Dinophyceae) and its relationship to the cyst-defined genus Operculodinium and yessotoxin-producing Protoceratium reticulatum. Harmful Algae, 71: 57-77. https://doi.org/10.1016/j.hal.2017.12.003
2017
Günther B., Raupach M.J., Knebelsberger T. (2016) Full-length and mini-length DNA barcoding for the identification of seafood commercially traded in Germany. Food Control 73, 922-929. https://doi.org/10.1016/j.foodcont.2016.10.016
Tillmann U., Hoppenrath M., Gottschling M., Kusber W.H. Elbrächter M. (2017) Plate pattern clarification of the marine dinophyte Heterocapsa triquetra sensu Stein (Dinophyceae) collected at the Kiel Fjord (Germany). Journal of Phycology 53: 1305-1324. https://doi.org/10.1111/jpy.12584
Laakmann S., Boos K., Knebelsberger T., Raupach M.J., Neumann H. (2017) Species identification of echinoderms from the North Sea by combining morphology and molecular data. Helgoland Marine Research, 70: 18. https://doi.org/10.1186/s10152-016-0468-5
Kieneke A., Nikoukar H. (2017) Integrative morphological and molecular investigation of Turbanella hyalina Schultze, 1853 (Gastrotricha: Macrodasyida), including a redescription of the species. Zoologischer Anzeiger, 267: 168–186. https://doi.org/10.1016/j.jcz.2017.03.005
Hoppenrath M., Yubuki N., Stern R., Leander B.S. (2017) Ultrastructure and molecular phylogenetic position of a new marine sand-dwelling dinoflagellate from British Columbia, Canada: Pseudadenoides polypyrenoides sp. nov. (Dinophyceae). European Journal of Phycology, 52(2), 208–224. https://doi.org/10.1080/09670262.2016.1274788
Hofmann T., Knebelsberger T., Kloppmann M., Ulleweit J., Raupach M.J. (2017) Egg identification of three economical important fish species using DNA barcoding in comparison to a morphological determination. Journal of Applied Ichthyology, 33: 925–932. https://doi.org/10.1111/jai.13389
Bode M., Laakmann S., Kaiser P., Hagen W., Auel H., Cornils A. (2017) Unravelling diversity of deep-sea copepods using integrated morphological and molecular techniques. Journal of Plankton Research, 39: 600–617. https://doi.org/10.1093/plankt/fbx031
2016
Gollner S., Stuckas H., Kihara T.C., Laurent S., Khodami S., Martínez Arbizu P. (2016) Mitochondrial DNA analyses indicate high diversity, expansive population growth and high genetic connectivity of vent copepods (Dirivultidae) across different oceans. PLOS ONE. 11 (10). https://doi.org/10.1371/journal.pone.0163776
Thiel R., Knebelsberger T. (2016) How reliably can northeast Atlantic sand lances of the genera Ammodytes and Hyperoplus be distinguished? A comparative application of morphological and molecular methods. ZooKeys, 617, 139-164, https://doi.org/10.3897/zookeys.617.8866
Schade F.M., Raupach M.J., Wegner K.M. (2016) Seasonal variation in parasite infection patterns of marine fish species from the Northern Wadden Sea in relation of interannual temperature fluctuations. Journal of the Sea 113: 73-84. https://doi.org/10.1016/j.seares.2015.09.002
Raupach M.J., Amann R., Wheeler Q. et al. (2016) The application of “-omics” technologies for the classification and identification of animals. Organisms Diversity & Evolution, 16: 1–12. https://doi.org/10.1007/s13127-015-0234-6
Oliveira L.M., Knebelsberger T., Landi M., Soares P., Raupach M.J., Costa F.O. (2016) Assembling and auditing a comprehensive DNA barcode reference library for European marine fishes. Journal of Fish Biology, 89: 2741–2754. https://doi.org/10.1111/jfb.13169
Miljutin D.M., Miljutina M.A. (2016) Intraspecific variability of morphological characters in the species-rich deep-sea genus Acantholaimus Allgén, 1933 (Nematoda: Chromadoridae). Nematology, 18(4), 455-473. https://doi.org/10.1163/15685411-00002970
