Metabarcoding and NGS Laboratory

Team

Leitung

Team Metabarcoding Khodami
Dr. Sahar Khodami
Leitung Metabarcoding and NGS Laboratory

Link zum Fachbereich Metabarcoding und NGS Labor

Link Metabarcoding and NGS Laboratory

Current position

Leader of the NGS laboratory at Senckenberg am Meer, German Centre for Marine Biodiversity Research, Wilhelmshaven, Germany

Major research Interest

  • Monitoring and rapid biodiversity assessment of macro and meiofauna, planktonic and associated microbiome communities of marine ecosystems using metabarcoding and eDNA approaches
  • Transcriptomics: Evolution and phylogeny of crustaceans specifically copepods
  • Genetic connectivity between populations of marine species from macro- and meiofauna communities using restriction associated DNA-markers (2b-RADs)
  • Reverse taxonomy and species delimitations in the deep sea

Employment history

07.2020 – today Leader of the NGS laboatories at Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB)
07.2018 – 2020 Postdoctoral researcher at Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB)
08.2012 – 2018 Ph.D. scholarship candidate at Carl von Ossietzky Universität Oldenburg

Academic Educations

2012 – 2018
Ph.D.   Carl von Ossietzky Universität Oldenburg, Institute of Biology, Oldenburg, Germany
Title of thesis: Molecular Phylogeny and Revision of Copepod Orders (Pancrustacea)

2007 – 2010
M.Sc.  University of Tehran, Science and Research Branch, Department of Marine Biology, Tehran, Iran
Title of thesis: Effects of abiotic factors on sexual maturity of Acartia clausi (Calanoida: Copepoda) from Caspian Sea 

2003 – 2006
B.Sc.  University of Mazandaran, Badeleh Branch, Department of Aquaculture and Fisheries Engineering, Sari, Iran

CAREER BREAK

2010 – 2012
Lab technician at University of Mazandaran, Department of Fisheries and Agriculture

Relevant Workshop/Trainings (last 10 years)

21.01 – 01.02.2013   Phylogenetic and Systematic and Molecular Dating at the University of Copenhagen (Denmark). Winner of the DEST-grant (Distributed European School of Taxonomy)
24 – 25.02.2016   Statistical Methods in Phylogeny with „R“ provided by Gesellschaft für Biologische Systematik (GfBS)”. Munich, Germany
22 – 23.06.2021   MiSeq training by Illumina Senckenberg am Meer, Wilhelmshaven, Germany
02 – 13.09.2018    Next Generation sequencing course Senckenberg institute, Frankfurt, Germany
19 – 24.02.2021   Analysis of hybridization capture data Centrum für Naturkunde (CENAK), Hamburg, Germany
06 – 15.06.2022   Genome assemblies and Genes expression Senckenberg am Meer, Wilhelmshaven, Germany

Funded projects as participant (last 5 years)

  • Project title: Genetic tools for Ecosystem health Assessment in the North Sea region (GEANS). Funded by the European Union (Interreg), Years: 2019–2023, PI: Dr De Backer A. (ILVO), Role: Postdoctoral Researcher (663,710.00 €)
  • Project title: MiningImpact – Environmental Impacts and Risks of Deep-Sea Mining. Funded by Federal Ministry of Education and Research (Germany), Years: 2018–2022, PI: Dr Haeckel M. (GEOMAR), Role: Postdoctoral researcher (~430,000.00 €)
  • Project title: Icelandic Marine Animals: Genetic and Ecology (IceAGE). Funded by: German Science Foundation (MerMet17-6), Years: 2011-2020, PI: Dr. Brix S. (DZMB), Role: Postdoctoral researcher. (~680,000.00 €)
  • Project title: Icelandic marine Animals meet Diversity along latitudinal gradients in the deep sea of the Atlantic (IceDivA). Funded by: German Science Foundation, Years: 2021-2023, PI: Dr. Brix S. (DZMB), Role: Postdoctoral researcher
  • Project title: JPIO Oceans – Ecological Aspects of Deep-sea Mining. Funded by Federal Ministry of Education and Research (Germany), Years: 2017-2018, PI: Dr Haeckel M. (GEOMAR), Role: Postdoctoral researcher. (474,647.00 €)
  • Project title: Exclusion of mobile bottom-contact fishing in marine protected areas of the German Exclusive Economic Zone (EEZ) of the North Sea and Baltic Sea (MGF Baltic Sea). Funded by Federal Ministry of Education and Research (BMBF). Years: 2022-2023. PI:  Prof. Dr. Jürgens K. (IOW), Role: Postdoctoral researcher

PUBLICATIONS

2021

  • Sánchez N., González-Casarrubios A., Cepeda D., Khodami S., Pardos F., Vink A., Martínez Arbizu P. in press. Revision of diversity and distribution of Kinorhyncha in abyssal polymetallic nodule areas with the description of three new species. Marine Biodiversity.
  • 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. 10.3389/fenvs.2021.642098.
  • Mercado-Salas N., Khodami S., Martinez Arbizu P. 2021. Copepods and ostracods associated with bromeliads in the Yucatán Peninsula, Mexico. PLOS ONE. 16. e0248863. 10.1371/journal.pone.0248863.
  • Rahlff J., Khodami S., Voskuhl L., Humphreys M., Stolle C., Martinez 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. 10.3354/meps13561.

