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Research Projects

3rd German Intercalibration Exercise Benthic Diatoms 2022/23

The third intercalibration exercise benthic diatoms will take place from fall 2022 to fall 2023. The intercalibration exercise is aimed at laboratories as well as facilities, which professionally assess water quality based on benthic diatom analyses and other interested diatomists.
Each participant receives two prepared permanent slides. The samples are taken from a lowland lake in northern Germany and from a stream in the Central German Uplands. Species identification and recording have to be carried out according to the German instruction protocol for implementing the European Water Framework Directive (Schaumburg et al. 2011 & 2012 in German, English: Schaumburg et al. 2007 & 2011). The results will be submitted in a predefined excel table and contribute to the final report. Participants have time to process the slides from November 2022 to the end of March 2023. Each participant will receive a certificate. There will be no workshop.
Dr. Krisztina Buczko (Hungarian Natural History Museum, Budapest), Prof. Dr. Bart Van De Vijver (Botanic Garden Meise, Belgium) and Dr. Carlos Wetzel (Luxembourg Institute of Science and Technology (LIST) agreed to function as auditors.
More information will follow soon.

The Research Group Diatoms at the Botanic Garden and Botanical Museum Berlin Freie Universität Berlin:
Dr. Nélida Abarca, Wolf-Henning Kusber and Dr. Jonas Zimmermann
In co-operation with Dr. Mirko Dreßler (University Rostock) and Dr. Petra Werner (translator)

Further reading:

Second German Benthic Diatom Intercalibration Exercise 2014/2015. Report, November 2019 PDF icon 2019_schwarz_et_al_intercalibration_exercise_2014-2015_final_report.pdf(7 MB)

First German Benthic Diatom Intercalibration Exercise 2011/2012. Report, September 2014 [PDF icon 2014_dressler_et_al_intercalibration_diatoms_2011-2012_final_report.pdf(4 MB)


Current Research Projects
Endemism vs. Cosmopolitanism: assessing polar benthic diatom diversity and biogeography patterns as baseline for environmental change using an integrative approach
Forschungsprojekt im Schwerpunktprogramm SPP 1158 „Antarktisforschung“ der Deutschen Forschungsgemeinschaft DFG gemeinsam mit der Universität Rostock (Prof. Dr. Ulf Karsten)
DNA-Metabarcoding für die Bewertung von Gewässern in der behördlichen Praxis "GeDNA"
Ressortforschungsplan (REFOPLAN) des Umweltbundesamtes (UBA) gemeinsam mit Universität Duisburg-Essen (UDE), AG Aquatische Ökosystemforschung (Prof. Dr. Florian Leese und Prof. Dr. Daniel Hering)
The ultimate aim of FRESHBAR is to establish DNA-barcoding techniques in operative national monitoring and improve assessment of biodiversity human-induced stress on freshwater ecosystems. The specific tasks are providing new reference sequences for diatoms and invertebrates that are important for monitoring, guaranteeing the taxonomical correctness of new sequence identifications by molecular and morphological taxonomical curation, contribute to the development of metabarcoding using long marker sequences (diatoms) and testing shorter barcodes (invertebrates) comparing morphological and DNA-based identifications across environmental gradients, and depositing results and samples in quality-assured public databases and collections.

German Barcode of Life Project Phase 2 (GBOL2) – Innovative, NGS-based tool to assess Water Framework Directive relevant diatoms  []