Meissner K., Bick A., Götting M. (2016) Arctic Pholoe (Polychaeta, Pholoidae): when integrative taxonomy helps to sort out barcodes. Zoological Journal of the Linnean Society. https://doi.org/10.1111/zoj.12468
Laakmann S., Boos K., Knebelsberger T., Raupach M.J., Neumann H. (2016) Species identification of echinoderms from the North Sea by combining morphology and molecular data. Helgoland Marine Research 70:18. https://doi.org/10.1186/s10152-016-0468-5
Barco A., Raupach M.J., Laakmann S., Neumann H., Knebelsberger T. (2016) Identification of North Sea molluscs with DNA barcoding. Molecular Ecology Resources, 16: 288–297. https://doi.org/10.1111/1755-0998.12440
2015
Raupach M.J., Barco A., Steinke D., Beermann J., Laakmann S., Mohrbeck I., Neumann H., Kihara T.C., Pointner K., Radulovici A., Segelken-voigt A., Wesse C., Knebelsberger T. (2015) The application of DNA barcodes for the identification of marine crustaceans from the North Sea and adjacent regions. Public Library of Science ONE 10 (9): e0139421. https://doi.org/10.1371/journal.pone.0139421
Raupach M.J., Radulovici A.E. (2015) Looking back on a decade of barcoding crustaceans. Zookeys. 23 (539), 53-81. https://doi.org/10.3897/zookeys.539.6530.
Mohrbeck I., Raupach M.J., Martínez Arbizu P., Knebelsberger T., Laakmann S. (2015) High-Throughput Sequencing—The Key to Rapid Biodiversity Assessment of Marine Metazoa?. PLOS ONE 10(10): e0140342. https://doi.org/10.1371/journal.pone.0140342
Miljutina M.A., Miljutin D.M. (2015) A revision of the genus Paracanthonchus (Cyatholaimidae, Nematoda) with a tabular key to species and a description of P. mamubiae sp. n. from the deep North-Western Pacific. Deep-sea Research II 111, 104-118. https://doi.org/10.1016/j.dsr2.2014.08.002.
Meißner K., Götting M. (2015) Spionidae (Annelida: ‘Polychaeta’: Canalipalpata) from Lizard Island, Great Barrier Reef, Australia: the genera Malacoceros, Scolelepis, Spio, Microspio, and Spiophanes. Zootaxa, 4019: 378–413. https://doi.org/10.11646/zootaxa.4019.1.15
Knebelsberger T., Dunz A.R., Neumann D., Geiger M.F. (2015) Molecular diversity of Germany’s freshwater fishes and lampreys assessed by DNA barcoding. Molecular Ecology Resources, 15: 562–572. https://doi.org/10.1111/1755-0998.12322
Janssen A., Kaiser S., Meißner K., Brenke N., Menot L., Martínez Arbízu P. (2015) Reverse taxonomy reveals long-range distribution of abyssal species on polymetallic nodule fields: A comparison of the polychaete and isopod faunas between the French and German Exploration License Areas in the Clarion-Clipperton Zone (CCZ, NE-equatorial Pacific). PLOS ONE, 10(2): e0117790. https://doi.org/10.1371/journal.pone.0117790
Hofmann T., Raupach M.J., Martinez Arbízu P., Knebelsberger T. (2015) An application of in situ hybridization for the identification of commercially important fish species. Fisheries Research, 170: 1–8. https://doi.org/10.1016/j.fishres.2015.05.002
Gebhardt K., Knebelsberger T. (2015) Identification of cephalopod species from the North and Baltic Seas using morphology, COI and 18S rDNA sequences. Helgoland Marine Research, 69: 259–271. https://doi.org/10.1007/s10152-015-0434-7
Boeters H.D., Callot-Girardi H., Knebelsberger T. (2015) News of Pseudamnicola (Corrosella) of Spain and France (Mollusca: Gastropoda: Truncatelloidea). Folia Malacologica, 23: 95–119. https://doi.org/10.12657/folmal.023.007
2014
Brix S., Leese F., Riehl T., Kihara T.C. (2014) A new genus and new species of Desmosomatidae Sars, 1897 (Isopoda) from the east South-Atlantic abyss described by means of integrative taxonomy. Marine Biodiversity. https://doi.org/10.1007/s12526-014-0218-3
