Abstract
DNA barcoding uses a short fragment of a DNA sequence to identify a taxon. After obtaining the target sequence it is compared to reference sequences stored in a database to assign an organism name to it. The quality of data in the reference database is the key to the success of the analysis. In the here presented study, multiple types of data have been combined and critically examined in order to create best practice guidelines for taxonomic reference libraries for environmental barcoding. 70 unialgal diatom strains from Berlin waters have been established and cultured to obtain morphological and molecular data. The strains were sequenced for 18S V4 rDNA (the pre-Barcode for protists) as well as rbcL data, and identified by microscopy. LM and for some strains also SEM pictures were taken and physical vouchers deposited at the BGBM. 37 freshwater taxa from 15 naviculoid diatom genera were identified. Four taxa from the genera Amphora, Mayamaea, Planothidium and Stauroneis are described here as new. Names, molecular, morphological and habitat data as well as additional images of living cells are also available electronically in the AlgaTerra Information System. All reference sequences (or reference barcodes) presented here are linked to voucher specimens in order to provide a complete chain of evidence back to the formal taxonomic literature.
Highlights
Diatoms are unicellular and usually photoautotroph micro algae which are responsible for about 25% of global CO2 fixation [1,2,3] and contribute approximately 20% of the global net primary production [4].Diatoms are important bioindicators for monitoring water quality because they are sensitive to changes in pollution, nutrient availability, acidity and salinity, e.g. [5,6]
They are the most ubiquitous group within the microscopic algae as they occur in all types of water bodies and play an important part in benthic and planktonic biocoenoses [7]. They are routinely used as bioindicators within the EU Water Framework Directive (WFD) as well as in water quality monitoring worldwide [8,9,10,11,12,13]
This paper focuses on naviculoid diatom strains from Berlin waters since its diatom flora has been well studied for almost two centuries by light microscopy [31] and a recent diatom flora is available for water quality assessments [32]
Summary
Diatoms are unicellular and usually photoautotroph micro algae which are responsible for about 25% of global CO2 fixation [1,2,3] and contribute approximately 20% of the global net primary production [4].Diatoms are important bioindicators for monitoring water quality because they are sensitive to changes in pollution, nutrient availability, acidity and salinity, e.g. [5,6]. [5,6] They are the most ubiquitous group within the microscopic algae as they occur in all types of water bodies and play an important part in benthic and planktonic biocoenoses [7]. They are routinely used as bioindicators within the EU Water Framework Directive (WFD) as well as in water quality monitoring worldwide [8,9,10,11,12,13]. Current identification of diatoms is based on a morphological and mostly descriptive species concept (Zimmermann et al subm.) and relies exclusively on micro-characters of the frustule such as size, symmetry, shape, and sculpture which can be seen by light microscopy [14]; more detailed analyses of the siliceous structures lead to more and more refined differentiation of species, which is possible through the development of higher resolution techniques, e.g. electron microscopy
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