2020

  • Khodami S., Mercado-Salas N., Martinez 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.
  • Christodoulou M., O’Hara T., Hugall A., Khodami S., Rodrigues C.F., et al. 2020. Unexpected high abyssal ophiuroid diversity in polymetallic nodule fields of the Northeast Pacific Ocean, and implications for conservation. Biogeosiences. DOI: 10.5194/bg-2019-360
  • Steinert G., Busch K., Bayer K., Khodami, S., Martinez Arbizu, P., et al. 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

2019

  • Rossel S., Khodami S., Martinez Arbizu P. 2019. Comparison of Rapid Biodiversity Assessment of Meiobenthos Using MALDI-TOF MS and Metabarcoding. Frontiers in Marine Science 6. DOI: 10.3389/fmars.2019.00659
  • Khodami S., Mercado-Salas N., 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. DOI: 10.1016/j.ympev.2019.05.019

2018

  • Mercado-Salas N., Martinez Arbizu P., Khodami S. 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.DOI: 10.1007/s12526-018-0932-3
  • Mercado-Salas N., Khodami S., Kihara T., Elias-Gutierrez M., Martinez Arbizu P. 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 and Phylogeny 76(3):487-507. senckenberg.de/arthropod-systematics.

2017

  • Khodami S., McArthur V., Blanco-Bercial L., Martinez Arbizu P. 2017. Molecular phylogeny and revision of copepod orders (Crustacea: Copepoda). Scientific Reports, 7: 9164. DOI: 10.1038/s41598-017-06656-4.

2016

  • Gollner S., Stuckas H., Kihara T.C., Laurent S., Khodami S., Martinez 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): e0163776. DOI: 10.1371/journal.

2014

  • Khodami S., Martinez Arbizu P., Stöhr S., Laakmann S. 2014, Molecular species delimitation of Icelandic brittle stars (Ophiuroidea). Polish Polar Research, 35 (2): 243-260. DOI: 10.2478/popore−2014−0011

 

BOOK CHAPTER

 Submitted

  • Mercado-Salas NF., Khodami S., Martínez-Arbizu P. Chapter 41C. In: Vaupel Klein JC (Ed.) Traité de Zoologie C. Brill Academic Publishers, Leiden, Netherlands.
  • Mercado- Salas NF., Martínez A., Khodami S., Martínez Arbizu P. Chapter 42F. Anchialine Copepoda. In: Vaupel Klein JC (Ed.) Traité de Zoologie C. Brill Academic Publishers, Leiden, Netherlands.

2020

  • George K, Khodami S., Kihara TC, Martínez Arbizu P, Martínez García A, Mercado-Salas NF, Pointner K, Veit-Köhler G. 2020. Chapter 28. Copepoda. In: Schmidt-Rhaesa A (Ed.) Guide to the determination of marine meiofauna. Pfeil-Verlag, Munich, Germany.
  • Martínez Arbizu P, Martínez García A, Mercado-Salas NF, Khodami S. Chapter 28.5.3. Order Misophioida Gurney, 1933. In: Schmidt-Rhaesa A (Ed.). Guide to the determination of marine meiofauna. Pfeil-Verlag, Munich, Germany.
  • Martínez Arbizu P, Mercado-Salas NF, Khodami S. Chapter 28.5.4. Order Cyclopoida Burmeister, 1834. In: Schmidt-Rhaesa A (Ed.) (2020). Guide to the determination of marine meiofauna. Pfeil-Verlag, Munich, Germany.

 