Vogt P., Miljutina M., Raupach M.J. (2014) The use of DNA sequence data for the identification of benthic nematodes from the North Sea. Helgoland Marine Research, 68: 549–558. https://doi.org/10.1007/s10152-014-0411-6
Raupach M.J., Bininda-Emonds O.R.P., Knebelsberger T., Laakmann S., Pfänder J., Leese F. (2014) Phylogeographic analysis of Ligia oceanica (Crustacea: Isopoda) reveals two deeply divergent mitochondrial lineages. Biological Journal of the Linnean Society, 112: 16–30. https://doi.org/10.1111/bij.12254
Meißner K., Bick A., Guggolz T., Götting M. (2014) Spionidae (Polychaeta: Canalipalpata: Spionida) from seamounts in the NE Atlantic. Zootaxa, 3786: 201–245. https://doi.org/10.11646/zootaxa.3786.3.1
Markhaseva E.L., Laakmann S., Renz J. (2014) An interim synopsis of the Bradfordian families with a description of Thoxancalanus spinatus (Copepoda: Calanoida), a new diaxid genus and species from the deep Atlantic Ocean. Marine Biodiversity, 44: 63–88. https://doi.org/10.1007/s12526-013-0185-0
Markert A., Raupach M.J., Segelken-Voigt A., Wehrmann A. (2014) Molecular identification and morphological characteristics of Asian brush-clawed crabs from native Japanese and invasive German sites: Hemigrapsus penicillatus (De Haan, 1835) versus H. takanoi Asakura & Watanabe 2005 (Crustacea: Brachyura). Organisms Diversity & Evolution, 14: 369–382. https://doi.org/10.1007/s13127-014-0176-4
Laakmann S., Holst S. (2014) Emphasizing the diversity of North Sea hydromedusae by combined morphological and molecular methods. Journal of Plankton Research, 36: 64–76. https://doi.org/10.1093/plankt/fbt078
Knebelsberger T., Thiel R. (2014) Identification of gobies (Teleostei: Perciformes: Gobiidae) from the North and Baltic Seas combining morphological analysis and DNA barcoding. Zoological Journal of the Linnean Society, 172: 831–845. https://doi.org/10.1111/zoj.12189
Knebelsberger T., Landi M., Neumann H., Kloppmann M., Sell A., Campbell P., Laakmann S., Raupach M.J., Carvalho G., Costa F. (2014) A reliable DNA barcode reference library for the identification of the European shelf fish fauna. Molecular Ecology Resources, 14: 1060–1071. https://doi.org/10.1111/1755-0998.12238
Khodami S., Martínez-Arbizu P., Stöhr S., Laakmann S. (2014) Molecular species delimitation of Icelandic brittle stars (Ophiuroidea). Polish Polar Research, 35: 243–260. https://doi: 10.2478/popore−2014−0011
Holst S., Laakmann S. (2014) Morphological and molecular discrimination of two closely related jellyfish species, Cyanea capillata and C. lamarckii (Cnidaria, Scyphozoa), from the northeast Atlantic. Journal of Plankton Research, 36: 48–63. https://doi.org/10.1093/plankt/fbt093
2013
Stöger I., Sigwart J.D., Kano Y., Knebelsberger T., Marshall B.A., Schwabe E., Schrödl M. (2013) The continuing debate on deep molluscan phylogeny: Evidence for Serialia (Mollusca, Monoplacophora + Polyplacophora). BioMed Research International, Article ID 407072. https://doi.org/10.1155/2013/407072
Lejzerowicz F., Esling P., Majewski W., Szczuciński W., Decelle J., Obadia C., Martínez Arbizu P.M., Pawlowski J. (2013) Ancient DNA complements microfossil record in deep-sea subsurface sediments. Biology Letters, 9(4). https://doi.org/10.1098/rsbl.2013.0283
Laakmann S., Gerdts G., Erler R., Knebelsberger T., Martínez Arbizu P., Raupach M.J. (2013) Comparison of molecular species identification for North Sea calanoid copepods (Crustacea) using proteome fingerprints and DNA sequences. Molecular Ecology Resources, 13: 862–876. https://doi.org/10.1111/1755-0998.12139
2012
