Regine Jahn

CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

A group of protist experts proposes a two-step DNA barcoding approach, comprising a universal eukaryotic pre-barcode followed by group-specific barcodes, to unveil the hidden biodiversity of microbial eukaryotes.

Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

Diatoms are frequently used for water quality assessments; however, identification to species level is difficult, time‐consuming and needs in‐depth knowledge of the organisms under investigation, as nonhomoplastic species‐specific morphological characters are scarce. We here investigate how identification methods based on DNA (metabarcoding using NGS platforms) perform in comparison to morphological diatom identification and propose a workflow to optimize diatom fresh water quality assessments. Diatom diversity at seven different sites along the course of the river system Odra and Lusatian Neisse from the source to the mouth is analysed with DNA and morphological methods, which are compared. The NGS technology almost always leads to a higher number of identified taxa (270 via NGS vs. 103 by light microscopy LM), whose presence could subsequently be verified by LM. The sequence‐based approach allows for a much more graduated insight into the taxonomic diversity of the environmental samples. Taxa retrieval varies considerably throughout the river system, depending on species occurrences and the taxonomic depth of the reference databases. Mostly rare taxa from oligotrophic parts of the river systems are less well represented in the reference database used. A workflow for DNA‐based NGS diatom identification is presented. 28 000 diatom sequences were evaluated. Our findings provide evidence that metabarcoding of diatoms via NGS sequencing of the V4 region (18S) has a great potential for water quality assessments and could complement and maybe even improve the identification via light microscopy.

USING THE EHRENBERG COLLECTION

The Christian Gottfried Ehrenberg Collection at the Museum fur Naturkunde in Berlin holds type specimens and original material for thousands of taxa of microscopic organisms. Ehrenberg did not explicitly designate types for his many taxa, or label types in his collection. This, and the rather complex, sample oriented organisation of the materials makes using the collection more difficult. Nonetheless, through the use of unpublished taxonomic and geographic index volumes compiled by Ehrenbergs daughter Clara, by examination of unpublished notations made by Ehrenberg on his original drawings, and by examination of other documentation in the collection it is usually possible to locate both the original type specimen and unprocessed original material for new studies. Clara Ehrenbergs index volumes have now been scanned and placed onto a CD-ROM which can be ordered from the senior author.

Does the cosmopolitan diatom Gomphonema parvulum (Kutzing) Kutzing have a biogeography

Diatom cultures of the G. parvulum species complex were established from seven different sites in the Faroe Islands, Sweden, Germany, Mexico and Korea, and were studied in detail. Eight morphodemes were identified which corresponded to the descriptions of the cosmopolitan taxon G. parvulum (Kützing) Kützing sensu lato: its nominate variety (var. parvulum), G. parvulum var. exilissimum Grunow and G. parvulum f. saprophilum Lange-Bertalot & Reichardt, G. [parvulum var.] lagenula Kützing plus four unidentifiable morphodemes. The concatenated analysis of the sequences of the markers 18SV4, rbcL, and ITS as well as morphological data resulted in a separation of four taxa based on their biogeography in Mexico, Korea, central Continental Europe and Northern Atlantic Europe. Mantel tests showed a significant correlation between molecular and geographical distances. The diagnoses of two taxa, G. parvulum sensu stricto, and G. lagenula, were emended, G. saprophilum elevated to species rank and epitypes designated. One species was newly described.

Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.

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.

Algae of the Ehrenberg collection - 1. Typification of 32 names of diatom taxa described by C. G. Ehrenberg

Abstract Jahn, R. & Kusber, W.-H.: Algae of the Ehrenberg collection — 1. Typification of 32 names of diatom taxa described by C. G. Ehrenberg. — Willdenowia 34: 577–595. — ISSN 0511-9618;

Morphology and Identity of Aulacoseira italica and typification of Aulacoseira (Bacillariophyta)

Original material of Ehrenbergs from Santa Fiora (Tuscany, Italy) was examined to establish the identity of the diatom to which Ehrenberg gave the name Gaillonella italica. It was compared with other Ehrenberg material, notably from New England, and with numerous other samples, both fossil and recent, with a view to understanding the taxonomy of this species. Although Ehrenberg later discarded the name, it was validly published and we consider it synonymous with G. crenulata. However, despite the earlier publication of G. italica, G. crenulata remains the type of the name of the genus Aulacoseira. New observations on the rimoportulae and the velum together with recent illustrations of separation valves have been added to the features used to distinguish the species from others in the genus, of which, the most important, though hitherto neglected, is the curving of the pore rows to the left (sinistrorse). We draw attention to the fact that A. italica has often been confused with A. valida.

Rare Surirella taxa (Bacillariophyta) from East Africa described by Otto Müller: typifications, recombinations, new names, annotations and distributions

Abstract Cocquyt, C. & Jahn, R.: Rare Surirella taxa (Bacillariophyta) from East Africa described by Otto Müller: typifications, recombinations, new names, annotations and distributions. — Willdenowia 35: 359–371. —ISSN 0511-9618;

REINSTATEMENT OF THE GENUS CERATONEIS EHRENBERG AND LECTOTYPIFICATION OF ITS TYPE SPECIMEN: C. CLOSTERIUM EHRENBERG

A preparation in the Ehrenberg Collection was designated as lectotype of Ceratoneis closterium Ehrenb., the type of the name of the genus Ceratoneis. The lectotype specimen was studied using the light microscopy and found to agree morphologically with recently studied material of taxa of the genus Cylindrotheca Rabenh. (1859) observed by Reimann & Lewin (1964). Ceratoneis Ehrenb., having priority over Cylindrotheca Rabenh., is reinstated and appropriate transfers are made.

Typification of Cocconeis lineata and Cocconeis euglypta (Bacillariophyta)

The nominate varieties of the monoraphid diatoms Cocconeis lineata Ehrenberg and C. euglypta Ehrenberg are typified. Lectotypes of both taxa are preserved at the Ehrenberg Collection, Museum für Naturkunde, Berlin, Germany. The lectotype of C. lineata is a poorly detailed drawing, showing an ovoid valve (or frustule?) with two to three apical lines on each hemivalve. The lectotype of C. euglypta, contained in a mica, shows a unique, broadly elliptical sternum valve with up to five apical striae on each hemivalve, displaying a zigzag pattern. This is roughly consistent with the current concept of C. lineata and C. euglypta and with their usage over the last 160 years. To ensure stabilization of the names and current concepts for these two taxa, culture-based epitypes of C. lineata and C. euglypta are designated. Light and electron microscopy observations, as well as morphometric data from clones for both taxa, are presented and an amended description for each taxon is provided.