The German Barcode of Life 2 project, funded by the Federal Ministry of Education and Research (BMBF), is phase two of the GBOL project to extend the DNA barcode reference library by integrating all frequent and common organisms, important indicators, FFH and German Red List species as well as health-relevant invasive organisms and important agricultural pests. The network consists of 19 German research institutions. The Research Group Diatoms executes the sub-project “Environmental DNA in the Water Framework Directive context (diatoms)” with the focus on compiling a taxonomically curated DNA barcode reference library for the relevant diatom taxa for water quality assessments in Northern Germany.  Another focal area is the improvement of the bioinformatic pipeline for eDNA metabarcoding purposes. This endeavour is a key prerequisite for developing a sequence-based time- and cost-efficient method for analysing the diatom community composition in environmental samples via eDNA metabarcoding for water quality assessments. All samples and data deposited will be made available through the GGBN Data Portal. The project was financed by the Federal Ministry of Education and Research (BMBF).
Building a Global Registration and Index System for Scientific Names and Types of Algae []
Scientific names of organisms are the key to biodiversity information, because all observations, experimental and specimen data are linked to them. Even in the age of Internet accessibility of information, many scientific names remain hidden, because they are published in books or journals that are available in print only, or because publishing policies do not permit open access. On the other hand, many scientific names are accessible without available information on their source or on their reliability. To overcome these shortcomings the International Association for Plant Taxonomy (IAPT) constituted a Special Committee on Registration of Algal and Plant Names (including fossils) to report to the XIX International Botanical Congress in 2017. In phycology a new attempt for the registration of scientific names, including their name-bearing types was started in 2016 at the BGBM, modelling workflows and a database on basis of the EDIT Common Data Model (CDM). A Web-based user interface will allow data input, data quality check, and data access. Furthermore an automatic registration tool for electronic journals is planned and  an index to all existing algal names was implemented. It was a joint project between the Research Group Diatoms and the Research Group Biodiversity Informatics and was financed by the German Science Foundation (DFG). Now it is institutionalised as by the BGBM Berlin.
Diversity Assessment and Taxonomy of Freshwater Diatoms in Subtropical Mexico 
Very little is known about diatom diversity in the tropics in general and in Central America and the Caribbean especially where diatoms not only occur in water bodies but also in any moist places such as soil, leaves, bark, mosses, and phytothelmata. Only with modern methods (SEM, Molecular) and modern taxonomic concepts, the different species can be detected. High diatom diversity is to be expected because of numerous different biotopes in favorable climates, the geological age of the different islands, the structure and distribution of surface elements, the components of relief, hydrological and hydrochemical regimes and aquatic vegetation. Mexico is considered a center of high biodiversity, and parts of its territory have been identified as hotspots, centers of great wealth and high ecological fragility with exceptional concentrations of endemic species concerning plants and animals. As a consequence of its physiography, the tropical parts of Mexico are covered by a very complex mosaic of vegetation types. Not only topography but also latitude, climate, and soils play important roles and produce a varied spectrum of environmental situations. Since tropical Mexico is not so highly industrialized yet, it is expected that the typical “Kulturfolger” (diatom weeds, cosmopolitan European species) have not taken over yet all the water bodies. Especially in oligotrophic and electrolyte poor habitats such as in forests and in springs, diatoms are expected to be still indigenous. For Central America and the Caribbean a high endemism for higher plants is known; it should be tested whether this is also true for diatoms.  
DNAqua-Net – Developing new genetic tools for bioassessment of aquatic ecosystems in Europe (EU COST Action CA15219) []
DNAqua-Net is an EU COST Action (Co-Operation in Science & Technology program of the European Commission) with the Memorandum of Understanding (MoU) “To advance the application of DNA-tools for biodiversity assessments and develop a roadmap to include these in standardised ecological assessments of aquatic ecosystems in Europe and beyond.” The project provides a platform to connect researchers from all over Europe, EU Near Neighbour Countries (NNC) as well as EU International Partner Countries (IPC) and aims to nucleate these researchers across disciplines with the task to identify gold-standard genomic tools and novel eco-genomic indices for routine application for ecological assessments in water bodies (e.g. EU Water Framework Directive, US Clean Water Act).