Tang C.Q., Leasi F., Obertegger U., Kieneke A., Barraclough T.G., Fontaneto D. (2012) The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna. Proceedings of the National Academy of Sciences, 109: 16208–16212. https://doi.org/10.1073/pnas.1209160109
Kieneke A., Martínez Arbizu P.M., Fontaneto D. (2012) Spatially structured populations with a low level of cryptic diversity in European marine Gastrotricha. Molecular Ecology, 21: 1239–1254. https://doi.org/10.1111/j.1365-294X.2011.05421.x
Boeters H.D., Knebelsberger T. (2012) Revision of selected species of Bythinella Moquin-Tandon 1856 from Central Europe using morphology, anatomy and DNA barcodes (Caenogastropoda: Rissooidea). Archiv für Molluskenkunde, 141: 115–136. https://doi.org/10.1127/arch.moll/1869-0963/141/115-136
2011
Meißner K., Bick A., Bastrop R. (2011) On the identity of Spio filicornis (O.F. Müller, 1776) – with the designation of a neotype, and the description of two new species from the North East Atlantic Ocean based on morphological and genetic studies. Zootaxa, 2815: 1–27. https://doi.org/10.11646/zootaxa.2815.1.1
Gollner S., Fontaneto D., Martínez Arbizu P.M. (2011) Molecular taxonomy confirms morphological classification of deep-sea hydrothermal vent copepods (Dirivultidae) and suggests broad physiological tolerance of species and frequent dispersal along ridges. Marine Biology, 158: 221–231. https://doi.org/10.1007/s00227-010-1553-y
Brix S., Riehl T., Leese F. (2011) First genetic data for species of the genus Haploniscus Richardson, 1908 (Isopoda: Asellota: Haploniscidae) from neighbouring deep-sea basins in the South Atlantic. Zootaxa, 2838: 79–84.
2010
Knebelsberger T., Ditzler S., Laakmann S., Mohrbeck I., Raupach M.J. (2010) Molecular techniques for identifying North Sea fauna. In: Nimis P.L., Vignes Lebbe R. (eds.) Tools for identifying Biodiversity: progress and problems. Edizioni Università di Trieste, Trieste: 349.
Grabbert S., Renz J., Hirche H., Bucklin A. (2010) Species-specific PCR discrimination of species of the calanoid copepod Pseudocalanus, P. acuspes and P. elongatus, in the Baltic and North Seas. Hydrobiologia, 652: 289–297. https://doi.org/10.1007/s10750-010-0351-9
2009
Meißner K., Blank M. (2009) Spiophanes norrisi sp. nov. (Polychaeta: Spionidae) – a new species from the NE Pacific coast, separated from the Spiophanes bombyx complex based on both morphological and genetic studies. Zootaxa, 2278: 1–25. https://doi.org/10.11646/zootaxa.2278.1.1
Proteomic Laboratory
Species identification is a fundamental component of ecological and scientific studies. At the same time, it is time-consuming and requires a high level of taxonomic knowledge. With the help of proteome fingerprinting, species can be identified quickly, cost-effectively, and reliably, even without years of accumulated expertise. In our laboratory, we use MALDI-TOF mass spectrometry to determine the protein fingerprint.
MALDI-TOF MS stands for Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. In this method, the substances to be analyzed are embedded in a matrix and ionized with a laser. This releases them from the matrix; they are then accelerated at different speeds depending on their size by an electromagnetic field and finally detected by a detector. This allows for the measurement of macromolecules such as peptides and proteins without them being destroyed by radiation. The totality of the measured peptides and proteins then constitutes the protein fingerprint. In the field of microbiology, measuring the protein fingerprint has long been a standard method for identifying various types of bacteria, fungi, and viruses. In recent years, this method has also found application in the identification of animals.