PUBLICATION IN PREPARATION

  • Khodami S., Gatzemeier N., Peter J., Renz J., Martinez Arbizu P.. Genetic monitoring of Zooplankton communities in the German Bight (North Sea). Frontiers.
  • Khodami S., Mercado-Salas NF., Martínez Arbizu P. Evaluation of marine zooplankton community structure at polymetallic nodule field from Clarion-Clipperton Fracture Zone through DNA metabarcoding. Environment International.
  • Khodami S., Martinez A., Mercado-Salas NF., Martínez Arbizu P. Phylogenetic reconstruction of the misophrioid’s (Copepoda) evolution, inferred from NGS data. Molecular Phylogenetics and Evolution.
  • Martínez Arbizu P., Mercado-Salas N.F., Khodami S., Macheriotou L., Vanreusel A. Ecological patterns of meiofauna from the polymetallic nodule area at the Clarion-Clipperton Fracture Zone applying metabarcoding. Scientific Reports.
  • Reñé A., Khodami S., Martínez Arbizu P., Hoppenrath M., Benthic dinoflagellate’s genetic structure and dynamics in the North Sea and Mediterranean waters. Progress in Oceanography.
  • Khodami S., George K., Packmor J., Martinez P., Influence of marker choice on biodiversity estimate and community structure of Baltic meiofauna.“
  • 2) „Martinez P., Khodami S., Packmor J., Lessons learned from molecular rapid assessment of meiofauna for monitoring purposes
  • Packmor J., Khodami S., George K., Martinez P. Effect of fisheries on metazoan meiofauna communities

 

REPORT

 2021

  • Kieneke A., Khodami S., Kamyab E., Galarza-Verkovitc D., Bonc F., Bierschenk T., Martinez P. Icelandic marine Animals meet Diversity along latitudinal gradients in the deep sea of the Atlantic, Meiofauna (IceDivA II). Cruise report.

2020

  • Kieneke A., Khodami S., Martinez P., Brix S. Icelandic marine Animals meet Diversity along latitudinal gradients in the deep sea of the Atlantic; Meiofauna (IceDivA I). Cruise report.
  • Uhlenkott K., Khodami S., Menke S., Gatzemeier N.,Mercado-Salas N., Martínez Arbizu P. Biodiversity of benthic fauna within the polymetallic nodule belt, NE Pacific (Clarion Clipperton Fracture Zone). Final Report Mangan 18 . Bundesanstalt für Geowissenchaften und Rohstoffe.
  • Uhlenkott K., Khodami S., Menke S., Rossel S., Martínez Arbizu P.JPIO MiningImpact – Environmental impacts and risks of deep-sea mining; Molecular chapter. Final report MiningImpactI 2021. Bundesanstalt für Geowissenchaften und Rohstoffe.

2018

  • Mercado-Salas NF., Gatzemeier N., Martínez Arbizu P., Khodami S., Uhlenkott K., Menke S., Ercan T. Chapter 11. Planktonic Diversity. In: Rühlemann C, Vink A (Eds.). Cruise Report SO-262 Mangan 2018. Bundesanstalt für Geowissenchaften und Rohstoffe.
  • Uhlenkott K., Edullantes C., Ercan T., Gatzemeier N., Khodami S., Martínez Arbizu P., Mercado-Salas NF. 2018. Chapter 12. Benthic biodiversity. In: Rühlemann C, Vink A (Eds.). Cruise Report SO-262 Mangan 2018. Bundesanstalt für Geowissenchaften und Rohstoffe.

2015

  • Vanreusel A., Macheriotou L., Khodami S., Raschka U., Martinez Arbizu P. 2015. Metazoan meiofauna. In P. Martinez Arbizu et al.: SO239 EcoResponse, Assessing the Ecology, Connectivity and Resilience of Polymetallice Nodule field Systems. Balboa (Panama)- Manzanillo (Mexico), 11th March – 30th April 2015. SONNE – Fahrtberichte.

2011

  • Ostmann, A., Khodami S., Schnurr S., Bauernfeld W., Yasuhara M., Martinez P. 2012. Meiofauna communities around Icelandic waters. In S. Brix et al.: Overflow, Circulation, and Biodiversity Cruise No. 85, Leg 3 August 27 – September 28, 2011 Reykjavik (Iceland) – Cuxhaven (Germany). Meteor – Berichte.

 

CONFERENCE

oral

    07 – 12/06/2019

  • Khodami S., Mercado-Salas N.F., Martinez Arbizu P. Gradual morphological adaptation to deep-sea and pelagic habitats in Aegisthidae Giesbrecht, 1893 (Copepoda: Harpacticoida) inferred from genus level molecular phylogeny seventIMCO (17th International Meiofauna Conference 2019). Évora, Portugal.

    16 – 18/07/2018

  • Martinez Arbizu, P., Khodami S., Mercado-Salas N.F. The Senckenberg Metabarcoding Pipeline: Examples from Meiofauna and Plankton. Marine ‘omics Workshop. Delmenhorst, Germany.