Assessing the diatom diversity for water quality evaluation in the Euphrates-Tigris-Catchment area using eDNA Metabarcoding and classical microscopical analysis
The purpose of this project is to introduce advanced molecular techniques with DNA barcoding, as well as environmental DNA (eDNA) metabarcoding for diatom identification to monitor biodiversity and create a first baseline for future screening of biodiversity in the Euphrat-Tigris-Catchment area. This will allow the assessment of water bodies and their ecosystem services. Thus, providing the prerequisites for the establishment of new means to evaluate water quality. The research focuses on the following three questions:
1. Which diatom species diversity can be found in the Euphrates-Tigris-Area?
2. Which species occur under specific ecological conditions and therefore can be used as indicator-species associated with water quality?
3. Can metabarcoding be applied as an alternative method for the assessment of water quality?
Implementation of eDNA metabarcoding for water quality assessments in cooperation with AquaPlus (Switzerland)
Main goal is the evaluation and the possible implementation of eDNA metabarcoding for water quality assessments in the context of the Swiss Diatom Index (DI-CH). Therefor the classical microscopy based approach and eDNA metabarcoding are analysed complementarily comparing the outcome of the different methods. It will be tested, if an adaptive calibration of the DI-CH is required as well.
Technical report “For the routine sampling of benthic diatoms from rivers and lakes adapted for metabarcoding analyses” and “DNA barcoding libraries” (CEN)
Diatoms are unicellular microalgae present in all types of water bodies. They are an important component of aquatic ecosystems and have been used widely for ecological assessment required by the EU Water Framework Directive (2000/60/EC) and Urban Waste Water Treatment Directive (91/217/EEC) in addition to other EU Directives and international agreements. Concerning this issue the technical committee CEN/TC 230 – working group 23 “Water analysis” agreed on, proposed, submitted specific standard requirements for the routine sampling of benthic diatoms from rivers and lakes adapted for metabarcoding analyses as well as the development of DNA barcoding libraries for eDNA metabarcoding. These standards are now accepted by the CEN (European Committee for Standardization).
Red Lists and Checklists of Algae for Berlin and Germany
Checklists are species inventory of groups of organism; when combined with Red Lists they provide information with regard to threatened species. Therefore, red lists are valuable tools for conservation. In the RG Diatoms Red Lists are being established for Germany (desmids) and for Berlin (red algae, brown algae, stoneworts). 
The Diatom Flora of Ecosystems Distrito Capital and Caribbean Tropical Dry Forest as a Baseline for the Development of an Aquatic Bio-Monitoring System for Colombia.
To set the basis for a time- and cost-efficient identification system based on DNA barcoding of freshwater diatoms, the proposed project focuses on the establishment of the first DNA reference library for diatoms of Colombia. To achieve this, the objectives are (1) to characterize composition and diversity of the diatom communities in the region of Distrito capital and Caribbean Tropical Dry Forest with morphological (floristic) and molecular methods (eDNA-Metabarcoding), (2) to set up a diatom culture collection as reference and source for molecular studies, (3) to generate a baseline for the occurrence of diatoms in both regions (river basin), (4) to lay the foundation for a diatom-based biomonitoring instrument that will help to define the species or assemblages that could be used as biological indicators for water quality of Distrito capital and Caribbean Tropical Dry Forest for future monitoring of the water quality of the Colombia rivers, (5) to recommend the use of diatoms in water quality monitoring for the Environmental Protection Agency of Colombia.



Sustained Projects and Resources

AlgaTerra - An information system for micro algal biodiversity [

Originally a 3-year research and implementation project at the BGBM (2001 to 2004) financed by the German Federal Ministry of Research under the BIOLOG Programme, the information system offers researched data on diatom names, concepts, images, type and specimen information, molecular data, morphological, and environmental data. Data has been migrated to the common data model of the EDIT Platform for Cybertaxonomy. AlgaTerra is sustained in the framework of several projects and as a core activity of the BGBM’s Diatom Research Group. 
GBIF-D Algae & Protists
GBIF-D Algae & Protists is part of the Botanical Node for GBIF-Germany with special emphasis on algae and protists. The BGBM supports the German phycological and protozoological community in their efforts to mobilise biodiversity data using the BioCASE software and to  facilitate data sharing via  the GBIF Network, e.g. using the GBIF-D Algae & Protozoa data portal. 
The project was financed by the Federal Ministry of Education and Research (BMBF) within the GBIF-D Programme.