In our section, we are working to adapt this method for use in biodiversity research. To this end, we are first testing the method on various animal groups. In addition, we are developing workflows that enable the rapid analysis of MALDI-TOF MS data. In community analyses in particular, it is the morphological identification of many individuals that takes up a significant amount of time. MALDI-TOF mass spectrometry is expected to significantly reduce this time, as it requires only a few preparation steps compared to other methods such as COI barcoding. In addition to the time savings, MALDI-TOF mass spectrometry also incurs significantly lower costs, making it particularly attractive when dealing with large numbers of individuals. As a result, this technique is especially well-suited for use in meiofauna research as well as the analysis of plankton communities and time series. Furthermore, we have already been able to identify cryptic species—that is, species that are morphologically indistinguishable. This makes the method quite interesting in the field of macro- and megafauna as well and can be used to assist with species that are morphologically difficult to identify, without requiring time-consuming sample preparation.
Head
Dr. Sven Rossel
Leitung Proteomic Laboratory
2022
18. KÜRZEL, K., KAISER, S., LÖRZ, A.-N., ROSSEL, S., PAULUS, E., PETERS, J., SCHWENTNER, M., MARTÍNEZ ARBIZU, P., COLEMAN, C. O., SVAVARSSON, J., & BRIX, S. (2022). Correct Species Identification and Its Implications for Conservation Using Haploniscidae (Crustacea, Isopoda) in Icelandic Waters as a Proxy. Frontiers in Marine Science, 8(795196). https://doi.org/doi: 10.3389/fmars.2021.795196
17. ROSSEL, S., UHLENKOTT, K., PETERS, J., VINK, A., & MARTÍNEZ ARBIZU, P. (2022). Evaluating species richness using proteomic fingerprinting and DNA-barcoding – a case study on meiobenthic copepods from the Clarion Clipperton Fracture Zone. Marine Biodiversity.
16. KORFHAGE, S. A., ROSSEL, S., BRIX, S., MCFADDEN, C. S., ÓLAFSDÓTTIR, S. H., & MARTÍNEZ ARBIZU, P. (2022). Species Delimitation of Hexacorallia and Octocorallia Around Iceland Using Nuclear and Mitochondrial DNA and Proteome Fingerprinting. Frontiers in Marine Science, 9. https://www.frontiersin.org/article/10.3389/fmars.2022.838201
15. ROSSEL, S., KAISER, P., BODE-DALBY, M., RENZ, J., LAAKMANN, S., AUEL, H., HAGEN, W., MARTÍNEZ ARBIZU, P., & PETERS, J. (2022). Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean. Molecular Ecology Resources, n/a(n/a). https://doi.org/10.1111/1755-0998.13714
2021
14. RENZ, J., MARKHASEVA, E. L., LAAKMANN, S., ROSSEL, S., MARTÍNEZ ARBIZU, P., & PETERS, J. (2021). Proteomic fingerprinting facilitates biodiversity assessments in understudied ecosystems: A case study on integrated taxonomy of deep sea copepods. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13405
13. PAULUS, E., BRIX, S., SIEBERT, A., MARTÍNEZ ARBIZU, P., ROSSEL, S., PETERS, J., SVAVARSSON, J., & SCHWENTNER, M. (2022). Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics. Molecular Ecology, 31(1), 313–330. https://doi.org/10.1111/mec.16234
2020
12. ROSSEL, S., & MARTÍNEZ ARBIZU, P. (2020). Unsupervised biodiversity estimation using proteomic fingerprints from MALDI-TOF MS data. Limnology and Oceanography: Methods. https://doi.org/10.1002/lom3.10358
11. ROSSEL, S., BARCO, A., KLOPPMANN, M., MARTÍNEZ ARBIZU, P., HUWER, B., & KNEBELSBERGER, T. (2020). Rapid species level identification of fish eggs by proteome fingerprinting using MALDI-TOF MS. Journal of Proteomics, 103993. https://doi.org/10.1016/j.jprot.2020.103993
10. PETERS, J., LAAKMANN, S., ROSSEL, S., MARTÍNEZ ARBIZU, P., & RENZ, J. (2022). Perspectives of species identification by MALDI-TOF MS in monitoring—Stability of proteomic fingerprints in marine epipelagic copepods [Preprint]. Preprints. https://doi.org/10.22541/au.166671183.32080869/v1
9. WILKE, T., RENZ, J., HAUFFE, T., DELICADO, D., & PETERS, J. (2020). Proteomic Fingerprinting Discriminates Cryptic Gastropod Species. Malacologia, 63(1), 131–137. https://doi.org/10.4002/040.063.0113
2019
8. HOLST, S., HEINS, A., AND LAAKMANN, S. (2019). Morphological and molecular diagnostic species characters of Staurozoa (Cnidaria) collected on the coast of Helgoland (German Bight, North Sea). Marine Biodiversity. doi:10.1007/s12526-019-00943-1.