    16 – 21/07/2017

  • Khodami S., McArthur V., Blanco-Bercial L., Martinez Arbizu P. Molecular phylogeny and revision of Copepod. 13ICOC (13 International Copepoda Conference). Los Angeles. The U.S.A.
  • Khodami S., Mercado-Salas N.F., Martinez Arbizu P. Molecular phylogeny of Aegisthidae Giesbrecht, 1893 (Copepoda: Harpacticoida) reveals quick morphological adaptation to deep-sea and pelagic habitats. 13ICOC (13 International Copepoda Conference 2017). Los Angeles. The U.S.A.
  • Mercado-Salas N.F., Khodami S., Martinez Arbizu P. How diverse are bromeliad copepods and ostracods in the tropical forest of the Yucatan Peninsula? 13ICOC (13 International Copepoda Conference 2017). Los Angeles. The U.S.A.
  • Mercado-Salas N.F., Khodami S., Martinez Arbizu P. How diverse are bromeliad copepods and ostracods in the tropical forest of the Yucatan Peninsula? 13ICOC (13 International Copepoda Conference 2017). Los Angeles. The U.S.A.

03- 08/07/2016

  • Khodami S., Martinez Arbizu P.. First parasitic Aegisthidae Giesbrecht, 1893 (Copepoda: Harpacticoida) showing convergent evolution with Siphonostomatoida and its phylogenetic position within the family. 16th International Meiofauna Conference (ISIMCO 2016). Crete. Greece.

21- 24/02/2016

  • Khodami S., Martinez Arbizu P.. A new phylogeny of copepod (Crustacean) orders based on 18S rRNA. 17th Annual Meeting of the Gesellschaft für Biologische Systematik (GfBS) “Taxa in Time and Space” 2016. Munich. Germany.

09-13/07/2014

  • Khodami S., Martinez Arbizu P. Phylogenetic relationship of Copepoda orders based on 18S rRNA. 12ICOC (12 International Copepoda Conference 2014). Seoul. Korea


Poster

26 – 28/02/2020

  • Khodami S., Gatzemeier N., Peter J., Renz J., Martinez Arbizu P. Genetic monitoring of Zooplankton communities in the German Bight (North Sea). 4th Annual Meeting in Conservation Genetics – From Genomes to Application, Frankfurt am Main, Germany.

07 – 12/06/2019

  • Khodami S., Mercado-Salas N.F., Tang D., Martinez Arbizu P. New phylogeny and systematics for Cyclopoida (Copepoda). seventIMCO (17th International Meiofauna Conference 2019). Évora, Portugal.

16 – 18/07/2018

  • Khodami S., Rossel S., Martinez Arbizu P. Comparison of Metabarcoding and MALDI-TOF for rapid biodiversity assessment of Harpacticoid Copepods (Crustacea) on a tidal flat (Hooksiel, Germany). Marine ‘omics Workshop. Delmenhorst, Germany.

 

EXPEDITIONS

2021

  • SO286 IceDivA II Expedition (Emden–Las Palmas). Icelandic Marine Animals: Genetic and Ecology. 05th November – 07th December 2021 on board of RV SONNE
  • SO280 IceDivA I Expedition (Emden–Emden). Icelandic Marine Animals: Genetic and Ecology. 08th January – 07th February 2021 on board of RV SONNE

2018

  • SO262 Mangan 2018 Expedition (Guayaquil- Suva). Geology, Biodiversity and environmental of the German License Area for the Exploration of Polymetallic Nodules in the Equatorial NE Pacific. 4th April – 29th May 2018 on board of RV SONNE.

2015

  • SO239 EcoResponse Expedition (Balboa – Manzanillo). Assessing the Ecology, Connectivity, and Resilience of Polymetallic Nodule Field Systems. 11th March – 30th April 2015 on board of RV SONNE.

2011

  • IceAGE1 Expedition (Reykjavik – Cuxhaven). Icelandic Marine Animals: Genetics and Ecology. 19th August – 28th September 2011 on board of RV Meteor (ME 85/3).

 

SUPERVISED STUDENTS 

M.Sc.

2022

  • Bonc F., Analysis of distribution and diversity of deep-sea Copepoda (Crustacea) and Meiofauna in the North-East Atlantic using a metabarcoding approach. Carl von Ossietzky Universität Oldenburg.
  • Korfhage S. Is the Mitochondrial Genome of Octocorals Circular or Linear? A Review and Experimental Approach. Carl von Ossietzky Universität Oldenburg.

B.Sc.

2022

  • Esteban-Vázquez B. Integrative taxonomy of the sea star Astropecten irregularis (Pennant, 1777) species complex in the North Sea. Erasmus Mundus Joint Master Degree in Marine Environment.

2021

  • Bonc F. Morphological and molecular characterization of meiofauna communities from Hooksiel tidal area of the North Sea. Carl von Ossietzky Universität Oldenburg.
  • Weßels A., Biodiversity assesment of meiofauna communities of North Sea using multi gene metabarcoding. Carl von Ossietzky Universität Oldenburg.

2019

  • Eichsteller A., DNA barcoding of the ophiuroids shows no barrier in the Kuril-Kamchatka Trench, Northwest Pacific reveals. Carl von Ossietzky Universität Oldenburg.