7. ROSSEL, S., KHODAMI, S., AND MARTÍNEZ ARBIZU, P. (2019). Comparison of rapid biodiversity assessment of meiobenthos using MALDI-TOF MS and Metabarcoding. Frontiers in Marine Science 6, 659. doi: 10.3389/fmars.2019.00659
6. ROSSEL, S., AND MARTÍNEZ ARBIZU, P. (2019). Revealing higher than expected diversity of Harpacticoida (Crustacea: Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding. Scientific Reports 9, 9182. doi: 10.1038/s41598-019-45718-7
2018
5. ROSSEL, S., AND MARTÍNEZ ARBIZU, P. (2018). Effects of Sample Fixation on Specimen Identification in Biodiversity Assemblies based on Proteomic Data (MALDI-TOF). Frontiers in Marine Science 5, 149. doi: 10.3389/fmars.2018.00149
4. ROSSEL, S., AND MARTÍNEZ ARBIZU, P. (2018). Automatic specimen identification of Harpacticoids (Crustacea: Copepoda) using Random Forest and MALDI-TOF mass spectra, including a post hoc test for false positive discovery. Methods in Ecology and Evolution 00, 1–14. doi: 10.1111/2041-210X.13000
3. KAISER, P., BODE, M., CORNILS, A., HAGEN, W., MARTÍNEZ ARBIZU, P., AUEL, H., AND LAAKMANN, S. (2018). High-resolution community analysis of deep-sea copepods using MALDI-TOF protein fingerprinting. Deep Sea Research Part I: Oceanographic Research Papers. doi:10.1093/plankt/fbx031
2017
2. BODE, M., LAAKMANN, S., KAISER, P., HAGEN, W., AUEL, H., AND CORNILS, A. (2017). Unravelling diversity of deep-sea copepods using integrated morphological and molecular techniques. Journal of Plankton Research 39, 600–617. doi: 10.1016/j.dsr.2018.06.005
2013
1. LAAKMANN, S., GERDTS, G., ERLER, R., KNEBELSBERGER, T., MARTÍNEZ ARBIZU, P., AND RAUPACH, M. J. (2013). Comparison of molecular species identification for North Sea calanoid copepods (Crustacea) using proteome fingerprints and DNA sequences. Mol Ecol Resour 13, 862–76. doi:10.1111/1755-0998.12139.
Research
Not all samples are suitable for analysis using MALDI-TOF mass spectrometry. Certain fixatives and storage methods can prevent the successful measurement of the protein fingerprint. An important task of our laboratory is therefore to determine how samples must be treated to enable successful identification based on mass spectrometry data. To this end, extensive studies have already been conducted on meiofauna from sediment samples.
The analysis of samples fixed with various ethanol concentrations and stored under different conditions revealed a strong influence of storage temperature on the resulting quality of the mass spectra. Ethanol-fixed samples stored at low temperatures (-25°C) showed only a slight change in signal quality compared to fresh samples. Storage at room temperature, on the other hand, led to a significant decrease in signal quality even after a short time. This resulted in samples becoming unmeasurable after just a few weeks.
To date, all samples processed in our laboratory have been fixed with high-concentration ethanol. Further studies will determine whether other commonly used fixatives are also suitable for fixing samples intended for MALDI-TOF mass spectrometry.
Pilot studies on various species
Since the use of MALDI-TOF mass spectrometry for the identification of animals is not yet widespread, it remains to be determined for most animal groups whether this method can be successfully applied. To this end, the animals are first identified morphologically and molecularly, and the extent to which ontogenetic or other differences affect identification via mass spectrometry is examined. In our laboratory, we primarily study marine organisms.
We have already demonstrated that calanoid copepods from the North Sea can be easily distinguished using a protein fingerprint, and that it is even possible to differentiate between larval stages. MALDI-TOF MS analysis has also been successful for the significantly smaller harpacticoid copepods of the North Sea. Furthermore, larger animal species such as Cnidaria (cnidarians), whose morphological identification is very difficult, could be identified quickly and reliably.
Thanks to previous projects at the DZMB (MOLTAX working group), we have access to a large tissue database of morphologically and molecularly identified organisms from the North Sea, which has yet to be analyzed using MALDI-TOF.
Methods for Rapid Biodiversity Assessment
The availability of appropriate analytical techniques is crucial for the future application of this method in ecological research and biodiversity assessment. Among other things, it is essential that organisms can be identified using reference databases. We are working to develop open-source software solutions for working with mass spectrometry data.
Using Random Forest, a machine learning tool, we have already developed a solution for database-based identification that enables the detection of species not present in the reference database, thereby preventing false-positive identifications. Moving forward, the focus will be on creating additional tools, such as the automatic calculation of biodiversity indices, to enable ecological surveys even in areas without reference databases.
Biodiversity Surveys Already Conducted
In addition to method development and pilot studies, we have already conducted biodiversity surveys using MALDI-TOF MS. This involves measuring the protein fingerprints of a large number of organisms so that, based on the resulting species identification, we can draw conclusions about the communities of these animals. Initial studies showed that the communities identified using MALDI-TOF MS corresponded highly with those identified morphologically or through molecular genetics. This allowed the speed of identifying the studied animals to be accelerated many times over. For example, in the case of spinocalanid copepods from the deep sea, it was demonstrated that the vertical stratification of habitats plays a major role in the reproductive isolation and coexistence of cryptic species.
In future projects, the method will be used to study the species-rich meiofaunal communities of the North Sea. Meiofaunal communities in the CCZ in the North Pacific, an area where deep-sea mining for manganese nodules may occur, will also be studied using protein fingerprinting. The use of MALDI-TOF MS frees up scientific capacity for exploring new research areas that were previously tied up in time-consuming morphological data collection.
Figure Sources
Figure Sample Condition.png: Rossel, S. & Martínez Arbizu, P. (2018). Effects of Sample Fixation on Specimen Identification in Biodiversity Assemblies based on Proteomic Data (MALDI-TOF). Frontiers in Marine Science, 5, 149.
Figure Pilotstudien.tif: Holst, S., Heins, A., & Laakmann, S. (2019). Morphological and molecular diagnostic species characters of Staurozoa (Cnidaria) collected on the coast of Helgoland (German Bight, North Sea). Marine Biodiversity. Retrieved from https://doi.org/10.1007/s12526-019-00943-1
Figure caption Figure Biodiversity Surveys.png: Kaiser, P., Bode, M., Cornils, A., Hagen, W., Arbizu, P.M., Auel, H. & Laakmann, S. (2018). High-resolution community analysis of deep-sea copepods using MALDI-TOF protein fingerprinting. Deep Sea Research Part I: Oceanographic Research Papers.
Confocal laser scanning microscopy
The documentation, quantification, and description of morphological characteristics of species form the indispensable foundation for all taxonomic, systematic, and morphological research. A wide variety of imaging techniques are now available for the study of marine protists, plants, and animals.
Confocal laser scanning microscopy (CLSM) is an ideal tool for the examination of microscopic organisms from marine benthic and pelagic habitats in particular.
The CLSM laboratory at the German Center for Marine Biodiversity Research (DZMB) is currently frequently used to examine the external morphology of small crustaceans, as well as to reconstruct the internal organ systems of soft-bodied meiofauna taxa. Various histochemical and immunohistochemical labeling techniques are employed for this purpose. Additionally, new application areas and preparation techniques are being explored and further developed, such as the enhancement of cuticular autofluorescence or the imaging and examination of micro-bioeroding organisms.
Our department’s CLSM laboratory is equipped with a Leica® TCS SP5 system mounted on a DM5000B microscope base. Six visible laser wavelengths (458, 476, 488, 514, 561, and 633 nm), two fluorescence detectors, and an additional detector for the transmitted light channel are available for our experiments. The fluorescent objects are excited by a diffraction-limited focused laser beam that is scanned line by line across the sample. The confocal arrangement of two adjustable apertures allows for the suppression of signals that do not originate from the focal plane. The stepwise change in the stage position ultimately allows for the generation of three-dimensional image stacks. Such datasets can be processed in a variety of ways, ranging from the creation of depth-of-field projection images to three-dimensional reconstructions of the external morphology and internal anatomy of the organisms under investigation, including quantifications such as the measurement of the biovolume of organ systems.
Head
Dr. Alexander Kieneke
Fachgebietsleiter Evolution und Biogeographie von Meiofauna
Laserschutzbeauftragter
Laserschutzbeauftragter
93. Paulus, E., Brix, S., Siebert, A., Martínez Arbizu, P., Sven Rossel, S., Peters, J., Svavarsson, J., Schwentner, M. (2022): Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics. Molecular Ecology 31: 313-330. https://doi.org/10.1111/mec.16234
92. Kunze, M., Khodami, S., Ostmann, A., Packmor, J., George, K.H. (2026) Redescription of Enhydrosoma sarsi (Scott, 1905) (Copepoda, Harpacticoida, Cletodidae T. Scott) from the western Baltic Sea (Germany) and remarks on the systematics of Enhydrosoma Boeck, 1873. Zootaxa 5768: 335-369. https://doi.org/10.11646/zootaxa.5768.3.2
91. Minowa, A.K., Araújo, T.Q., Garraffoni, A.R.S., Kieneke, A. (2025): A threefold, specimen-saving morphological protocol for aquatic micrometazoans: proof of concept with an integrative re-investigation of the rare freshwater gastrotrich Dichaetura surreyi Martin, 1990. Zoomorphology 144: 61. https://doi.org/10.1007/s00435-025-00748-w
90. Kuru, S., Martínez Arbizu, P.M., Rossel, S. (2025): Revealing high genetic divergence masked by low morphological variability in harpacticoid genus Leptastacus Scott T., 1906 (Copepoda, Harpacticoida, Leptastacidae) including the description of five new species. Marine Biodiversity 55: 113. https://doi.org/10.1007/s12526-025-01583-4
89. Hughes, L.E., Tandberg, A.H.S. (2026). Synopiidae Dana, 1853 (Amphipoda, Crustacea) of the Clarion Clipperton Zone. ZooKeys 1274: 255-270. DOI: 10.3897/zookeys.1274.141366
88. Peart, R.A., Lörz, A.-N. (2026). A new species from the genus Lepechinelloides Thurston, 1980 (Amphipoda, Lepechinellidae) from the Clarion-Clipperton Zone, Pacific Ocean. ZooKeys 1274: 175-184. DOI: 10.3897/zookeys.1274.142630
87. Horton, T., Valls Domedel, G., Stewart, E.C.D., Hendrycks, E.A. (2026). A revision of the genus Elimedon J.L. Barnard, 1962 (Crustacea, Amphipoda, Tryphosidae) with the addition of two new species from the Clarion-Clipperton Zone, Central Pacific Ocean. ZooKeys 1274: 119-140. DOI: 10.3897/zookeys.1274.139884
86. Horton, T., Valls Domedel, G., Hendrycks, E.A. (2026). A new species of Thrombasia J.L. Barnard, 1966 (Crustacea, Amphipoda, Tryphosidae) from the Clarion-Clipperton Zone, Central Pacific Ocean. ZooKeys 1274: 161-174. DOI: 10.3897/zookeys.1274.140063
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